Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold485
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: 999764
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 8
Found at i:474026 original size:32 final size:32
Alignment explanation
Indices: 473984--474047 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
473974 CCTGCAAAGG
*
473984 CGATATGGAACTACGAGAAGTTCTTGGCGATA
1 CGATACGGAACTACGAGAAGTTCTTGGCGATA
474016 CGATACGGAACTACGAGAAGTTCTTGGCGATA
1 CGATACGGAACTACGAGAAGTTCTTGGCGATA
474048 GCATTGGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (32 bp):
CGATACGGAACTACGAGAAGTTCTTGGCGATA
Found at i:477896 original size:53 final size:52
Alignment explanation
Indices: 477839--478039 Score: 183
Period size: 53 Copynumber: 3.8 Consensus size: 52
477829 AATTTAGTTT
* * *
477839 TTAAATCTGACAAAAATATTAGAGTTTCAATTCGTGACATTCAAATTTAATGA
1 TTAAATCCGACAAAAATATTAGAGTTTCGATACGTGACATTCAAATTTAAT-A
* * * * * * *
477892 TTAAATTCGATAAAAATTTTTGAGTCTT-GATACGTAATACTCAAATTTAATA
1 TTAAATCCGACAAAAATATTAGAGT-TTCGATACGTGACATTCAAATTTAATA
* * * * * *
477944 CTTAAATCCGACAAAAATATTTGAGTCTCGAT-CTGCGAGACTCAAATCTAATA
1 -TTAAATCCGACAAAAATATTAGAGTTTCGATAC-GTGACATTCAAATTTAATA
477997 TCTAAATCCGACAAAAATATTTA-AGTTTCGATACGTGACATTC
1 T-TAAATCCGACAAAAATA-TTAGAGTTTCGATACGTGACATTC
478040 GAATCCGACA
Statistics
Matches: 118, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
52 4 0.03
53 109 0.92
54 5 0.04
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (52 bp):
TTAAATCCGACAAAAATATTAGAGTTTCGATACGTGACATTCAAATTTAATA
Found at i:477989 original size:106 final size:105
Alignment explanation
Indices: 477820--478032 Score: 243
Period size: 106 Copynumber: 2.0 Consensus size: 105
477810 TTTTAATTTA
* ** * * *
477820 TAATACTCAAATTTAGTTTTTAAATCTGACAAAAATATTAGAGTTTCAATTCGTGACATTCAAAT
1 TAATACTCAAATTTAATACTTAAATCCGACAAAAATATTAGAGTCTCAATTCGAGACA-TCAAAT
* * * * *
477885 TTAATGAT-TAAATTCGATAAAAATTTTTGAGTCTT-GATACG
65 CTAAT-ATCTAAATCCGACAAAAATATTTAAGT-TTCGATACG
* *
477926 TAATACTCAAATTTAATACTTAAATCCGACAAAAATATTTGAGTCTCGATCTGCGAGAC-TCAAA
1 TAATACTCAAATTTAATACTTAAATCCGACAAAAATATTAGAGTCTCAAT-T-CGAGACATCAAA
477990 TCTAATATCTAAATCCGACAAAAATATTTAAGTTTCGATACG
64 TCTAATATCTAAATCCGACAAAAATATTTAAGTTTCGATACG
478032 T
1 T
478033 GACATTCGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
105 4 0.04
106 80 0.89
107 1 0.01
108 5 0.06
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (105 bp):
TAATACTCAAATTTAATACTTAAATCCGACAAAAATATTAGAGTCTCAATTCGAGACATCAAATC
TAATATCTAAATCCGACAAAAATATTTAAGTTTCGATACG
Found at i:478782 original size:6 final size:6
Alignment explanation
Indices: 478771--478795 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
478761 ATTTAAAAAA
478771 TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT T
478796 AAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:479019 original size:15 final size:16
Alignment explanation
Indices: 478992--479041 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
478982 AAGAAATCTC
*
478992 AAATTCAAAATAATTT
1 AAATTTAAAATAATTT
* *
479008 AAATTT-AAATAAATA
1 AAATTTAAAATAATTT
*
479023 AAATTTAAAATCATTT
1 AAATTTAAAATAATTT
479039 AAA
1 AAA
479042 CTCAAACTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:479263 original size:21 final size:20
Alignment explanation
Indices: 479224--479267 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
479214 ATATTAAACC
*
479224 TTAAATCTTAAACAATAAGCT
1 TTAAATCCTAAACAATAAG-T
* *
479245 TTAAATCCTAAGCATTAAGT
1 TTAAATCCTAAACAATAAGT
479265 TTA
1 TTA
479268 TACTTTGAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (20 bp):
TTAAATCCTAAACAATAAGT
Found at i:480194 original size:24 final size:24
Alignment explanation
Indices: 480158--480203 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
480148 TAAATCGATT
* *
480158 GAATTGAAATATTTAATTAAAAAA
1 GAATTGAAATATTAAATGAAAAAA
* *
480182 GAATTTAAGTATTAAATGAAAA
1 GAATTGAAATATTAAATGAAAA
480204 TTTTAATATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.33
Consensus pattern (24 bp):
GAATTGAAATATTAAATGAAAAAA
Found at i:490729 original size:19 final size:19
Alignment explanation
Indices: 490705--490766 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
490695 TTTATGTCGA
490705 TAATAAATATAATTAAAAT
1 TAATAAATATAATTAAAAT
490724 TAATAAATAT-ATTAAAAT
1 TAATAAATATAATTAAAAT
* *
490742 T-TTAAATATTAATTTAAAT
1 TAATAAATA-TAATTAAAAT
*
490761 AAATAA
1 TAATAA
490767 TATCATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.17
18 10 0.28
19 17 0.47
20 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAAATATAATTAAAAT
Found at i:491090 original size:27 final size:27
Alignment explanation
Indices: 491038--491090 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
491028 TCTTTTGAAT
**
491038 TTTTTTTAATTATATAATATTCATTAA
1 TTTTTTTAATTATATAATATAAATTAA
491065 TTTTTTTAATTATATAAGTA-AAATTA
1 TTTTTTTAATTATATAA-TATAAATTA
491091 TGAAACTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTTTAATTATATAATATAAATTAA
Found at i:491276 original size:28 final size:27
Alignment explanation
Indices: 491240--491300 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
491230 GAATCAACGA
* *
491240 AAATAATTACTATATTTATTTTATTTTT
1 AAATAATTACTATAATT-TTTTATTATT
* *
491268 AAATTATTATTATAATTTTTTATTATT
1 AAATAATTACTATAATTTTTTATTATT
491295 -AATAAT
1 AAATAAT
491301 ACTTATCTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 5 0.18
27 9 0.32
28 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
AAATAATTACTATAATTTTTTATTATT
Found at i:491715 original size:20 final size:20
Alignment explanation
Indices: 491665--491703 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
491655 GTTTATTAAC
491665 AATT-GTTT-TTACTTTTTT
1 AATTAGTTTCTTACTTTTTT
491683 AATTAGTTTCTTACTTTTTT
1 AATTAGTTTCTTACTTTTTT
491703 A
1 A
491704 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (20 bp):
AATTAGTTTCTTACTTTTTT
Found at i:492393 original size:2 final size:2
Alignment explanation
Indices: 492386--492412 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
492376 GGCATTGACT
492386 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
492413 TTCATAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:492668 original size:16 final size:16
Alignment explanation
Indices: 492647--492683 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
492637 CAAACCTGAG
492647 TTAAATCTAAAATAAT
1 TTAAATCTAAAATAAT
* *
492663 TTAAATTTAAAATTAT
1 TTAAATCTAAAATAAT
492679 TTAAA
1 TTAAA
492684 CCCGAACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAATCTAAAATAAT
Found at i:492859 original size:16 final size:17
Alignment explanation
Indices: 492838--492870 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
492828 TCAAAATTAC
492838 TAAATTT-AAAATAATT
1 TAAATTTAAAAATAATT
492854 TAAATTTAAAAATAATT
1 TAAATTTAAAAATAATT
492871 CAAAAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAAAATAATT
Found at i:493143 original size:15 final size:15
Alignment explanation
Indices: 493123--493181 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
493113 TTAAAATATT
493123 TTATAATTATATAAA
1 TTATAATTATATAAA
*
493138 TTATAATATATTAATAAT
1 TTATAAT-TA-T-ATAAA
493156 TTAT-ATTATATAAA
1 TTATAATTATATAAA
*
493170 TTTTAATT-TATA
1 TTATAATTATATA
493182 TTTGTAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 11 0.30
15 11 0.30
16 4 0.11
17 3 0.08
18 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAATTATATAAA
Found at i:493159 original size:18 final size:18
Alignment explanation
Indices: 493117--493166 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
493107 TTATATTTAA
*
493117 AATATTTTATAAT-TA-T
1 AATAATTTATAATATATT
*
493133 -ATAAATTATAATATATT
1 AATAATTTATAATATATT
*
493150 AATAATTTATATTATAT
1 AATAATTTATAATATAT
493167 AAATTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 1 0.04
18 14 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATAATTTATAATATATT
Found at i:493166 original size:32 final size:34
Alignment explanation
Indices: 493087--493176 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 34
493077 TAATTCGTAT
*
493087 ATTTATATTAT-T-CATTATAATTATATTTAAAATA
1 ATTTATATTATATAAATTATAA-TATATTT-AAATA
