Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008855.1 Hibiscus syriacus cultivar Beakdansim tig00112072_pilon, 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: 1316246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:230098 original size:23 final size:23
Alignment explanation
Indices: 230069--230128 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
230059 CTTCTTTTTC
*
230069 TTTATTTTCTTTATTTTTTTATA
1 TTTATTTTCTTTATTATTTTATA
* *
230092 TTTATTTTAC-TTACTATTTTATC
1 TTTATTTT-CTTTATTATTTTATA
*
230115 TTTACTTTCTTTAT
1 TTTATTTTCTTTAT
230129 CTTATCTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.93
24 1 0.03
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATTTTCTTTATTATTTTATA
Found at i:236981 original size:36 final size:36
Alignment explanation
Indices: 236941--237060 Score: 118
Period size: 36 Copynumber: 3.3 Consensus size: 36
236931 CAGATGATTA
*
236941 TCTCACTTGAGATTGTTTTTCTTAAAACATACTTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
* * * *
236977 TCTCACTTGAGACTGTTTTACTCGAAAGA-AGA-TTTA
1 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAGACTTTG
* ** * *
237013 TTTCACTCAAGTTTGCTTTTCTTAAAACAGACTTTG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
237049 TCTCACTTGAGA
1 TCTCACTTGAGA
237061 CCGTTTTCAC
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
34 1 0.02
35 6 0.10
36 49 0.79
37 5 0.08
38 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (36 bp):
TCTCACTTGAGATTGTTTTTCTTAAAACAGACTTTG
Found at i:236987 original size:72 final size:72
Alignment explanation
Indices: 236901--237113 Score: 180
Period size: 72 Copynumber: 2.9 Consensus size: 72
236891 CAAAATAAAT
* ** * ** *
236901 TTTGTCTCGCTTGAGACAGTCTCA-T-TTAAGCAGATGATTATCTCACTTGAGATTGTTTTTCTT
1 TTTGTCTCACTTGAGACAGTCTCACTCGAAAGAAGAT--TTATCTCACTCAAGATTGCTTTTCTT
*
236964 AAAACATAC
64 AAAACAGAC
* * * * *
236973 TTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCACTCAAGTTTGCTTTTCTTAA
1 TTTGTCTCACTTGAGACAGTCTCACTCGAAAGAAGATTTATCTCACTCAAGATTGCTTTTCTTAA
237038 AACAGAC
66 AACAGAC
* * * * * *
237045 TTTGTCTCACTTGAGACCGTTTTCACTAGAAAGAAGGCATTTCATTTCACTCAAGACTG-TTTTT
1 TTTGTCTCACTTGAGACAG-TCTCACTCGAAAGAA-G-ATTT-ATCTCACTCAAGATTGCTTTTC
237109 TTAAA
62 TTAAA
237114 GAAATTTTGT
Statistics
Matches: 116, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
72 67 0.58
73 14 0.12
74 8 0.07
75 13 0.11
76 14 0.12
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (72 bp):
TTTGTCTCACTTGAGACAGTCTCACTCGAAAGAAGATTTATCTCACTCAAGATTGCTTTTCTTAA
AACAGAC
Found at i:237304 original size:102 final size:102
Alignment explanation
Indices: 237181--237379 Score: 353
Period size: 102 Copynumber: 2.0 Consensus size: 102
237171 ATAGGTTTCA
*
237181 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTG
1 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTG
237246 TCTCTCTTGAGATAGGTTCCCTTGAAACAAAAATTTT
66 TCTCTCTTGAGATAGGTTCCCTTGAAACAAAAATTTT
*
237283 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTG
1 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTG
* * *
237348 TTTCTCTTGAGATAGTTTCTCTTGAAACAAAA
66 TCTCTCTTGAGATAGGTTCCCTTGAAACAAAA
237380 TCTTTGAATC
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (102 bp):
TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAAATTTCCCTTGAAATGAATTTTG
TCTCTCTTGAGATAGGTTCCCTTGAAACAAAAATTTT
Found at i:237307 original size:37 final size:38
Alignment explanation
Indices: 237239--237311 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
237229 CCTTGAAATG
* *
237239 AATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAA
1 AATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACAAA
* *
237277 AATTTT-TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACA
237312 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (38 bp):
AATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACAAA
Found at i:237410 original size:65 final size:65
Alignment explanation
Indices: 237266--237432 Score: 178
Period size: 65 Copynumber: 2.6 Consensus size: 65
237256 GATAGGTTCC
237266 CTTGAAACAAAAATTTT-TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTT
1 CTTGAAAC--AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTT
*
237330 CC
64 CA
** * * * * * *
237332 CTTGAAATGAATTTTGTTTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AATCTGTTT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA-CATTGAAAAC-ATTT
237395 CA
64 CA
* *
237397 CTTGAAACAAATTTCGTCTCCCTTGAGACATTTTCT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
237433 TTTGGAACTA
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
64 12 0.15
65 63 0.77
66 7 0.09
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (65 bp):
CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCA
Found at i:237526 original size:102 final size:101
Alignment explanation
Indices: 237326--237611 Score: 299
Period size: 102 Copynumber: 2.8 Consensus size: 101
237316 CATTGAAAAC
** * *
237326 ATTTCCCTTGAAATGAATTTTGTTTCTCTTGAGATAGTTTCTCTTGAAACA-AAATCTTTG-AAT
1 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAA-CTTTGAAAA
* * **
237389 CTGTTTCACTTGAAACAAATTTCGTCTCCCTTGAGACA
65 C-ATTTCACTTGAAACAAATTTCGTCACCAATGAGACA
* ** * * *
237427 TTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1 ATTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACTTTGAAAA
* ** * * *
237492 CATTTCCCTTGAAATGAATTTTGTCACTAATGAGATA
65 CATTTCACTTGAAACAAATTTCGTCACCAATGAGACA
* * *
237529 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAAC
1 ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACTTTGAAAAC
237594 AGTTT-ACTTTGAAACAAA
66 A-TTTCAC-TTGAAACAAA
237612 ATCTTTGAAT
Statistics
Matches: 148, Mismatches: 32, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
101 57 0.39
102 85 0.57
103 6 0.04
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (101 bp):
ATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACTTTGAAAAC
ATTTCACTTGAAACAAATTTCGTCACCAATGAGACA
Found at i:237562 original size:36 final size:36
Alignment explanation
Indices: 237493--237576 Score: 87
Period size: 36 Copynumber: 2.3 Consensus size: 36
237483 CATTGAAAAC
** * *
237493 ATTTCCCTTGAAATGAATTTTGTCACTAATGAGATA
1 ATTTCCCTTGAAACAAATTTTGTCACCAATGAGACA
* **
237529 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTTGTCACCAATGAGACA
* *
237565 GTTTCTCTTGAA
1 ATTTCCCTTGAA
237577 GCATAAACTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTTGTCACCAATGAGACA
Found at i:237596 original size:30 final size:30
Alignment explanation
Indices: 237562--237620 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
237552 CTCCCTTGAG
*
237562 ACAGTTT-CTCTTGAAGCATAAA-CTTTGAAA
1 ACAGTTTACT-TTGAAACA-AAATCTTTGAAA
237592 ACAGTTTACTTTGAAACAAAATCTTTGAA
1 ACAGTTTACTTTGAAACAAAATCTTTGAA
237621 TATGTTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 21 0.81
31 2 0.08
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (30 bp):
ACAGTTTACTTTGAAACAAAATCTTTGAAA
Found at i:237809 original size:36 final size:36
Alignment explanation
Indices: 237750--237829 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
237740 ATACATTTTC
* *
237750 TCTTGAAACAC---AAAAAACCTTTGAAATTGTTTA
1 TCTTGAAACACAAAAAAAAACATTTGAAAATGTTTA
* *
237783 TCTTGGAACACAAAAAAAAACATTTGAAAATGTTTC
1 TCTTGAAACACAAAAAAAAACATTTGAAAATGTTTA
237819 TCTTGAAACAC
1 TCTTGAAACAC
237830 CAAACCCTCG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 10 0.26
36 29 0.74
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (36 bp):
TCTTGAAACACAAAAAAAAACATTTGAAAATGTTTA
Found at i:237973 original size:84 final size:85
Alignment explanation
Indices: 237837--237994 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 85
237827 CACCAAACCC
* * * *
237837 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGACTAGAAGGGT
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGACAAGAAGGGC
*
237902 TATCTGTCACCAAAAGACCT
66 TATATGTCACCAAAAGACCT
** * * * *
237922 TCGAGTTCGACTATGCTCAGC-TCTAAGGCACATCATTTACAGTATAGCTCAAGGCAAGAAGGGC
1 TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGACAAGAAGGGC
237986 TATATGTCA
66 TATATGTCA
237995 ATAAAATTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 44 0.71
85 18 0.29
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (85 bp):
TCGAGTTCGACTACACTCAGCTTCGAAGGCACATCATTTACAGCATAACTCAAGACAAGAAGGGC
TATATGTCACCAAAAGACCT
Found at i:238959 original size:24 final size:24
Alignment explanation
Indices: 238915--238997 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
238905 GATGTAATAT
** *
238915 TTTTTTACATT-TTATGCATTTTC
1 TTTTTTACATTATTATATATTTTA
*
238938 TTTTTTACTTTATTATATATTTTTA
1 TTTTTTACATTATTATATA-TTTTA
*
238963 TTTTTTAGATTATATATATATATATATA
1 TTTTTTACATTAT-TATATAT-T-T-TA
238991 TTTTTTA
1 TTTTTTA
238998 TTATCAGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 10 0.21
24 5 0.10
25 16 0.33
26 7 0.15
27 1 0.02
28 9 0.19
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTTACATTATTATATATTTTA
Found at i:239000 original size:26 final size:25
Alignment explanation
Indices: 238938--239001 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 25
238928 ATGCATTTTC
* *
238938 TTTTTTACTT-TATTATATATTTTTA
1 TTTTTTA-TTATATTATATATATATA
238963 TTTTTTAGATTATATATATATATATATA
1 TTTTTT--ATTATAT-TATATATATATA
238991 TTTTTTATTAT
1 TTTTTTATTAT
239002 CAGTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 6 0.18
26 7 0.21
27 4 0.12
28 16 0.48
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTTTATTATATTATATATATATA
Found at i:239023 original size:43 final size:39
Alignment explanation
Indices: 238972--239090 Score: 120
Period size: 43 Copynumber: 2.9 Consensus size: 39
238962 ATTTTTTAGA
*
238972 TTATATATATATATATATATTTTTTATTATCAGTTTTATTAAT
1 TTATATATATATATATATATTTTTTATT-T---TGTTATTAAT
*
239015 TTATATATATATATATTTACTATTTTTTATTTTGTTATTTAT
1 TTATATATATATATA--TA-TATTTTTTATTTTGTTATTAAT
239057 TT-TATATATATATAT-TA-TTTTTACTTTT-TTATTA
1 TTATATATATATATATATATTTTTTA-TTTTGTTATTA
239091 TTATTTTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
36 11 0.16
37 6 0.09
39 1 0.01
41 12 0.17
42 10 0.14
43 15 0.22
45 3 0.04
46 11 0.16
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (39 bp):
TTATATATATATATATATATTTTTTATTTTGTTATTAAT
Found at i:239092 original size:39 final size:38
Alignment explanation
