Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 13 of 18
Found at i:2195716 original size:2 final size:2
Alignment explanation
Indices: 2195709--2195748 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2195699 CAGCAGCAAA
2195709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2195749 TGAACTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2195989 original size:23 final size:24
Alignment explanation
Indices: 2195934--2195997 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
2195924 GATTTGCTGG
*
2195934 AATAGTTATTTTATTATTTTATGT
1 AATAGTTATTTTATTATTTTATAT
*
2195958 AATAATTATTTTATTATTTT-TAT
1 AATAGTTATTTTATTATTTTATAT
2195981 AATAGTTATTTTATTAT
1 AATAGTTATTTTATTAT
2195998 GAATTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (24 bp):
AATAGTTATTTTATTATTTTATAT
Found at i:2196234 original size:19 final size:19
Alignment explanation
Indices: 2196210--2196248 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2196200 TAATATTCTA
2196210 TTTCATTGAATTAAACTAC
1 TTTCATTGAATTAAACTAC
2196229 TTTCATTGAATTAAACTAC
1 TTTCATTGAATTAAACTAC
2196248 T
1 T
2196249 GTTATAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (19 bp):
TTTCATTGAATTAAACTAC
Found at i:2197796 original size:16 final size:16
Alignment explanation
Indices: 2197775--2197806 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2197765 AAAATATTTT
2197775 TATATCACTTTTGTAA
1 TATATCACTTTTGTAA
2197791 TATATCACTTTTGTAA
1 TATATCACTTTTGTAA
2197807 GGTATAGATA
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:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TATATCACTTTTGTAA
Found at i:2198212 original size:20 final size:22
Alignment explanation
Indices: 2198177--2198239 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
2198167 TATCTTCTTA
2198177 ATTT-TTATATATTAAAAATTAT
1 ATTTATTATA-ATTAAAAATTAT
*
2198199 A-TTATTA-AATTAAATA-TAT
1 ATTTATTATAATTAAAAATTAT
* *
2198218 ATTTATTATATTTAATAATTAT
1 ATTTATTATAATTAAAAATTAT
2198240 TGAATATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 4 0.12
20 13 0.39
21 9 0.27
22 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTATTATAATTAAAAATTAT
Found at i:2201812 original size:3 final size:3
Alignment explanation
Indices: 2201804--2201840 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2201794 TCACTAAAGC
2201804 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2201841 AGCTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2203072 original size:17 final size:19
Alignment explanation
Indices: 2203032--2203075 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
2203022 TCTTTCAAAT
*
2203032 AATTTGTTACAAAATTTTA
1 AATTTGTTACAAAATCTTA
*
2203051 TATTT-TTA-AAAATCTTA
1 AATTTGTTACAAAATCTTA
2203068 AATTTGTT
1 AATTTGTT
2203076 TACCAACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
19 4 0.19
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (19 bp):
AATTTGTTACAAAATCTTA
Found at i:2203494 original size:2 final size:2
Alignment explanation
Indices: 2203487--2203518 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2203477 TTTGTCTTTG
2203487 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
2203519 TCACACATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2205197 original size:16 final size:16
Alignment explanation
Indices: 2205176--2205209 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2205166 ATAAGAGTGC
*
2205176 AATGTAAATACTCTTG
1 AATGTAAATACTCATG
2205192 AATGTAAATACTCATG
1 AATGTAAATACTCATG
2205208 AA
1 AA
2205210 AAAAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (16 bp):
AATGTAAATACTCATG
Found at i:2206353 original size:27 final size:27
Alignment explanation
Indices: 2206322--2206376 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2206312 AATTGATTTG
*
2206322 ATTTTTTTTTA-T-TTTAAAAAAAATA
1 ATTTTTTATTATTATTTAAAAAAAATA
*
2206347 ATTTTTTATTATTATTTAAAAAAATTA
1 ATTTTTTATTATTATTTAAAAAAAATA
2206374 ATT
1 ATT
2206377 GAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 10 0.38
26 1 0.04
27 15 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTTTATTATTATTTAAAAAAAATA
Found at i:2207666 original size:10 final size:9
Alignment explanation
Indices: 2207647--2207689 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2207637 AAAGATACCC
*
2207647 AAAAGGAAA
1 AAAAAGAAA
*
2207656 AAAATGAAA
1 AAAAAGAAA
2207665 AAAAAGAAA
1 AAAAAGAAA
2207674 AGAAAAGAAA
1 A-AAAAGAAA
*
2207684 AGAAAG
1 AAAAAG
2207690 TTGGTGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:2207676 original size:5 final size:5