*
493121 TTTTATAATTATATAAATTATAATATA-TT-AATA
1 ATTTAT-ATTATATAAATTATAATATATTTAAATA
*
493154 ATTTATATTATATAAATTTTAAT
1 ATTTATATTATATAAATTATAAT
493177 TTATATTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
32 16 0.33
33 9 0.18
34 5 0.10
35 7 0.14
36 5 0.10
37 7 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTTATATTATATAAATTATAATATATTTAAATA
Found at i:497869 original size:8 final size:8
Alignment explanation
Indices: 497842--497930 Score: 58
Period size: 8 Copynumber: 10.8 Consensus size: 8
497832 TTTTGTTTTA
497842 TTATAT-T
1 TTATATAT
*
497849 TTATTATAA
1 TTA-TATAT
497858 TTATATAT
1 TTATATAT
497866 TTATATAATT
1 TTATAT-A-T
497876 TTAATATAT
1 TT-ATATAT
*
497885 TAATA-AT
1 TTATATAT
497892 TTATAT-T
1 TTATATAT
* *
497899 TTTTAAAAT
1 TTAT-ATAT
497908 TTATTATAT
1 TTA-TATAT
*
497917 TTATATTT
1 TTATATAT
497925 TTATAT
1 TTATAT
497931 TACATTATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
7 13 0.20
8 27 0.42
9 15 0.23
10 5 0.08
11 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATATAT
Found at i:497916 original size:32 final size:32
Alignment explanation
Indices: 497845--497931 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 32
497835 TGTTTTATTA
* *
497845 TATTTTATTATAA-TTATATATTTATATAATTT
1 TATTATATTATAATTTATAT-TTTATATAAATT
* *
497877 TAATATATTAATAATTTATATTTTTTA-AAATT
1 TATTATATT-ATAATTTATATTTTATATAAATT
*
497909 TATTATATTTATATTTTTATATT
1 TATTATA-TTATA-ATTTATATT
497932 ACATTATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
32 20 0.44
33 19 0.42
34 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TATTATATTATAATTTATATTTTATATAAATT
Found at i:497942 original size:25 final size:22
Alignment explanation
Indices: 497910--497965 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
497900 TTTAAAATTT
497910 ATTATATTTATATTTTTATATTAC
1 ATTATATTTA-ATTTTT-TATTAC
*
497934 ATTATTATTTAATTTTTTATTAT
1 ATTA-TATTTAATTTTTTATTAC
497957 ATTTATATT
1 A-TTATATT
497966 ATATCTAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 10 0.34
24 13 0.45
25 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTATATTTAATTTTTTATTAC
Found at i:497961 original size:51 final size:52
Alignment explanation
Indices: 497838--497962 Score: 127
Period size: 51 Copynumber: 2.4 Consensus size: 52
497828 GATATTTTGT
* * *
497838 TTTATTATATTTTATTATAATTA-TATATTTATATAATTTTAATATATTAATAA
1 TTTA-TATTTTTTATTATATTTATTATATTTATAT-ATTTTAATACATTAATAA
* *
497891 TTTATATTTTTTA--AAATTTATTATATTTATAT-TTTTATATTACATT-ATTA
1 TTTATATTTTTTATTATATTTATTATATTTATATATTTTA-A-TACATTAATAA
497941 TTTA-ATTTTTTATTATATTTAT
1 TTTATATTTTTTATTATATTTAT
497963 ATTATATCTA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
49 13 0.21
50 13 0.21
51 23 0.38
52 8 0.13
53 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (52 bp):
TTTATATTTTTTATTATATTTATTATATTTATATATTTTAATACATTAATAA
Found at i:498052 original size:16 final size:17
Alignment explanation
Indices: 498015--498052 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
498005 ATGAAAATAT
498015 TTAA-TTAAAAATAAAA
1 TTAATTTAAAAATAAAA
498031 TT-ATTTAAAAAT-AAA
1 TTAATTTAAAAATAAAA
498046 TTAATTT
1 TTAATTT
498053 TATTCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAATTTAAAAATAAAA
Found at i:499020 original size:4 final size:4
Alignment explanation
Indices: 499011--499035 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
499001 CCTTAATTGC
499011 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
499036 TAATAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:499039 original size:3 final size:3
Alignment explanation
Indices: 499031--499063 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
499021 TAAATAAATA
499031 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
499064 TTTATATAGT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:502994 original size:21 final size:22
Alignment explanation
Indices: 502961--503004 Score: 56
Period size: 20 Copynumber: 2.0 Consensus size: 22
502951 ATTAATTATA
502961 AAATATAATAATCAAATTAAAAT
1 AAATATAATAATC-AATTAAAAT
*
502984 AAATAT-A-AATCATTTAAAAT
1 AAATATAATAATCAATTAAAAT
503004 A
1 A
503005 TTTTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 1 0.05
23 6 0.30
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATATAATAATCAATTAAAAT
Found at i:503040 original size:19 final size:20
Alignment explanation
Indices: 503016--503055 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
503006 TTTAAAAACG
503016 TGTAAAATTA-ATTTTTCAT
1 TGTAAAATTATATTTTTCAT
*
503035 TGTAAAATTATCTTTTTCAT
1 TGTAAAATTATATTTTTCAT
503055 T
1 T
503056 AATTAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (20 bp):
TGTAAAATTATATTTTTCAT
Found at i:504414 original size:10 final size:10
Alignment explanation
Indices: 504378--504433 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
504368 TTATTATAAA
*
504378 ATAAAATAAT
1 ATAAAATTAT
*
504388 AAAAAATTAT
1 ATAAAATTAT
504398 ATAAAATTA-
1 ATAAAATTAT
504407 ATATAAA-TAT
1 ATA-AAATTAT
504417 ATTAAAATT-T
1 A-TAAAATTAT
504427 ATAAAAT
1 ATAAAAT
504434 ATAAATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 11 0.28
10 25 0.64
11 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAATTAT
Found at i:504433 original size:19 final size:20
Alignment explanation
Indices: 504378--504436 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
504368 TTATTATAAA
*
504378 ATAAAA-TAATAAAAAATTAT
1 ATAAAATTAATAAAATA-TAT
504398 ATAAAATTAATATAAATATAT
1 ATAAAATTAATA-AAATATAT
*
504419 -TAAAATTTATAAAATATA
1 ATAAAATTAATAAAATATA
504437 AATTATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 7 0.20
20 16 0.46
21 8 0.23
22 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAATTAATAAAATATAT
Found at i:504781 original size:16 final size:16
Alignment explanation
Indices: 504760--504795 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
504750 CTTTAAAAAG
*
504760 AATATTATATGAATAT
1 AATATTATATAAATAT
504776 AATATTATATAAATAT
1 AATATTATATAAATAT
504792 AATA
1 AATA
504796 ATATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATATTATATAAATAT
Found at i:504805 original size:16 final size:16
Alignment explanation
Indices: 504760--504803 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
504750 CTTTAAAAAG
* *
504760 AATATTATATGAATAT
1 AATAATATATAAATAT
*
504776 AATATTATATAAATAT
1 AATAATATATAAATAT
504792 AATAATAT-TAAA
1 AATAATATATAAA
504804 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AATAATATATAAATAT
Found at i:511697 original size:21 final size:21
Alignment explanation
Indices: 511655--511714 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
511645 TAATAATTTT
* *
511655 ATATTAA-ACTAATATATTTAA
1 ATATTAATA-TAAAATATATAA
511676 AT-TTAAATATAAAATATATAA
1 ATATT-AATATAAAATATATAA
511697 ATATTAATATAAAA-ATAT
1 ATATTAATATAAAATATAT
511715 TTTTAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.18
21 25 0.74
22 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATTAATATAAAATATATAA
Found at i:511723 original size:21 final size:21
Alignment explanation
Indices: 511699--511741 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
511689 ATATATAAAT
*
511699 ATTAATATAAA-AATATTTTTA
1 ATTAA-ATAAATAATAATTTTA
511720 ATTAAATAAATAATAATTTTA
1 ATTAAATAAATAATAATTTTA
511741 A
1 A
511742 ATTTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAATAAATAATAATTTTA
Found at i:512392 original size:16 final size:16
Alignment explanation
Indices: 512371--512426 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
512361 ATTTTATATA
512371 AAATATTATATTAATT
1 AAATATTATATTAATT
*
512387 AAATATTA-ATTTTATT
1 AAATATTATA-TTAATT
512403 AAATATT-TATTATATT
1 AAATATTATATTA-ATT
*
512419 TAATATTA
1 AAATATTA
512427 AATATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 3 0.09
16 30 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTATATTAATT
Found at i:512424 original size:32 final size:34
Alignment explanation
Indices: 512350--512427 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 34
512340 ATATAAGATT
*
512350 TTAAATTTTAAATTTTATATAAAATATTATATTAA
1 TTAAATATT-AATTTTATATAAAATATTATATTAA
512385 TTAAATATTAATTTTAT-T-AAATATT-TATTATA
1 TTAAATATTAATTTTATATAAAATATTATATTA-A