Indices: 238951--239094 Score: 127
Period size: 37 Copynumber: 3.7 Consensus size: 38
238941 TTTACTTTAT
*
238951 TATA-TATTTTTATTTTTTA-GATTATATATATATATA
1 TATATTATTTTTATTTTTTATTATTATATATATATATA
* *
238987 TATATTTTTTATTATCAGTTTTATTAATTTATATATATATATA
1 TATATTATTT-TTAT--TTTTTATT-A-TTATATATATATATA
* * *
239030 TTTACTATTTTTTATTTTGTTA-T-TTAT-TTTATATATA
1 TATATTA-TTTTTATTTT-TTATTATTATATATATATATA
239067 TATATTATTTTTACTTTTTTATTATTAT
1 TATATTATTTTTA-TTTTTTATTATTAT
239095 TTTATTTATT
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
36 13 0.15
37 23 0.27
38 12 0.14
40 5 0.06
41 3 0.03
42 4 0.05
43 23 0.27
44 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (38 bp):
TATATTATTTTTATTTTTTATTATTATATATATATATA
Found at i:239099 original size:43 final size:43
Alignment explanation
Indices: 238941--239101 Score: 125
Period size: 45 Copynumber: 3.6 Consensus size: 43
238931 CATTTTCTTT
* * *
238941 TTTACTTTATTATATATT-TTTATTTTTTAGATTATATATATATATA
1 TTTACTTTTTTAT-TATTATTT-TATTTTATA-TATATATAT-TATA
* *
238987 TATA-TTTTTTATTATCAGTTTTATTAATT-TATATATATA-TATA
1 TTTACTTTTTTATTATTA-TTTTATT--TTATATATATATATTATA
* *
239030 TTTACTATTTTTTATT-TTGTTATTTATTTTATATATATATATTATT
1 TTTAC--TTTTTTATTATT-AT-TTTATTTTATATATATATATTATA
239076 TTTACTTTTTTATTATTATTTTATTT
1 TTTACTTTTTTATTATTATTTTATTT
239102 ATTTGTTTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 27
0.72 0.08 0.21
Matches are distributed among these distances:
43 14 0.15
44 15 0.16
45 32 0.34
46 30 0.32
47 2 0.02
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (43 bp):
TTTACTTTTTTATTATTATTTTATTTTATATATATATATTATA
Found at i:239103 original size:9 final size:9
Alignment explanation
Indices: 239039--239158 Score: 52
Period size: 9 Copynumber: 12.9 Consensus size: 9
239029 ATTTACTATT
239039 TTTTATTT-
1 TTTTATTTA
*
239047 TGTTATTTA
1 TTTTATTTA
*
239056 TTTTATATA
1 TTTTATTTA
*
239065 -TATATATTA
1 TTTTAT-TTA
*
239074 TTTTTACTT-
1 -TTTTATTTA
239083 TTTTATTATTA
1 TTTTA-T-TTA
239094 TTTTATTTA
1 TTTTATTTA
239103 TTTGT-TTTA
1 TTT-TATTTA
*
239112 TTTATATATTT
1 TTT-TAT-TTA
*
239123 TTTTCTTCT-
1 TTTTATT-TA
*
239132 TTTTCTTTA
1 TTTTATTTA
*
239141 TTTTCTTTA
1 TTTTATTTA
239150 TTTTTATTT
1 -TTTTATTT
239159 TACTTACTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 24
0.71 0.10 0.20
Matches are distributed among these distances:
8 17 0.20
9 40 0.46
10 17 0.20
11 13 0.15
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:239121 original size:17 final size:16
Alignment explanation
Indices: 239037--239126 Score: 51
Period size: 17 Copynumber: 5.4 Consensus size: 16
239027 ATATTTACTA
*
239037 TTTTTTATTT-TGTTAT
1 TTTTTTATTTAT-ATAT
239053 TTATTTTATATATATATAT
1 TT-TTTTAT-T-TATATAT
*
239072 TATTTTTACTTT-TTTAT
1 T-TTTTTA-TTTATATAT
* * *
239089 TATTAT-TTTATTTAT
1 TTTTTTATTTATATAT
239104 TTGTTTTATTTATATAT
1 TT-TTTTATTTATATAT
239121 TTTTTT
1 TTTTTT
239127 CTTCTTTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 12 0.21
17 21 0.36
18 2 0.03
19 11 0.19
20 3 0.05
ACGTcount: A:0.22, C:0.01, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTTTATTTATATAT
Found at i:239124 original size:38 final size:36
Alignment explanation
Indices: 239071--239201 Score: 90
Period size: 38 Copynumber: 3.5 Consensus size: 36
239061 TATATATATA
239071 TTATTTTTACTTTTTTATTATTATTTTATTTATTTGT-T
1 TTATTTTTA--TTTTTATTATTATTTTATTTATTT-TCT
* * *
239109 TTATTTATATATTTTT-TTCTTCTTTTTCTTTATTTTCT
1 TTATTT-T-TATTTTTATTATT-ATTTTATTTATTTTCT
* *
239147 TTATTTTTA-TTTTACTTACTATTTTATCTTTACTTTCT
1 TTATTTTTATTTTTA-TTATTATTTTA--TTTATTTTCT
*
239185 TTA-TCTTATCTTTTATT
1 TTATTTTTAT-TTTTATT
239202 TAATTTGTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
35 4 0.05
36 6 0.08
37 13 0.18
38 43 0.58
39 6 0.08
40 2 0.03
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.73
Consensus pattern (36 bp):
TTATTTTTATTTTTATTATTATTTTATTTATTTTCT
Found at i:239125 original size:47 final size:45
Alignment explanation
Indices: 238972--239154 Score: 146
Period size: 47 Copynumber: 4.0 Consensus size: 45
238962 ATTTTTTAGA
* * * *
238972 TTATATATATATATATATA-TTTTTTATTATCAGTTTTA-TTA--AT
1 TTATATATATATATTTTTACTTTTTT-TTATTA-TTTTATTTATTTT
* *
239015 TTATATATATATATATTTACTATTTTTTATT-TTGTTATTTATTTT
1 TTATATATATATATTTTTACTTTTTTTTATTATT-TTATTTATTTT
*
239060 ATATATATATATTATTTTTACTTTTTTATTATTATTTTATTTATTTGT
1 TTATATATATA-TATTTTTACTTTTTT-TTATTATTTTATTTATTT-T
* * *
239108 TT-TATTTATATATTTTTTTCTTCTTTTTCT-TTATTTTCTTTATTTT
1 TTATATATATATA-TTTTTACTT-TTTTT-TATTATTTTATTTATTTT
239154 T
1 T
239155 ATTTTACTTA
Statistics
Matches: 117, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 25 0.21
44 5 0.04
45 11 0.09
46 17 0.15
47 45 0.38
48 9 0.08
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (45 bp):
TTATATATATATATTTTTACTTTTTTTTATTATTTTATTTATTTT
Found at i:239148 original size:15 final size:15
Alignment explanation
Indices: 239071--239159 Score: 67
Period size: 15 Copynumber: 5.9 Consensus size: 15
239061 TATATATATA
*
239071 TTATTTTTACTTT-T
1 TTATTTTTATTTTCT
* *
239085 TTATTATTATTTTAT
1 TTATTTTTATTTTCT
* *
239100 TTATTTGTTTTATTTAT
1 TTATTT-TTAT-TTTCT
*
239117 ATATTTTT-TTCTTCT
1 TTATTTTTATT-TTCT
239132 TT-TTCTTTATTTTCT
1 TTATT-TTTATTTTCT
239147 TTATTTTTATTTT
1 TTATTTTTATTTT
239160 ACTTACTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
14 14 0.23
15 28 0.46
16 9 0.15
17 10 0.16
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.78
Consensus pattern (15 bp):
TTATTTTTATTTTCT
Found at i:239169 original size:18 final size:15
Alignment explanation
Indices: 239091--239182 Score: 52
Period size: 13 Copynumber: 6.1 Consensus size: 15
239081 TTTTTTATTA
239091 TTATTTTA-TTTA-T
1 TTATTTTATTTTACT
*
239104 TTGTTTTA-TTTA-T
1 TTATTTTATTTTACT
* *
239117 ATATTTT-TTTCTTCT
1 TTATTTTATTT-TACT
*
239132 TTTTCTTTATTTT-CT
1 TTAT-TTTATTTTACT
239147 TTATTTTTATTTTACT
1 TTA-TTTTATTTTACT
239163 TACTATTTTATCTTTACT
1 T--TATTTTAT-TTTACT
239181 TT
1 TT
239183 CTTTATCTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
13 19 0.31
14 1 0.02
15 15 0.24
16 9 0.15
17 9 0.15
18 9 0.15
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (15 bp):
TTATTTTATTTTACT
Found at i:241738 original size:133 final size:133
Alignment explanation
Indices: 241300--242493 Score: 1444
Period size: 133 Copynumber: 9.0 Consensus size: 133
241290 TAGGATGAGA
* * *
241300 GATATG-TTCTGCTTCTTCTTGAGGGAAAAGT-AGATATGGGGATGTTGAT-TCATTCAACTTTC
1 GATATGTTTC-GCTTCTTCTTGAGGGAAAA-TCAGATCTGGGGA-GTTGATCT-ATTCCACTGTC
* * * * * *
241362 AGTTAGGGAAGAATAAATCAAGGCAGACTTGTTCCACTGTTACTCAGAAAATATCAAATCTTGAA
62 ACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAAATATCAAATCTTGAA
*
241427 AGAGATG
127 AGAGAGG
* * * * * *
241434 GATATGCTTCACTTCTTCTTAAGGGAAAATTAGATCTAGGGGAGTTGATCCATTCCACTCTCACT
1 GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCT-GGGGAGTTGATCTATTCCACTGTCACT
* * * ** * * *
241499 CAGGGAAGATTGAATCAAAGTAGACTTGTTCCACCATCACTCAGGGAATATTAAATCTTGAAAGA
65 CAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAAATATCAAATCTTGAAAGA
* *
241564 CAAG
130 GAGG
* * * * * * *
241568 GATCTGTTCCGTTTCTTCTTGAGGGAAAATCAGATCTGGGGGAGTTGATCTATTTCAATATCACC
1 GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCT-GGGGAGTTGATCTATTCCACTGTCACT
* *
241633 CAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTCACTC-GGAAATATCAAATCTTGAAAGA
65 CAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAAATATCAAATCTTGAAAGA
*
241697 GAAG
130 GAGG
* * *
241701 GATCTATTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGATCTATTCCACTATCACT
1 GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGA-GTTGATCTATTCCACTGTCACT
*
241766 CAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAGGGAAA-ATCAAATCTTGAAAG
65 CAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA-GGAAATATCAAATCTTGAAAG
241830 AGAGG
129 AGAGG
* * * * * * **
241835 GATATG-TTCTGCTTCTTCTTAAAGGAAAATCAAATATGGGGTGTTGATCCATTTTACTGTCACT
1 GATATGTTTC-GCTTCTTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCTATTCCACTGTCACT
* *
241899 CAAGGAAGATTGAATCGAGGCAGACTTATTCCACTGTTACTCAGTGAAA-ATCAAATCTTGAAAG
65 CAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAG-GAAATATCAAATCTTGAAAG
241963 AGAGG
129 AGAGG
* * * *
241968 GATATGTTCCACTTCTTCTTGAGGGAAAATCAGATCTAGGGAGTTGATCCATTCCACTGTCACTC
1 GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCTATTCCACTGTCACTC
*
242033 AGGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAAA-ATCAAATCTTGAAAGA
66 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA-GGAAATATCAAATCTTGAAAGA
242097 GAGG
130 GAGG
* * * *
242101 GATTTGTTTTGTTTCTTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCCATTCCACTGTCACTC
1 GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCTATTCCACTGTCACTC
* * *
242166 AGGGAAGATTGAATCAAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAAATCTTAAAAGA
66 AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAAATATC-AAATCTTGAAAGA
242231 GAGG
130 GAGG
* *
242235 GATATGTTAT-ACTTCTTCTTGAGGGAAAATCAGATCTGGAGG-GTTAAT-TATTCCACTGTCAC
1 GATATGTT-TCGCTTCTTCTTGAGGGAAAATCAGATCTGG-GGAGTTGATCTATTCCACTGTCAC
* * *
242297 TCAGGGAAGATTGAATCGAGGCAGAATTGTTCCACTATTACTAAGGGAAA-ATCAAATCTTGAAA
64 TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCA-GGAAATATCAAATCTTGAAA
*
242361 GAAAGG
128 GAGAGG
* * * * * * *
242367 GATCTGTTCCTCTTTTTCTTGAGGGAAAATCATATATAGGGACGTTGAT-TCATTCCACTGTCAC
1 GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGA-GTTGATCT-ATTCCACTGTCAC
* *
242431 TCATGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATC-TGAAA
64 TCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAAATATCAAATCTTGAAA
242494 ATTAAACATT
Statistics
Matches: 927, Mismatches: 112, Indels: 43
0.86 0.10 0.04
Matches are distributed among these distances:
131 2 0.00
132 56 0.06
133 489 0.53
134 364 0.39
135 16 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (133 bp):
GATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCTATTCCACTGTCACTC
AGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGAAATATCAAATCTTGAAAGAG
AGG
Found at i:246747 original size:90 final size:88
Alignment explanation
Indices: 246638--246807 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 88
246628 TCCTGAATAT
*
246638 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCCAATATGATTAG
*
246703 GGTAACTTGGATATAAGAGGATTA
