Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold262
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: 1141274
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 8
Found at i:503851 original size:7 final size:7
Alignment explanation
Indices: 503839--503893 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
503829 TTAAAATATG
503839 ATATAAA
1 ATATAAA
503846 ATAT--A
1 ATATAAA
*
503851 ATATAAT
1 ATATAAA
*
503858 ATAAAAA
1 ATATAAA
503865 ATAATAAA
1 AT-ATAAA
503873 A-ATAAA
1 ATATAAA
503879 ATATAAAA
1 ATAT-AAA
503887 ATATAAA
1 ATATAAA
503894 TGTATCAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
5 5 0.13
6 6 0.15
7 16 0.41
8 12 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATATAAA
Found at i:503853 original size:17 final size:17
Alignment explanation
Indices: 503833--503893 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
503823 TATGATTTAA
*
503833 AATATGATATAAAATAT
1 AATATAATATAAAATAT
*
503850 AATATAATATAAAAAAT
1 AATATAATATAAAATAT
*
503867 AATA-AAAATAAAATAT
1 AATATAATATAAAATAT
503883 AA-A-AATATAAA
1 AATATAATATAAA
503894 TGTATCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.21
16 12 0.31
17 19 0.49
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
AATATAATATAAAATAT
Found at i:504239 original size:3 final size:3
Alignment explanation
Indices: 504231--504263 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
504221 TATATTCTAC
504231 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
504264 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:504268 original size:3 final size:3
Alignment explanation
Indices: 504262--504306 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
504252 CATCATCATC
504262 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
504307 CAATAATCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:505118 original size:3 final size:3
Alignment explanation
Indices: 505112--505137 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
505102 CCACCAACTT
505112 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
505138 TAGCCTGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:505343 original size:2 final size:2
Alignment explanation
Indices: 505338--505370 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
505328 CTGGGTGCTT
*
505338 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
505371 TTTAAATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:505616 original size:6 final size:6
Alignment explanation
Indices: 505605--505637 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
505595 TAAATTTACG
505605 TATATT TATATT TA-ATGT TATATT TATATT TAT
1 TATATT TATATT TATAT-T TATATT TATATT TAT
505638 TTACGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 2 0.08
6 21 0.84
7 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:505709 original size:17 final size:17
Alignment explanation
Indices: 505677--505722 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
505667 ATAAATTTAA
* *
505677 AATATTTAATTATTTTT
1 AATAATTAAATATTTTT
505694 --TAATGTAAATATTTTT
1 AATAAT-TAAATATTTTT
505710 AATAATTAAATAT
1 AATAATTAAATAT
505723 ATAGTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 7 0.29
18 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
AATAATTAAATATTTTT
Found at i:506233 original size:45 final size:45
Alignment explanation
Indices: 506177--506308 Score: 192
Period size: 45 Copynumber: 2.9 Consensus size: 45
506167 AAAAAGATTA
* *
506177 AAAAAATCAAAACTTTCATCACCGGTCTATATAAAAAATAAAGTT
1 AAAAAATCAAAATTTTCATCATCGGTCTATATAAAAAATAAAGTT
* * *
506222 GAAAAATCAAAATTTTCGTCATTGGTCTATATAAAAAATAAAGTT
1 AAAAAATCAAAATTTTCATCATCGGTCTATATAAAAAATAAAGTT
* *
506267 AAAAAATTAAAATTTTCATTATCGGTCTATATAAAAAGATAA
1 AAAAAATCAAAATTTTCATCATCGGTCTATATAAAAA-ATAA
506309 TATAATTAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
45 72 0.95
46 4 0.05
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (45 bp):
AAAAAATCAAAATTTTCATCATCGGTCTATATAAAAAATAAAGTT
Found at i:513179 original size:14 final size:14
Alignment explanation
Indices: 513146--513179 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
513136 TTATAATATA
513146 AAATTTTTAAAATT
1 AAATTTTTAAAATT
* *
513160 ATATTTTTAAATTT
1 AAATTTTTAAAATT
513174 AAATTT
1 AAATTT
513180 AGTTACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATTTTTAAAATT
Found at i:513273 original size:19 final size:19
Alignment explanation
Indices: 513215--513273 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
513205 TAATTTTTTA
* *
513215 TTTATTTTATTATTAAAAT
1 TTTATTTTATAATTAAATT
*
513234 ATTATTTT-TATATTAATATT
1 TTTATTTTATA-ATTAA-ATT
513254 TTTATTTTATAATTAAATT
1 TTTATTTTATAATTAAATT
513273 T
1 T
513274 AAATAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.03
19 16 0.48
20 14 0.42
21 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTATAATTAAATT
Found at i:513302 original size:19 final size:19
Alignment explanation
Indices: 513219--513303 Score: 51
Period size: 19 Copynumber: 4.8 Consensus size: 19
513209 TTTTTATTTA
513219 TTTTATTATTAAAATATTAT
1 TTTTATTATT-AAATATTAT
513239 TTTTA-TATT--A-A-TAT
1 TTTTATTATTAAATATTAT
* *
513253 TTTTATT-TTATA-ATTAA
1 TTTTATTATTAAATATTAT
* * *
513270 ATTTA-AATAAAAATATTAT
1 TTTTATTAT-TAAATATTAT
513289 TTTTATTATTAAATA
1 TTTTATTATTAAATA
513304 ATAATTTAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 17
0.65 0.12 0.23
Matches are distributed among these distances:
14 10 0.21
15 2 0.04
16 3 0.06
17 7 0.15
18 2 0.04
19 17 0.35
20 7 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATTATTAAATATTAT
Found at i:513897 original size:17 final size:17
Alignment explanation
Indices: 513855--513906 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
513845 AAATAACTCG
*
513855 AAATCAAAATAATTT-A
1 AAATTAAAATAATTTAA
*
513871 AATTTAAAAATAATTTAA
1 AAATT-AAAATAATTTAA
*
513889 AAATTAAAA-AACTTAA
1 AAATTAAAATAATTTAA
513905 AA
1 AA
513907 TAATTCAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.37
17 14 0.47
18 5 0.17
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTAAAATAATTTAA
Found at i:513897 original size:18 final size:17
Alignment explanation
Indices: 513860--513898 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
513850 ACTCGAAATC
*
513860 AAAATAATTTAAATTTA
1 AAAATAATTTAAAATTA
513877 AAAATAATTTAAAAATTA
1 AAAATAATTT-AAAATTA
513895 AAAA
1 AAAA
513899 ACTTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATTTAAAATTA
Found at i:514123 original size:25 final size:25
Alignment explanation
Indices: 514093--514142 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
514083 CTATATCATA
*
514093 TTATTTTGATTCGAAAATGATTATT
1 TTATTTTAATTCGAAAATGATTATT
514118 TTATTTTAATTCGAAAATGATTATT
1 TTATTTTAATTCGAAAATGATTATT
514143 AATTATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.10, T:0.52
Consensus pattern (25 bp):
TTATTTTAATTCGAAAATGATTATT
Found at i:515199 original size:19 final size:20
Alignment explanation
Indices: 515172--515209 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
515162 ATCAAATACT
*
515172 AAATCAAATTATA-ATATAA
1 AAATAAAATTATATATATAA
515191 AAATAAAATTATATATATA
1 AAATAAAATTATATATATA
515210 TATAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAAATTATATATATAA
Found at i:518848 original size:16 final size:15
Alignment explanation