*
512417 TTTAATATTAA
1 TTAAATATTAA
512428 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 5 0.12
32 18 0.45
33 1 0.03
34 8 0.20
35 8 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TTAAATATTAATTTTATATAAAATATTATATTAA
Found at i:512437 original size:32 final size:32
Alignment explanation
Indices: 512371--512437 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
512361 ATTTTATATA
*
512371 AAATATTATATTAATTAAATATTAATTTTATT
1 AAATATTATATTAATTAAATATTAATATTATT
*
512403 AAATATT-TATTATATTTAATATTAAATATT-TT
1 AAATATTATATTA-ATTAAATATT-AATATTATT
512435 AAA
1 AAA
512438 ATAATTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 5 0.16
32 21 0.68
33 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AAATATTATATTAATTAAATATTAATATTATT
Found at i:512445 original size:24 final size:23
Alignment explanation
Indices: 512399--512447 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
512389 ATATTAATTT
** *
512399 TATTAAATATTTATTATATTTAA
1 TATTAAATATTTAAAATAATTAA
512422 TATTAAATATTTTAAAATAATTAA
1 TATTAAATA-TTTAAAATAATTAA
512446 TA
1 TA
512448 AATCAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTAAATATTTAAAATAATTAA
Found at i:513090 original size:61 final size:60
Alignment explanation
Indices: 512967--513093 Score: 168
Period size: 61 Copynumber: 2.1 Consensus size: 60
512957 TTTTTAATAT
* * *
512967 TTTTAATTTATTAATTATATTTTAAATAGTATTTTATTAAAAAATGATACAATTAATTGTA
1 TTTTAATTTATTAATTATATTTTAAATAATATTTTATTAAAAAATAATACAA-TAATAGTA
*
513028 TTTTAATTTATTAATTGTATTTTAAATAATATTTTATTAAATAGAATTAATA-AA-AATAGTA
1 TTTTAATTTATTAATTATATTTTAAATAATATTTTATTAAA-A-AA-TAATACAATAATAGTA
513089 TTTTA
1 TTTTA
513094 TTAATTGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
61 50 0.85
62 1 0.02
63 4 0.07
64 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (60 bp):
TTTTAATTTATTAATTATATTTTAAATAATATTTTATTAAAAAATAATACAATAATAGTA
Found at i:513110 original size:17 final size:17
Alignment explanation
Indices: 513088--513151 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
513078 TAAAAATAGT
513088 ATTTTATTAATTGTATC
1 ATTTTATTAATTGTATC
* * *
513105 ATTTTAAATAGTATT-TTTT
1 ATTTT-ATTA--ATTGTATC
513124 ATTTTTATTAATTGTATC
1 A-TTTTATTAATTGTATC
513142 ATTTTATTAA
1 ATTTTATTAA
513152 AAATAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 17 0.47
18 6 0.17
19 6 0.17
20 7 0.19
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (17 bp):
ATTTTATTAATTGTATC
Found at i:513169 original size:15 final size:15
Alignment explanation
Indices: 513149--513179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
513139 ATCATTTTAT
513149 TAAAAATAAAATTAA
1 TAAAAATAAAATTAA
*
513164 TAAAAATAGAATTAA
1 TAAAAATAAAATTAA
513179 T
1 T
513180 GGCACTTGGT
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:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
TAAAAATAAAATTAA
Found at i:514019 original size:22 final size:22
Alignment explanation
Indices: 513993--514034 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
513983 GGTCATAGAG
*
513993 TTTAAACTTA-AATTTTAATTTT
1 TTTAAAATTATAA-TTTAATTTT
514015 TTTAAAATTATAATTTAATT
1 TTTAAAATTATAATTTAATT
514035 CATAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAAATTATAATTTAATTTT
Found at i:517130 original size:16 final size:16
Alignment explanation
Indices: 517109--517140 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
517099 ATAAAGCTAT
517109 ACTCAAAAATCAAGGA
1 ACTCAAAAATCAAGGA
517125 ACTCAAAAATCAAGGA
1 ACTCAAAAATCAAGGA
517141 GAATAGTTGG
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:0.56, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
ACTCAAAAATCAAGGA
Found at i:518472 original size:30 final size:30
Alignment explanation
Indices: 518412--518478 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
518402 ATTTAAGTAT
*
518412 TTTTAA-TATTTAATTTAAATAATTTAAAA
1 TTTTAATTATTTAATTTAAATAATATAAAA
* *
518441 TTTTAATTATTTTATTTTTAATAATAT-AAA
1 TTTTAATTA-TTTAATTTAAATAATATAAAA
*
518471 TTTAAATT
1 TTTTAATT
518479 TAAAATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 6 0.19
30 12 0.38
31 14 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTTAATTATTTAATTTAAATAATATAAAA
Found at i:518574 original size:13 final size:13
Alignment explanation
Indices: 518556--518622 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
518546 TTATTTTAAA
518556 TTAAATTTAAATT
1 TTAAATTTAAATT
*
518569 TTAAATATAAATT
1 TTAAATTTAAATT
**
518582 TT-AA-CCAAA-T
1 TTAAATTTAAATT
518592 TTAAA-TTAAATT
1 TTAAATTTAAATT
* * *
518604 ATATACTTAAATT
1 TTAAATTTAAATT
518617 TTAAAT
1 TTAAAT
518623 CCAACATAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
10 3 0.07
11 8 0.20
12 6 0.15
13 24 0.59
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATTTAAATT
Found at i:518591 original size:24 final size:25
Alignment explanation
Indices: 518564--518622 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
518554 AATTAAATTT
*
518564 AAATTTTAAATATAAATTTTA-AC-C
1 AAATTTTAAAT-TAAATTATATACTC
*
518588 AAA-TTTAAATTAAATTATATACTT
1 AAATTTTAAATTAAATTATATACTC
518612 AAATTTTAAAT
1 AAATTTTAAAT
518623 CCAACATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.27
23 9 0.30
24 6 0.20
25 7 0.23
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTTTAAATTAAATTATATACTC
Found at i:518785 original size:2 final size:2
Alignment explanation
Indices: 518778--518807 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
518768 GTCATTTCAT
518778 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
518808 CCGTTGTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:519944 original size:29 final size:28
Alignment explanation
Indices: 519878--519945 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
519868 CTTTTGAAAC
*
519878 TTTCCACTAACACTATCACTACTTGAAA
1 TTTCCACTAACACTATCACTACTTCAAA
* *
519906 CTACCTACTAACA-TAATCACTACTTCAAA
1 TTTCC-ACTAACACT-ATCACTACTTCAAA
519935 TTTCTCACTAA
1 TTTC-CACTAA
519946 TCAACCACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.12
29 27 0.84
30 1 0.03
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.32
Consensus pattern (28 bp):
TTTCCACTAACACTATCACTACTTCAAA
Found at i:527495 original size:23 final size:25
Alignment explanation
Indices: 527468--527521 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
527458 GATACATTTT
*
527468 AATATTTTAT-TA-AAAAATTTAAA
1 AATATATTATATATAAAAATTTAAA
*
527491 AATATATTATATATAAATATTTAAA
1 AATATATTATATATAAAAATTTAAA
527516 AA-ATAT
1 AATATAT
527522 CAATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 6 0.22
25 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATATATTATATATAAAAATTTAAA
Found at i:527547 original size:19 final size:18
Alignment explanation
Indices: 527499--527547 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
527489 AAAATATATT
*
527499 ATATATAAATATTTAAAAA
1 ATATATTAA-ATTTAAAAA
*
527518 ATATCAATAAATTTAAAATA
1 ATAT-ATTAAATTTAAAA-A
527538 ATATATTAAA
1 ATATATTAAA
527548 ATTTGTGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATATTAAATTTAAAAA
Found at i:527610 original size:2 final size:2
Alignment explanation
Indices: 527603--527639 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
527593 TACTGCCTCA
527603 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
527640 CTTATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:534289 original size:15 final size:15
Alignment explanation
Indices: 534253--534308 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
534243 TTTTTATCCT
* *
534253 TTTTATTTAATATAA
1 TTTTATATAAAATAA
534268 -TTT-TATAAAATAA
1 TTTTATATAAAATAA
*
534281 TTTTATATATAATTAA
1 TTTTATATA-AAATAA
*
534297 TTATATATAAAA
1 TTTTATATAAAA
534309 ATAAATAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 8 0.24
14 6 0.18
15 6 0.18
16 13 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTTATATAAAATAA
Found at i:534294 original size:12 final size:12
Alignment explanation
Indices: 534258--534306 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
534248 ATCCTTTTTA
534258 TTTA-ATATAAT
1 TTTATATATAAT
*
534269 TTTATAAAATAAT
1 TTTAT-ATATAAT
534282 TTTATATATAAT
1 TTTATATATAAT
534294 TAATTATATATAA
1 T--TTATATATAA
