Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011743.1 Kokia drynarioides strain JFW-HI SEQ_126737, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 184780
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 39 characters in sequence are not A, C, G, or T
Found at i:753 original size:23 final size:23
Alignment explanation
Indices: 727--874 Score: 181
Period size: 23 Copynumber: 6.3 Consensus size: 23
717 ACACTAGCAC
727 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
750 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
*
773 GCTCTCTGTTATTAGCACTGTGTTT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
798 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
821 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
844 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
867 GCTCTCTG
1 GCTCTCTG
875 TTGCCCAGCA
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.03
23 84 0.79
25 16 0.15
26 3 0.03
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:795 original size:46 final size:44
Alignment explanation
Indices: 727--902 Score: 156
Period size: 48 Copynumber: 3.8 Consensus size: 44
717 ACACTAGCAC
727 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACT-TGTGTGCTCTCTGTTTAGCACGTCT-GT
* * * *
773 GCTCTCTGTTATTAGCACTGTGTTTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACT-TGTGTGCTCTCTGTTTAGCAC-GTCTGT
* * * *
821 GCTCTCTGACTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCAC-TTGTGTGCTCTCTGTTTAGCAC-GTCTGT
*
867 GCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTT
1 GCTCTCTGATT----AGCACTTGTGTGCTCTCTGTTT
903 GTTCCGTATA
Statistics
Matches: 108, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
45 1 0.01
46 46 0.43
47 1 0.01
48 54 0.50
49 6 0.06
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (44 bp):
GCTCTCTGATTAGCACTTGTGTGCTCTCTGTTTAGCACGTCTGT
Found at i:875 original size:23 final size:23
Alignment explanation
Indices: 727--902 Score: 176
Period size: 23 Copynumber: 7.5 Consensus size: 23
717 ACACTAGCAC
*
727 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
750 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
773 GCTCTCTGTTATTAGCACTGTGTTT
1 GCTCTCTG-T-TTAGCACTGTGTGT
* *
798 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
** * *
821 GCTCTCTGACTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
844 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
867 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
892 GCTCTCTGTTT
1 GCTCTCTGTTT
903 GTTCCGTATA
Statistics
Matches: 128, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.02
23 85 0.66
24 1 0.01
25 30 0.23
26 9 0.07
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:10776 original size:21 final size:21
Alignment explanation
Indices: 10730--10777 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
10720 ATCTTGGCTG
* * * *
10730 AGATATAATGAGATAGGGCTC
1 AGATCTAAAGAGATAGAGCCC
10751 AGATCTAAAGAGATAGAGCCC
1 AGATCTAAAGAGATAGAGCCC
10772 AGATCT
1 AGATCT
10778 TTGAAAGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (21 bp):
AGATCTAAAGAGATAGAGCCC
Found at i:11351 original size:9 final size:9
Alignment explanation
Indices: 11339--11366 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11329 TTTTTTTTTA
11339 TTAGGCTTG
1 TTAGGCTTG
11348 TTAGGCTTG
1 TTAGGCTTG
11357 TTAGGCTTG
1 TTAGGCTTG
11366 T
1 T
11367 ATGGGTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.32, T:0.46
Consensus pattern (9 bp):
TTAGGCTTG
Found at i:11503 original size:11 final size:11
Alignment explanation
Indices: 11487--11511 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11477 TTTAAAAATG
11487 TTTATTTTTAT
1 TTTATTTTTAT
11498 TTTATTTTTAT
1 TTTATTTTTAT
11509 TTT
1 TTT
11512 TGGGTTTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:14864 original size:20 final size:19
Alignment explanation
Indices: 14818--14873 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
14808 ATTTTAAAAT
* *
14818 CAAGTTAAAATAATTTTTAA
1 CAAGTCAAAATAA-TTTGAA
*
14838 CATGTCAAAATAATTTGAA
1 CAAGTCAAAATAATTTGAA
*
14857 CTAAGTCAAAATCATTT
1 C-AAGTCAAAATAATTT
14874 TAAAACTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (19 bp):
CAAGTCAAAATAATTTGAA
Found at i:21069 original size:2 final size:2
Alignment explanation
Indices: 21062--21104 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21052 TTCACTGTCC
21062 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21104 C
1 C
21105 AAGAGCACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:25588 original size:19 final size:20
Alignment explanation
Indices: 25548--25588 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
25538 CAAAAACCCT
*
25548 CAAAACTTTTTATTTTCCCC
1 CAAAACTTTTTATCTTCCCC
25568 CAAAA-TTTTTA-CTTCCTCC
1 CAAAACTTTTTATCTTCC-CC
25587 CA
1 CA
25589 CTTTCTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (20 bp):
CAAAACTTTTTATCTTCCCC
Found at i:33975 original size:14 final size:12
Alignment explanation
Indices: 33948--33972 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33938 GCCTACTCAT
33948 ATTATTTTTTAA
1 ATTATTTTTTAA
33960 ATTATTTTTTAA
1 ATTATTTTTTAA
33972 A
1 A
33973 AATGTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTTTTTAA
Found at i:44661 original size:22 final size:23
Alignment explanation
Indices: 44608--44664 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
44598 CGTTGAACGA
*
44608 ACCCGTTGATCGACCCGACCCAG
1 ACCCGTTGACCGACCCGACCCAG
44631 ACCCGTTGACCGACCCGACCCAG
1 ACCCGTTGACCGACCCGACCCAG
44654 A-CCGTTGACCG
1 ACCCGTTGACCG
44665 TTAACTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.21, C:0.44, G:0.23, T:0.12
Consensus pattern (23 bp):
ACCCGTTGACCGACCCGACCCAG
Found at i:50135 original size:76 final size:76
Alignment explanation