Alignment explanation
Indices: 2207647--2207688 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
2207637 AAAGATACCC
*
2207647 AAAAGG AAAA- AAATG AAAA- AAAAG AAAAG AAAAG AAAAG AAA
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
2207689 GTTGGTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
4 7 0.22
5 21 0.66
6 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:2208858 original size:21 final size:21
Alignment explanation
Indices: 2208812--2208859 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2208802 ATTATATATT
*
2208812 ATATATTAATAAATTAATAAT
1 ATATATTAATAAATTAATAAA
* *
2208833 TTATATTATATAAATT-TTAAA
1 ATATATTA-ATAAATTAATAAA
2208854 ATATAT
1 ATATAT
2208860 ATTTATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATATTAATAAATTAATAAA
Found at i:2208874 original size:15 final size:15
Alignment explanation
Indices: 2208831--2208874 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2208821 TAAATTAATA
* *
2208831 ATTTATATTATATAA
1 ATTTATAATATATAT
*
2208846 ATTT-TAAAATATAT
1 ATTTATAATATATAT
2208860 ATTTATAATATATAT
1 ATTTATAATATATAT
2208875 TTAATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATAATATATAT
Found at i:2209290 original size:6 final size:6
Alignment explanation
Indices: 2209281--2209328 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
2209271 TGGTTGATTA
*
2209281 TATATA TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
2209329 AGAAGGTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:2210014 original size:24 final size:25
Alignment explanation
Indices: 2209942--2210034 Score: 68
Period size: 24 Copynumber: 3.9 Consensus size: 25
2209932 AAGATACACA
* *
2209942 TATTAAATATA-TAATTTTA-ATTA
1 TATTAAATATATTATTTTTATATTT
* ***
2209965 TATTAATTATATT-TAAATATATTT
1 TATTAAATATATTATTTTTATATTT
* *
2209989 TATTTATTATATTATTTTTATA-TT
1 TATTAAATATATTATTTTTATATTT
* *
2210013 TATTAAATGTGTTATTTTTATA
1 TATTAAATATATTATTTTTATA
2210035 ACGTCTAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
23 12 0.23
24 36 0.68
25 5 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTAAATATATTATTTTTATATTT
Found at i:2210016 original size:29 final size:30
Alignment explanation
Indices: 2209941--2210008 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 30
2209931 TAAGATACAC
*
2209941 ATATTAAATATATAATTTTAATTATATTAATT
1 ATATTTAA-ATAT-ATTTTAATTATATTAATT
2209973 ATATTTAAATATATTTT-ATT-TATTATATT
1 ATATTTAAATATATTTTAATTATATTA-ATT
*
2210002 ATTTTTA
1 ATATTTA
2210009 TATTTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 5 0.15
29 12 0.36
30 5 0.15
31 4 0.12
32 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
ATATTTAAATATATTTTAATTATATTAATT
Found at i:2211202 original size:3 final size:3
Alignment explanation
Indices: 2211194--2211242 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
2211184 ATCAATCTCA
2211194 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2211242 T
1 T
2211243 CAATGTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2211741 original size:25 final size:26
Alignment explanation
Indices: 2211689--2211741 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
2211679 ACATAAATGC
* * *
2211689 ATTTTATATTATTATTTAATATTTTA
1 ATTTTATATAATTATTTAATAATATA
2211715 ATTTTAT-TAATTATTTAATAATATA
1 ATTTTATATAATTATTTAATAATATA
2211740 AT
1 AT
2211742 AATTTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTATATAATTATTTAATAATATA
Found at i:2211917 original size:19 final size:18
Alignment explanation
Indices: 2211886--2211949 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
2211876 GATACGAGAA
2211886 AAATA-ATAAAAATATA-
1 AAATATATAAAAATATAC
*
2211902 ATATGATATGAAAAATAGTAC
1 AAAT-ATAT-AAAAATA-TAC
*
2211923 AAATATATAAAAATATAT
1 AAATATATAAAAATATAC
*
2211941 AAAAATATA
1 AAATATATA
2211950 TATATATAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.08
17 1 0.03
18 12 0.31
19 14 0.36
20 6 0.15
21 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATATATAAAAATATAC
Found at i:2211938 original size:10 final size:10
Alignment explanation
Indices: 2211923--2211951 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2211913 AAAATAGTAC
2211923 AAATATATAA
1 AAATATATAA
2211933 AAATATATAA
1 AAATATATAA
2211943 AAATATATA
1 AAATATATA
2211952 TATATAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAATATATAA
Found at i:2212501 original size:11 final size:11
Alignment explanation
Indices: 2212487--2212529 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
2212477 TAATTTAATA
