Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold435
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: 524057
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:244013 original size:13 final size:13
Alignment explanation
Indices: 243995--244019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243985 TGTCAAATAT
243995 ATATTAATATTTG
1 ATATTAATATTTG
244008 ATATTAATATTT
1 ATATTAATATTT
244020 AAATTTGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATTAATATTTG
Found at i:244062 original size:14 final size:14
Alignment explanation
Indices: 244019--244083 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
244009 TATTAATATT
* *
244019 TAAATTTGAGTAACA
1 TAAATTTTA-TAAAA
244034 TAAATTTTA-AAAA
1 TAAATTTTATAAAA
*
244047 TAATTTTTATAAAA
1 TAAATTTTATAAAA
*
244061 TAAAATTTATAAAA
1 TAAATTTTATAAAA
244075 TAAAATTTT
1 T-AAATTTT
244084 TTGTATGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.26
14 17 0.40
15 14 0.33
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (14 bp):
TAAATTTTATAAAA
Found at i:244376 original size:14 final size:14
Alignment explanation
Indices: 244342--244397 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
244332 TTGGTTTGGC
244342 TAAACATAAATTTTA
1 TAAA-ATAAATTTTA
*
244357 -AAAATAATTTTTA
1 TAAAATAAATTTTA
*
244370 TAAAATAAAATTTA
1 TAAAATAAATTTTA
244384 TAAAATAAAATTTT
1 TAAAAT-AAATTTT
244398 TTGTATGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 9 0.26
14 20 0.57
15 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATAAATTTTA
Found at i:244599 original size:314 final size:314
Alignment explanation
Indices: 244030--244654 Score: 1250
Period size: 314 Copynumber: 2.0 Consensus size: 314
244020 AAATTTGAGT
244030 AACATAAATTTTAAAAATAATTTTTATAAAATAAAATTTATAAAATAAAATTTTTTGTATGATAA
1 AACATAAATTTTAAAAATAATTTTTATAAAATAAAATTTATAAAATAAAATTTTTTGTATGATAA
244095 ATGAATAATAAAAGATTATTAATATATTTAAAGAATTAAATTATCGTTTTTACGAAATAAATTAA
66 ATGAATAATAAAAGATTATTAATATATTTAAAGAATTAAATTATCGTTTTTACGAAATAAATTAA
244160 TATTTATGGGGGATCAAGATGAAGCCTATTGTGGCGGGGATTATGAAATTTTTCTAGGATTGTTT
131 TATTTATGGGGGATCAAGATGAAGCCTATTGTGGCGGGGATTATGAAATTTTTCTAGGATTGTTT
244225 TGTTGCCGACTTCCTTAAAATTACAAGAGTAATATTCCTGTGATTTAGGCCTGGCTAAACTTCAA
196 TGTTGCCGACTTCCTTAAAATTACAAGAGTAATATTCCTGTGATTTAGGCCTGGCTAAACTTCAA
244290 AATGTACTGCTTAAAATTGTTGGTTCTGACCGTGGACACAATTTGGTTTGGCTA
261 AATGTACTGCTTAAAATTGTTGGTTCTGACCGTGGACACAATTTGGTTTGGCTA
244344 AACATAAATTTTAAAAATAATTTTTATAAAATAAAATTTATAAAATAAAATTTTTTGTATGATAA
1 AACATAAATTTTAAAAATAATTTTTATAAAATAAAATTTATAAAATAAAATTTTTTGTATGATAA
244409 ATGAATAATAAAAGATTATTAATATATTTAAAGAATTAAATTATCGTTTTTACGAAATAAATTAA
66 ATGAATAATAAAAGATTATTAATATATTTAAAGAATTAAATTATCGTTTTTACGAAATAAATTAA
244474 TATTTATGGGGGATCAAGATGAAGCCTATTGTGGCGGGGATTATGAAATTTTTCTAGGATTGTTT
131 TATTTATGGGGGATCAAGATGAAGCCTATTGTGGCGGGGATTATGAAATTTTTCTAGGATTGTTT
244539 TGTTGCCGACTTCCTTAAAATTACAAGAGTAATATTCCTGTGATTTAGGCCTGGCTAAACTTCAA
196 TGTTGCCGACTTCCTTAAAATTACAAGAGTAATATTCCTGTGATTTAGGCCTGGCTAAACTTCAA
244604 AATGTACTGCTTAAAATTGTTGGTTCTGACCGTGGACACAATTTGGTTTGG
261 AATGTACTGCTTAAAATTGTTGGTTCTGACCGTGGACACAATTTGGTTTGG
244655 TTTGGTTTGG
Statistics
Matches: 311, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
314 311 1.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (314 bp):
AACATAAATTTTAAAAATAATTTTTATAAAATAAAATTTATAAAATAAAATTTTTTGTATGATAA
ATGAATAATAAAAGATTATTAATATATTTAAAGAATTAAATTATCGTTTTTACGAAATAAATTAA
TATTTATGGGGGATCAAGATGAAGCCTATTGTGGCGGGGATTATGAAATTTTTCTAGGATTGTTT
TGTTGCCGACTTCCTTAAAATTACAAGAGTAATATTCCTGTGATTTAGGCCTGGCTAAACTTCAA
AATGTACTGCTTAAAATTGTTGGTTCTGACCGTGGACACAATTTGGTTTGGCTA
Found at i:244943 original size:15 final size:16
Alignment explanation
Indices: 244925--244968 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
244915 TTTATATTAT
244925 TTAAAAT-TATTTAAA
1 TTAAAATATATTTAAA
*
244940 TT-AAATATATTTACA
1 TTAAAATATATTTAAA
244955 TTAAATATATATTT
1 TTAAA-ATATATTT
244969 TTAATATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 11 0.44
16 2 0.08
17 8 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATATATTTAAA
Found at i:244968 original size:17 final size:15
Alignment explanation
Indices: 244928--244964 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
244918 ATATTATTTA
244928 AAAT-TATTTAAATT
1 AAATATATTTAAATT
*
244942 AAATATATTTACATT
1 AAATATATTTAAATT
244957 AAATATAT
1 AAATATAT
244965 ATTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATATTTAAATT
Found at i:245424 original size:12 final size:13
Alignment explanation
Indices: 245407--245435 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
245397 CTTTATTATT
245407 TTAAATAAATTC-
1 TTAAATAAATTCA
245419 TTAAATAAATTCA
1 TTAAATAAATTCA
245432 TTAA
1 TTAA
245436 TTAAGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATAAATTCA
Found at i:245919 original size:20 final size:20
Alignment explanation
Indices: 245896--245982 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
245886 AAGGAGAGAG
*
245896 AAAAAAGAAAAGATAAAGGA
1 AAAAAAGAAAAGAGAAAGGA
*
245916 AAAAAAGAAAA-AAAAAGGA
1 AAAAAAGAAAAGAGAAAGGA
* * *
245935 ACAGAAGGAAAGAGAAA-GA
1 AAAAAAGAAAAGAGAAAGGA
245954 ACAAAAAGAGAAGAGAGAAAGGA
1 A-AAAAAGA-AA-AGAGAAAGGA
245977 AAAAAA
1 AAAAAA
245983 AAAGAAAGAG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
19 18 0.33
20 19 0.35
21 2 0.04
22 12 0.22
23 3 0.06
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAAGAGAAAGGA
Found at i:245972 original size:22 final size:24
Alignment explanation
Indices: 245922--245995 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 24
245912 AGGAAAAAAA
*
245922 GAAAAAAAAAGGAACAGA-AGGAAAG
1 GAAAAAAAAAAGAA-AGAGA-GAAAG
245947 AGAAAGAACAAAAAGAGAAGAGAGAAAG
1 -GAAA-AA-AAAAAGA-AAGAGAGAAAG
245975 GAAAAAAAAAAGAAAGAGAGA
1 GAAAAAAAAAAGAAAGAGAGA
245996 GAAAAATTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
24 8 0.19
25 7 0.16
26 6 0.14
27 6 0.14
28 14 0.33
29 2 0.05
ACGTcount: A:0.70, C:0.03, G:0.27, T:0.00
Consensus pattern (24 bp):
GAAAAAAAAAAGAAAGAGAGAAAG
Found at i:245987 original size:20 final size:19
Alignment explanation
Indices: 245881--245985 Score: 63
Period size: 19 Copynumber: 5.3 Consensus size: 19
245871 GGAAGGAAGG
*
245881 AAAAAAAG-GAGAGAGAAAA
1 AAAAAAAGAGAAAG-GAAAA
* *
245900 AAGAAAAGATAAAGGAAAA
1 AAAAAAAGAGAAAGGAAAA
* *
245919 AAAGAAAA-AAAAAGGAACAG
1 AAA-AAAAGAGAAAGGAA-AA
**
245939 AAGGAAAGAGAAA-GAACAA
1 AAAAAAAGAGAAAGGAA-AA
245958 AAAGAGAAGAGAGAAAGGAAAA
1 AAA-A-AA-AGAGAAAGGAAAA
245980 AAAAAA
1 AAAAAA
245986 GAAAGAGAGA
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
19 32 0.48
20 16 0.24
21 3 0.05
22 12 0.18
23 3 0.05
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.01
Consensus pattern (19 bp):
AAAAAAAGAGAAAGGAAAA
Found at i:246000 original size:20 final size:20
Alignment explanation
Indices: 245896--246001 Score: 70
Period size: 20 Copynumber: 5.1 Consensus size: 20
245886 AAGGAGAGAG
* *
245896 AAAAAAGAAAAGATAAAG-GA
1 AAAAAAG-AAAGAGAAAGAAA
* * *
245916 AAAAAAGAAAAAAAAAGGAA
1 AAAAAAGAAAGAGAAAGAAA
* * *
245936 CAGAAGGAAAGAGAAAGAACA
1 AAAAAAGAAAGAGAAAGAA-A
*
245957 AAAAGAGAAGAGAGAAAGGAAAA
1 AAAAAAGAA-AGAGAAA-G-AAA
*
245980 AAAAAAGAAAGAGAGAGAAA
1 AAAAAAGAAAGAGAAAGAAA
246000 AA
1 AA
246002 TTATATTTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
19 8 0.12
20 26 0.39
21 7 0.11
22 13 0.20
23 10 0.15
24 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAGAGAAAGAAA
Found at i:246001 original size:22 final size:25
Alignment explanation
Indices: 245937--246001 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 25
245927 AAAAAGGAAC
*
245937 AGAAG-GAAAGAGAAAGAACAAAAAG
1 AGAAGAGAGAGAGAAA-AACAAAAAG
* *
245962 AGAAGAGAGAAAGGAAAA-AAAAA-
1 AGAAGAGAGAGAGAAAAACAAAAAG
245985 AGAA-AGAGAGAGAAAAA
1 AGAAGAGAGAGAGAAAAA
246002 TTATATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 11 0.32
23 4 0.12
24 5 0.15
25 7 0.21
26 7 0.21
ACGTcount: A:0.71, C:0.02, G:0.28, T:0.00
