Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1688
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: 613586
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:531924 original size:20 final size:20
Alignment explanation
Indices: 531879--531930 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
531869 GTAGCCAAAC
**
531879 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
531899 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
531918 TTGTATCGATACA
1 TTGTATCGATACA
531931 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:533172 original size:42 final size:42
Alignment explanation
Indices: 533120--533238 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
533110 TTCTTCTCTC
*
533120 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* * * *
533162 CTCCTCCTATCATCCCTCCTATTTGTACTATCTTTCCTATCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
* * *
533204 CTCCTTC-ATTCATCCCT-CTCATCTCTTCTTTCTCT
1 CTCCTCCTA-TCATCCCTCCTC-TCTCTACTATCTCT
533239 TTGAGGGCTA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 3 0.05
42 60 0.95
ACGTcount: A:0.12, C:0.42, G:0.01, T:0.45
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTATCT
Found at i:548009 original size:9 final size:9
Alignment explanation
Indices: 547997--548056 Score: 57
Period size: 9 Copynumber: 6.1 Consensus size: 9
547987 CTCTCTCTAT
547997 TATCTCTCC
1 TATCTCTCC
548006 TATCTCTCCTC
1 TATCTCT-C-C
548017 TATCATCCCTCC
1 TATC-T--CTCC
*
548029 TATCTCTAC
1 TATCTCTCC
548038 TATCTCTCC
1 TATCTCTCC
*
548047 TATATCTCC
1 TATCTCTCC
548056 T
1 T
548057 CCTATCATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
9 27 0.63
10 1 0.02
11 6 0.14
12 6 0.14
13 1 0.02
14 2 0.05
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:548011 original size:18 final size:18
Alignment explanation
Indices: 547984--548049 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
547974 CTTGTCATCC
*
547984 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTATTATCT
*
548002 CTCCTATCTCTCCTCTATCAT
1 CTCCTATCTCT-AT-TATC-T
*
548023 CCCTCCTATCTCTACTATCT
1 --CTCCTATCTCTATTATCT
548043 CTCCTAT
1 CTCCTAT
548050 ATCTCCTCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 17 0.44
19 1 0.03
20 5 0.13
21 5 0.13
23 11 0.28
ACGTcount: A:0.14, C:0.42, G:0.00, T:0.44
Consensus pattern (18 bp):
CTCCTATCTCTATTATCT
Found at i:548026 original size:41 final size:41
Alignment explanation
Indices: 547968--548086 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 41
547958 CTTCTTCTCT
* * * *
547968 TCTCCTCTTGTCATCCCTCCTCTCTCTATTATCTCTCCTATC
1 TCTCCTC-TATCATCCCTCCTATCTCTACTATCTCTCCTATA
548010 TCTCCTCTATCATCCCTCCTATCTCTACTATCTCTCCTATA
1 TCTCCTCTATCATCCCTCCTATCTCTACTATCTCTCCTATA
* *
548051 TCTCCTCCTATCATCCCTCCTATCTCTTCTTTCTCT
1 TCTCCT-CTATCATCCCTCCTATCTCTACTATCTCT
548087 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 36 0.51
42 34 0.49
ACGTcount: A:0.12, C:0.43, G:0.01, T:0.45
Consensus pattern (41 bp):
TCTCCTCTATCATCCCTCCTATCTCTACTATCTCTCCTATA
Found at i:548074 original size:12 final size:11
Alignment explanation
Indices: 548002--548076 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
547992 TCTATTATCT
548002 CTCCTATCTCTC
1 CTCCTATCTC-C
548014 CT-CTATCATCC
1 CTCCTATC-TCC
548025 CTCCTATCT--
1 CTCCTATCTCC
*
548034 CTACTATCT--
1 CTCCTATCTCC
*
548043 CTCCTATATCTC
1 CTCCTATCTC-C
548055 CTCCTATCATCC
1 CTCCTATC-TCC
548067 CTCCTATCTC
1 CTCCTATCTC
548077 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
9 15 0.28
11 11 0.21
12 25 0.47
13 2 0.04
ACGTcount: A:0.15, C:0.45, G:0.00, T:0.40
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:552906 original size:12 final size:11
Alignment explanation
Indices: 552890--552999 Score: 74
Period size: 12 Copynumber: 10.2 Consensus size: 11
552880 GAACTCATTT
552890 GATAGGAGGGA
1 GATAGGAGGGA
*
552901 TGATAGTAGGAGA
1 -GATAGGAGG-GA
552914 GATAGGA--GA
1 GATAGGAGGGA
*
552923 GATAGTA--GA
1 GATAGGAGGGA
552932 GATAGGAGGGA
1 GATAGGAGGGA
552943 TGATAGGAGGAGA
1 -GATAGGAGG-GA
*
552956 GACAGGA--GA
1 GATAGGAGGGA
*
552965 GATAGTA--GA
1 GATAGGAGGGA
552974 GATAGGAGGGA
1 GATAGGAGGGA
552985 TGATAGGAGGAGA
1 -GATAGGAGG-GA
552998 GA
1 GA
553000 CAGGGAGATA
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
9 31 0.38
11 4 0.05
12 40 0.49
13 6 0.07