65 GGCAACTTGGATATAAGAGGATTA
*
246727 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCCAATATGATTAG
*
246792 GGCAACTTGGCTATAA
65 GGCAACTTGGATATAA
246808 AAGGGTGTGT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 35 0.46
90 41 0.54
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCCAATATGATTAGG
GCAACTTGGATATAAGAGGATTA
Found at i:254977 original size:130 final size:130
Alignment explanation
Indices: 254752--255056 Score: 421
Period size: 130 Copynumber: 2.3 Consensus size: 130
254742 AAGTGAAATG
* * * * *
254752 ATAATATCTAATTACTTCCAATCGAGAATAAATTACCTTTCGTGAATTAAAACAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCAT-CATTAAAACAGTCAATTATTA
* * * * *
254817 CTCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCGATTTAAGTGAAAAC
65 CCCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAAATCAATATCAATTCAAGAGAAAAC
254882 A
130 A
*
254883 ATAATATCTAATGATTTCCAATCGAGAATAAATGACCTTTCATCATTAAAACAGTCAATTATTAC
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATCATTAAAACAGTCAATTATTAC
* * * * **
254948 CCCAATTGAAATAAAGAGATATTAGTATTTCGTCTTAAAAATCAATATTAATTCGAGAGAAAATT
66 CCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAAATCAATATCAATTCAAGAGAAAACA
* * *
255013 ACAATATCAAATTATTTCCAATCGAGAATAAATGACCTCTCATC
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATC
255057 CCTTAAAGCA
Statistics
Matches: 153, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 114 0.75
131 39 0.25
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (130 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCATCATTAAAACAGTCAATTATTAC
CCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAAATCAATATCAATTCAAGAGAAAACA
Found at i:257503 original size:20 final size:21
Alignment explanation
Indices: 257467--257510 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
257457 GAAGTGCCAT
*
257467 ATAATTTTCCTGAAGGACCAC
1 ATAATTATCCTGAAGGACCAC
257488 ATAATTATCC-GAAGGACCAC
1 ATAATTATCCTGAAGGACCAC
257508 ATA
1 ATA
257511 GACCCTCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (21 bp):
ATAATTATCCTGAAGGACCAC
Found at i:258068 original size:55 final size:55
Alignment explanation
Indices: 257984--258126 Score: 250
Period size: 55 Copynumber: 2.6 Consensus size: 55
257974 ATACTTGGGA
*
257984 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGAGG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCAATGTTTTGAGG
* *
258039 GTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCAATGTTTTGAGG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCAATGTTTTGAGG
*
258094 ATATCGATACACTCCTCAGTGTACCGATACACA
1 GTATCGATACACTCCTCAGTGTACCGATACACA
258127 CTCAAACAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 84 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (55 bp):
GTATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCAATGTTTTGAGG
Found at i:262957 original size:21 final size:21
Alignment explanation
Indices: 262925--262977 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
262915 ATAATTTGCA
262925 CCGAAGTG-CCACATAATTATC
1 CCGAAG-GACCACATAATTATC
* * * *
262946 TCGAATGACCACTTAATTGTC
1 CCGAAGGACCACATAATTATC
262967 CCGAAGGACCA
1 CCGAAGGACCA
262978 TATAGACCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:263841 original size:55 final size:55
Alignment explanation
Indices: 263700--263843 Score: 200
Period size: 54 Copynumber: 2.6 Consensus size: 55
263690 TTATACTTAG
263700 GGATATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGA
1 GGATATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGA
* * * * * * *
263755 GGGTAT-GATAGACTCCTCAGTGTATCGATACACTACTGGCATTCGATGTTTTGA
1 GGATATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGA
* *
263809 GGATATCGATACACTCCTCACTATACCGATACACA
1 GGATATCGATACACTCCTCAGTGTACCGATACACA
263844 CTCAAACAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
54 47 0.63
55 28 0.37
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (55 bp):
GGATATCGATACACTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGA
Found at i:264107 original size:23 final size:23
Alignment explanation
Indices: 264077--264129 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
264067 CTTCAAATCG
264077 TACCCAACATTCAAACATGTTAT
1 TACCCAACATTCAAACATGTTAT
264100 TACCCAACATTCAAACATGTTAT
1 TACCCAACATTCAAACATGTTAT
264123 TACCCAA
1 TACCCAA
264130 TTTTACCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.28, G:0.04, T:0.28
Consensus pattern (23 bp):
TACCCAACATTCAAACATGTTAT
Found at i:264957 original size:3 final size:3
Alignment explanation
Indices: 264949--264999 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
264939 AAGTATTTAT
* *
264949 TAA TAA TAA TAT TAA TAA TAA TAA -AGA TAA AAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
264993 TAA TAA T
1 TAA TAA T
265000 GGGACGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.07
3 37 0.90
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:264963 original size:12 final size:12
Alignment explanation
Indices: 264946--264971 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
264936 ACAAAGTATT
264946 TATTAATAATAA
1 TATTAATAATAA
264958 TATTAATAATAA
1 TATTAATAATAA
264970 TA
1 TA
264972 AAGATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTAATAATAA
Found at i:265378 original size:134 final size:133
Alignment explanation
Indices: 265137--266315 Score: 1326
Period size: 134 Copynumber: 8.8 Consensus size: 133
265127 GTTTCATTTT
* * * * *
265137 TTCTTGAGGGAAAATCAGATCT-GAGACGTTGATTCATTCAACTGTCACTTAGGGAAGATTGAAC
1 TTCTTGAGGGAAAATCAGATCTGGGGA-GTTGATCCATTCCACTGTCACTCAGGGAAGATTGAAT
* * * * * * *
265201 CGAGGCAGTCTTGTTCCACTGTTACTCAGGGAATTTCATATCTTAAAAGATAGGGATATGCTCTG
65 CGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCG
265266 CTTC
130 CTTC
* * *
265270 TTCTTGAGGGAAAATCAGATCTGGGGGAGTTAATCCATTCCACTATCACTTAGGGAAGATTGAAT
1 TTCTTGAGGGAAAATCAGATCT-GGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAAT
* * * * * * * *
265335 CGAGGAAGACTTGTTCCGCTATCACTTAGGGAATATTAAATCTTGAAAGAGAGGGATATATTCTG
65 CGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCG
*
265400 TTTC
130 CTTC
* * ** **
265404 TTCTTGAGAGAAAATTAGATCTGGGGGAGTTGATCCATTATACTGTCACTCAAAGAAGATTGAAT
1 TTCTTGAGGGAAAATCAGATCT-GGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAAT
* * * * *
265469 CGAGGTAGACTTGTTCCACTGTCACTTAGGGAATATCAAATCTTGAAAGAGATGGATATGTTCTG
65 CGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCG
*
265534 TTTC
130 CTTC
* * * * * * *
265538 TTCTTAAGGGAAAATCAGATTTGGAGGAGTTGATTCCATTCCATTGTTACTCTGGGAATATTCAA
1 TTCTTGAGGGAAAATCAGATCTGG-GGAGTTGA-TCCATTCCACTGTCACTCAGGGAAGATTGAA
* * * * * *
265603 TCAAAGCAGATTTGTTCCACTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTGCTCC
64 TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCC
265668 GCTTC
129 GCTTC
* * * * *
265673 TTTTTGAGGGAAAATCAGATAT-GGGATTTGATCTATTCCACTATCACTCAGGGAAGATTGAATC
1 TTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATC
* * * * * * *
265737 AAGGTAGAATTGTTTCACTGTTACTCAGAGAATATCAAATCTTGAAAGAGAGAGATCTGTTCCGC
66 GAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGC
265802 TT-
131 TTC
* * * * * * *
265804 TTTTTTAGGGAAAATCGGATCTGGGGAGTTGATCCATGCCACTGTAACTTAGGGAAGATTGAATT
1 TTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATC
* * * * * *
265869 GAGGTAGACTTGTTCCAATGTTACTCAGGGAAAATCAAATCTTGAAATAAAGGGATATGTTCCAC
66 GAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGC
*
265934 TTA
131 TTC
* *
265937 TTCTTGAGGAAAAATCAGATCTAGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATC
1 TTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATC
* * *
266002 GAGGTAGACTTATTCCACTGTTACTCAGGGAATATCAAAATCTTCAAAGAGAGGGAT-TAGTTCC
66 GAGGCAGACTTGTTCCACTGTTACTCAGGGAATATC-AAATCTTGAAAGAGAGGGATAT-GTTCC
*
266066 ACTTC
129 GCTTC
* * * *
266071 TTCTTGAGGGAAAATTAGATTTGGAGGAGTT-AGTTCATTCCACTGTCACTCAGAGAAGATTGAA
1 TTCTTGAGGGAAAATCAGATCTGG-GGAGTTGA-TCCATTCCACTGTCACTCAGGGAAGATTGAA
* * *
266135 TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAAAATCAAAACTTGAAAGAGAGGGATCTGTTCC
64 TCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCC
** *
266200 AATTT
129 GCTTC
* * * ** * *
266205 TTCTTGAGGGAAAATCAGATTTGGGGAGTTTATCTATTCCACTAACACTAAGGAAAGATTGAATC
1 TTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATC
* * *
266270 GAGGCAGACATGTTCCACTATTGCTCAGGGAATATCAAATC-TGAAA
66 GAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAA
266316 ATTAAACATT
Statistics
Matches: 894, Mismatches: 140, Indels: 25
0.84 0.13 0.02
Matches are distributed among these distances:
131 19 0.02
132 181 0.20
133 189 0.21
134 330 0.37
135 175 0.20
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (133 bp):
TTCTTGAGGGAAAATCAGATCTGGGGAGTTGATCCATTCCACTGTCACTCAGGGAAGATTGAATC
GAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGC
TTC
Found at i:267966 original size:2 final size:2
Alignment explanation
Indices: 267961--268001 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
267951 TGTGCGTGTG
267961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
268002 ATTTCCTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:273039 original size:130 final size:131
Alignment explanation
Indices: 272695--273042 Score: 445
Period size: 129 Copynumber: 2.7 Consensus size: 131
272685 ACGATGATAT
*
272695 CTAATTACTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAGTCATTTATTACTCCAAT
1 CTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAGTCATTTATTACTCCAAT
* * *
272760 TGAAATAAAGAGATATTACTATTTCGTCTTAAAATTCAATATCGATTCAAGTGAAAACAATAATA
66 TGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCAATTCAAGAGAAAACAATAATA
272825 A
131 A
* * * *
272826 CTAATGATTTTCAATCGAGAATAAATGAACTTTCGTGCATTAAAATAGTCATTTATTAC-CCAAT
1 CTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAGTCATTTATTACTCCAAT
* *
272890 TGAAATAAAGAGATATTACTATTTCATCTTAAAA-TCAATATTAATTCAAGAGAAAAC-GTCAAT
66 TGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCAATTCAAGAGAAAACAAT-AAT
272953 -A
130 AA
* * * * * * * *
272954 TTAAATTATTTCCAAACGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTACTCCGA
1 CT-AATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAGTCATTTATTACTCCAA
***
273019 CCAAAATGAAA-AGATATTACTATT
65 TTGAAAT-AAAGAGATATTACTATT
273043 CTCAATGTCG
Statistics