Consensus pattern (25 bp):
AGAAGAGAGAGAGAAAAACAAAAAG
Found at i:246087 original size:26 final size:26
Alignment explanation
Indices: 246026--246101 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 26
246016 AGGGTTATTT
*
246026 TTATATATT-TAAATTATTATAAAAAAA
1 TTATATATTATAAA-T-TTATATAAAAA
*
246053 TT-TATTATTATAAATTTATATAAAAC
1 TTATA-TATTATAAATTTATATAAAAA
246079 TTATATATTA-ATAATTTGATATA
1 TTATATATTATA-AATTT-ATATA
246102 TATATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
25 1 0.02
26 23 0.55
27 14 0.33
28 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
TTATATATTATAAATTTATATAAAAA
Found at i:246137 original size:38 final size:38
Alignment explanation
Indices: 246094--246172 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
246084 TATTAATAAT
*
246094 TTGATA-TATATATT-TATT-TGTTTTATATTTTTATTATA
1 TTGATATTAT-TATTGTATTAT-TTTTA-ATTATTATTATA
*
246132 TTGATATTATTTTTGTATTATTTTTAATTATTATTATA
1 TTGATATTATTATTGTATTATTTTTAATTATTATTATA
246170 TTG
1 TTG
246173 TGTTTGTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
38 23 0.64
39 12 0.33
40 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (38 bp):
TTGATATTATTATTGTATTATTTTTAATTATTATTATA
Found at i:246162 original size:32 final size:31
Alignment explanation
Indices: 246104--246180 Score: 83
Period size: 32 Copynumber: 2.6 Consensus size: 31
246094 TTGATATATA
246104 TATT-TATT-TGTTT-TA-TATTTTTATTA-
1 TATTATATTATGTTTGTATTATTTTTATTAT
*
246130 TATTGATATTATTTTTGTATTATTTTTAATTAT
1 TATT-ATATTATGTTTGTATTATTTTT-ATTAT
*
246163 TATTATATTGTGTTTGTA
1 TATTATATTATGTTTGTA
246181 AATTTAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.10
28 4 0.10
29 4 0.10
30 2 0.05
31 7 0.17
32 16 0.39
33 4 0.10
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (31 bp):
TATTATATTATGTTTGTATTATTTTTATTAT
Found at i:246238 original size:17 final size:17
Alignment explanation
Indices: 246216--246248 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
246206 TGATATTACG
*
246216 TTTGTGCTATATTTTAA
1 TTTGTGATATATTTTAA
246233 TTTGTGATATATTTTA
1 TTTGTGATATATTTTA
246249 TATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.61
Consensus pattern (17 bp):
TTTGTGATATATTTTAA
Found at i:247053 original size:19 final size:17
Alignment explanation
Indices: 247013--247055 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
247003 ATTTAATTTA
*
247013 AAATTAATTTTTATAAT
1 AAATTAATTTTTATAAG
*
247030 TAATTAATGATTTTATAAG
1 AAATTAAT--TTTTATAAG
247049 AAATTAA
1 AAATTAA
247056 GAAGCCCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
19 14 0.67
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AAATTAATTTTTATAAG
Found at i:253084 original size:51 final size:51
Alignment explanation
Indices: 253027--253257 Score: 234
Period size: 51 Copynumber: 4.7 Consensus size: 51
253017 TTTTAACTAG
* *
253027 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
* * *
253078 ATGTATCGATACATTGAATAATGTATCGATACA--T---T---CATACATG-
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACA-GA
* * *
253121 -TGT-T-GATACATTGAAGAATGTATCGATATATCTGGGTAAAAGGAATTCATA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAG-A--CAGA
* *
253172 CATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAGGATAGA
1 -ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
*
253224 ATGTATCGATATATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAGAATGTATCGATACAT
253258 TCATACATGT
Statistics
Matches: 149, Mismatches: 14, Indels: 34
0.76 0.07 0.17
Matches are distributed among these distances:
40 24 0.16
41 1 0.01
42 4 0.03
43 4 0.03
44 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
51 67 0.45
52 2 0.01
53 3 0.02
54 2 0.01
55 38 0.26
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (51 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:253102 original size:20 final size:20
Alignment explanation
Indices: 253077--253297 Score: 109
Period size: 20 Copynumber: 10.8 Consensus size: 20
253067 AAAAAGACAG
253077 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
*
253097 AATGTATCGATACATT-CAT
1 AATGTATCGATACATTGAAT
* * *
253116 ACATGTGTTGATACATTGAAG
1 A-ATGTATCGATACATTGAAT
* **
253137 AATGTATCGATATATCTGGGT
1 AATGTATCGATACAT-TGAAT
* * *
253158 AA---A-AG-GA-ATT-CAT
1 AATGTATCGATACATTGAAT
*
253171 ACATGTATCGATACATTGAAG
1 A-ATGTATCGATACATTGAAT
253192 AATGTATCGATACATCTGGGTAAAAGGAT
1 AATGTATCGATACAT-T--G----A--AT
* *
253221 AGAATGTATCGATATATTGAAG
1 --AATGTATCGATACATTGAAT
*
253243 AATGTATCGATACATT-CAT
1 AATGTATCGATACATTGAAT
*
253262 ACATGTATCGATACATTGAAG
1 A-ATGTATCGATACATTGAAT
253283 AATGTATCGATACAT
1 AATGTATCGATACAT
253298 CTGGGTACCT
Statistics
Matches: 150, Mismatches: 27, Indels: 48
0.67 0.12 0.21
Matches are distributed among these distances:
13 2 0.01
14 2 0.01
15 2 0.01
16 1 0.01
17 2 0.01
18 2 0.01
19 6 0.04
20 101 0.67
21 11 0.07
22 1 0.01
23 1 0.01
24 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 14 0.09
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:253184 original size:55 final size:54
Alignment explanation
Indices: 253110--253257 Score: 221
Period size: 55 Copynumber: 2.8 Consensus size: 54
253100 GTATCGATAC
* * *
253110 ATTCATACATGTGTTGATACATTGAAGAATGTATCGATATATCTGGGTAAAAGG
1 ATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAGG
253164 AATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAGG
1 -ATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAGG
* *
253219 A-T-AGA-ATGTATCGATATATTGAAGAATGTATCGATACAT
1 ATTCATACATGTATCGATACATTGAAGAATGTATCGATACAT
253258 TCATACATGT
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 33 0.38
52 2 0.02
53 1 0.01
54 1 0.01
55 51 0.58
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (54 bp):
ATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAGG
Found at i:253231 original size:146 final size:146
Alignment explanation
Indices: 253027--253304 Score: 475
Period size: 146 Copynumber: 1.9 Consensus size: 146
253017 TTTTAACTAG
253027 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
* * * *
253092 TGAATAATGTATCGATACATTCATACATGTGTTGATACATTGAAGAATGTATCGATATATCTGGG
66 TGAAGAATGTATCGATACATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGG
253157 TAAAAGGAATTCATAC
131 TAAAAGGAATTCATAC
* * * * *
253173 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAGGATAGAATGTATCGATATAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
253238 TGAAGAATGTATCGATACATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGG
66 TGAAGAATGTATCGATACATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGG
253303 TA
131 TA
253305 CCTTTCCATA
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
146 123 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (146 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGTATCGATACAT
TGAAGAATGTATCGATACATTCATACATGTATCGATACATTGAAGAATGTATCGATACATCTGGG
TAAAAGGAATTCATAC
Found at i:255647 original size:14 final size:14
Alignment explanation
Indices: 255628--255673 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
255618 TCATGAATAA
255628 TAAACAAACAAATC
1 TAAACAAACAAATC
*
255642 T----AAACAAATT
1 TAAACAAACAAATC
255652 TAAACAAACAAATC
1 TAAACAAACAAATC
255666 TAAACAAA
1 TAAACAAA
255674 TATGTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
10 9 0.35
14 17 0.65
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACAAACAAATC
Found at i:255655 original size:24 final size:24
Alignment explanation
Indices: 255628--255674 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
255618 TCATGAATAA
255628 TAAACAAACAAATCTAAACAAATT
1 TAAACAAACAAATCTAAACAAATT
255652 TAAACAAACAAATCTAAACAAAT
1 TAAACAAACAAATCTAAACAAAT
255675 ATGTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (24 bp):
TAAACAAACAAATCTAAACAAATT
Found at i:258944 original size:2 final size:2
Alignment explanation
Indices: 258937--258971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
258927 TACAATTGTT
