Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold199
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: 611138
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 5
Found at i:126113 original size:17 final size:18
Alignment explanation
Indices: 126091--126128 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
126081 AAATTATACC
126091 ATTAAA-AAAAATAAAA-A
1 ATTAAAGAAAAA-AAAACA
126108 ATTAAAGAAAAAAAAACA
1 ATTAAAGAAAAAAAAACA
126126 ATT
1 ATT
126129 GACCCATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
ATTAAAGAAAAAAAAACA
Found at i:127668 original size:22 final size:22
Alignment explanation
Indices: 127642--127724 Score: 78
Period size: 22 Copynumber: 3.6 Consensus size: 22
127632 TGTAATTTTG
127642 AATATAATATAAAAATAATTAT
1 AATATAATATAAAAATAATTAT
* *
127664 AATATAATAAAAATATCATAAATAT
1 AATATAATATAAA-A--ATAATTAT
* *
127689 AATATAAGTATATAAATATATTAA
1 AATATAA-TATAAAAATA-ATTAT
127713 AATAT-ATATAAA
1 AATATAATATAAA
127725 CAGTAAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
22 17 0.35
23 5 0.10
24 8 0.16
25 15 0.31
26 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (22 bp):
AATATAATATAAAAATAATTAT
Found at i:127670 original size:11 final size:10
Alignment explanation
Indices: 127642--127723 Score: 55
Period size: 11 Copynumber: 8.2 Consensus size: 10
127632 TGTAATTTTG
127642 AATATAATAT
1 AATATAATAT
*
127652 AAAAATAATTAT
1 -AATATAA-TAT
*
127664 AATATAATAAA
1 AATATAAT-AT
*
127675 AATATCATA-
1 AATATAATAT
127684 AATATAATAT
1 AATATAATAT
127694 AAGTAT-ATA-
1 AA-TATAATAT
* *
127703 AATATATTAA
1 AATATAATAT
127713 AATAT-ATAT
1 AATATAATAT
127722 AA
1 AA
127724 ACAGTAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
8 3 0.05
9 16 0.28
10 12 0.21
11 23 0.40
12 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (10 bp):
AATATAATAT
Found at i:127675 original size:20 final size:20
Alignment explanation
Indices: 127650--127724 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
127640 TGAATATAAT
*
127650 ATAAAAATAATTAT-AATATA
1 ATAAAAAT-ATCATAAATATA
127670 ATAAAAATATCATAAATATA
1 ATAAAAATATCATAAATATA
* *
127690 ATATAAGTAT-ATAAATATA
1 ATAAAAATATCATAAATATA
*
127709 TTAAAATATAT-ATAAA
1 ATAAAA-ATATCATAAA
127725 CAGTAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
ATAAAAATATCATAAATATA
Found at i:127721 original size:28 final size:28
Alignment explanation
Indices: 127647--127723 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
127637 TTTTGAATAT
127647 AATATAAAAATA-ATTATAATATAATAAA
1 AATATAAAAATATA-TATAATATAATAAA
*
127675 AATATCATAAATATAATATAAGTAT-ATAAA
1 AATAT-AAAAATAT-ATATAA-TATAATAAA
* *
127705 TATATTAAAATATATATAA
1 AATATAAAAATATATATAA
127724 ACAGTAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 11 0.27
29 12 0.29
30 14 0.34
31 4 0.10
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (28 bp):
AATATAAAAATATATATAATATAATAAA
Found at i:127915 original size:16 final size:17
Alignment explanation
Indices: 127895--127930 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
127885 TTAATTATTC
127895 ATTTTT-ATT-CAAAAT
1 ATTTTTAATTACAAAAT
127910 ATTTTTAATTACAAAAT
1 ATTTTTAATTACAAAAT
127927 ATTT
1 ATTT
127931 AAAATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 3 0.16
17 10 0.53
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTAATTACAAAAT
Found at i:128185 original size:8 final size:8
Alignment explanation
Indices: 128170--128198 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
128160 GAAAAAGAAG
128170 AATA-AAA
1 AATATAAA
128177 AATATAAA
1 AATATAAA
128185 AATATAAA
1 AATATAAA
128193 AATATA
1 AATATA
128199 TTTTATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 4 0.19
8 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATATAAA
Found at i:131615 original size:15 final size:15
Alignment explanation
Indices: 131595--131634 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
131585 AAATTGAATT
131595 AAATTATTTTATTTA
1 AAATTATTTTATTTA
*
131610 AAATTATTAT-TTTA
1 AAATTATTTTATTTA
*
131624 AAATTAATTTA
1 AAATTATTTTA
131635 ATTTTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTATTTTATTTA
Found at i:131773 original size:27 final size:27
Alignment explanation
Indices: 131686--131775 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 27
131676 ATTAAATCAA
* * *
131686 TTAACTTTGATATAATTTAATTTTTTAT
1 TTAAATTTAATATAAATTAA-TTTTTAT
*
131714 TTAAAATTTAATATTAATTAATTTTTAT
1 TT-AAATTTAATATAAATTAATTTTTAT
*
131742 ATTAAATTTAAT-TAAATTAATTTTGAAT
1 -TTAAATTTAATATAAATTAATTTT-TAT
131770 TTAAAT
1 TTAAAT
131776 AAACTGAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 17 0.32
28 20 0.38
29 16 0.30
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAATTTAATATAAATTAATTTTTAT
Found at i:132848 original size:24 final size:24
Alignment explanation
Indices: 132821--132866 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
132811 AAAAAAATTA
*
132821 TCATTACTATTTATGGCAAGTCTG
1 TCATTACTATTTATGACAAGTCTG
* *
132845 TCATTATTTTTTATGACAAGTC
1 TCATTACTATTTATGACAAGTC
132867 ATACATGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (24 bp):
TCATTACTATTTATGACAAGTCTG
Found at i:136787 original size:25 final size:25
Alignment explanation
Indices: 136754--136801 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
136744 TATTTTTTTA
* *
136754 TTTATATAAATTATAATCATTAAAT
1 TTTAAATAAATTAAAATCATTAAAT
*
136779 TTTAAATAAATTAAAATGATTAA
1 TTTAAATAAATTAAAATCATTAA
136802 TTATTTGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAAATAAATTAAAATCATTAAAT
Found at i:137372 original size:12 final size:12
Alignment explanation
Indices: 137355--137421 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
137345 TCAGTCTAAA
*
137355 ATTTATTTTATT
1 ATTTATTATATT
137367 ATTTATTATATT
1 ATTTATTATATT
**
137379 A-TTAAAATATT
1 ATTTATTATATT
*
137390 ACTTT-TTATTAAT
1 A-TTTATTA-TATT
137403 ATTTA-TATATT
1 ATTTATTATATT
137414 -TTTATTAT
1 ATTTATTAT
137422 TAAATAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
10 4 0.09
11 15 0.35
12 18 0.42
13 6 0.14
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:137434 original size:20 final size:20
Alignment explanation
Indices: 137375--137434 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
137365 TTATTTATTA
* *
137375 TATTATTAAAATATTACTTTT
1 TATTATT-AAATAATAATTTT
* * *
137396 TATTAAT-ATTTATATATTTT
1 TATTATTAAATAATA-ATTTT
137416 TATTATTAAATAATAATTT
1 TATTATTAAATAATAATTT
137435 AAAATGAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTATTAAATAATAATTTT
Found at i:137938 original size:21 final size:22
Alignment explanation
Indices: 137895--137938 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
137885 TATTTTTAAA
*
137895 ATTTTTTTACATTTAATATATT
1 ATTTTTTTACATTTAATAAATT
137917 ATTTTTTTA-ATTTTAA-AAATT
1 ATTTTTTTACA-TTTAATAAATT
137938 A
1 A
137939 ATGTATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTTTACATTTAATAAATT
Found at i:137940 original size:29 final size:29
Alignment explanation
Indices: 137870--137946 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
137860 TAGATATTAA
137870 TTAAAAATTAATTATTATTTTTAAAATTTT
1 TTAAAAATTAATTATTATTTTTAAAA-TTT
* * * **
137900 TTTACATTTAATATATTATTTTTTTAA-TT
1 TTAAAAATTAAT-TATTATTTTTAAAATTT
137929 TTAAAAATTAATGTATTA
1 TTAAAAATTAAT-TATTA
