Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold560
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: 122116
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:134 original size:22 final size:22
Alignment explanation
Indices: 104--146 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
94 TAGGATGGAA
*
104 GAATAAAAAAATTATTTAAATG
1 GAATAAAAAAATTATATAAATG
*
126 GAATTAAAAAATTATATAAAT
1 GAATAAAAAAATTATATAAAT
147 ATTAGTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (22 bp):
GAATAAAAAAATTATATAAATG
Found at i:2100 original size:22 final size:23
Alignment explanation
Indices: 2052--2121 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 23
2042 TATACTTATT
* *
2052 TATATTTATTT-TTAA-AAATTT
1 TATATTTATTTATTAATAAAATA
2073 TATATTTATTTATTAATAAAATA
1 TATATTTATTTATTAATAAAATA
2096 T-TA-TTATTTAATTAACTAATAATA
1 TATATTTATTT-ATTAA-TAA-AATA
2120 TA
1 TA
2122 CAAAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 17 0.41
22 11 0.27
23 8 0.20
24 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATTTATTTATTAATAAAATA
Found at i:16004 original size:17 final size:17
Alignment explanation
Indices: 15957--16004 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
15947 ATAATATAAT
15957 TTTATTACTTTTAAATA
1 TTTATTACTTTTAAATA
**
15974 TATT-TTACAATTAAATA
1 T-TTATTACTTTTAAATA
*
15991 TTTATTATTTTTAA
1 TTTATTACTTTTAA
16005 TAAAATAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATTACTTTTAAATA
Found at i:19121 original size:16 final size:16
Alignment explanation
Indices: 19102--19135 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
19092 TAATTTTATT
19102 ATTTTTA-TATTTTTAA
1 ATTTTTATTA-TTTTAA
19118 ATTTTTATTATTTTAA
1 ATTTTTATTATTTTAA
19134 AT
1 AT
19136 ATATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATTATTTTAA
Found at i:22163 original size:29 final size:31
Alignment explanation
Indices: 22125--22185 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
22115 TATAGAATTA
*
22125 TTATTCTAAATAAAT-TACATAT-TTTTATTT
1 TTATTCTAAA-AAATATAAATATATTTTATTT
*
22155 TTATT-TAAAATATATAAATATATTTTATTT
1 TTATTCTAAAAAATATAAATATATTTTATTT
22185 T
1 T
22186 GTTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.11
29 10 0.37
30 14 0.52
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (31 bp):
TTATTCTAAAAAATATAAATATATTTTATTT
Found at i:22918 original size:106 final size:107
Alignment explanation
Indices: 22793--23247 Score: 300
Period size: 106 Copynumber: 4.3 Consensus size: 107
22783 TGTAAGTAAT
* *
22793 TTTAAGTTATTATTAAATATAAAAGAATAAAATGCAAATATAATTAAATTTAAGTTAAT-TATTA
1 TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAA-TTAATATATAA
22857 TAAATATAAACAATAAAACACAAATATTATTA-AAGTATTAAA
65 TAAATATAAACAATAAAACACAAATATTATTACAAGTATTAAA
* ** * * * *
22899 TTTAATTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTAT-ATT-ATGA-ATAA
1 TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAATTAAT-ATATAA
* ** **
22961 GTAAATATAAATAATAATATTATTAAT-TATATTACAA-TA--AAA
65 -TAAATATAAACAATAA-AACACAAATAT-TATTACAAGTATTAAA
** ** * ** * * ** ** *
23003 CAATAAGCAAGTT-TTAAACGATTTATTAAAAAAATGTTAA-ACGATTCAATAATTAA-TAATAT
1 -TTTAAGTTA-TTATTAAA-TATAAAATAATAAAATGCAAATATAATT-AA-ATTTAATTAATAT
* * * ** * * *
23065 AAAAACAAATCTAAACAAATTTTAA-ACAAATA--A--ACATGTAAGTAAT
61 -ATAATAAATATAAAC-AA-TAAAACACAAATATTATTACAAGT-ATTAAA
*
23111 TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAAGTTAAT-TATTA
1 TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAA-TTAATATATAA
23175 TAAATATAAACAATAAAACACAAATATTATTA-AAGTATTAAA
65 TAAATATAAACAATAAAACACAAATATTATTACAAGTATTAAA
*
23217 TTTAATTTATTATTAAATATAAAATAATAAA
1 TTTAAGTTATTATTAAATATAAAATAATAAA
23248 GCACAAAAAT
Statistics
Matches: 250, Mismatches: 68, Indels: 62
0.66 0.18 0.16
Matches are distributed among these distances:
103 5 0.02
104 20 0.08
105 47 0.19
106 127 0.51
107 26 0.10
108 18 0.07
109 6 0.02
110 1 0.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (107 bp):
TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAATTAATATATAAT
AAATATAAACAATAAAACACAAATATTATTACAAGTATTAAA
Found at i:22934 original size:56 final size:58
Alignment explanation
Indices: 22835--22945 Score: 165
Period size: 56 Copynumber: 1.9 Consensus size: 58
22825 TGCAAATATA
*
22835 ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAATATTATTAAAGT
1 ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGT
* *
22893 ATTAAATTTAA-TTTATTA-T-TAAATATAAAATAATAAAACACAAAAATTATTAA
1 ATTAAATTTAAGTTAATTATTATAAATAT-AAACAATAAAACACAAAAATTATTAA
22946 CTATATTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 7 0.14
56 25 0.51
57 6 0.12
58 11 0.22
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (58 bp):
ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGT
Found at i:23253 original size:56 final size:58
Alignment explanation
Indices: 23153--23263 Score: 156
Period size: 56 Copynumber: 1.9 Consensus size: 58
23143 TGCAAATATA
*
23153 ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAATATTATTAAAGT
1 ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGT
* * *
23211 ATTAAATTTAA-TTTATTA-T-TAAATATAAAATAATAAAGCACAAAAATTATTAA
1 ATTAAATTTAAGTTAATTATTATAAATAT-AAACAATAAAACACAAAAATTATTAA
23264 CTATATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
55 7 0.15
56 24 0.50
57 6 0.12
58 11 0.23
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.37
Consensus pattern (58 bp):
ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGT
