Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold404
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: 638648
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 4
Found at i:356702 original size:116 final size:115
Alignment explanation
Indices: 356467--356846 Score: 404
Period size: 116 Copynumber: 3.3 Consensus size: 115
356457 GATCCGATAG
* *
356467 TTAAATAAAATAGGCTCC-AAATAAATTAATTAAATATGTACATGGATCC-CATTTTATCTAATG
1 TTAAATAAAATA-G-TCCTAAATAAATTAATTAAATATGTACGTGGA-CCTTATTTTATCTAATG
*
356530 TATA-TTTTTTAT-AGAACTTGACTTTAAATTAAATAATTTATGACCAAATATAA
63 TATATTTTTTTATAAG-ACTTGACCTTAAATTAAAT-ATTTATGACCAAATATAA
* *
356583 TTAAAT-AAATAGATCCTAAATAAATTAATTAAATATGTATGTGGACCTTATTTTATGTAATGTA
1 TTAAATAAAATAG-TCCTAAATAAATTAATTAAATATGTACGTGGACCTTATTTTATCTAATGTA
* * *
356647 TATTTTTTTATAAGGCTTGACCTTAAATTAAATATTTAATAAATC-AATATAA
65 TATTTTTTTATAAGACTTGACCTTAAATTAAATATTT-AT-GACCAAATATAA
* * *
356699 TTAAATAAAATAG-GCTCAAATAAATTAATTAAATAAGCACGTGGGA-CTTATTTTATCTAA--T
1 TTAAATAAAATAGTCCT-AAATAAATTAATTAAATATGTACGT-GGACCTTATTTTATCTAATGT
* * * * * *
356760 ATATATTTTTATATGATTTGACGTTAAATTAAACAATTTATGACCTAATATAA
64 ATATTTTTTTATAAGACTTGACCTTAAATTAAA-TATTTATGACCAAATATAA
* *
356813 TTAAATAAAATAGGT-TTAAATTAATTAATTAAAT
1 TTAAATAAAATA-GTCCTAAATAAATTAATTAAAT
356847 CAGCATGTGG
Statistics
Matches: 227, Mismatches: 24, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
113 2 0.01
114 72 0.32
115 59 0.26
116 81 0.36
117 13 0.06
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (115 bp):
TTAAATAAAATAGTCCTAAATAAATTAATTAAATATGTACGTGGACCTTATTTTATCTAATGTAT
ATTTTTTTATAAGACTTGACCTTAAATTAAATATTTATGACCAAATATAA
Found at i:356823 original size:114 final size:114
Alignment explanation
Indices: 356467--356911 Score: 444
Period size: 114 Copynumber: 3.9 Consensus size: 114
356457 GATCCGATAG
* * * * *
356467 TTAAATAAAATAGGCTCCAAATAAATTAATTAAATATGTACATGGATCC-CATTTTATCTAATGT
1 TTAAATAAAATAGGCTCCAAATAAATTAATTAAATAAGCACGTGGA-CCTTATTTTATCTAATAT
*
356531 ATATTTTT-TATAGAACTTGACTTTAAATTAAATAATTTATGACCAAATATAA
65 ATATTTTTATA-AG-ACTTGAC-TTAAATTAAATAATTTATGACCTAATATAA
* * * * *
356583 TTAAAT-AAATA-GATCCTAAATAAATTAATTAAATATGTATGTGGACCTTATTTTATGTAATGT
1 TTAAATAAAATAGGCTCC-AAATAAATTAATTAAATAAGCACGTGGACCTTATTTTATCTAA--T
* * **
356646 ATATTTTTTTATAAGGCTTGACCTTAAATTAAAT-ATTTAAT-AAATCAATATAA
63 ATATATTTTTATAAGACTTGA-CTTAAATTAAATAATTT-ATGACCT-AATATAA
356699 TTAAATAAAATAGGCT-CAAATAAATTAATTAAATAAGCACGTGGGA-CTTATTTTATCTAATAT
1 TTAAATAAAATAGGCTCCAAATAAATTAATTAAATAAGCACGT-GGACCTTATTTTATCTAATAT
* * *
356762 ATATTTTTATATGATTTGACGTTAAATTAAACAATTTATGACCTAATATAA
65 ATATTTTTATAAGACTTGAC-TTAAATTAAATAATTTATGACCTAATATAA
** * * * * *
356813 TTAAATAAAATAGG-TTTAAATTAATTAATTAAATCAGCATGTGGGATC-TATTTAATCTAATAT
1 TTAAATAAAATAGGCTCCAAATAAATTAATTAAATAAGCACGT-GGACCTTATTTTATCTAATAT
* *
356876 ATA-ATTTATAAGACTTTGTCTTAAATTAAATAATTT
65 ATATTTTTATAAGAC-TTGACTTAAATTAAATAATTT
356912 GCGACCTTAC
Statistics
Matches: 279, Mismatches: 33, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
113 25 0.09
114 104 0.37
115 53 0.19
116 72 0.26
117 21 0.08
118 4 0.01
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (114 bp):
TTAAATAAAATAGGCTCCAAATAAATTAATTAAATAAGCACGTGGACCTTATTTTATCTAATATA
TATTTTTATAAGACTTGACTTAAATTAAATAATTTATGACCTAATATAA
Found at i:357153 original size:22 final size:22
Alignment explanation
Indices: 357113--357167 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
357103 TATTCCTTTT
** *
357113 CTATTCTATTTTCATTGAATAG
1 CTATTCTATTCCCACTGAATAG
*
357135 TTATTCTATTCCCACTGAATAG
1 CTATTCTATTCCCACTGAATAG
*
357157 CTATTTTATTC
1 CTATTCTATTC
357168 TTTCTTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (22 bp):
CTATTCTATTCCCACTGAATAG
Found at i:358155 original size:22 final size:23
Alignment explanation
Indices: 358130--358177 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
358120 CGTTCTAATA
* *
358130 AATAATTTTTTATATAT-AATTT
1 AATAATATTTCATATATAAATTT
*
358152 AATAATATTTCATATTTAAATTT
1 AATAATATTTCATATATAAATTT
358175 AAT
1 AAT
358178 TTTAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
AATAATATTTCATATATAAATTT
Found at i:358971 original size:12 final size:12
Alignment explanation
Indices: 358954--358980 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
358944 ATGATTATTT
358954 TAACAATAATAA
1 TAACAATAATAA
358966 TAACAATAATAA
1 TAACAATAATAA
358978 TAA
1 TAA
358981 TGACGATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
TAACAATAATAA
Found at i:359585 original size:16 final size:15
Alignment explanation
Indices: 359538--359590 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
359528 GAAAAAAAAT
359538 ATTTTATATCTTCTCA
1 ATTTTATATCTTC-CA
* * *
359554 ATTTTCTCTCCCTCCA
1 ATTTTATAT-CTTCCA
359570 ATTTTATATCTTTCCA
1 ATTTTATATC-TTCCA
359586 ATTTT
1 ATTTT
359591 CTTTTTATCC
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 25 0.86
17 3 0.10
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTATATCTTCCA
Found at i:360451 original size:18 final size:18
Alignment explanation
Indices: 360428--360489 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
360418 AATTTAAGTA
360428 TTAAATTGTGAATTTTTT
1 TTAAATTGTGAATTTTTT
** * *
360446 TTAAATAT-AAAATTTAAGTA
1 TTAAAT-TGTGAATTT--TTT
360466 TTAAATTGTGAATTTTTT
1 TTAAATTGTGAATTTTTT
360484 TTAAAT
1 TTAAAT
360490 ATAAAATTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
18 18 0.56
19 2 0.06
20 12 0.38
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TTAAATTGTGAATTTTTT
Found at i:360460 original size:38 final size:38
Alignment explanation
Indices: 360409--360498 Score: 180
Period size: 38 Copynumber: 2.4 Consensus size: 38
360399 AATATGTTAA
360409 TAAATATAAAATTTAAGTATTAAATTGTGAATTTTTTT
1 TAAATATAAAATTTAAGTATTAAATTGTGAATTTTTTT
360447 TAAATATAAAATTTAAGTATTAAATTGTGAATTTTTTT
1 TAAATATAAAATTTAAGTATTAAATTGTGAATTTTTTT
360485 TAAATATAAAATTT
1 TAAATATAAAATTT
360499 TTAATCAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (38 bp):
TAAATATAAAATTTAAGTATTAAATTGTGAATTTTTTT
Found at i:364776 original size:14 final size:14
Alignment explanation
Indices: 364756--364797 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
364746 TTGAGGTAAG
364756 TTAAATTAT-AATT
1 TTAAATTATAAATT
*
364769 TATAAATTTTAAATT
1 T-TAAATTATAAATT
364784 TTAAATT-TAAATT
1 TTAAATTATAAATT
364797 T
1 T
364798 AATTTAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 8 0.31
14 13 0.50
15 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATTATAAATT
Found at i:364950 original size:15 final size:15
Alignment explanation
Indices: 364928--364963 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
364918 TATGAGATAA
364928 AAATAATTAAAA-AT
1 AAATAATTAAAAGAT
364942 AATATAATTAAAAGAT
1 AA-ATAATTAAAAGAT
364958 AAATAA
1 AAATAA
364964 AAAACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 14 0.70
16 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATAATTAAAAGAT
Found at i:365259 original size:36 final size:33
Alignment explanation
Indices: 365216--365305 Score: 94
Period size: 36 Copynumber: 2.6 Consensus size: 33
365206 TTAATTTAAT
365216 TTAAAAATATTTAAAAATTAAATTAAAATAATACTA
1 TTAAAAATATTTAAAAATTAAATTAAAA-AA-A-TA
* *
365252 TTAAAAATATTTATATAATTTTAAATTTAAAAAATA
1 TTAAAAATATTTA-A-AA-ATTAAATTAAAAAAATA
365288 TT-AAAAT-TTTAAAAATTA
1 TTAAAAATATTTAAAAATTA
365306 TTTATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
31 3 0.06
32 2 0.04
33 1 0.02
34 4 0.08
35 5 0.10
36 17 0.35
37 2 0.04
38 4 0.08
39 10 0.21
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
TTAAAAATATTTAAAAATTAAATTAAAAAAATA
Found at i:365374 original size:18 final size:18
Alignment explanation
Indices: 365351--365404 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
365341 ACTACTCAAA
365351 ATTTATTTTTTAAAAAAT
1 ATTTATTTTTTAAAAAAT
**
365369 ATTTATTTAAATTTAAATTAT
1 ATTTATTT---TTTAAAAAAT
*
365390 TTTTATTTTTTAAAA
1 ATTTATTTTTTAAAA
365405 TTTTCATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 14 0.48
21 15 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTATTTTTTAAAAAAT
Found at i:369139 original size:109 final size:109
Alignment explanation
Indices: 368935--369140 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 109
368925 TTTTAGATTA
* * * *
368935 ATAATGTGTTATGAATAAAAATAAATTCTTATGTTTTGTTATTTTGTTGTTTATTTTTTAAATAT
1 ATAATGTGTTATCAATAAAAATAAATTCTTATATTTTGTTATTTTATTATTTATTTTTTAAATAT
* * *
369000 TAATAAAAATATATTATTTTTATAACTGTTATACAATTATATTG
66 AAATAAAAATATAATAGTTTTATAACTGTTATACAATTATATTG
*
369044 ATAATGTGTTATCAATAAAAATAAATTTTTTATATTTT-TTATGTTTTATTATTTATTTTTTAAA
1 ATAATGTGTTATCAATAAAAATAAA-TTCTTATATTTTGTTA--TTTTATTATTTATTTTTTAAA
* * *