Indices: 50004--50157 Score: 272
Period size: 76 Copynumber: 2.0 Consensus size: 76
49994 CATAGTATGA
*
50004 CATGTCTAAATCTTGAGTGCATGATAAACTATGTATATGTGACTCATATACTTTGATGTAAGTAA
1 CATGCCTAAATCTTGAGTGCATGATAAACTATGTATATGTGACTCATATACTTTGATGTAAGTAA
50069 AAGCCTGAGTT
66 AAGCCTGAGTT
* * *
50080 CATGCCTAAATTTTGAGTGCATGATGAACTATGTATATGTGACTCGTATACTTTGATGTAAGTAA
1 CATGCCTAAATCTTGAGTGCATGATAAACTATGTATATGTGACTCATATACTTTGATGTAAGTAA
50145 AAGCCTGAGTT
66 AAGCCTGAGTT
50156 CA
1 CA
50158 AATAGATAAG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (76 bp):
CATGCCTAAATCTTGAGTGCATGATAAACTATGTATATGTGACTCATATACTTTGATGTAAGTAA
AAGCCTGAGTT
Found at i:51846 original size:104 final size:104
Alignment explanation
Indices: 51666--51873 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
51656 AGAGCTAATA
51666 AGTGGTAATCATTTTGAAAGTGAAATATGAAATTATAATGAACTATAGTTGAGCCTTAAGAAAGA
1 AGTGGTAATCATTTTGAAAGTGAAATATGAAATTATAATGAACTATAGTTGAGCCTTAAGAAAGA
51731 ATGAATTGGTGTATGGACCTGAGTGATTGTTAGTAAATG
66 ATGAATTGGTGTATGGACCTGAGTGATTGTTAGTAAATG
51770 AGTGGTAATCATTTTGAAAGTGAAATATGAAATTATAATGAACTATAGTTGAGCCTTAAGAAAGA
1 AGTGGTAATCATTTTGAAAGTGAAATATGAAATTATAATGAACTATAGTTGAGCCTTAAGAAAGA
51835 ATGAATTGGTGTATGGACCTGAGTGATTGTTAGTAAATG
66 ATGAATTGGTGTATGGACCTGAGTGATTGTTAGTAAATG
51874 GCATACTTAA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (104 bp):
AGTGGTAATCATTTTGAAAGTGAAATATGAAATTATAATGAACTATAGTTGAGCCTTAAGAAAGA
ATGAATTGGTGTATGGACCTGAGTGATTGTTAGTAAATG
Found at i:59627 original size:51 final size:51
Alignment explanation
Indices: 59551--59785 Score: 274
Period size: 51 Copynumber: 4.6 Consensus size: 51
59541 CTATAAACGA
*
59551 AAAGGTCCGATGACTAAGTGTCATCGTGAGGAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
59602 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * * * *
59653 AAAGGTCCAATGATTAAGTGTCATCCTAAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * * * **
59704 AAAGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
59756 AAGAGGTTCGATGACTATA-TGTCATCGTGA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGA
59786 ATATGAAATG
Statistics
Matches: 154, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
51 121 0.79
52 10 0.06
53 23 0.15
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:62113 original size:15 final size:16
Alignment explanation
Indices: 62088--62119 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
62078 AGGGGTTTTA
62088 AGAGAAGAATTATCAC
1 AGAGAAGAATTATCAC
62104 AGAG-AGAATTATCAC
1 AGAGAAGAATTATCAC
62119 A
1 A
62120 ATAAGAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (16 bp):
AGAGAAGAATTATCAC
Found at i:65812 original size:29 final size:29
Alignment explanation
Indices: 65763--65828 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
65753 TAATAACTTA
*
65763 TATATTTATAAAGAATTAAATCA-AATTTT
1 TATATTTATAAAGAATAAAAT-ATAATTTT
*
65792 TATATTT-TAAGGAGATAAAATATAA-TTT
1 TATATTTATAAAGA-ATAAAATATAATTTT
*
65820 TATCTTTAT
1 TATATTTAT
65829 TAACTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (29 bp):
TATATTTATAAAGAATAAAATATAATTTT
Found at i:67642 original size:17 final size:17
Alignment explanation
Indices: 67617--67649 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
67607 AAAGTAAAAA
67617 TAATAATATAA-ATTTT
1 TAATAATATAACATTTT
67633 TAATATATATAACATTT
1 TAATA-ATATAACATTT
67650 ATAAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATAATATAACATTTT
Found at i:67775 original size:21 final size:18
Alignment explanation
Indices: 67744--67782 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 18
67734 AAAAAATTAT
67744 AATAATTTTTTTATGAATA
1 AATAATTTTTTTAT-AATA
67763 AATATATTATTTTTATAATA
1 AATA-ATT-TTTTTATAATA
67783 TTTAGCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AATAATTTTTTTATAATA
Found at i:70774 original size:23 final size:23
Alignment explanation
Indices: 70741--70786 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
70731 TCCATTTTAA
*
70741 ATAAATAATATGTTGACAATATT
1 ATAAATAATATCTTGACAATATT
*
70764 ATAAATCATATCTTGACAATATT
1 ATAAATAATATCTTGACAATATT
70787 GAGGCATTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (23 bp):
ATAAATAATATCTTGACAATATT
Found at i:70872 original size:24 final size:27
Alignment explanation
Indices: 70826--70874 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
70816 ACACCACATC
70826 ATTTAATTATGAATATTTCTTTTAATT
1 ATTTAATTATGAATATTTCTTTTAATT
70853 ATTTAATTAT-AAT-TTT-TTTTAA
1 ATTTAATTATGAATATTTCTTTTAA
70875 ATTAATAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 3 0.14
26 3 0.14
27 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
ATTTAATTATGAATATTTCTTTTAATT
Found at i:71157 original size:21 final size:21
Alignment explanation
Indices: 71133--71175 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
71123 AGTATAATAA
* *
71133 TAAATTTAAGGGCTAAATTTG
1 TAAAGTTAAAGGCTAAATTTG
*
71154 TAAAGTTAAAGGTTAAATTTG
1 TAAAGTTAAAGGCTAAATTTG
71175 T
1 T
71176 TATTATACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (21 bp):
TAAAGTTAAAGGCTAAATTTG
Found at i:74740 original size:23 final size:23
Alignment explanation
Indices: 74706--74763 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
74696 ACGCTAGCGC
*
74706 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTATTTCGCACTTCGTGT
74729 GCTTACTATTTCGCACTTCGTGT
1 GCTTACTATTTCGCACTTCGTGT
*
74752 GCCTACTGATTT
1 GCTTACT-ATTT
74764 GCGCTATGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.43
Consensus pattern (23 bp):
GCTTACTATTTCGCACTTCGTGT
Found at i:74814 original size:23 final size:23
Alignment explanation
Indices: 74778--74827 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
74768 TATGTGCGCC
*
74778 TACT-GATTGTACTGTGTGTGCT
1 TACTGGATTGCACTGTGTGTGCT
74800 TACTGGATTGCACTGTGTGTGCT
1 TACTGGATTGCACTGTGTGTGCT
74823 TACTG