Found at i:23305 original size:318 final size:318
Alignment explanation
Indices: 22728--23368 Score: 1201
Period size: 318 Copynumber: 2.0 Consensus size: 318
22718 ATAATTAAAA
22728 ATTCAATAATGAATAATATAAAAACAAATCTAAACAAATTTTAAACAAATAAACATGTAAGTAAT
1 ATTCAATAATGAATAATATAAAAACAAATCTAAACAAATTTTAAACAAATAAACATGTAAGTAAT
22793 TTTAAGTTATTATTAAATATAAAAGAATAAAATGCAAATATAATTAAATTTAAGTTAATTATTAT
66 TTTAAGTTATTATTAAATATAAAAGAATAAAATGCAAATATAATTAAATTTAAGTTAATTATTAT
22858 AAATATAAACAATAAAACACAAATATTATTAAAGTATTAAATTTAATTTATTATTAAATATAAAA
131 AAATATAAACAATAAAACACAAATATTATTAAAGTATTAAATTTAATTTATTATTAAATATAAAA
*
22923 TAATAAAACACAAAAATTATTAACTATATTATGAATAAGTAAATATAAATAATAATATTATTAAT
196 TAATAAAACACAAAAATTATTAACTATATTATAAATAAGTAAATATAAATAATAATATTATTAAT
* *
22988 TATATTACAATAAAACAATAAGCAAGTTTTAAACGATTTATTAAAAAAATGTTAAACG
261 TATATTAAAATAAAACAATAAGCAAGTTTTAAACGATTTATTAAAAAAATATTAAACG
*
23046 ATTCAATAATTAATAATATAAAAACAAATCTAAACAAATTTTAAACAAATAAACATGTAAGTAAT
1 ATTCAATAATGAATAATATAAAAACAAATCTAAACAAATTTTAAACAAATAAACATGTAAGTAAT
*
23111 TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAAGTTAATTATTAT
66 TTTAAGTTATTATTAAATATAAAAGAATAAAATGCAAATATAATTAAATTTAAGTTAATTATTAT
23176 AAATATAAACAATAAAACACAAATATTATTAAAGTATTAAATTTAATTTATTATTAAATATAAAA
131 AAATATAAACAATAAAACACAAATATTATTAAAGTATTAAATTTAATTTATTATTAAATATAAAA
*
23241 TAATAAAGCACAAAAATTATTAACTATATTATAAATAAGTAAATATAAATAATAATATTATTAAT
196 TAATAAAACACAAAAATTATTAACTATATTATAAATAAGTAAATATAAATAATAATATTATTAAT
* * *
23306 TATATTAAAATCAAACAATAAGTAAGTTTTAAACGATTTATTAAAAAAATATTAAATG
261 TATATTAAAATAAAACAATAAGCAAGTTTTAAACGATTTATTAAAAAAATATTAAACG
23364 ATTCA
1 ATTCA
23369 TAAATAAATT
Statistics
Matches: 314, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
318 314 1.00
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (318 bp):
ATTCAATAATGAATAATATAAAAACAAATCTAAACAAATTTTAAACAAATAAACATGTAAGTAAT
TTTAAGTTATTATTAAATATAAAAGAATAAAATGCAAATATAATTAAATTTAAGTTAATTATTAT
AAATATAAACAATAAAACACAAATATTATTAAAGTATTAAATTTAATTTATTATTAAATATAAAA
TAATAAAACACAAAAATTATTAACTATATTATAAATAAGTAAATATAAATAATAATATTATTAAT
TATATTAAAATAAAACAATAAGCAAGTTTTAAACGATTTATTAAAAAAATATTAAACG
Found at i:23312 original size:106 final size:104
Alignment explanation
Indices: 22793--23314 Score: 251
Period size: 106 Copynumber: 4.9 Consensus size: 104
22783 TGTAAGTAAT
* ** * * * * * *
22793 TTTAAGTTATTATTAAATATAAAAGAATAAAATGCAAATATAATTAAATTTAAGTTA-ATTATTA
1 TTTAAGTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTAT-A-TTATA-AATAA
* ** *
22857 TAAATATAAACAATAAAACA-CAAATATTATTAAAGTATTAAA
63 TAAATATAAATAATAAATTATTAAATA-TATTAAAGTATTAAA
* *
22899 TTTAATTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTATATTATGAATAAGTA
1 TTTAAGTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTATATTATAAATAA-TA
*
22964 AATATAAATAATAATATTATTAATTATATTACAA-TA--AAA
65 AATATAAATAATAA-ATTATTAAATATATTA-AAGTATTAAA
** ** * ** * * *** * * * *
23003 CAATAAGCAAGTT-TTAAACGATTTATTAAAAAAATGTTAAACGATTCAATAATTAATAATATAA
1 -TTTAAGTTA-TTATTAAA-TATAAAATAATAAAA-CACAAA-AATT-ATTAACT-ATATTATAA
* * * * * * * *
23067 A-AACAAATCT--A-AACAAATT-TTAAACAAATAAACATGTAAGTAAT
59 ATAATAAATATAAATAATAAATTATTAAATATATTAA-A-GT-ATTAAA
** * * * * * *
23111 TTTAAGTTATTATTAAATATAAAATAATAAAATGCAAATATAATTAAATTTAAGTTA-ATTATTA
1 TTTAAGTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTAT-A-TTATA-AATAA
* ** *
23175 TAAATATAAACAATAAAACA-CAAATATTATTAAAGTATTAAA
63 TAAATATAAATAATAAATTATTAAATA-TATTAAAGTATTAAA
* *
23217 TTTAATTTATTATTAAATATAAAATAATAAAGCACAAAAATTATTAACTATATTATAAATAAGTA
1 TTTAAGTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTATATTATAAATAA-TA
*
23282 AATATAAATAATAATATTATTAATTATATTAAA
65 AATATAAATAATAA-ATTATTAAATATATTAAA
23315 ATCAAACAAT
Statistics
Matches: 296, Mismatches: 88, Indels: 64
0.66 0.20 0.14
Matches are distributed among these distances:
102 2 0.01
103 16 0.05
104 23 0.08
105 56 0.19
106 134 0.45
107 26 0.09
108 20 0.07
109 11 0.04
110 8 0.03
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (104 bp):
TTTAAGTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAACTATATTATAAATAATAA
ATATAAATAATAAATTATTAAATATATTAAAGTATTAAA
Found at i:26429 original size:34 final size:34
Alignment explanation
Indices: 26383--26563 Score: 240
Period size: 34 Copynumber: 5.4 Consensus size: 34
26373 GTAAAAACCA
*
26383 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
26417 TCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
26451 CCATTTAATTAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
26485 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
26519 CCATTTAGTCAACAATGGTAAACTATCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
26552 CCATTTAATCAA
1 CCATTTAATCAA
26564 TAATTCTCTC
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 14 0.11
34 112 0.86
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:31052 original size:34 final size:34
Alignment explanation
Indices: 31014--31126 Score: 133
Period size: 34 Copynumber: 3.4 Consensus size: 34
31004 CAAATCACTT
*
31014 ATTTAATCAACAATGATAAGTTACCAAAACTCCC
1 ATTTAATCAACAATGATAAGCTACCAAAACTCCC
* *
31048 ATTTAATCAACAATGATAAGCTATCAAATCTCCC
1 ATTTAATCAACAATGATAAGCTACCAAAACTCCC
* * *
31082 ATTTAGTCAACAAT-AGTAAACTACC-AAA-TCATC
1 ATTTAATCAACAATGA-TAAGCTACCAAAACTC-CC
31115 ATTTAATCAACA
1 ATTTAATCAACA
31127 TGTCAGTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.03
33 15 0.22
34 51 0.75
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.28
Consensus pattern (34 bp):