ACGTcount: A:0.40, C:0.01, G:0.45, T:0.14
Consensus pattern (11 bp):
GATAGGAGGGA
Found at i:552921 original size:9 final size:9
Alignment explanation
Indices: 552907--552981 Score: 75
Period size: 9 Copynumber: 8.7 Consensus size: 9
552897 GGGATGATAG
552907 TAGGAGAGA
1 TAGGAGAGA
552916 TAGGAGAGA
1 TAGGAGAGA
*
552925 TAGTAGAGA
1 TAGGAGAGA
*
552934 TAGGAGGGA
1 TAGGAGAGA
*
552943 T--GATAG-
1 TAGGAGAGA
*
552949 GAGGAGAGA
1 TAGGAGAGA
*
552958 CAGGAGAGA
1 TAGGAGAGA
*
552967 TAGTAGAGA
1 TAGGAGAGA
552976 TAGGAG
1 TAGGAG
552982 GGATGATAGG
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 45 0.87
ACGTcount: A:0.41, C:0.01, G:0.44, T:0.13
Consensus pattern (9 bp):
TAGGAGAGA
Found at i:552928 original size:21 final size:20
Alignment explanation
Indices: 552902--552975 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 20
552892 TAGGAGGGAT
552902 GATAGTAGGAGAGATAGGAGA
1 GATAGTA-GAGAGATAGGAGA
552923 GATAGT--AGAGATAGGAGGGA
1 GATAGTAGAGAGATAGGA--GA
* *
552943 TGATAGGAGGAGAGACAGGAGA
1 -GATAGTA-GAGAGATAGGAGA
552965 GATAGTAGAGA
1 GATAGTAGAGA
552976 TAGGAGGGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
18 10 0.23
20 6 0.14
21 17 0.39
22 2 0.05
24 9 0.20
ACGTcount: A:0.42, C:0.01, G:0.43, T:0.14
Consensus pattern (20 bp):
GATAGTAGAGAGATAGGAGA
Found at i:552954 original size:42 final size:42
Alignment explanation
Indices: 552890--553036 Score: 235
Period size: 42 Copynumber: 3.5 Consensus size: 42
552880 GAACTCATTT
* *
552890 GATAGGAGGGATGATAGTAGGAGAGATAGGAGAGATAGTAGA
1 GATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAGA
552932 GATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAGA
1 GATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAGA
*
552974 GATAGGAGGGATGATAGGAGGAGAGACAGG-GAGATAATAGA
1 GATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAGA
* *
553015 GA-GGGAGGGATGACAGGAGGAG
1 GATAGGAGGGATGATAGGAGGAG
553037 GAGAGAAGAA
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 18 0.18
41 12 0.12
42 70 0.70
ACGTcount: A:0.39, C:0.02, G:0.46, T:0.12
Consensus pattern (42 bp):
GATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAGA
Found at i:555015 original size:16 final size:16
Alignment explanation
Indices: 554994--555024 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
554984 AAACTATTCA
554994 TGATGTTTCTATGGAC
1 TGATGTTTCTATGGAC
555010 TGATGTTTCTATGGA
1 TGATGTTTCTATGGA
555025 TTTCATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.45
Consensus pattern (16 bp):
TGATGTTTCTATGGAC
Found at i:564864 original size:9 final size:9
Alignment explanation
Indices: 564852--564909 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
564842 CTCTCTCTAT
564852 TATCTCTCC
1 TATCTCTCC
564861 TATCTCTCC
1 TATCTCTCC
* *
564870 T-CCTAT-C
1 TATCTCTCC
564877 -ATCTCTCC
1 TATCTCTCC
*
564885 TATCTCTAC
1 TATCTCTCC
*
564894 TATCTATCC
1 TATCTCTCC
564903 TATCTCT
1 TATCTCT
564910 GCTCCTATCA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
7 4 0.11
8 4 0.11
9 30 0.79
ACGTcount: A:0.16, C:0.40, G:0.00, T:0.45
Consensus pattern (9 bp):
TATCTCTCC
Found at i:564872 original size:12 final size:11
Alignment explanation
Indices: 564854--564933 Score: 60
Period size: 12 Copynumber: 7.3 Consensus size: 11
564844 CTCTCTATTA
564854 TCTCTCCTATC
1 TCTCTCCTATC
564865 TCTCCTCCTATC
1 TCT-CTCCTATC
564877 ATCTCTCCTA--
1 -TCTCTCCTATC
*
564887 TCTCTACTA--
1 TCTCTCCTATC
*
564896 TCTATCCTATC
1 TCTCTCCTATC
564907 TCTGCTCCTATC
1 TCT-CTCCTATC
* *
564919 ATCCCTCCTGTC
1 -TCTCTCCTATC
564931 TCT
1 TCT
564934 TCTTTCTCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
9 15 0.27
11 8 0.14
12 28 0.50
13 5 0.09
ACGTcount: A:0.12, C:0.42, G:0.03, T:0.42
Consensus pattern (11 bp):
TCTCTCCTATC
Found at i:564879 original size:42 final size:42
Alignment explanation
Indices: 564824--564933 Score: 157
Period size: 42 Copynumber: 2.6 Consensus size: 42
564814 TTCTTCTCTC
* * * *
564824 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTATCCTATCT
*
564866 CTCCTCCTATCATCTCTCCTATCTCTACTATCTATCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTATCCTATCT
* *
564908 CTGCTCCTATCATCCCTCCTGTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCT
564934 TCTTTCTCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.12, C:0.44, G:0.03, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTATCCTATCT
Found at i:569054 original size:51 final size:52
Alignment explanation
Indices: 568964--569080 Score: 193
Period size: 51 Copynumber: 2.3 Consensus size: 52
568954 AAGTTGCTTG
568964 CATGTATCGATACATTTAATAGTATATCGATACATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATTTAATAGTATATCGATACATCTGGGCAAATTTGCCTA
* *
569016 CATGTATCGATACATTATAA-A-TGTATCGATACATCTGGGCAAATTTGCCTG
1 CATGTATCGATACATT-TAATAGTATATCGATACATCTGGGCAAATTTGCCTA
569067 CATGTATCGATACA
1 CATGTATCGATACA
569081 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 42 0.68
52 17 0.27
53 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (52 bp):
CATGTATCGATACATTTAATAGTATATCGATACATCTGGGCAAATTTGCCTA
Found at i:569107 original size:13 final size:13
Alignment explanation
Indices: 569089--569113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
569079 CAAAGATCAG
569089 TGTATCGATACAA
1 TGTATCGATACAA
569102 TGTATCGATACA
1 TGTATCGATACA
569114 TTTGAGTATC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:569192 original size:20 final size:20
Alignment explanation
Indices: 569167--569220 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
569157 TAGCTTAAAG
569167 TGTATCGATACAAAAAAATA
1 TGTATCGATACAAAAAAATA
* ***
569187 TGTATCGATACAACATTTTA
1 TGTATCGATACAAAAAAATA
569207 TGTATCGATACAAA
1 TGTATCGATACAAA
569221 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAAAAATA
Found at i:570601 original size:49 final size:49
Alignment explanation
Indices: 570377--570899 Score: 500
Period size: 49 Copynumber: 11.0 Consensus size: 49
570367 TGAGAAAAGT
* * * * * *
570377 GATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* ** * *
570426 GATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1 GAT-----AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
570481 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
570529 --TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGATTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
570576 GATAAAGGTTCCAATATGTTGATTCAAGGCCAGCGATATTGGACTT---
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
570622 -A-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
570669 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
570718 GGTGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T---
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
570763 --TAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGATATTGGACTT---
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
570807 -A-AAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
570853 GA-AGAAGGTGCCAATATGCTGATTCAAGGCCATCTATATTGGGCTTA
1 GATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
570900 GAAGGGTTGC
Statistics
Matches: 401, Mismatches: 48, Indels: 50
0.80 0.10 0.10
Matches are distributed among these distances:
43 113 0.28
44 43 0.11
45 1 0.00
46 1 0.00
47 2 0.00
48 4 0.01
49 160 0.40
51 1 0.00
52 31 0.08
53 7 0.02
54 4 0.01
55 34 0.08
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
Found at i:570615 original size:92 final size:92
Alignment explanation
Indices: 570447--570904 Score: 615
Period size: 92 Copynumber: 4.9 Consensus size: 92
570437 GGATGTCAAC
*
570447 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATTCAAG
*
570512 GCCAGCTATATTGGACTTAAAGGTGCCAAT
63 GCCAGCGATATTGGACTTAAAGGTGCCAAT
* * *
570542 GTGCTGATTCAAGGCCAGCTACATTGGATTTAAAGATAAAGGTTCCAATATGTTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
570607 AGCGATATTGGACTTAAAAGGTGCCAAT
66 AGCGATATTGGACTT-AAAGGTGCCAAT
* *
570635 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
570700 AGCGATATTGGACTTAAAGGTGAAGGTGCCAAT
66 AGCGATATTGGACTT--A----AAGGTGCCAAT
* * * * *
570733 ATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TAAAGGTGCTAATGTGCTGATTCAAGGCC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
*
570792 AGCGATATTGGACTTAAAAGTGCCAAT
66 AGCGATATTGGACTTAAAGGTGCCAAT
570819 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCAAGGC
* * *
570883 CATCTATATTGGGCTTAGAAGG
65 CAGCGATATTGGACTTA-AAGG
570905 GTTGCCACCG
Statistics
Matches: 322, Mismatches: 27, Indels: 30
0.85 0.07 0.08
Matches are distributed among these distances:
86 36 0.11
87 1 0.00
90 1 0.00
91 1 0.00
92 118 0.37
93 90 0.28
94 2 0.01
95 35 0.11
97 1 0.00