258937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
258972 TTATCTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:261732 original size:23 final size:24
Alignment explanation
Indices: 261706--261753 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
261696 TAGATGCTCA
* *
261706 AAATGAATGAAT-GATTTAAATCT
1 AAATGAATAAATAGATTCAAATCT
*
261729 AAATTAATAAATAGATTCAAATCT
1 AAATGAATAAATAGATTCAAATCT
261753 A
1 A
261754 TCTCCATAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATGAATAAATAGATTCAAATCT
Found at i:263501 original size:2 final size:2
Alignment explanation
Indices: 263496--263520 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
263486 AATTAGCATG
263496 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
263521 AGTTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:264563 original size:2 final size:2
Alignment explanation
Indices: 264558--264601 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
264548 TGTGTGTGTG
*
264558 TA TA TA TA TA TA -A TA TA TG TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264598 -A TA T
1 TA TA T
264602 TTAATTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:265147 original size:31 final size:31
Alignment explanation
Indices: 265091--265175 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
265081 AAAATCAATA
* * *
265091 TTGAGTA-AAAAATTCAATAAAAAAATAGAAG
1 TTGAGTAGTAAAATTCAAT-CAAAAATAAAAG
*
265122 TTGAGTAGTAAAATTCAATCAAAAATAAAAT
1 TTGAGTAGTAAAATTCAATCAAAAATAAAAG
* * *
265153 TTTAATTGTAAAATTCAATCAAA
1 TTGAGTAGTAAAATTCAATCAAA
265176 TGAACATAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 36 0.78
32 10 0.22
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.29
Consensus pattern (31 bp):
TTGAGTAGTAAAATTCAATCAAAAATAAAAG
Found at i:265384 original size:15 final size:15
Alignment explanation
Indices: 265364--265392 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
265354 TCGAAACTTA
265364 ACTCAATTAGTTTGT
1 ACTCAATTAGTTTGT
265379 ACTCAATTAGTTTG
1 ACTCAATTAGTTTG
265393 AGAGTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
ACTCAATTAGTTTGT
Found at i:270313 original size:17 final size:17
Alignment explanation
Indices: 270291--270327 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
270281 TAAAATTATA
270291 AATAAAATTA-ATATATT
1 AATAAAATTATATA-ATT
270308 AATAAAATTATATAATT
1 AATAAAATTATATAATT
270325 AAT
1 AAT
270328 TTAAGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAAAATTATATAATT
Found at i:270797 original size:22 final size:21
Alignment explanation
Indices: 270766--270809 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
270756 AAAATTTATT
270766 TAAATTTAAT-TATAAAATATA
1 TAAATTTAATATA-AAAATATA
270787 TAAATATTAATATAAAAATATA
1 TAAAT-TTAATATAAAAATATA
270809 T
1 T
270810 TTTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATATAAAAATATA
Found at i:272559 original size:5 final size:5
Alignment explanation
Indices: 272509--272542 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
272499 TTTAAAATTA
*
272509 AAAAT ATAA- AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
272543 GCATCAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:284730 original size:2 final size:2
Alignment explanation
Indices: 284723--284761 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
284713 TAAACGGAAA
284723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
284762 AAGATTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:285058 original size:20 final size:18
Alignment explanation
Indices: 285030--285097 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
285020 TTTAAAATTC
285030 TTTATTATTAAAAATATTA
1 TTTATTATT-AAAATATTA
285049 TTTAATTATTAAAA-ATTA
1 TTT-ATTATTAAAATATTA
* *
285067 TTTTATT-TTAATATTTTA
1 -TTTATTATTAAAATATTA
*
285085 TTTATAATTAAAA
1 TTTATTATTAAAA
285098 ATAAAACTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
17 10 0.24
18 15 0.37
19 10 0.24
20 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATTATTAAAATATTA
Found at i:285068 original size:18 final size:17
Alignment explanation
Indices: 285023--285099 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 17
285013 TTATTTTTTT
*
285023 AAAATTCTTTATTATTAA
1 AAAATTATTTATTATT-A
285041 AAATATTATTTAATTATTA
1 AAA-ATTATTT-ATTATTA
285060 AAAATTATTTTATT-TTA
1 AAAATTA-TTTATTATTA
** *
285077 ATATTTTATTTATAATTA
1 A-AAATTATTTATTATTA
285095 AAAAT
1 AAAAT
285100 AAAACTTAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
17 11 0.23
18 18 0.38
19 13 0.27
20 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATTATTTATTATTA
Found at i:285287 original size:2 final size:2
Alignment explanation
Indices: 285280--285304 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
285270 ATGTATGTAC
285280 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
285305 AACTAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:285498 original size:6 final size:6
Alignment explanation
Indices: 285480--285524 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
285470 GCTAGGACAA
* *
285480 TGAGGC TGCGGC TGAGGC TGAGGT TGAGGC TGAGGC TGAGGC TGA
1 TGAGGC TGAGGC TGAGGC TGAGGC TGAGGC TGAGGC TGAGGC TGA
285525 TACCGCATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.16, G:0.49, T:0.20
Consensus pattern (6 bp):
TGAGGC
Found at i:286186 original size:5 final size:5
Alignment explanation
Indices: 286176--286203 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
286166 TGTATGCATC
286176 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
286204 TCAAGTGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:286836 original size:2 final size:2
Alignment explanation
Indices: 286829--286870 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
286819 AACTTGGCTA
286829 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
286871 CACAAAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:288666 original size:16 final size:17
Alignment explanation
Indices: 288635--288669 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
288625 AAGGAAGATG
*
288635 AAGAAGAAAGAAAGAAA
1 AAGAAGAAAAAAAGAAA
288652 AAGAA-AAAAAAAGAAA
1 AAGAAGAAAAAAAGAAA
288668 AA
1 AA
288670 ATATGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAGAAA
Found at i:288677 original size:10 final size:10
Alignment explanation
Indices: 288641--288670 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
288631 GATGAAGAAG
*
288641 AAAGAAAGAA
1 AAAGAAAAAA
288651 AAAGAAAAAA
1 AAAGAAAAAA
288661 AAAGAAAAAA
1 AAAGAAAAAA
288671 TATGAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:288953 original size:16 final size:17
Alignment explanation
Indices: 288922--288956 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
288912 AAGGAAGATG
*
288922 AAGAAGAAAGAAAGAAA
1 AAGAAGAAAAAAAGAAA
288939 AAGAA-AAAAAAAGAAA
1 AAGAAGAAAAAAAGAAA
288955 AA
1 AA
288957 ATATGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAGAAA
Found at i:288964 original size:10 final size:10
Alignment explanation
Indices: 288928--288957 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
288918 GATGAAGAAG
*
288928 AAAGAAAGAA
1 AAAGAAAAAA
288938 AAAGAAAAAA
1 AAAGAAAAAA
288948 AAAGAAAAAA
1 AAAGAAAAAA
288958 TATGAAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:289013 original size:287 final size:287
Alignment explanation
Indices: 288497--289070 Score: 1148
Period size: 287 Copynumber: 2.0 Consensus size: 287
288487 GTCTAGAACT
288497 GAAATTTGGGAGCCAACGGCCACCGGTGAGCGGTGGCCGACGGTGGTCGCCGGCAACCGGCGTGG
1 GAAATTTGGGAGCCAACGGCCACCGGTGAGCGGTGGCCGACGGTGGTCGCCGGCAACCGGCGTGG
288562 TGGCCGGTCGCCGGTTTCTGGGTTACTTTTTTTGTCATTTGTGGTTATGGGCGGGAAAGAAAGAA
66 TGGCCGGTCGCCGGTTTCTGGGTTACTTTTTTTGTCATTTGTGGTTATGGGCGGGAAAGAAAGAA
288627 GGAAGATGAAGAAGAAAGAAAGAAAAAGAAAAAAAAAGAAAAAATATGAAATGGAGTGGCCTGGG
131 GGAAGATGAAGAAGAAAGAAAGAAAAAGAAAAAAAAAGAAAAAATATGAAATGGAGTGGCCTGGG
288692 ATTTGAACCCAGGCCACCCATAATGGAAAACAACCACTAACCACTTTGTCACGTTCATTTTTTAG