ATTTAATCAACAATGATAAGCTACCAAAACTCCC
Found at i:36734 original size:18 final size:19
Alignment explanation
Indices: 36711--36747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
36701 GCTTAAGGTT
36711 GGAGAT-GAAGTTTATCTG
1 GGAGATAGAAGTTTATCTG
36729 GGAGATGAGAAGTTTATCT
1 GGAGAT-AGAAGTTTATCT
36748 ACATTCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.32
Consensus pattern (19 bp):
GGAGATAGAAGTTTATCTG
Found at i:37552 original size:34 final size:32
Alignment explanation
Indices: 37494--37560 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
37484 ACTATTATAC
*
37494 AATATTTTTATAATATAATTTTATTACTTTTA
1 AATATTTTTATAATATAATATTATTACTTTTA
*
37526 AATATATTTTATAAT-TAAATAATTATTATTTTTA
1 AATAT-TTTTATAATAT-AAT-ATTATTACTTTTA
37560 A
1 A
37561 CAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.20
33 12 0.40
34 12 0.40
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
AATATTTTTATAATATAATATTATTACTTTTA
Found at i:37560 original size:17 final size:17
Alignment explanation
Indices: 37514--37579 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
37504 TAATATAATT
*
37514 TTATTACTTTTAAATATA
1 TTATTATTTTTAAATA-A
**
37532 TT-TTATAATTAAATAA
1 TTATTATTTTTAAATAA
37548 TTATTATTTTTAACA-AA
1 TTATTATTTTTAA-ATAA
* *
37565 ATAATATTTTTAAAT
1 TTATTATTTTTAAAT
37580 TAGATTTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 4 0.11
17 31 0.82
18 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTATTTTTAAATAA
Found at i:39970 original size:25 final size:26
Alignment explanation
Indices: 39941--39998 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
39931 TATAATTGTG
*
39941 AAAATT-ATTTATTTCTAA-AATTATA
1 AAAATTAATTTATTTATAATAA-TATA
*
39966 TAAATTGAATTTATTTATAATAATATA
1 AAAATT-AATTTATTTATAATAATATA
39993 AAAATT
1 AAAATT
39999 GTTTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
27 20 0.74
28 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
AAAATTAATTTATTTATAATAATATA
Found at i:39992 original size:27 final size:27
Alignment explanation
Indices: 39947--39999 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39937 TGTGAAAATT
* *
39947 ATTTATTTCTAAAATTATATAAATTGA
1 ATTTATTTATAAAATTATAAAAATTGA
39974 ATTTATTTATAATAA-TATAAAAATTG
1 ATTTATTTATAA-AATTATAAAAATTG
40000 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (27 bp):
ATTTATTTATAAAATTATAAAAATTGA
Found at i:45696 original size:12 final size:11
Alignment explanation
Indices: 45676--45713 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
45666 ATAATAGATT
45676 TTTTATATTTA
1 TTTTATATTTA
45687 TTTTAGTATTTA
1 TTTTA-TATTTA
45699 TATTTATA-TTA
1 T-TTTATATTTA
45710 TTTT
1 TTTT
45714 TAAGGCACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.12
11 9 0.36
12 9 0.36
13 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:46072 original size:21 final size:22
Alignment explanation
Indices: 46046--46092 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
46036 TGATTGTTAG
* *
46046 ATATAATTTTTCAT-ATTTTGA
1 ATATAATTATTAATCATTTTGA
*
46067 ATATAATTATTAATCATTTTTA
1 ATATAATTATTAATCATTTTGA
46089 ATAT
1 ATAT
46093 TTTCAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATAATTATTAATCATTTTGA
Found at i:50887 original size:27 final size:27
Alignment explanation
Indices: 50856--50951 Score: 135
Period size: 27 Copynumber: 3.7 Consensus size: 27
50846 CAAAAGCCAC
50856 CCTTTGTGTTTGTCAAAAATGGTGATT
1 CCTTTGTGTTTGTCAAAAATGGTGATT
50883 CCTTTGTGTTTGTCAAAAATGGTGATT
1 CCTTTGTGTTTGTCAAAAATGGTGATT
* * *
50910 CCTTTGTGTTTATAAAAAATGGCGA--
1 CCTTTGTGTTTGTCAAAAATGGTGATT
*
50935 CCTGT-TGTTTGTCAAAA
1 CCTTTGTGTTTGTCAAAA
50952 TTAGTGACTA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.16
25 4 0.06
27 49 0.78
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATGGTGATT
Found at i:51442 original size:2 final size:2
Alignment explanation
Indices: 51435--51465 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
51425 TTCTAAAGAA
*
51435 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51466 AAATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:51528 original size:7 final size:7
Alignment explanation
Indices: 51518--51546 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
51508 TAAATGAAAA
51518 ATAAATT
1 ATAAATT
51525 ATAAATT
1 ATAAATT
51532 ATAAATT
1 ATAAATT
51539 ATAAATT
1 ATAAATT
51546 A
1 A
51547 AATCTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATAAATT
Found at i:51563 original size:21 final size:21
Alignment explanation
Indices: 51514--51563 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
51504 TTCATAAATG
51514 AAAAATAAATTATAAATTATA
1 AAAAATAAATTATAAATTATA
**
51535 AATTATAAA-T-TAAATCTATA
1 AAAAATAAATTATAAAT-TATA
51555 TAAAAATAA
1 -AAAAATAA
51564 TTTACAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 5 0.22
20 5 0.22
21 13 0.57
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATAAATTATAAATTATA
Found at i:51612 original size:17 final size:17
Alignment explanation
Indices: 51580--51612 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
51570 ACCATAAACA
51580 TAATTTTTATATATCAC
1 TAATTTTTATATATCAC
51597 TAATTATTTATA-ATCA
1 TAATT-TTTATATATCA
51613 ATTACTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTTTTATATATCAC
Found at i:52868 original size:8 final size:7
Alignment explanation
Indices: 52852--52933 Score: 51
Period size: 7 Copynumber: 11.4 Consensus size: 7
52842 ATAAATTTTT
52852 AAATTAA
1 AAATTAA
52859 AAATTAA
1 AAATTAA
*
52866 AAAATAA
1 AAATTAA
*