Indices: 518829--518895 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 15
518819 TATATTATAA
518829 TTATATTTAAAATATT
1 TTATATTTAAAA-ATT
518845 TTATATTTATATAAATT
1 TTATATTTA-A-AAATT
* **
518862 TAATATATTAATTA-T
1 TTATAT-TTAAAAATT
518877 TTATATTATAAAAATT
1 TTATATT-TAAAAATT
518893 TTA
1 TTA
518896 AAATATTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 1 0.03
15 10 0.25
16 14 0.35
17 10 0.25
18 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTTAAAAATT
Found at i:518896 original size:32 final size:32
Alignment explanation
Indices: 518839--518917 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
518829 TTATATTTAA
* *
518839 AATAT-TTTATATTTATATAAATTTAATATATT
1 AATATATTTATA-TTATAAAAATTTAAAATATT
518871 AAT-TATTTATATTATAAAAATTTTAAAATATT
1 AATATATTTATATTATAAAAA-TTTAAAATATT
*
518903 CATATATTTATATTA
1 AATATATTTATATTA
518918 ATTTTTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 9 0.22
32 21 0.51
33 11 0.27
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (32 bp):
AATATATTTATATTATAAAAATTTAAAATATT
Found at i:518929 original size:19 final size:19
Alignment explanation
Indices: 518905--518941 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
518895 AAAATATTCA
518905 TATATTTATATTA-ATTTTT
1 TATATTT-TATTATATTTTT
518924 TATATTTTATTATATTTT
1 TATATTTTATTATATTTT
518942 AATTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TATATTTTATTATATTTTT
Found at i:518936 original size:10 final size:10
Alignment explanation
Indices: 518905--518957 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 10
518895 AAAATATTCA
518905 TATATTTATAT
1 TATATTT-TAT
518916 TA-ATTTT-T
1 TATATTTTAT
518924 TATATTTTAT
1 TATATTTTAT
*
518934 TATATTTTAA
1 TATATTTTAT
518944 T-TATTTT-T
1 TATATTTTAT
518952 TATATT
1 TATATT
518958 ATATAATCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 4 0.11
9 16 0.43
10 15 0.41
11 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TATATTTTAT
Found at i:518949 original size:28 final size:32
Alignment explanation
Indices: 518899--518957 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 32
518889 AATTTTAAAA
518899 TATTCATATATTTATATTAATTTTTTATATTT
1 TATTCATATATTTATATTAATTTTTTATATTT
518931 TATT-ATAT-TTTA-ATT-ATTTTTTATATT
1 TATTCATATATTTATATTAATTTTTTATATT
518958 ATATAATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 12 0.44
29 3 0.11
30 4 0.15
31 4 0.15
32 4 0.15
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
TATTCATATATTTATATTAATTTTTTATATTT
Found at i:519110 original size:5 final size:5
Alignment explanation
Indices: 519100--519139 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
519090 TTAAAAATAA
*
519100 TAATT TAATT TAATT TAATT TAATT TAATT TTATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT
519140 AATAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:519193 original size:28 final size:29
Alignment explanation
Indices: 519175--519229 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
519165 TTAATTAAAA
519175 TATTAAT-ATAAAATAAATTTTTAAATAT
1 TATTAATAATAAAATAAATTTTTAAATAT
*
519203 TTTTAATAATAAAATAAATTTTTAAAT
1 TATTAATAATAAAATAAATTTTTAAAT
519230 CAATTTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTAATAATAAAATAAATTTTTAAATAT
Found at i:519816 original size:14 final size:15
Alignment explanation
Indices: 519736--519840 Score: 56
Period size: 15 Copynumber: 6.9 Consensus size: 15
519726 TGTTATTATA
*
519736 TATATAAATTTAATT
1 TATATAATTTTAATT
*
519751 TAT-TTATTTT-ATT
1 TATATAATTTTAATT
*
519764 ATATCATAATTAT-ATT
1 -TAT-ATAATTTTAATT
* * *
519780 TAAGATATTTTTTATT
1 T-ATATAATTTTAATT
519796 TATATAATTTTAATT
1 TATATAATTTTAATT
* *
519811 TA-ATAATAATTCATAT
1 TATATAAT-TTTAAT-T
519827 TATATAAATTTTAA
1 TATAT-AATTTTAA
519841 AAAATATATT
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
13 3 0.04
14 13 0.19
15 27 0.40
16 16 0.24
17 5 0.07
18 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (15 bp):
TATATAATTTTAATT
Found at i:519861 original size:11 final size:10
Alignment explanation
Indices: 519845--519896 Score: 61
Period size: 11 Copynumber: 5.0 Consensus size: 10
519835 TTTTAAAAAA
519845 TATATTCATAT
1 TATATT-ATAT
519856 TATATTATA-
1 TATATTATAT
*
519865 TATTTTATAT
1 TATATTATAT
519875 TATATATATAT
1 TATAT-TATAT
519886 TATATTCATAT
1 TATATT-ATAT
519897 AAATATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 8 0.22
10 8 0.22
11 20 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATTATAT
Found at i:519864 original size:16 final size:15
Alignment explanation
Indices: 519845--519896 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
519835 TTTTAAAAAA
519845 TATATTCATATTATAT
1 TATATT-ATATTATAT
*
519861 TATA-TATTTTATAT
1 TATATTATATTATAT
519875 TATATATATATTATAT
1 TATAT-TATATTATAT
519891 TCATAT
1 T-ATAT
519897 AAATATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 12 0.39
15 1 0.03
16 14 0.45
17 4 0.13
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTATATTATAT
Found at i:521805 original size:17 final size:17
Alignment explanation
Indices: 521785--521826 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
521775 AATAAATTAA
521785 ATATATTTATATTAAAT
1 ATATATTTATATTAAAT
* *
521802 ATATTTTTATATTTAAT
1 ATATATTTATATTAAAT
*
521819 ATTTATTT
1 ATATATTT
521827 GAATCTGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTTATATTAAAT
Found at i:523364 original size:2 final size:2
Alignment explanation
Indices: 523359--523383 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
523349 ATGTATATAT
523359 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
523384 AACTCCATCA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:524406 original size:15 final size:15
Alignment explanation
Indices: 524386--524436 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
524376 TATTAATTCA
524386 TATATTTTATTATAT
1 TATATTTTATTATAT
*
524401 TATATTTATATT-TAA
1 TATATTT-TATTATAT
*
524416 AATATTTTA-TAT-T
1 TATATTTTATTATAT
524429 TATATTTT
1 TATATTTT
524437 TTTAATATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 8 0.27
14 3 0.10
15 15 0.50
16 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTTATTATAT
Found at i:525568 original size:2 final size:2
Alignment explanation
Indices: 525561--525596 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
525551 ATTGGCATCA
*
525561 AT AT AT AT CT 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
525597 GAGATTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:527468 original size:14 final size:14
Alignment explanation
Indices: 527446--527487 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
527436 TAATAATGAT
*
527446 TAAATTTTAAAATA
1 TAAATTTTAAAAAA
*
527460 TATATTTTAAAAAA
1 TAAATTTTAAAAAA
*
527474 TAAATTATAAAAAA
1 TAAATTTTAAAAAA
527488 ATAATATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTTTAAAAAA
Found at i:527828 original size:14 final size:14
Alignment explanation
Indices: 527806--527850 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
527796 TAATAATGAT
*
527806 TAAATTTTAAAATA
1 TAAATTTTAAAAAA
*
527820 TATATTTTAAAAAA
1 TAAATTTTAAAAAA
*
527834 TAAATTATAAAAAA
1 TAAATTTTAAAAAA
527848 TAA
1 TAA
527851 TATGAATCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTTTAAAAAA
Found at i:527882 original size:359 final size:359
Alignment explanation
Indices: 527222--527918 Score: 1188
Period size: 359 Copynumber: 1.9 Consensus size: 359