1 TACTG
74828 TTAAGTACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42
Consensus pattern (23 bp):
TACTGGATTGCACTGTGTGTGCT
Found at i:77135 original size:16 final size:16
Alignment explanation
Indices: 77114--77167 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
77104 TTTGGTTCGT
77114 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAAC
* *
77130 TGTAATGGAGTAGAGC
1 TGTAATGGAATAGAAC
*
77146 TGTAATGGAATAGGAC
1 TGTAATGGAATAGAAC
77162 TGTAAT
1 TGTAAT
77168 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.06, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAAC
Found at i:77404 original size:58 final size:58
Alignment explanation
Indices: 77337--77497 Score: 193
Period size: 58 Copynumber: 2.8 Consensus size: 58
77327 GACTATTGTT
* *
77337 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAAATAATAAATTATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* * * *
77395 ATTATATTTTAACATAATTATCATTAAATACAATTTAAT-AAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
* *
77452 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAA
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAA
77498 CCATAATATA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
57 21 0.24
58 50 0.57
59 10 0.11
60 6 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
Found at i:84221 original size:13 final size:13
Alignment explanation
Indices: 84203--84241 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
84193 AATATTATCA
84203 TTTTTATAATTTT
1 TTTTTATAATTTT
*
84216 TTTTTATAAATTT
1 TTTTTATAATTTT
*
84229 TGTTTATAATTTT
1 TTTTTATAATTTT
84242 CATATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTTATAATTTT
Found at i:90212 original size:12 final size:12
Alignment explanation
Indices: 90195--90246 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
90185 ATTTCACCCA
90195 AAAAAAAGAAAG
1 AAAAAAAGAAAG
90207 AAAAAAAGAAA-
1 AAAAAAAGAAAG
90218 AGAAAAAAGAAAG
1 A-AAAAAAGAAAG
* *
90231 ACAAGAA-AAAG
1 AAAAAAAGAAAG
90242 AAAAA
1 AAAAA
90247 GGAGTGGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 8 0.24
12 25 0.74
13 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:90228 original size:24 final size:26
Alignment explanation
Indices: 90196--90245 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
90186 TTTCACCCAA
90196 AAAAAAGAAAG-AA-AAAAAGAAAAG
1 AAAAAAGAAAGAAAGAAAAAGAAAAG
90220 AAAAAAGAAAGACAAGAAAAAGAAAA
1 AAAAAAGAAAGA-AAGAAAAAGAAAA
90246 AGGAGTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.48
26 2 0.09
27 10 0.43
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAGAAAGAAAAAGAAAAG
Found at i:90230 original size:16 final size:16
Alignment explanation
Indices: 90198--90244 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
90188 TCACCCAAAA
*
90198 AAAAGAAAGAAAAAAAG
1 AAAAGAAA-AAAGAAAG
90215 AAAAGAAAAAAGAAAG
1 AAAAGAAAAAAGAAAG
*
90231 ACAAG-AAAAAGAAA
1 AAAAGAAAAAAGAAA
90245 AAGGAGTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 9 0.32
16 11 0.39
17 8 0.29
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAGAAAG
Found at i:92679 original size:49 final size:49
Alignment explanation
Indices: 92609--92745 Score: 150
Period size: 49 Copynumber: 2.8 Consensus size: 49
92599 AAAGACATGA
* * *
92609 AGGGAAATATTAAAGTCGCAATGGTGAATCTTATACCTTAGAGATATAG
1 AGGGAAAGATTAAAGCCGCAATGGTGAATCTTATACCCTAGAGATATAG
* * * * * *
92658 AGGGAAAGGTTGAAA-CTGCAATGGCGAGTCTTATACCCTAGAGATGTGG
1 AGGGAAAGATT-AAAGCCGCAATGGTGAATCTTATACCCTAGAGATATAG
* * *
92707 GGGGAAAGATTAAAGCCACAACGGTGAATCTTATACCCT
1 AGGGAAAGATTAAAGCCGCAATGGTGAATCTTATACCCT
92746 GAAAATGATG
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
48 3 0.04
49 64 0.91
50 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (49 bp):
AGGGAAAGATTAAAGCCGCAATGGTGAATCTTATACCCTAGAGATATAG
Found at i:93154 original size:50 final size:50
Alignment explanation
Indices: 93075--93204 Score: 129
Period size: 50 Copynumber: 2.6 Consensus size: 50
93065 AACCTTTATC
* * * *
93075 TCCCTAAAGTTACAGTGGAGCAAGATGAAGCTATAACATC-AAATCCTATA
1 TCCCTAAAGTTACAGTGGAGCAAGATGAAGATACAAAAGCGAAA-CCTATA
* * * *
93125 TCCCTGAAGTTACAGTGGATC-GGATTGAAGATACAAAAGCGAAACTTATA
1 TCCCTAAAGTTACAGTGGAGCAAGA-TGAAGATACAAAAGCGAAACCTATA
** *
93175 TCCCTAAAGTTACAGTAAAGCAGGATGAAG
1 TCCCTAAAGTTACAGTGGAGCAAGATGAAG
93205 CTACCTATAC
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
49 2 0.03
50 57 0.88
51 6 0.09
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (50 bp):
TCCCTAAAGTTACAGTGGAGCAAGATGAAGATACAAAAGCGAAACCTATA
Found at i:94096 original size:5 final size:5
Alignment explanation
Indices: 94081--94120 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
94071 GTTTATTTTG
94081 TATTT TA-TT TATTT TATTT TATTT TATTT TATTTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT
94121 CAAAAAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 24 0.73
6 5 0.15
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:105083 original size:15 final size:15
Alignment explanation
Indices: 105063--105118 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
105053 TAAAGTTCAG
105063 TAAAAATTTAAATGT
1 TAAAAATTTAAATGT
** *
105078 TAAAAAAATAAGTGT
1 TAAAAATTTAAATGT
* *
105093 TAAAAATTTAATTAT
1 TAAAAATTTAAATGT
*
105108 TGAAAATTTAA
1 TAAAAATTTAA
105119 GTATTGAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (15 bp):
TAAAAATTTAAATGT
Found at i:105123 original size:15 final size:15
Alignment explanation
Indices: 105095--105126 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
105085 ATAAGTGTTA
*
105095 AAAATTTAATTATTG
1 AAAATTTAAGTATTG
105110 AAAATTTAAGTATTG
1 AAAATTTAAGTATTG
105125 AA
1 AA
105127 TTTAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (15 bp):
AAAATTTAAGTATTG
Found at i:106410 original size:12 final size:13