52873 ATTAATAAA
1 A--AATTAA
*
52882 AAAATAA
1 AAATTAA
*
52889 GATTATTAA
1 -A-AATTAA
52898 AAATT-A
1 AAATTAA
* *
52904 ATATAAA
1 AAATTAA
*
52911 AAATT-T
1 AAATTAA
52917 AAATTAA
1 AAATTAA
52924 AAATTAA
1 AAATTAA
52931 AAA
1 AAA
52934 AATTTAAAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
6 9 0.16
7 35 0.64
8 2 0.04
9 9 0.16
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (7 bp):
AAATTAA
Found at i:52885 original size:16 final size:17
Alignment explanation
Indices: 52864--52900 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
52854 ATTAAAAATT
52864 AAAAAATAA-ATTAATA
1 AAAAAATAAGATTAATA
*
52880 AAAAAATAAGATTATTA
1 AAAAAATAAGATTAATA
52897 AAAA
1 AAAA
52901 TTAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAAAATAAGATTAATA
Found at i:52914 original size:13 final size:13
Alignment explanation
Indices: 52857--52930 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
52847 TTTTTAAATT
52857 AAAAATTAA-A-A
1 AAAAATTAATATA
52868 AATAAATTAATA-A
1 AA-AAATTAATATA
* *
52881 AAAAATAAGATTATT
1 AAAAATTA-A-TATA
52896 AAAAATTAATATA
1 AAAAATTAATATA
*
52909 AAAAATTTAA-ATT
1 AAAAA-TTAATATA
52922 AAAAATTAA
1 AAAAATTAA
52931 AAAAATTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
11 2 0.04
12 16 0.31
13 20 0.38
14 7 0.13
15 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (13 bp):
AAAAATTAATATA
Found at i:56207 original size:21 final size:20
Alignment explanation
Indices: 56174--56214 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
56164 AGTTTAAATT
*
56174 ATTTTTATATTAAATTTATA
1 ATTTTGATATTAAATTTATA
56194 ATTTTGATAATTAAATTTATA
1 ATTTTGAT-ATTAAATTTATA
56215 TCAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTGATATTAAATTTATA
Found at i:61735 original size:13 final size:13
Alignment explanation
Indices: 61713--61743 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
61703 AAAGAATTGA
*
61713 AGAGGGATGCTTG
1 AGAGGAATGCTTG
61726 AGAGGAATGCTTG
1 AGAGGAATGCTTG
61739 AGAGG
1 AGAGG
61744 GAGGAGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.45, T:0.19
Consensus pattern (13 bp):
AGAGGAATGCTTG
Found at i:61875 original size:27 final size:27
Alignment explanation
Indices: 61845--61897 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
61835 TAATAAATAA
*
61845 AAAGAAACTACCATTTTTGAAAAACAC
1 AAAGAAACCACCATTTTTGAAAAACAC
* *
61872 AAAGTAACCACCATTTTTGACAAACA
1 AAAGAAACCACCATTTTTGAAAAACA
61898 AATGGTGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.23
Consensus pattern (27 bp):
AAAGAAACCACCATTTTTGAAAAACAC
Found at i:66425 original size:26 final size:28
Alignment explanation
Indices: 66380--66439 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
66370 ACAAGCTACA
* * *
66380 ATTTTTGAGAAATAAAAAAG-AACTATT
1 ATTTTTGACAAATAAAAAAGTAACCACT
*
66407 ATTTTTGACAAAT-ACAAAGTAACCACT
1 ATTTTTGACAAATAAAAAAGTAACCACT
66434 ATTTTT
1 ATTTTT
66440 TAAAAAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (28 bp):
ATTTTTGACAAATAAAAAAGTAACCACT
Found at i:68887 original size:13 final size:13
Alignment explanation
Indices: 68869--68895 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
68859 TATATATAAA
68869 AAAACATGATATG
1 AAAACATGATATG
68882 AAAACATGATATG
1 AAAACATGATATG
68895 A
1 A
68896 GATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (13 bp):
AAAACATGATATG
Found at i:69711 original size:25 final size:25
Alignment explanation
Indices: 69665--69729 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
69655 AGATAATGTG
*
69665 TATTTTTATAT-TTT-ATTCTGTTT
1 TATTTTTATATATTTAATTATGTTT
69688 TATTTTTATATATTTAATTATGTTT
1 TATTTTTATATATTTAATTATGTTT
* *
69713 AATATATTATATATTTA
1 TAT-TTTTATATATTTA
69730 TATAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 11 0.31
24 3 0.08
25 10 0.28
26 12 0.33
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (25 bp):
TATTTTTATATATTTAATTATGTTT
Found at i:69727 original size:26 final size:25
Alignment explanation
Indices: 69671--69729 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
69661 TGTGTATTTT
* * * *
69671 TATATTTTATTCTGTTTTATTTTTA
1 TATATTTAATTATGTTTAATTATTA
69696 TATATTTAATTATGTTTAATATATTA
1 TATATTTAATTATGTTTAAT-TATTA
69722 TATATTTA
1 TATATTTA
69730 TATAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (25 bp):
TATATTTAATTATGTTTAATTATTA
Found at i:69744 original size:18 final size:18
Alignment explanation
Indices: 69692--69745 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
69682 CTGTTTTATT
* *
69692 TTTATAT-ATTTAATTATG
1 TTTATATAAATTAA-TATA
*
69710 TTTA-ATATATT-ATATA
1 TTTATATAAATTAATATA
69726 TTTATATAAATTAATATA
1 TTTATATAAATTAATATA
69744 TT
1 TT
69746 AATAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 7 0.24
17 9 0.31
18 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTATATAAATTAATATA
Found at i:69745 original size:25 final size:25
Alignment explanation
Indices: 69711--69759 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
69701 TTAATTATGT
69711 TTAATATATT-ATATATTTATATAAA
1 TTAATATATTAATA-ATTTATATAAA
69736 TTAATATATTAATAATTTATATAA
1 TTAATATATTAATAATTTATATAA
69760 TATAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAATATATTAATAATTTATATAAA
Found at i:69795 original size:11 final size:11
Alignment explanation
Indices: 69779--69830 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
69769 TGATTCGTTT
69779 ATATTTATATA
1 ATATTTATATA
69790 ATATTTATATTA
1 ATATTTATA-TA
* *
69802 ATTTTTTATATT
1 A-TATTTATATA
69814 ATATTATATATA
1 ATATT-TATATA
69826 TATAT