527212 AAATAAGTTT
* * *
527222 TTTGCAAATGGGTCGGGCCTTTACTGCAACTTCCAAGGCCCAAGTCTTGCCCAATCTATTTTACT
1 TTTGCAAATGGGTCGGGCCTTTACTGCAACTTCCAAGGCCCAAGTCCTGACCAATCCATTTTACT
*
527287 ATTATATAATATTTATTAATTTTATATTTTATATGTCATGTAATTTTTATAAAATAAAAAATACA
66 ATTACATAATATTTATTAATTTTATATTTTATATGTCATGTAATTTTTATAAAATAAAAAATACA
527352 TATATGTAATATTATAATATAAACATTAAAAACTTGGTTAAATTATTTATAATTTTTTAACTTAA
131 TATATGTAATATTATAATATAAACATTAAAAACTTGGTTAAATTATTTATAATTTTTTAACTTAA
527417 TAAAAGAAAATTATTAAATTAATAATGATTAAATTTTAAAATATATATTTTAAAAAATAAATTAT
196 TAAAAGAAAATTATTAAATTAATAATGATTAAATTTTAAAATATATATTTTAAAAAATAAATTAT
*
527482 AAAAAAATAATATGAACTGACCTAAACGAACTTTGACTATCTATTTATAAATATAAACGAACATA
261 AAAAAAATAATATGAACTGACCTAAACGAACTTTAACTATCTATTTATAAATATAAACGAACATA
527547 AATAAAATTCAAAACTCATAAAAAAAATAAACTC
326 AATAAAATTCAAAACTCATAAAAAAAATAAACTC
* * * *
527581 TTTGCAAATGGGTCGGGCTTTTACTGTAACTTCCAAGGCCCAAGTCCT-ACTAGGTCCATTTTAC
1 TTTGCAAATGGGTCGGGCCTTTACTGCAACTTCCAAGGCCCAAGTCCTGACCA-ATCCATTTTAC
527645 TATTACATAATATTTATTAATTTTATATTTTATATGTCATGTAATTTTTATAAAATAAAAAATAT
65 TATTACATAATATTTATTAATTTTATATTTTATATGTCATGTAATTTTTATAAAAT-AAAAA-AT
* *
527710 ATATATATGTAATATTATAATATAAACATTAAAAACTTGG-TAAATTATTTAT-ATTTGTTTGAC
128 ACATATATGTAATATTATAATATAAACATTAAAAACTTGGTTAAATTATTTATAATTT-TTTAAC
527773 TTAATAAAAGAAAATTATTAAATTAATAATGATTAAATTTTAAAATATATATTTTAAAAAATAAA
192 TTAATAAAAGAAAATTATTAAATTAATAATGATTAAATTTTAAAATATATATTTTAAAAAATAAA
* **
527838 TTAT-AAAAAATAATATGAA-TCGACCTAAACTAACTTTAACTATCTATTTATAAATATGGACGA
257 TTATAAAAAAATAATATGAACT-GACCTAAACGAACTTTAACTATCTATTTATAAATATAAACGA
527901 ACATAAATAAAATTCAAA
321 ACATAAATAAAATTCAAA
527919 GCCTATATTT
Statistics
Matches: 319, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
358 3 0.01
359 184 0.58
360 91 0.29
361 41 0.13
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (359 bp):
TTTGCAAATGGGTCGGGCCTTTACTGCAACTTCCAAGGCCCAAGTCCTGACCAATCCATTTTACT
ATTACATAATATTTATTAATTTTATATTTTATATGTCATGTAATTTTTATAAAATAAAAAATACA
TATATGTAATATTATAATATAAACATTAAAAACTTGGTTAAATTATTTATAATTTTTTAACTTAA
TAAAAGAAAATTATTAAATTAATAATGATTAAATTTTAAAATATATATTTTAAAAAATAAATTAT
AAAAAAATAATATGAACTGACCTAAACGAACTTTAACTATCTATTTATAAATATAAACGAACATA
AATAAAATTCAAAACTCATAAAAAAAATAAACTC
Found at i:528402 original size:2 final size:2
Alignment explanation
Indices: 528395--528461 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
528385 TTCTCTTTTC
528395 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
528437 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
528462 AAAGTGGATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:528514 original size:19 final size:19
Alignment explanation
Indices: 528490--528529 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
528480 ATACAAGAGA
528490 TTTTATAC-ATTTTATAATT
1 TTTTATACGATTTTAT-ATT
528509 TTTTATACGATTTTATATT
1 TTTTATACGATTTTATATT
528528 TT
1 TT
528530 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTATACGATTTTATATT
Found at i:530907 original size:2 final size:2
Alignment explanation
Indices: 530894--530929 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
530884 GTAGAACACC
*
530894 AT AT AT AA 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
530930 GCTTAATCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:532740 original size:2 final size:2
Alignment explanation
Indices: 532729--532768 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
532719 ATGACTTATT
*
532729 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
532769 TATGCATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:539685 original size:7 final size:7
Alignment explanation
Indices: 539659--539699 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
539649 TAAAATATTT
*
539659 ATTTAAT
1 ATTTAAA
539666 ATTATAAA
1 ATT-TAAA
539674 A-TTAAA
1 ATTTAAA
539680 ATTTAAA
1 ATTTAAA
539687 ATTTAAA
1 ATTTAAA
539694 ATTTAA
1 ATTTAA
539700 TTTAATTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 5 0.16
7 22 0.71
8 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:539818 original size:21 final size:22
Alignment explanation
Indices: 539780--539821 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
539770 TTTAATTATT
* *
539780 ATTTGAATTAAAATCAAATTAA
1 ATTTGAATAAAAACCAAATTAA
539802 ATTT-AATAAAAACCAAATTA
1 ATTTGAATAAAAACCAAATTA
539822 CAAAAGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTTGAATAAAAACCAAATTAA
Found at i:540905 original size:16 final size:16
Alignment explanation
Indices: 540856--540906 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
540846 ATGTAAATCT
* *
540856 TAAAATTTATATAATA
1 TAAAATTAATATAAAA
540872 TAAATTATTAATAT--AA
1 TAAA--ATTAATATAAAA
540888 TAAAATTAATATAAAA
1 TAAAATTAATATAAAA
540904 TAA
1 TAA
540907 TATATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.28
16 14 0.48
18 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATTAATATAAAA
Found at i:541114 original size:11 final size:12
Alignment explanation
Indices: 541081--541106 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
541071 CAATAATTTC
541081 AAATATGATATA
1 AAATATGATATA
541093 AAATATGATATA
1 AAATATGATATA
541105 AA
1 AA
541107 TATTATATGT
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AAATATGATATA
Found at i:542761 original size:16 final size:17
Alignment explanation
Indices: 542728--542762 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
542718 GTTTGATAAA
542728 TCATTAAAAATTATTAAT
1 TCATTAAAAA-TATTAAT
542746 TCATTAAAAA-ATTAAT
1 TCATTAAAAATATTAAT
542762 T
1 T
542763 TAGACATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TCATTAAAAATATTAAT
Found at i:543742 original size:16 final size:16
Alignment explanation
Indices: 543718--543802 Score: 107
Period size: 16 Copynumber: 5.2 Consensus size: 16
543708 TTAATTAAAT
*
543718 TTTTTAATTATTTTAA
1 TTTTAAATTATTTTAA
543734 TTTTAAATTATTTTAA
1 TTTTAAATTATTTTAA
* * *
543750 GTTTGATTTATTTTAA
1 TTTTAAATTATTTTAA
*
543766 ATTTAAATTATTTTAA
1 TTTTAAATTATTTTAA
*
543782 TTTTATATTATTTTAAA
1 TTTTAAATTATTTT-AA
543799 TTTT
1 TTTT
543803 GATTAATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
16 53 0.90
17 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTAAATTATTTTAA
Found at i:543771 original size:32 final size:31
Alignment explanation
Indices: 543725--543801 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 31
543715 AATTTTTTAA
*
543725 TTATTTTAATTTTAAATTATTTTAAGTTTGAT
1 TTATTTTAAATTTAAATTATTTTAA-TTTGAT
*
543757 TTATTTTAAATTTAAATTATTTTAATTTTAT
1 TTATTTTAAATTTAAATTATTTTAATTTGAT
543788 ATTATTTTAAATTT
1 -TTATTTTAAATTT
543802 TGATTAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 5 0.12
32 37 0.88
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TTATTTTAAATTTAAATTATTTTAATTTGAT
Found at i:543807 original size:16 final size:15
Alignment explanation
Indices: 543702--543807 Score: 99
Period size: 16 Copynumber: 6.9 Consensus size: 15
543692 GTCCGTCAAA
**
543702 TTAATTTTAATTAAA
1 TTAATTTTAATTATT
543717 TT--TTTTAATTATT
1 TTAATTTTAATTATT
543730 TTAATTTTAAATTATT
1 TTAATTTT-AATTATT
* *
543746 TTAAGTTTGATTTATT
1 TTAA-TTTTAATTATT
*
543762 TTAAATTTAAATTATT
1 TT-AATTTTAATTATT
543778 TTAATTTTATATTATT
1 TTAATTTTA-ATTATT
*
543794 TTAAATTTTGATTA
1 TT-AATTTTAATTA
543808 ATTAAGTTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
13 11 0.14
15 12 0.16
16 42 0.55
17 11 0.14