98 37 0.11
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (92 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAGGTGCCAAT
Found at i:570768 original size:22 final size:22
Alignment explanation
Indices: 570743--570809 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
570733 ATGCTGATTC
570743 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
* * *
570765 AAGG--TGCTA-ATGTGCTGA-TTC
1 AAGGCCAGCGATAT-TG--GACTTA
570786 AAGGCCAGCGATATTGGACTTA
1 AAGGCCAGCGATATTGGACTTA
570808 AA
1 AA
570810 AGTGCCAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 8 0.25
22 10 0.31
23 5 0.16
24 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (22 bp):
AAGGCCAGCGATATTGGACTTA
Found at i:570984 original size:32 final size:31
Alignment explanation
Indices: 570892--570994 Score: 154
Period size: 33 Copynumber: 3.3 Consensus size: 31
570882 CCATCTATAT
570892 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
570922 TGGGCTTTAGAGAGTGGTTGCCACCAACTTGTG
1 TGGGCTTTAGA-AG-GGTTGCCACCGACTTGTG
*
570955 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACCGACTTGTG
570987 TGGGCTTT
1 TGGGCTTT
570995 GGGAAAGGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
30 5 0.08
31 5 0.08
32 26 0.39
33 28 0.42
34 2 0.03
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:571109 original size:71 final size:68
Alignment explanation
Indices: 571005--571549 Score: 714
Period size: 71 Copynumber: 7.9 Consensus size: 68
570995 GGGAAAGGAG
* *
571005 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGG-AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
571068 AAGAA
64 AAGAA
*
571073 AAAGGTACCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
571138 AAAGAA
63 AAAGAA
* *
571144 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAAAGTGCCACGGAGTTGTAGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GG-AAAAAGGTGCCACGGAGTTGTGGGCTTTAA
571209 AAAGAA
63 AAAGAA
571215 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
571280 AAAGAA
63 AAAGAA
* *
571286 AAA-GTGCCACGGAGTGGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
571350 GGGAA
66 --GAA
* *
571355 AAAGAGTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
571420 AGGGAA
65 A--GAA
* *
571426 AAAGAGTGCCACGGAGTTGTGGGCTTTGAGAA-GAAAAAGGTTGCCACGGAATTGTGGGCTTT-A
1 AAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGG-TGCCACGGAGTTGTGGGCTTTAA
571489 AAAG--
63 AAAGAA
* * * *
571493 ---GGTACCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGGCTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT
571550 GAAGACACTG
Statistics
Matches: 443, Mismatches: 21, Indels: 32
0.89 0.04 0.06
Matches are distributed among these distances:
62 22 0.05
63 28 0.06
64 1 0.00
67 27 0.06
68 27 0.06
69 13 0.03
70 59 0.13
71 238 0.54
72 28 0.06
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.21
Consensus pattern (68 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
GAA
Found at i:571225 original size:175 final size:176
Alignment explanation
Indices: 571005--571549 Score: 780
Period size: 175 Copynumber: 3.1 Consensus size: 176
570995 GGGAAAGGAG
* *
571005 AAAGATGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1 AAAG-TGCCACGGAGTTGTGGGCTTTAAAAAG-AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
*
571068 AA-GAAAAAG-GTACCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
63 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAAAAGAGTGCCACGGAGTTGTGG
571131 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
126 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
*
571182 AAAGTGCCACGGAGTTGTAGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA-
* *
571247 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG-AAAA-AGTGCCACGGAGTGGTGGGCTT
65 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
571310 TAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
130 TAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
* *
571357 AGAGTGCCACGGAATTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA-
* *
571422 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAG-GTTGCCACGGAATTGTGGGCT
65 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGAG-TGCCACGGAGTTGTGGGCT
* *
571486 TT-AAAAG-----GGTACCACGGAGTTGTGGACTTTAAAAA--G-AAA
129 TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