Matches: 188, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
128 3 0.02
129 70 0.37
130 58 0.31
131 57 0.30
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.33
Consensus pattern (131 bp):
CTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAGTCATTTATTACTCCAAT
TGAAATAAAGAGATATTACTATTTCATCTTAAAATTCAATATCAATTCAAGAGAAAACAATAATA
A
Found at i:275147 original size:3 final size:3
Alignment explanation
Indices: 275139--275187 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
275129 AAGTATTTAT
* * * *
275139 TAA TAA TAA TAT TAA TAA CAA TAA TGA TAA AAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
275186 TA
1 TA
275188 GCGGGACGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:275732 original size:8 final size:8
Alignment explanation
Indices: 275687--275733 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
275677 GACAAAAATT
275687 AAATATTA
1 AAATATTA
275695 AATATAATTTA
1 AA-AT-A-TTA
275706 AAATA-TA
1 AAATATTA
*
275713 AAAAATTA
1 AAATATTA
275721 AAATATTA
1 AAATATTA
275729 AAATA
1 AAATA
275734 AACTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 6 0.18
8 16 0.48
9 3 0.09
10 3 0.09
11 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATATTA
Found at i:275741 original size:33 final size:33
Alignment explanation
Indices: 275680--275742 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
275670 AAAATGAGAC
**
275680 AAAAATTAAATATTAAATATAATTTAAAATATA
1 AAAAATTAAATATTAAATATAAACTAAAATATA
275713 AAAAATTAAAATATTAAA-ATAAACTAAAAT
1 AAAAATT-AAATATTAAATATAAACTAAAAT
275743 TAATAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 17 0.63
34 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (33 bp):
AAAAATTAAATATTAAATATAAACTAAAATATA
Found at i:275754 original size:24 final size:23
Alignment explanation
Indices: 275698--275754 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
275688 AATATTAAAT
275698 ATAATTTAAAATATAAAAAATTA
1 ATAATTTAAAATATAAAAAATTA
275721 A-AATATTAAAATA-AACTAAAATTA
1 ATAAT-TTAAAATATAA--AAAATTA
*
275745 ATAATCTAAA
1 ATAATTTAAA
275755 TACTAAACGC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.17
23 9 0.31
24 12 0.41
25 3 0.10
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAATTTAAAATATAAAAAATTA
Found at i:275837 original size:149 final size:150
Alignment explanation
Indices: 275674--275972 Score: 591
Period size: 149 Copynumber: 2.0 Consensus size: 150
275664 TGTACTAAAA
275674 TGAGACAAAAATTAAATATTAAATATAATTTAAAATATAAAAAATTAAAATATTAAAATAAACTA
1 TGAGACAAAAATTAAATATTAAATATAATTTAAAATATAAAAAATTAAAATATTAAAATAAACTA
275739 AAATTAATAATCTAAATACTAAACGCGCAGTTTATCATTTAATGAATGTTGTAGAGGA-TTTGGG
66 AAATTAATAATCTAAATACTAAACGCGCAGTTTATCATTTAATGAATGTTGTAGAGGATTTTGGG
275803 ACGAAGAGTACGAGACATTG
131 ACGAAGAGTACGAGACATTG
275823 TGAGACAAAAATTAAATATTAAATATAATTTAAAATATAAAAAATTAAAATATTAAAATAAACTA
1 TGAGACAAAAATTAAATATTAAATATAATTTAAAATATAAAAAATTAAAATATTAAAATAAACTA
275888 AAATTAATAATCTAAATACTAAACGCGCAGTTTATCATTTAATGAATGTTGTAGAGGATTTTGGG
66 AAATTAATAATCTAAATACTAAACGCGCAGTTTATCATTTAATGAATGTTGTAGAGGATTTTGGG
275953 ACGAAGAGTACGAGACATTG
131 ACGAAGAGTACGAGACATTG
275973 GGCAATTAAT
Statistics
Matches: 149, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
149 123 0.83
150 26 0.17
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.30
Consensus pattern (150 bp):
TGAGACAAAAATTAAATATTAAATATAATTTAAAATATAAAAAATTAAAATATTAAAATAAACTA
AAATTAATAATCTAAATACTAAACGCGCAGTTTATCATTTAATGAATGTTGTAGAGGATTTTGGG
ACGAAGAGTACGAGACATTG
Found at i:275881 original size:8 final size:8
Alignment explanation
Indices: 275836--275882 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
275826 GACAAAAATT
275836 AAATATTA
1 AAATATTA
275844 AATATAATTTA
1 AA-AT-A-TTA
275855 AAATA-TA
1 AAATATTA
*
275862 AAAAATTA
1 AAATATTA
275870 AAATATTA
1 AAATATTA
275878 AAATA
1 AAATA
275883 AACTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 6 0.18
8 16 0.48
9 3 0.09
10 3 0.09
11 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATATTA
Found at i:275890 original size:33 final size:33
Alignment explanation
Indices: 275829--275891 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
275819 ATTGTGAGAC
**
275829 AAAAATTAAATATTAAATATAATTTAAAATATA
1 AAAAATTAAATATTAAATATAAACTAAAATATA
275862 AAAAATTAAAATATTAAA-ATAAACTAAAAT
1 AAAAATT-AAATATTAAATATAAACTAAAAT
275892 TAATAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 17 0.63
34 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (33 bp):
AAAAATTAAATATTAAATATAAACTAAAATATA
Found at i:275903 original size:24 final size:23
Alignment explanation
Indices: 275847--275903 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
275837 AATATTAAAT
275847 ATAATTTAAAATATAAAAAATTA
1 ATAATTTAAAATATAAAAAATTA
275870 A-AATATTAAAATA-AACTAAAATTA
1 ATAAT-TTAAAATATAA--AAAATTA
*
275894 ATAATCTAAA
1 ATAATTTAAA
275904 TACTAAACGC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 5 0.17
23 9 0.31
24 12 0.41
25 3 0.10
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAATTTAAAATATAAAAAATTA
Found at i:280165 original size:27 final size:28
Alignment explanation
Indices: 280127--280195 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
280117 GTGCACATTA
280127 TCAACTTGGGTGTTA-TTTTTTTAAGAT
1 TCAACTTGGGTGTTATTTTTTTTAAGAT
280154 TCAACTTGGGTGTTATTTTTTTTAAGAT
1 TCAACTTGGGTGTTATTTTTTTTAAGAT
280182 TCAACTTGGGTGTT
1 TCAACTTGGGTGTT
280196 TAATGCAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 15 0.37
28 26 0.63
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (28 bp):
TCAACTTGGGTGTTATTTTTTTTAAGAT
Found at i:288195 original size:17 final size:20
Alignment explanation
Indices: 288159--288196 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
288149 TGTTTTTCAA
288159 ATAATCATATATAAATAAAT
1 ATAATCATATATAAATAAAT
288179 ATAAT-ATA-ATAAA-AAAT
1 ATAATCATATATAAATAAAT
288196 A
1 A
288197 ATTTTACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 3 0.17
20 5 0.28
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATCATATATAAATAAAT
Found at i:291913 original size:6 final size:6
Alignment explanation
Indices: 291902--291934 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
291892 TTGATGCAAG
291902 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATT
291935 TGTTTACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATTAAA
Found at i:293107 original size:2 final size:2
Alignment explanation
Indices: 293100--293151 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
293090 AATTATTTTA
293100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293142 AT AT AT AT AT
1 AT AT AT AT AT
293152 TCGACTTATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295599 original size:27 final size:27
Alignment explanation
Indices: 295546--295600 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
295536 GACAAATGCA
* * **
295546 AATATGAACAACATAAATGAATGACAC
1 AATATAAACAACAGAAATGAACAACAC
*
295573 AATATAAACAATAGAAATGAACAACAC
1 AATATAAACAACAGAAATGAACAACAC
295600 A
1 A
295601 CACCCAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.15, G:0.09, T:0.16
Consensus pattern (27 bp):
AATATAAACAACAGAAATGAACAACAC
Found at i:295930 original size:17 final size:17
Alignment explanation
Indices: 295910--295948 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
295900 AGAAAAAAAT
*
295910 AAAAT-TAATAAAATAAC
1 AAAATCTAA-AAAATAAA
295927 AAAATCTAAAAAATAAA
1 AAAATCTAAAAAATAAA
295944 AAAAT
1 AAAAT
295949 GAAAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATCTAAAAAATAAA
Found at i:306369 original size:11 final size:11
Alignment explanation
Indices: 306353--306384 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
306343 ATTGCATGGC
306353 ATTTAGTTTAT
1 ATTTAGTTTAT
306364 ATTTAGTTTAT
1 ATTTAGTTTAT
306375 ATTTAGTTTA
1 ATTTAGTTTA
306385 GTTCTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (11 bp):
ATTTAGTTTAT
Found at i:319697 original size:82 final size:83
Alignment explanation
Indices: 319320--319747 Score: 359
Period size: 82 Copynumber: 5.2 Consensus size: 83
319310 ACAATTGTGG
** * * * **
319320 CGTTTATTACAAAAACGTCGCTAAGGTGCATGACTATAG-GGCGTTTATTACAAAAACACCGCTA
1 CGTTTATTA-AAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATTACAAAAATACTACTA
* *
319384 AAGTGCATGATTATTGCGG
65 AAGTGCATGACTATTGCGA
* * * * **
319403 CGTTCATTACAAAAACACCGCTAAAGTACATGATTATGGCGGCGTTTATT--AAAAACGCTACTA
1 CGTTTATTA-AAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATTACAAAAATACTACTA
*
319466 ACA-TGCATGACTACTGCGA
65 A-AGTGCATGACTATTGCGA
* * * * * * * *
319485 CGTTTATTGCAAAAATACCACTAAAGTGCAAGACTATTGTGTCATTTATTACAAAAATACCACTA
1 CGTTTATT-AAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATTACAAAAATACTACTA
319550 AAGTGCATGACTATTGC-A
65 AAGTGCATGACTATTGCGA
* * * ** * * * *
319568 GCGTTTA-TCAAAAACACCGCTAAAGGGAAAAATTATTGCGGCATTTATTATAAAAATGCTACTA
1 -CGTTTATTAAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATTACAAAAATACTACTA
*
319632 AAGTGCATGATTATTGCGA
65 AAGTGCATGACTATTGCGA
* * ** *
319651 TGTTTA-TAAAAAACGCCGCTAAAGTGCATGACTATTATGGCGTTTATTACAAAAATA-TCGCTA
1 CGTTTATTAAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATTACAAAAATACT-ACTA
* *
319714 AGGTGCATGACTATTGCGG
65 AAGTGCATGACTATTGCGA
*
319733 TGTTTATTACAAAAA
1 CGTTTATTA-AAAAA
319748 TGCTGCCTAA
Statistics
Matches: 277, Mismatches: 57, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
81 1 0.00
82 192 0.69
83 39 0.14
84 45 0.16
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (83 bp):
CGTTTATTAAAAAACACCGCTAAAGTGCATGACTATTGCGGCGTTTATTACAAAAATACTACTAA
AGTGCATGACTATTGCGA
Found at i:319748 original size:42 final size:42
Alignment explanation
Indices: 319313--319747 Score: 391
Period size: 42 Copynumber: 10.5 Consensus size: 42
319303 TGATTGTACA
* ** *
319313 ATTGTGGCGTTTATTACAAAAACGTCGCTAAGGTGCATGACT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* *
319355 ATAG-GGCGTTTATTACAAAAACACCGCTAAAGTGCATGATT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * *
319396 ATTGCGGCGTTCATTACAAAAACACCGCTAAAGTACATGATT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * **
319438 ATGGCGGCGTTTATT--AAAAACGCTACTAACA-TGCATGACT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAA-AGTGCATGACT
* * * * * *
319478 ACTGCGACGTTTATTGCAAAAATACCACTAAAGTGCAAGACT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * * * *
319520 ATTGTGTCATTTATTACAAAAATACCACTAAAGTGCATGACT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * * ** *
319562 ATTGCAGCGTTTA-T-CAAAAACACCGCTAAAGGGAAAAATT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * ** ** *
319602 ATTGCGGCATTTATTATAAAAATGCTACTAAAGTGCATGATT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
** *
319644 ATTGCGATGTTTA-TA-AAAAACGCCGCTAAAGTGCATGACT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
** * * *
319684 ATTATGGCGTTTATTACAAAAATATCGCTAAGGTGCATGACT
1 ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
*
319726 ATTGCGGTGTTTATTACAAAAA
1 ATTGCGGCGTTTATTACAAAAA
319748 TGCTGCCTAA
Statistics
Matches: 316, Mismatches: 68, Indels: 18
0.79 0.17 0.04
Matches are distributed among these distances:
40 90 0.28
41 44 0.14
42 182 0.58
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (42 bp):
ATTGCGGCGTTTATTACAAAAACACCGCTAAAGTGCATGACT
Found at i:319751 original size:124 final size:125
Alignment explanation
Indices: 319313--319748 Score: 422
Period size: 124 Copynumber: 3.5 Consensus size: 125
319303 TGATTGTACA
* * * *
319313 ATTGTGGCGTTTATTACAAAAACGTCGCTAAGGTGCATGACTATAG-GGCGTTTATTACAAAAAC
1 ATTGCGGCGTTTATTACAAAAACATCGCTAAGGTGCATGACTATTGCGGCGTTTATTACAAAAAT
* * * * *
319377 ACCGCTAAAGTGCATGATTATTGCGGCGTTCATTACAAAAACACCGCTAAAGTACATGATT
66 ACCACTAAAGTGCATGATTATTGC-GTGTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * * ** * * *
319438 ATGGCGGCGTTTATT--AAAAAC-GCTACTAACATGCATGACTACTGCGACGTTTATTGCAAAAA
1 ATTGCGGCGTTTATTACAAAAACATC-GCTAAGGTGCATGACTATTGCGGCGTTTATTACAAAAA
* * * * * *
319500 TACCACTAAAGTGCAAGACTATTGTGTCATTTATTACAAAAATACCACTAAAGTGCATGACT
65 TACCACTAAAGTGCATGATTATTGCGT-GTTTATTACAAAAACACCGCTAAAGTGCATGACT
* * * ** * * *
319562 ATTGCAGCGTTTA-T-CAAAAACACCGCTAAAGG-GAAAAATTATTGCGGCATTTATTATAAAAA
1 ATTGCGGCGTTTATTACAAAAACATCGCT-AAGGTGCATGACTATTGCGGCGTTTATTACAAAAA
* * *
319624 TGCTACTAAAGTGCATGATTATTGCGATGTTTA-TA-AAAAACGCCGCTAAAGTGCATGACT
65 TACCACTAAAGTGCATGATTATTGCG-TGTTTATTACAAAAACACCGCTAAAGTGCATGACT
** * *
319684 ATTATGGCGTTTATTACAAAAATATCGCTAAGGTGCATGACTATTGCGGTGTTTATTACAAAAAT
1 ATTGCGGCGTTTATTACAAAAACATCGCTAAGGTGCATGACTATTGCGGCGTTTATTACAAAAAT
319749 GCTGCCTAAT
Statistics
Matches: 243, Mismatches: 58, Indels: 21
0.75 0.18 0.07
Matches are distributed among these distances:
122 33 0.14
123 30 0.12
124 163 0.67
125 17 0.07
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (125 bp):
ATTGCGGCGTTTATTACAAAAACATCGCTAAGGTGCATGACTATTGCGGCGTTTATTACAAAAAT
ACCACTAAAGTGCATGATTATTGCGTGTTTATTACAAAAACACCGCTAAAGTGCATGACT
Found at i:331242 original size:20 final size:19
Alignment explanation
Indices: 331212--331262 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
331202 AAAAGGGAAA
*
331212 TATTCTTTTATTCTTTATTTC
1 TATTATTTTATTC--TATTTC
331233 T-TTATTTTATTCTATTTC
1 TATTATTTTATTCTATTTC
*
331251 TATTTTTTTATT
1 TATTATTTTATT
331263 TCTCTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.26
19 9 0.33
20 10 0.37
21 1 0.04
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TATTATTTTATTCTATTTC
Found at i:338941 original size:2 final size:2
Alignment explanation
Indices: 338914--338961 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
338904 CGAGCCTTTA
* *
338914 AT AT GT AT AT AT CT AT GAT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
338956 AT AT AT
1 AT AT AT
338962 GTAAATAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:351852 original size:3 final size:3
Alignment explanation
Indices: 351846--351900 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
351836 TTTTGAACTA
351846 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
351893 TAT TAT TA
1 TAT TAT TA
351901 CCAAAAATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:354037 original size:2 final size:2
Alignment explanation
Indices: 354030--354059 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
354020 TTAAATAACA
354030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
354060 TAAATTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355514 original size:18 final size:18
Alignment explanation
Indices: 355491--355527 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
355481 CAACCAGATC
355491 GACCCGTTAACCCGACCT
1 GACCCGTTAACCCGACCT
*
355509 GACCCGTTGACCCGACCT
1 GACCCGTTAACCCGACCT
355527 G
1 G
355528 TTGACCGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.43, G:0.22, T:0.16
Consensus pattern (18 bp):
GACCCGTTAACCCGACCT
Found at i:358020 original size:24 final size:24
Alignment explanation
Indices: 357993--358080 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
357983 TTCTATTATA
* *
357993 ATACCTGACCTAGATTCTGATCGG
1 ATACTTGACCTAGATTTTGATCGG
* *
358017 ATACTTGACCTAGATTTTGATTGA
1 ATACTTGACCTAGATTTTGATCGG
* *
358041 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTAGATTTTGATCGG
*
358065 ATACTTGACCTGGATT
1 ATACTTGACCTAGATT
358081 ATTTTATGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
ATACTTGACCTAGATTTTGATCGG
Found at i:358090 original size:24 final size:23
Alignment explanation
Indices: 358016--358090 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
358006 ATTCTGATCG
* *
358016 GATACTTGACCTAGA-TTTTGATT
1 GATACTTGACCTGGATTTTTTA-T
* *
358039 GAATACTTGACCTGGATTTTGATCT
1 G-ATACTTGACCTGGATTTT-TTAT
358064 GATACTTGACCTGGATTATTTTAT
1 GATACTTGACCTGGATT-TTTTAT
358088 GAT
1 GAT
358091 TTTTGATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.02
24 34 0.81
25 7 0.17
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (23 bp):
GATACTTGACCTGGATTTTTTAT
Found at i:358294 original size:2 final size:2
Alignment explanation
Indices: 358287--358317 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
358277 CGGATGGGGG
358287 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 T
358318 GTTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:360243 original size:18 final size:17
Alignment explanation
Indices: 360214--360250 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
360204 ACCGGTCACA
360214 ACCCGACCGACCCGTTG
1 ACCCGACCGACCCGTTG
360231 ACCCGACCCGACCCGTTG
1 ACCCGA-CCGACCCGTTG
360249 AC
1 AC
360251 TGTTGACCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (17 bp):
ACCCGACCGACCCGTTG
Found at i:362728 original size:24 final size:24
Alignment explanation
Indices: 362701--362836 Score: 191
Period size: 24 Copynumber: 5.7 Consensus size: 24
362691 TTCTATTAAA
* *
362701 ATACCTGACCTGGATTCTAATCGG
1 ATACTTGACCTGGATTCTGATCGG
362725 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
362749 ATACTTGACCTGGATTTTGATTGG
1 ATACTTGACCTGGATTCTGATCGG
* *
362773 ATACTTGACCTGGATTCTGATTGA
1 ATACTTGACCTGGATTCTGATCGG
* * *
362797 ATACTTGACCTGGATTTTGAACTG
1 ATACTTGACCTGGATTCTGATCGG
362821 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
362837 ATTTTATGAT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 101 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:362780 original size:12 final size:13
Alignment explanation
Indices: 362723--362835 Score: 89
Period size: 12 Copynumber: 9.3 Consensus size: 13
362713 GATTCTAATC
362723 GGATACTTGACCT
1 GGATACTTGACCT
* *
362736 GGATTC-TGATC-
1 GGATACTTGACCT
362747 GGATACTTGACCT
1 GGATACTTGACCT
* *
362760 GGAT-TTTGA-TT
1 GGATACTTGACCT
362771 GGATACTTGACCT
1 GGATACTTGACCT
* *
362784 GGATTC-TGA-TT
1 GGATACTTGACCT
*
362795 GAATACTTGACCT
1 GGATACTTGACCT
* *
362808 GGAT-TTTGAACT
1 GGATACTTGACCT
362820 -GATACTTGACCT
1 GGATACTTGACCT
362832 GGAT
1 GGAT
362836 TATTTTATGA
Statistics
Matches: 74, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
11 18 0.24
12 34 0.46
13 22 0.30
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (13 bp):
GGATACTTGACCT
Found at i:366587 original size:23 final size:24
Alignment explanation
Indices: 366543--366592 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
366533 ATTCTTTCTC
366543 TGATTCAAAATGGAGAAATGGTCG
1 TGATTCAAAATGGAGAAATGGTCG
*
366567 TGATTCAAAA-GGTGAAATGGTCG
1 TGATTCAAAATGGAGAAATGGTCG
366590 TGA
1 TGA
366593 AATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.36, C:0.08, G:0.30, T:0.26
Consensus pattern (24 bp):
TGATTCAAAATGGAGAAATGGTCG
Found at i:366760 original size:18 final size:18
Alignment explanation
Indices: 366739--366806 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
366729 CATTTAAATA
366739 TATAAATATATTTTTATT
1 TATAAATATATTTTTATT
** **
366757 TATAAATTTAAATACATTTAAA
1 TATAAA--T--ATATTTTTATT
*
366779 TATAAATATATTTTCATT
1 TATAAATATATTTTTATT
366797 TATAAATATA
1 TATAAATATA
366807 AATACATTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
18 22 0.59
20 2 0.05
22 13 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATATATTTTTATT
Found at i:366784 original size:16 final size:16
Alignment explanation
Indices: 366759--366831 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 16
366749 TTTTTATTTA
*
366759 TAAATTTAAATACATT
1 TAAATATAAATACATT
366775 TAAATATAAATATATTTTCATT
1 TAAATAT-AA-ATA----CATT
366797 TATAAATATAAATACATT
1 T--AAATATAAATACATT
*
366815 TAAATATAAATATATT
1 TAAATATAAATACATT
366831 T
1 T
366832 TCATTTTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
16 21 0.45
17 2 0.04
18 8 0.17
22 8 0.17
23 2 0.04
24 6 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATAAATACATT
Found at i:366798 original size:40 final size:40
Alignment explanation
Indices: 366725--366854 Score: 192
Period size: 40 Copynumber: 3.2 Consensus size: 40
366715 ATAAATGACT
*
366725 AATACATTTAAATATATAAATATATTTTTATTTATAAATTTA
1 AATACATTT-AA-ATATAAATATATTTTCATTTATAAATTTA
*
366767 AATACATTTAAATATAAATATATTTTCATTTATAAATATA
1 AATACATTTAAATATAAATATATTTTCATTTATAAATTTA
*
366807 AATACATTTAAATATAAATATATTTTCATTT-TCATATTTA
1 AATACATTTAAATATAAATATATTTTCATTTAT-AAATTTA
366847 AATA-ATTT
1 AATACATTT
366855 TTATTAAAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
39 5 0.06
40 67 0.81
41 2 0.02
42 9 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (40 bp):
AATACATTTAAATATAAATATATTTTCATTTATAAATTTA
Found at i:366836 original size:22 final size:22
Alignment explanation
Indices: 366771--366877 Score: 89
Period size: 22 Copynumber: 5.0 Consensus size: 22
366761 AATTTAAATA
366771 CATTTAAATATAAATATATTTT
1 CATTTAAATATAAATATATTTT
** *
366793 CA-TT---TATAAATATAAATA
1 CATTTAAATATAAATATATTTT
366811 CATTTAAATATAAATATATTTT
1 CATTTAAATATAAATATATTTT