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTAATTTTAATTATT
Found at i:543822 original size:32 final size:33
Alignment explanation
Indices: 543724--543822 Score: 114
Period size: 32 Copynumber: 3.1 Consensus size: 33
543714 AAATTTTTTA
* * *
543724 ATTATTTTAATTTTAAATTATTTTAAGTTTGAT
1 ATTATTTTAAATTTAAATTATATTAAGTTTAAT
* *
543757 -TTATTTTAAATTTAAATTATTTTAA-TTTTAT
1 ATTATTTTAAATTTAAATTATATTAAGTTTAAT
**
543788 ATTATTTTAAATTTTGATTA-ATTAAGTTTAAT
1 ATTATTTTAAATTTAAATTATATTAAGTTTAAT
543820 ATT
1 ATT
543823 TAAGTTATCA
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
31 9 0.16
32 49 0.84
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (33 bp):
ATTATTTTAAATTTAAATTATATTAAGTTTAAT
Found at i:543843 original size:68 final size:70
Alignment explanation
Indices: 543764--543913 Score: 182
Period size: 69 Copynumber: 2.2 Consensus size: 70
543754 GATTTATTTT
* * * * *
543764 AAATTTAAATTATT-TTAATTTTATATTATTTTAAA-TTTTGA-TTAATTAAGTTTAATATTTAA
1 AAATTTAAATTATTCTTAATTTGA-ATTA-TTTAAAGATTTGAGTCAATCAAATTTAATATTTAA
*
543826 GTT-ATC
64 ATTAATC
543832 AAATTTAAATTATTCTTAATTTGAATTATTTAAAGATTTGAGTCAATCAAATTTAATATTTAAAT
1 AAATTTAAATTATTCTTAATTTGAATTATTTAAAGATTTGAGTCAATCAAATTTAATATTTAAAT
*
543897 TAATT
66 TAATC
*
543902 AAGTTTAAATTA
1 AAATTTAAATTA
543914 ATTAAGTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
67 6 0.09
68 23 0.33
69 28 0.40
70 13 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (70 bp):
AAATTTAAATTATTCTTAATTTGAATTATTTAAAGATTTGAGTCAATCAAATTTAATATTTAAAT
TAATC
Found at i:543853 original size:52 final size:51
Alignment explanation
Indices: 543783--543969 Score: 148
Period size: 52 Copynumber: 3.5 Consensus size: 51
543773 TTATTTTAAT
* **
543783 TTTATATTATTTTAAATTTTGATTAATTAAGTTTAATATTTAAGTTATCAAA
1 TTTAAATTATTTT-AATTTAAATTAATTAAGTTTAATATTTAAGTTATCAAA
* * * * * *
543835 TTTAAATTATTCTTAATTTGAATTATTTAAAGATTTGAGTCAATCAAATT-T-AATA
1 TTTAAATTATT-TTAATTTAAATTAATT-AAG-TTT-AAT-ATTTAAGTTATCAA-A
* * *
543890 TTTAAATTA-ATTAAGTTTAAATTAATTAAGTTTAATATTTAAGTTTATCGAG
1 TTTAAATTATTTTAA-TTTAAATTAATTAAGTTTAATATTTAAG-TTATCAAA
543942 TTT-AATTATTTTTAATTTAAATTAATTA
1 TTTAAATTA-TTTTAATTTAAATTAATTA
543970 TTCGAATCAT
Statistics
Matches: 105, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
50 4 0.04
51 9 0.09
52 41 0.39
53 17 0.16
54 15 0.14
55 13 0.12
56 6 0.06
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (51 bp):
TTTAAATTATTTTAATTTAAATTAATTAAGTTTAATATTTAAGTTATCAAA
Found at i:543910 original size:15 final size:15
Alignment explanation
Indices: 543890--543936 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
543880 AAATTTAATA
543890 TTTAAATTAATTAAG
1 TTTAAATTAATTAAG
543905 TTTAAATTAATTAAG
1 TTTAAATTAATTAAG
*
543920 TTT-AA-TATTTAAG
1 TTTAAATTAATTAAG
543933 TTTA
1 TTTA
543937 TCGAGTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 18 0.60
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
TTTAAATTAATTAAG
Found at i:543961 original size:37 final size:36
Alignment explanation
Indices: 543881--543967 Score: 87
Period size: 37 Copynumber: 2.6 Consensus size: 36
543871 GAGTCAATCA
*
543881 AATTTAATATTTAAATTAATTAAGTTTAAATTAATT
1 AATTTAATATTTAAATTAATCAAGTTTAAATTAATT
* * *
543917 AAGTTTAATATTTAAGTTTATCGAGTTT-AATT-ATT
1 AA-TTTAATATTTAAATTAATCAAGTTTAAATTAATT
543952 --TTT-A-ATTTAAATTAAT
1 AATTTAATATTTAAATTAAT
543968 TATTCGAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
30 10 0.23
31 1 0.02
32 3 0.07
35 3 0.07
36 6 0.14
37 21 0.48
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (36 bp):
AATTTAATATTTAAATTAATCAAGTTTAAATTAATT
Found at i:545282 original size:29 final size:28
Alignment explanation
Indices: 545225--545284 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
545215 TTAACGAGCC
*
545225 TAACTATTTTTTTAATTATTATATATAA
1 TAACTATTTTTTTAATTATTATAAATAA
545253 TAAC-ATTTTTATCTAATATATTA-AAATAA
1 TAACTATTTTT-T-TAAT-TATTATAAATAA
545282 TAA
1 TAA
545285 TTTTTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.21
28 5 0.18
29 12 0.43
30 5 0.18
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (28 bp):
TAACTATTTTTTTAATTATTATAAATAA
Found at i:551385 original size:2 final size:2
Alignment explanation
Indices: 551378--551405 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
551368 CAAACTGTGA
551378 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
551406 TTTCAACATC
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:557117 original size:16 final size:16
Alignment explanation
Indices: 557091--557164 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
557081 TTAATTAGTC
557091 AAATCATTTTAAATTTT
1 AAAT-ATTTTAAATTTT
557108 AAATATTTT--ATTTT
1 AAATATTTTAAATTTT
* *
557122 --AT-TTTTTAA-TTC
1 AAATATTTTAAATTTT
557134 AAATCATTTTAAA-TTT
1 AAAT-ATTTTAAATTTT
557150 AAATTATTTTAAATT
1 AAA-TATTTTAAATT
557165 CGGATCAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 1 0.02
14 7 0.15
16 24 0.52
17 6 0.13
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTAAATTTT
Found at i:557552 original size:2 final size:2
Alignment explanation
Indices: 557547--557580 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
557537 AGTCTGCATT
557547 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
557581 TGGTGAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:563263 original size:17 final size:17
Alignment explanation
Indices: 563238--563277 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
563228 TGAGATTATT
563238 TTAAAAATTTATAAATA
1 TTAAAAATTTATAAATA
* *
563255 TTAATAATTTTTAAATA
1 TTAAAAATTTATAAATA
*
563272 ATAAAA
1 TTAAAA
563278 TAAATTTACG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAATTTATAAATA
Found at i:564925 original size:19 final size:19
Alignment explanation
Indices: 564903--564945 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
564893 TATCAACTCA
*
564903 TATATAA-ATTATATCATCT
1 TATATAATATTATATC-TAT
564922 TATA-AATATTATATCTAT
1 TATATAATATTATATCTAT
564940 TATATA
1 TATATA
564946 TTAAAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATAATATTATATCTAT
Found at i:566013 original size:21 final size:21
Alignment explanation
Indices: 565976--566015 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
565966 GTTATGTTAA
*
565976 TATTTATTACTATAAAATAAT
1 TATTTATTAATATAAAATAAT
565997 TATTTATTTAATA-AAAATA
1 TATTTA-TTAATATAAAATA
566016 TTGTTATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTATTAATATAAAATAAT
Found at i:566957 original size:44 final size:45
Alignment explanation
Indices: 566879--566980 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 45
566869 ATATTTTATG
* * *
566879 TTATATTTTTGAATAATTTTATATATTTTAATTATATTTAAATATT
1 TTATATTTTTGAATAATTTTATATAATATAATTATATATAAAT-TT
566925 TTATATTTTT-AA-AATTTTA-ATAATATATATTATATATAAATTT
1 TTATATTTTTGAATAATTTTATATAATATA-ATTATATATAAATTT
566968 TAATATATTTTTG
1 T--TATATTTTTG
566981 TAATTATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
43 9 0.18
44 19 0.39
45 11 0.22
46 10 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (45 bp):
TTATATTTTTGAATAATTTTATATAATATAATTATATATAAATTT
Found at i:567011 original size:18 final size:19
Alignment explanation
Indices: 566981--567016 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
566971 TATATTTTTG
566981 TAATTATATTTTTTTATTT
1 TAATTATATTTTTTTATTT
567000 TAATTA-ATTTTTTTATT
1 TAATTATATTTTTTTATT