196 ATTTGAACCCAGGCCACCCATAATGGAAAACAACCACTAACCACTTTGTCACGTTCATTTTTTAG
288757 TTAGAAATTACCAAAACAGTTATTTAA
261 TTAGAAATTACCAAAACAGTTATTTAA
288784 GAAATTTGGGAGCCAACGGCCACCGGTGAGCGGTGGCCGACGGTGGTCGCCGGCAACCGGCGTGG
1 GAAATTTGGGAGCCAACGGCCACCGGTGAGCGGTGGCCGACGGTGGTCGCCGGCAACCGGCGTGG
288849 TGGCCGGTCGCCGGTTTCTGGGTTACTTTTTTTGTCATTTGTGGTTATGGGCGGGAAAGAAAGAA
66 TGGCCGGTCGCCGGTTTCTGGGTTACTTTTTTTGTCATTTGTGGTTATGGGCGGGAAAGAAAGAA
288914 GGAAGATGAAGAAGAAAGAAAGAAAAAGAAAAAAAAAGAAAAAATATGAAATGGAGTGGCCTGGG
131 GGAAGATGAAGAAGAAAGAAAGAAAAAGAAAAAAAAAGAAAAAATATGAAATGGAGTGGCCTGGG
288979 ATTTGAACCCAGGCCACCCATAATGGAAAACAACCACTAACCACTTTGTCACGTTCATTTTTTAG
196 ATTTGAACCCAGGCCACCCATAATGGAAAACAACCACTAACCACTTTGTCACGTTCATTTTTTAG
289044 TTAGAAATTACCAAAACAGTTATTTAA
261 TTAGAAATTACCAAAACAGTTATTTAA
289071 CTTGTTGATT
Statistics
Matches: 287, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 287 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (287 bp):
GAAATTTGGGAGCCAACGGCCACCGGTGAGCGGTGGCCGACGGTGGTCGCCGGCAACCGGCGTGG
TGGCCGGTCGCCGGTTTCTGGGTTACTTTTTTTGTCATTTGTGGTTATGGGCGGGAAAGAAAGAA
GGAAGATGAAGAAGAAAGAAAGAAAAAGAAAAAAAAAGAAAAAATATGAAATGGAGTGGCCTGGG
ATTTGAACCCAGGCCACCCATAATGGAAAACAACCACTAACCACTTTGTCACGTTCATTTTTTAG
TTAGAAATTACCAAAACAGTTATTTAA
Found at i:293708 original size:189 final size:190
Alignment explanation
Indices: 293188--294120 Score: 1400
Period size: 190 Copynumber: 4.9 Consensus size: 190
293178 ATACATCAAT
* * * * *
293188 AAAAAATGAAGCATTCATCAATTCTATAATCTTATATACATGAATGTCAAAAATTTCTGACTT-T
1 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTAAAAAATTTTTGACTTAT
** * * * *
293252 -CACATAGGGAAATGATAAGCAACATTATTGTTTGCATATAAAATGAATATGCAATCTATAGTTT
66 ACACA-A-GGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATATGCAATCTATAGTCT
* *
293316 TAAGTCCAATCTTAACCTTTTTAGGCGTAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
129 TAAGTCCAATCTTGACCTTTTTAGGCGGAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
*
293378 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATGCATGAATGTAAAAAATTTTTGACTTAT
1 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTAAAAAATTTTTGACTTAT
293443 ACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATATGCAATCTATAGTCTTA
66 ACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATATGCAATCTATAGTCTTA
*
293508 AGTCCAATCTTGACCTTTTTAGGCGGAGGACATGCCACTTTAGTAAGGAAATTCATCCTT
131 AGTCCAATCTTGACCTTTTTAGGCGGAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
293568 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACA-GAATGTAAAAAATTTTTGACTTAT
1 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTAAAAAATTTTTGACTTAT
* * *
293632 ACACAAGGAAACGATAAGTCACACTATTGTTTGCATATCAAATGAATATGCAATTTATAGTCTTA
66 ACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATATGCAATCTATAGTCTTA
* * *
293697 GGTCCAATCTTGACTTTTTTAGGCAGAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
131 AGTCCAATCTTGACCTTTTTAGGCGGAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
* *
293757 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTCAAAAA--TTTGACTTAG
1 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTAAAAAATTTTTGACTTAT
* *
293820 ACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATAATGTAATCTATAGTTTT
66 ACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAAT-ATGCAATCTATAGTCTT
* * * * *
293885 AGGTCCAATCTTGACCTTTTTA---GGTGGACATGCCACCTTAGTAAGGAAATCCATCCTA
130 AAGTCCAATCTTGACCTTTTTAGGCGGAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
293943 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTCAAAAAA-TTTTGACTTA
1 AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGT-AAAAAATTTTTGACTTA
** * * *
294007 TGTATAAAGAAACAATAAGCCACACTGTTGTTTGCATATCAAATGAATATGCAATCTATAGTCTT
65 TACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATATGCAATCTATAGTCTT
* * * *
294072 AAGTCCAATCTTGAACTTTTTAGGTGGAGGA-ATTGTCACTTTAGCAAGG
130 AAGTCCAATCTTGACCTTTTTAGGCGGAGGACA-TGCCACTTTAGTAAGG
294121 TACCCTCACA
Statistics
Matches: 682, Mismatches: 51, Indels: 20
0.91 0.07 0.03
Matches are distributed among these distances:
186 78 0.11
187 40 0.06
188 105 0.15
189 218 0.32
190 235 0.34
191 2 0.00
192 4 0.01
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (190 bp):
AAAAAATAAAGCATTCCTCAATTCTATAATTTTATATACATGAATGTAAAAAATTTTTGACTTAT
ACACAAGGAAACAATAAGCCACACTATTGTTTGCATATCAAATGAATATGCAATCTATAGTCTTA
AGTCCAATCTTGACCTTTTTAGGCGGAGGACATGCCACTTTAGTAAGGAAATTCATCCTC
Found at i:303019 original size:10 final size:10
Alignment explanation
Indices: 303004--303082 Score: 51
Period size: 11 Copynumber: 8.1 Consensus size: 10
302994 AATATATAAT
303004 TAATTTAAAA
1 TAATTTAAAA
303014 TAATTT-AAA
1 TAATTTAAAA
*
303023 T-ATTTAACA
1 TAATTTAAAA
*
303032 TATATTTAAAT
1 TA-ATTTAAAA
*
303043 TAA---AATA
1 TAATTTAAAA
*
303050 TAACTTAATAA
1 TAATTTAA-AA
*
303061 TAATTAAAAA
1 TAATTTAAAA
303071 TAATTTTAAAA
1 TAA-TTTAAAA
303082 T
1 T
303083 TAATCAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
7 5 0.10
8 4 0.08
9 7 0.13
10 14 0.27
11 22 0.42
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATTTAAAA
Found at i:303027 original size:18 final size:19
Alignment explanation
Indices: 303006--303042 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
302996 TATATAATTA
303006 ATTTAAAATA-ATTTAAAT
1 ATTTAAAATATATTTAAAT
*
303024 ATTTAACATATATTTAAAT
1 ATTTAAAATATATTTAAAT
303043 TAAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTAAAATATATTTAAAT
Found at i:303085 original size:18 final size:18
Alignment explanation
Indices: 303005--303085 Score: 51
Period size: 18 Copynumber: 4.3 Consensus size: 18
302995 ATATATAATT
*
303005 AATTTAAAATAA-TTTAA
1 AATTAAAAATAATTTTAA
* *
303022 ATATTTAACAT-ATATTT-A
1 A-ATTAAAAATAAT-TTTAA
*
303040 AATTAAAATATAACTTAATAA
1 AATTAAAA-ATAA-TT-TTAA
303061 TAATTAAAAATAATTTTAA
1 -AATTAAAAATAATTTTAA
303080 AATTAA
1 AATTAA
303086 TCAAAATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
17 7 0.14
18 18 0.36
19 8 0.16
20 4 0.08
21 5 0.10
22 8 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAAAAATAATTTTAA
Found at i:303964 original size:5 final size:5
Alignment explanation
Indices: 303954--303985 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
303944 ACATATATAA
303954 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
303986 TTAATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:304005 original size:17 final size:16
Alignment explanation
Indices: 303979--304013 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
303969 AAAATAAAAT
*
303979 AAAATAATTAATTTAA
1 AAAATAATTAAATTAA
303995 AAAATTAATTAAATTAA
1 AAAA-TAATTAAATTAA
304012 AA
1 AA
304014 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAATTAAATTAA
Found at i:307151 original size:33 final size:33
Alignment explanation
Indices: 307114--307178 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
307104 CATTTAATTA
307114 AATACATA-TTAATATTAAATATT-TATTATTTAT
1 AATACATATTTAATATTAAA-ATTATA-TATTTAT
* *
307147 AATACTTATTTATTATTAAAATTATATATTTA
1 AATACATATTTAATATTAAAATTATATATTTA
307179 ATATTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (33 bp):
AATACATATTTAATATTAAAATTATATATTTAT
Found at i:307164 original size:40 final size:36
Alignment explanation
Indices: 307120--307203 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 36
307110 ATTAAATACA
*
307120 TATTAATATTAAATATTTATTATTTATAATACTTATTTAT
1 TATTAATATTAAATATTTAATATTTA-AAT--TT-TTTAT
* *
307160 TATTAAAATTATATATTTAATATTTAAATTTTTTAT
1 TATTAATATTAAATATTTAATATTTAAATTTTTTAT
307196 T-TTAATAT
1 TATTAATAT
307204 AATTAACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 6 0.15
36 6 0.15
37 2 0.05
39 3 0.08
40 23 0.57
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (36 bp):
TATTAATATTAAATATTTAATATTTAAATTTTTTAT
Found at i:307176 original size:20 final size:20
Alignment explanation
Indices: 307120--307189 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
307110 ATTAAATACA
* *
307120 TATTAATATTAAATATTTAT