369108 TATAAAT-ATAATTTAATAGTTTT-TAATTGTTAT
63 TATAAATAAAAATATAATAGTTTTATAACTGTTAT
369141 TTAATAATAC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
109 36 0.43
110 22 0.27
111 25 0.30
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (109 bp):
ATAATGTGTTATCAATAAAAATAAATTCTTATATTTTGTTATTTTATTATTTATTTTTTAAATAT
AAATAAAAATATAATAGTTTTATAACTGTTATACAATTATATTG
Found at i:369174 original size:25 final size:23
Alignment explanation
Indices: 369128--369227 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 23
369118 ATTTAATAGT
* * *
369128 TTTTAATTGTTATTTAATAATACAA
1 TTTTAATTTTTATAT-A-AATAAAA
369153 TTTTAATTATTTACTATAAAT---A
1 TTTTAATT-TTTA-TATAAATAAAA
369175 -TTT-ATTTTTAATATAAATATAAA
1 TTTTAATTTTT-ATATAAATA-AAA
*
369198 TTTTTATTTTTA-ATAAATAAAA
1 TTTTAATTTTTATATAAATAAAA
369220 TTTTAATT
1 TTTTAATT
369228 ATCATTTAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
19 10 0.16
20 4 0.06
21 3 0.05
22 11 0.17
23 8 0.13
24 4 0.06
25 17 0.27
26 4 0.06
27 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (23 bp):
TTTTAATTTTTATATAAATAAAA
Found at i:369189 original size:19 final size:21
Alignment explanation
Indices: 369137--369194 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 21
369127 TTTTTAATTG
369137 TTATTTAATAATACAAT-TTTAA
1 TTATTTAAT-ATA-AATATTTAA
*
369159 TTATTTACTATAAATATTT-A
1 TTATTTAATATAAATATTTAA
369179 TT-TTTAATATAAATAT
1 TTATTTAATATAAATAT
369195 AAATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
19 13 0.39
20 6 0.18
21 6 0.18
22 8 0.24
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTTAATATAAATATTTAA
Found at i:369212 original size:19 final size:20
Alignment explanation
Indices: 369137--369203 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
369127 TTTTTAATTG
*
369137 TTATTTAATAATACAATTTTAA
1 TTATTTAAT-ATA-AATATTAA
* *
369159 TTATTTACTATAAATATTTA
1 TTATTTAATATAAATATTAA
*
369179 TT-TTTAATATAAATATAAA
1 TTATTTAATATAAATATTAA
369198 TT-TTTA
1 TTATTTA
369204 TTTTTAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 20 0.51
20 8 0.21
21 3 0.08
22 8 0.21
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTTAATATAAATATTAA
Found at i:369242 original size:26 final size:27
Alignment explanation
Indices: 369187--369312 Score: 102
Period size: 26 Copynumber: 4.7 Consensus size: 27
369177 TATTTTTAAT
*
369187 ATAAATATAAATTT--TTATT--TTTA
1 ATAAATATAATTTTAATTATTCATTTA
*
369210 ATAAATAAAATTTTAATTA-TCATTTA
1 ATAAATATAATTTTAATTATTCATTTA
* * *
369236 ACAAATATAATTCTAATTATTCTTTTA
1 ATAAATATAATTTTAATTATTCATTTA
* *
369263 ATAAATATAATTTTGAAACTATT-ATTCAA
1 ATAAATATAATTTT--AATTATTCATT-TA
*
369292 TATAAATATAATTTTATTTAT
1 -ATAAATATAATTTTAATTAT
369313 ATTTTATTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
23 12 0.15
24 1 0.01
25 3 0.04
26 20 0.25
27 18 0.22
28 6 0.07
29 7 0.09
30 14 0.17
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (27 bp):
ATAAATATAATTTTAATTATTCATTTA
Found at i:369371 original size:19 final size:19
Alignment explanation
Indices: 369322--369371 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
369312 TATTTTATTA
369322 TTTAATATAA-ATATAAAT
1 TTTAATATAATATATAAAT
* *
369340 ATTAAT-TATATATATACAT
1 TTTAATATA-ATATATAAAT
369359 TTTAATATAATAT
1 TTTAATATAATAT
369372 CTTTAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.08
18 6 0.23
19 16 0.62
20 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATATAATATATAAAT
Found at i:369371 original size:42 final size:40
Alignment explanation
Indices: 369290--369371 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 40
369280 ACTATTATTC
* * *
369290 AATATAAATATAATTTTATTTATATTTTATTATTTAATATA
1 AATATAAATATAATTTTATATACATTTTA-TATATAATATA
369331 AATATAAATATTAATTATATATATACATTTTA-ATATAATAT
1 AATATAAATA-TAATT-T-TATATACATTTTATATATAATAT
369372 CTTTAATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
41 10 0.29
42 13 0.37
43 1 0.03
44 11 0.31
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (40 bp):
AATATAAATATAATTTTATATACATTTTATATATAATATA
Found at i:369882 original size:21 final size:21
Alignment explanation
Indices: 369834--369882 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
369824 AAATGTTACA
369834 TAAATAAAAATATTATAAAAAT
1 TAAATAAAAATA-TATAAAAAT
*
369856 T-CATAAAAATA-ATAAATAAT
1 TAAATAAAAATATATAAA-AAT
369876 TAAATAA
1 TAAATAA
369883 TATTTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 13 0.57
22 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATAAAAATATATAAAAAT
Found at i:370335 original size:27 final size:27
Alignment explanation
Indices: 370305--370364 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
370295 CTGAATAATA
* *
370305 ATTAAAAATTATTAAAATTATATTTAT
1 ATTAAAAAGTATTAAAATTATAATTAT
* * *
370332 ATTAGAAAGTGTTAAAATTCTAATTAT
1 ATTAAAAAGTATTAAAATTATAATTAT
370359 ATTAAA
1 ATTAAA
370365 TAATAAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (27 bp):
ATTAAAAAGTATTAAAATTATAATTAT
Found at i:370521 original size:83 final size:81
Alignment explanation
Indices: 370354--370522 Score: 189
Period size: 83 Copynumber: 2.0 Consensus size: 81
370344 TAAAATTCTA
* * *
370354 ATTATATTAAATAATAAAATATAAATAAAAATTATATCATATTGAATAATAGTTAAAAATTATAT
1 ATTATATTAAATAATAAAATATAAATAAAAATTATATCATATTAAATAATAATTAAAAATTACAT
* *
370419 TTATATTAAAAGAATAT
66 TTATA-TAAAAAAAAAT
* * * * *
370436 ATTATATT-TATAATAAAATATAAATTAAAACTATATGTGATTTTAAATAATAATTAAAAATTAC
1 ATTATATTAAATAATAAAATATAAA-TAAAAAT-TATATCATATTAAATAATAATTAAAAATTAC
370500 ATTTACTA-AAAATAAAAAT
64 ATTTA-TATAAAA-AAAAAT
370519 ATTA
1 ATTA
370523 GAAAATAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
81 15 0.21
82 18 0.25
83 38 0.52
84 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (81 bp):
ATTATATTAAATAATAAAATATAAATAAAAATTATATCATATTAAATAATAATTAAAAATTACAT
TTATATAAAAAAAAAT
Found at i:370913 original size:21 final size:21
Alignment explanation
Indices: 370866--370906 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
370856 AAAATAACAG
*
370866 TTATAATAATAAGATTAGTTA
1 TTATAATAATAAAATTAGTTA
370887 TTATAATAATAAAATTAGTT
1 TTATAATAATAAAATTAGTT
370907 TTAATAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
TTATAATAATAAAATTAGTTA
Found at i:370920 original size:21 final size:21
Alignment explanation
Indices: 370866--370921 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
370856 AAAATAACAG
* *
370866 TTATAATAATAAGATTAGTTA
1 TTATAAGAATAAAATTAGTTA
*
370887 TTATAATAATAAAATTAGTT-
1 TTATAAGAATAAAATTAGTTA
*
370907 TTAATAAGATTAAAA
1 TT-ATAAGAATAAAA
370922 ATAATGACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
TTATAAGAATAAAATTAGTTA
Found at i:372761 original size:23 final size:23
Alignment explanation
Indices: 372700--372763 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
372690 AATTTCATTA
372700 ATAAAATATTTTTTAA-ATTAAT
1 ATAAAATATTTTTTAATATTAAT
* *
372722 -TATAAA-ATTTATAAATATTAAT
1 ATA-AAATATTTTTTAATATTAAT
372744 ATAAAATATTTTTTAATATT
1 ATAAAATATTTTTTAATATT
372764 TTAATACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 9 0.26
22 12 0.35
23 13 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAAAATATTTTTTAATATTAAT
Found at i:373458 original size:13 final size:14
Alignment explanation
Indices: 373442--373474 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
373432 AATATTTGTG
373442 TATATTATTATA-T
1 TATATTATTATATT
*
373455 TATAATATTATATT
1 TATATTATTATATT
373469 TATATT
1 TATATT
373475 TTAAGATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATTATATT
Found at i:374752 original size:15 final size:16
Alignment explanation
Indices: 374732--374770 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
374722 TTATTGATAG
374732 TATAATAAATATT-AT
1 TATAATAAATATTGAT
*
374747 TATAATAATTATTGAT
1 TATAATAAATATTGAT
374763 TATGAATA
1 TAT-AATA
374771 TTAATAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
TATAATAAATATTGAT
Found at i:377220 original size:2 final size:2
Alignment explanation
Indices: 377213--377243 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
377203 AGCAAAAGGT
377213 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 A
377244 AGAAGGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:377569 original size:2 final size:2
Alignment explanation
Indices: 377522--377554 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
377512 TCTCTCTCTC
*
377522 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
377555 TTTACACAGT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:377656 original size:22 final size:23
Alignment explanation
Indices: 377621--377675 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
377611 ATATAAAAAT
* *
377621 TAAAATATAGTAT-AATATTAAA
1 TAAAAAATAGTATAAATATGAAA
* *
377643 TAAAAAATATTATAAATATGACA