567017 ATATGACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TAATTATATTTTTTTATTT
Found at i:567164 original size:2 final size:2
Alignment explanation
Indices: 567157--567189 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
567147 CAAACGAAAA
567157 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
567190 ACTTTGAAAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:573847 original size:3 final size:3
Alignment explanation
Indices: 573839--573864 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
573829 AGCAAAAGTA
573839 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
573865 AAGTCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:581786 original size:11 final size:11
Alignment explanation
Indices: 581770--581804 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
581760 TCGATCAAGG
581770 TTTCTTCCAGT
1 TTTCTTCCAGT
581781 TTTCTTCAGCAGT
1 TTTCTTC--CAGT
581794 TTTCTTCCAGT
1 TTTCTTCCAGT
581805 CCAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.11, C:0.26, G:0.11, T:0.51
Consensus pattern (11 bp):
TTTCTTCCAGT
Found at i:587642 original size:13 final size:13
Alignment explanation
Indices: 587624--587650 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
587614 TTCCATGTGC
587624 TACCAGTCATTCA
1 TACCAGTCATTCA
587637 TACCAGTCATTCA
1 TACCAGTCATTCA
587650 T
1 T
587651 CTAGAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (13 bp):
TACCAGTCATTCA
Found at i:591298 original size:44 final size:44
Alignment explanation
Indices: 591234--591331 Score: 178
Period size: 44 Copynumber: 2.2 Consensus size: 44
591224 TGATGAGATG
591234 GAAATCTTTTAACTTAATTCAACAGTCCCTGGTTGTTCACTGGCT
1 GAAAT-TTTTAACTTAATTCAACAGTCCCTGGTTGTTCACTGGCT
*
591279 GAAATTTTTAACTTAATTCAACAGTCCCTGGTTTTTCACTGGCT
1 GAAATTTTTAACTTAATTCAACAGTCCCTGGTTGTTCACTGGCT
591323 GAAATTTTT
1 GAAATTTTT
591332 TGGATGGCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 47 0.90
45 5 0.10
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (44 bp):
GAAATTTTTAACTTAATTCAACAGTCCCTGGTTGTTCACTGGCT
Found at i:594472 original size:11 final size:11
Alignment explanation
Indices: 594456--594497 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
594446 TAATATCAAA
594456 ATTTAATATTT
1 ATTTAATATTT
594467 ATTTAAT-TTAT
1 ATTTAATATT-T
* *
594478 AATTAATTTTT
1 ATTTAATATTT
594489 ATTTAATAT
1 ATTTAATAT
594498 AATATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.08
11 22 0.85
12 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTAATATTT
Found at i:595015 original size:28 final size:27
Alignment explanation
Indices: 594976--595028 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
594966 AAAAATATAT
594976 ATTTTTATAATTATTAAATATCAATAA
1 ATTTTTATAATTATTAAATATCAATAA
595003 ATTTTTATTAATTATTAAATATCAAT
1 ATTTTTA-TAATTATTAAATATCAAT
595029 TTGGCGGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTTTATAATTATTAAATATCAATAA
Found at i:596519 original size:15 final size:16
Alignment explanation
Indices: 596499--596567 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
596489 ATTCAATCTA
596499 TAAATAA-ATTTATAT
1 TAAATAATATTTATAT
596514 TAAATAAATATTTATAT
1 TAAAT-AATATTTATAT
* * * *
596531 TCAATACTCATATAAATT
1 TAAATAAT-ATTTATA-T
*
596549 TAAATAATATAT-TAT
1 TAAATAATATTTATAT
596564 TAAA
1 TAAA
596568 AAAAACTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 10 0.23
16 5 0.12
17 21 0.49
18 7 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATAATATTTATAT
Found at i:597530 original size:20 final size:19
Alignment explanation
Indices: 597500--597538 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
597490 ATTTAAATAT
597500 ATTTTTTATTTTATTTTTA
1 ATTTTTTATTTTATTTTTA
597519 ATTTTTTAATTTTATTTTTA
1 ATTTTTT-ATTTTATTTTTA
597539 TTATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTTATTTTATTTTTA
Found at i:597596 original size:22 final size:21
Alignment explanation
Indices: 597568--597611 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
597558 AAATTTTAAA
597568 ATATATTTT-TATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
597590 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
597611 A
1 A
597612 AATAAAAATA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:599435 original size:20 final size:20
Alignment explanation
Indices: 599405--599456 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
599395 TAAGTTATTT
*
599405 ATATT-TTAAAATTTAATAAA
1 ATATTATTAAAAATTAA-AAA
599425 A-ATTATTAAAAATTAAAAA
1 ATATTATTAAAAATTAAAAA
*
599444 ATATTTTTAAAAA
1 ATATTATTAAAAA
599457 ATATAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTATTAAAAATTAAAAA
Found at i:599526 original size:16 final size:16
Alignment explanation
Indices: 599500--599547 Score: 71
Period size: 16 Copynumber: 2.9 Consensus size: 16
599490 TTAATATAAA
599500 TAAATTTAAATTAAATT
1 TAAA-TTAAATTAAATT
599517 TAAATTAAATTAAATT
1 TAAATTAAATTAAATT
599533 TAAA-TAAATATAAAT
1 TAAATTAAAT-TAAAT
599548 ATAATTACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTAAATTAAATT
Found at i:599551 original size:6 final size:5
Alignment explanation
Indices: 599496--599547 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 5
599486 TTTATTAATA
599496 TAAA- TAAATT TAAAT TAAATT TAAAT TAAAT TAAATT TAAA- TAAAT
1 TAAAT TAAA-T TAAAT TAAA-T TAAAT TAAAT TAAA-T TAAAT TAAAT
599542 ATAAAT
1 -TAAAT
599548 ATAATTACGT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 8 0.19
5 15 0.36
6 19 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:600692 original size:35 final size:35
Alignment explanation
Indices: 600646--600712 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
600636 AGGCATAGAA
600646 CTTTTATTTACATTTGATTGTACATTATTCTTCAT
1 CTTTTATTTACATTTGATTGTACATTATTCTTCAT
600681 CTTTTATTTACATTTGATTGTACATTATTCTT
1 CTTTTATTTACATTTGATTGTACATTATTCTT
600713 TATAGCACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.22, C:0.13, G:0.06, T:0.58
Consensus pattern (35 bp):
CTTTTATTTACATTTGATTGTACATTATTCTTCAT
Found at i:603584 original size:128 final size:127
Alignment explanation
Indices: 603344--603654 Score: 327
Period size: 128 Copynumber: 2.5 Consensus size: 127
603334 AAATAATCTG
* * **
603344 GGTAACGTAGTCTTGAGCATATAACTTGATATGACTTGAACCTAATAGCTCCTTTGTCTATGCGT
1 GGTAACATAGTCTTAAGCATATAACTTGATATGACTTGAACCTAATAGCTCCTTCATCTATGCGT
* *
603409 GAAAGAGCAAATATGTGTCTGACATAAATGTTAGATATTTAAAAAAAATAAATAAAGAGTTCA
66 GAAAGAGCAAATATGTGTATGACATAAAAGTTA-ATATTTAAAAAAAATAAATAAAGAGTTCA
* * * *
603472 GGTAACATAGTTTTAAGCATATAACTTGCTATGGCTTGAACCCT-ATAGCTCCTTCATCTATGCT
1 GGTAACATAGTCTTAAGCATATAACTTGATATGACTTGAA-CCTAATAGCTCCTTCATCTATGCG
* * * *
603536 TGAAAGAGCAAATATGTGTATGTCGGATAACAAG-T-AT-TTT-----AAATAAAAAAAGAATCC
65 TGAAAGAGCAAATATGTGTATGAC--ATAA-AAGTTAATATTTAAAAAAAATAAATAAAGAGTTC
603593 TA
127 -A
* * * **
603595 -GTAACATAATCTTGAGCATATAACTTGATATGACTTGAACCTGATAGCTAATTCATCTAT
1 GGTAACATAGTCTTAAGCATATAACTTGATATGACTTGAACCTAATAGCTCCTTCATCTAT
603655 ATGCATGAAA
Statistics
Matches: 156, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
121 3 0.02
122 63 0.40
123 1 0.01
127 3 0.02
128 76 0.49
129 3 0.02
130 5 0.03
131 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (127 bp):
GGTAACATAGTCTTAAGCATATAACTTGATATGACTTGAACCTAATAGCTCCTTCATCTATGCGT
GAAAGAGCAAATATGTGTATGACATAAAAGTTAATATTTAAAAAAAATAAATAAAGAGTTCA
Found at i:605720 original size:32 final size:32