1 -ATAT
69831 AATTATATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 12 0.36
12 10 0.30
13 11 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTATATA
Found at i:69827 original size:29 final size:31
Alignment explanation
Indices: 69750--69834 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
69740 TATATTAATA
* * * *
69750 ATTTATATAATATAAAT-TTTGATTCGTTTAT
1 ATTTATATAATATATATATATAATT-TTTTAT
*
69781 ATTTATATAATATTTATAT-TAATTTTTTAT
1 ATTTATATAATATATATATATAATTTTTTAT
*
69811 A-TTATATTATATATATATATAATT
1 ATTTATATAATATATATATATAATT
69835 ATATCTTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
29 15 0.33
30 11 0.24
31 19 0.41
32 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (31 bp):
ATTTATATAATATATATATATAATTTTTTAT
Found at i:70421 original size:24 final size:24
Alignment explanation
Indices: 70393--70438 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
70383 AATAAAAATT
70393 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* * *
70417 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
70439 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:70464 original size:28 final size:28
Alignment explanation
Indices: 70433--70496 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
70423 CATTTTTTAC
70433 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
*
70461 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
70489 ATACAAAG
1 ATACAAAG
70497 GGTGGCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:70497 original size:28 final size:28
Alignment explanation
Indices: 70443--70497 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
70433 ATACAAAAAT
70443 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
70471 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
70498 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:72439 original size:21 final size:22
Alignment explanation
Indices: 72401--72446 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
72391 ATCTGTTGAA
* **
72401 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
72422 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
72444 ACT
1 ACT
72447 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:74986 original size:24 final size:24
Alignment explanation
Indices: 74958--75003 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
74948 AATAAAAATT
74958 AGCCACCAATTTTGACAAACAACC
1 AGCCACCAATTTTGACAAACAACC
* * *
74982 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
75004 AAATAACCGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.30, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACC
Found at i:75029 original size:28 final size:28
Alignment explanation
Indices: 74998--75061 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
74988 CATTTTTTAC
*
74998 ATACAAA-AATAACCGCCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
* *
75026 ATACAAAGGAAACCACTATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
75054 ATACAAAG
1 ATACAAAG
75062 GGTGGCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.52, C:0.19, G:0.09, T:0.20
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:78713 original size:427 final size:427
Alignment explanation
Indices: 77913--78720 Score: 1163
Period size: 427 Copynumber: 1.9 Consensus size: 427
77903 TTTTATTAAA
* *
77913 TTATTATTTGAACAAAAATAAAATAAAATTTAATTAAGTTAATATCATTTTATATTAGACTTTAG
1 TTATTATTTGAACAAAAATAAAATAAAATTTAATTAAGTTAATATCATTTTATATCAGACTTTAA
* * * * *
77978 ATCATTTAGGTTTGAATCTTTTTGAGTTCGCATTAGTTTGAATTCAAGATGGCTGGATTTAAATT
66 ATCATCTAGGCTTGAATATTTTTGAGTTCGCATTAGTTTAAATTCAAGATGGATGGATTTAAATT
* * *
78043 ATAATTCTTTTTATTGAACCAGGTTGGTTAATAGTTGAAATAGACACATCTTTTAAGTTTAGATC
131 ATAATTCCTTTCATTGAACCAGGTTGGTAAATAGTTGAAATAGACACATCTTTTAAGTTTAGATC
* * * * *
78108 AATCTCGTCAATTCTAATTCAGATATTCAAGATACCAAATAGGATTCATGTGATAATTTAAGAAT
196 AACCTCGTCAACTCTAATTCAGATATTCAAAATACCAAATAAGATTCATGTGATAATTTAAAAAT
* * * *
78173 TAAATGTAAGATATATTCTTAATATAGAGATCGTAATTGATGCTCTTTCATCTAGCTATCTGTTT
261 TAAATGTAAGATATATTCTTAAAATAGAGATCGTAACTGATGATCTTTCATCTAGCTATCCGTTT
* * *
78238 TTCTTTGGTTGTAAGAGGCTAAGCTTCTTTATTATGATCTTGGTTAGCATTAATGTTGATTTTAA
326 ATCTTTGATTGTAAGAGGCTAAACTTCTTTATTATGATCTTGGTTAGCATTAATGTTGATTTTAA
78303 AGATAATTTATTAGTAGACTACTAATTTTTGTAATAT
391 AGATAATTTATTAGTAGACTACTAATTTTTGTAATAT
* ** **
78340 TTATTATTTTAACAAAAATTTAATTTAATTTAATTAAGTTAATATCATTTTATATCAGACTTTAA
1 TTATTATTTGAACAAAAATAAAATAAAATTTAATTAAGTTAATATCATTTTATATCAGACTTTAA
* * *
78405 ATTATCTAGGCTTGGATATTTTTGAGTTCGCATTAGTTTAAATTCAAGTTGGATGGATTTAAATT
66 ATCATCTAGGCTTGAATATTTTTGAGTTCGCATTAGTTTAAATTCAAGATGGATGGATTTAAATT
* * **
78470 ATAATTCCTTTCGTTGAACTAGGTTGGTAAATAGTTGAAATAGACATGT-TTTTCAAGTTTAGAT
131 ATAATTCCTTTCATTGAACCAGGTTGGTAAATAGTTGAAATAGACACATCTTTT-AAGTTTAGAT
* * * *
78534 CAACCTTGTTAACTCTAATTTAGATATTTAAAATACCAAATAAGATTCATGTGATAATTTAAAAA
195 CAACCTCGTCAACTCTAATTCAGATATTCAAAATACCAAATAAGATTCATGTGATAATTTAAAAA
* * * * * *
78599 TTAAATGTGATATGTGTTCTTAAAATAGAGATGGTAACTGATGATCTTTCATTTAGCTATCCGTT
260 TTAAATGTAAGATATATTCTTAAAATAGAGATCGTAACTGATGATCTTTCATCTAGCTATCCGTT
*
78664 TATCTTTGATTGTAAGAGGTTAAACTTCTTTATTAT-AGTCATT-GTTAGCATTAATGT
325 TATCTTTGATTGTAAGAGGCTAAACTTCTTTATTATGA-TC-TTGGTTAGCATTAATGT
78721 AGATGTAATT
Statistics
Matches: 333, Mismatches: 45, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
426 5 0.02
427 326 0.98
428 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (427 bp):
TTATTATTTGAACAAAAATAAAATAAAATTTAATTAAGTTAATATCATTTTATATCAGACTTTAA