Alignment explanation
Indices: 106386--106414 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
106376 CTAATGGTAA
106386 TAATATATTTTAT
1 TAATATATTTTAT
106399 TAATAT-TTTTAT
1 TAATATATTTTAT
106411 TAAT
1 TAAT
106415 TAATGACATT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATATATTTTAT
Found at i:106507 original size:13 final size:13
Alignment explanation
Indices: 106489--106521 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
106479 GATTTAAAAA
106489 TCATTTTAACTTT
1 TCATTTTAACTTT
*
106502 TCA-TTTAATTTT
1 TCATTTTAACTTT
106514 TCATTTTA
1 TCATTTTA
106522 TTAACCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TCATTTTAACTTT
Found at i:106695 original size:19 final size:19
Alignment explanation
Indices: 106643--106699 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
106633 CAATTAATTG
*
106643 ATTTTTTAAAATTTAAAAAT
1 ATTTTTT-AAATTTTAAAAT
* ** *
106663 ATTTTATACTTTTTAATAT
1 ATTTTTTAAATTTTAAAAT
106682 ATTTTTTAAATTTTAAAA
1 ATTTTTTAAATTTTAAAA
106700 ATCAATTAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTTTTAAATTTTAAAAT
Found at i:108510 original size:22 final size:22
Alignment explanation
Indices: 108478--108519 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
108468 ACTTCGTGTT
108478 ATTTTTTTTAT-TAATTTTATG
1 ATTTTTTTTATATAATTTTATG
*
108499 ATTTTTTATTATATATTTTTA
1 ATTTTTT-TTATATAATTTTA
108520 AATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
ATTTTTTTTATATAATTTTATG
Found at i:108536 original size:20 final size:20
Alignment explanation
Indices: 108482--108546 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
108472 CGTGTTATTT
* * *
108482 TTTTTATTAATTTTATGATTT
1 TTTTTATAAATTTTA-AATTA
*
108503 TTTATTATATATTTTTAAA-TA
1 TTT-TTATA-AATTTTAAATTA
108524 TTTTTATAAATTTTAAATTA
1 TTTTTATAAATTTTAAATTA
108544 TTT
1 TTT
108547 GTTGACTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 8 0.22
20 10 0.28
21 7 0.19
22 5 0.14
23 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTATAAATTTTAAATTA
Found at i:109106 original size:7 final size:7
Alignment explanation
Indices: 109094--109124 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
109084 TGGTAATAAA
109094 AATATTT
1 AATATTT
109101 AATATTT
1 AATATTT
109108 AATATTT
1 AATATTT
109115 AAT-TTT
1 AATATTT
109121 AATA
1 AATA
109125 AAAAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATATTT
Found at i:113605 original size:26 final size:27
Alignment explanation
Indices: 113545--113618 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
113535 TATTTTCTTT
113545 AAATTTTATC-AGAGGTAAAATCATCAA
1 AAATTTTATCGAG-GGTAAAATCATCAA
* * *
113572 AAACTTTATCGAGGGTAAAATCGT-TA
1 AAATTTTATCGAGGGTAAAATCATCAA
*
113598 AAATTTTA-CTGGGGGTAAAAT
1 AAATTTTATC-GAGGGTAAAAT
113619 AGAGATGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 18 0.45
27 19 0.47
28 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31
Consensus pattern (27 bp):
AAATTTTATCGAGGGTAAAATCATCAA
Found at i:117061 original size:158 final size:157
Alignment explanation
Indices: 116732--117063 Score: 477
Period size: 157 Copynumber: 2.1 Consensus size: 157
116722 GTAACCATAT
* * * * *
116732 ATGCTCACACGAGATGTGAAATGGGCCTGCTCACATGAGTTGTGGGTCGAGAAGTGGGGGTACAT
1 ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATGAGCTGTGGGTCGAGAAGTGAGGCTACAC
* * *
116797 GATGCTGCTCACATGAGCTGTGGAGGAACCGAATAAATATCGGACCTCAGCCATAAGTAGGACAT
66 GATGCTGCTCACACGAGCTGTGGAGGAACCGAACAAATATAGGACCTCAGCCATAAGTAGGACAT
* *
116862 CTAAGACCAGCAGCCATATAACATGTA
131 CTAAGACCAACACCCATATAACATGTA
*
116889 ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATGAGCTGTGGGTCGAGATGTGAGGCTACAC
1 ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATGAGCTGTGGGTCGAGAAGTGAGGCTACAC
* * * **
116954 GATGCTGCTCACACGAGTTGTGGA-GAATCCGCAACCAATGTAGGACCTCAGCCATCGGTAGGAC
66 GATGCTGCTCACACGAGCTGTGGAGGAA-CCG-AACAAATATAGGACCTCAGCCATAAGTAGGAC
*
117018 ATCTAAGACCAACACCCATATAACCTGTA
129 ATCTAAGACCAACACCCATATAACATGTA
*
117047 ATGCTCACATGAGCTGT
1 ATGCTCACACGAGCTGT
117064 AACTGTAACA
Statistics
Matches: 155, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
156 3 0.02
157 84 0.54
158 68 0.44
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (157 bp):
ATGCTCACACGAGCTGTGAAATGGGCCTGCTCACATGAGCTGTGGGTCGAGAAGTGAGGCTACAC
GATGCTGCTCACACGAGCTGTGGAGGAACCGAACAAATATAGGACCTCAGCCATAAGTAGGACAT
CTAAGACCAACACCCATATAACATGTA
Found at i:118785 original size:2 final size:2
Alignment explanation
Indices: 118780--118814 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
118770 TTTACATTAT
118780 TA TA TA TA TA 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 TA TA TA TA TA T
118815 TCATACACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:120435 original size:2 final size:2
Alignment explanation
Indices: 120428--120452 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
120418 AAGTTCGTAC
120428 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
120453 AGAGTCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:120623 original size:23 final size:23
Alignment explanation
Indices: 120597--120657 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
120587 GCTCATTAGT
*
120597 ATGATATGTTTACGCTCGTCAGC
1 ATGATAAGTTTACGCTCGTCAGC
* *
120620 ATGATAAATTTATGCTCGTCAGC
1 ATGATAAGTTTACGCTCGTCAGC
*
120643 ATGATACGTTTACGC
1 ATGATAAGTTTACGC
120658 ATACTTCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (23 bp):
ATGATAAGTTTACGCTCGTCAGC
Found at i:127209 original size:29 final size:28
Alignment explanation
Indices: 127162--127267 Score: 106
Period size: 29 Copynumber: 3.7 Consensus size: 28
127152 CGGAGAGTTT
* *
127162 GGGGTTAAAACATAATTTTGGAAAGTTGA
1 GGGGTAAAAATATAATTTT-GAAAGTTGA
* * *
127191 GGAGTAAAAATATGATTTTTAGAAGTTTG-
1 GGGGTAAAAATATAATTTTGA-AAG-TTGA
*
127220 GGGGTAAAAATATAATTTTTGAAAGTTTA