Alignment explanation
Indices: 605684--605753 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
605674 TATTATTATT
*
605684 TTATATAAATATTGACACATAAATAATTTAAA
1 TTATATAAATATTAACACATAAATAATTTAAA
* ** **
605716 TTATATAAATTTTAACACATTTATAATTTTTA
1 TTATATAAATATTAACACATAAATAATTTAAA
605748 TTATAT
1 TTATAT
605754 TCATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (32 bp):
TTATATAAATATTAACACATAAATAATTTAAA
Found at i:605766 original size:20 final size:20
Alignment explanation
Indices: 605741--605798 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 20
605731 CACATTTATA
605741 ATTTTTATTATATTCATAA-T
1 ATTTTTATTATATT-ATAATT
*
605761 ATTTTTCATATTATATTTTAATT
1 A-TTTT--TATTATATTATAATT
605784 ATTTTTATTATATTA
1 ATTTTTATTATATTA
605799 ATGTAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 10 0.31
21 4 0.12
22 7 0.22
23 11 0.34
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTATTATATTATAATT
Found at i:606542 original size:2 final size:2
Alignment explanation
Indices: 606535--606574 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
606525 TTCAATTTGT
606535 TA TA TA TA TA TA TA TA TA TA TA 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
606575 ATTTTGGTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:608185 original size:3 final size:3
Alignment explanation
Indices: 608177--608203 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
608167 AATTTAGTTA
608177 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
608204 TTTTGGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:611436 original size:2 final size:2
Alignment explanation
Indices: 611431--611465 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
611421 TATATATATA
611431 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
611466 TTGTACATTT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:615860 original size:20 final size:21
Alignment explanation
Indices: 615823--615862 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
615813 AAAACATTGA
* *
615823 AAATAAATATTTTTAATTAAT
1 AAATAAATAATTTAAATTAAT
615844 AAAT-AATAATTTAAATTAA
1 AAATAAATAATTTAAATTAA
615863 ATCAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATAATTTAAATTAAT
Found at i:615884 original size:15 final size:15
Alignment explanation
Indices: 615851--615886 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
615841 AATAAATAAT
**
615851 AATTTAAATTAAATC
1 AATTTAAATTAAAAA
615866 AATTTAAATTAAAAA
1 AATTTAAATTAAAAA
615881 AATTTA
1 AATTTA
615887 TTTATGTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTTAAATTAAAAA
Found at i:616203 original size:32 final size:33
Alignment explanation
Indices: 616147--616222 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
616137 TTATACGAAA
*
616147 ATAATATAAATATATTAATGTAT-AAAATTTAAT
1 ATAATATAAATATATTAATATATAAAAATTT-AT
616180 ATAATATAAAT-TATTAATATATAAAAATTTAT
1 ATAATATAAATATATTAATATATAAAAATTTAT
616212 ATAAATATAAA
1 AT-AATATAAA
616223 AATTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 14 0.35
33 26 0.65
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (33 bp):
ATAATATAAATATATTAATATATAAAAATTTAT
Found at i:616211 original size:18 final size:18
Alignment explanation
Indices: 616154--616231 Score: 69
Period size: 18 Copynumber: 4.6 Consensus size: 18
616144 AAAATAATAT
* *
616154 AAATATATTAATGTAT-A
1 AAATTTATTAATATATAA
* *
616171 AAATTTAAT-ATA-ATAT
1 AAATTTATTAATATATAA
616187 AAA-TTATTAATATATAA
1 AAATTTATTAATATATAA
616204 AAATTTATATAA-ATATAA
1 AAATTTAT-TAATATATAA
616222 AAATTT-TTAA
1 AAATTTATTAA
616232 ATAGGATTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
15 6 0.12
16 11 0.22
17 14 0.28
18 16 0.32
19 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
AAATTTATTAATATATAA
Found at i:616221 original size:38 final size:38
Alignment explanation
Indices: 616134--616221 Score: 91
Period size: 33 Copynumber: 2.4 Consensus size: 38
616124 GAAAATGCTT
* *
616134 AATTTATACGAAA-ATAATATAAATATATTAATGTATAA
1 AATTTATA-TAAATATAATATAAATATATTAATATATAA
616172 AA--T-T-T-AATATAATATAAAT-TATTAATATATAAA
1 AATTTATATAAATATAATATAAATATATTAATATAT-AA
616205 AATTTATATAAATATAA
1 AATTTATATAAATATAA
616222 AAATTTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
32 12 0.29
33 15 0.37
35 2 0.05
36 2 0.05
37 1 0.02
38 9 0.22
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (38 bp):
AATTTATATAAATATAATATAAATATATTAATATATAA
Found at i:616364 original size:17 final size:19
Alignment explanation
Indices: 616339--616397 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 19
616329 GGATAAATAG
*
616339 ATTTTTTTATA-T-TTTTA
1 ATTTATTTATATTATTTTA
616356 ATTTATTTATATTATTTTA
1 ATTTATTTATATTATTTTA
*
616375 ATTTTTATTTA-ATTAATTTA
1 A--TTTATTTATATTATTTTA
616395 ATT
1 ATT
616398 AAAAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 10 0.28
18 3 0.08
19 6 0.17
20 9 0.25
21 8 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTATTTATATTATTTTA
Found at i:616389 original size:20 final size:21
Alignment explanation
Indices: 616357--616397 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
616347 ATATTTTTAA
*
616357 TTTATTTATATTATTTTAATT
1 TTTATTTATATTAATTTAATT
616378 TTTATTTA-ATTAATTTAATT
1 TTTATTTATATTAATTTAATT
616398 AAAAAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTATATTAATTTAATT
Found at i:618341 original size:45 final size:45
Alignment explanation
Indices: 618277--618439 Score: 245
Period size: 45 Copynumber: 3.6 Consensus size: 45
618267 TATCATGTTG
* *
618277 AATGGGTTAGGCCTTCGAGTCCGGTTAGGTACCATGCCGAAGAAA
1 AATGGGTTAGGCCTTCGAGTCCGGTTCGGTACCATGCCGAAGAGA
*
618322 AATGGGTTAGGCCTTCGAGTCCGATTCGGTACCATGCCGAAGAGA
1 AATGGGTTAGGCCTTCGAGTCCGGTTCGGTACCATGCCGAAGAGA
* * * ** *
618367 AATGGGTTAGACCTTCGAGTCCGGTTCGTTGCCATGGTGAACAGA
1 AATGGGTTAGGCCTTCGAGTCCGGTTCGGTACCATGCCGAAGAGA
618412 AATGGGTTAGGCCTTCGAGTCCGGTTCG
1 AATGGGTTAGGCCTTCGAGTCCGGTTCG
618440 ATCCATTAGG
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 107 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (45 bp):
AATGGGTTAGGCCTTCGAGTCCGGTTCGGTACCATGCCGAAGAGA
Found at i:619062 original size:32 final size:32
Alignment explanation
Indices: 619026--619088 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
619016 ATACGAATCG
* * *
619026 ATAATTATTATATAATATTAAAA-AATATTTTA
1 ATAATTATAATA-AATAATAAAATAAAATTTTA
619058 ATAATTATAATAAATAATAAAATAAAATTTT
1 ATAATTATAATAAATAATAAAATAAAATTTT
619089 TAATCAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATAATTATAATAAATAATAAAATAAAATTTTA
Found at i:619389 original size:17 final size:19
Alignment explanation
Indices: 619336--619428 Score: 74
Period size: 18 Copynumber: 5.1 Consensus size: 19
619326 CATAAATCTA
*
619336 AATTATTT-TTTATTATTT
1 AATTATTTATTTAATATTT
619354 AATTATTTA-TT-ATATTT
1 AATTATTTATTTAATATTT
*
619371 AA-TATTTATTTAATATTAA
1 AATTATTTATTTAATATT-T
619390 AATTAATTT-TTTAAATATTT
1 AATT-ATTTATTT-AATATTT
*
619410 AA-AATTTCATTTAA-ATTT
1 AATTATTT-ATTTAATATTT
619428 A
1 A
619429 TTAACAAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
16 6 0.10
17 9 0.15
18 24 0.39
19 4 0.06
20 9 0.15
21 10 0.16
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTATTTATTTAATATTT
Found at i:619406 original size:21 final size:22
Alignment explanation
Indices: 619374--619415 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