ATCATCTAGGCTTGAATATTTTTGAGTTCGCATTAGTTTAAATTCAAGATGGATGGATTTAAATT
ATAATTCCTTTCATTGAACCAGGTTGGTAAATAGTTGAAATAGACACATCTTTTAAGTTTAGATC
AACCTCGTCAACTCTAATTCAGATATTCAAAATACCAAATAAGATTCATGTGATAATTTAAAAAT
TAAATGTAAGATATATTCTTAAAATAGAGATCGTAACTGATGATCTTTCATCTAGCTATCCGTTT
ATCTTTGATTGTAAGAGGCTAAACTTCTTTATTATGATCTTGGTTAGCATTAATGTTGATTTTAA
AGATAATTTATTAGTAGACTACTAATTTTTGTAATAT
Found at i:82660 original size:56 final size:58
Alignment explanation
Indices: 82552--82662 Score: 165
Period size: 56 Copynumber: 1.9 Consensus size: 58
82542 TACAAATGTA
* *
82552 ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACATAAATATTATTAAAGT
1 ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGT
*
82610 ATTAAATTTAAGTT-ATTA-T-TAAATATAAAATAATAAAACACAAAAATTATTAA
1 ATTAAATTTAAGTTAATTATTATAAATAT-AAACAATAAAACACAAAAATTATTAA
82663 TTATATTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
55 7 0.14
56 24 0.49
57 4 0.08
58 14 0.29
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (58 bp):
ATTAAATTTAAGTTAATTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGT
Found at i:82679 original size:57 final size:54
Alignment explanation
Indices: 82512--82662 Score: 148
Period size: 56 Copynumber: 2.8 Consensus size: 54
82502 TAAGTAATTT
* * ** * *
82512 TAAGTTAATATTAAATATATAACAATAAAATACAAATGTAATTAAA-T-TTAAGT-
1 TAAGTTATTA-TAAATATA-AACAATAAAACACAAAAATTATTAAAGTATTAAATA
* * *
82565 TAA-TTATTATAAATATAAACAATAAAACATAAATATTATTAAAGTATTAAATT
1 TAAGTTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGTATTAAATA
*
82618 TAAGTTATTATTAAATATAAAATAATAAAACACAAAAATTATTAA
1 TAAGTTATTA-TAAATAT-AAACAATAAAACACAAAAATTATTAA
82663 TTATATTATA
Statistics
Matches: 83, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
50 22 0.27
51 9 0.11
52 10 0.12
53 6 0.07
54 6 0.07
55 7 0.08
56 23 0.28
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (54 bp):
TAAGTTATTATAAATATAAACAATAAAACACAAAAATTATTAAAGTATTAAATA
Found at i:82689 original size:56 final size:54
Alignment explanation
Indices: 82572--82690 Score: 125
Period size: 56 Copynumber: 2.1 Consensus size: 54
82562 AGTTAATTAT
* * * * *
82572 TATAAATATAAACAATAAAACATAAATATTATTAAAGTATTAAATTTAAGTTAT
1 TATAAATATAAACAATAAAACACAAAAATTATTAAAGTATTAAATATAAGTAAA
*
82626 TATTAAATATAAAATAATAAAACACAAAAATTATTAATTA-TATTATAA-ATAAGTAAA
1 TA-TAAATAT-AAACAATAAAACACAAAAATTATTAA--AGTATTA-AATATAAGTAAA
82683 TATAAATA
1 TATAAATA
82691 ATAATATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
54 2 0.04
55 7 0.13
56 29 0.54
57 13 0.24
58 3 0.06
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (54 bp):
TATAAATATAAACAATAAAACACAAAAATTATTAAAGTATTAAATATAAGTAAA
Found at i:84061 original size:22 final size:23
Alignment explanation
Indices: 84018--84061 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
84008 AATAATTTAC
*
84018 TAAAATTTTATAAATTATCTAAA
1 TAAAATTTTATAAATTAACTAAA
84041 TAAAA-TTTA-AAATTAAACTAA
1 TAAAATTTTATAAATT-AACTAA
84062 TTAATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAATTTTATAAATTAACTAAA
Found at i:85514 original size:32 final size:33
Alignment explanation
Indices: 85473--85536 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
85463 TTTTTACTTA
* *
85473 AATTTAATAATATTAGAACA-AATTTTATTTTT
1 AATTTAATAATATTAGAAAAGAATATTATTTTT
85505 AATTTAATAATATTAGAAAAGAATATTATTTT
1 AATTTAATAATATTAGAAAAGAATATTATTTT
85537 AAAATTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (33 bp):
AATTTAATAATATTAGAAAAGAATATTATTTTT
Found at i:86232 original size:21 final size:22
Alignment explanation
Indices: 86190--86232 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
86180 CAATTAAATT
* *
86190 TTTTTTAACTCTGTTAAGTTTA
1 TTTTTTAACTCTGATAAATTTA
*
86212 TTTTTTAA-TTTGATAAATTTA
1 TTTTTTAACTCTGATAAATTTA
86233 ATTTATATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
TTTTTTAACTCTGATAAATTTA
Found at i:92823 original size:5 final size:5
Alignment explanation
Indices: 92813--92856 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
92803 AGGGTAATGC
*
92813 AATAA AATAA AATAA AATAA AATAA AATAA ACA-AA CATAA AATA
1 AATAA AATAA AATAA AATAA AATAA AATAA A-ATAA AATAA AATA
92857 TTTATGTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 33 0.94
6 1 0.03
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:93664 original size:21 final size:21
Alignment explanation
Indices: 93634--93710 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 21
93624 CTTTATTCAT
93634 AATA-AAAATAATTA-AAATAA
1 AATATAAAAT-ATTATAAATAA
*
93654 AATATAAAATATTATAAATAT
1 AATATAAAATATTATAAATAA
* *
93675 AATGT-AAATA-CAT-AATAA
1 AATATAAAATATTATAAATAA
*
93693 TAT-TAAAATATATATAAA
1 AATATAAAATAT-TATAAA
93711 ATATTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
17 1 0.02
18 11 0.24
19 2 0.04
20 15 0.33
21 16 0.36
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (21 bp):
AATATAAAATATTATAAATAA
Found at i:93887 original size:22 final size:22
Alignment explanation
Indices: 93859--93902 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
93849 AGCACTAATT
*
93859 ATCTTCTGTTCTTACTTGAAAA
1 ATCTTCTCTTCTTACTTGAAAA
*
93881 ATCTTCTCTTGTTACTTGAAAA
1 ATCTTCTCTTCTTACTTGAAAA
93903 TATAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (22 bp):
ATCTTCTCTTCTTACTTGAAAA
Found at i:95667 original size:21 final size:21
Alignment explanation
Indices: 95652--95696 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
95642 AATATTTATA
95652 ATTT-TATATTTTATATAAAT
1 ATTTATATATTTTATATAAAT