1 TAAAAAATAGTATAAATATGAAA
377666 TAAATAAATA
1 TAAA-AAATA
377676 ACAATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 11 0.41
23 11 0.41
24 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
TAAAAAATAGTATAAATATGAAA
Found at i:378028 original size:19 final size:20
Alignment explanation
Indices: 378004--378057 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
377994 ACATTATGCT
***
378004 TTGTATCGATACATG-TTTA
1 TTGTATCGATACATGCACAA
*
378023 TTGTATCAATACATGCACAA
1 TTGTATCGATACATGCACAA
378043 TTGTATCGATACATG
1 TTGTATCGATACATG
378058 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGCACAA
Found at i:378147 original size:20 final size:20
Alignment explanation
Indices: 378122--378173 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
378112 CGATACAATA
378122 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTG
378142 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTG
*
378162 TATTGATACATG
1 TATCGATACATG
378174 GCTTCAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (20 bp):
TATCGATACATGATGAATTG
Found at i:385745 original size:52 final size:52
Alignment explanation
Indices: 385667--385795 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
385657 CGAATTATGA
* * *
385667 AAATTTCCCTGCATGTATCGATACATTTCGTAGTGTATTGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
385719 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATATATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
385771 AAATTTACCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
385796 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:385806 original size:52 final size:51
Alignment explanation
Indices: 385667--385815 Score: 158
Period size: 52 Copynumber: 2.9 Consensus size: 51
385657 CGAATTATGA
* ** *
385667 AAATTTCCCTGCATGTATCGATAC-ATTTCGTAGTGTATTGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACAACATC--AGTGTATCGATACATCTGGGC
* * * *
385719 AAATTTGCCTGTATGTATCGATACATTTCAT-AGTGTATCGATATATCTGGGC
1 AAATTTACCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
*
385771 AAATTTACCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATAC-AACATCAGTGTATCGATACA
385816 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
51 2 0.03
52 76 0.95
53 1 0.01
55 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACAACATCAGTGTATCGATACATCTGGGC
Found at i:385822 original size:13 final size:13
Alignment explanation
Indices: 385804--385828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385794 CAAAGATCAG
385804 TGTATCGATACAA
1 TGTATCGATACAA
385817 TGTATCGATACA
1 TGTATCGATACA
385829 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:385917 original size:32 final size:32
Alignment explanation
Indices: 385874--385975 Score: 177
Period size: 32 Copynumber: 3.2 Consensus size: 32
385864 GCTTCGTAGT
* *
385874 GATACATTGTATCGATACAAAACTTATGTATC
1 GATACACTGTATCGATACAACACTTATGTATC
385906 GATACACTGTATCGATACAACACTTATGTATC
1 GATACACTGTATCGATACAACACTTATGTATC
*
385938 GATACACTATATCGATACAACACTTATGTATC
1 GATACACTGTATCGATACAACACTTATGTATC
385970 GATACA
1 GATACA
385976 ACACTTATGT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (32 bp):
GATACACTGTATCGATACAACACTTATGTATC
Found at i:385918 original size:13 final size:13
Alignment explanation
Indices: 385900--385956 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
385890 ACAAAACTTA
385900 TGTATCGATACAC
1 TGTATCGATACAC
385913 TGTATCGATACAACAC
1 TGTATCGAT---ACAC
385929 TTATGTATCGATACAC
1 ---TGTATCGATACAC
*
385945 TATATCGATACA
1 TGTATCGATACA
385957 ACACTTATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
16 8 0.22
19 9 0.24
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:385968 original size:51 final size:51
Alignment explanation
Indices: 385913--386027 Score: 221
Period size: 51 Copynumber: 2.3 Consensus size: 51
385903 ATCGATACAC
385913 TGTATCGATACAACACTTATGTATCGATACACTATATCGATACAACACTTA
1 TGTATCGATACAACACTTATGTATCGATACACTATATCGATACAACACTTA
*
385964 TGTATCGATACAACACTTATGTATCGATACACTGTATCGATACAACACTTA
1 TGTATCGATACAACACTTATGTATCGATACACTATATCGATACAACACTTA
386015 TGTATCGATACAA
1 TGTATCGATACAA
386028 ATCGTTGAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (51 bp):
TGTATCGATACAACACTTATGTATCGATACACTATATCGATACAACACTTA
Found at i:386000 original size:32 final size:32
Alignment explanation
Indices: 385964--386026 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
385954 ACAACACTTA
385964 TGTATCGATACAACACTTATGTATCGATACAC
1 TGTATCGATACAACACTTATGTATCGATACAC
385996 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
386027 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAC
Found at i:386001 original size:13 final size:13
Alignment explanation
Indices: 385983--386007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
385973 ACAACACTTA
385983 TGTATCGATACAC
1 TGTATCGATACAC
385996 TGTATCGATACA
1 TGTATCGATACA
386008 ACACTTATGT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:390550 original size:20 final size:19
Alignment explanation
Indices: 390497--390557 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
390487 GTTTTGTATC
*
390497 GATACATTGTATCAATACAT
1 GATA-ATTGTATCGATACAT
* * *
390517 GTTTATTGTGTCGATACAT
1 GATAATTGTATCGATACAT
*
390536 GCATAATTGTATCGATATAT
1 G-ATAATTGTATCGATACAT
390556 GA
1 GA
390558 ACTGCAGTAG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.39
Consensus pattern (19 bp):
GATAATTGTATCGATACAT
Found at i:390628 original size:33 final size:32
Alignment explanation
Indices: 390586--390648 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
390576 CCGCTGTTTG
390586 TATCGATACATG-GCACATTGTATCGATACAATA
1 TATCGATACATGAG-A-ATTGTATCGATACAATA
390619 TATCGATACATGATGAATTGTATCGATACA
1 TATCGATACATGA-GAATTGTATCGATACA
390649 TGGCTTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TATCGATACATGAGAATTGTATCGATACAATA
Found at i:391446 original size:16 final size:15
Alignment explanation
Indices: 391421--391456 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
391411 TATCAAGATT
*
391421 TATATGAATATATCAA
1 TATATAAATATAT-AA
391437 TATATAAATATATAA
1 TATATAAATATATAA
391452 TATAT
1 TATAT
391457 TATTAACGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATAAATATATAA
Found at i:391726 original size:24 final size:26
Alignment explanation
Indices: 391693--391744 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
391683 AATTTTTAAA
* *
391693 AATAATATAA-ATAATTTTATTT-TT
1 AATAAAATAACATAATTTAATTTATT
*
391717 AATAAAATAACATCATTTAATTTATT
1 AATAAAATAACATAATTTAATTTATT
391743 AA
1 AA
391745 AAATGTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
AATAAAATAACATAATTTAATTTATT
Found at i:392043 original size:2 final size:2
Alignment explanation
Indices: 392036--392078 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
392026 GTGCAAGAAT
392036 TA 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 TA
392078 T
1 T
392079 TGCTAGATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:392644 original size:14 final size:14
Alignment explanation
Indices: 392627--392656 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
392617 CCCTGAAGTA
392627 CTGAGTCTGATCAT
1 CTGAGTCTGATCAT
392641 CTGAGTCTGATCAT
1 CTGAGTCTGATCAT
392655 CT
1 CT
392657 TCAATAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (14 bp):
CTGAGTCTGATCAT
Found at i:394363 original size:27 final size:26
Alignment explanation
Indices: 394313--394370 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
394303 TCATATTTAT
*
394313 ATATTTTTTATTATAAATATATTAAG
1 ATATTTTATATTATAAATATATTAAG
*
394339 ATATTTTATATTTATATAATA-ATTAAT
1 ATATTTTATA-TTATA-AATATATTAAG
394366 ATATT
1 ATATT
394371 GATAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.32
27 15 0.54
28 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATATTTTATATTATAAATATATTAAG
Found at i:394378 original size:27 final size:27
Alignment explanation
Indices: 394323--394378 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
394313 ATATTTTTTA
*
394323 TTATAAATATATTAAGATATTTTATAT
1 TTATAAATATATTAAGATATTATATAT
*
394350 TTATATAATA-ATTAATATATTGATA-AT
1 TTATA-AATATATTAAGATATT-ATATAT
394377 TT
1 TT
394379 GTATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TTATAAATATATTAAGATATTATATAT
Found at i:400677 original size:20 final size:20
Alignment explanation
Indices: 400649--400723 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
400639 TTTTACCCAG
400649 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
400669 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
400689 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
*
400709 ATGTATCAATACATT
1 ATGTATCGATACATT