137947 ATTAAATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 16 0.43
30 9 0.24
31 12 0.32
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TTAAAAATTAATTATTATTTTTAAAATTT
Found at i:138224 original size:17 final size:17
Alignment explanation
Indices: 138202--138235 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
138192 CAGTAAGTAG
138202 TTATTTTTTAATAATAA
1 TTATTTTTTAATAATAA
138219 TTATTTTTTAATAATAA
1 TTATTTTTTAATAATAA
138236 AAAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTTTTAATAATAA
Found at i:139428 original size:30 final size:30
Alignment explanation
Indices: 139355--139428 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
139345 CTTTCTACAT
139355 ATAAA-AAATC-ATATTTAATATATTAATA
1 ATAAATAAATCTATATTTAATATATTAATA
*
139383 ATATATAAATCTATATTT-AT-TATTAATTA
1 ATAAATAAATCTATATTTAATATATTAA-TA
139412 ATCAAATAATAT-TATAT
1 AT-AAATAA-ATCTATAT
139429 AATTAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 10 0.26
29 11 0.28
30 16 0.41
31 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (30 bp):
ATAAATAAATCTATATTTAATATATTAATA
Found at i:139569 original size:8 final size:8
Alignment explanation
Indices: 139556--139612 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
139546 ACAGATTTAT
139556 TATGTGTA
1 TATGTGTA
139564 TATGTGTA
1 TATGTGTA
*
139572 TA--TATA
1 TATGTGTA
* *
139578 TATATATA
1 TATGTGTA
* *
139586 TATTTATA
1 TATGTGTA
139594 TATGTGTA
1 TATGTGTA
139602 TATGTGTA
1 TATGTGTA
139610 TAT
1 TAT
139613 CAAGCCGGCT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 5 0.12
8 38 0.88
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (8 bp):
TATGTGTA
Found at i:139603 original size:10 final size:10
Alignment explanation
Indices: 139562--139612 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
139552 TTATTATGTG
139562 TATATGTGTA
1 TATATGTGTA
* *
139572 TATATATATA
1 TATATGTGTA
* *
139582 TATATATTTA
1 TATATGTGTA
139592 TATATGTG--
1 TATATGTGTA
139600 TATATGTGTA
1 TATATGTGTA
139610 TAT
1 TAT
139613 CAAGCCGGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 8 0.24
10 26 0.76
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (10 bp):
TATATGTGTA
Found at i:143799 original size:54 final size:54
Alignment explanation
Indices: 143717--143824 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
143707 AGCGAATCCA
143717 TTACAAATGTGGAAACTGTCATCATTTTAGGTTATGATAATGACTCTGTTAGTG
1 TTACAAATGTGGAAACTGTCATCATTTTAGGTTATGATAATGACTCTGTTAGTG
143771 TTACAAATGTGGAAACTGTCATCATTTTAGGTTATGATAATGACTCTGTTAGTG
1 TTACAAATGTGGAAACTGTCATCATTTTAGGTTATGATAATGACTCTGTTAGTG
143825 CGGTTGCTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (54 bp):
TTACAAATGTGGAAACTGTCATCATTTTAGGTTATGATAATGACTCTGTTAGTG
Found at i:145600 original size:16 final size:16
Alignment explanation
Indices: 145579--145609 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
145569 AGACAATAGC
145579 TTATTTTATTATAGTT
1 TTATTTTATTATAGTT
*
145595 TTATTTTATTTTAGT
1 TTATTTTATTATAGT
145610 AAATTAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTATTTTATTATAGTT
Found at i:146906 original size:31 final size:29
Alignment explanation
Indices: 146862--146967 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 29
146852 TTATGTTATT
*
146862 TTTATTATATATTTATATGAAATTTAAAATA
1 TTTATTATTTATTTATAT-AAATTT-AAATA
* *
146893 TTTATAATTTATTTTATATAAATTTTAATA
1 TTTATTATTTA-TTTATATAAATTTAAATA
* *
146923 TGTTATTTATTTATTTATATTATTTTAAATTA
1 T-TTA-TTATTTATTTATATAAATTTAAA-TA
*
146955 TTTGTTATATTAT
1 TTTATTAT-TTAT
146968 GTAATATTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
30 9 0.15
31 37 0.60
32 16 0.26
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (29 bp):
TTTATTATTTATTTATATAAATTTAAATA
Found at i:148485 original size:17 final size:18
Alignment explanation
Indices: 148463--148507 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
148453 TATTTATAAG
*
148463 TATTTATATTTAATA-CA
1 TATTTATATATAATATCA
*
148480 TATTTAAATATAATATCA
1 TATTTATATATAATATCA
148498 TATTTATATA
1 TATTTATATA
148508 ACATAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTATATATAATATCA
Found at i:149291 original size:4 final size:4
Alignment explanation
Indices: 149282--149326 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
149272 AGAATCCAAG
149282 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
149327 ATACCAGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:149962 original size:21 final size:21
Alignment explanation
Indices: 149937--149984 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
149927 ATAATAACTC
149937 ATAATATATCAAAAATATAGT
1 ATAATATATCAAAAATATAGT
*
149958 GTAATATATCAAAAATATAGT
1 ATAATATATCAAAAATATAGT
149979 ATAATA
1 ATAATA
149985 AATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (21 bp):
ATAATATATCAAAAATATAGT
Found at i:149989 original size:14 final size:14
Alignment explanation
Indices: 149970--150013 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
149960 AATATATCAA
149970 AAATATAGTATA-AT
1 AAATATA-TATATAT
149984 AAATATATATATAT
1 AAATATATATATAT
*
149998 ATATATATATATAT
1 AAATATATATATAT
150012 AA
1 AA
150014 TCCATTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:149993 original size:2 final size:2
Alignment explanation
Indices: 149972--150012 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
149962 TATATCAAAA
*
149972 AT AT AGT AT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
150013 ATCCATTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:152529 original size:21 final size:21
Alignment explanation
Indices: 152505--152546 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
152495 ATATTTTATA
152505 ATTAAATTTAA-ATAAAAATAT
1 ATTAAA-TTAATATAAAAATAT
* *
152526 ATTATATTAATTTAAAAATAT
1 ATTAAATTAATATAAAAATAT
152547 TATTTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAATTAATATAAAAATAT
Found at i:155292 original size:2 final size:2
Alignment explanation
Indices: 155285--155322 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
155275 CAAATCTGGA
155285 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
155323 TTGATTGAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155870 original size:2 final size:2
Alignment explanation
Indices: 155863--155896 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
155853 AAAACGCAAA
155863 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
155897 TTATTACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:157968 original size:13 final size:13
Alignment explanation
Indices: 157938--157977 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
157928 AACTCTTTAG
* *
157938 GTTTTTTTTTTTC
1 GTTTCTTTTTCTC
*
157951 TTTTCTTTTTCTC
1 GTTTCTTTTTCTC
157964 GTTTCTTTTTCTC
1 GTTTCTTTTTCTC
157977 G
1 G
157978 AAACCCAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.75
Consensus pattern (13 bp):
GTTTCTTTTTCTC
Found at i:160713 original size:2 final size:2
Alignment explanation
Indices: 160706--160734 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
160696 GTGCTTCCAT
160706 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
160735 GGGTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:161566 original size:40 final size:40
Alignment explanation