* *
366833 CATTTTCATATTTAAATA-ATTTT
1 CA-TTT-AAATATAAATATATTTT
* * *
366856 TATTAAAATATAATTATATTTT
1 CATTTAAATATAAATATATTTT
366878 AAATACTAGT
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
18 13 0.20
19 2 0.03
21 10 0.15
22 22 0.34
23 9 0.14
24 9 0.14
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
CATTTAAATATAAATATATTTT
Found at i:367273 original size:27 final size:30
Alignment explanation
Indices: 367242--367297 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 30
367232 TAATATCTGG
367242 TTTTAGAAAATA-T-TTTTT-ATTTTTTAT
1 TTTTAGAAAATAGTATTTTTAATTTTTTAT
367269 TTTTAGAAAATAGTATTTTTAATTTTTTA
1 TTTTAGAAAATAGTATTTTTAATTTTTTA
367298 AAAATTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.46
28 1 0.04
29 5 0.19
30 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTAGAAAATAGTATTTTTAATTTTTTAT
Found at i:367969 original size:24 final size:25
Alignment explanation
Indices: 367939--367988 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
367929 ATTTAATTTT
* *
367939 TTAAAAATTTAAA-AATTATTTAGA
1 TTAAAAATATAAACAATTATTAAGA
367963 TTAAAAATATAAACAATTATTAAGA
1 TTAAAAATATAAACAATTATTAAGA
367988 T
1 T
367989 ATTCAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAAAAATATAAACAATTATTAAGA
Found at i:368038 original size:15 final size:15
Alignment explanation
Indices: 367998--368040 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
367988 TATTCAATAC
*
367998 ATTAAAAATAAAAAT
1 ATTAAAAATTAAAAT
*
368013 ATTACAAAATTAAACT
1 ATTA-AAAATTAAAAT
368029 ATTAAAAATTAA
1 ATTAAAAATTAA
368041 TTTAATGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAAAAATTAAAAT
Found at i:374317 original size:28 final size:28
Alignment explanation
Indices: 374277--374336 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
374267 CACGGTAATA
* *
374277 CCCTCCAACCGAATACTGGTATTAAATT
1 CCCTCCAACCGAACACGGGTATTAAATT
374305 CCCTCCAACCGAACACGGGTATTAAATT
1 CCCTCCAACCGAACACGGGTATTAAATT
374333 CCCT
1 CCCT
374337 AGAATTGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.25
Consensus pattern (28 bp):
CCCTCCAACCGAACACGGGTATTAAATT
Found at i:377898 original size:30 final size:30
Alignment explanation
Indices: 377831--377898 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
377821 TTAATTAATT
*
377831 AGACCACCCAACTATTTAAATGCTTCAATC
1 AGACCACTCAACTATTTAAATGCTTCAATC
377861 AGACCACTCAACTATTTAAATGCTTCAATC
1 AGACCACTCAACTATTTAAATGCTTCAATC
*
377891 ATACCACT
1 AGACCACT
377899 AGCCATTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28
Consensus pattern (30 bp):
AGACCACTCAACTATTTAAATGCTTCAATC
Found at i:378276 original size:473 final size:471
Alignment explanation
Indices: 377376--378833 Score: 2258
Period size: 472 Copynumber: 3.1 Consensus size: 471
377366 TTTGATTTAA
* * * ** *
377376 TCAACCAGACCACCCAACTATTTAAATGCTTCAATAAGACTGCTAACCATTAACATTTAATGAAA
1 TCAATCAGACCACTCAACTATTTAAATGCTTCAATCAGACCACTAGCCATTAACATTTAATGAAA
** * ***
377441 ATGATGACATGACAATTAATAAAACCGATATATTTATACATTTGGTCTTTAATGTTTACGCGTTC
66 ATGATGAC--G----TTAATAAAATTGCTATATTTATACATTTGGTCTTTAATGTTTACATATTC
* *
377506 TATCAATCTAGTACTAATTTCAATTTATTCAATAAATTTAATCCTCTATATAAATAATGTCACGT
125 TATCAATCTAGTACTAATTTCAATTTATTCAATAAATTTAATCCTCCA-ATAAATAATGTCACAT
* * *
377571 TTCACCATTTAATTAAAATATTTTTAA-TAATTTTAAATCATTTAATTTAAAAAATTTATTTCTT
189 TTCACCATTTAATT-AAAT-TTTTTAATTAATTTTAATTTATTTAATTTAAATAATTTATTTC-T
*
377635 TCAATCATATGGTGGTGACACATGTCTCTATATTATTAAAAG-AAATACTTGATATAAATTGGTG
251 TCAATCATATGGTGGTGACACATGTCACTATATTATTAAAAGAAAATACTTGATATAAATTGGTG
* * *
377699 TTAGAAACAAACGAACTTGCTTCGATGTTTATTTTATGAAATGGCTAATTTATTTTATGGTAAAC
316 TTAGAAACAATCGAACCTGCTTCGATGTTTATTTTATGAAATGACTAATTTATTTTATGGTAAAC
* * * * *
377764 TATACATGTGACCACTTAACTATTGCACTGTTCCACTTCGACCATCGATGTTTTAATTTAATTAA
381 TACACATGTGACCACTTAACTATTGCACCGTTTCACTTCGACCATCGATGTTTTGATTTAATCAA
*
377829 TTAGACCACCCAACTATTTAAATGCT
446 TCAGACCACCCAACTATTTAAATGCT
*
377855 TCAATCAGACCACTCAACTATTTAAATGCTTCAATCATACCACTAGCCATTAACATTTAATGAAA
1 TCAATCAGACCACTCAACTATTTAAATGCTTCAATCAGACCACTAGCCATTAACATTTAATGAAA
* * * * *
377920 ATGATGACGTTATTAAAATTTCTATATTTATATATTTGGTCCTTAATTTTTACATATTCTATCAA
66 ATGATGACGTTAATAAAATTGCTATATTTATACATTTGGTCTTTAATGTTTACATATTCTATCAA
* *
377985 TCTAGTACT-ATTTTAATTTATTCAATAAATTTAATCCTCCAATCATATAATGTCACATTTCACC
131 TCTAGTACTAATTTCAATTTATTCAATAAATTTAATCCTCCAAT-AAATAATGTCACATTTCACC
*
378049 ATTTAATTATTATTTTTTAATTAATTTTAATTTATTTAATTTAAATAATTTATTTCTTCGAATCA
195 ATTTAATTA-AATTTTTTAATTAATTTTAATTTATTTAATTTAAATAATTTATTTCTTC-AATCA
* *
378114 TACGGTGGTGACACATGTCGCTATATTATTAAAAGAAAATACTTGATATAAATTGGTGTTAGAAA
258 TATGGTGGTGACACATGTCACTATATTATTAAAAGAAAATACTTGATATAAATTGGTGTTAGAAA
378179 CAATCGAACCTGCTTCGATGTTTATTTTATGAAATGACTAATTTATTTTATGGTAAACTACACAT
323 CAATCGAACCTGCTTCGATGTTTATTTTATGAAATGACTAATTTATTTTATGGTAAACTACACAT
378244 GTGACCACTTAACTATTGCACCGTTTCACTTCGACCATCGATGTTTTGATTTAATCAATCAGACC
388 GTGACCACTTAACTATTGCACCGTTTCACTTCGACCATCGATGTTTTGATTTAATCAATCAGACC
378309 ACCCAACTATTTAAATGCT
453 ACCCAACTATTTAAATGCT
*
378328 TCAATCATACCACTCAACTATTTAAATGCTTCAATCAGACCACTAGCCATTAACATTTAATGAAA
1 TCAATCAGACCACTCAACTATTTAAATGCTTCAATCAGACCACTAGCCATTAACATTTAATGAAA
* * * *
378393 ATGACGATGCTAATAAAATTGCTATAATTATACATTTGGTCTTTAATGTTTACATATTCTATCAA
66 ATGATGACGTTAATAAAATTGCTATATTTATACATTTGGTCTTTAATGTTTACATATTCTATCAA
378458 TCTAGTACTAATTTCAATTTATTCAATAAATTTAATCCTCCAATTAAATAATGTCACATTTCACC
131 TCTAGTACTAATTTCAATTTATTCAATAAATTTAATCCTCCAA-TAAATAATGTCACATTTCACC
* * * *
378523 ATTTAATTAAAATTTTT-ATTAATTTTTATCTATTTAATTTAAATAATTTATTTTTTCCAATCAT
195 ATTTAATTAAATTTTTTAATTAATTTTAATTTATTTAATTTAAATAATTTATTTCTT-CAATCAT
*
378587 ATGGTGGTGACACATGTCACTATATTATTAAAAGAAAATACTTTATATAAATTGGTGTTAGAAAC
259 ATGGTGGTGACACATGTCACTATATTATTAAAAGAAAATACTTGATATAAATTGGTGTTAGAAAC
* *
378652 AATCAAACCTGCTTCGATATTTATTTTATGAAATGACTAATTTATTTTATGGTAAACTACACATG
324 AATCGAACCTGCTTCGATGTTTATTTTATGAAATGACTAATTTATTTTATGGTAAACTACACATG
*
378717 TGACCACTTAACTATTGCACCGTTTCACTTCGACCATCAATGTTTTGATTTAATCAATCAGACCA
389 TGACCACTTAACTATTGCACCGTTTCACTTCGACCATCGATGTTTTGATTTAATCAATCAGACCA
*
378782 CCCAACTATTTAAATACT
454 CCCAACTATTTAAATGCT
* * *
378800 TCAATCAAATCAATCAACTATTTAAATGCTTCAA
1 TCAATCAGACCACTCAACTATTTAAATGCTTCAA
378834 ATCAATCAAC
Statistics
Matches: 906, Mismatches: 65, Indels: 23
0.91 0.07 0.02
Matches are distributed among these distances:
471 13 0.01
472 407 0.45
473 358 0.40
474 60 0.07
475 1 0.00
477 1 0.00
479 66 0.07
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (471 bp):
TCAATCAGACCACTCAACTATTTAAATGCTTCAATCAGACCACTAGCCATTAACATTTAATGAAA
ATGATGACGTTAATAAAATTGCTATATTTATACATTTGGTCTTTAATGTTTACATATTCTATCAA
TCTAGTACTAATTTCAATTTATTCAATAAATTTAATCCTCCAATAAATAATGTCACATTTCACCA
TTTAATTAAATTTTTTAATTAATTTTAATTTATTTAATTTAAATAATTTATTTCTTCAATCATAT
GGTGGTGACACATGTCACTATATTATTAAAAGAAAATACTTGATATAAATTGGTGTTAGAAACAA
TCGAACCTGCTTCGATGTTTATTTTATGAAATGACTAATTTATTTTATGGTAAACTACACATGTG
ACCACTTAACTATTGCACCGTTTCACTTCGACCATCGATGTTTTGATTTAATCAATCAGACCACC
CAACTATTTAAATGCT
Found at i:378371 original size:30 final size:30
Alignment explanation
Indices: 378298--378371 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
378288 TTTGATTTAA
*
378298 TCAATCAGACCACCCAACTATTTAAATGCT
1 TCAATCAGACCACTCAACTATTTAAATGCT
*
378328 TCAATCATACCACTCAACTATTTAAATGCT
1 TCAATCAGACCACTCAACTATTTAAATGCT
378358 TCAATCAGACCACT
1 TCAATCAGACCACT
378372 AGCCATTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.36, C:0.30, G:0.05, T:0.28
Consensus pattern (30 bp):
TCAATCAGACCACTCAACTATTTAAATGCT
Found at i:378804 original size:30 final size:29
Alignment explanation
Indices: 378770--378883 Score: 117
Period size: 30 Copynumber: 3.9 Consensus size: 29
378760 TTTGATTTAA
* *
378770 TCAATCAGACCACCCAACTATTTAAATACT
1 TCAATCA-ACCAACCAACTATTTAAATGCT
* *
378800 TCAATCAAATCAATCAACTATTTAAATGCT
1 TCAATC-AACCAACCAACTATTTAAATGCT
* *
378830 TC-A--AATCAATCAACTATTTAAATGCT
1 TCAATCAACCAACCAACTATTTAAATGCT
*
378856 TCAATCATACCAACCTACTATTTAAATG
1 TCAATCA-ACCAACCAACTATTTAAATG
378884 GTGCCCATCG
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
26 25 0.35
27 1 0.01
29 2 0.03
30 43 0.60
31 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.04, T:0.32
Consensus pattern (29 bp):
TCAATCAACCAACCAACTATTTAAATGCT
Found at i:378840 original size:26 final size:26
Alignment explanation
Indices: 378804--378859 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
378794 AATACTTCAA
378804 TCAAATCAATCAACTATTTAAATGCT
1 TCAAATCAATCAACTATTTAAATGCT
378830 TCAAATCAATCAACTATTTAAATGCT
1 TCAAATCAATCAACTATTTAAATGCT
378856 TCAA
1 TCAA
378860 TCATACCAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.34
Consensus pattern (26 bp):
TCAAATCAATCAACTATTTAAATGCT
Found at i:378869 original size:26 final size:26
Alignment explanation
Indices: 378783--378869 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 26
378773 ATCAGACCAC
*
378783 CCAACTATTTAAATACTTCAATCAAATCAA
1 CCAACTATTTAAATGCTTCAATC--AT--A
*
378813 TCAACTATTTAAATGCTTCAAATCA-A
1 CCAACTATTTAAATGCTTC-AATCATA
*
378839 TCAACTATTTAAATGCTTCAATCATA
1 CCAACTATTTAAATGCTTCAATCATA
378865 CCAAC
1 CCAAC
378870 CTACTATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
25 5 0.10
26 25 0.48
29 1 0.02
30 17 0.33
31 4 0.08
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (26 bp):
CCAACTATTTAAATGCTTCAATCATA
Found at i:379100 original size:13 final size:14
Alignment explanation
Indices: 379077--379108 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
379067 TAAAATTAAC
379077 TCTTCTCTTCTTCT
1 TCTTCTCTTCTTCT
379091 TCTT-TCTTCTTCT
1 TCTTCTCTTCTTCT
379104 TCTTC
1 TCTTC
379109 CTTATTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TCTTCTCTTCTTCT
Found at i:385423 original size:13 final size:13
Alignment explanation
Indices: 385405--385429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385395 ATTACAATTG
385405 AAAATATATATTA
1 AAAATATATATTA
385418 AAAATATATATT
1 AAAATATATATT
385430 TTGAATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATATATTA
Found at i:386658 original size:25 final size:24
Alignment explanation
Indices: 386601--386659 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 24
386591 ATTGATATTA
*
386601 TAAATATATTTTTATAATATTTTAG
1 TAAATATA-TATTATAATATTTTAG
* *
386626 --AATTTATATTATAATATATTTTG
1 TAAATATATATTATAATAT-TTTAG