400724 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:400709 original size:40 final size:39
Alignment explanation
Indices: 400649--400726 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
400639 TTTTACCCAG
* *
400649 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCAATACAT-TATGA
* *
400689 ATGTATCGATATATTCTTCAATGTATCAATACATTATG
1 ATGTATCGATACATTCTTCAATATATCAATACATTATG
400727 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCAATACATTATGA
Found at i:414540 original size:5 final size:5
Alignment explanation
Indices: 414530--414562 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
414520 CCTTTACAAA
414530 AAAAC AAAAC AAAAC AAAAC AAAA- AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
414563 AACCAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:414563 original size:10 final size:10
Alignment explanation
Indices: 414527--414588 Score: 54
Period size: 10 Copynumber: 5.7 Consensus size: 10
414517 CGTCCTTTAC
414527 AAAAAAACAA
1 AAAAAAACAA
*
414537 AACAAAACAA
1 AAAAAAACAA
414547 AACAAAAA-AA
1 AA-AAAAACAA
414557 ACAAAAAACCAA
1 A-AAAAAA-CAA
414569 GAAAAAATAGCAA
1 -AAAAAA-A-CAA
414582 AAAAAAA
1 AAAAAAA
414589 GGGTCTAGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
10 19 0.44
11 6 0.14
12 13 0.30
13 5 0.12
ACGTcount: A:0.82, C:0.13, G:0.03, T:0.02
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:415840 original size:29 final size:29
Alignment explanation
Indices: 415799--417142 Score: 1648
Period size: 29 Copynumber: 46.9 Consensus size: 29
415789 TGATCGTCCC
* *
415799 TTTCAAAGCTCACAGGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
** * * *
415828 TTTCAAAGTTCACGAGTCAGTGGTAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
415856 TTTCAAAGCACATAAGTCAGTGGCACTGT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
415885 TTTCGAAA-CCCACAATTCAGTGGCACTCT
1 TTTC-AAAGCCCACAAGTCAGTGGCACTCT
* *
415914 TTTCAAAGCCCACAAGTTAGTGGCACACT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
** *
415943 TTTCAAAGCTTACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
415972 TTTCAAAGCCCACAAGTCAGTGACAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
416000 TTTCAATGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
416028 TTTCAAAACCCACAAGTCAATTGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
416057 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416086 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
416115 TTTCAAAGCCCACAGGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416143 TTTCAAAGCCCACAAATC-GATGGCACTCT
1 TTTCAAAGCCCACAAGTCAG-TGGCACTCT
*
416172 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
416201 TTT-AAAACCTACAATTCACTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416229 TTTCAAAGCCCACAAGTCAGTGGCACTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416258 TTTCAAAGCCCACAAATCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416287 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
416315 TTTCAAAGCCCACAAGTCAATGGTACTAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416344 TTTCAAAGCCAACAAGTTAGTGGCA-TCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
416373 TTT-AAAGCCCACAAGTCAGTAGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416400 TTTCAAAACCCATAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416429 TTTCAAAGCCCACAAGTCAGTGACACTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416458 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416487 TTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
416516 TTT-AAAGCCCACAAATTAATGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416544 TTT-AAAACCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416572 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
416601 TTTCAAAGCCTACAAATCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416630 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416658 TTTCAAAGCCCACAATTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416687 TTTCAAAGCCCATAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416716 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416745 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
416773 TATCAAAACCCACAAGTCAATGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416802 TTTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416831 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416860 TTTCAAAGCCCATAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
416888 TTTCAAATCTCACAAATTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
416917 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416945 TTTCAAAGCCCACAATTCAGTAGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
416974 TTCCAAAGCCCACAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
417003 TTTCAAAGCCCACAAATCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
417031 TTTCAAAGCCCACAAGTCAATGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
417060 TTTCAAAGCCCACAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
417088 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
417116 TTTCAAAACCCATGCAAGTCGGTGGCA
1 TTTCAAAGCCCA--CAAGTCAGTGGCA
417143 ACCTTTTTCA
Statistics
Matches: 1126, Mismatches: 167, Indels: 43
0.84 0.12 0.03
Matches are distributed among these distances:
27 5 0.00
28 389 0.35
29 717 0.64
30 15 0.01
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:416005 original size:86 final size:87
Alignment explanation
Indices: 415799--417142 Score: 1648
Period size: 86 Copynumber: 15.6 Consensus size: 87
415789 TGATCGTCCC
* * ** * * *
415799 TTTCAAAGCTCACAGGTCAGTGGCACTCTTTTCAAAGTTCACGAGTCAGTGGTAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
415863 GCACATAAGTCAGTGGCACTGT
66 GCCCACAAGTCAGTGGCACTCT
* * *
415885 TTTCGAAA-CCCACAATTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACACTTTTCAA
1 TTTC-AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
** *
415949 AGCTTACAAATCAGTGGCACTCT
65 AGCCCACAAGTCAGTGGCACTCT
* * * * *
415972 TTTCAAAGCCCACAAGTCAGTGACAC-CCTTTCAATGCCCACAAGTTAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * *
416035 ACCCACAAGTCAATTGCACTCC
66 GCCCACAAGTCAGTGGCACTCT
*
416057 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
416122 GCCCACAGGTTAGTGGCAC-CC
66 GCCCACAAGTCAGTGGCACTCT
* *
416143 TTTCAAAGCCCACAAATC-GATGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACTCTTTT-AA
1 TTTCAAAGCCCACAAGTCAG-TGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAA
* * * *
416206 AACCTACAATTCACTGGCACTCT
65 AGCCCACAAGTCAGTGGCACTCT
* * *
416229 TTTCAAAGCCCACAAGTCAGTGGCACTATTTTCAAAGCCCACAAATCAATGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
416294 GCCCACAAGTCAGTGGCAC-CC
66 GCCCACAAGTCAGTGGCACTCT
* * * * *
416315 TTTCAAAGCCCACAAGTCAATGGTACTATTTTCAAAGCCAACAAGTTAGTGGCA-TCCTTTT-AA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTTCAA
* *
416378 AGCCCACAAGTCAGTAGCAC-CC
65 AGCCCACAAGTCAGTGGCACTCT
* * * *
416400 TTTCAAAACCCATAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACACTTTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
416465 GCCCACAAATCAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * * * *
416487 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTT-AAAGCCCACAAATTAATGGCACCCTTTT-AAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* *
416550 ACCCACAAGTCAATGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * * *
416572 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAATCAATGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
416637 GCCCACAAGTCAGTGGCAC-CC
66 GCCCACAAGTCAGTGGCACTCT
* * *
416658 TTTCAAAGCCCACAATTTAGTGGCACTCTTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
416723 GCCCACAAATCAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * * * * *
416745 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTATCAAAACCCACAAGTCAATGGCACTCCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
416809 GCCCACAAGTTAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * *
416831 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCATAAGTCAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * *
416895 TCTCACAAATTAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * * *
416917 TTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAATTCAGTAGCACTCTTTCCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
*
416981 GCCCACAAGTTAGTGGCACTCT
66 GCCCACAAGTCAGTGGCACTCT
* * *
417003 TTTCAAAGCCCACAAATCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAATGGCATTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* *
417067 GCCCACAAGTTAGTGGCA-TCC
66 GCCCACAAGTCAGTGGCACTCT
* * * *
417088 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAACCCATGCAAGTCGGTGGCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAGTGGCA
417143 ACCTTTTTCA
Statistics
Matches: 1092, Mismatches: 146, Indels: 39
0.86 0.11 0.03
Matches are distributed among these distances:
85 253 0.23
86 640 0.59
87 199 0.18
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (87 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
GCCCACAAGTCAGTGGCACTCT
Found at i:416101 original size:143 final size:145
Alignment explanation
Indices: 415799--417142 Score: 1648
Period size: 143 Copynumber: 9.4 Consensus size: 145
415789 TGATCGTCCC
* * ** * * *
415799 TTTCAAAGCTCACAGGTCAGTGGCACTCTTTTCAAAGTTCACGAGTCAGTGGTAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * *
415863 GCACATAAGTCAGTGGCACTGTTTTCGAAA-CCCACAATTCAGTGGCACTCTTTTCAAAGCCCAC
66 GCCCACAAGTCAGTGGCACTCTTTTC-AAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAC
* *
415927 AAGTTAGTGGCACACT
130 AAGTCAGTGGCACTCT
** * * * *
415943 TTTCAAAGCTTACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGACAC-CCTTTCAAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * * * *
416007 GCCCACAAGTTAGTGGCAC-CCTTTCAAAACCCACAAGTCAATTGCACTCCTTTCAAAGCCCACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
416071 AGTCAGTGGCACTCT
131 AGTCAGTGGCACTCT
* * * *
416086 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAGGTTAGTGGCAC-CCTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * *
416150 GCCCACAAATC-GATGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACTCTTTT-AAAACCTAC
66 GCCCACAAGTCAG-TGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAC
* *
416213 AATTCACTGGCACTCT
130 AAGTCAGTGGCACTCT
* * *
416229 TTTCAAAGCCCACAAGTCAGTGGCACTATTTTCAAAGCCCACAAATCAATGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * * *
416294 GCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAATGGTACTATTTTCAAAGCCAACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
*
416358 AGTTAGTGGCA-TCCT
131 AGTCAGTGGCACT-CT
* * * *
416373 TTT-AAAGCCCACAAGTCAGTAGCAC-CCTTTCAAAACCCATAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
416436 GCCCACAAGTCAGTGACACTTTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
*
416501 AGTCAGTGGCACCCT
131 AGTCAGTGGCACTCT
* * * * * *
416516 TTT-AAAGCCCACAAATTAATGGCACCCTTTT-AAAACCCACAAGTCAATGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * *
416579 GCCCACAAGTTAGTGGCACTCTTTTCAAAGCCTACAAATCAATGGCACTCTTTTCAAAGCCCACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
*
416644 AGTCAGTGGCAC-CC
131 AGTCAGTGGCACTCT
* * *
416658 TTTCAAAGCCCACAATTTAGTGGCACTCTTTTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * * *
416723 GCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CCTATCAAAACCCACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
* *
416787 AGTCAATGGCACTCC
131 AGTCAGTGGCACTCT
* *
416802 TTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * * * * *
416867 GCCCATAAGTCAGTGGCAC-CCTTTCAAATCTCACAAATTAGTGGCACTCTTTTCAAAGCCCACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
*
416931 AGTCAGTGGCAC-CC
131 AGTCAGTGGCACTCT
* * * *
416945 TTTCAAAGCCCACAATTCAGTAGCACTCTTTCCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
* * *
417010 GCCCACAAATCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAATGGCATTCTTTTCAAAGCCCACA
66 GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
* *
417074 AGTTAGTGGCA-TCC
131 AGTCAGTGGCACTCT
* * * *
417088 TTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAACCCATGCAAGTCGGTGGCA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAGTGGCA
417143 ACCTTTTTCA
Statistics
Matches: 1044, Mismatches: 139, Indels: 34
0.86 0.11 0.03
Matches are distributed among these distances:
142 69 0.07
143 639 0.61
144 335 0.32
145 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (145 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
GCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACA
AGTCAGTGGCACTCT
Found at i:417691 original size:20 final size:20
Alignment explanation
Indices: 417666--417740 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
417656 TTTTACCCAG
*
417666 ATATATCGATGCATTTTTCA
1 ATATATCGATACATTTTTCA
* * *
417686 ATATATCGATACATGTATGA
1 ATATATCGATACATTTTTCA
* * *
417706 ATGTATCGATATATTCTTCA
1 ATATATCGATACATTTTTCA
417726 ATATATCGATACATT
1 ATATATCGATACATT
417741 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATATATCGATACATTTTTCA
Found at i:417792 original size:20 final size:20
Alignment explanation
Indices: 417767--417804 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
417757 ATGTATCGAT
417767 AATAATGTATCGATACATTG
1 AATAATGTATCGATACATTG
417787 AATAATGTATCGATACAT
1 AATAATGTATCGATACAT
417805 CTAGTTAAAA
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:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (20 bp):
AATAATGTATCGATACATTG
Found at i:424855 original size:53 final size:54
Alignment explanation
Indices: 424775--424877 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
424765 AGGCATTAGA
* * *
424775 AATCTATATGTGTGATGTAATTTTTTGTTT-CTCTAAAGTAACCTTAGTTTTTT
1 AATCTATATGTGTGATGCAATTCTTTGTTTCCCCTAAAGTAACCTTAGTTTTTT
*
424828 AATCTATATGTGTGATGCAATTCTTTGTTTCCCCTAAAGTAGCCTTAGTT
1 AATCTATATGTGTGATGCAATTCTTTGTTTCCCCTAAAGTAACCTTAGTT
424878 CAAGATTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 28 0.62
54 17 0.38
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.48
Consensus pattern (54 bp):
AATCTATATGTGTGATGCAATTCTTTGTTTCCCCTAAAGTAACCTTAGTTTTTT
Found at i:427228 original size:4 final size:4
Alignment explanation
Indices: 427219--427246 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
427209 CTTTTCTCTC
427219 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
427247 TATCTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:428050 original size:50 final size:50
Alignment explanation
Indices: 427842--428037 Score: 331
Period size: 50 Copynumber: 3.9 Consensus size: 50
427832 TATACTTAGA
* *
427842 GTCAACAATTATGGCCACATTTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
427892 GTCAACAATAATGGCCACCTCT-TCCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCT-CTATTGTCAAAGGTTGGTGAAGAATC
* *
427942 GTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
427992 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAG
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAG
428038 GATAATCAAC
Statistics
Matches: 136, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
49 1 0.01
50 134 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:432513 original size:50 final size:50
Alignment explanation
Indices: 432436--432629 Score: 255
Period size: 50 Copynumber: 3.9 Consensus size: 50
432426 TATACTTAGA
* *
432436 GTCAACAATTATGGTCACATTTCTCTATTATCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
* * * * * * *
432486 GTCAATAATAATGGCCACCTCTTTCTATTGTCAAAAGTTGATGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
* *
432536 GTCAACAATTACGGTCATCTCTCTCTATTATCAAAGG-TGGTGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
* * *
432585 GTCAACAATTATGGTCACATCTCTCTATTATTAAAGGTTAGTGAA
1 GTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAA
432630 TGATAATCAA
Statistics
Matches: 120, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
49 44 0.37
50 76 0.63
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (50 bp):
GTCAACAATTATGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATC
Found at i:432998 original size:22 final size:21
Alignment explanation
Indices: 432973--433014 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
432963 AAAATTAAAA
432973 ATATTATTAT-ATTAATATTTAT
1 ATATT-TTATAATTAA-ATTTAT
432995 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
433015 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:433172 original size:15 final size:16
Alignment explanation
Indices: 433138--433180 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
433128 GGTCTAAATA
433138 TAAATTAAAATTTCATT
1 TAAA-TAAAATTTCATT
433155 TAAATAAAATTT-ATT
1 TAAATAAAATTTCATT
433170 TAAATATAAAT
1 TAAATA-AAAT
433181 AAAAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.36
16 12 0.48
17 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATAAAATTTCATT
Found at i:433196 original size:30 final size:30
Alignment explanation
Indices: 433156--433246 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 30
433146 AATTTCATTT
433156 AAAT-AAAATTTATTTAAATATAAATAAAA
1 AAATAAAAATTTATTTAAATATAAATAAAA
433185 AAATAAAAATTTTATTTAAAGTAT-AAT--AA
1 AAATAAAAA-TTTATTTAAA-TATAAATAAAA
* * * *
433214 AAGTATAAATTTATCTAAATA-AAATAATA
1 AAATAAAAATTTATTTAAATATAAATAAAA
433243 AAAT
1 AAAT
433247 TTAATAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
27 5 0.10