Indices: 161520--161597 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
161510 ACCCTGCCAC
161520 TTTCAAGTTCCAAACAACCACCCCACCCCCCAACGCCCGT
1 TTTCAAGTTCCAAACAACCACCCCACCCCCCAACGCCCGT
* * *
161560 TTTCAAGTTCCCAACAACCACCCCATCCTCCAACGCCC
1 TTTCAAGTTCCAAACAACCACCCCACCCCCCAACGCCC
161598 ACCAGACCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.50, G:0.06, T:0.17
Consensus pattern (40 bp):
TTTCAAGTTCCAAACAACCACCCCACCCCCCAACGCCCGT
Found at i:163893 original size:2 final size:2
Alignment explanation
Indices: 163886--163920 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
163876 AATTTAGCAA
163886 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 A
163921 GTGTGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:164805 original size:27 final size:26
Alignment explanation
Indices: 164794--164855 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 26
164784 TTTTTTATAT
*
164794 TTTATTTAAATTAAAAATATTTTATA
1 TTTATATAAATTAAAAATATTTTATA
164820 TTTATATAAATTTTAAAAATATTTATATA
1 TTTATATAAA--TTAAAAATATTT-TATA
164849 TTTATAT
1 TTTATAT
164856 TATATTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 9 0.28
28 12 0.38
29 11 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATATAAATTAAAAATATTTTATA
Found at i:164814 original size:29 final size:29
Alignment explanation
Indices: 164785--164856 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 29
164775 AATTATATAT
164785 TTTTTATATTTTATTTAAA-TTAAAAATA
1 TTTTTATATTTTATTTAAATTTAAAAATA
*
164813 -TTTTATA-TTTATATAAATTTTAAAAATA
1 TTTTTATATTTTATTTAAA-TTTAAAAATA
*
164841 TTTATATATTTATATT
1 TTTTTATATTT-TATT
164857 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 9 0.25
27 7 0.19
28 9 0.25
29 6 0.17
30 2 0.06
31 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTTATATTTTATTTAAATTTAAAAATA
Found at i:169057 original size:250 final size:250
Alignment explanation
Indices: 168611--169105 Score: 814
Period size: 250 Copynumber: 2.0 Consensus size: 250
168601 AACTTCAGTT
* * * *
168611 CCATCTCTGAATCGTATGAGGGTACTTTGGAGTTTCCTGAACGAGAACTTGGTTGAGCAGTCAGA
1 CCATCTCTGAATCATATGAGGATACCTTGGAGTTTCCTGAACAAGAACTTGGTTGAGCAGTCAGA
* *
168676 AAACTATATTCAATATGTTCTAAGCTACCTGATCGCAGTCCTTCAAAACCCGATTCACTGCTGCA
66 AAACTATATTCAATATGTTCTAAGCTACCTGATCGCAGCCCTTCAAAACCCGATACACTGCTGCA
*
168741 CTTCCCACTAACGTTGAACATTTCACTTTCACCCTGTCCATTACAACAAAATTGCACATCCAAAT
131 CTTCCCACTAACGTTGAACATCTCACTTTCACCCTGTCCATTACAACAAAATTGCACATCCAAAT
* *
168806 TTCATTAAGCAGACTTACACTAATTCATTTTCAGCATTTATTTACTTATTCAGAG
196 TTCATTAAGCAAACTAACACTAATTCATTTTCAGCATTTATTTACTTATTCAGAG
*
168861 CCATCTCTGAATCATATGATGATACCTTGGAGTTTCCTGAACAAGAACTTGGTTGAGCAGTCAGA
1 CCATCTCTGAATCATATGAGGATACCTTGGAGTTTCCTGAACAAGAACTTGGTTGAGCAGTCAGA
* * * *
168926 AAATTATATTCCATATGTTCTATGCTATCC-GATCGCAGCCCTTCAAAACCGGATACACTGCTGC
66 AAACTATATTCAATATGTTCTAAGCTA-CCTGATCGCAGCCCTTCAAAACCCGATACACTGCTGC
*
168990 ACTTCCCACTAATGTTGAACATCTCACTTTCACCCTGTCCATTACAACAAAATTGCACAGT-CAA
130 ACTTCCCACTAACGTTGAACATCTCACTTTCACCCTGTCCATTACAACAAAATTGCACA-TCCAA
*
169054 ATTTCATTAAGCAAACTAACTCTAATTCATTTTCAGCATTTATTTACTTATT
194 ATTTCATTAAGCAAACTAACACTAATTCATTTTCAGCATTTATTTACTTATT
169106 TACTTAGAAG
Statistics
Matches: 227, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
250 224 0.99
251 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.32
Consensus pattern (250 bp):
CCATCTCTGAATCATATGAGGATACCTTGGAGTTTCCTGAACAAGAACTTGGTTGAGCAGTCAGA
AAACTATATTCAATATGTTCTAAGCTACCTGATCGCAGCCCTTCAAAACCCGATACACTGCTGCA
CTTCCCACTAACGTTGAACATCTCACTTTCACCCTGTCCATTACAACAAAATTGCACATCCAAAT
TTCATTAAGCAAACTAACACTAATTCATTTTCAGCATTTATTTACTTATTCAGAG
Found at i:171833 original size:1 final size:1
Alignment explanation
Indices: 171829--171859 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
171819 ATTTTTTTTT
*
171829 GGGGGGGGGGGGGGGGGGGGAGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
171860 AGGGTGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:171860 original size:11 final size:11
Alignment explanation
Indices: 171829--171863 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
171819 ATTTTTTTTT
171829 GGGGGGGGGG-
1 GGGGGGGGGGA
171839 GGGGGGGGGGA
1 GGGGGGGGGGA
171850 GGGGGGGGGGA
1 GGGGGGGGGGA
171861 GGG
1 GGG
171864 TGTAGAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.06, C:0.00, G:0.94, T:0.00
Consensus pattern (11 bp):
GGGGGGGGGGA
Found at i:174902 original size:17 final size:16
Alignment explanation
Indices: 174876--174940 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
174866 TAAGTCAAAT
* *
174876 TAATTTTAAAGATTCA
1 TAATTATAAACATTCA
* *
174892 TGAATTATAAATATTTA
1 T-AATTATAAACATTCA
*
174909 TATATTATGAACATTCA
1 TA-ATTATAAACATTCA
174926 TAAATTATAAACATT
1 T-AATTATAAACATT
174941 TATATATGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.05
17 36 0.92
18 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (16 bp):
TAATTATAAACATTCA
Found at i:177663 original size:15 final size:16
Alignment explanation
Indices: 177643--177672 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
177633 AGTTGAAGAT
177643 TTTGTTA-TATATTTA
1 TTTGTTATTATATTTA
177658 TTTGTTATTATATTT
1 TTTGTTATTATATTT
177673 TAAGAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTGTTATTATATTTA
Found at i:177936 original size:18 final size:19
Alignment explanation
Indices: 177905--177947 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
177895 ATTTATTTAC
177905 ATATTTTAAAAATATATT-T
1 ATATTTTAAAAATA-ATTAT
177924 ATATTTT-AAAATAATTAT
1 ATATTTTAAAAATAATTAT
177942 ATATTT
1 ATATTT
177948 AATATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTAAAAATAATTAT
Found at i:177954 original size:17 final size:16
Alignment explanation
Indices: 177915--177954 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
177905 ATATTTTAAA
*
177915 AATATATTTATATTTT
1 AATATAATTATATTTT
*
177931 AAAATAATTATATATTT
1 AATATAATTATAT-TTT
177948 AATATAA
1 AATATAA
177955 ATATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATAATTATATTTT
Found at i:178627 original size:12 final size:12
Alignment explanation
Indices: 178610--178644 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
178600 ATGACAAGAA
*
178610 TATATATTTATG
1 TATATATATATG
178622 TATATATATATG
1 TATATATATATG
*
178634 TATATGTATAT
1 TATATATATAT
178645 ATGGCAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (12 bp):
TATATATATATG
Found at i:179176 original size:14 final size:14
Alignment explanation
Indices: 179151--179188 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
179141 ATATTAATTT
*
179151 TTTTATAATT-AAA
1 TTTTAAAATTAAAA
179164 TTATTAAAATTAAAA
1 TT-TTAAAATTAAAA
179179 TTTTAAAATT
1 TTTTAAAATT
179189 TTATCAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 15 0.68
15 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAAAATTAAAA
Found at i:179527 original size:21 final size:21
Alignment explanation
Indices: 179489--179533 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
179479 ACCAACCATT
* *
179489 TAAATATATTTATCATAATTA
1 TAAATATATTAATCATAATCA
179510 TAAATATATTAAAT-ATAATCA
1 TAAATATATT-AATCATAATCA
179531 TAA
1 TAA
179534 TTGATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATATTAATCATAATCA
Found at i:186920 original size:32 final size:34
Alignment explanation