1 TATTAAAATTATATATTTAT
*
307140 TATTTATAA-TACT-TATTTAT
1 TA-TTAAAATTA-TATATTTAT
*
307160 TATTAAAATTATATATTTAA
1 TATTAAAATTATATATTTAT
*
307180 TATTTAAATT
1 TATTAAAATT
307190 TTTTATTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 6 0.15
20 30 0.75
21 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAAAATTATATATTTAT
Found at i:307196 original size:20 final size:20
Alignment explanation
Indices: 307152--307203 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
307142 TTTATAATAC
*
307152 TTATTTATTATTAAAATTAT
1 TTATTTAATATTAAAATTAT
* * *
307172 ATATTTAATATTTAAATTTT
1 TTATTTAATATTAAAATTAT
307192 TTATTTTAATAT
1 TTA-TTTAATAT
307204 AATTAACCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTAATATTAAAATTAT
Found at i:317385 original size:2 final size:2
Alignment explanation
Indices: 317378--317410 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
317368 TTTGCATGTG
*
317378 TA TA TA TA TA TA TA TA TT TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
317411 AAATAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:317753 original size:20 final size:20
Alignment explanation
Indices: 317708--317755 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
317698 CGAAAATTTC
*
317708 ATTAAAAATAATTAATTTTT
1 ATTAAAAATAAGTAATTTTT
* *
317728 AGTTAAAAATGAGTATTTTTT
1 A-TTAAAAATAAGTAATTTTT
317749 ATTAAAA
1 ATTAAAA
317756 TTTCATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
ATTAAAAATAAGTAATTTTT
Found at i:321379 original size:24 final size:24
Alignment explanation
Indices: 321351--321404 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
321341 TATAAACATT
*
321351 ATCATCTATC-TCATCATCATTGTC
1 ATCAT-TATCTTCAACATCATTGTC
* *
321375 CTCATTGTCTTCAACATCATTGTC
1 ATCATTATCTTCAACATCATTGTC
321399 ATCATT
1 ATCATT
321405 TTCATTATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.24, C:0.28, G:0.06, T:0.43
Consensus pattern (24 bp):
ATCATTATCTTCAACATCATTGTC
Found at i:325995 original size:27 final size:27
Alignment explanation
Indices: 325948--326026 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
325938 ATATTTAAAT
* *
325948 CACATTAATT-AT-CAA-ACACATTGTG
1 CACA-TAATTAATACAATACACATTATA
325973 CACATAATTAATACAATACACATTATA
1 CACATAATTAATACAATACACATTATA
*
326000 CACCTAATTAATACAATACACATTATA
1 CACATAATTAATACAATACACATTATA
326027 AACAATTCAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
24 5 0.10
25 6 0.12
26 3 0.06
27 34 0.71
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (27 bp):
CACATAATTAATACAATACACATTATA
Found at i:327510 original size:20 final size:20
Alignment explanation
Indices: 327474--327515 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
327464 AGTCCTCCAT
* *
327474 TTAATTTAGCTTCTATTTAA
1 TTAATTTAACTTCTATTGAA
327494 TTAATTTAAACTT-TATTGAA
1 TTAATTT-AACTTCTATTGAA
327514 TT
1 TT
327516 CTAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TTAATTTAACTTCTATTGAA
Found at i:329312 original size:31 final size:30
Alignment explanation
Indices: 329231--329319 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 30
329221 CCCCTAAAGT
*
329231 TTTATAAAAAATACACTTATCCCT-TAA-C
1 TTTATAAAAAATACACTTATCCCTCTAAGG
*
329259 ATT-TAAAAAATACCCACTTATCCCTCTAAGG
1 TTTATAAAAAATA--CACTTATCCCTCTAAGG
*
329290 TTTGATAAAAAATATACTTATCCCTCTAAG
1 TTT-ATAAAAAATACACTTATCCCTCTAAG
329320 CTATTATTCA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
27 9 0.18
28 2 0.04
29 11 0.22
30 3 0.06
31 17 0.33
33 9 0.18
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.34
Consensus pattern (30 bp):
TTTATAAAAAATACACTTATCCCTCTAAGG
Found at i:329606 original size:23 final size:24
Alignment explanation
Indices: 329563--329608 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
329553 CTTTAAAATA
* *
329563 AATTTATTAAAATATTTTTATTTC
1 AATTAATTAAAATATTATTATTTC
329587 AATTAATT-AAATATTATTATTT
1 AATTAATTAAAATATTATTATTT
329609 AAAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTAATTAAAATATTATTATTTC
Found at i:331396 original size:2 final size:2
Alignment explanation
Indices: 331389--331426 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
331379 GGATTGGTAG
*
331389 AT AT AT AT AC 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
331427 TAATAAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:332840 original size:2 final size:2
Alignment explanation
Indices: 332827--332858 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
332817 ATTAAAATTC
*
332827 AT AT AT AC 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
332859 CAACCATCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:337935 original size:16 final size:15
Alignment explanation
Indices: 337914--337943 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
337904 AATAATTAAG
337914 TTTTTTATGCTTTTTC
1 TTTTTTATG-TTTTTC
337930 TTTTTTATGTTTTT
1 TTTTTTATGTTTTT
337944 AGATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (15 bp):
TTTTTTATGTTTTTC
Found at i:337951 original size:2 final size:2
Alignment explanation
Indices: 337946--337973 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
337936 ATGTTTTTAG
337946 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
337974 TCTCTTTCAA
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:338302 original size:2 final size:2
Alignment explanation
Indices: 338295--338328 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
338285 TGTTACGTCC
*
338295 AT AT AT AT AA 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
338329 TTGTTTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:343364 original size:15 final size:16
Alignment explanation
Indices: 343337--343366 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
343327 ATTTATATAA
343337 AAAATTATTAATTTTT
1 AAAATTATTAATTTTT
343353 AAAATT-TTAATTTT
1 AAAATTATTAATTTT
343367 AGTAATCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAAATTATTAATTTTT
Found at i:343602 original size:6 final size:6
Alignment explanation
Indices: 343591--343637 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
343581 AATCTAAAAT
* *
343591 AATTTA AATTTA AA-ATA AATTTA AATTTA AA-AT- AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
343636 AA
1 AA
343638 AATAACCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
4 2 0.06
5 6 0.18
6 26 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:343642 original size:17 final size:16
Alignment explanation
Indices: 343585--343638 Score: 99
Period size: 16 Copynumber: 3.3 Consensus size: 16
343575 TGTTTGAATC
343585 TAAAATAATTTAAATT
1 TAAAATAATTTAAATT
343601 TAAAATAAATTTAAATT
1 TAAAAT-AATTTAAATT
343618 TAAAATAATTTAAATT
1 TAAAATAATTTAAATT
343634 TAAAA
1 TAAAA
343639 ATAACCCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:344862 original size:2 final size:2
Alignment explanation
Indices: 344855--344892 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
344845 TTGACTTCCC
* *
344855 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
344893 TCCTAGAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:346036 original size:2 final size:2
Alignment explanation
Indices: 346029--346066 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
346019 TCTTACTAGG
346029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
346067 AATTGGCCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351729 original size:3 final size:3
Alignment explanation
Indices: 351707--351805 Score: 72
Period size: 3 Copynumber: 33.0 Consensus size: 3
351697 TTACTTCTTG
* * * * * * * *
351707 ATC ATC CTC ATC ATC CTC ATC ATC CTC CTC ATC CTC TTC CTC ATC ACC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
351755 ATC CTC ATC GTC TTC ACC ATC ATC GTC TTC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
351803 ATC
1 ATC
351806 TATATCTAGC
Statistics
Matches: 74, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:351735 original size:12 final size:12
Alignment explanation
Indices: 351714--351805 Score: 87