1 GGGGTAAAAATATAA-TTTTGAAAGTTGA
*
127249 GGGGTAAAAATGTAATTTT
1 GGGGTAAAAATATAATTTT
127268 AAGAAGTTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
28 7 0.11
29 48 0.76
30 8 0.13
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.36
Consensus pattern (28 bp):
GGGGTAAAAATATAATTTTGAAAGTTGA
Found at i:127274 original size:29 final size:29
Alignment explanation
Indices: 127184--127435 Score: 140
Period size: 29 Copynumber: 8.6 Consensus size: 29
127174 TAATTTTGGA
* * * * *
127184 AAGTTGAGGAGTAAAAATATGATTTTTAG
1 AAGTTTAGGGGTAAAAATGTAATTTTAAG
* * *
127213 AAGTTTGGGGGTAAAAATATAATTTT-TG
1 AAGTTTAGGGGTAAAAATGTAATTTTAAG
127241 AAAGTTTAGGGGTAAAAATGTAATTTTAAG
1 -AAGTTTAGGGGTAAAAATGTAATTTTAAG
* ** *
127271 AAGTTCAGTAG-CAAAATGTAATTTTTAAG
1 AAGTTTAGGGGTAAAAATGTAA-TTTTAAG
* * **
127300 AAGTTTAGGGGTCAAAATGTGATTTTTGG
1 AAGTTTAGGGGTAAAAATGTAATTTTAAG
* * *
127329 AAG-TTCGAGGGCAAAAATGTAATTTTTGAG
1 AAGTTTAG-GGGTAAAAATGTAA-TTTTAAG
* * * *
127359 AAGTTT-GATGGTTAAAATGTGATTTT-TG
1 AAGTTTAG-GGGTAAAAATGTAATTTTAAG
*
127387 AAAGTTTGAGGGCT-AAAATGTAATTTTTAA-
1 -AAGTTT-AGGGGTAAAAATGTAA-TTTTAAG
* *
127417 AAGATTTAAGGTTAAAAAT
1 AAG-TTTAGGGGTAAAAAT
127436 ATGATTTGTG
Statistics
Matches: 174, Mismatches: 35, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
28 14 0.08
29 113 0.65
30 44 0.25
31 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (29 bp):
AAGTTTAGGGGTAAAAATGTAATTTTAAG
Found at i:127311 original size:87 final size:87
Alignment explanation
Indices: 127205--127363 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 87
127195 TAAAAATATG
* *
127205 ATTTTTAGAAGTTTGGGGGTAAAAATATAATTTTTGAAAGTTTAG-GGGTAAAAATGTAA-TTTT
1 ATTTTTAGAAGTTTAGGGGTAAAAATATAATTTTTGAAAG-TTAGAGGGCAAAAATGTAATTTTT
127268 AAGAAGTTCAGTAGCAAAATGTA
65 AAGAAGTTCAGTAGCAAAATGTA
* * * * *
127291 ATTTTTAAGAAGTTTAGGGGTCAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTT
1 ATTTTT-AGAAGTTTAGGGGTAAAAATATAATTTTTGAAAGTTAGAGGGCAAAAATGTAATTTTT
*
127356 GAGAAGTT
65 AAGAAGTT
127364 TGATGGTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 9 0.15
87 42 0.68
88 11 0.18
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (87 bp):
ATTTTTAGAAGTTTAGGGGTAAAAATATAATTTTTGAAAGTTAGAGGGCAAAAATGTAATTTTTA
AGAAGTTCAGTAGCAAAATGTA
Found at i:127376 original size:59 final size:59
Alignment explanation
Indices: 127174--127453 Score: 241
Period size: 59 Copynumber: 4.8 Consensus size: 59
127164 GGTTAAAACA
* * * * * * * * * *
127174 TAATTTTGGA-AAGTTGAGGAGTAAAAATATGATTTTTAGAAGTTTGGGGGTAAAAATA
1 TAATTTTTGAGAAGTTTAGGGGTTAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATG
* * ** *
127232 TAATTTTTGA-AAGTTTAGGGGTAAAAATGTAATTTTAAGAAGTTC-AGTAGC-AAAATG
1 TAATTTTTGAGAAGTTTAGGGGTTAAAATGTGATTTTTGGAAGTTCGAG-GGCAAAAATG
* *
127289 TAATTTTTAAGAAGTTTAGGGGTCAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATG
1 TAATTTTTGAGAAGTTTAGGGGTTAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATG
* * * *
127348 TAATTTTTGAGAAGTTT-GATGGTTAAAATGTGATTTTTGAAAGTTTGAGGGCTAAAATG
1 TAATTTTTGAGAAGTTTAG-GGGTTAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATG
* * * *
127407 TAATTTTT-AAAAGATTTA-AGGTTAAAAATATGATTTGTGGACAGTTC
1 TAATTTTTGAGAAG-TTTAGGGGTT-AAAATGTGATTTTTGGA-AGTTC
127454 AAGGATCTTC
Statistics
Matches: 184, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
57 15 0.08
58 81 0.44
59 84 0.46
60 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (59 bp):
TAATTTTTGAGAAGTTTAGGGGTTAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATG
Found at i:128590 original size:15 final size:16
Alignment explanation
Indices: 128570--128625 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 16
128560 GACTGCTTTT
128570 TTATTATT-TTATTTA
1 TTATTATTATTATTTA
*
128585 TTATTATTAATATTGTAA
1 TTATTATTATTATT-T-A
128603 TTATTTATTATGTATTTA
1 TTA-TTATTAT-TATTTA
128621 TTATT
1 TTATT
128626 TAATGAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 3 0.09
18 8 0.24
19 7 0.21
20 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:128623 original size:18 final size:18
Alignment explanation
Indices: 128569--128627 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
128559 TGACTGCTTT
*
128569 TTTATTATTTTATTTATTA
1 TTTATTA-TATATTTATTA
128588 -TTATTA-ATATTGTAATTA
1 TTTATTATATATT-T-ATTA
*
128606 TTTATTATGTATTTATTA
1 TTTATTATATATTTATTA
128624 TTTA
1 TTTA
128628 ATGAAATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.12
17 1 0.03
18 18 0.53
19 7 0.21
20 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTATTATATATTTATTA
Found at i:129264 original size:10 final size:10
Alignment explanation
Indices: 129249--129274 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
129239 TTATTTATTT
129249 TAAATTTAAA
1 TAAATTTAAA
129259 TAAATTTAAA
1 TAAATTTAAA
129269 TAAATT
1 TAAATT
129275 AAACTTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:129826 original size:78 final size:77
Alignment explanation
Indices: 129720--130084 Score: 401
Period size: 78 Copynumber: 4.7 Consensus size: 77
129710 TTCCTCATGA
* * ** **
129720 TCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAGGTTCTAGGTAAAAGATCGAATGGTTGCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGTT-GGGGTAAAAGATCGAATGACTGCA
129785 ATCTGCCCTAGGC
65 ATCTGCCCTAGGC
*
129798 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTTGGGGTAAGAGATCGAATGACTGCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG-TTGGGGTAAAAGATCGAATGACTGCA
* *
129863 ATCTATCCC-AAGC
65 ATCT-GCCCTAGGC
* *
129876 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGACTGCA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCC-AGGTTGGGGTAAAAGATCGAATGACTGCA
* * *
129941 ATTTGCCCTATGT
65 ATCTGCCCTAGGC
* * * * * * * *
129954 TAGGGGTAAGAAATTGGCCGATGGTGATTTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCCGTA
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGG-TTGGGGTAAAAGATCGAATGACTGCA
* * *
130019 ATCTACCCCAGAC
65 ATCTGCCCTAGGC
* * * *
130032 TCAGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGACTCGGGGTAAAAGATC
1 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAG-GTTGGGGTAAAAGATC
130085 AGATGATTGT
Statistics
Matches: 242, Mismatches: 39, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
77 25 0.10
78 210 0.87
79 7 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGTTGGGGTAAAAGATCGAATGACTGCAA
TCTGCCCTAGGC
Found at i:129828 original size:39 final size:39
Alignment explanation
Indices: 129720--130126 Score: 219
Period size: 39 Copynumber: 10.5 Consensus size: 39
129710 TTCCTCATGA
* * * *
129720 TCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAGGT
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
** * * * * * ** *
129759 TCTAGGTAAAAGATCGAATGGTTGCAATCTGCCCTAGGC
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
*
129798 TCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
* * * ** ** *
129837 TTGGGGTAAGAGATCGAATGACT-GCAATCTATCCCAAGC
1 TCGGGGTAAGAGATTGGATGA-TGGTGATCTGCCCCAGGC
* *
129876 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
* * * * ** * * * *
129915 TTGGGGTAAAAGATCGAATGACT-GCAATTTGCCCTATGT
1 TCGGGGTAAGAGATTGGATGA-TGGTGATCTGCCCCAGGC
* * ** *
129954 TAGGGGTAAGAAATTGGCCGATGGTGATTTGCCCCAGGC
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
* * * *** * * *
129993 TCGGGGTAAAAGATCGAATGGCCGTAATCTACCCCAGAC
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
* * *
130032 TCAGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGAC
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
* ** * * * *
130070 TCGGGGTAAAAGATCAGATGATTGTAATTTGCCCCATAG-
1 TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCA-GGC
*
130109 TCGGGATAAGAGATTGGA
1 TCGGGGTAAGAGATTGGA
130127 ATCTTCAATT
Statistics
Matches: 259, Mismatches: 103, Indels: 12
0.69 0.28 0.03
Matches are distributed among these distances:
38 32 0.12
39 225 0.87
40 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGATGATGGTGATCTGCCCCAGGC
Found at i:129978 original size:156 final size:155
Alignment explanation
Indices: 129720--130103 Score: 486
Period size: 156 Copynumber: 2.5 Consensus size: 155
129710 TTCCTCATGA
* * * * ** *
129720 TCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAGGTTCTAGGTAAAAGATCGAATGGTTGCA
1 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGCTT-GGGGTAAAAGATCGAATGATTGCA
* * * * * *
129785 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTTGGGGTAAGAGA
65 ATTTGCCCTAGGCTAGGGGTAAGAAATTGGCCGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
*
129850 TCGAATGACTGCAATCTATCCCAAG-C
130 TCGAATGACCGCAATCTA-CCCAAGAC
*
129876 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGAATGACTGCA
1 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCC-AGCTTGGGGTAAAAGATCGAATGATTGCA
* * *
129941 ATTTGCCCTATGTTAGGGGTAAGAAATTGGCCGATGGTGATTTGCCCCAGGCTCGGGGTAAAAGA
65 ATTTGCCCTAGGCTAGGGGTAAGAAATTGGCCGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGA
* * *
130006 TCGAATGGCCGTAATCTACCCCAGAC
130 TCGAATGACCGCAATCTACCCAAGAC
* * *
130032 TCAGGGTAAGAGATTGGTTGATGGTGATCTG-CCCAGACTCGGGGTAAAAGATC-AGATGATTGT
1 TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAG-CTTGGGGTAAAAGATCGA-ATGATTGC
130095 AATTTGCCC
64 AATTTGCCC
130104 CATAGTCGGG
Statistics
Matches: 199, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
154 3 0.02
155 38 0.19
156 154 0.77
157 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (155 bp):
TCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGCTTGGGGTAAAAGATCGAATGATTGCAA
TTTGCCCTAGGCTAGGGGTAAGAAATTGGCCGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGAT
CGAATGACCGCAATCTACCCAAGAC
Found at i:130103 original size:38 final size:37
Alignment explanation
Indices: 129980--130103 Score: 86
Period size: 38 Copynumber: 3.2 Consensus size: 37
129970 GCCGATGGTG
* **
129980 ATTTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCCGTA
1 ATTTG-CCCAGACTCGGGGTAAAAGATCG-ATGATCGTA
** * * * * * *
130019 ATCTACCCCAGACTCAGGGTAAGAGATTGGTTGATGGTG
1 AT-TTGCCCAGACTCGGGGTAAAAGA-TCGATGATCGTA
* *
130058 ATCTGCCCAGACTCGGGGTAAAAGATCAGATGATTGTA
1 ATTTGCCCAGACTCGGGGTAAAAGATC-GATGATCGTA
130096 ATTTGCCC
1 ATTTGCCC
130104 CATAGTCGGG
Statistics
Matches: 61, Mismatches: 21, Indels: 7
0.69 0.24 0.08
Matches are distributed among these distances:
37 1 0.02
38 32 0.52
39 25 0.41
40 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (37 bp):
ATTTGCCCAGACTCGGGGTAAAAGATCGATGATCGTA
Found at i:135244 original size:3 final size:3
Alignment explanation
Indices: 135236--135261 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
135226 AGTCAACCCT
135236 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
135262 ATTCACTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:144793 original size:14 final size:14
Alignment explanation
Indices: 144774--144815 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
144764 AGTACGGATG
144774 AATAAATATACGAA
1 AATAAATATACGAA
*
144788 AATAAATATAAGAAA
1 AATAAATATACG-AA
144803 AATAAA-ATACGAA
1 AATAAATATACGAA
144816 TTATGAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 15 0.60
15 8 0.32
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:145012 original size:28 final size:28
Alignment explanation
Indices: 144961--145181 Score: 196
Period size: 29 Copynumber: 7.7 Consensus size: 28
144951 AAATTTTTAG
* *
144961 GGGTAAATATGTGATTTTTGAAAGTTCAA
1 GGGTAAA-ATGTAATTTTTGAAAGTTCGA
*
144990 GGGTAAAATATAATTTTTGAAAGTTCGA
1 GGGTAAAATGTAATTTTTGAAAGTTCGA
* * *
145018 GGGCAAAAATGCAATTTTTAAAAGTTC-A
1 GGG-TAAAATGTAATTTTTGAAAGTTCGA
* * *
145046 GGGGGAAAATGCAATTTTTGGAAAGTTCAA