Indices: 186858--186931 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 34
186848 TAGTTTTTAT
* *
186858 TTATATTTTAAAAATTAAAGTAGAAAATAAATAAA
1 TTATA-TTTAAAAATTAAAGTAAAAAATAAAAAAA
*
186893 TTATATTT-AAAATT-ATGTAAAAAATAAAAAAA
1 TTATATTTAAAAATTAAAGTAAAAAATAAAAAAA
186925 TTA-ATTT
1 TTATATTT
186932 TGTTCACGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 4 0.11
32 18 0.50
33 6 0.17
34 3 0.08
35 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (34 bp):
TTATATTTAAAAATTAAAGTAAAAAATAAAAAAA
Found at i:187722 original size:20 final size:20
Alignment explanation
Indices: 187692--187739 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
187682 AATTATTAAT
* *
187692 TTATAAAATTTTATATA-AA
1 TTATAATATTTTAAATATAA
187711 TATATAATATTTTAAATATAA
1 T-TATAATATTTTAAATATAA
187732 TTATAATA
1 TTATAATA
187740 AAAATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATAATATTTTAAATATAA
Found at i:187736 original size:22 final size:20
Alignment explanation
Indices: 187684--187742 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
187674 AATGTATAAA
187684 TTAT-TAATT-TATAAAATT
1 TTATATAATTATATAAAATT
* *
187702 TTATATAAATATATAATATT
1 TTATATAATTATATAAAATT
187722 TTAAATATAATTATAATAAAA
1 TT--ATATAATTAT-ATAAAA
187743 ATAATATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 10 0.31
22 9 0.28
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATATAATTATATAAAATT
Found at i:188924 original size:14 final size:14
Alignment explanation
Indices: 188893--188943 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
188883 TTGACCAAAA
* *
188893 TATATATATACATA
1 TATATATATATATG
*
188907 TATACATATATATG
1 TATATATATATATG
*
188921 TATATGTATATATG
1 TATATATATATATG
188935 TATATATAT
1 TATATATAT
188944 CACTCTCTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (14 bp):
TATATATATATATG
Found at i:192553 original size:16 final size:17
Alignment explanation
Indices: 192532--192566 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
192522 TTGGTAAATT
*
192532 AAATTAAA-AAATTTTA
1 AAATTAAATAAATATTA
192548 AAATTAAATAAATATTA
1 AAATTAAATAAATATTA
192565 AA
1 AA
192567 TATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTAAATAAATATTA
Found at i:192567 original size:16 final size:16
Alignment explanation
Indices: 192529--192582 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
192519 GGATTGGTAA
192529 ATTAAATTAAA-AAAT
1 ATTAAATTAAATAAAT
*
192544 TTTAAAATTAAATAAAT
1 ATT-AAATTAAATAAAT
192561 ATTAAA-TATAATAAAT
1 ATTAAATTA-AATAAAT
192577 AATTAA
1 -ATTAA
192583 GTAAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 4 0.12
16 18 0.55
17 11 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAAATTAAATAAAT
Found at i:192590 original size:17 final size:16
Alignment explanation
Indices: 192529--192590 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
192519 GGATTGGTAA
*
192529 ATTAAATTAAA-AAAT
1 ATTAAATAAAATAAAT
* *
192544 TTTAAAATTAAATAAAT
1 ATT-AAATAAAATAAAT
*
192561 ATTAAATATAATAAAT
1 ATTAAATAAAATAAAT
*
192577 AATTAAGTAAAATA
1 -ATTAAATAAAATA
192591 TTTATTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 2 0.05
16 19 0.50
17 17 0.45
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
ATTAAATAAAATAAAT
Found at i:193596 original size:2 final size:2
Alignment explanation
Indices: 193589--193629 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
193579 CCAAGGTTCG
*
193589 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
193630 AAAAATAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:195374 original size:3 final size:3
Alignment explanation
Indices: 195366--195391 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
195356 GCTCTTTATC
195366 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
195392 GTTGCTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:195850 original size:13 final size:13
Alignment explanation
Indices: 195825--195870 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
195815 TTTATCAACT
195825 TATTTTTATATTAA
1 TATTTTTA-ATTAA
*
195839 TATTTTTAATTAT
1 TATTTTTAATTAA
*
195852 TATTTTTAATTAC
1 TATTTTTAATTAA
195865 TATTTT
1 TATTTT
195871 ATCATCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 22 0.73
14 8 0.27
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTTAATTAA
Found at i:195857 original size:26 final size:27
Alignment explanation
Indices: 195828--195888 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
195818 ATCAACTTAT
*
195828 TTTTATATTAATATTTT-TAATTATTA
1 TTTTATATTAATATTTTATAATCATTA
* *
195854 TTTT-TAATTACTATTTTATCATCATTA
1 TTTTAT-ATTAATATTTTATAATCATTA
195881 -TTTATATT
1 TTTTATATT
195889 TACATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 1 0.03
26 20 0.69
27 8 0.28
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTATATTAATATTTTATAATCATTA
Found at i:195880 original size:27 final size:28
Alignment explanation
Indices: 195815--195883 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 28
195805 ATAAAATAAA
*
195815 TTTATCAAC-TTATTTTTATATTAATAT
1 TTTATCATCATTATTTTTATATTAATAT
* * *
195842 TTT-TAATTATTATTTTTA-ATTACTAT
1 TTTATCATCATTATTTTTATATTAATAT
195868 TTTATCATCATTATTT
1 TTTATCATCATTATTT
195884 ATATTTACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 12 0.35
27 22 0.65
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATCATCATTATTTTTATATTAATAT
Found at i:195891 original size:27 final size:27
Alignment explanation
Indices: 195815--195891 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
195805 ATAAAATAAA
* *
195815 TTTATCAAC-TTATTTTTATATTAATAT
1 TTTATCATCATTATTTTTAT-TTACTAT
* * *
195842 TTT-TAATTATTATTTTTAATTACTAT
1 TTTATCATCATTATTTTTATTTACTAT
*
195868 TTTATCATCATTATTTATATTTAC
1 TTTATCATCATTATTTTTATTTAC
195892 ATTCAAACGT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 11 0.28
27 28 0.72
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTATCATCATTATTTTTATTTACTAT
Found at i:196148 original size:2 final size:2
Alignment explanation
Indices: 196141--196187 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
196131 TTTATGCCTC
196141 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
196183 TA TA T
1 TA TA T
196188 GAAGTAGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:196806 original size:5 final size:5
Alignment explanation
Indices: 196798--196866 Score: 65
Period size: 5 Copynumber: 14.6 Consensus size: 5
196788 TTAATTAAAA
** *
196798 AATTT AATTT AATTT AATTT AA-TT AA-AA AATTT AATTA AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
* *
196846 AA-TC AATTT TA-TT AATTT AAT
1 AATTT AATTT AATTT AATTT AAT
196867 ATAAATTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
4 12 0.24
5 39 0.76
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (5 bp):
AATTT
Found at i:196809 original size:23 final size:23
Alignment explanation
Indices: 196803--196871 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
196793 TAAAAAATTT
196803 AATTTAATTTAATTTAATTAAAA
1 AATTTAATTTAATTTAATTAAAA
* **
196826 AATTTAATTAAATTTAATTTAATC
1 AATTTAATTTAATTTAA-TTAAAA
*
196850 AATTTTA-TTAATTTAATATAAA
1 AATTTAATTTAATTTAAT-TAAA
196872 TTTTGATCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 27 0.71
24 10 0.26
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTTAATTTAATTTAATTAAAA
Found at i:196814 original size:28 final size:28
Alignment explanation
Indices: 196776--196848 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
196766 ACAAAAGTCG
*
196776 ATTAAAATTAATTTAATTAAAAAATTTA
1 ATTAAATTTAATTTAATTAAAAAATTTA
*
196804 ATTTAATTTAATTTAATTAAAAAATTTA
1 ATTAAATTTAATTTAATTAAAAAATTTA
196832 ATTAAATTTAATTTAAT
1 ATTAAATTTAATTTAAT
196849 CAATTTTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTAAATTTAATTTAATTAAAAAATTTA
Found at i:197040 original size:14 final size:14
Alignment explanation
Indices: 196970--197042 Score: 74
Period size: 14 Copynumber: 5.0 Consensus size: 14
196960 AAATTAATAT
196970 TTAAAATATATTTA
1 TTAAAATATATTTA
* * *
196984 ATAACATATAAATATA
1 TTAA-A-ATATATTTA
*
197000 TTAAAATATATATA
1 TTAAAATATATTTA
*
197014 TTTAAAATTTATTTA
1 -TTAAAATATATTTA
197029 TTAAAATATATTTA
1 TTAAAATATATTTA
197043 AAAACAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 24 0.50
15 14 0.29
16 10 0.21
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAAAATATATTTA
Found at i:198441 original size:21 final size:22
Alignment explanation
Indices: 198401--198442 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
198391 ATTTTAAAAA
198401 TTATTTTTACATTAATATTTAT
1 TTATTTTTACATTAATATTTAT
198423 TTATTTTATA-ATTAA-ATTTA
1 TTATTTT-TACATTAATATTTA
198443 AATAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTTTTACATTAATATTTAT
Found at i:198483 original size:10 final size:10
Alignment explanation
Indices: 198459--198509 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
198449 TTTTTAATTA
198459 TTAAATATTATT
1 TTAAAT-TTA-T
198471 TTAAATTTAT
1 TTAAATTTAT
*
198481 TTAAATTAAT
1 TTAAATTTAT
**
198491 AAAAATTTAT
1 TTAAATTTAT
198501 TTAAATTTA
1 TTAAATTTA
198510 ACTTGAATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 24 0.73
11 3 0.09
12 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTAAATTTAT
Found at i:198488 original size:20 final size:20
Alignment explanation
Indices: 198423--198507 Score: 64
Period size: 20 Copynumber: 4.1 Consensus size: 20
198413 TAATATTTAT
*
198423 TTATTTTATAATTAAATTTAAA
1 TTATTTTA-AATT-TATTTAAA
* * *
198445 TAATTTTTTAA-TTATTAAATA
1 TTA-TTTTAAATTTATTTAA-A
198466 TTATTTTAAATTTATTTAAA
1 TTATTTTAAATTTATTTAAA
* **
198486 TTAATAAAAATTTATTTAAA
1 TTATTTTAAATTTATTTAAA
198506 TT
1 TT
198508 TAACTTGAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
20 31 0.62
21 11 0.22
22 4 0.08
23 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTTTAAATTTATTTAAA
Found at i:200144 original size:9 final size:10
Alignment explanation
Indices: 200090--200147 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
200080 TTATTAAAAT
200090 TTTAAATATA
1 TTTAAATATA
*
200100 TTTTAAATAAA
1 -TTTAAATATA
* *
200111 ATT--ATATT
1 TTTAAATATA
*
200119 TTTATATATA
1 TTTAAATATA
200129 TTTAAATATA
1 TTTAAATATA
200139 -TTAAATATA
1 TTTAAATATA
200148 ATTATTATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 5 0.13
9 9 0.24
10 15 0.39
11 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTAAATATA
Found at i:200162 original size:37 final size:38
Alignment explanation
Indices: 200090--200162 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
200080 TTATTAAAAT
*
200090 TTTAAATATATTTTAAATAAAATTATATTTTTATATATA
1 TTTAAATATA-TTTAAATAAAATTATATTTATATATATA
*
200129 TTTAAATATA-TTAAATATAATTAT-TATTATATAT
1 TTTAAATATATTTAAATAAAATTATAT-TTATATAT
200163 TAATACTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 1 0.03
37 20 0.65
39 10 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTAAATATATTTAAATAAAATTATATTTATATATATA
Found at i:200712 original size:20 final size:20
Alignment explanation
Indices: 200687--200726 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
200677 TTTTAACTTT
200687 TGTAAAA-ATTATTTTTTTAA
1 TGTAAAATATT-TTTTTTTAA
200707 TGTAAAATATTTTTTTTTAA
1 TGTAAAATATTTTTTTTTAA
200727 AAAAATTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TGTAAAATATTTTTTTTTAA
Found at i:201218 original size:17 final size:17
Alignment explanation
Indices: 201189--201224 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
201179 CAAAGTTGCA
201189 TTATATTATTTTTATAT
1 TTATATTATTTTTATAT
201206 TTATAATTA-TTTTATAT
1 TTAT-ATTATTTTTATAT
201223 TT
1 TT
201225 GTTTCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATATTATTTTTATAT
Found at i:203744 original size:33 final size:31
Alignment explanation
Indices: 203685--203748 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
203675 AGATTATGAT
*
203685 TTAATAATAAAAATTTTATTTAATTTTATTTA
1 TTAATAATAAAAATTTAATTTAATTTT-TTTA
*
203717 TTAA-AATATAAAATATTAATTTTATTTTTTTA
1 TTAATAATA-AAAAT-TTAATTTAATTTTTTTA
203749 ATGTTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.14
32 13 0.46
33 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAATAATAAAAATTTAATTTAATTTTTTTA
Found at i:204334 original size:21 final size:21
Alignment explanation
Indices: 204294--204345 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
204284 TAAATATATT
* **
204294 ATTTTTATTATATTTTAATTA
1 ATTTTTATAATATTCAAATTA
204315 ATTTTTATAATATTCAAATTA
1 ATTTTTATAATATTCAAATTA
*
204336 TTTATTTATA
1 ATT-TTTATA
204346 TTAAACCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATAATATTCAAATTA
Found at i:207979 original size:2 final size:2
Alignment explanation
Indices: 207972--207997 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
207962 TTGAGGATTT
207972 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
207998 AGCCTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:209099 original size:78 final size:78
Alignment explanation
Indices: 208951--209099 Score: 212
Period size: 78 Copynumber: 1.9 Consensus size: 78
208941 AACTATGTAA
* * *
208951 CAAAAATAATAAAAAATTTATTTTTATATTAATATATATATTTTAACTAAATTTACATAAATATT
1 CAAAAATAATAAAAAATTTATTTTTATATTAATATATATATTTTAACTAAATTTAAATAAAAATA
*
209016 TTTTTATCAGTAG
66 GTTTTATCAGTAG
* *
209029 CAAAAGTAATAAAAAA-TTATTTTTATATTAATATATA-ATTTTATAATTAAATTTAAATAAAAA
1 CAAAAATAATAAAAAATTTATTTTTATATTAATATATATA-TTT-TAACTAAATTTAAATAAAAA
209092 TAGTTTTA
64 TAGTTTTA
209100 ATCATCAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
76 1 0.02
77 24 0.38
78 38 0.60
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (78 bp):
CAAAAATAATAAAAAATTTATTTTTATATTAATATATATATTTTAACTAAATTTAAATAAAAATA
GTTTTATCAGTAG
Found at i:209585 original size:3 final size:3
Alignment explanation
Indices: 209577--209615 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
209567 CATAGTCCCA
209577 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
209616 TCACAGCCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:209823 original size:24 final size:25
Alignment explanation
Indices: 209770--209823 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
209760 ATTTAATTTG
*
209770 AATATTATTTAAATAATAAAATATT
1 AATATTATTAAAATAATAAAATATT
*
209795 -TTATTA-TAAAAT-ATATAAATATT
1 AATATTATTAAAATAATA-AAATATT
209818 AATATT
1 AATATT
209824 TTATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 3 0.12
23 12 0.50
24 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATATTATTAAAATAATAAAATATT
Found at i:213219 original size:17 final size:18
Alignment explanation
Indices: 213200--213260 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 18