534307 AAATAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.12
12 7 0.22
13 11 0.34
14 10 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTTATATATAAT
Found at i:540144 original size:16 final size:17
Alignment explanation
Indices: 540102--540151 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
540092 TATTTAATAA
540102 TTAATT-TAAATTAATAT
1 TTAATTATAAATT-ATAT
540119 TT-ATTAATAAATT-TAT
1 TTAATT-ATAAATTATAT
*
540135 TTAATTATAAAATATAT
1 TTAATTATAAATTATAT
540152 AAATATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 14 0.50
17 8 0.29
18 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTATAAATTATAT
Found at i:540158 original size:23 final size:24
Alignment explanation
Indices: 540132--540182 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
540122 TTAATAAATT
*
540132 TATTTAATTATAAAATATA-TAAA
1 TATTTAATTATAAAAAATATTAAA
* *
540155 TA-TTAATTTTAAAAAATATTTAA
1 TATTTAATTATAAAAAATATTAAA
540178 TATTT
1 TATTT
540183 TTAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 14 0.61
23 7 0.30
24 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTTAATTATAAAAAATATTAAA
Found at i:540231 original size:18 final size:18
Alignment explanation
Indices: 540182--540232 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
540172 ATTTAATATT
540182 TTTAAATAATAAATTAAA
1 TTTAAATAATAAATTAAA
540200 TTT--ATAAGTTAAATTAAA
1 TTTAAATAA--TAAATTAAA
*
540218 TTTAAATAAAAAATT
1 TTTAAATAATAAATT
540233 TTATCAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
16 4 0.14
18 20 0.71
20 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTAAATAATAAATTAAA
Found at i:546632 original size:22 final size:19
Alignment explanation
Indices: 546603--546650 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
546593 ATTTTTATTT
546603 AAATTTAATTATAAAATATAA
1 AAATTTAA-TATAAAA-ATAA
546624 AAATATTAATATAAAAATAA
1 AAAT-TTAATATAAAAATAA
*
546644 AATTTTA
1 AAATTTA
546651 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 7 0.28
21 11 0.44
22 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTAATATAAAAATAA
Found at i:554464 original size:51 final size:51
Alignment explanation
Indices: 554405--554501 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 51
554395 TGCCTAAATA
* * *
554405 TAATCAAATTGAATTCCCAGGTTTAAAAGAGCATCTAAATCTAAATTAATC
1 TAATCAAATTAAACTCCCAAGTTTAAAAGAGCATCTAAATCTAAATTAATC
** *
554456 TAATCAAATTAAACTCCCAAGTTTAATGGAGTATCTAAATCTAAAT
1 TAATCAAATTAAACTCCCAAGTTTAAAAGAGCATCTAAATCTAAAT
554502 CCAAATTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (51 bp):
TAATCAAATTAAACTCCCAAGTTTAAAAGAGCATCTAAATCTAAATTAATC
Found at i:555972 original size:36 final size:38
Alignment explanation
Indices: 555932--556023 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 38
555922 GTTGCTTTTG
555932 TTTTTTTTAATAT-T-AATA-TTTAAATAAA-AAATAT-
1 TTTTTTTTAATATATAAATATTTTAAA-AAATAAATATA
*
555966 TATTTTTTAATATATAAATATTTTAAAAAATAAATATA
1 TTTTTTTTAATATATAAATATTTTAAAAAATAAATATA
*
556004 -TTTTTATAA-ATA-AAATATTT
1 TTTTTTTTAATATATAAATATTT
556024 ATATTTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
34 12 0.24
35 9 0.18
36 10 0.20
37 19 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
TTTTTTTTAATATATAAATATTTTAAAAAATAAATATA
Found at i:555987 original size:18 final size:18
Alignment explanation
Indices: 555966--556023 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 18
555956 TAAAAAATAT
*
555966 TATTTTTTAATATATAAA
1 TATTTTTTAATAAATAAA
*
555984 TA--TTTTAAAAAATAAA
1 TATTTTTTAATAAATAAA
556000 TATATTTTT-ATAAATAAAA
1 TAT-TTTTTAATAAAT-AAA
556019 TATTT
1 TATTT
556024 ATATTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 14 0.42
18 9 0.27
19 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTTTAATAAATAAA
Found at i:556020 original size:35 final size:37
Alignment explanation
Indices: 555934--556023 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 37
555924 TGCTTTTGTT
555934 TTTTTTAATAT-T-AATA-TTTAAATAAAAAATATTA
1 TTTTTTAATATATAAATATTTTAAATAAAAAATATTA
555968 TTTTTTAATATATAAATATTTTAAA-AAATAAATA-TA
1 TTTTTTAATATATAAATATTTTAAATAAA-AAATATTA
556004 TTTTTATAA-ATA-AAATATTT
1 TTTTT-TAATATATAAATATTT
556024 ATATTTAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
34 11 0.22
35 9 0.18
36 17 0.33
37 14 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
TTTTTTAATATATAAATATTTTAAATAAAAAATATTA
Found at i:556033 original size:18 final size:18
Alignment explanation
Indices: 555947--556027 Score: 62
Period size: 17 Copynumber: 4.6 Consensus size: 18
555937 TTTAATATTA
*
555947 ATATTTAAATAAA-AAAT
1 ATATTTATATAAATAAAT
* *
555964 ATTATTTTTTAATATATAAAT
1 A-TA-TTTAT-ATAAATAAAT
*
555985 AT-TTTA-AAAAATAAAT
1 ATATTTATATAAATAAAT
*
556001 ATATTTTTATAAATAAA-
1 ATATTTATATAAATAAAT
556018 ATATTTATAT
1 ATATTTATAT
556028 TTAATATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 10 0.20
17 13 0.27
18 13 0.27
19 3 0.06
20 5 0.10
21 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTATATAAATAAAT
Found at i:556338 original size:22 final size:22
Alignment explanation
Indices: 556301--556351 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
556291 ATTTAAATTT
*
556301 AATAATTTTAAATATAATATAAA
1 AATAA-TTAAAATATAATATAAA
*
556324 AATAATTAAAATATAATATTAA
1 AATAATTAAAATATAATATAAA
*
556346 TATAAT
1 AATAAT
556352 ATTAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAATTAAAATATAATATAAA
Found at i:556346 original size:28 final size:27
Alignment explanation
Indices: 556311--556363 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
556301 AATAATTTTA
556311 AATATAATATAAAAATAATTAAAATAT
1 AATATAATATAAAAATAATTAAAATAT
* *
556338 AATATTAATATAATATTAATTAAAAT
1 AATA-TAATATAAAAATAATTAAAAT
556364 TATTCATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AATATAATATAAAAATAATTAAAATAT
Found at i:556357 original size:11 final size:11
Alignment explanation
Indices: 556309--556353 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
556299 TTAATAATTT
556309 TAAATATAATA
1 TAAATATAATA
*
556320 TAAAAATAAT-
1 TAAATATAATA
556330 TAAAATATAATA
1 T-AAATATAATA
*
556342 TTAATATAATA
1 TAAATATAATA
556353 T
1 T
556354 TAATTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATATAATA
Found at i:556901 original size:14 final size:13
Alignment explanation
Indices: 556882--556924 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
556872 AACAAAGCAA
*
556882 ATATCATACATCAT
1 ATATCATATAT-AT
556896 ATATCATATATAT
1 ATATCATATATAT
556909 ATAT-ATATATAT
1 ATATCATATATAT
556921 ATAT
1 ATAT
556925 ATAAAAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 12 0.43
13 6 0.21
14 10 0.36
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATCATATATAT
Found at i:556906 original size:2 final size:2
Alignment explanation
Indices: 556894--556927 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
556884 ATCATACATC
556894 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
556928 AAAGTAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:557925 original size:28 final size:28
Alignment explanation
Indices: 557872--557928 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
557862 GAATATATAA
*
557872 ATTTATACATTATCGATATATCAAATAT
1 ATTTATACATTATCGATACATCAAATAT
* * *
557900 ATTTATATATTATCGATGCATGAAATAT
1 ATTTATACATTATCGATACATCAAATAT
557928 A
1 A
557929 AATCCGTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (28 bp):
ATTTATACATTATCGATACATCAAATAT
Found at i:559884 original size:21 final size:21
Alignment explanation
Indices: 559841--559882 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
559831 ATTAATATAA
* *
559841 AAATAATATTTTATATATTTT
1 AAATAATAATTTAAATATTTT
559862 AAATAATAATTTAAATTATTT
1 AAATAATAATTTAAA-TATTT
559883 AATTAGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATAATAATTTAAATATTTT
Found at i:560057 original size:13 final size:13
Alignment explanation
Indices: 560018--560058 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
560008 GTACGGAAAA
560018 TAATATTTTATAT
1 TAATATTTTATAT
* *
560031 TATTTTTTTAATAT
1 TAATATTTT-ATAT
560045 TAATATTTTATAT
1 TAATATTTTATAT
560058 T
1 T
560059 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TAATATTTTATAT
Found at i:560140 original size:19 final size:20