* *
571525 AAGGTGCCATGGAGTTGTGGGCTTT
1 AAAGTGCCACGGAGTTGTGGGCTTT
571550 GAAGACACTG
Statistics
Matches: 341, Mismatches: 19, Indels: 25
0.89 0.05 0.06
Matches are distributed among these distances:
168 24 0.07
169 1 0.00
171 26 0.08
175 187 0.55
176 40 0.12
177 31 0.09
178 7 0.02
179 25 0.07
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.21
Consensus pattern (176 bp):
AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
AAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAA
Found at i:571419 original size:246 final size:241
Alignment explanation
Indices: 571003--571549 Score: 838
Period size: 246 Copynumber: 2.3 Consensus size: 241
570993 TTGGGAAAGG
*
571003 AGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AGAAAGAGTGCCACGGAGTTGTGGACTTTAAAA--AGAAAA-AGTGCCACGGAGTTGTGGGCTTT
* *
571066 AAAAGAAAAAGGTACCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
63 AAAAGAAAAAGGTACCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAATTGTGG
571131 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAAAGTGCCACGGAG
128 GCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAAAGTGCCACGGAG
*
571196 TTGTAGGCTTTAAAAAGAAAAAGG-TGCCACGGAGTTGTGGGCTTTAAAA
193 TTGTAGGCTTTAAAAAGAAAAAGGTTGCCACGGAATTGTGGGCTTT-AAA
* *
571245 AGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTT
1 A--G--AAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGGAGTTGTGGGCTT
*
571310 TAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAATTGT
62 T-AAAAGAAAAAGGTACCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAATTGT
*
571375 GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGG
126 GGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAAAGTGCCACGG
* * *
571440 AGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAA
191 AGTTGTAGGCTTTAAAAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAA
* *
571491 AG---G-GTACCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGGCTTT
1 AGAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAA-GTGCCACGGAGTTGTGGGCTTT
571550 GAAGACACTG
Statistics
Matches: 281, Mismatches: 15, Indels: 21
0.89 0.05 0.07
Matches are distributed among these distances:
238 31 0.11
239 21 0.07
242 1 0.00
244 2 0.01
245 22 0.08
246 161 0.57
247 37 0.13
248 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (241 bp):
AGAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
AGAAAAAGGTACCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAATTGTGGGCT
TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAAAGTGCCACGGAGTTG
TAGGCTTTAAAAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAA
Found at i:571500 original size:28 final size:28
Alignment explanation
Indices: 571460--571519 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
571450 TTTGAGAAGA
* * *
571460 AAAAGGTTGCCACGGAATTGTGGGCTTT
1 AAAAGGGTACCACGGAATTGTGGACTTT
*
571488 AAAAGGGTACCACGGAGTTGTGGACTTT
1 AAAAGGGTACCACGGAATTGTGGACTTT
571516 AAAA
1 AAAA
571520 AGAAAAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.25
Consensus pattern (28 bp):
AAAAGGGTACCACGGAATTGTGGACTTT
Found at i:571524 original size:63 final size:62
Alignment explanation
Indices: 571425--571549 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
571415 TAAAAAGGGA
* * * *
571425 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTT
1 AAAAGAGTACCACGGAGTTGTGGACTTTAAAAAGAAAAAGG-TGCCACGGAATTGTGGGCTTT
* * *
571488 AAAAGGGTACCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCATGGAGTTGTGGGCTTT
1 AAAAGAGTACCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAATTGTGGGCTTT
571550 GAAGACACTG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 19 0.35
63 36 0.65
ACGTcount: A:0.30, C:0.12, G:0.34, T:0.24
Consensus pattern (62 bp):
AAAAGAGTACCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAATTGTGGGCTTT
Found at i:571562 original size:23 final size:22
Alignment explanation
Indices: 571536--571578 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
571526 AGGTGCCATG
* *
571536 GAGTTGTGGGCTTTGAAGACACT
1 GAGTCGTGGACTTTG-AGACACT
571559 GAGTCGTGGACTTTGAGACA
1 GAGTCGTGGACTTTGAGACA
571579 AAATGCCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.23, C:0.14, G:0.35, T:0.28
Consensus pattern (22 bp):
GAGTCGTGGACTTTGAGACACT
Found at i:571649 original size:31 final size:30