Period size: 12 Copynumber: 7.7 Consensus size: 12
351704 TTGATCATCC
351714 TCATCATCCTCA
1 TCATCATCCTCA
*
351726 TCATCCTCCTCA
1 TCATCATCCTCA
* *
351738 TCCTCTTCCTCA
1 TCATCATCCTCA
*
351750 TCACCATCCTCA
1 TCATCATCCTCA
* *
351762 TCGTCTTCAC-CA
1 TCATCATC-CTCA
* *
351774 TCATCGTCTTCA
1 TCATCATCCTCA
*
351786 TCATCATCATCA
1 TCATCATCCTCA
351798 TCATCATC
1 TCATCATC
351806 TATATCTAGC
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
12 63 0.98
13 1 0.02
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.35
Consensus pattern (12 bp):
TCATCATCCTCA
Found at i:357248 original size:42 final size:43
Alignment explanation
Indices: 357201--357282 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
357191 ATTTTTGGGC
*
357201 TTTTTTT-AACCCAATTGTAATTTATT-ATTATT-TTTTTGAAT
1 TTTTTTTCAACCCAACTGTAATTTATTAATT-TTATTTTTGAAT
*
357242 TTTTTTTCAATCCAACTGTAATTTATTAATTTTATTTTTGA
1 TTTTTTTCAACCCAACTGTAATTTATTAATTTTATTTTTGA
357283 GCTTTTAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 7 0.19
42 19 0.53
43 10 0.28
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.60
Consensus pattern (43 bp):
TTTTTTTCAACCCAACTGTAATTTATTAATTTTATTTTTGAAT
Found at i:357956 original size:38 final size:38
Alignment explanation
Indices: 357856--357957 Score: 141
Period size: 38 Copynumber: 2.7 Consensus size: 38
357846 TCAAAGAGAG
* ** *
357856 TTCAATTTGGAATTCTCTAGCCACCAGCCACCGGCCAAT
1 TTCAAATT-GAATTCTCTAGCCGTCAGCCACCAGCCAAT
*
357895 TTCAAATTGAATTCTCTAGCCGTCAGTCACCAGCCAAT
1 TTCAAATTGAATTCTCTAGCCGTCAGCCACCAGCCAAT
*
357933 TTCAAATTGAATTCTCTAACCGTCA
1 TTCAAATTGAATTCTCTAGCCGTCA
357958 ACTAATTCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 50 0.88
39 7 0.12
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (38 bp):
TTCAAATTGAATTCTCTAGCCGTCAGCCACCAGCCAAT
Found at i:361533 original size:38 final size:36
Alignment explanation
Indices: 361481--361606 Score: 136
Period size: 38 Copynumber: 3.5 Consensus size: 36
361471 TCAAAGAGAG
*
361481 TTCAATTTGGAATTCTCTAGCCACCAGCCACCGGCCAAT
1 TTCAAATT-GAATTCTCTAG-C-CCAGCCACCGGCCAAT
* * *
361520 TTCAAATTGAATTCTCTAGTCGTCAGCCGCCGGTCAAT
1 TTCAAATTGAATTCTCTAG-C-CCAGCCACCGGCCAAT
361558 TTCAAATTGAATTCTCTAG-CC-GCCA---GCCAAT
1 TTCAAATTGAATTCTCTAGCCCAGCCACCGGCCAAT
361589 TTCAAATTGAATTCTCTA
1 TTCAAATTGAATTCTCTA
361607 ACCGTCAACT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
31 23 0.29
34 3 0.04
35 1 0.01
38 44 0.56
39 7 0.09
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (36 bp):
TTCAAATTGAATTCTCTAGCCCAGCCACCGGCCAAT
Found at i:361589 original size:31 final size:31
Alignment explanation
Indices: 361544--361606 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
361534 TCTAGTCGTC
* *
361544 AGCCGCCGGTCAATTTCAAATTGAATTCTCT
1 AGCCGCCAGCCAATTTCAAATTGAATTCTCT
361575 AGCCGCCAGCCAATTTCAAATTGAATTCTCT
1 AGCCGCCAGCCAATTTCAAATTGAATTCTCT
361606 A
1 A
361607 ACCGTCAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (31 bp):
AGCCGCCAGCCAATTTCAAATTGAATTCTCT
Found at i:361629 original size:30 final size:31
Alignment explanation
Indices: 361554--361631 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
361544 AGCCGCCGGT
* *
361554 CAATTTCAAATTGAATTCTCTAGCCGCCAGC
1 CAATTTCAAATTGAATTCTCTAACCGCCAAC
*
361585 CAATTTCAAATTGAATTCTCTAACCGTCAAC
1 CAATTTCAAATTGAATTCTCTAACCGCCAAC
* *
361616 TAA-TTCAATTTGAATT
1 CAATTTCAAATTGAATT
361632 TGATTTGCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 12 0.29
31 30 0.71
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (31 bp):
CAATTTCAAATTGAATTCTCTAACCGCCAAC
Found at i:363534 original size:2 final size:2
Alignment explanation
Indices: 363529--363561 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
363519 GTAATTAGGG
363529 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
363562 ACAATACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:363860 original size:21 final size:19
Alignment explanation
Indices: 363806--363866 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 19
363796 AATTTTTATC
*
363806 ATATAAAAAATACATATAA
1 ATATAAAAAATATATATAA
* *
363825 ATATATAATATTATAGTATAA
1 ATATA-AAAAATATA-TATAA
363846 ATATTAAAAAATATAT-TAA
1 ATA-TAAAAAATATATATAA
363865 AT
1 AT
363867 TATTTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.29
20 7 0.21
21 15 0.44
22 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
ATATAAAAAATATATATAA
Found at i:367681 original size:14 final size:14
Alignment explanation
Indices: 367664--367699 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
367654 GATGGATATA
*
367664 TATCGTATAATTCT
1 TATCATATAATTCT
367678 TATCATATAATTCT
1 TATCATATAATTCT
367692 TAT-ATATA
1 TATCATATA
367700 TTGTACAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (14 bp):
TATCATATAATTCT
Found at i:369494 original size:21 final size:21
Alignment explanation
Indices: 369468--369509 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
369458 TCCATATTTT
369468 AAAATAAGTTAAATACAATAC
1 AAAATAAGTTAAATACAATAC
*
369489 AAAATAAGTTAAATATAATAC
1 AAAATAAGTTAAATACAATAC
369510 TATTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAATAAGTTAAATACAATAC
Found at i:374484 original size:15 final size:16
Alignment explanation
Indices: 374466--374500 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
374456 TATAAAGGAT
374466 ATTAATTATAT-TATA
1 ATTAATTATATATATA
*
374481 ATTACTTATATATATA
1 ATTAATTATATATATA
374497 ATTA
1 ATTA
374501 TGTATTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAATTATATATATA
Found at i:375432 original size:16 final size:16
Alignment explanation
Indices: 375390--375433 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
375380 AATCTTAAAA
*
375390 AAAAATTATTCTGAAC
1 AAAAATTATTTTGAAC
*
375406 AAAAATTATTTTGAAT
1 AAAAATTATTTTGAAC
375422 AAAAATTATTTT
1 AAAAATTATTTT
375434 AAATTCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (16 bp):
AAAAATTATTTTGAAC
Found at i:377976 original size:19 final size:20
Alignment explanation
Indices: 377929--377966 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
377919 CATTATTTAA
377929 TGTAATTTTTTTAAAATAAT
1 TGTAATTTTTTTAAAATAAT
377949 TGTAATTTTTTTAAAATA
1 TGTAATTTTTTTAAAATA
377967 TATTAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTAATTTTTTTAAAATAAT
Found at i:378741 original size:26 final size:26
Alignment explanation
Indices: 378696--378746 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
378686 AAGTGATGCT
378696 TAATTATTTAATTCAGTTATTATTAC
1 TAATTATTTAATTCAGTTATTATTAC
378722 TAATGTATTTAATAT-A-TTATTATTA
1 TAAT-TATTTAAT-TCAGTTATTATTA
378747 TTTTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.57
27 9 0.39
28 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (26 bp):
TAATTATTTAATTCAGTTATTATTAC
Found at i:378794 original size:3 final size:3
Alignment explanation
Indices: 378786--378872 Score: 65
Period size: 3 Copynumber: 29.3 Consensus size: 3
378776 ATATGTATAT
* *
378786 TTA TTA TTA TTA TTA TT- TATA TT- TAA TATA TTA TTT TTA TTAA TT-
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA TTA TT-A TTA
** **
378831 TTA AAA AAA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
378873 GAGATTCATT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
2 6 0.09
3 57 0.83
4 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:382759 original size:3 final size:3
Alignment explanation
Indices: 382751--382793 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
382741 ACCCAAAACT
382751 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
382794 AAGGATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:386574 original size:190 final size:189
Alignment explanation
Indices: 386331--386710 Score: 520
Period size: 190 Copynumber: 2.0 Consensus size: 189
386321 ATCCAATATA
* * *
386331 TAAATTTTGAACAAATCCTTGAAAGCTGAGCCTATCCATGTGTCAGTTATTA-TTAT-TATT-TT
1 TAAATTTTAAACAAATCCCTGAAAGCTGAGCCTATCCATGTGTCAGCTATTATTTATGTATTATT
* * *
386393 TTTCCTTTGGTTGC-CATGTAGCCATTTCTATT-GTTTTTTCTCAATTCTTTGTACTTAACTTAT