Alignment explanation
Indices: 560098--560145 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
560088 ATTTAAATAT
* *
560098 AAATATAAAATTAATTTTTTA
1 AAATAT-AAATTAATATTTAA
560119 AAATATAAA-TAATATTTAA
1 AAATATAAATTAATATTTAA
560138 AAAT-TAAA
1 AAATATAAA
560146 AAAATTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.16
19 12 0.48
20 3 0.12
21 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATAAATTAATATTTAA
Found at i:562092 original size:15 final size:15
Alignment explanation
Indices: 562072--562115 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
562062 TTTTATTATA
562072 ATTATAATAAATATT
1 ATTATAATAAATATT
562087 ATTATAAT---TA--
1 ATTATAATAAATATT
562097 ATTATAATAAATATT
1 ATTATAATAAATATT
562112 ATTA
1 ATTA
562116 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
10 8 0.33
12 2 0.08
13 2 0.08
15 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATAAATATT
Found at i:562329 original size:22 final size:22
Alignment explanation
Indices: 562291--562356 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
562281 TATAATATTT
562291 AATA-TTTAATAAA-ATTATG-A
1 AATATTTTAA-AAATATTATGTA
*
562311 AATATTATTAAAAATATTATGTT
1 AATATT-TTAAAAATATTATGTA
*
562334 ATTATTTTGAAAAATATTATGTA
1 AATATTTT-AAAAATATTATGTA
562357 TCATAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 12 0.32
23 18 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
AATATTTTAAAAATATTATGTA
Found at i:562409 original size:20 final size:20
Alignment explanation
Indices: 562384--562429 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
562374 GTTAAATATT
*
562384 AAATTAATATTTATTTAATA
1 AAATTAATATGTATTTAATA
562404 AAATTAATATGTATTTAATA
1 AAATTAATATGTATTTAATA
562424 AAATTA
1 AAATTA
562430 TAATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATTAATATGTATTTAATA
Found at i:562996 original size:33 final size:33
Alignment explanation
Indices: 562959--563032 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
562949 AATAATCTTT
* * *
562959 TTTATTTTTTTATATTTATAATTAATAAATATA
1 TTTATTTATTTATATTAAAAATTAATAAATATA
* * *
562992 TTTATTTATTTATCTTAAAAATTATTAAATTTA
1 TTTATTTATTTATATTAAAAATTAATAAATATA
563025 TTT-TTTAT
1 TTTATTTAT
563033 CATTGTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
32 5 0.14
33 30 0.86
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTATTTATTTATATTAAAAATTAATAAATATA
Found at i:563000 original size:37 final size:38
Alignment explanation
Indices: 562914--563002 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 38
562904 GAATTAATAT
* * *
562914 TAATATTATTTA-TGTTTTATTATTTATAAATAATTAA
1 TAATCTTATTTATTTTTTTATTATTTATAAATAATAAA
* *
562951 TAATCTTTTTTATTTTTTTA-TATTTATAATTAATAAA
1 TAATCTTATTTATTTTTTTATTATTTATAAATAATAAA
562988 TATAT-TTATTTATTT
1 TA-ATCTTATTTATTT
563003 ATCTTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
37 36 0.82
38 8 0.18
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (38 bp):
TAATCTTATTTATTTTTTTATTATTTATAAATAATAAA
Found at i:563584 original size:18 final size:18
Alignment explanation
Indices: 563563--563656 Score: 51
Period size: 16 Copynumber: 5.6 Consensus size: 18
563553 TAATAAAATT
563563 TATATATAAAATATAATA
1 TATATATAAAATATAATA
* * *
563581 TATAAAT-TAAT-TAAAA
1 TATATATAAAATATAATA
*
563597 TTTATATAAAATA-AAT-
1 TATATATAAAATATAATA
*
563613 TAT-TA-AAATATTTAA-A
1 TATATATAAA-ATATAATA
* *
563629 TTTATAT-AAATAAAATA
1 TATATATAAAATATAATA
563646 TATAATATAAA
1 TAT-ATATAAA
563657 TATTAAATTA
Statistics
Matches: 53, Mismatches: 13, Indels: 19
0.62 0.15 0.22
Matches are distributed among these distances:
14 3 0.06
15 4 0.08
16 19 0.36
17 15 0.28
18 10 0.19
19 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATATAAAATATAATA
Found at i:563596 original size:36 final size:35
Alignment explanation
Indices: 563556--563663 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
563546 ACGAACGTAA
563556 TAAAATTTATATATAAAATATAATATATAAATTAAT
1 TAAAATTTATATATAAAATATAATATATAAATT-AT
*
563592 TAAAA-TT-TATATAAAATA-AAT-TATTAAAATAT
1 TAAAATTTATATATAAAATATAATATA-TAAATTAT
*
563624 TTAAATTTATATAAATAAAATAT-ATAATATAAA-TAT
1 TAAAATTTATAT--ATAAAATATAAT-ATATAAATTAT
563660 TAAA
1 TAAA
563664 TTATTAATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
32 8 0.13
33 10 0.16
34 14 0.23
35 2 0.03
36 21 0.34
37 4 0.07
38 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAAATTTATATATAAAATATAATATATAAATTAT
Found at i:563608 original size:11 final size:11
Alignment explanation
Indices: 563555--563608 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 11
563545 TACGAACGTA
563555 ATAAAATTTATAT
1 ATAAAA-TTA-AT
563568 ATAAAATATAAT
1 ATAAAAT-TAAT
563580 ATATAAATTAAT
1 ATA-AAATTAAT
*
563592 -TAAAATTTAT
1 ATAAAATTAAT
563602 ATAAAAT
1 ATAAAAT
563609 AAATTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 7 0.19
11 8 0.22
12 10 0.27
13 12 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
ATAAAATTAAT
Found at i:563610 original size:25 final size:26
Alignment explanation
Indices: 563573--563621 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
563563 TATATATAAA
563573 ATATAATATATAAATTAATTAAAATTT
1 ATATAATATATAAATT-ATTAAAATTT
563600 ATATAA-A-ATAAATTATTAAAAT
1 ATATAATATATAAATTATTAAAAT
563622 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 1 0.05
27 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAATATATAAATTATTAAAATTT
Found at i:563635 original size:32 final size:33
Alignment explanation
Indices: 563556--563655 Score: 107
Period size: 32 Copynumber: 3.0 Consensus size: 33
563546 ACGAACGTAA
*
563556 TAAAATTTATATATAAAATATAATATATAAATTAAT
1 TAAAA-TT-TATATAAAATA-AATATATAAAATAAT
563592 TAAAATTTATATAAAATAAAT-TATTAAAAT-AT
1 TAAAATTTATATAAAATAAATATA-TAAAATAAT
* *
563624 TTAAATTTATAT-AAATAAAATATATAATATAA
1 TAAAATTTATATAAAAT-AAATATATAAAATAA
563656 ATATTAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
31 4 0.07
32 24 0.42
33 11 0.19
34 11 0.19
35 2 0.04
36 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TAAAATTTATATAAAATAAATATATAAAATAAT
Found at i:563657 original size:18 final size:17
Alignment explanation
Indices: 563554--563658 Score: 62
Period size: 18 Copynumber: 6.2 Consensus size: 17
563544 ATACGAACGT
*
563554 AATAAAATTTATATATAA
1 AATAAAATATATATAT-A
* *
563572 AATATAATATATAAATTA
1 AATAAAATATATATA-TA
* *
563590 ATTAAAATTTATATA-A
1 AATAAAATATATATATA
563606 AAT-AAAT-TAT-TA-A
1 AATAAAATATATATATA
563619 AATATTTAAAT-T-TATATA
1 AATA---AAATATATATATA
563637 AATAAAATATATAATATA
1 AATAAAATATAT-ATATA
563655 AATA
1 AATA
563659 TTAAATTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
13 6 0.09
14 3 0.04
15 8 0.12
16 5 0.07
17 8 0.12
18 38 0.55
19 1 0.01
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAAAATATATATATA
Found at i:563688 original size:43 final size:45
Alignment explanation
Indices: 563599--563690 Score: 118
Period size: 43 Copynumber: 2.1 Consensus size: 45
563589 AATTAAAATT
563599 TATATAAAATAAATTATTAAAATATTTAAATTTATATAAATAAAA
1 TATATAAAATAAATTATTAAAATATTTAAATTTATATAAATAAAA
* * * *
563644 TATATAATATAAA-TATTAAATTA-TTAATTTTATTTTAAAT-AAA
1 TATATAAAATAAATTATTAAAATATTTAAATTTA-TATAAATAAAA
563687 TATA
1 TATA
563691 ATGATACGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 15 0.36
44 15 0.36
45 12 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (45 bp):
TATATAAAATAAATTATTAAAATATTTAAATTTATATAAATAAAA
Found at i:563874 original size:20 final size:18
Alignment explanation
Indices: 563808--563873 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 18
563798 ATTAATAATA
563808 AAAATAATATATAAATATT
1 AAAATAATATAT-AATATT
*
563827 AATATAA-AT-TAATATT
1 AAAATAATATATAATATT
**
563843 TTAATAATATAATAGATATT
1 AAAATAATAT-ATA-ATATT
563863 AAAATAATATA
1 AAAATAATATA
563874 AGAAAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 10 0.27
17 3 0.08
18 2 0.05
19 9 0.24
20 13 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAAATAATATATAATATT
Found at i:566323 original size:66 final size:66
Alignment explanation
Indices: 566217--566348 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
566207 GCCCAAACAT
* * **
566217 TGTTTCAATATACAGGTATTGATGCACACTTTAGCATTTACTCTACCAGAGAGATTTTCTCTTTT