1 -GGGTAAAATGTAATTTTT-GAAAGTTCGA
*
145076 GGGTTAAAATGTGATTTTT-AGAAGTTCGA
1 GGG-TAAAATGTAATTTTTGA-AAGTTCGA
*** *
145105 GCCAAAAATGTAATTTTTGAGAAGTTTGA
1 GGGTAAAATGTAATTTTTGA-AAGTTCGA
* * *
145134 GGGT-AAATGTGATTTTTGGAAGTTCGG
1 GGGTAAAATGTAATTTTTGAAAGTTCGA
145161 GGGTAAAAATGTAATTTTTGA
1 GGGT-AAAATGTAATTTTTGA
145182 GAGGTTTGGA
Statistics
Matches: 156, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
27 10 0.06
28 63 0.40
29 70 0.45
30 13 0.08
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGAAAGTTCGA
Found at i:145189 original size:57 final size:58
Alignment explanation
Indices: 144959--145218 Score: 210
Period size: 58 Copynumber: 4.5 Consensus size: 58
144949 AAAAATTTTT
* * ** *
144959 AGGGGTAAATATGTGATTTTTGAAAGTTCAAGGGTAAAATATAATTTTTGA-AAGTTCG
1 AGGGATAAA-ATGTGATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTTGAGAAGTTCG
** ** * *
145017 AGGGCA-AAAATGCAATTTTTAAAAGTTCAGGGGG-AAAATGCAATTTTTG-GAAAGTTCA
1 AGGG-ATAAAATGTGATTTTTGGAAGTTC-GGGGGTAAAATGTAATTTTTGAG-AAGTTCG
* * * *** *
145075 AGGGTTAAAATGTGATTTTTAGAAGTTCGAGCCAAAAATGTAATTTTTGAGAAGTTTG
1 AGGGATAAAATGTGATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTTGAGAAGTTCG
* *
145133 AGGG-T-AAATGTGATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGAGAGGTTTGG
1 AGGGATAAAATGTGATTTTTGGAAGTTCGGGGGT-AAAATGTAATTTTTGAGAAG-TTCG
* *
145191 AAGTA-AAAATGTGATTTTTGGATAGTTC
1 AGGGATAAAATGTGATTTTTGGA-AGTTC
145219 AAAGACCTTC
Statistics
Matches: 162, Mismatches: 28, Indels: 22
0.76 0.13 0.10
Matches are distributed among these distances:
56 22 0.14
57 51 0.31
58 67 0.41
59 17 0.10
60 5 0.03
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (58 bp):
AGGGATAAAATGTGATTTTTGGAAGTTCGGGGGTAAAATGTAATTTTTGAGAAGTTCG
Found at i:145199 original size:30 final size:30
Alignment explanation
Indices: 145081--145210 Score: 119
Period size: 28 Copynumber: 4.5 Consensus size: 30
145071 TTCAAGGGTT
* * **
145081 AAAATGTGATTTTT-AGAAG-TTCGAGCCA
1 AAAATGTAATTTTTGAGAAGTTTGGAGGTA
145109 AAAATGTAATTTTTGAGAAGTTT-GAGGGT-
1 AAAATGTAATTTTTGAGAAGTTTGGA-GGTA
* * *
145138 -AAATGTGATTTTTG-GAAGTTCGGGGGTA
1 AAAATGTAATTTTTGAGAAGTTTGGAGGTA
* *
145166 AAAATGTAATTTTTGAGAGGTTTGGAAGTA
1 AAAATGTAATTTTTGAGAAGTTTGGAGGTA
*
145196 AAAATGTGATTTTTG
1 AAAATGTAATTTTTG
145211 GATAGTTCAA
Statistics
Matches: 83, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
27 9 0.11
28 27 0.33
29 20 0.24
30 27 0.33
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTGGAGGTA
Found at i:146382 original size:3 final size:3
Alignment explanation
Indices: 146364--146419 Score: 51
Period size: 3 Copynumber: 17.7 Consensus size: 3
146354 GATTGCCTTT
* *
146364 TTA TTA TT- TTA TTTA TTA TTA TTA ATA TTA TAA TTA TTTA TTA TGTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA
146411 TTTA TTA TT
1 -TTA TTA TT
146420 TAATTAAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 2 0.05
3 31 0.70
4 10 0.23
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:146384 original size:15 final size:16
Alignment explanation
Indices: 146364--146419 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 16
146354 GATTGCCTTT
146364 TTATTATT-TTATTTA
1 TTATTATTATTATTTA
*
146379 TTATTATTAATATTATAA
1 TTATTATTATTATT-T-A
146397 TTATTTATTATGTATTTA
1 TTA-TTATTAT-TATTTA
146415 TTATT
1 TTATT
146420 TAATTAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 3 0.09
18 8 0.24
19 7 0.21
20 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:146420 original size:18 final size:18
Alignment explanation
Indices: 146363--146421 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
146353 CGATTGCCTT
*
146363 TTTATTATTTTATTTATTA
1 TTTATTA-TATATTTATTA
146382 -TTATTA-ATATTATAATTA
1 TTTATTATATATT-T-ATTA
*
146400 TTTATTATGTATTTATTA
1 TTTATTATATATTTATTA
146418 TTTA
1 TTTA
146422 ATTAAATCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.12
17 1 0.03
18 18 0.53
19 7 0.21
20 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTATTATATATTTATTA
Found at i:147054 original size:6 final size:6
Alignment explanation
Indices: 147043--147086 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
147033 CATCATTTAT
*
147043 TTTAAA TTTAAA TTTAAA --TAAA TTTAAA TTTAAA -GTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
147087 GAATGAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.12
5 4 0.12
6 25 0.76
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:147066 original size:16 final size:17
Alignment explanation
Indices: 147045--147086 Score: 77
Period size: 16 Copynumber: 2.5 Consensus size: 17
147035 TCATTTATTT
147045 TAAATTTAAATTTAAA-
1 TAAATTTAAATTTAAAG
147061 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
147078 TAAATTTAA
1 TAAATTTAA
147087 GAATGAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:148236 original size:11 final size:11
Alignment explanation
Indices: 148222--148254 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
148212 TCTAAAAAGA
148222 TAAATATAAAT
1 TAAATATAAAT
*
148233 TAAATACAAAT
1 TAAATATAAAT
148244 TAAATATAAAT
1 TAAATATAAAT
148255 AATATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:148647 original size:52 final size:52
Alignment explanation
Indices: 148581--148743 Score: 231
Period size: 52 Copynumber: 3.1 Consensus size: 52
148571 CAAGACCTGC
* *
148581 TAATCATCGGCTCGAAGCTTGCTATTTAATCACC-AGCTTC-AGGCCTGTTATA
1 TAATCACCGGCTCGAAGCTTGCTATTTAATCACCGA-C-TCAAGGCCTGCTATA
* * * *
148633 TAATCACCGACTCGAAGCCTGCTATGTAATCACCGACTCAAGGCCTGCTATG
1 TAATCACCGGCTCGAAGCTTGCTATTTAATCACCGACTCAAGGCCTGCTATA
*
148685 TAATCACCGGCTCAAAGCTTGCTATTTAATCACCGACTCAAGGCCTGCTATA
1 TAATCACCGGCTCGAAGCTTGCTATTTAATCACCGACTCAAGGCCTGCTATA
148737 TAATCAC
1 TAATCAC
148744 TTCTTTTCTA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
51 2 0.02
52 95 0.97