Alignment explanation
Indices: 571555--571675 Score: 172
Period size: 31 Copynumber: 3.9 Consensus size: 30
571545 GCTTTGAAGA
571555 CACTGAGTCGTGGACTTTGAGACAAA-ATGC
1 CACTGAGTCGTGGACTTTGAGA-AAAGATGC
*
571585 CACTAAGTCGTGGACTTTGAAGAAAAGGATGC
1 CACTGAGTCGTGGACTTTG-AGAAAA-GATGC
571617 CACTGAGTCGTGGACTTTGAGAAAAGATTGC
1 CACTGAGTCGTGGACTTTGAGAAAAGA-TGC
* *
571648 CACTGAGTCGTGGGCTTTGAGAAGAGAT
1 CACTGAGTCGTGGACTTTGAGAAAAGAT
571676 TTGAAGAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
30 24 0.29
31 37 0.45
32 22 0.27
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (30 bp):
CACTGAGTCGTGGACTTTGAGAAAAGATGC
Found at i:577801 original size:9 final size:9
Alignment explanation
Indices: 577789--577891 Score: 92
Period size: 9 Copynumber: 12.1 Consensus size: 9
577779 CTCTCTCTAT
577789 TATCTCTCC
1 TATCTCTCC
577798 TATCTCTCC
1 TATCTCTCC
* *
577807 T-CCTAT-C
1 TATCTCTCC
*
577814 -ATCCCTCC
1 TATCTCTCC
*
577822 TATCTCTAC
1 TATCTCTCC
577831 TATCTCTCC
1 TATCTCTCC
577840 TATCTCTCC
1 TATCTCTCC
* *
577849 T-CCTAT-C
1 TATCTCTCC
*
577856 -ATCCCTCC
1 TATCTCTCC
*
577864 TATCTCTAC
1 TATCTCTCC
577873 TATCTCTCC
1 TATCTCTCC
577882 TATCTCTCC
1 TATCTCTCC
577891 T
1 T
577892 CCTATCATCC
Statistics
Matches: 72, Mismatches: 16, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
7 6 0.08
8 8 0.11
9 58 0.81
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:577809 original size:12 final size:12
Alignment explanation
Indices: 577794--577912 Score: 88
Period size: 12 Copynumber: 10.9 Consensus size: 12
577784 TCTATTATCT
577794 CTCCTATCTCTC
1 CTCCTATCTCTC
577806 CTCCTATCATC-C
1 CTCCTATC-TCTC
577818 CTCCTA--TCT-
1 CTCCTATCTCTC
*
577827 CTACTA--TCT-
1 CTCCTATCTCTC
577836 CTCCTATCTCTC
1 CTCCTATCTCTC
577848 CTCCTATCATC-C
1 CTCCTATC-TCTC
577860 CTCCTA--TCT-
1 CTCCTATCTCTC
*
577869 CTACTA--TCT-
1 CTCCTATCTCTC
577878 CTCCTATCTCTC
1 CTCCTATCTCTC
577890 CTCCTATCATC-C
1 CTCCTATC-TCTC
577902 CTCCTATCTCT
1 CTCCTATCTCT
577913 TCTTTCTCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 24
0.76 0.03 0.20
Matches are distributed among these distances:
9 30 0.33
11 8 0.09
12 47 0.52
13 6 0.07
ACGTcount: A:0.13, C:0.46, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:577817 original size:42 final size:42
Alignment explanation
Indices: 577760--577921 Score: 270
Period size: 42 Copynumber: 3.9 Consensus size: 42
577750 CTTCTTCTCT
* * * *
577760 TCTCCTTCTTTCATCCCTCCTCTCTCTATTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
577802 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
577844 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
* *
577886 TCTCCTCCTATCATCCCTCCTATCTCTTCTTTCTCT
1 TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
577922 TTGAGGGCTA
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 114 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (42 bp):
TCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
Found at i:583399 original size:15 final size:15
Alignment explanation
Indices: 583361--583399 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
583351 AGAATACAAA
583361 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
* * *
583376 AATACAAAAAGAGAG
1 AAAAAAAAAAGAAAG
583391 AAAAAAAAA
1 AAAAAAAAA
583400 CCAGTATTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:584168 original size:12 final size:11
Alignment explanation
Indices: 584146--584221 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
584136 AGAGAAAGAA
*
584146 GAGAGAGGAGG
1 GAGATAGGAGG
584157 GATGATAGGAGG
1 GA-GATAGGAGG
*
584169 AGAGACAGGA--
1 -GAGATAGGAGG
*
584179 GAGATAGTA--
1 GAGATAGGAGG
584188 GAGATAGGAGG
1 GAGATAGGAGG
584199 GATGATAGGAGG
1 GA-GATAGGAGG
*
584211 AGAGACAGGAG
1 -GAGATAGGAG
584222 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:584178 original size:24 final size:24
Alignment explanation
Indices: 584145--584230 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
584135 AAGAGAAAGA
*
584145 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
584169 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
584187 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
584211 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
584231 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:584197 original size:42 final size:42