1 TGTTTCAATATACAGGCATTGATGCACACTTTAGCATTTACTCTACCAAAGAGAAGTTCTCTTTT
566282 C
66 C
* *
566283 TGTTTCAATATACAGGCATTGATGCTCATTTTAGCATTTACTCTACCAAAGAGAAGTTCTCTTTT
1 TGTTTCAATATACAGGCATTGATGCACACTTTAGCATTTACTCTACCAAAGAGAAGTTCTCTTTT
566348 C
66 C
566349 ACTACAAGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.40
Consensus pattern (66 bp):
TGTTTCAATATACAGGCATTGATGCACACTTTAGCATTTACTCTACCAAAGAGAAGTTCTCTTTT
C
Found at i:568146 original size:7 final size:7
Alignment explanation
Indices: 568131--568182 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
568121 AGACGAAAAG
*
568131 AAAATTA
1 AAAAATA
568138 AAAAATA
1 AAAAATA
568145 AAAAATTA
1 AAAAA-TA
* *
568153 GAAAAGA
1 AAAAATA
568160 AAAAAGTA
1 AAAAA-TA
568168 CAAAAATA
1 -AAAAATA
568176 AAAAATA
1 AAAAATA
568183 TTTATGTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 23 0.62
8 9 0.24
9 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:568151 original size:15 final size:15
Alignment explanation
Indices: 568131--568181 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
568121 AGACGAAAAG
568131 AAAATTAAAAAATAA
1 AAAATTAAAAAATAA
* *
568146 AAAATTAGAAAAGAA
1 AAAATTAAAAAATAA
*
568161 AAAAGTACAAAAATAA
1 AAAATTA-AAAAATAA
568177 AAAAT
1 AAAAT
568182 ATTTATGTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 19 0.66
16 10 0.34
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (15 bp):
AAAATTAAAAAATAA
Found at i:568240 original size:16 final size:15
Alignment explanation
Indices: 568219--568248 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
568209 TGTGCTTAGT
568219 TGAAAAGAAGAAAAAG
1 TGAAAAGAA-AAAAAG
568235 TGAAAAGAAAAAAA
1 TGAAAAGAAAAAAA
568249 TTAATATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
TGAAAAGAAAAAAAG
Found at i:568493 original size:16 final size:15
Alignment explanation
Indices: 568463--568498 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
568453 AAATAATAAA
*
568463 CTTTTTTTTTATTTT
1 CTTTTCTTTTATTTT
568478 CTTTTCTTTTACTTTT
1 CTTTTCTTTTA-TTTT
568494 CTTTT
1 CTTTT
568499 TCAAACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.81
Consensus pattern (15 bp):
CTTTTCTTTTATTTT
Found at i:569136 original size:22 final size:22
Alignment explanation
Indices: 569102--569156 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
569092 TGATTAAGGT
*
569102 TTTTCTAATTATAAATAT-TATA
1 TTTTATAA-TATAAATATATATA
*
569124 TTTATATAATATAATTATATATA
1 TTT-TATAATATAAATATATATA
569147 TTTTATAATA
1 TTTTATAATA
569157 ATAGTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATAATATAAATATATATA
Found at i:569164 original size:23 final size:23
Alignment explanation
Indices: 569111--569172 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
569101 TTTTTCTAAT
*
569111 TATAAATAT-TATATTTATATAA
1 TATAATTATATATATTTATATAA
569133 TATAATTATATATATTT-TATAA
1 TATAATTATATATATTTATATAA
*
569155 TAATAGTTATA-AT-TTTAT
1 T-ATAATTATATATATTTAT
569173 TTAACTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.09
22 17 0.49
23 15 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATAATTATATATATTTATATAA
Found at i:569169 original size:20 final size:20
Alignment explanation
Indices: 569141--569191 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
569131 AATATAATTA
569141 TATATATTTTATAATAA-TAGT
1 TATA-ATTTTAT-ATAACTAGT
*
569162 TATAATTTTATTTAACTAGT
1 TATAATTTTATATAACTAGT
569182 TATTAATTTT
1 TA-TAATTTT
569192 TAAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 11 0.41
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TATAATTTTATATAACTAGT
Found at i:575780 original size:18 final size:18
Alignment explanation
Indices: 575757--575799 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
575747 GGATTTAACC
*
575757 CTGACTCCATTCGGAACT
1 CTGACTCCATTCGAAACT
575775 CTGACTCCATTCGAAACT
1 CTGACTCCATTCGAAACT
*
575793 CAGACTC
1 CTGACTC
575800 TGTTGGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.26
Consensus pattern (18 bp):
CTGACTCCATTCGAAACT
Found at i:579363 original size:22 final size:22
Alignment explanation
Indices: 579336--579388 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
579326 TTAGGTTAAA
*
579336 TATATATTTTTATTAATT-AAAT
1 TATATATTTTTAAT-ATTAAAAT
* *
579358 TTTATATTATTAATATTAAAAT
1 TATATATTTTTAATATTAAAAT
579380 TATATATTT
1 TATATATTT
579389 ACTATATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATATTTTTAATATTAAAAT
Found at i:579497 original size:22 final size:23
Alignment explanation
Indices: 579466--579513 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
579456 TTTATTACAT
*
579466 AAAAAGTTATAAAT-TTAAAATA
1 AAAAAATTATAAATATTAAAATA
*
579488 AAAAAATTATAAATATTAAATTA
1 AAAAAATTATAAATATTAAAATA
579511 AAA
1 AAA
579514 TTTTATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAAATTATAAATATTAAAATA
Found at i:580164 original size:16 final size:16
Alignment explanation
Indices: 580143--580232 Score: 90
Period size: 16 Copynumber: 5.6 Consensus size: 16
580133 TTTAATAAAG
580143 TAAATATAATTACTTT
1 TAAATATAATTACTTT
* * *
580159 TAAATATAATAAATAT
1 TAAATATAATTACTTT
* *
580175 TAAATAAAATTACTTA
1 TAAATATAATTACTTT
* * * *
580191 TAAATTTAATAAATAT
1 TAAATATAATTACTTT
580207 TAAATATAATTACTTT
1 TAAATATAATTACTTT
*
580223 TAAATTTAAT
1 TAAATATAAT
580233 AACCATTAAA
Statistics
Matches: 55, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 55 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTACTTT
Found at i:580214 original size:22 final size:23
Alignment explanation
Indices: 580167--580215 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
580157 TTTAAATATA
**
580167 ATAAATATTAAATAAAATTACTT
1 ATAAATATTAAATAAAATTAAAT
580190 ATAAAT-TT-AATAAATATTAAAT
1 ATAAATATTAAATAAA-ATTAAAT
580212 ATAA
1 ATAA
580216 TTACTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 11 0.48
23 6 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAAATATTAAATAAAATTAAAT
Found at i:580241 original size:16 final size:16
Alignment explanation
Indices: 580129--580242 Score: 72
Period size: 16 Copynumber: 7.2 Consensus size: 16
580119 ATATTGATAA
*
580129 TAAATTTAATAA--AG
1 TAAATTTAATAACTAT
* * *
580143 TAAATATAATTACTTT
1 TAAATTTAATAACTAT
* *
580159 TAAATATAATAAATAT
1 TAAATTTAATAACTAT
** *
580175 TAAATAAAATTACT-T
1 TAAATTTAATAACTAT
*
580190 ATAAATTTAATAAATAT
1 -TAAATTTAATAACTAT
* * *
580207 TAAATATAATTACTTT
1 TAAATTTAATAACTAT
*
580223 TAAATTTAATAACCAT
1 TAAATTTAATAACTAT
580239 TAAA
1 TAAA
580243 ATATTTTAAT
Statistics
Matches: 74, Mismatches: 22, Indels: 6
0.73 0.22 0.06
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 62 0.84
17 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (16 bp):
TAAATTTAATAACTAT
Found at i:580242 original size:32 final size:32
Alignment explanation
Indices: 580129--580234 Score: 162
Period size: 32 Copynumber: 3.4 Consensus size: 32
580119 ATATTGATAA
*
580129 TAAATTTAAT-AA-AGTAAATATAATTACTTT
1 TAAATTTAATAAATATTAAATATAATTACTTT
* * *
580159 TAAATATAATAAATATTAAATAAAATTACTTA
1 TAAATTTAATAAATATTAAATATAATTACTTT
580191 TAAATTTAATAAATATTAAATATAATTACTTT
1 TAAATTTAATAAATATTAAATATAATTACTTT
580223 TAAATTTAATAA
1 TAAATTTAATAA
580235 CCATTAAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.13
31 2 0.03
32 56 0.84
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (32 bp):
TAAATTTAATAAATATTAAATATAATTACTTT
Found at i:580256 original size:32 final size:32
Alignment explanation
Indices: 580129--580256 Score: 127
Period size: 32 Copynumber: 4.1 Consensus size: 32
580119 ATATTGATAA
* *
580129 TAAATTTAAT-AA-AGTAAATATAATTACTTT
1 TAAATTTAATAAACATTAAATATAATTAATTT
* * * * *
580159 TAAATATAATAAATATTAAATAAAATTACTTA
1 TAAATTTAATAAACATTAAATATAATTAATTT
* *
580191 TAAATTTAATAAATATTAAATATAATTACTTT
1 TAAATTTAATAAACATTAAATATAATTAATTT
* *
580223 TAAATTTAATAACCATTAAA-ATATTTTAATTT
1 TAAATTTAATAAACATTAAATATA-ATTAATTT
580255 TA
1 TA
580257 CTATTTAGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
30 9 0.11
31 5 0.06
32 70 0.83
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (32 bp):
TAAATTTAATAAACATTAAATATAATTAATTT
Found at i:580424 original size:44 final size:44
Alignment explanation
Indices: 580370--580453 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