95672 ATTTATATATTTTATAATTAAAT
1 ATTTATATATTTTAT-A-TAAAT
95695 AT
1 AT
95697 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 10 0.45
22 1 0.05
23 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTATATATTTTATATAAAT
Found at i:95684 original size:28 final size:29
Alignment explanation
Indices: 95634--95724 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
95624 ACTATTTAAA
95634 AAATATTAAATATTTATA-ATTTTAT-ATT
1 AAATA-TAAATATTTATATATTTTATAATT
**
95662 TTATATAAATATTTATATATTTTATAATT
1 AAATATAAATATTTATATATTTTATAATT
** *
95691 AAATATAAATA-AAATATATTTTATTAAAT
1 AAATATAAATATTTATATATTTTA-TAATT
95720 AAATA
1 AAATA
95725 ATTATTTGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
27 12 0.23
28 20 0.38
29 21 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AAATATAAATATTTATATATTTTATAATT
Found at i:98004 original size:20 final size:20
Alignment explanation
Indices: 97979--98032 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
97969 GTTACAAGCA
* *
97979 ATGTATTGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
*
97999 ATGTATCGATATAATGTACC
1 ATGTATCGATACAATGTACC
98019 ATGTATCGATACAA
1 ATGTATCGATACAA
98033 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:98799 original size:23 final size:23
Alignment explanation
Indices: 98773--98817 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
98763 TTTCTCCCCC
98773 TTTTCAAAGCAAAATTTATTTTA
1 TTTTCAAAGCAAAATTTATTTTA
* *
98796 TTTTCAAAGCAATATTTTTTTT
1 TTTTCAAAGCAAAATTTATTTT
98818 TCCCTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTCAAAGCAAAATTTATTTTA
Found at i:100718 original size:20 final size:20
Alignment explanation
Indices: 100693--100808 Score: 205
Period size: 20 Copynumber: 5.8 Consensus size: 20
100683 GGATTTTCTA
100693 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
100713 AATGTATCGATATATTTTTC
1 AATGTATCGATACATTTTTC
100733 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
100753 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
*
100773 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
100793 AATGTATCGATACATT
1 AATGTATCGATACATT
100809 CTAAAAAATT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:101825 original size:13 final size:13
Alignment explanation
Indices: 101807--101832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
101797 TACACAAAGT
101807 ATGTATCGATACA
1 ATGTATCGATACA
101820 ATGTATCGATACA
1 ATGTATCGATACA
101833 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:101830 original size:32 final size:33
Alignment explanation
Indices: 101789--101852 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
101779 TAGCCAAACT
*
101789 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
101821 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
101853 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:101917 original size:20 final size:22
Alignment explanation
Indices: 101886--101929 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
101876 GCTATATTTT
101886 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
101907 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
101928 CA
1 CA
101930 CGGAAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:104078 original size:22 final size:21
Alignment explanation
Indices: 104051--104102 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
104041 TTGCAAGTTG
104051 AAATAAAAAATTTAGCTAATG-A
1 AAATAAAAAA-TTAGCTAA-GAA
**
104073 AAATAATGAATTAGCTAAGAA
1 AAATAAAAAATTAGCTAAGAA
104094 AAATAAAAA
1 AAATAAAAA
104103 CTTGCATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 16 0.64
22 8 0.32
ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23
Consensus pattern (21 bp):
AAATAAAAAATTAGCTAAGAA
Found at i:108026 original size:13 final size:13
Alignment explanation
Indices: 108008--108046 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
107998 ACATTTTCCT
108008 TTGTATCGATACA
1 TTGTATCGATACA
108021 TTGTATCGATACA
1 TTGTATCGATACA
* *
108034 CTGTATTGATACA
1 TTGTATCGATACA
108047 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:109711 original size:22 final size:20
Alignment explanation
Indices: 109669--109711 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
109659 GTGTTTAAAG
*
109669 TATTTGCTTGACTTTGTTTT
1 TATTTGCTTGACTTTGATTT
109689 TATTTGCATTGTACTTTGATTT
1 TATTTGC-TTG-ACTTTGATTT
109711 T
1 T
109712 TTAATCTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.14, C:0.09, G:0.14, T:0.63
Consensus pattern (20 bp):
TATTTGCTTGACTTTGATTT
Found at i:110639 original size:13 final size:13
Alignment explanation
Indices: 110621--110646 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
110611 TACACAAAGT
110621 ATGTATCGATACA
1 ATGTATCGATACA
110634 ATGTATCGATACA
1 ATGTATCGATACA
110647 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:110644 original size:32 final size:33
Alignment explanation
Indices: 110603--110666 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
110593 TAGCCAAACT
*
110603 TGTATCGATACA-C-AAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAAT-TGTATCGATACAA
110635 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
110667 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 13 0.45
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:110731 original size:20 final size:22
Alignment explanation
Indices: 110700--110743 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
110690 GCTATATTTT
110700 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