28 9 0.18
29 17 0.33
30 4 0.08
31 13 0.25
32 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATAAAAATTTATTTAAATATAAATAAAA
Found at i:433202 original size:31 final size:29
Alignment explanation
Indices: 433156--433246 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 29
433146 AATTTCATTT
433156 AAATAAAATTTATTTAAA-TATAAATAAAA
1 AAATAAAATTTATTTAAAGTAT-AATAAAA
433185 AAATAAAAATTTTATTTAAAGTATAATAAAA
1 AAAT-AAAA-TTTATTTAAAGTATAATAAAA
** * * *
433216 GTAT-AAATTTATCTAAA-TAAAATAATA
1 AAATAAAATTTATTTAAAGTATAATAAAA
433243 AAAT
1 AAAT
433247 TTAATAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
27 10 0.19
28 9 0.17
29 7 0.13
30 4 0.08
31 19 0.37
32 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATAAAATTTATTTAAAGTATAATAAAA
Found at i:433909 original size:15 final size:15
Alignment explanation
Indices: 433873--433903 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
433863 TGTTTTTATA
*
433873 AAAATAACAAATTTT
1 AAAATAAAAAATTTT
433888 AAAATAAAAAATTTT
1 AAAATAAAAAATTTT
433903 A
1 A
433904 TTATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAAAAAATTTT
Found at i:433991 original size:122 final size:124
Alignment explanation
Indices: 433673--434005 Score: 387
Period size: 121 Copynumber: 2.7 Consensus size: 124
433663 TTTTTTAATT
*
433673 AAAAATAATATTTAATTAAAATTTTAAAAAAATTATATTAACAAATTAAAATATT-A--A-T-TA
1 AAAAATAATATTTAATT-AAA-TTT-AAAAAATTAAATTAACAAATTAAAATATTAATTATTATA
* *
433733 TTTTTTAAAAATAAAAAAATTTTAAATAAAAAATAAAAAGGTTTTTTTATTATTATTTTTTAATA
63 TTTTTTAAAAAT-AAAAAA-TTT--AT-AAAAATAAAAA-G--ATTTTATTATTAATTTTTAATA
*
433798 AAATT
120 AAATA
* * * *
433803 AGAAATAATATTTAATTAAATTTAAAAAATTAAATTAATAAAGTAAAATATTAATTATTATGTTT
1 AAAAATAATATTTAATTAAATTTAAAAAATTAAATTAACAAATTAAAATATTAATTATTATATTT
*
433868 TTATAAAAATAACAAATTT-T-AAAATAAAAA-ATTTTATTA-TAATTTTTAATAAAATA
66 TT-TAAAAATAAAAAATTTATAAAAATAAAAAGATTTTATTATTAATTTTTAATAAAATA
* *
433924 AAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATATT
1 AAAAATAATATTTAATTAAATTTAAAAAA-TTAAATTAACAAATTAAAATATTAATTATTATATT
433989 TTTTAAAAATAAAAAAT
65 TTTTAAAAATAAAAAAT
434006 ATTTTTGATT
Statistics
Matches: 180, Mismatches: 16, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
121 55 0.31
122 42 0.23
126 10 0.06
127 26 0.14
128 5 0.03
129 3 0.02
130 17 0.09
131 4 0.02
132 11 0.06
133 7 0.04
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (124 bp):
AAAAATAATATTTAATTAAATTTAAAAAATTAAATTAACAAATTAAAATATTAATTATTATATTT
TTTAAAAATAAAAAATTTATAAAAATAAAAAGATTTTATTATTAATTTTTAATAAAATA
Found at i:434346 original size:14 final size:15
Alignment explanation
Indices: 434327--434355 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
434317 AATAAAAACT
434327 TTTTTTA-TTTAAAA
1 TTTTTTATTTTAAAA
434341 TTTTTTATTTTAAAA
1 TTTTTTATTTTAAAA
434356 AATATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTTATTTTAAAA
Found at i:434459 original size:7 final size:7
Alignment explanation
Indices: 434447--434480 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
434437 TAATAAAAAC
434447 TTTTTAA
1 TTTTTAA
434454 TTTTTAA
1 TTTTTAA
*
434461 TTTTAAA
1 TTTTTAA
*
434468 TTTTTTA
1 TTTTTAA
434475 TTTTTA
1 TTTTTA
434481 TAAAAATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTAA
Found at i:434461 original size:21 final size:20
Alignment explanation
Indices: 434437--434487 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
434427 TTAAAAATTA
434437 TAATAAAAACTTTTTAATTTT
1 TAATAAAAA-TTTTTAATTTT
** *
434458 TAATTTTAAATTTTTTATTTT
1 TAA-TAAAAATTTTTAATTTT
434479 T-ATAAAAAT
1 TAATAAAAAT
434488 ATAATAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 5 0.21
20 1 0.04
21 14 0.58
22 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATAAAAATTTTTAATTTT
Found at i:435576 original size:26 final size:26
Alignment explanation
Indices: 435527--435575 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
435517 GTGAAGTAAT
* *
435527 AAATAATTAAATAATATATAAAAATA
1 AAATAATTAAATAATAAAAAAAAATA
435553 AAATAATTAAA-AATAAAAAAAAA
1 AAATAATTAAATAATAAAAAAAAA
435576 AGTAGCGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (26 bp):
AAATAATTAAATAATAAAAAAAAATA
Found at i:435681 original size:21 final size:22
Alignment explanation
Indices: 435658--435710 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
435648 TGGATTAACA
435658 AAAAAAAT-AATA-TTATTTTG
1 AAAAAAATAAATATTTATTTTG
*
435678 AAAAAATTAAATATTTATTTTG
1 AAAAAAATAAATATTTATTTTG
*
435700 CAAAAAATAAA
1 AAAAAAATAAA
435711 CTTAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 7 0.25
21 4 0.14
22 17 0.61
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (22 bp):
AAAAAAATAAATATTTATTTTG
Found at i:435982 original size:34 final size:34
Alignment explanation
Indices: 435885--435982 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 34
435875 GTCAATATTG
* * * *
435885 AGTTACAAAATTTAATCAAAAATCAAAGTTAAAT
1 AGTTACAAAATTCAATCAAAAATAAAAATAAAAT
* *
435919 -G--ACAAAATTCTAT-AAAAAAAAAAACTAAAAT
1 AGTTACAAAATTCAATCAAAAATAAAAA-TAAAAT
*
435950 AGTTACAAAATTCAATCAAATATAAAAATAAAA
1 AGTTACAAAATTCAATCAAAAATAAAAATAAAA
435983 AGATAAATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
30 8 0.16
31 15 0.30
32 1 0.02
33 1 0.02
34 16 0.32
35 9 0.18
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.24
Consensus pattern (34 bp):
AGTTACAAAATTCAATCAAAAATAAAAATAAAAT
Found at i:436154 original size:3 final size:3
Alignment explanation
Indices: 436146--436179 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
436136 TTCAAACAAC
436146 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
436180 GGTCATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:438012 original size:21 final size:21
Alignment explanation
Indices: 437988--438027 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
437978 AATTAAGTTT
*
437988 ATAA-AATAAATAATTTATAAA
1 ATAATAATAAA-AATATATAAA
438009 ATAATAATAAAAATATATA
1 ATAATAATAAAAATATATA
438028 TGGCATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAATAAAAATATATAAA
Found at i:438016 original size:15 final size:16
Alignment explanation
Indices: 437985--438016 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
437975 ATCAATTAAG
437985 TTTATAAAATAAATAA
1 TTTATAAAATAAATAA
438001 TTTATAAAAT-AATAA
1 TTTATAAAATAAATAA
438016 T
1 T
438017 AAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTATAAAATAAATAA
Found at i:438132 original size:14 final size:16
Alignment explanation
Indices: 438099--438137 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
438089 TCTAGTTTAT
*
438099 AAATAAATACTTAGAA
1 AAATAAATACATAGAA
438115 AAATAAATA-ATA-AA
1 AAATAAATACATAGAA
438129 AAATAAATA
1 AAATAAATA
438138 TTTATAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 2 0.09
16 9 0.41
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATAAATACATAGAA
Found at i:438149 original size:30 final size:30
Alignment explanation
Indices: 438099--438157 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
438089 TCTAGTTTAT
438099 AAATAAATACTTAGAAAAATA-AATAATAAA
1 AAATAAATACTTAGAAAAATATAA-AATAAA
* * *
438129 AAATAAATATTTATAGAAATATAAAATAA
1 AAATAAATACTTAGAAAAATATAAAATAA
438158 TTATTTACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATAAATACTTAGAAAAATATAAAATAAA
Found at i:438703 original size:18 final size:18
Alignment explanation
Indices: 438647--438696 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
438637 ATTAATGTAA
*
438647 ATAAA-TATTTTATATTT
1 ATAAATTATTTAATATTT
438664 ATAAATTATTTAATATTT
1 ATAAATTATTTAATATTT
438682 ATAAAGTTAATTTAA
1 ATAAA-TT-ATTTAA
438697 ATTATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 5 0.17
18 16 0.55
19 2 0.07
20 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATAAATTATTTAATATTT
Found at i:439568 original size:48 final size:47
Alignment explanation
Indices: 439493--439590 Score: 151
Period size: 48 Copynumber: 2.1 Consensus size: 47
439483 ATCAGTACTC
** *
439493 ATTAGTTTAACATATGTGTATAGTTTTTATATAATTTATATTTTTTTA
1 ATTAGTTTAACATATGTACATAATTTTTATATAATTTATA-TTTTTTA
*
439541 ATTAGTTTAACATATTTACATAATTTTTATATAATTTATATTTTTTA
1 ATTAGTTTAACATATGTACATAATTTTTATATAATTTATATTTTTTA
439588 ATT
1 ATT
439591 GAATCATCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 10 0.22
48 36 0.78
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (47 bp):
ATTAGTTTAACATATGTACATAATTTTTATATAATTTATATTTTTTA
Found at i:441163 original size:21 final size:22
Alignment explanation
Indices: 441114--441164 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
441104 GAATTTAACA
*
441114 AATAATATTTATATATAATATT
1 AATAATATCTATATATAATATT
*
441136 AAAAATATCT-TATATAATATT
1 AATAATATCTATATATAATATT
*
441157 ACTAATAT
1 AATAATAT