53 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (52 bp):
TAATCACCGGCTCGAAGCTTGCTATTTAATCACCGACTCAAGGCCTGCTATA
Found at i:148652 original size:26 final size:26
Alignment explanation
Indices: 148600--148743 Score: 168
Period size: 26 Copynumber: 5.5 Consensus size: 26
148590 GCTCGAAGCT
*
148600 TGCTATTTAATCACC-AGCTTC-AGGCC
1 TGCTATATAATCACCGA-C-TCAAGGCC
*
148626 TGTTATATAATCACCGACTCGAA-GCC
1 TGCTATATAATCACCGACTC-AAGGCC
*
148652 TGCTATGTAATCACCGACTCAAGGCC
1 TGCTATATAATCACCGACTCAAGGCC
* * * *
148678 TGCTATGTAATCACCGGCTCAAAGCT
1 TGCTATATAATCACCGACTCAAGGCC
*
148704 TGCTATTTAATCACCGACTCAAGGCC
1 TGCTATATAATCACCGACTCAAGGCC
148730 TGCTATATAATCAC
1 TGCTATATAATCAC
148744 TTCTTTTCTA
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
25 4 0.04
26 96 0.94
27 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (26 bp):
TGCTATATAATCACCGACTCAAGGCC
Found at i:148682 original size:78 final size:78
Alignment explanation
Indices: 148600--148743 Score: 193
Period size: 78 Copynumber: 1.8 Consensus size: 78
148590 GCTCGAAGCT
* * * *
148600 TGCTATTTAATCACCAGCTTC-AGGCCTGTTATATAATCACCGACTCGAA-GCCTGCTATGTAAT
1 TGCTATGTAATCACCAGC-TCAAAGCCTGCTATATAATCACCGACTC-AAGGCCTGCTATATAAT
148663 CACCGACTCAAGGCC
64 CACCGACTCAAGGCC
* * *
148678 TGCTATGTAATCACCGGCTCAAAGCTTGCTATTTAATCACCGACTCAAGGCCTGCTATATAATCA
1 TGCTATGTAATCACCAGCTCAAAGCCTGCTATATAATCACCGACTCAAGGCCTGCTATATAATCA
148743 C
66 C
148744 TTCTTTTCTA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
77 4 0.07
78 53 0.93
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (78 bp):
TGCTATGTAATCACCAGCTCAAAGCCTGCTATATAATCACCGACTCAAGGCCTGCTATATAATCA
CCGACTCAAGGCC
Found at i:155892 original size:9 final size:9
Alignment explanation
Indices: 155868--155906 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
155858 ATATATTATC
155868 AATTCGGTT
1 AATTCGGTT
*
155877 AATTTTGGTT
1 AA-TTCGGTT
*
155887 AATTTGGTT
1 AATTCGGTT
155896 AATTCGGTT
1 AATTCGGTT
155905 AA
1 AA
155907 ATGAACATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (9 bp):
AATTCGGTT
Found at i:156388 original size:73 final size:73
Alignment explanation
Indices: 156269--156422 Score: 290
Period size: 73 Copynumber: 2.1 Consensus size: 73
156259 CAAAAACATT
156269 AGGCTCGAAAATGGATTTGGGTAAAAAATTAGGCCTATTTAAAATATGGGTAGAGCTTGGGCTTG
1 AGGCTCGAAAATGGATTTGGGTAAAAAATTAGGCCTATTTAAAATATGGGTAGAGCTTGGGCTTG
156334 AACATTCA
66 AACATTCA
*
156342 AGGCTCGAAAATGGGTTTGGGTAAAAAATTAGGCCTATTTAAAATATGGGTAGAGCTTGGGCTTG
1 AGGCTCGAAAATGGATTTGGGTAAAAAATTAGGCCTATTTAAAATATGGGTAGAGCTTGGGCTTG
156407 AACATTCA
66 AACATTCA
156415 AGGGCTCG
1 A-GGCTCG
156423 GCTCGACTCG
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 73 0.92
74 6 0.08
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (73 bp):
AGGCTCGAAAATGGATTTGGGTAAAAAATTAGGCCTATTTAAAATATGGGTAGAGCTTGGGCTTG
AACATTCA
Found at i:159456 original size:21 final size:21
Alignment explanation
Indices: 159432--159483 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
159422 CATCCATGCT
159432 ATATATTATAAAAAATAATAC
1 ATATATTATAAAAAATAATAC
159453 ATATATTATAAAAAATAATAC
1 ATATATTATAAAAAATAATAC
159474 ACT-TATTATA
1 A-TATATTATA
159484 TGAAAACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATATTATAAAAAATAATAC
Found at i:172874 original size:21 final size:22
Alignment explanation
Indices: 172850--172909 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
172840 CGATCTGAGG
*
172850 AAAAATAGAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
172871 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATAGAATT
*
172893 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
172910 AGGAAGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.29
22 23 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:172875 original size:22 final size:23
Alignment explanation
Indices: 172850--172905 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
172840 CGATCTGAGG
172850 AAAAATAGAAG-AAATAGAATT-
1 AAAAATAGAAGAAAATAGAATTA
* *
172871 AAAAATAAAAGAAAATATAATTAA
1 AAAAATAGAAGAAAATAGAATT-A
172895 AAGAAATAGAA
1 AA-AAATAGAA
172906 AATAAGGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
22 9 0.32
24 2 0.07
25 7 0.25
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATAGAAGAAAATAGAATTA
Found at i:176972 original size:21 final size:21
Alignment explanation
Indices: 176927--176986 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
176917 GATATAAGGA
*
176927 AAAATAGAAGAAACA-AAATTG
1 AAAATAAAAGAAA-ATAAATTG
176948 AAAATAAAAGAAAATATAATT-
1 AAAATAAAAGAAAATA-AATTG
*
176969 AAAAGAAATAGAAAATAA
1 AAAATAAA-AGAAAATAA
176987 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 21 0.62
22 12 0.35
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATAAAAGAAAATAAATTG
Found at i:179018 original size:14 final size:14
Alignment explanation
Indices: 178969--179029 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
178959 TTTCCTGGAT
178969 AAAAATAAATAAATAA
1 AAAAAT-AAT-AATAA
* *
178985 ATAAAATAA-GATAG
1 A-AAAATAATAATAA
178999 AAAAATAATAATAA
1 AAAAATAATAATAA
*
179013 AAAAATAAAAATAA
1 AAAAATAATAATAA
179027 AAA
1 AAA
179030 TAATTGGGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 7 0.18
14 23 0.61
16 3 0.08
17 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:184406 original size:21 final size:21
Alignment explanation
Indices: 184361--184420 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
184351 GATATAAGGA
*
184361 AAAATAGAAGAAACA-AAATTG
1 AAAATAAAAGAAA-ATAAATTG
184382 AAAATAAAAGAAAATATAATT-
1 AAAATAAAAGAAAATA-AATTG
*
184403 AAAAGAAATAGAAAATAA
1 AAAATAAA-AGAAAATAA
184421 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 21 0.62
22 12 0.35
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATAAAAGAAAATAAATTG
Done.