110721 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
110742 CA
1 CA
110744 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:112061 original size:3 final size:3
Alignment explanation
Indices: 112055--112103 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
112045 CTGTGGCAAG
112055 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
112103 A
1 A
112104 ACATTTAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:113363 original size:22 final size:23
Alignment explanation
Indices: 113333--113378 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
113323 ATATTTTTAA
* *
113333 TTATAATTTAGTTATTCTTAAAT
1 TTATAATTTAATTACTCTTAAAT
*
113356 TTAT-ATTTAATTACTGTTAAAT
1 TTATAATTTAATTACTCTTAAAT
113378 T
1 T
113379 AAATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTATAATTTAATTACTCTTAAAT
Found at i:113518 original size:28 final size:29
Alignment explanation
Indices: 113437--113520 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 29
113427 AAATCTATTT
* *
113437 TTAATTCAATTATATATTACATTTGAAATGAA
1 TTAATTAAATTAT-TATT--ATTTTAAATGAA
* * * *
113469 TTTATTAAAATATTTTTA-TTTAAATTAA
1 TTAATTAAATTATTATTATTTTAAATGAA
113497 TTAATT-AATTATTATTATTTTAAA
1 TTAATTAAATTATTATTATTTTAAA
113521 ATTTTAGTGA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
27 9 0.21
28 19 0.45
29 1 0.02
31 3 0.07
32 10 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAATTAAATTATTATTATTTTAAATGAA
Found at i:114257 original size:14 final size:13
Alignment explanation
Indices: 114234--114290 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
114224 TGAAAATAAT
114234 AAAAAAATACCAG
1 AAAAAAATACCAG
114247 AAAAAACATACCAG
1 AAAAAA-ATACCAG
* *
114261 AAAATCAAT-TCAG
1 AAAA-AAATACCAG
*
114274 AAAAATATACCAG
1 AAAAAAATACCAG
114287 AAAA
1 AAAA
114291 TCAGAAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 2 0.06
13 20 0.56
14 13 0.36
15 1 0.03
ACGTcount: A:0.65, C:0.16, G:0.07, T:0.12
Consensus pattern (13 bp):
AAAAAAATACCAG
Found at i:117548 original size:15 final size:15
Alignment explanation
Indices: 117528--117581 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
117518 TTTATTTCAA
117528 AATAAAAAATAAAAT
1 AATAAAAAATAAAAT
*
117543 AATAAATTAA-AAAAT
1 AATAAA-AAATAAAAT
*
117558 ATTAAAAAAATAAAATT
1 AAT-AAAAAATAAAA-T
117575 AATAAAA
1 AATAAAA
117582 TTTAATTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 15 0.48
16 13 0.42
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAAAAAATAAAAT
Found at i:117583 original size:9 final size:8
Alignment explanation
Indices: 117528--117582 Score: 60
Period size: 8 Copynumber: 7.0 Consensus size: 8
117518 TTTATTTCAA
117528 AATAAAA-
1 AATAAAAT
117535 AATAAAAT
1 AATAAAAT
*
117543 AATAAATT
1 AATAAAAT
117551 AA-AAAAT
1 AATAAAAT
* *
117558 ATTAAAAA
1 AATAAAAT
117566 AATAAAATT
1 AATAAAA-T
117575 AATAAAAT
1 AATAAAAT
117583 TTAATTCATC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
7 12 0.31
8 20 0.51
9 7 0.18
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAAAAT
Found at i:118193 original size:28 final size:30
Alignment explanation
Indices: 118162--118223 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
118152 TAAATTAATA
*
118162 ATAATTAAAAT-TAATTTAAATAT-TAAAT
1 ATAATTAAAATCTAATTAAAATATATAAAT
* *
118190 ATAATTATAATCTAATTAAAATATATGAAT
1 ATAATTAAAATCTAATTAAAATATATAAAT
118220 ATAA
1 ATAA
118224 AAAAAAAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.34
29 11 0.38
30 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
ATAATTAAAATCTAATTAAAATATATAAAT
Found at i:119166 original size:9 final size:10
Alignment explanation
Indices: 119131--119181 Score: 52
Period size: 9 Copynumber: 5.1 Consensus size: 10
119121 TTTATTAATT
119131 ATATATAATAA
1 ATATA-AATAA
119142 ATATAAAT-A
1 ATATAAATAA
119151 ATATAAATAA
1 ATATAAATAA
*
119161 AT-TAAACAAA
1 ATATAAA-TAA
*
119171 ATAAAAATAA
1 ATATAAATAA
119181 A
1 A
119182 CTTATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 13 0.38
10 13 0.38
11 8 0.24
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
ATATAAATAA
Found at i:120105 original size:10 final size:10
Alignment explanation
Indices: 120090--120122 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
120080 ATAAAAATTT
120090 TTAATTTAAA
1 TTAATTTAAA
120100 TTAATTT-AA
1 TTAATTTAAA
120109 TATAATTTAAA
1 T-TAATTTAAA
120120 TTA
1 TTA
120123 TTATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.14
10 15 0.71
11 3 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:120206 original size:16 final size:16
Alignment explanation
Indices: 120185--120218 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
120175 ATATAAAATT
*
120185 AATTTTTAATATAATA
1 AATTTTTAAAATAATA
120201 AATTTTTAAAATAATA
1 AATTTTTAAAATAATA
120217 AA
1 AA
120219 ATAAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTTTAAAATAATA
Found at i:121828 original size:42 final size:46
Alignment explanation
Indices: 121767--121852 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 46
121757 ATTATTCTTT
*
121767 TAGTCTTACTGAAGTTTTAATTTT-AAGTTAGCTTT-TGCATCATTG
1 TAGTCTTACTGAAGTTTTAATTTTAAAGTTA-CTTTATACATCATTG
121812 TAGTCTTAC-G-A-TTTTAATTTTAAAGTTACTTTATACATCAT
1 TAGTCTTACTGAAGTTTTAATTTTAAAGTTACTTTATACATCAT
121853 CATAGTGAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
42 14 0.37
43 14 0.37
44 1 0.03
45 9 0.24
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.49
Consensus pattern (46 bp):
TAGTCTTACTGAAGTTTTAATTTTAAAGTTACTTTATACATCATTG
Done.