213190 GTCTTTATTA
213200 ATATTTAAATAATTTTA-
1 ATATTTAAATAATTTTAC
**
213217 ATATTT--ATAATTAAAAC
1 ATATTTAAATAATT-TTAC
*
213234 ATATTTAAATAATTTTAT
1 ATATTTAAATAATTTTAC
*
213252 ATAATTAAA
1 ATATTTAAA
213261 ATTAGTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.18
16 1 0.03
17 12 0.35
18 9 0.26
19 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATTTAAATAATTTTAC
Found at i:213230 original size:30 final size:31
Alignment explanation
Indices: 213196--213278 Score: 80
Period size: 34 Copynumber: 2.6 Consensus size: 31
213186 TCCCGTCTTT
* *
213196 ATTAATATTTAAATAATTTTA-ATATTTATA
1 ATTAATATTTAAATAATTTTATATAATTAAA
213226 ATTAAAACATATTTAAATAATTTTATATAATTAAA
1 ATT---A-ATATTTAAATAATTTTATATAATTAAA
* *
213261 ATTAGT-TATAAATAATTT
1 ATTAATATTTAAATAATTT
213279 ATTTTATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
30 14 0.32
31 1 0.02
32 1 0.02
33 1 0.02
34 17 0.39
35 10 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
ATTAATATTTAAATAATTTTATATAATTAAA
Found at i:213256 original size:29 final size:30
Alignment explanation
Indices: 213222--213278 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
213212 TTTTAATATT
213222 TATAATTAAAACATA-TT-TAAATAATTTTA
1 TATAATTAAAA-ATAGTTATAAATAATTTTA
*
213251 TATAATTAAAATTAGTTATAAATAATTT
1 TATAATTAAAAATAGTTATAAATAATTT
213279 ATTTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 13 0.52
30 10 0.40
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (30 bp):
TATAATTAAAAATAGTTATAAATAATTTTA
Found at i:214050 original size:20 final size:20
Alignment explanation
Indices: 214025--214065 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
214015 AATTTTATTT
214025 AAATTATTATTTA-ATAATAA
1 AAATTA-TATTTATATAATAA
214045 AAATTATATTTATATAATAA
1 AAATTATATTTATATAATAA
214065 A
1 A
214066 CATCTTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTATATTTATATAATAA
Found at i:216147 original size:13 final size:13
Alignment explanation
Indices: 216129--216292 Score: 53
Period size: 13 Copynumber: 12.8 Consensus size: 13
216119 ATTTAGTAAT
216129 TTATATATTTATA
1 TTATATATTTATA
*
216142 TTATATATATATA
1 TTATATATTTATA
* *
216155 TTTATAGTATTAAAA
1 -TTATA-TATTTATA
* *
216170 TTATAT-TTAAAA
1 TTATATATTTATA
* *
216182 TT-TTTATTTTTA
1 TTATATATTTATA
*
216194 -TATAAATTTTATTAA
1 TTATATA-TTTA-T-A
*
216209 TTAATAAATTT-TA
1 TT-ATATATTTATA
216222 TTATATAATTT-TA
1 TTATAT-ATTTATA
*
216235 --AAATATTTATA
1 TTATATATTTATA
* *
216246 TTTTTTA-TTATA
1 TTATATATTTATA
216258 TTTATATTATTT-TA
1 -TTATA-TATTTATA
*
216272 TTATATA-ATAT-
1 TTATATATTTATA
216283 TTATATATTT
1 TTATATATTT
216293 TAATTATTTT
Statistics
Matches: 113, Mismatches: 20, Indels: 37
0.66 0.12 0.22
Matches are distributed among these distances:
10 4 0.04
11 16 0.14
12 25 0.22
13 35 0.31
14 16 0.14
15 8 0.07
16 4 0.04
17 5 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.60
Consensus pattern (13 bp):
TTATATATTTATA
Found at i:216251 original size:18 final size:19
Alignment explanation
Indices: 216222--216271 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
216212 ATAAATTTTA
*
216222 TTATATAATTTTAAAATAT
1 TTATATTATTTTAAAATAT
**
216241 TTATATT-TTTTATTATAT
1 TTATATTATTTTAAAATAT
216259 TTATATTATTTTA
1 TTATATTATTTTA
216272 TTATATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTATTTTAAAATAT
Found at i:216264 original size:24 final size:25
Alignment explanation
Indices: 216216--216288 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 25
216206 TAATTAATAA
216216 ATTTTATTATATAAT-TTTAAAATATTT
1 ATTTTATTATATAATATTT---ATATTT
*
216243 ATATTT-TT-TATTATATTTATA-TT
1 AT-TTTATTATATAATATTTATATTT
216266 ATTTTATTATATAATATTTATAT
1 ATTTTATTATATAATATTTATAT
216289 ATTTTAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
22 3 0.08
23 6 0.15
24 15 0.38
26 5 0.13
27 7 0.18
28 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTTATTATATAATATTTATATTT
Found at i:216266 original size:42 final size:42
Alignment explanation
Indices: 216216--216304 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
216206 TAATTAATAA
* *
216216 ATTTTATTATATAATTTTAAAATATTTATAT-TTTTTATTAT
1 ATTTTATTATATAATTATAAAATATTTATATATTTTAATTAT
* * *
216257 ATTTATATTATTTTATTATATAATATTTATATATTTTAATTAT
1 ATTT-TATTATATAATTATAAAATATTTATATATTTTAATTAT
*
216300 TTTTT
1 ATTTT
216305 CGCATATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 4 0.10
42 24 0.60
43 12 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (42 bp):
ATTTTATTATATAATTATAAAATATTTATATATTTTAATTAT
Found at i:216272 original size:19 final size:19
Alignment explanation
Indices: 216222--216277 Score: 78
Period size: 19 Copynumber: 3.0 Consensus size: 19
216212 ATAAATTTTA
* **
216222 TTATATAATTTTAAAATAT
1 TTATATTATTTTATTATAT
216241 TTATATT-TTTTATTATAT
1 TTATATTATTTTATTATAT
216259 TTATATTATTTTATTATAT
1 TTATATTATTTTATTATAT
216278 AATATTTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTATTTTATTATAT
Found at i:216286 original size:19 final size:19
Alignment explanation
Indices: 216223--216283 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
216213 TAAATTTTAT
* ** *
216223 TATATAATTTTAAAATATT
1 TATATTATTTTATTATATA
*
216242 TATATT-TTTTATTATATT
1 TATATTATTTTATTATATA
216260 TATATTATTTTATTATATA
1 TATATTATTTTATTATATA
216279 -ATATT
1 TATATT
216284 TATATATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 21 0.57
19 16 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTATTTTATTATATA
Found at i:216291 original size:18 final size:17
Alignment explanation
Indices: 216127--216301 Score: 64
Period size: 17 Copynumber: 10.2 Consensus size: 17
216117 GAATTTAGTA
216127 ATTTATATATTTATATTAT
1 ATTTATATATTTATA--AT
* *
216146 ATATATATATTTATAGT
1 ATTTATATATTTATAAT
*
216163 ATTAAAATTATATTTA-AA-
1 ATT--TA-TATATTTATAAT
* * *
216181 ATTTTTATTTTTATATAA
1 ATTTATATATTTATA-AT
*
216199 ATTT-TATTAATTAATAA-
1 ATTTATA-T-ATTTATAAT
*
216216 ATTT-TAT-TATATAAT
1 ATTTATATATTTATAAT
* *
216231 -TTTAAAATATTTATATT
1 ATTT-ATATATTTATAAT
* *
216248 TTTTATTATATTTATATT
1 ATTTA-TATATTTATAAT
*
216266 ATTT-TAT-TATATAAT
1 ATTTATATATTTATAAT
216281 ATTTATATATTT-TAATT
1 ATTTATATATTTATAA-T
216298 ATTT
1 ATTT
216302 TTTCGCATAT
Statistics
Matches: 119, Mismatches: 20, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.07
15 17 0.14
16 13 0.11
17 26 0.22
18 26 0.22
19 21 0.18
20 8 0.07
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (17 bp):
ATTTATATATTTATAAT
Found at i:218671 original size:15 final size:16
Alignment explanation
Indices: 218647--218676 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
218637 CAAATTTTAA
218647 AAAAATTAAATATATT
1 AAAAATTAAATATATT
218663 AAAAA-TAAATATAT
1 AAAAATTAAATATAT
218677 ACTTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATTAAATATATT
Found at i:219331 original size:12 final size:12
Alignment explanation
Indices: 219295--219358 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
219285 GAATTACGTG
*
219295 ATAATATTAAAT
1 ATAATATAAAAT
*
219307 ATGATTATAAAAAT
1 AT-AATAT-AAAAT
219321 ATAATATAAAAT
1 ATAATATAAAAT
219333 AATAAT-TAAAAT
1 -ATAATATAAAAT
*
219345 ATGATAT-AAAT
1 ATAATATAAAAT
219356 ATA
1 ATA
219359 TGTTTTAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 10 0.23
12 14 0.33
13 13 0.30
14 6 0.14