619364 TATATTTAAT
619374 ATTTATTTAATA-TTAAAATTA
1 ATTTATTTAATATTTAAAATTA
619395 ATTT-TTTAAATATTTAAAATT
1 ATTTATTT-AATATTTAAAATT
619416 TCATTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTATTTAATATTTAAAATTA
Found at i:620943 original size:16 final size:16
Alignment explanation
Indices: 620924--620955 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
620914 TTAGAAACTG
620924 TAGGAAAAGGAAAGAA
1 TAGGAAAAGGAAAGAA
620940 TAGGAAAAGGAAAGAA
1 TAGGAAAAGGAAAGAA
620956 AATGTAAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (16 bp):
TAGGAAAAGGAAAGAA
Found at i:622080 original size:3 final size:3
Alignment explanation
Indices: 622072--622100 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
622062 ACCAAGAAAC
622072 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
622101 GGTGAGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:623264 original size:71 final size:70
Alignment explanation
Indices: 623209--623351 Score: 164
Period size: 71 Copynumber: 2.0 Consensus size: 70
623199 AGATTTTAAC
* * * * *
623209 TTTA-AATTTAAAATTTAATTAA-ATTAAATTATGTAATTAAAAATTTAAATCATAATATTTATA
1 TTTACAATTCAAAACTTAATTAATA-TAAATTATATAATTAAAAATTTAAATCATAATATCTACA
623272 AATTTT
65 AATTTT
* * * *
623278 TTTACTAATTCAAAACTTAATTTATATAACTTATATAATTAAAAATTTAAATCATAATATATATA
1 TTTAC-AATTCAAAACTTAATTAATATAAATTATATAATTAAAAATTTAAATCATAATATCTACA
*
623343 ATTTTT
65 AATTTT
623349 TTT
1 TTT
623352 CTAACTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
69 4 0.06
71 59 0.92
72 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (70 bp):
TTTACAATTCAAAACTTAATTAATATAAATTATATAATTAAAAATTTAAATCATAATATCTACAA
ATTTT
Found at i:623274 original size:37 final size:36
Alignment explanation
Indices: 623233--623343 Score: 102
Period size: 37 Copynumber: 3.1 Consensus size: 36
623223 TTAATTAAAT
623233 TAAATTATGTAATTAAAAATTTAAATCATAATATTTA
1 TAAATTAT-TAATTAAAAATTTAAATCATAATATTTA
* ** * * *
623270 TAAATT-TT-TTTACTAATTCAAAACTTAAT-TTATA
1 TAAATTATTAATTAAAAATTTAAATCATAATATT-TA
* *
623304 TAACTTATATAATTAAAAATTTAAATCATAATATATA
1 TAAATTAT-TAATTAAAAATTTAAATCATAATATTTA
623341 TAA
1 TAA
623344 TTTTTTTTCT
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
33 2 0.04
34 22 0.40
35 2 0.04
36 2 0.04
37 26 0.47
38 1 0.02
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (36 bp):
TAAATTATTAATTAAAAATTTAAATCATAATATTTA
Found at i:625460 original size:2 final size:2
Alignment explanation
Indices: 625453--625477 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
625443 CCACTTGCTT
625453 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
625478 TCTTTTTTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:630129 original size:2 final size:2
Alignment explanation
Indices: 630122--630153 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
630112 AAGGGTTGGA
630122 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
630154 TTACAATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:630352 original size:3 final size:3
Alignment explanation
Indices: 630339--630384 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
630329 AGAGCATCAG
630339 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
630385 ATGCTTCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:635726 original size:50 final size:51
Alignment explanation
Indices: 635593--635745 Score: 299
Period size: 51 Copynumber: 3.0 Consensus size: 51
635583 TCTTGAGTTG
635593 ACTGGTGGTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
1 ACTGGTGGTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
635644 ACTGGTGGTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
1 ACTGGTGGTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
635695 ACTGGT-GTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
1 ACTGGTGGTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
635745 A
1 A
635746 TGGAAGATTA
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
50 45 0.44
51 57 0.56
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.24
Consensus pattern (51 bp):
ACTGGTGGTGCAATGAAGATCCAAGTGGATGTCTTCCACAAGGAGCTTCAC
Found at i:636486 original size:19 final size:21
Alignment explanation
Indices: 636443--636487 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
636433 CCGCTTATAG
* *
636443 TTAAATATATCAAAAATTGAT
1 TTAAATATATAAAAAATTGAA
636464 TTAAATA-ATAAAAAATT-AA
1 TTAAATATATAAAAAATTGAA
636483 TTAAA
1 TTAAA
636488 AAAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 9 0.41
21 7 0.32
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TTAAATATATAAAAAATTGAA
Found at i:637501 original size:19 final size:19
Alignment explanation
Indices: 637477--637583 Score: 76
Period size: 19 Copynumber: 5.3 Consensus size: 19
637467 TTTCATGTTA
637477 ATTATACAAATA-TAAATAT
1 ATTATA-AAATATTAAATAT
*
637496 ATTATAAATTATTAAATAT
1 ATTATAAAATATTAAATAT
* * *
637515 A-T-CAAAATTTTAAATAA
1 ATTATAAAATATTAAATAT
637532 ATATATAATATATATTAAATAT
1 AT-TATAA-A-ATATTAAATAT
637554 ATTATACTAATTATATTTAAATAT
1 ATTATA--AA--ATA-TTAAATAT
637578 ATTATA
1 ATTATA
637584 TGATAAAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
17 12 0.17
18 5 0.07
19 15 0.21
20 2 0.03
21 5 0.07
22 12 0.17
23 5 0.07
24 14 0.20
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTATAAAATATTAAATAT
Found at i:637503 original size:11 final size:11
Alignment explanation
Indices: 637487--637583 Score: 54
Period size: 11 Copynumber: 9.4 Consensus size: 11
637477 ATTATACAAA
637487 TATAAATATAT
1 TATAAATATAT
637498 TATAAAT-TA-
1 TATAAATATAT
637507 T-TAAATATA-
1 TATAAATATAT
*
637516 T-CAAA-AT-T
1 TATAAATATAT
*
637524 T-TAAATA-AA
1 TATAAATATAT
637533 TATATAATATA-
1 TATA-AATATAT
637544 TATTAAATATAT
1 TA-TAAATATAT
637556 TATACTAATTATAT
1 TATA--AA-TATAT
637570 T-TAAATATAT
1 TATAAATATAT
637580 TATA
1 TATA
637584 TGATAAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 26
0.71 0.03 0.26
Matches are distributed among these distances:
8 11 0.16
9 9 0.13
10 10 0.14
11 25 0.36
12 5 0.07
13 4 0.06
14 6 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (11 bp):
TATAAATATAT
Found at i:637573 original size:24 final size:22
Alignment explanation
Indices: 637523--637584 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 22
637513 ATATCAAAAT
*
637523 TTTAAATA-AATATATAATATA
1 TTTAAATATATTATATAATATA
637544 TATTAAATATATTATACTAATTATA
1 T-TTAAATATATTATA-TAA-TATA
637569 TTTAAATATATTATAT
1 TTTAAATATATTATAT
637585 GATAAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 1 0.03
22 7 0.19
23 6 0.17
24 17 0.47
25 5 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAAATATATTATATAATATA
Found at i:638094 original size:22 final size:22
Alignment explanation
Indices: 638069--638110 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
638059 TTAGTTTAAA
* *
638069 ATTTTATTTTATTATTTAAAAT
1 ATTTTATATTAATATTTAAAAT
638091 ATTTTATATTAATATTTAAA
1 ATTTTATATTAATATTTAAA
638111 TAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTATATTAATATTTAAAAT
Found at i:641032 original size:21 final size:21
Alignment explanation
Indices: 641008--641048 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
640998 ATATTAAATA
641008 ATATTTTAT-ATTATTATTTAT
1 ATATTTTATAATTA-TATTTAT
641029 ATATTTTATAATTATATTTA
1 ATATTTTATAATTATATTTA
641049 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTTTATAATTATATTTAT
Found at i:641191 original size:15 final size:16
Alignment explanation
Indices: 641165--641208 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
641155 TTCTCTGGAC
*
641165 ATATTTAATTATTAAT
1 ATATTTATTTATTAAT
*
641181 A-ATTTATTTATGAAT
1 ATATTTATTTATTAAT
*
641196 ATAATTATTTATT
1 ATATTTATTTATT
641209 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATATTTATTTATTAAT
Found at i:641330 original size:12 final size:12
Alignment explanation
Indices: 641313--641350 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
641303 TTAATTATAA
641313 AAATATTTAAAT
1 AAATATTTAAAT
*
641325 AAATATTTTAAT
1 AAATATTTAAAT
*
641337 ATA-ATTTAAAT
1 AAATATTTAAAT
641348 AAA
1 AAA
641351 AAATGAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATATTTAAAT
Found at i:641330 original size:28 final size:29
Alignment explanation
Indices: 641280--641340 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
641270 TATCTAATAA
* * *
641280 ATAAAAATATTTTTATTTAATA-TTTAATT
1 ATAAAAATATTTTAAATAAATATTTTAA-T
641309 ATAAAAATA-TTTAAATAAATATTTTAAT
1 ATAAAAATATTTTAAATAAATATTTTAAT
641337 ATAA
1 ATAA
641341 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
ATAAAAATATTTTAAATAAATATTTTAAT
Found at i:642752 original size:16 final size:16
Alignment explanation
Indices: 642731--642761 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
642721 TTTAAATTTA
*
642731 ATTTTTTTTTAAAAAT
1 ATTTTTTTGTAAAAAT
642747 ATTTTTTTGTAAAAA
1 ATTTTTTTGTAAAAA
642762 AATTAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTTTTGTAAAAAT
Found at i:643202 original size:3 final size:3
Alignment explanation
Indices: 643194--643239 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
643184 TTTAATAGCT
643194 TTA TTA TTA TTA TTA TTA 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 TTA T
643240 CATCTACTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:643837 original size:25 final size:25
Alignment explanation
Indices: 643803--643873 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 25
643793 AAACTGTTTG
* *
643803 AAATCAATTATATTTATATTATTTA
1 AAATTAATTATATTTAAATTATTTA
643828 AAATTAA-T-TATTTAAATTATTTA
1 AAATTAATTATATTTAAATTATTTA
643851 AAATTTTAATTAT-TTTAAATTAT
1 AAA--TTAATTATATTTAAATTAT
643874 AATTATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 17 0.43
24 1 0.03
25 10 0.25
26 11 0.28
27 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTAATTATATTTAAATTATTTA
Found at i:643845 original size:9 final size:9
Alignment explanation
Indices: 643813--643873 Score: 53
Period size: 9 Copynumber: 7.3 Consensus size: 9
643803 AAATCAATTA
*
643813 TATTTATAT
1 TATTTAAAT
643822 TATTTAAA-
1 TATTTAAAT
643830 -A-TT-AAT
1 TATTTAAAT
643836 TATTTAAAT
1 TATTTAAAT
643845 TATTTAAA-
1 TATTTAAAT
*
643853 -ATTTTAAT
1 TATTTAAAT
643861 TATTTTAAAT
1 TA-TTTAAAT
643871 TAT
1 TAT
643874 AATTATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
5 2 0.05
6 2 0.05
7 8 0.19
8 2 0.05
9 20 0.48
10 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTTAAAT
Found at i:643846 original size:23 final size:24
Alignment explanation
Indices: 643813--643873 Score: 88
Period size: 23 Copynumber: 2.5 Consensus size: 24
643803 AAATCAATTA
*
643813 TATTTATATTATTTAAAA-TTAAT
1 TATTTAAATTATTTAAAATTTAAT
643836 TATTTAAATTATTTAAAATTTTAAT
1 TATTTAAATTATTTAAAA-TTTAAT
643861 TATTTTAAATTAT
1 TA-TTTAAATTAT
643874 AATTATTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 17 0.50
25 7 0.21
26 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTAAATTATTTAAAATTTAAT
Found at i:643861 original size:16 final size:16
Alignment explanation
Indices: 643837--643911 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
643827 AAAATTAATT
*
643837 ATTTAAATTATTTAAA
1 ATTTAAATTATTTTAA
*
643853 ATTTTAATTATTTTAA
1 ATTTAAATTATTTTAA
643869 A-TTATAATTATTTTAA
1 ATTTA-AATTATTTTAA
* *
643885 ATTTAAATT-TATTAT
1 ATTTAAATTATTTTAA
*
643900 TTTTAAATTATT
1 ATTTAAATTATT
643912 AATTTTGTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
15 14 0.29
16 32 0.65
17 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:643912 original size:14 final size:16
Alignment explanation
Indices: 643886--643917 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
643876 TTATTTTAAA
643886 TTTAAATTTATT-ATT
1 TTTAAATTTATTAATT
643901 TTTAAA-TTATTAATT
1 TTTAAATTTATTAATT
643916 TT
1 TT
643918 GTAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAAATTTATTAATT
Found at i:644273 original size:28 final size:30
Alignment explanation
Indices: 644206--644306 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 30
644196 TATTAAAAAT
* *
644206 ATTATATATTTATATAAATTTTAATATATA
1 ATTATATAATTATATTAATTTTAATATATA
*
644236 ATT-TAT-ATTATATTACTTTTAATAT-T-
1 ATTATATAATTATATTAATTTTAATATATA
* *
644262 TTTATATAATTATATT-ATTTTTATATAATA
1 ATTATATAATTATATTAATTTTAATAT-ATA
*
644292 TATTATTTTAATTAT
1 -ATTA-TATAATTAT
644307 TTTTATCACA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
26 2 0.04
27 12 0.21
28 24 0.43
29 4 0.07
30 3 0.05
31 3 0.05
32 8 0.14
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
ATTATATAATTATATTAATTTTAATATATA
Found at i:644293 original size:18 final size:19
Alignment explanation
Indices: 644258--644300 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
644248 TTACTTTTAA
644258 TATTTTTATATAATTATAT
1 TATTTTTATATAATTATAT
644277 TATTTTTATATAA-TATAT
1 TATTTTTATATAATTATAT
644295 TATTTT
1 TATTTT
644301 AATTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATATAATTATAT
Found at i:644430 original size:16 final size:16
Alignment explanation
Indices: 644409--644439 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
644399 AGGTTAATTA
*
644409 ATTTTTTATTTTTAAG
1 ATTTTTTATTATTAAG
644425 ATTTTTTATTATTAA
1 ATTTTTTATTATTAA
644440 AAACATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTTATTATTAAG
Found at i:644946 original size:18 final size:18
Alignment explanation
Indices: 644887--644950 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
644877 TTAAAAAGTA
644887 AATAAATAATATTAATT-T
1 AATAAA-AATATTAATTAT
* * *
644905 AATTAAAA-ATT-AGTAA
1 AATAAAAATATTAATTAT
644921 AAGTTAAAAATATTAATTAT
1 AA--TAAAAATATTAATTAT
644941 AATAAAAATA
1 AATAAAAATA
644951 ACATAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
15 2 0.06
16 5 0.14
17 2 0.06
18 18 0.51
19 3 0.09
20 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATAAAAATATTAATTAT
Found at i:647077 original size:24 final size:24
Alignment explanation
Indices: 647043--647093 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
647033 TAAAATATTA
*
647043 ATATTTTATATTTATATATAATAT
1 ATATTTAATATTTATATATAATAT
647067 ATATTTAATATTTATATATAATAT
1 ATATTTAATATTTATATATAATAT
647091 ATA
1 ATA
647094 ACTTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTTAATATTTATATATAATAT
Found at i:647088 original size:13 final size:13
Alignment explanation
Indices: 647023--647090 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
647013 TACAGTTTCT
*
647023 TAATTTTTAT-TA
1 TAATATTTATATA
* * *
647035 AAATATTAATATT
1 TAATATTTATATA
*
647048 TTATATTTATATA
1 TAATATTTATATA
*
647061 TAATA--TATATT
1 TAATATTTATATA
647072 TAATATTTATATA
1 TAATATTTATATA
647085 TAATAT
1 TAATAT
647091 ATAACTTTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
11 10 0.24
12 7 0.17
13 25 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATTTATATA
Done.