580360 TTTATACTTA
* *
580370 AAAAATTTAAAATTTTATAAATTTTAAATGATATATTAAAATAT
1 AAAAATTTAAAATTTAATAAATTTAAAATGATATATTAAAATAT
580414 AAAAATTTAAAATTTAATAAATTTAAAATGATATATTAAA
1 AAAAATTTAAAATTTAATAAATTTAAAATGATATATTAAA
580454 TTACATCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (44 bp):
AAAAATTTAAAATTTAATAAATTTAAAATGATATATTAAAATAT
Found at i:580425 original size:15 final size:16
Alignment explanation
Indices: 580372--580442 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 16
580362 TATACTTAAA
* *
580372 AAATTTAAAATTTTAT
1 AAATTTAAAATATAAT
*
580388 AAATTTTAAATGAT-AT
1 AAATTTAAAAT-ATAAT
580404 --A-TTAAAATATAA-
1 AAATTTAAAATATAAT
*
580416 AAATTTAAAATTTAAT
1 AAATTTAAAATATAAT
580432 AAATTTAAAAT
1 AAATTTAAAAT
580443 GATATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 2 0.04
13 7 0.16
14 2 0.04
15 10 0.22
16 23 0.51
17 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
AAATTTAAAATATAAT
Found at i:580950 original size:19 final size:18
Alignment explanation
Indices: 580918--580955 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
580908 TATTATATTT
580918 TTTAATAAAATTAATTAAA
1 TTTAATAAAATTAA-TAAA
580937 TTTAA-AAAATTTAATAAA
1 TTTAATAAAA-TTAATAAA
580955 T
1 T
580956 AATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTAATAAAATTAATAAA
Found at i:580975 original size:5 final size:6
Alignment explanation
Indices: 580958--580984 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
580948 TAATAAATAA
580958 TATTTT TATTTT TATTTT TATTTT TAT
1 TATTTT TATTTT TATTTT TATTTT TAT
580985 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:581314 original size:11 final size:11
Alignment explanation
Indices: 581298--581334 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
581288 TTATTACTAT
581298 TTATTTATAAA
1 TTATTTATAAA
* *
581309 TTATTTTTAAT
1 TTATTTATAAA
581320 TTATTTATAAA
1 TTATTTATAAA
581331 TTAT
1 TTAT
581335 ACAAATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTATAAA
Found at i:582311 original size:43 final size:43
Alignment explanation
Indices: 582263--582348 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
582253 CGATAACTTA
582263 TTCGTCTAGATTTTCCAATTCTTCAATAAGAAAAGATTAATTT
1 TTCGTCTAGATTTTCCAATTCTTCAATAAGAAAAGATTAATTT
*
582306 TTCGTCTAGATTTTTCAATTCTTCAATAAGAAAAGATTAATTT
1 TTCGTCTAGATTTTCCAATTCTTCAATAAGAAAAGATTAATTT
582349 GCTTGTGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (43 bp):
TTCGTCTAGATTTTCCAATTCTTCAATAAGAAAAGATTAATTT
Found at i:585042 original size:87 final size:90
Alignment explanation
Indices: 584888--585087 Score: 271
Period size: 87 Copynumber: 2.2 Consensus size: 90
584878 CAACTGTGAT
* * *
584888 ATTTACAATCAATCAACTTTTTATCTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTTAT
1 ATTTACAATCAGTCAAC--TTTATCTTTTCTATAAAAAAGAATCTGACTCTCAAATATAATTCAT
* *
584953 GCATTAGTCTAATCCTTGCAGTCTGAC
64 GCATTAGTCTAATCCTTGCAATCTAAC
* *
584980 ATTTACAATCAGTCAACTTT-T-TTTT-TATAAAAAAGAATCTGACTCTTAGATATAATTCATGC
1 ATTTACAATCAGTCAACTTTATCTTTTCTATAAAAAAGAATCTGACTCTCAAATATAATTCATGC
*
585042 ATTAGTCTAATCCTTGTAATCTAAC
66 ATTAGTCTAATCCTTGCAATCTAAC
* *
585067 ACTTACCATCAGTCAACTTTA
1 ATTTACAATCAGTCAACTTTA
585088 AAAAATAAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
87 73 0.75
88 4 0.04
89 1 0.01
90 3 0.03
92 16 0.16
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (90 bp):
ATTTACAATCAGTCAACTTTATCTTTTCTATAAAAAAGAATCTGACTCTCAAATATAATTCATGC
ATTAGTCTAATCCTTGCAATCTAAC
Found at i:585212 original size:117 final size:115
Alignment explanation
Indices: 585088--585422 Score: 276
Period size: 122 Copynumber: 2.8 Consensus size: 115
585078 GTCAACTTTA
*
585088 AAAAATAAATAATAATGTATTAATTATTATTTT-T-AA-TAAAA-AATAATTAATTAACTTTAAA
1 AAAAATAAA-AA-AATGTATT-ATTATT-TTTTATAAATTAAAATAATAATTAATTAAATTT--A
585149 AAAATT-CTATTAACAAATTAAAATATTAATTATTTTTTAAAATAAAAAATTTAAAT
60 AAAATTAC-ATTAACAAATTAAAATATTAATTATTTTTTAAAATAAAAAATTTAAAT
** * * *
585205 AAAAATAAAAAGGTTTGTTATTATTTTTTAATAAAATTAAAATAATATTTAATTAAATTTAAAAA
1 AAAAATAAAAAAATGTATTATTATTTTTT-AT-AAATTAAAATAATAATTAATTAAATTTAAAAA
*
585270 TTACATTAACAAATTAAAATATTAATTATTATGTTTTTGTAAAA-ATAAAATTT---T
64 TTACATTAACAAATTAAAATATT-A--ATTA--TTTTT-TAAAATAAAAAATTTAAAT
* * * * *
585324 -AAAATAAAAAAAGTTTTTTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAATTTTA
1 AAAAATAAAAAAA-TGTATTATTAT--TTTTT-AT-AAAT-TAAAATAATAATTAATTAAATTTA
* *
585388 AATATTTACATTAACAAATTAAACTATTAATTATT
60 AA-AATTACATTAACAAATTAAAATATTAATTATT
585423 ATGTTTTTTT
Statistics
Matches: 186, Mismatches: 14, Indels: 35
0.79 0.06 0.15
Matches are distributed among these distances:
113 4 0.02
114 6 0.03
115 5 0.03
116 2 0.01
117 37 0.20
118 19 0.10
119 26 0.14
120 8 0.04
121 13 0.07
122 38 0.20
123 28 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (115 bp):
AAAAATAAAAAAATGTATTATTATTTTTTATAAATTAAAATAATAATTAATTAAATTTAAAAATT
ACATTAACAAATTAAAATATTAATTATTTTTTAAAATAAAAAATTTAAAT
Found at i:585283 original size:21 final size:20
Alignment explanation
Indices: 585238--585297 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
585228 TTTTTTAATA
* * *
585238 AAATTAAAATAATATTTAATT
1 AAATTAAAATATTAATTAA-C
585259 AAATTTAAAA-ATTACATTAAC
1 AAA-TTAAAATATTA-ATTAAC
585280 AAATTAAAATATTAATTA
1 AAATTAAAATATTAATTA
585298 TTATGTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 10 0.30
21 13 0.39
22 10 0.30
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTAAAATATTAATTAAC
Found at i:585499 original size:123 final size:122
Alignment explanation
Indices: 585122--585472 Score: 417
Period size: 122 Copynumber: 2.9 Consensus size: 122
585112 TATTATTTTT
*
585122 AATAAAAAAT-A-A-TTAATTAACTTTAAAAAAATT-CTATTAACAAATTAAAATATT-A--ATT
1 AATAAAAAATAATATTTAATTAAATTT--AAAAATTAC-ATTAACAAATTAAAATATTAATTATT
* *
585180 A--TTTTT-TAAAATAAAAAATTTAAATAAAAATAAAAAGGTTTGTTATTAT--TTTTTAATAA
63 ATGTTTTTGTAAAA-AAAAAATTTTAA-AATAA-AAAAAGGTTT-TTATTATAATTTTTAATAA
*
585239 AAT-TAAAATAATATTTAATTAAATTTAAAAATTACATTAACAAATTAAAATATTAATTATTATG
1 AATAAAAAATAATATTTAATTAAATTTAAAAATTACATTAACAAATTAAAATATTAATTATTATG
* *
585303 TTTTTGTAAAAATAAAATTTTAAAATAAAAAAAGTTTTTTATTATAATTTTTAATAA
66 TTTTTGTAAAAAAAAAATTTTAAAATAAAAAAAGGTTTTTATTATAATTTTTAATAA
* * *
585360 AATAAAAAATAATATTTAATTAATTTTAAATATTTACATTAACAAATTAAACTATTAATTATTAT
1 AATAAAAAATAATATTTAATTAAATTTAAA-AATTACATTAACAAATTAAAATATTAATTATTAT
* *
585425 GTTTTTTTAAAATAAAAAATTTT-AAAT-TAAAAAGGTTTTTATTATAAT
65 GTTTTTGTAAAA-AAAAAATTTTAAAATAAAAAAAGGTTTTTATTATAAT
585473 AATATTTTTT
Statistics
Matches: 205, Mismatches: 14, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
116 5 0.02
117 30 0.15
118 3 0.01
119 18 0.09
120 13 0.06
121 17 0.08
122 58 0.28
123 52 0.25
124 9 0.04
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (122 bp):
AATAAAAAATAATATTTAATTAAATTTAAAAATTACATTAACAAATTAAAATATTAATTATTATG
TTTTTGTAAAAAAAAAATTTTAAAATAAAAAAAGGTTTTTATTATAATTTTTAATAA
Found at i:585813 original size:22 final size:23
Alignment explanation
Indices: 585764--585816 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
585754 AATAATCATA
585764 AATTTTTTTAATTCCTTAAATAT
1 AATTTTTTTAATTCCTTAAATAT
* ** *
585787 TATTTTTTTAATTTGTT-AATGT
1 AATTTTTTTAATTCCTTAAATAT
585809 AATTTTTT
1 AATTTTTT
585817 AAAAATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (23 bp):
AATTTTTTTAATTCCTTAAATAT
Found at i:585884 original size:37 final size:38
Alignment explanation
Indices: 585823--585904 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 38
585813 TTTTAAAAAT
585823 TTAATTAAATATCATTTTTATTTTATTAAAAA-ATAATAA
1 TTAA-TAAATATCATTTTTATTTTA-TAAAAATATAATAA
*
585862 -TAATAAATA-CTTTTTTATTTTTATAAAAATATAATAA
1 TTAATAAATATCATTTTTA-TTTTATAAAAATATAATAA
585899 TTAATA
1 TTAATA
585905 TTTAATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
36 13 0.33
37 18 0.46
38 8 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (38 bp):
TTAATAAATATCATTTTTATTTTATAAAAATATAATAA
Found at i:585918 original size:112 final size:113
Alignment explanation
Indices: 585792--586176 Score: 428
Period size: 112 Copynumber: 3.4 Consensus size: 113
585782 AATATTATTT
* * * *
585792 TTTTAATTTGTTAATGTAATTTTTTAAAAATTTAATTAAATATCATTTTTATTTTATTAAAAAAT