441165 ATAAAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATATCTATATATAATATT
Found at i:441290 original size:13 final size:13
Alignment explanation
Indices: 441240--441293 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
441230 AAATTTTCAA
*
441240 TAAAAATTAATATC
1 TAAAAA-TAATATT
441254 TAAAAAT-AT-TT
1 TAAAAATAATATT
*
441265 TAATAAATTATATT
1 TAA-AAATAATATT
441279 TAAAAATAATATT
1 TAAAAATAATATT
441292 TA
1 TA
441294 GAATTCATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 4 0.11
12 6 0.17
13 14 0.40
14 11 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAAAATAATATT
Found at i:441941 original size:22 final size:21
Alignment explanation
Indices: 441910--441951 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
441900 AATTATTATT
* *
441910 TAAATTTAATTATAAAATATA
1 TAAATTTAATAAAAAAATATA
441931 TAAATATTAATAAAAAAATAT
1 TAAAT-TTAATAAAAAAATAT
441952 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATAAAAAAATATA
Found at i:441947 original size:21 final size:20
Alignment explanation
Indices: 441910--441951 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
441900 AATTATTATT
*
441910 TAAATTTAATTATAAAATATA
1 TAAATTTAATTA-AAAAAATA
441931 TAAATATTAA-TAAAAAAATA
1 TAAAT-TTAATTAAAAAAATA
441951 T
1 T
441952 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTAAAAAAATA
Found at i:450144 original size:19 final size:20
Alignment explanation
Indices: 450097--450133 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
450087 GGAAATGCAT
450097 AGGT-TTTTTTTTAAAAAAA
1 AGGTATTTTTTTTAAAAAAA
*
450116 AGGTAATTTTTTTAAAAA
1 AGGTATTTTTTTTAAAAA
450134 TAGTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (20 bp):
AGGTATTTTTTTTAAAAAAA
Found at i:453509 original size:16 final size:16
Alignment explanation
Indices: 453470--453524 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
453460 AATTTACATA
453470 TAAAATAATTCAAAAT
1 TAAAATAATTCAAAAT
* *
453486 T--GATAATTTAAAAT
1 TAAAATAATTCAAAAT
453500 TAAAATAATTCAAAAT
1 TAAAATAATTCAAAAT
*
453516 TAAATTAAT
1 TAAAATAAT
453525 CATTTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 12 0.38
16 20 0.62
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAATAATTCAAAAT
Found at i:454235 original size:2 final size:2
Alignment explanation
Indices: 454228--454265 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
454218 TCTCTGTTCC
454228 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
454266 TTTCTTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:454456 original size:9 final size:10
Alignment explanation
Indices: 454436--454465 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
454426 AAATTATGAA
*
454436 TTTCTTTTTT
1 TTTCATTTTT
454446 TTTCATTTTT
1 TTTCATTTTT
454456 TTTCATTTTT
1 TTTCATTTTT
454466 AATTTTAAAA
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:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:454480 original size:17 final size:18
Alignment explanation
Indices: 454460--454494 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
454450 ATTTTTTTTC
454460 ATTTTT-AATTTTAAAAT
1 ATTTTTCAATTTTAAAAT
*
454477 ATTTTTCATTTTTAAAAT
1 ATTTTTCAATTTTAAAAT
454495 TTAAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTCAATTTTAAAAT
Found at i:454481 original size:24 final size:25
Alignment explanation
Indices: 454454--454500 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
454444 TTTTTCATTT
*
454454 TTTTTCATTTTT-AATTTTAAAATA
1 TTTTTCATTTTTAAAATTTAAAATA
454478 TTTTTCATTTTTAAAATTTAAAA
1 TTTTTCATTTTTAAAATTTAAAA
454501 ATGAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTTCATTTTTAAAATTTAAAATA
Found at i:456090 original size:16 final size:15
Alignment explanation
Indices: 456032--456095 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
456022 AGATTCAAAA
*
456032 TTTTTTAAGTTGAA-
1 TTTTTTAAGTTTAAG
** *
456046 TTTATTCGAGTTTAAA
1 TTT-TTTAAGTTTAAG
456062 TTTTTTAAGTTTAAG
1 TTTTTTAAGTTTAAG
*
456077 TTTTTTTAGATTTAAG
1 TTTTTTAAG-TTTAAG
456093 TTT
1 TTT
456096 ATTTGGACTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 3 0.08
15 25 0.62
16 12 0.30
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTTTTAAGTTTAAG
Found at i:456317 original size:15 final size:14
Alignment explanation
Indices: 456297--456340 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
456287 TCTATATTTA
456297 TATATAAAATTAATT
1 TATAT-AAATTAATT
456312 TATATAAATTAATT
1 TATATAAATTAATT
*
456326 T-TTTAAA-TAATT
1 TATATAAATTAATT
456338 TAT
1 TAT
456341 TATTATAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 6 0.22
13 6 0.22
14 10 0.37
15 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATATAAATTAATT
Found at i:457918 original size:19 final size:19
Alignment explanation
Indices: 457877--457918 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
457867 ATTCATTCCC
* *
457877 TTTTTTTTTTTTTAACAAT
1 TTTTTTTTTATTTAACAAG
457896 TTTTATTTTTATTTAA-AAG
1 TTTT-TTTTTATTTAACAAG
457915 TTTT
1 TTTT
457919 CCAACTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTTTTATTTAACAAG
Found at i:458062 original size:39 final size:42
Alignment explanation
Indices: 457982--458080 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 42
457972 AAACTTTTCA
**
457982 AATAATTTATTTAAAATAATAAATAAATTTAAATACTTATAT
1 AATAATTTATTTAAAATAATAAATAAATTTAAATAAATATAT
*
458024 AATAA-TTATTT--AATAATAAA-ATTATTTAAATAAATATAT
1 AATAATTTATTTAAAATAATAAATA-AATTTAAATAAATATAT
* *
458063 ACTAGTTTATGTTAAAAT
1 AATAATTTAT-TTAAAAT
458081 TTTAAATAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
38 1 0.02
39 26 0.55
40 4 0.09
41 8 0.17
42 5 0.11
43 3 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
AATAATTTATTTAAAATAATAAATAAATTTAAATAAATATAT
Found at i:458143 original size:27 final size:28
Alignment explanation
Indices: 458113--458168 Score: 64
Period size: 27 Copynumber: 2.0 Consensus size: 28
458103 AATATATAAA
458113 AATAGCTTGACAAT-AT-ATTTTTA-TATT
1 AATA-CTTGA-AATGATCATTTTTATTATT
*
458140 AATACTTTAAATGATCATTTTTATTATT
1 AATACTTGAAATGATCATTTTTATTATT
458168 A
1 A
458169 TCTCACCGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.12
26 6 0.24
27 11 0.44
28 5 0.20
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (28 bp):
AATACTTGAAATGATCATTTTTATTATT
Found at i:459796 original size:22 final size:22
Alignment explanation
Indices: 459771--459815 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
459761 AGATATCGGG
* * *
459771 CTGGCGCTATAGCCTTGGCTTT
1 CTGGCGCTACAGCATTAGCTTT
459793 CTGGCGCTACAGCATTAGCTTT
1 CTGGCGCTACAGCATTAGCTTT
459815 C
1 C
459816 ATATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.29, G:0.24, T:0.33
Consensus pattern (22 bp):
CTGGCGCTACAGCATTAGCTTT
Found at i:461981 original size:20 final size:20
Alignment explanation
Indices: 461956--462001 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
461946 AAGAATTGAA
*
461956 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
461976 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
461996 GAGGGA
1 GAGGGA
462002 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:466714 original size:28 final size:27
Alignment explanation
Indices: 466683--466736 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
466673 TGACAAATAC
* *
466683 AAAAGAAACTATCATTTTTTACAAACAT
1 AAAA-AAACTACCATTTTTAACAAACAT
* *
466711 AAAATAATTACCATTTTTAACAAACA
1 AAAAAAACTACCATTTTTAACAAACA
466737 AATGAGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAAAAACTACCATTTTTAACAAACAT
Found at i:467477 original size:20 final size:20
Alignment explanation
Indices: 467441--467500 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
467431 ATTAAATAAG
*
467441 AATAAAAAGAAATAAAAATA
1 AATAAAAAGAAACAAAAATA
467461 AATAAATAA-AAACAAAAAATA
1 AATAAA-AAGAAAC-AAAAATA
* **
467482 TATAAAGTGAAA-AAAAATA
1 AATAAAAAGAAACAAAAATA
467501 TTAAAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.21
20 9 0.27
21 17 0.52
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.17
Consensus pattern (20 bp):
AATAAAAAGAAACAAAAATA
Found at i:468594 original size:20 final size:20
Alignment explanation
Indices: 468547--468594 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
468537 TTGCAATCGG
*
468547 TCCTCTTAAAAATAATTAAT
1 TCCTCTTAAAAATAATCAAT
*
468567 ACCTTCTT-AAAATAAATCAAT
1 TCC-TCTTAAAAAT-AATCAAT
468588 TCCTCTT
1 TCCTCTT
468595 TTGATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.40
Consensus pattern (20 bp):
TCCTCTTAAAAATAATCAAT
Found at i:471523 original size:12 final size:13
Alignment explanation
Indices: 471497--471521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
471487 TTGTACTAAT
471497 TTCATTAAAAAAA
1 TTCATTAAAAAAA
471510 TTCATTAAAAAA
1 TTCATTAAAAAA