Alignment explanation
Indices: 584136--584254 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
584126 TAGCCCTCAA
* *
584136 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
584178 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
584220 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
584255 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:590608 original size:42 final size:42
Alignment explanation
Indices: 590553--590713 Score: 259
Period size: 42 Copynumber: 3.8 Consensus size: 42
590543 TTCTTCTCTC
* * *
590553 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
590595 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
*
590637 CTACTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
* * *
590679 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
590714 TTGAGGGCTA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 111 1.00
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
Found at i:590612 original size:12 final size:11
Alignment explanation
Indices: 590586--590703 Score: 63
Period size: 12 Copynumber: 10.9 Consensus size: 11
590576 TCTATTATCT
*
590586 CTCCTGTCTCTC
1 CTCCTATCTC-C
590598 CTCCTATCATCC
1 CTCCTATC-TCC
590610 CTCCTATCT--
1 CTCCTATCTCC
*
590619 CTACTATCT--
1 CTCCTATCTCC
* *
590628 CTCCTGTCTCTA
1 CTCCTATCTC-C
590640 CTCCTATCATCC
1 CTCCTATC-TCC
590652 CTCCTATCT--
1 CTCCTATCTCC
*
590661 CTACTATCT--
1 CTCCTATCTCC
*
590670 CTCCTGTCTCTC
1 CTCCTATCTC-C
590682 CTCCTATCATCC
1 CTCCTATC-TCC
*
590694 CTCCTCTCTC
1 CTCCTATCTC
590704 TTCTTTCTCT
Statistics
Matches: 86, Mismatches: 11, Indels: 19
0.74 0.09 0.16
Matches are distributed among these distances:
9 30 0.35
11 4 0.05
12 46 0.53
13 6 0.07
ACGTcount: A:0.11, C:0.47, G:0.03, T:0.40
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:590637 original size:18 final size:18
Alignment explanation
Indices: 590568--590680 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
590558 CCTGTCATCC
* *
590568 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
590586 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
590608 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
590628 CTCCTGTCTCTACTCCTATCAT
1 CTCCTGTCTCTA---CTATC-T
*
590650 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
590670 CTCCTGTCTCT
1 CTCCTGTCTCT
590681 CCTCCTATCA
Statistics
Matches: 75, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
18 26 0.35
20 5 0.07
21 23 0.31
22 5 0.07
24 16 0.21
ACGTcount: A:0.12, C:0.43, G:0.03, T:0.42
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:590679 original size:9 final size:9
Alignment explanation
Indices: 590581--590683 Score: 59
Period size: 9 Copynumber: 11.1 Consensus size: 9
590571 CTCTCTCTAT
590581 TATCTCTCC
1 TATCTCTCC
*
590590 TGTCTCTCC
1 TATCTCTCC
* *
590599 T-CCTAT-C
1 TATCTCTCC
*
590606 -ATCCCTCC
1 TATCTCTCC
*
590614 TATCTCTAC
1 TATCTCTCC
590623 TATCTCTCC
1 TATCTCTCC
*
590632 TGTCTCTACTCC
1 --TATCT-CTCC
590644 TATCATCCCTCC
1 TATC-T--CTCC
*
590656 TATCTCTAC
1 TATCTCTCC
590665 TATCTCTCC
1 TATCTCTCC
*
590674 TGTCTCTCC
1 TATCTCTCC
590683 T
1 T
590684 CCTATCATCC
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
7 3 0.04
8 4 0.06
9 43 0.61
10 3 0.04
11 6 0.08
12 12 0.17
ACGTcount: A:0.12, C:0.44, G:0.03, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:595794 original size:42 final size:42
Alignment explanation
Indices: 595739--595857 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
595729 TTTTTCTCTC
* *
595739 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
595781 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
595823 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
595858 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:595798 original size:12 final size:11
Alignment explanation
Indices: 595772--595847 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
595762 TCTATTATCT
*
595772 CTCCTGTCTCTC
1 CTCCTATCTC-C
595784 CTCCTATCATCC
1 CTCCTATC-TCC
595796 CTCCTATCT--
1 CTCCTATCTCC
*
595805 CTACTATCT--
1 CTCCTATCTCC
*
595814 CTCCTGTCTCTC
1 CTCCTATCTC-C
595826 CTCCTATCATCC
1 CTCCTATC-TCC
*
595838 CTCCTCTCTC
1 CTCCTATCTC
595848 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:595799 original size:24 final size:24
Alignment explanation