1 TTTTAATTTATTAATATAATTTTTT--AAACTTAATTAAATATTATTTTTATTTTATTAAAAAAT
585857 AATAATAATAAATA-CTTT-TTTA-TTTTTA-TAAAAATATAATAATTAATA
64 AATAATAATAAATATCTTTATTTATTTTTTATTAAAAA-A-AATAATTAATA
*
585905 -TTTAATTTATTAATATAATTTTTTAAACTTAATTAAATATTATTTTAATTTTATTAAAAATAAT
1 TTTTAATTTATTAATATAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATT-AAAA-AAT
* **
585969 AATAATAATAAATATTTTTAATTTATTTTTTATTTTTAAAAAATAATTAATA
64 AATAATAATAAATATCTTT-ATTTATTTTTTA-TTAAAAAAAATAATTAATA
*
586021 TTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTTTATTAAAAAAT
1 TTTTAATTTATTAATATAA-TTTTTTAAACTTAATTAAATATTATTTTT-ATTTTATTAAAAAAT
* * *** *
586086 AATAATAA-AAACT-T-TTAATTTAATGTTTTATTTTTAAAAATAATTGATA
64 AATAATAATAAA-TATCTTTATTT-ATTTTTTATTAAAAAAAATAATTAATA
* * *
586135 TTTTAA-TTATTAATGTAATTTTTTTAGAGTTAATTAAATATT
1 TTTTAATTTATTAATATAA-TTTTTTAAACTTAATTAAATATT
586177 TTTATTAAAA
Statistics
Matches: 243, Mismatches: 16, Indels: 26
0.85 0.06 0.09
Matches are distributed among these distances:
110 28 0.12
111 4 0.02
112 39 0.16
113 37 0.15
114 27 0.11
115 13 0.05
116 21 0.09
117 31 0.13
118 35 0.14
119 8 0.03
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (113 bp):
TTTTAATTTATTAATATAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATAA
TAATAATAAATATCTTTATTTATTTTTTATTAAAAAAAATAATTAATA
Found at i:585922 original size:35 final size:35
Alignment explanation
Indices: 585851--585922 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
585841 TATTTTATTA
**
585851 AAAAATAATAATAATAAATACTTTTTTATTTTTAT
1 AAAAATAATAATAATAAATACTTTTTTATTAATAT
*
585886 AAAAAT-ATAATAATTAATA-TTTAATTTATTAATAT
1 AAAAATAATAATAATAAATACTTT--TTTATTAATAT
585921 AA
1 AA
585923 TTTTTTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 3 0.09
34 12 0.38
35 17 0.53
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
AAAAATAATAATAATAAATACTTTTTTATTAATAT
Found at i:585962 original size:21 final size:20
Alignment explanation
Indices: 585905--585962 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 20
585895 ATAATTAATA
585905 TTTAATTTATTAATATAATTT
1 TTTAATTTATTAA-ATAATTT
*
585926 TTTAAACTTAATTAAAT-ATTAT
1 TTT-AA-TTTATTAAATAATT-T
585948 TTTAATTTTATTAAA
1 TTTAA-TTTATTAAA
585963 AATAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 16 0.52
22 8 0.26
23 7 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTAATTTATTAAATAATTT
Found at i:585999 original size:72 final size:73
Alignment explanation
Indices: 585865--586000 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
585855 ATAATAATAA
* **
585865 TAAATACTTTTTTATTTTTATAAAAATATAATAATTAATATTTAATTTATTAATATAATTTTTTA
1 TAAATACTTTTTTAATTTTATAAAAATATAATAATTAATAAATAATTTATTAATATAATTTTTTA
585930 AACTTAAT
66 AACTTAAT
*
585938 TAAATA-TTATTTTAATTTTATTAAAAATAATAATAA-TAATAAAT-ATTT-TTAAT-TTATTTT
1 TAAATACTT-TTTTAATTTTA-TAAAAAT-ATAATAATTAATAAATAATTTATTAATATAATTTT
585998 TTA
63 TTA
586001 TTTTTAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
71 9 0.16
72 7 0.12
73 20 0.36
74 13 0.23
75 7 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (73 bp):
TAAATACTTTTTTAATTTTATAAAAATATAATAATTAATAAATAATTTATTAATATAATTTTTTA
AACTTAAT
Found at i:586004 original size:78 final size:71
Alignment explanation
Indices: 585860--586024 Score: 165
Period size: 78 Copynumber: 2.2 Consensus size: 71
585850 AAAAAATAAT
*
585860 AATAA-TAAATACTTTTTTATTTTTATAAAAATATAATAATTAATATTTAATTTATTAATATAAT
1 AATAATTAAATA-TTTTTTAATTTTATAAAAATATAATAATTAATATTTAATTTATT-ATATAAT
*
585924 TTTTTAAA
64 TTTTAAAA
**
585932 CTTAATTAAATATTATTTTAATTTTATTAAAAATAATAATAATAATAAATATTTTTAATTTATT-
1 AATAATTAAATATT-TTTTAATTTTA-TAAAAAT-ATAATAAT--T-AATA--TTTAATTTATTA
* *
585996 TTTTATTTTTAAAA
58 TATAATTTTTAAAA
586010 AATAATT-AATATTTT
1 AATAATTAAATATTTT
586025 AATTTATTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
72 5 0.07
73 16 0.21
74 7 0.09
75 8 0.11
76 2 0.03
77 7 0.09
78 20 0.26
80 11 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (71 bp):
AATAATTAAATATTTTTTAATTTTATAAAAATATAATAATTAATATTTAATTTATTATATAATTT
TTAAAA
Found at i:586079 original size:22 final size:21
Alignment explanation
Indices: 586021--586081 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 21
586011 ATAATTAATA
586021 TTTTAATTTATTAATATAATTT
1 TTTTAATTTATTAA-ATAATTT
*
586043 TTTTAAAGTTAATTAAAT-ATTAT
1 TTTT-AA-TTTATTAAATAATT-T
586066 TTTTAATTTTATTAAA
1 TTTTAA-TTTATTAAA
586082 AAATAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 17 0.52
23 9 0.27
24 7 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAATTTATTAAATAATTT
Found at i:586136 original size:114 final size:119
Alignment explanation
Indices: 585894--586184 Score: 433
Period size: 113 Copynumber: 2.5 Consensus size: 119
585884 ATAAAAATAT
*
585894 AATAATTAATA-TTTAATTTATTAATATAA-TTTTTTAAACTTAATTAAATATTA-TTTTAATTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
* *
585956 TATTAAAAATAATAATAATAATAAATATTTTTAATTTATTTTTTATTTTTAAAA
66 TATTAAAAATAATAATAATAATAAATACTTTTAATTTATGTTTTATTTTTAAAA
586010 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
586075 TATT-AAAA-AATAATAAT-A-AAA-ACTTTTAATTTAATGTTTTATTTTT-AAA
66 TATTAAAAATAATAATAATAATAAATACTTTTAATTT-ATGTTTTATTTTTAAAA
* * *
586124 AATAATTGATATTTTAA-TTATTAATGTAATTTTTTTAGAGTTAATTAAATATT-TTTATTAA
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTT-TTAA
586185 AAATAATAAT
Statistics
Matches: 164, Mismatches: 6, Indels: 13
0.90 0.03 0.07
Matches are distributed among these distances:
112 3 0.02
113 38 0.23
114 29 0.18
115 15 0.09
116 12 0.07
117 27 0.16
118 27 0.16
119 13 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (119 bp):
AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTTTTAATTT
TATTAAAAATAATAATAATAATAAATACTTTTAATTTATGTTTTATTTTTAAAA
Found at i:586221 original size:113 final size:115
Alignment explanation
Indices: 585894--586221 Score: 283
Period size: 113 Copynumber: 2.9 Consensus size: 115
585884 ATAAAAATAT
*
585894 AATAATTAATA-TTTAATTTATTAATATAA-TTTTTTAAACTTAATTAAATATTATTTTAATTTT
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATT-AA-A-TA---T--TTTT
* *
585957 ATTAAAAATAATAA-TAATAATAAATATTTTT--AA---TTT-ATTTTTTATTTTTAAAA
58 ATTAAAAATAATAATTAAT-AT-ATTATTTTTAAAATTTTTTAATGTTTTATTTTTAAAA
586010 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTATTT-TT---A
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATT-TTTATTAAAA
* * * * * ** *
586071 AT-TTTATTAAAAAATAATAATAAAAACTTTTAATTTAATGTTTTATTTTT-AAA
65 ATAATAATTAATATATTATTTTTAAAA--TTT--TTTAATGTTTTATTTTTAAAA
* * *
586124 AATAATTGATATTTTAA-TTATTAATGTAATTTTTTTAGAGTTAATTAAATATTTTTATTAAAAA
1 AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTTTTATTAAAAA
586188 TAATAATTAATATATTATTTTTAAAATTTTTTAA
66 TAATAATTAATATATTATTTTTAAAATTTTTTAA
586222 ATTTAATTAC
Statistics
Matches: 171, Mismatches: 22, Indels: 41
0.73 0.09 0.18
Matches are distributed among these distances:
105 4 0.02
106 3 0.02
107 8 0.05
110 3 0.02
111 3 0.02
112 4 0.02
113 41 0.24
114 22 0.13
115 17 0.10
116 15 0.09
117 36 0.21
118 15 0.09
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (115 bp):
AATAATTAATATTTTAATTTATTAATATAATTTTTTTAAAGTTAATTAAATATTTTTATTAAAAA
TAATAATTAATATATTATTTTTAAAATTTTTTAATGTTTTATTTTTAAAA
Found at i:586598 original size:24 final size:25
Alignment explanation
Indices: 586556--586612 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
586546 ATTACTTTAG
*
586556 ATTTAATAAGTTAAAATAA-ATAAT
1 ATTTAATAAATTAAAATAATATAAT
* *
586580 ATTTAATAAATTTATATAAGTTATAAT
1 ATTTAATAAATTAAAATAA--TATAAT
586607 ATTTAA
1 ATTTAA
586613 AATTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 16 0.59
27 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
ATTTAATAAATTAAAATAATATAAT
Found at i:587838 original size:13 final size:13
Alignment explanation
Indices: 587822--587870 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
587812 GATTTATGTA
*
587822 TTTATATTATTTT
1 TTTATATTATATT
*
587835 TTTAAATTATATT
1 TTTATATTATATT
587848 TTTATATTATA--
1 TTTATATTATATT
587859 TTTATATTATAT
1 TTTATATTATAT
587871 AATTTATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.34
13 21 0.66
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATATTATATT
Done.