471522 TTTATTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCATTAAAAAAA
Found at i:472471 original size:3 final size:3
Alignment explanation
Indices: 472463--472496 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
472453 TGAGAAGTTG
*
472463 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
472497 AATAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:482508 original size:74 final size:74
Alignment explanation
Indices: 482427--482574 Score: 260
Period size: 74 Copynumber: 2.0 Consensus size: 74
482417 CCTTTTCTTT
*
482427 CCAGTCCTTTCCTTTTTCTTTAATTCCTTATATCCAAACATAGTGAAAACCTAAGACCACAATAA
1 CCAGTCCTTTCCTTTTTCTTTAATTCCTTATATCCAAACATAGTGAAAACCTAAAACCACAATAA
482492 GTCAAAATC
66 GTCAAAATC
* * *
482501 CCAGTCCTTTCCTTTTTCTTTAATTTCTTATATCCAAACATGGTGAAAACTTAAAACCACAATAA
1 CCAGTCCTTTCCTTTTTCTTTAATTCCTTATATCCAAACATAGTGAAAACCTAAAACCACAATAA
482566 GTCAAAATC
66 GTCAAAATC
482575 TTTTAGGAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (74 bp):
CCAGTCCTTTCCTTTTTCTTTAATTCCTTATATCCAAACATAGTGAAAACCTAAAACCACAATAA
GTCAAAATC
Found at i:487484 original size:43 final size:43
Alignment explanation
Indices: 487426--487513 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
487416 AAAAAGTAAT
* * ** *
487426 AAATGAAATTAATATATTATATTAAATTCAATGAATGAAGATA
1 AAATAAAATAAATATATTATATTAAACACAATGAATGAAAATA
*
487469 AAATAAAATAAATATATTATATTACACACAATGAATGAAAATA
1 AAATAAAATAAATATATTATATTAAACACAATGAATGAAAATA
487512 AA
1 AA
487514 TGAGATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (43 bp):
AAATAAAATAAATATATTATATTAAACACAATGAATGAAAATA
Found at i:488250 original size:20 final size:20
Alignment explanation
Indices: 488195--488277 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
488185 AAAAACATGT
*
488195 AATTATATTTT-TTTAATTGA
1 AATTAT-TTTTATTTAATTTA
* *
488215 AACTTA-CTTGATTTAATTTA
1 AA-TTATTTTTATTTAATTTA
*
488235 AATTATTATTTA-TTAA-TAA
1 AATTATT-TTTATTTAATTTA
*
488254 AAATATTTTTATTTAAATTTA
1 AATTATTTTTATTT-AATTTA
488275 AAT
1 AAT
488278 ATAAAAATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
18 4 0.09
19 15 0.32
20 18 0.38
21 10 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTATTTTTATTTAATTTA
Found at i:488279 original size:20 final size:20
Alignment explanation
Indices: 488225--488279 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
488215 AACTTACTTG
488225 ATTTAATTTAAATTATTATTT
1 ATTTAATTTAAA-TATTATTT
**
488246 A-TTAATAAAAATATT-TTT
1 ATTTAATTTAAATATTATTT
488264 ATTTAAATTTAAATAT
1 ATTT-AATTTAAATAT
488280 AAAAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 17 0.61
21 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTAATTTAAATATTATTT
Found at i:488942 original size:19 final size:19
Alignment explanation
Indices: 488918--489003 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
488908 TTTCAGCGAT
*
488918 TTGTATCGATACATAAATG
1 TTGTATCGATACATAAATA
488937 TTGTATCGATAC----A-A
1 TTGTATCGATACATAAATA
* *
488951 -TGTATTGATACATAAGTA
1 TTGTATCGATACATAAATA
*
488969 TTGTATCGATACATAAGTA
1 TTGTATCGATACATAAATA
488988 TTGTATCGATACATAA
1 TTGTATCGATACATAA
489004 TTAGCTACTG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
13 10 0.18
15 1 0.02
18 1 0.02
19 45 0.79
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAATA
Found at i:488955 original size:32 final size:32
Alignment explanation
Indices: 488919--488981 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
488909 TTCAGCGATT
*
488919 TGTATCGATACATAAATGTTGTATCGATACAA
1 TGTATCGATACATAAATATTGTATCGATACAA
* *
488951 TGTATTGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAATATTGTATCGATACA
488982 TAAGTATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAATATTGTATCGATACAA
Found at i:489062 original size:13 final size:13
Alignment explanation
Indices: 489044--489069 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
489034 ATTTTTCTTG
489044 TGTATCGATACAT
1 TGTATCGATACAT
489057 TGTATCGATACAT
1 TGTATCGATACAT
489070 CTAGGAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:491271 original size:15 final size:15
Alignment explanation
Indices: 491251--491287 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
491241 ATTTATAAAT
491251 TTATCACTCGAGTTG
1 TTATCACTCGAGTTG
*
491266 TTATCAATCGAGTTG
1 TTATCACTCGAGTTG
491281 TTATCAC
1 TTATCAC
491288 ATGGTATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (15 bp):
TTATCACTCGAGTTG
Found at i:491887 original size:21 final size:21
Alignment explanation
Indices: 491858--491925 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
491848 TTATTTTATA
491858 AAATA-AAATAAAATAATATTT
1 AAATATAAATAAAATAAT-TTT
* **
491879 -AATTTAAATTTAATAATTTT
1 AAATATAAATAAAATAATTTT
* *
491899 AAATATAAATAAATTTAAATTT
1 AAATATAAATAAA-ATAATTTT
491921 AAATA
1 AAATA
491926 ATTTTAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
20 6 0.17
21 19 0.53
22 11 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATAAATAAAATAATTTT
Found at i:491936 original size:16 final size:16
Alignment explanation
Indices: 491881--491941 Score: 88
Period size: 16 Copynumber: 3.8 Consensus size: 16
491871 TAATATTTAA
491881 TTTAAATTT-AATAAT
1 TTTAAATTTAAATAAT
* *
491896 TTTAAATATAAATAAA
1 TTTAAATTTAAATAAT
491912 TTTAAATTTAAATAAT
1 TTTAAATTTAAATAAT
491928 TTTAAATTTTAAAT
1 TTTAAA-TTTAAAT
491942 GCTTTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.20
16 25 0.62
17 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAATTTAAATAAT
Found at i:496360 original size:2 final size:2
Alignment explanation
Indices: 496355--496386 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
496345 TGATATATGC
496355 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
496387 ACATATATAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:498889 original size:17 final size:16
Alignment explanation
Indices: 498855--498893 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
498845 TGTTAATGAC
*
498855 TTAT-TTTATATATTT
1 TTATATTTATATATAT
498870 TTATATTTATATAATAT
1 TTATATTTATAT-ATAT
498887 TTATATT
1 TTATATT
498894 ATTTTTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTTATATATAT
Found at i:499195 original size:26 final size:26
Alignment explanation
Indices: 499166--499222 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
499156 TTTTTATATA
*
499166 GATTTTAATAT-ATTTGTGTTTAATTT
1 GATTTTAATATCATGT-TGTTTAATTT
**
499192 GATTTTCGTATCATGTTGTTTAATTT
1 GATTTTAATATCATGTTGTTTAATTT
499218 -ATTTT
1 GATTTT
499223 TTGTGTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.23, C:0.04, G:0.12, T:0.61
Consensus pattern (26 bp):
GATTTTAATATCATGTTGTTTAATTT
Found at i:499296 original size:40 final size:40
Alignment explanation
Indices: 499250--499327 Score: 140
Period size: 40 Copynumber: 1.9 Consensus size: 40
499240 TGCATATCAA
499250 TTCATCTCATATTTTTCT-TAATTTATCATAATTAATTACT
1 TTCATCTCATATTTTT-TATAATTTATCATAATTAATTACT
499290 TTCATCTCATATTTTTTATAATTTATCATAATTAATTA
1 TTCATCTCATATTTTTTATAATTTATCATAATTAATTA
499328 ATTTTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (40 bp):
TTCATCTCATATTTTTTATAATTTATCATAATTAATTACT
Found at i:499870 original size:2 final size:2
Alignment explanation
Indices: 499863--499904 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
499853 CCTTTATTGC
499863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
499904 A
1 A
499905 CAAAAATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:505920 original size:17 final size:17
Alignment explanation
Indices: 505898--505931 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
505888 TGATTTTTTA
505898 TATTTAAATAATAAATT
1 TATTTAAATAATAAATT
*
505915 TATTTATATAATAAATT
1 TATTTAAATAATAAATT
505932 AATAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTAAATAATAAATT
Found at i:506274 original size:21 final size:21
Alignment explanation
Indices: 506249--506292 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
506239 AAATACTTTT
* * *
506249 AATTTTATTATTATGATACTC
1 AATTTTACTATTATAATAATC
506270 AATTTTACTATTATAATAATC
1 AATTTTACTATTATAATAATC
506291 AA
1 AA
506293 GCTTACCGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTTTACTATTATAATAATC
Found at i:508699 original size:36 final size:36
Alignment explanation
Indices: 508652--508724 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
508642 GAAACAAGTA
*
508652 ACCAAAGAATGTTGGAATTAAC-TTGAAGTCATTCAT
1 ACCAAAGAATGTTCGAATT-ACGTTGAAGTCATTCAT
508688 ACCAAAGAATGTTCGAATTACGTTGAAGTCATTCAT
1 ACCAAAGAATGTTCGAATTACGTTGAAGTCATTCAT
508724 A
1 A
508725 AATGAAGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 2 0.06
36 33 0.94
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (36 bp):
ACCAAAGAATGTTCGAATTACGTTGAAGTCATTCAT
Done.