Indices: 595763--595848 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
595753 CCTCCTCTCT
* *
595763 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
595787 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
595808 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
595829 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
595849 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:595823 original size:18 final size:18
Alignment explanation
Indices: 595754--595824 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
595744 CCTGTCATCC
* *
595754 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
595772 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
595794 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
595814 CTCCTGTCTCT
1 CTCCTGTCTCT
595825 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:605536 original size:245 final size:246
Alignment explanation
Indices: 605079--605570 Score: 905
Period size: 245 Copynumber: 2.0 Consensus size: 246
605069 GCTACATTTT
* * *
605079 TGATGACAACCATTAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTAACAATAAATA
1 TGATGACAACCATGAACCAAGGTTGCCTAAACAATGATCTTGAGATGGATTTCTAACAATAAACA
*
605144 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTA
66 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATCGAATAGATTA
* *
605209 GAGATGAAGGATGGCGCCACAATCATAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
131 GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTC
605274 TTGGCCTCTTGATAAGATCCAGAAAAATTGGATCACTCAAGAACCTAAGAA
196 TTGGCCTCTTGATAAGATCCAGAAAAATTGGATCACTCAAGAACCTAAGAA
605325 TGATGACAACCATGAACCAAGGTTGCCTAAACAATGATCTTGAGATGGATTTCTAACAATAAACA
1 TGATGACAACCATGAACCAAGGTTGCCTAAACAATGATCTTGAGATGGATTTCTAACAATAAACA
605390 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAG-AAAAAAATAACAAAATCGAATAGATTA
66 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATCGAATAGATTA
*
605454 GAGATGGAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTC
131 GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTC
*
605519 TTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAA
196 TTGGCCTCTTGATAAGATCCAGAAAAATTGGATCACTCAAGAACCTAAGAA
605570 T
1 T
605571 CACACTCTCA
Statistics
Matches: 238, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
245 139 0.58
246 99 0.42
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.21
Consensus pattern (246 bp):
TGATGACAACCATGAACCAAGGTTGCCTAAACAATGATCTTGAGATGGATTTCTAACAATAAACA
GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATCGAATAGATTA
GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCACCACAAGAGTC
TTGGCCTCTTGATAAGATCCAGAAAAATTGGATCACTCAAGAACCTAAGAA
Found at i:610318 original size:18 final size:18
Alignment explanation
Indices: 610295--610402 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
610285 ATCTTCTTCT
610295 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
610313 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
610334 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
610355 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
610376 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
610397 CTCCTC
1 CTCCTC
610403 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 14 0.20
19 4 0.06
20 6 0.09
21 22 0.31
22 6 0.09
23 4 0.06
24 8 0.11
25 3 0.04
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:610350 original size:42 final size:42
Alignment explanation
Indices: 610298--610416 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
610288 TTCTTCTCTC
*
610298 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
610340 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
610382 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
610417 TTGAGGGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:610357 original size:12 final size:11
Alignment explanation
Indices: 610331--610406 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
610321 TCTATTATCT
*
610331 CTCCTGTCTCTC
1 CTCCTATCTC-C
610343 CTCCTATCATCC
1 CTCCTATC-TCC
610355 CTCCTATCT--
1 CTCCTATCTCC
*
610364 CTACTATCT--
1 CTCCTATCTCC
*
610373 CTCCTGTCTCTC
1 CTCCTATCTC-C
610385 CTCCTATCATCC
1 CTCCTATC-TCC
*
610397 CTCCTCTCTC
1 CTCCTATCTC
610407 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Done.