386649 TAAATATATAT
1 TAAATATATAT
386660 AATTAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
22 10 0.37
23 9 0.33
25 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (24 bp):
TAAATATATATTATAATATTTTAG
Found at i:389060 original size:23 final size:23
Alignment explanation
Indices: 388982--389044 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
388972 GATCCTTTGA
388982 GACAATTCTACGTGGTCCTTCAG
1 GACAATTCTACGTGGTCCTTCAG
389005 GACAATTCTACGTGGTCCTTCAG
1 GACAATTCTACGTGGTCCTTCAG
*
389028 GACATTTCTACGTGGTC
1 GACAATTCTACGTGGTC
389045 ATATGGGACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (23 bp):
GACAATTCTACGTGGTCCTTCAG
Found at i:392004 original size:16 final size:16
Alignment explanation
Indices: 391983--392020 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
391973 TCCATATAAT
391983 TCACATGTCACATATA
1 TCACATGTCACATATA
391999 TCACATGTCACATATA
1 TCACATGTCACATATA
392015 TCACAT
1 TCACAT
392021 AGCTTTTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (16 bp):
TCACATGTCACATATA
Found at i:392761 original size:21 final size:21
Alignment explanation
Indices: 392737--392782 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
392727 CCAGTCTTTG
*
392737 GTATGGACACCAGCTCATCTA
1 GTATGGACACCAACTCATCTA
* * *
392758 GTATGGATACTAACTCATCTC
1 GTATGGACACCAACTCATCTA
392779 GTAT
1 GTAT
392783 CAATACAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (21 bp):
GTATGGACACCAACTCATCTA
Found at i:395248 original size:19 final size:19
Alignment explanation
Indices: 395224--395267 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
395214 AATATGCTCA
395224 TAGTCGATCCTCCAAGTAC
1 TAGTCGATCCTCCAAGTAC
395243 TAGTCGATCCTCCAAGTAC
1 TAGTCGATCCTCCAAGTAC
395262 TAGTCG
1 TAGTCG
395268 GAACTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (19 bp):
TAGTCGATCCTCCAAGTAC
Found at i:402630 original size:46 final size:46
Alignment explanation
Indices: 402580--402709 Score: 251
Period size: 46 Copynumber: 2.8 Consensus size: 46
402570 TTATTTTTGA
*
402580 AAACTTTGAATAAGTTCAATTCAAGTCCAAAACCAATTAATTTTAT
1 AAACTTTGAATAAATTCAATTCAAGTCCAAAACCAATTAATTTTAT
402626 AAACTTTGAATAAATTCAATTCAAGTCCAAAACCAATTAATTTTAT
1 AAACTTTGAATAAATTCAATTCAAGTCCAAAACCAATTAATTTTAT
402672 AAACTTTGAATAAATTCAATTCAAGTCCAAAACCAATT
1 AAACTTTGAATAAATTCAATTCAAGTCCAAAACCAATT
402710 TTGTCTTAAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 83 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.33
Consensus pattern (46 bp):
AAACTTTGAATAAATTCAATTCAAGTCCAAAACCAATTAATTTTAT
Found at i:407278 original size:20 final size:20
Alignment explanation
Indices: 407253--407303 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
407243 CAGTTGAACA
407253 AGTACCGATACTGTTCATAT
1 AGTACCGATACTGTTCATAT
407273 AGTACCGATACTGTTCATAT
1 AGTACCGATACTGTTCATAT
* *
407293 GGTACTGATAC
1 AGTACCGATAC
407304 AAAGGTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (20 bp):
AGTACCGATACTGTTCATAT
Found at i:412571 original size:26 final size:25
Alignment explanation
Indices: 412542--412599 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
412532 ATTAAGTACA
*
412542 TGAATGGAAGGGAATAATGTTTTGGC
1 TGAATGGAAGGGAAT-ATCTTTTGGC
* * *
412568 TGAATGGAGGGGCATGTCTTTTGGC
1 TGAATGGAAGGGAATATCTTTTGGC
412593 TGAATGG
1 TGAATGG
412600 TGCTTGAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.24, C:0.07, G:0.38, T:0.31
Consensus pattern (25 bp):
TGAATGGAAGGGAATATCTTTTGGC
Found at i:415979 original size:21 final size:21
Alignment explanation
Indices: 415949--415989 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
415939 ATATTCCAAC
*
415949 TTAAACTTCAACATTCAATAA
1 TTAAAATTCAACATTCAATAA
*
415970 TTAAAATTCAACATTGAATA
1 TTAAAATTCAACATTCAATA
415990 CCCATAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAAAATTCAACATTCAATAA
Found at i:419592 original size:2 final size:2
Alignment explanation
Indices: 419587--419612 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
419577 TTTATTTTTC
419587 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
419613 TTAATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:420933 original size:17 final size:17
Alignment explanation
Indices: 420911--420963 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
420901 AATTAAGATT
420911 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
420928 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
420945 CAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
420962 TA
1 TA
420964 ACTTTATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:422842 original size:33 final size:33
Alignment explanation
Indices: 422797--422866 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
422787 CATTTACAAA
*
422797 TCCCTAAGTTTTCACGGGCTAAACTAGAACCTT
1 TCCCTAAGTTTTCACGGGATAAACTAGAACCTT
* *
422830 TCCCT-AGCTTTTCACGGGATCAGCTAGAACCTT
1 TCCCTAAG-TTTTCACGGGATAAACTAGAACCTT
422863 TCCC
1 TCCC
422867 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.30
Consensus pattern (33 bp):
TCCCTAAGTTTTCACGGGATAAACTAGAACCTT
Found at i:423135 original size:21 final size:21
Alignment explanation
Indices: 423109--423149 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
423099 CCATAATAGG
**
423109 GGGTATCGGTACCCCTTCATA
1 GGGTATCGGTAAACCTTCATA
423130 GGGTATCGGTAAACCTTCAT
1 GGGTATCGGTAAACCTTCAT
423150 TAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
GGGTATCGGTAAACCTTCATA
Found at i:423239 original size:36 final size:36
Alignment explanation
Indices: 423192--423260 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
423182 TTGTAGCCAG
423192 AGTGTATGGATACAC-TACAGGGTGTATCGGTACACC
1 AGTGTATGGATACACATACAGGG-GTATCGGTACACC
*
423228 AGTGTATGGATACACATATAGGGGTATCGGTAC
1 AGTGTATGGATACACATACAGGGGTATCGGTAC
423261 CCTTTTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 25 0.81
37 6 0.19
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (36 bp):
AGTGTATGGATACACATACAGGGGTATCGGTACACC
Found at i:423241 original size:16 final size:17
Alignment explanation
Indices: 423192--423243 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 17
423182 TTGTAGCCAG
423192 AGTGTATGGATACACTAC
1 AGTGTATGGATACAC-AC
423210 AGGGTGTATCGG-TACAC-C
1 A--GTGTAT-GGATACACAC
423228 AGTGTATGGATACACA
1 AGTGTATGGATACACA
423244 TATAGGGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
15 2 0.07
16 11 0.38
18 3 0.10
20 11 0.38
21 2 0.07
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (17 bp):
AGTGTATGGATACACAC
Found at i:423622 original size:18 final size:19
Alignment explanation
Indices: 423576--423633 Score: 82
Period size: 18 Copynumber: 3.0 Consensus size: 19
423566 TTGTTTAATG
423576 AAAAGATACCAATTGTTAAC
1 AAAAGATACCAATTGTT-AC
*
423596 AAAAGGATATCAATTGTTA-
1 AAAA-GATACCAATTGTTAC
423615 AAAAGATACCAATTGTTAC
1 AAAAGATACCAATTGTTAC
423634 CAATTGTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 5 0.15
21 12 0.35
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAGATACCAATTGTTAC
Found at i:426672 original size:21 final size:21
Alignment explanation
Indices: 426646--426685 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
426636 CCATAATAGG
*
426646 GGGTATTGATACCCCTTCATA
1 GGGTATTGATACACCTTCATA
*
426667 GGGTATTGGTACACCTTCA
1 GGGTATTGATACACCTTCA
426686 ATAAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
GGGTATTGATACACCTTCATA
Found at i:427045 original size:18 final size:18
Alignment explanation
Indices: 427022--427078 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 18
427012 TATATTTTCC
*
427022 AACAATTGGTATCTTTTT
1 AACAATTGATATCTTTTT
427040 AACAATTGATATCCTTTTGTT
1 AACAATTGATAT-C-TTT-TT
427061 AACAATTGATATCTTTTT
1 AACAATTGATATCTTTTT
427079 CATTAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (18 bp):
AACAATTGATATCTTTTT
Found at i:427361 original size:21 final size:21
Alignment explanation
Indices: 427335--427392 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
427325 TCCATACAAT
427335 GGTGTA-CCAATACACCCTGTA
1 GGTGTATCC-ATACACCCTGTA
427356 GGTGTATCCATACACCCTGTA
1 GGTGTATCCATACACCCTGTA
427377 GGTGTATCCATACACC
1 GGTGTATCCATACACC
427393 TATGACTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (21 bp):
GGTGTATCCATACACCCTGTA
Found at i:427880 original size:33 final size:33
Alignment explanation
Indices: 427836--427902 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
427826 CATTGTAAAG
* *
427836 GGGAAAGGTTCTAGCTGATCCCGTGAAAAGCTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
* * *
427869 GGGAAATGTTCTAGTTTAGCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
427902 G
1 G
427903 AGACTTGTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTGAGCCCGTGAAAAACTA
Found at i:430536 original size:17 final size:17
Alignment explanation
Indices: 430514--430566 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
430504 TATTAAGATT
430514 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
430531 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
430548 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
430565 TA
1 TA
430567 ACTTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:430579 original size:18 final size:18
Alignment explanation
Indices: 430517--430585 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
430507 TAAGATTTAG
* *
430517 TTTAATAAATGAACT-AG
1 TTTAATTAATGAACTAAC
* * *
430534 TTTGATGAATGAACT-AG
1 TTTAATTAATGAACTAAC
430551 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACTAAC
430569 TTT-ATTCAATGAACTAA
1 TTTAATT-AATGAACTAA
430586 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTAATTAATGAACTAAC
Found at i:431359 original size:16 final size:17
Alignment explanation
Indices: 431338--431369 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
431328 AATCAAAATT
431338 GAAATTTG-TAACACTC
1 GAAATTTGATAACACTC
431354 GAAATTTGATAACACT
1 GAAATTTGATAACACT
431370 AAAATAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (17 bp):
GAAATTTGATAACACTC
Found at i:432027 original size:186 final size:186
Alignment explanation
Indices: 431708--432088 Score: 613
Period size: 186 Copynumber: 2.0 Consensus size: 186
431698 ATAAAATTTT
* * *
431708 AAAATTTAAATATATTATATATAACATATGGGCTCAACCCAAACTATTTAAAACCAATTAATAAT
1 AAAATTTAAATATATAATATATAACATATGAGCTCAACCCAAACCATTTAAAACCAATTAATAAT
* * *
431773 TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTGAAAAATTTATATACAATTTT
66 TTAAGATCCAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTT
* * **
431838 TATTTTATAATTATATATTATTTAAATTAATTGTACACTGTTTTTTTGAATT-TAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTACTTTTTTGAATTATAA
*
431893 AAAATATTAAATATATAATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATA
1 AAAAT-TTAAATATATAATATATAACATATGAGCTCAACCCAAACCATTTAAAA-CCAATTAATA
*
431958 ATTTAAGGTCCAATAA-ATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
64 ATTTAAGATCCAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
432022 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTACTTTTTTGAATTATAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTACTTTTTTGAATTATAA
*
432080 AACATTTAA
1 AAAATTTAA
432089 TTTTTATATA
Statistics
Matches: 180, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
185 5 0.03
186 143 0.79
187 32 0.18
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.41
Consensus pattern (186 bp):
AAAATTTAAATATATAATATATAACATATGAGCTCAACCCAAACCATTTAAAACCAATTAATAAT
TTAAGATCCAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTACTTTTTTGAATTATAA
Found at i:446428 original size:390 final size:390
Alignment explanation
Indices: 445709--446491 Score: 1311
Period size: 390 Copynumber: 2.0 Consensus size: 390
445699 GGTTTGATGC
*
445709 TAGAATTAATTACCCGATATCCAATAGTTCGTGGGTCAGCCTGATCTAATGTGTACCTAAGAAAG
1 TAGAATTAATTACCCGATATCCAATAGTTCGTGGGTCAGCCTGATCTAATGTGTACCCAAGAAAG
* * * **
445774 GAGGCATGATCGTGGTGAGCAATGAGGACAACGAACTACTACCTTCAAGAACTGTCATGAGATGG
66 GAGGCATGACCGTGGTAAGCAATGAGGACAACGAACTACTAACTTCAAGAACCATCATGAGATGG
* * * * *
445839 AGGATTTTCATGGATTATCTAAAGCTTAACAAGGCAACCAAGTAGGACCGATTTCTATCCCATTC
131 AGGATTTTCATGGATTATCAAAAGCTTAACAAGGCAACAAAGAAGAACCGATTTCCATCCCATTC
* * * * * *
445904 ATCGATCAAATGATGGATCGATTGGCAGTAAATCCTTTTATTGTTTTCTCAATTGTTATTTTGGG
196 ATCAATCAAATGATAGATCAATTAGCAGTAAATCCTTTTATTGTTTTCTCAATGGTTATTCTGGG
445969 TACAACCAGATTGCTATATTGTCGGAGTACCAAGAGAAGACAACCTTCACGAGCCCTTATGGTAT
261 TACAACCAGATTGCTATATTGTCGGAGTACCAAGAGAAGACAACCTTCACGAGCCCTTATGGTAT
** *
446034 CTAGGCCTTTAGGAGGATGCCTTTTGGACTTTGCAATGCTCTAACTACTTTTCAAATGTGTATGT
326 CTAGGCCTTTAGGAGGATGCCTTTTGGACTTTGCAACACTCTAACTACTTTTCAAAGGTGTATGT
*
446099 TAGAATTAATTACCCGATATCCAATAGTTCGTGGGTCAGTCTGATAC-AATGTGTACCCAAGAAA
1 TAGAATTAATTACCCGATATCCAATAGTTCGTGGGTCAGCCTGAT-CTAATGTGTACCCAAGAAA
446163 GGAGGCATGACCGTGGTAAGCAATGAGGACAACGAACTACTAACTTCAAGAACCATCATGAGATG
65 GGAGGCATGACCGTGGTAAGCAATGAGGACAACGAACTACTAACTTCAAGAACCATCATGAGATG
*
446228 GAGGATTTTCATGGATTATCAAAAGCTTAATAAGGCAACAAAGAAGAACC-ATTTTCCCATCCCA
130 GAGGATTTTCATGGATTATCAAAAGCTTAACAAGGCAACAAAGAAGAACCGA-TTT-CCATCCCA
*
446292 TTCATCAATCAAATGATAGATCAATTAGCGGTAAATCCTTTTATT-TTTTCTCAATGGTTATTCT
193 TTCATCAATCAAATGATAGATCAATTAGCAGTAAATCCTTTTATTGTTTTCTCAATGGTTATTCT
446356 GGGTACAACCAGATTGCTATATTGTCGGAGTACCAAGAGAAGACAACCTTCACGAGCCCTTATGG
258 GGGTACAACCAGATTGCTATATTGTCGGAGTACCAAGAGAAGACAACCTTCACGAGCCCTTATGG
446421 TATCTAGGCCTTTAGGAGGATGCCTTTTGGACTTTGCAACACTCTAACTACTTTTCAAAGGTGTA
323 TATCTAGGCCTTTAGGAGGATGCCTTTTGGACTTTGCAACACTCTAACTACTTTTCAAAGGTGTA
446486 TGT
388 TGT
446489 TAG
1 TAG
446492 CCATCTTGTC
Statistics
Matches: 367, Mismatches: 23, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
389 1 0.00
390 318 0.87
391 48 0.13
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (390 bp):
TAGAATTAATTACCCGATATCCAATAGTTCGTGGGTCAGCCTGATCTAATGTGTACCCAAGAAAG
GAGGCATGACCGTGGTAAGCAATGAGGACAACGAACTACTAACTTCAAGAACCATCATGAGATGG
AGGATTTTCATGGATTATCAAAAGCTTAACAAGGCAACAAAGAAGAACCGATTTCCATCCCATTC
ATCAATCAAATGATAGATCAATTAGCAGTAAATCCTTTTATTGTTTTCTCAATGGTTATTCTGGG
TACAACCAGATTGCTATATTGTCGGAGTACCAAGAGAAGACAACCTTCACGAGCCCTTATGGTAT
CTAGGCCTTTAGGAGGATGCCTTTTGGACTTTGCAACACTCTAACTACTTTTCAAAGGTGTATGT
Found at i:449749 original size:26 final size:26
Alignment explanation
Indices: 449713--449767 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
449703 CTCAGATGTC
449713 ACGCAATTGTGTGTCATAAATCTATG
1 ACGCAATTGTGTGTCATAAATCTATG
449739 ACGCAATTGTGTGTCATAAATCTATG
1 ACGCAATTGTGTGTCATAAATCTATG
449765 ACG
1 ACG
449768 TACATTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (26 bp):
ACGCAATTGTGTGTCATAAATCTATG
Found at i:449779 original size:13 final size:13
Alignment explanation
Indices: 449761--449825 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
449751 GTCATAAATC
449761 TATGACGTACATT
1 TATGACGTACATT
449774 TATGAC--ACGAATT
1 TATGACGTAC--ATT
**
449787 TATGACACACATT
1 TATGACGTACATT
449800 TATGACGCT-CATT
1 TATGACG-TACATT
*
449813 TATGACGTGCATT
1 TATGACGTACATT
449826 GAGCATCATT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
11 2 0.05
12 1 0.02
13 39 0.89
15 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TATGACGTACATT
Found at i:449790 original size:26 final size:26
Alignment explanation
Indices: 449761--449825 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
449751 GTCATAAATC
449761 TATGACGTACATTTATGACACGAATT
1 TATGACGTACATTTATGACACGAATT
** * **
449787 TATGACACACATTTATGACGCTCATT
1 TATGACGTACATTTATGACACGAATT
*
449813 TATGACGTGCATT
1 TATGACGTACATT
449826 GAGCATCATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (26 bp):
TATGACGTACATTTATGACACGAATT
Found at i:450858 original size:46 final size:45
Alignment explanation
Indices: 450766--450858 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 45
450756 ACAAGAAATC
* * * *
450766 TTATTATATTTTTTTTATAAAAAAATCAATTCATAAATATTAATA
1 TTATTATAATTTATTTATAAAAAAATAAAATCATAAATATTAATA
* *
450811 TTATTAATAATTTATTTCTAAAAAAATAAAATCTTAATATATT-ATA
1 TTATT-ATAATTTATTTATAAAAAAATAAAATCATAA-ATATTAATA
450857 TT
1 TT
450859 TTCGAGCTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
45 5 0.12
46 30 0.75
47 5 0.12
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.48
Consensus pattern (45 bp):
TTATTATAATTTATTTATAAAAAAATAAAATCATAAATATTAATA
Found at i:456845 original size:2 final size:2
Alignment explanation
Indices: 456801--456828 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
456791 AATTTACGAG
456801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
456829 TATTTTGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:458866 original size:17 final size:16
Alignment explanation
Indices: 458835--458885 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
458825 CAAAAGGACT
458835 AAAATGAATTATAATA
1 AAAATGAATTATAATA
*
458851 AAAATGAAATTCTAATTCA
1 AAAATG-AATTATAA-T-A
*
458870 AAAA-GAATTAAAATA
1 AAAATGAATTATAATA
458885 A
1 A
458886 GATTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 2 0.07
16 7 0.24
17 13 0.45
18 2 0.07
19 5 0.17
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (16 bp):
AAAATGAATTATAATA
Found at i:460209 original size:21 final size:21
Alignment explanation
Indices: 460176--460218 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
460166 TTGAATTTAT
460176 TAAAATGACAAGAAGC-AATAA
1 TAAAATGACAAGAA-CAAATAA
* *
460197 TAAAATTATAAGAACAAATAA
1 TAAAATGACAAGAACAAATAA
460218 T
1 T
460219 TTCTCAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAAATGACAAGAACAAATAA
Found at i:466046 original size:20 final size:19
Alignment explanation
Indices: 466023--466062 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
466013 TAATTCATTT
*
466023 TATTAGTTCATAAGCATTCA
1 TATTAGCTCATAAGC-TTCA
*
466043 TATTAGCTCTTAAGCTTCA
1 TATTAGCTCATAAGCTTCA
466062 T
1 T
466063 GCATTATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (19 bp):
TATTAGCTCATAAGCTTCA
Found at i:469315 original size:25 final size:25
Alignment explanation
Indices: 469277--469344 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
469267 ATAAAGCTTC
*
469277 AAGGAG-TGGCGAGCTAGGAGCCGA
1 AAGGAGCTAGCGAGCTAGGAGCCGA
*
469301 AAGGAGCTAGCGAGCTAGGAGTCGA
1 AAGGAGCTAGCGAGCTAGGAGCCGA
469326 AAGGAGCTAGCGAGCTAGG
1 AAGGAGCTAGCGAGCTAGG
469345 TGGTTCACGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 6 0.15
25 35 0.85
ACGTcount: A:0.31, C:0.16, G:0.43, T:0.10
Consensus pattern (25 bp):
AAGGAGCTAGCGAGCTAGGAGCCGA
Found at i:469548 original size:24 final size:24
Alignment explanation
Indices: 469519--469568 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
469509 TGGTGGTAGA
*
469519 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
469543 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
469567 TT
1 TT
469569 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:470064 original size:16 final size:16
Alignment explanation
Indices: 470043--470075 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
470033 CACGTGAGGA
470043 TTATTT-TCTTTTCATT
1 TTATTTATCTTTT-ATT
470059 TTATTTATCTTTTATT
1 TTATTTATCTTTTATT
470075 T
1 T
470076 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTATCTTTTATT
Found at i:475082 original size:26 final size:25
Alignment explanation
Indices: 475051--475121 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 25
475041 CCTCTTAAAT
475051 TTTTAACTTTTTCTTTTCTCTTTC-
1 TTTTAACTTTTTCTTTTCTCTTTCA
*
475075 -TTT-A-TTAATT-TTTTCTCTTTCA
1 TTTTAACTT-TTTCTTTTCTCTTTCA
*
475097 TTTTAACTTTTACTTTTTCTCTTTC
1 TTTTAACTTTTTC-TTTTCTCTTTC
475122 CTTCATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.35
22 3 0.08
23 6 0.16
24 2 0.05
25 2 0.05
26 11 0.30
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTAACTTTTTCTTTTCTCTTTCA
Found at i:475141 original size:47 final size:46
Alignment explanation
Indices: 475051--475141 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 46
475041 CCTCTTAAAT
* * * *
475051 TTTTAACTTTTTCTTTTCTCTTTCTTTATTAATTTTTTCTCTTTCA
1 TTTTAACTTTTACTTTTCTCTTTCTTCATTAATTCTTTATCTTTCA
*
475097 TTTTAACTTTTACTTTTTCTCTTTCCTTCATTCA-TCTTTATCTTT
1 TTTTAACTTTTAC-TTTTCTCTTT-CTTCATTAATTCTTTATCTTT
475142 TGTTATTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 12 0.32
47 19 0.50
48 7 0.18
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (46 bp):
TTTTAACTTTTACTTTTCTCTTTCTTCATTAATTCTTTATCTTTCA
Found at i:475711 original size:20 final size:20
Alignment explanation
Indices: 475688--475729 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
475678 GCGTCAAACA
475688 AGTCGATACTCGGTCAACCG
1 AGTCGATACTCGGTCAACCG
475708 AGTCGATACTCGGTCAACCG
1 AGTCGATACTCGGTCAACCG
475728 AG
1 AG
475730 AACGTCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (20 bp):
AGTCGATACTCGGTCAACCG
Done.