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:219465 original size:29 final size:30
Alignment explanation
Indices: 219418--219476 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
219408 TTATGTAAAT
*
219418 ATAAAATACTTTAAATATAA-ATATAATATA
1 ATAAAATACTGTAAATATAATATA-AATATA
219448 ATAAAATA-TGTAAATATAATATAAATATA
1 ATAAAATACTGTAAATATAATATAAATATA
219477 TTAATTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (30 bp):
ATAAAATACTGTAAATATAATATAAATATA
Found at i:220116 original size:17 final size:17
Alignment explanation
Indices: 220107--220141 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
220097 AAAAAAATTA
220107 ATTTAATAAATATAAAT
1 ATTTAATAAATATAAAT
*
220124 ATTTAATAAATGTAAAT
1 ATTTAATAAATATAAAT
220141 A
1 A
220142 AATAACGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATTTAATAAATATAAAT
Found at i:220252 original size:23 final size:24
Alignment explanation
Indices: 220208--220270 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
220198 AATAAATTTT
* *
220208 AAATTTTAAATTTAAAATATATTAAGT
1 AAATTATAAATTT-AAATAT-TTAA-A
220235 AAATTA-AAATTTAAATATTTAAA
1 AAATTATAAATTTAAATATTTAAA
220258 AAATTATAAATTT
1 AAATTATAAATTT
220271 TTAACCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 6 0.18
24 10 0.30
25 6 0.18
26 6 0.18
27 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATTATAAATTTAAATATTTAAA
Found at i:220273 original size:18 final size:17
Alignment explanation
Indices: 220240--220274 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
220230 TAAGTAAATT
220240 AAAATTTAAATATTTAA
1 AAAATTTAAATATTTAA
*
220257 AAAATTATAAATTTTTAA
1 AAAATT-TAAATATTTAA
220275 CCTATTATCA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTTAAATATTTAA
Found at i:220573 original size:45 final size:45
Alignment explanation
Indices: 220494--220603 Score: 120
Period size: 45 Copynumber: 2.4 Consensus size: 45
220484 TAAATGGTAA
* * *
220494 ATAATTT-ATTTGATTT-AATTATTTTAATTTAAATATAATAATTT
1 ATAATTTAATTTAATTTAAATTATTTT-ATATAAATAAAATAATTT
220538 ATAATTTAATTTAATTTAAATTATTATT-TATAAATAAAATAATTT
1 ATAATTTAATTTAATTTAAATTATT-TTATATAAATAAAATAATTT
*
220583 -TTATTTAAATTTAATTATAAA
1 ATAATTT-AATTTAATT-TAAA
220604 ATATATCAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
44 12 0.21
45 32 0.56
46 11 0.19
47 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (45 bp):
ATAATTTAATTTAATTTAAATTATTTTATATAAATAAAATAATTT
Found at i:220662 original size:16 final size:17
Alignment explanation
Indices: 220633--220673 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
220623 AAAATAATTT
*
220633 TTTAATATTTTAAT-AAA
1 TTTAA-ATTATAATCAAA
220650 TTTAAATTATAATCAAA
1 TTTAAATTATAATCAAA
220667 -TTAAATT
1 TTTAAATT
220674 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATTATAATCAAA
Found at i:226219 original size:26 final size:29
Alignment explanation
Indices: 226190--226258 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 29
226180 ATGAGTTATT
* *
226190 AATATATTAAATTTA-TATAA-A-TATAA
1 AATATATTAAATATATTATAATACGATAA
*
226216 AATATTTTAAATATATTATAATACGATAA
1 AATATATTAAATATATTATAATACGATAA
226245 AATATA-TAAATATA
1 AATATATTAAATATA
226259 ATATGATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 13 0.36
27 5 0.14
28 9 0.25
29 9 0.25
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
AATATATTAAATATATTATAATACGATAA
Found at i:233138 original size:17 final size:17
Alignment explanation
Indices: 233108--233174 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
233098 GCTTTAATTT
* *
233108 ATATAATATGAATTTTA
1 ATATATTATAAATTTTA
233125 ATATATTAGT-AA-TTT-
1 ATATATTA-TAAATTTTA
*
233140 ATATTTTATAAATTTTA
1 ATATATTATAAATTTTA
*
233157 ATATATTTATATATTTTA
1 ATATA-TTATAAATTTTA
233175 TATTTGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.02
15 9 0.22
16 6 0.15
17 13 0.32
18 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATATATTATAAATTTTA
Found at i:233138 original size:32 final size:32
Alignment explanation
Indices: 233102--233163 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
233092 TTTTATGCTT
*
233102 TAATTTATATAATATGAATTTTAATATATTAG
1 TAATTTATATAATATAAATTTTAATATATTAG
**
233134 TAATTTATATTTTATAAATTTTAATATATT
1 TAATTTATATAATATAAATTTTAATATATT
233164 TATATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (32 bp):
TAATTTATATAATATAAATTTTAATATATTAG
Found at i:233156 original size:9 final size:9
Alignment explanation
Indices: 233139--233222 Score: 55
Period size: 9 Copynumber: 9.0 Consensus size: 9
233129 ATTAGTAATT
233139 TATATTTTA
1 TATATTTTA
*
233148 TAAATTTTA
1 TATATTTTA
233157 -ATATATTTA
1 TATAT-TTTA
233166 TATATTTTA
1 TATATTTTA
*
233175 TATTTGTGTTA
1 TATAT-T-TTA
*
233186 TTTA-TTTA
1 TATATTTTA
*
233194 TATTATATTA
1 TA-TATTTTA
* *
233204 TATTTTATTT
1 TATATT-TTA
233214 TATATTTTA
1 TATATTTTA
233223 AATTTTTTGG
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
8 7 0.12
9 27 0.48
10 17 0.30
11 5 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TATATTTTA
Found at i:233167 original size:18 final size:18
Alignment explanation
Indices: 233118--233174 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
233108 ATATAATATG
233118 AATTTTAATATA-TTAGT-
1 AATTTTAATATATTTA-TA
233135 AA-TTT-ATAT-TTTATA
1 AATTTTAATATATTTATA
233150 AATTTTAATATATTTATA
1 AATTTTAATATATTTATA
*
233168 TATTTTA
1 AATTTTA
233175 TATTTGTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
16 6 0.18
17 6 0.18
18 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATTTTAATATATTTATA
Found at i:238082 original size:19 final size:19
Alignment explanation
Indices: 238058--238111 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
238048 ATAATATAAT
* *
238058 AAAAATAAAAAATTAATGA
1 AAAAATAAAAAATCAATCA
*
238077 AAAAATTAAAAATCAATCA
1 AAAAATAAAAAATCAATCA
*
238096 AAAAATCAAAAATCAA
1 AAAAATAAAAAATCAA
238112 AGAAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAATAAAAAATCAATCA
Found at i:241495 original size:18 final size:17
Alignment explanation
Indices: 241472--241515 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
241462 ATTTAACTTA
241472 TTTTTAAATAAATTTTAT
1 TTTTTAAATAAA-TTTAT
**
241490 TTTTTATTTAAATTTAT
1 TTTTTAAATAAATTTAT
241507 TTTTTAAAT
1 TTTTTAAAT
241516 TTTATACGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTAAATAAATTTAT
Found at i:241873 original size:19 final size:20
Alignment explanation
Indices: 241835--241880 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
241825 AATTTGAATT
*
241835 TAAATTTTCTAATTAATTTAA
1 TAAA-TTTCTAATAAATTTAA
241856 TAAATTTC-AATAAATTTAA
1 TAAATTTCTAATAAATTTAA
*
241875 TTAATT
1 TAAATT
241881 ATTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 4 0.17
21 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATTTCTAATAAATTTAA
Found at i:242190 original size:16 final size:16
Alignment explanation
Indices: 242169--242227 Score: 73
Period size: 16 Copynumber: 3.5 Consensus size: 16
242159 TCTTGGAAAT
242169 AAGGAAAAGAAAAAGA
1 AAGGAAAAGAAAAAGA
*
242185 AAGGAAAGGAAAAAGA
1 AAGGAAAAGAAAAAGA
*
242201 AAGGAAGAGAAAGAACGA
1 AAGGAAAAGAAA-AA-GA
242219 AGAGGAAAA
1 A-AGGAAAA
242228 AAAGGGGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
16 25 0.69
17 2 0.06
18 3 0.08
19 6 0.17
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (16 bp):
AAGGAAAAGAAAAAGA