66 TTTCCTTTGG--GCACATGTAGCCATTTCTATTACTTTTTT-TC----CTTTGTACTCAACCTAT
* *
386456 TTGTCTAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTTTACAGAGATATTAAAAGATTTTATGT
124 TTGTCGAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGT
386521 T
189 T
* * *
386522 TAAATTTTAAACAAATCCCTGAAAG-TGAGTCTATCCATGTGTCAGCTATTATTTTTGTTTTCAT
1 TAAATTTTAAACAAATCCCTGAAAGCTGAGCCTATCCATGTGTCAGCTATTATTTATGTATT-AT
* *
386586 TTTTCCTTTGGGCATCGTGTAGTCATTTCTATTACTTTTTTTCCTTTGTACTCAACCTATTTGTC
65 TTTTCCTTTGGGCA-CATGTAGCCATTTCTATTACTTTTTTTCCTTTGTACTCAACCTATTTGTC
386651 GAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGT
129 GAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGT
386711 ATTATTTAAT
Statistics
Matches: 169, Mismatches: 13, Indels: 15
0.86 0.07 0.08
Matches are distributed among these distances:
190 102 0.60
191 26 0.15
192 5 0.03
194 30 0.18
195 6 0.04
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (189 bp):
TAAATTTTAAACAAATCCCTGAAAGCTGAGCCTATCCATGTGTCAGCTATTATTTATGTATTATT
TTTCCTTTGGGCACATGTAGCCATTTCTATTACTTTTTTTCCTTTGTACTCAACCTATTTGTCGA
AGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGTT
Found at i:392068 original size:50 final size:51
Alignment explanation
Indices: 391977--392121 Score: 231
Period size: 50 Copynumber: 2.9 Consensus size: 51
391967 TTTTAACTAG
*
391977 ATGTATCGATACATTGAAAAATGTATCCATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
392028 ATGTATCGATACATTG-AAAATGTATCGATACATCTAGGT-AAAAGACTGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
392077 ATATATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
392122 TATGACTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 23 0.27
50 43 0.50
51 20 0.23
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:397161 original size:20 final size:20
Alignment explanation
Indices: 397145--397183 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
397135 TAATATTGAC
397145 ATAAATATTAAAATATTATA
1 ATAAATATTAAAATATTATA
*
397165 ATAATTATTAAAATATTAT
1 ATAAATATTAAAATATTAT
397184 TTTTAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATATTAAAATATTATA
Found at i:397603 original size:21 final size:20
Alignment explanation
Indices: 397579--397667 Score: 55
Period size: 21 Copynumber: 4.5 Consensus size: 20
397569 GCATGTTACA
397579 ATTTATTATTAAAATAATAAT
1 ATTTATTATT-AAATAATAAT
397600 ATTT-TTAAATTAAATAAT-AT
1 ATTTATT--ATTAAATAATAAT
*
397620 -TTTA-TA-TAAATAA-ATTT
1 ATTTATTATTAAATAATA-AT
* *
397637 ATTTATTACTAAAATAATACT
1 ATTTATTA-TTAAATAATAAT
397658 ATTATATTAT
1 ATT-TATTAT
397668 ATTTTATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
16 7 0.13
17 2 0.04
18 4 0.07
19 6 0.11
20 4 0.07
21 22 0.41
22 9 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATTATTAAATAATAAT
Found at i:397607 original size:17 final size:17
Alignment explanation
Indices: 397582--397632 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
397572 TGTTACAATT
*
397582 TATTATTAAAATAATAA
1 TATTTTTAAAATAATAA
*
397599 TATTTTTAAATTAAATAA
1 TATTTTTAAAAT-AATAA
397617 TATTTTATATAAATAA
1 TATTTT-TA-AAATAA
397633 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 10 0.36
18 11 0.39
19 4 0.14
20 3 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTTTAAAATAATAA
Found at i:397631 original size:16 final size:17
Alignment explanation
Indices: 397594--397636 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
397584 TTATTAAAAT
397594 AATAATATTTTTAAATTA
1 AATAATA-TTTTAAATTA
*
397612 AATAATATTTTATA-TA
1 AATAATATTTTAAATTA
397628 AATAA-ATTT
1 AATAATATTT
397637 ATTTATTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 6 0.25
18 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATAATATTTTAAATTA
Found at i:398005 original size:14 final size:14
Alignment explanation
Indices: 397986--398014 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
397976 CAAAAAAATA
397986 AAAAAATATTTTTC
1 AAAAAATATTTTTC
398000 AAAAAATATTTTTC
1 AAAAAATATTTTTC
398014 A
1 A
398015 TTAAACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAAATATTTTTC
Found at i:399757 original size:22 final size:22
Alignment explanation
Indices: 399732--399779 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
399722 TTGACTCTAT
*
399732 TTTTGTCATTGATTTATATAT-A
1 TTTTGTCA-TGATTTAAATATAA
*
399754 TTTTTTCATGATTTAAATATAA
1 TTTTGTCATGATTTAAATATAA
399776 TTTT
1 TTTT
399780 TTGGAAAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTTGTCATGATTTAAATATAA
Found at i:399780 original size:22 final size:22
Alignment explanation
Indices: 399729--399781 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
399719 TGATTGACTC
*
399729 TATTTTTGTCATTGATTTATATA
1 TATTTTT-TCATTGATTTAAATA
399752 TATTTTTTCA-TGATTTAAATA
1 TATTTTTTCATTGATTTAAATA
399773 TAATTTTTT
1 T-ATTTTTT
399782 GGAAAGTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.39
22 10 0.36
23 7 0.25
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (22 bp):
TATTTTTTCATTGATTTAAATA
Found at i:402097 original size:15 final size:17
Alignment explanation
Indices: 402058--402098 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
402048 TTATATTTAT
*
402058 ATAAATTTTATTCATTA
1 ATAATTTTTATTCATTA
402075 ATAATTTTTATT-A-TA
1 ATAATTTTTATTCATTA
402090 AT-ATTTTTA
1 ATAATTTTTA
402099 GATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 1 0.04
17 11 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATTTTTATTCATTA
Found at i:402509 original size:41 final size:45
Alignment explanation
Indices: 402447--402529 Score: 111
Period size: 43 Copynumber: 1.9 Consensus size: 45
402437 TTTAATATAC
**
402447 TATTTTAATTATATTTAAATATATTATA-TCATATT-TATTTTAT
1 TATTTTAATTATATTTAAATATACAATATTCATATTATATTTTAT
*
402490 TATTTTTATT-TA-TTAAATATACAATATTCATATTATATTT
1 TATTTTAATTATATTTAAATATACAATATTCATATTATATTT
402530 AAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 12 0.34
42 9 0.26
43 14 0.40
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (45 bp):
TATTTTAATTATATTTAAATATACAATATTCATATTATATTTTAT
Found at i:406996 original size:12 final size:12
Alignment explanation
Indices: 406963--406996 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
406953 CTTGCAAGTG
406963 CTTTGCCTTTAA
1 CTTTGCCTTTAA
406975 CTTTAG-CTTTAA
1 CTTT-GCCTTTAA
406987 CTTTGCCTTT
1 CTTTGCCTTT
406997 TTCAATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.15, C:0.24, G:0.09, T:0.53
Consensus pattern (12 bp):
CTTTGCCTTTAA
Found at i:411302 original size:3 final size:3
Alignment explanation
Indices: 411296--411336 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
411286 GTTTTGAGAT
411296 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
411337 CTTATGGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:412963 original size:22 final size:21
Alignment explanation
Indices: 412920--412964 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
412910 AATATAATGG
*
412920 TAAAATTAATTATTATATAAA
1 TAAAATTAATTATGATATAAA
412941 TAAAATTAAATTAGTGATA-AAA
1 TAAAATT-AATTA-TGATATAAA
412963 TA
1 TA
412965 TATATTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 10 0.48
23 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAATTAATTATGATATAAA
Found at i:413161 original size:14 final size:14
Alignment explanation
Indices: 413142--413177 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
413132 TTTTATTAAA
413142 AATAAATATATTTT
1 AATAAATATATTTT
413156 AATAAATATATTTT
1 AATAAATATATTTT
413170 AATAAATA
1 AATAAATA
413178 ACTAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAAATATATTTT
Found at i:413206 original size:32 final size:31
Alignment explanation
Indices: 413170--413232 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
413160 AATATATTTT
*
413170 AATAAATAACTAAAAATTATATTTATATTAAA
1 AATAAATAA-TAAAAATCATATTTATATTAAA
* * *
413202 AATAAATTATTAAAATCATGTTTATATTAAA
1 AATAAATAATAAAAATCATATTTATATTAAA
413233 TAAATTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (31 bp):
AATAAATAATAAAAATCATATTTATATTAAA
Found at i:413298 original size:23 final size:23
Alignment explanation
Indices: 413263--413308 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
413253 ATTGGAGGTA
* *
413263 AAAAATAAAATTATATTTATATT
1 AAAAATAAAATTAAAATTATATT
**
413286 AAAAATATTATTAAAATTATATT
1 AAAAATAAAATTAAAATTATATT
413309 TATTTTAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAATAAAATTAAAATTATATT
Found at i:413301 original size:29 final size:29
Alignment explanation
Indices: 413182--413322 Score: 96
Period size: 31 Copynumber: 4.8 Consensus size: 29
413172 TAAATAACTA
413182 AAAATTATATTTATATTAAAAATAAATTATT
1 AAAATTATATTTATATTAAAAAT--ATTATT
* *
413213 AAAATCATGTTTATATTAAATAA-ATTAATT
1 AAAATTATATTTATATTAAA-AATATT-ATT
* * * ** *
413243 AATAGTATAAATTGGAGGT-AAAA-A--A-T
1 AAAATTAT-ATTTATA-TTAAAAATATTATT
413269 AAAATTATATTTATATTAAAAATATTATT
1 AAAATTATATTTATATTAAAAATATTATT
*
413298 AAAATTATATTTATTTTAAGAAATA
1 AAAATTATATTTATATTAA-AAATA
413323 AAATAACCAT
Statistics
Matches: 83, Mismatches: 17, Indels: 21
0.69 0.14 0.17
Matches are distributed among these distances:
24 1 0.01
25 8 0.10
26 8 0.10
27 1 0.01
28 1 0.01
29 22 0.27
30 16 0.19
31 23 0.28
32 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (29 bp):
AAAATTATATTTATATTAAAAATATTATT
Found at i:413827 original size:28 final size:29
Alignment explanation
Indices: 413781--413841 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
413771 TATAAATATG
* *
413781 ATTTATATTAGATTTAATTATTTTTAATT
1 ATTTATATTAGATTTAATTAATTTAAATT
413810 ATTTA-ATTAAGA-TTAATTAATTTAAATT
1 ATTTATATT-AGATTTAATTAATTTAAATT
413838 ATTT
1 ATTT
413842 TTTTTAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
ATTTATATTAGATTTAATTAATTTAAATT
Found at i:414731 original size:2 final size:2
Alignment explanation
Indices: 414724--414753 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
414714 CAAACACCCA
*
414724 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
414754 AGTCTCTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:416892 original size:17 final size:17
Alignment explanation
Indices: 416854--416899 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
416844 ATAAATAATG
416854 TTTTAAAT-AAAAT-TA
1 TTTTAAATAAAAATATA
*
416869 -ATTAAATAAAAATATA
1 TTTTAAATAAAAATATA
*
416885 TTTTAAATATAAATA
1 TTTTAAATAAAAATA
416900 GTTTATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 2 0.08
17 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTTAAATAAAAATATA
Found at i:421391 original size:21 final size:21
Alignment explanation
Indices: 421365--421422 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
421355 AAACTCAACA
*
421365 TTGTATCGACACAATATGACC
1 TTGTATCGATACAATATGACC
*
421386 TTGTATCGATAAAATATGACC
1 TTGTATCGATACAATATGACC
* *
421407 TTATATCAATACAATA
1 TTGTATCGATACAATA
421423 CATGTTTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACAATATGACC
Found at i:423439 original size:32 final size:33
Alignment explanation
Indices: 423398--423459 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
423388 CAATTCACTG
423398 TGTATCGATACCAAG-AA-CGTGTATCGATATAA
1 TGTATCGATACCAAGCAATC-TGTATCGATATAA
*
423430 TGTATCGATACTAAGCAATCTGTATCGATA
1 TGTATCGATACCAAGCAATCTGTATCGATA
423460 CATCTGGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 12 0.44
34 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (33 bp):
TGTATCGATACCAAGCAATCTGTATCGATATAA
Found at i:437560 original size:29 final size:27
Alignment explanation
Indices: 437510--437564 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
437500 ATTTTTTTAT
437510 TATTTAAAATATTATAATTTTATATAA
1 TATTTAAAATATTATAATTTTATATAA
* *
437537 TATTTATAAATATTTTTATGTTTATATA
1 TATTTA-AAATATTATAAT-TTTATATA
437565 TTTATGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 10 0.42
29 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TATTTAAAATATTATAATTTTATATAA
Found at i:437575 original size:31 final size:30
Alignment explanation
Indices: 437509--437599 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
437499 TATTTTTTTA
* *
437509 TTATTTA-AAATATTATAAT-TTTATATA-
1 TTATTTATAAATATTTTTATGTTTATATAT
*
437536 ATATTTATAAATATTTTTATGTTTATATAT
1 TTATTTATAAATATTTTTATGTTTATATAT
** *
437566 TTATGTTATATTTATTTTTTTGTATTATAT-T
1 TTAT-TTATAAATATTTTTATGT-TTATATAT
437597 TTA
1 TTA
437600 ATTAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.12
28 10 0.19
29 8 0.15
30 3 0.06
31 19 0.37
32 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (30 bp):
TTATTTATAAATATTTTTATGTTTATATAT
Found at i:437608 original size:31 final size:31
Alignment explanation
Indices: 437547--437619 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
437537 TATTTATAAA
*
437547 TATTTTTATGTTTATATATTTATGTTATATT
1 TATTTTTATGTTTATATATTTATGTAATATT
*
437578 TATTTTTTTGTATTATAT-TTTAAT-TAATATT
1 TATTTTTATGT-TTATATATTT-ATGTAATATT
437609 TAATGTTTTAT
1 T-AT-TTTTAT
437620 TTGTGTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
31 20 0.57
32 10 0.29
33 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (31 bp):
TATTTTTATGTTTATATATTTATGTAATATT
Found at i:438209 original size:14 final size:16
Alignment explanation
Indices: 438190--438221 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
438180 GTTTTATGTC
438190 ATGTATAT-T-TTTAT
1 ATGTATATGTATTTAT
438204 ATGTATATGTATTTAT
1 ATGTATATGTATTTAT
438220 AT
1 AT
438222 CATGTGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
ATGTATATGTATTTAT
Found at i:439382 original size:11 final size:11
Alignment explanation
Indices: 439368--439409 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
439358 TTGTATCATA
439368 TTTATATTATT
1 TTTATATTATT
*
439379 TTTATTTTATAT
1 TTTATATTAT-T
439391 TTTA-ATTATT
1 TTTATATTATT
439401 CTTTATATT
1 -TTTATATT
439410 GTGTTCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 1 0.04
11 17 0.65
12 8 0.31
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:439745 original size:9 final size:10
Alignment explanation
Indices: 439718--439750 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
439708 TATATATTCG
439718 TATATTTTTA
1 TATATTTTTA
439728 TCATATTTTTA
1 T-ATATTTTTA
439739 T-TATTTTTA
1 TATATTTTTA
439748 TAT
1 TAT
439751 CGTATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.43
10 2 0.10
11 10 0.48
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTTA
Found at i:439805 original size:17 final size:17
Alignment explanation
Indices: 439755--439816 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
439745 TTATATCGTA
*
439755 TTATATTTTAATTATTTTC
1 TTATATTTTAA-T-TTATC
* *
439774 TTATATTAT-ATTTATG
1 TTATATTTTAATTTATC
439790 TTATATTTTAATTTATC
1 TTATATTTTAATTTATC
439807 TTATATTTTA
1 TTATATTTTA
439817 TATATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 11 0.30
17 17 0.46
18 1 0.03
19 8 0.22
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATATTTTAATTTATC
Found at i:439886 original size:14 final size:14
Alignment explanation
Indices: 439823--439906 Score: 86
Period size: 14 Copynumber: 6.0 Consensus size: 14
439813 TTTATATATT
439823 TTTTATATAATTAAA
1 TTTTAT-TAATTAAA
439838 TTTTAATT--TTAAA
1 TTTT-ATTAATTAAA
*
439851 -TTTATTTATTAAA
1 TTTTATTAATTAAA
*
439864 TATTT-TTAAATAAA
1 T-TTTATTAATTAAA
439878 TTTTATTAATTAAA
1 TTTTATTAATTAAA
439892 TTTTATTTAATTAAA
1 TTTTA-TTAATTAAA
439907 AATTTTATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
11 3 0.05
12 3 0.05
13 13 0.22
14 21 0.36
15 17 0.29
16 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTATTAATTAAA
Found at i:440235 original size:23 final size:23
Alignment explanation
Indices: 440209--440258 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
440199 TTTTAATTTC
*
440209 AGAAAGAAATAAGTAAA-AAAGAA
1 AGAAA-AAATAAATAAATAAAGAA
*
440232 AGAAAAAATAAATAAATAAAGCA
1 AGAAAAAATAAATAAATAAAGAA
440255 AGAA
1 AGAA
440259 GCTTGAACTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (23 bp):
AGAAAAAATAAATAAATAAAGAA
Done.