Found at i:242293 original size:6 final size:6
Alignment explanation
Indices: 242282--242334 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
242272 AGAAAGAACG
242282 AAGAGA AAGAGA AAGA-A ATAGAGA ATA-AG- AAGAGA AAGAGA AA-A-A
1 AAGAGA AAGAGA AAGAGA A-AGAGA A-AGAGA AAGAGA AAGAGA AAGAGA
242327 AAGAGA AA
1 AAGAGA AA
242335 AATTTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
4 4 0.10
5 7 0.17
6 26 0.63
7 4 0.10
ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04
Consensus pattern (6 bp):
AAGAGA
Found at i:242306 original size:27 final size:25
Alignment explanation
Indices: 242276--242334 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 25
242266 AAGATGAGAA
*
242276 AGAACGAAGAGAAAGAGAAAGAAATAG
1 AGAAAGAAGAGAAAGAGAAA-AAA-AG
242303 AGAATAAGAAGAGAAAGAGAAAAAAAG
1 AG-A-AAGAAGAGAAAGAGAAAAAAAG
242330 AGAAA
1 AGAAA
242335 AATTTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 2 0.07
26 1 0.03
27 6 0.21
28 4 0.14
29 16 0.55
ACGTcount: A:0.68, C:0.02, G:0.27, T:0.03
Consensus pattern (25 bp):
AGAAAGAAGAGAAAGAGAAAAAAAG
Found at i:252505 original size:22 final size:22
Alignment explanation
Indices: 252480--252525 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
252470 TGTGTATACG
252480 TATATGTATGTATTTAAAATGA
1 TATATGTATGTATTTAAAATGA
*
252502 TATATGTGTGTATTTAAAATGA
1 TATATGTATGTATTTAAAATGA
252524 TA
1 TA
252526 AGAATAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (22 bp):
TATATGTATGTATTTAAAATGA
Found at i:254134 original size:24 final size:24
Alignment explanation
Indices: 254090--254146 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
254080 TCGCGTATTC
* *
254090 ATATCATA-TTTATTTAATTTTTT
1 ATATCATATTTTAATTAATTTTAT
* *
254113 ATATTATATTTTAATTATTTTTAT
1 ATATCATATTTTAATTAATTTTAT
254137 ATATCATATT
1 ATATCATATT
254147 CTTGTTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATCATATTTTAATTAATTTTAT
Found at i:254154 original size:24 final size:21
Alignment explanation
Indices: 254090--254146 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
254080 TCGCGTATTC
254090 ATATCATATTTATTTAATTTTTT
1 ATATCATATTT-TTT-ATTTTTT
*
254113 ATATTATATTTTAATTATTTTTAT
1 ATATCATATTTT--TTATTTTT-T
254137 ATATCATATT
1 ATATCATATT
254147 CTTGTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 1 0.03
23 16 0.55
24 12 0.41
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATCATATTTTTTATTTTTT
Found at i:256221 original size:20 final size:18
Alignment explanation
Indices: 256196--256248 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 18
256186 AGCTTAAACA
256196 TAAATTTTTATACTTTAAAT
1 TAAATTTTTA-A-TTTAAAT
256216 TAAATTAATTTAATTTAAAT
1 TAAATT--TTTAATTTAAAT
256236 TATTAATTTTTAA
1 TA--AATTTTTAA
256249 AAAATATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 20 0.69
21 1 0.03
22 8 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATTTTTAATTTAAAT
Found at i:257698 original size:23 final size:24
Alignment explanation
Indices: 257649--257709 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
257639 GTTAAGATTC
257649 TTATTTAATTACAAATTAAAAATT
1 TTATTTAATTACAAATTAAAAATT
257673 TTATTTTAA-TACAAATTAAAAA-T
1 TTA-TTTAATTACAAATTAAAAATT
257696 TTATTTAATTACAA
1 TTATTTAATTACAA
257710 TAAAATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.14
23 9 0.26
24 16 0.46
25 5 0.14
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATTTAATTACAAATTAAAAATT
Found at i:258522 original size:2 final size:2
Alignment explanation
Indices: 258475--258510 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
258465 GGTATTTCTA
258475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
258511 GCGTATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:259528 original size:24 final size:24
Alignment explanation
Indices: 259464--259531 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
259454 CATGGGAGGG
259464 GAAGAAGAAGAAGC-AGAAGATAAA
1 GAAGAAGAAGAA-CAAGAAGATAAA
* * * *
259488 GATGAAGAATAATAAGATGATAAA
1 GAAGAAGAAGAACAAGAAGATAAA
*
259512 GAAGACGAAGAACAAGAAGA
1 GAAGAAGAAGAACAAGAAGA
259532 AGCAGCTGCA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.60, C:0.04, G:0.26, T:0.09
Consensus pattern (24 bp):
GAAGAAGAAGAACAAGAAGATAAA
Found at i:260079 original size:24 final size:24
Alignment explanation
Indices: 260048--260128 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
260038 CATGTAAAAA
260048 ATATAATATAAATATTTTAAAATT
1 ATATAATATAAATATTTTAAAATT
* * *
260072 ATATAATATTAACAATTT-AAA-T
1 ATATAATATAAATATTTTAAAATT
* *
260094 AAAT-AT-TAAATATTTTAAATATA
1 ATATAATATAAATATTTTAAA-ATT
260117 ATTATAATATAA
1 A-TATAATATAA
260129 TAAAAATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
20 7 0.17
21 4 0.10
22 5 0.12
23 4 0.10
24 17 0.40
25 2 0.05
26 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAATATAAATATTTTAAAATT
Found at i:260108 original size:19 final size:20
Alignment explanation
Indices: 260076--260114 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
260066 AAAATTATAT
260076 AATATTAACAA-TTTAAATA
1 AATATTAACAATTTTAAATA
260095 AATATTAA-ATATTTTAAATA
1 AATATTAACA-ATTTTAAATA
260115 TAATTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.06
19 9 0.50
20 8 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTAACAATTTTAAATA
Found at i:260120 original size:19 final size:20
Alignment explanation
Indices: 260046--260123 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
260036 GCCATGTAAA
260046 AAATATAATATAAATATTTT
1 AAATATAATATAAATATTTT
* * *
260066 AAAATTATATAATATTAACAATTT
1 --AA--ATATAATATAAATATTTT
260090 AAATA-AATATTAAATATTTT
1 AAATATAATA-TAAATATTTT
260110 AAATATAATTATAA
1 AAATATAA-TATAA
260124 TATAATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
19 4 0.09
20 15 0.33
21 5 0.11
22 6 0.13
24 15 0.33
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATAATATAAATATTTT
Found at i:261231 original size:21 final size:21
Alignment explanation
Indices: 261207--261284 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
261197 GGTTTTAATG
261207 AAATTAAAAATAATAATAGTA
1 AAATTAAAAATAATAATAGTA
** * *
261228 AAATTAATCATTATAATAATA
1 AAATTAAAAATAATAATAGTA
* * **
261249 AGATTAAAAATGATAACGGTA
1 AAATTAAAAATAATAATAGTA
* *
261270 AAATTGAAATTAATA
1 AAATTAAAAATAATA
261285 TTAAGATATA
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (21 bp):
AAATTAAAAATAATAATAGTA
Found at i:264935 original size:15 final size:16
Alignment explanation
Indices: 264905--264938 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
264895 TATAAATTTA
264905 ATATAAATTATTAAAT
1 ATATAAATTATTAAAT
264921 ATATAAATT-TTAAAT
1 ATATAAATTATTAAAT
264936 ATA
1 ATA
264939 AACATGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATAAATTATTAAAT
Found at i:265009 original size:20 final size:20
Alignment explanation
Indices: 264980--265048 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 20
264970 AACAATAATA
*
264980 ATTATATTTAAATATATTAT
1 ATTATTTTTAAATATATTAT
*
265000 ATTATTTTTATTAAAATATTAT
1 ATTATTTTTA--AATATATTAT
265022 CA-TATTTATTAAATATATTCAT
1 -ATTATTT-TTAAATATATT-AT
265044 ATTAT
1 ATTAT
265049 ATTATATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 9 0.22
21 8 0.20
22 19 0.47
23 4 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTATTTTTAAATATATTAT
Done.