2212487 ATTTATATTAT
1 ATTTATATTAT
2212498 ATTTATATTATT
1 ATTTATATTA-T
*
2212510 TTTTATATTAT
1 ATTTATATTAT
*
2212521 AATTATATT
1 ATTTATATT
2212530 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2212517 original size:18 final size:18
Alignment explanation
Indices: 2212494--2212551 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
2212484 ATAATTTATA
*
2212494 TTATATTTATATTATTTT
1 TTATATTTATATTATATT
2212512 TTATA-TTATAATTATATT
1 TTATATTTAT-ATTATATT
*
2212530 TTAAATTT-TA-TATATT
1 TTATATTTATATTATATT
*
2212546 ATATAT
1 TTATAT
2212552 AAATTTTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.29
17 5 0.15
18 17 0.50
19 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATTTATATTATATT
Found at i:2212540 original size:20 final size:20
Alignment explanation
Indices: 2212517--2212558 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2212507 ATTTTTTATA
*
2212517 TTATA-ATTATATTTTAAATT
1 TTATATATTATA-TATAAATT
2212537 TTATATATTATATATAAATT
1 TTATATATTATATATAAATT
2212557 TT
1 TT
2212559 GATACATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATATTATATATAAATT
Found at i:2212751 original size:2 final size:2
Alignment explanation
Indices: 2212744--2212784 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2212734 ATTAATTTGC
*
2212744 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2212785 GACCCTACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2213322 original size:3 final size:3
Alignment explanation
Indices: 2213314--2213351 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2213304 TAGACACCAA
2213314 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2213352 ATAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2214206 original size:38 final size:38
Alignment explanation
Indices: 2214158--2214230 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
2214148 TTAGGTTTAA
* *
2214158 TTTATCAAAATAAAATAGAGTTAAAATAA-AATAATTAT
1 TTTATAAAAATAAAATAGA-ATAAAATAATAATAATTAT
*
2214196 TTTATAAAAATAAAATATAATAAAATAATAATAAT
1 TTTATAAAAATAAAATAGAATAAAATAATAATAAT
2214231 AATAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 8 0.26
38 23 0.74
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (38 bp):
TTTATAAAAATAAAATAGAATAAAATAATAATAATTAT
Found at i:2214225 original size:3 final size:3
Alignment explanation
Indices: 2214199--2214245 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
2214189 TAATTATTTT
*
2214199 ATA AAA ATA A-A AT- ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2214244 AT
1 AT
2214246 TTAATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2215239 original size:30 final size:30
Alignment explanation
Indices: 2215205--2215276 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
2215195 TAAAATTAAC
* * *
2215205 AATAATATTATTAAAAAATATTAACATTGT
1 AATAATATTAATAAAAAATAATAACATTAT
* *
2215235 AATAATATAAATAAAAATTAATAACATTAT
1 AATAATATTAATAAAAAATAATAACATTAT
2215265 AATAAATATTAA
1 AAT-AATATTAA
2215277 CCCTAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 28 0.80
31 7 0.20
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (30 bp):
AATAATATTAATAAAAAATAATAACATTAT
Found at i:2215566 original size:13 final size:13
Alignment explanation
Indices: 2215531--2215565 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
2215521 AAAATAATAA
2215531 TAATAATAATATTT
1 TAATAA-AATATTT
2215545 TAATAAAATATTT
1 TAATAAAATATTT
2215558 TAAATAAA
1 T-AATAAA
2215566 TTCTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAAAATATTT
Found at i:2215581 original size:14 final size:13
Alignment explanation
Indices: 2215556--2215593 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2215546 AATAAAATAT
2215556 TTTAAATAAATTCTA
1 TTTAAAT-AATT-TA
2215571 TTTAAATAATTTA
1 TTTAAATAATTTA
2215584 TTTAAA-AATT
1 TTTAAATAATT
2215594 AAAGATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 4 0.17
15 7 0.30
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAATAATTTA
Found at i:2216128 original size:2 final size:2
Alignment explanation
Indices: 2216117--2216163 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2216107 TTAAAAACTT
2216117 TA TA -A 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
2216158 TA TA TA
1 TA TA TA
2216164 ACCACAGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2217100 original size:23 final size:22
Alignment explanation
Indices: 2217073--2217140 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
2217063 TATCCATTTT
2217073 TTAAAAAACTACTATTTTTTCAC
1 TTAAAAAACTACTATTTTTT-AC
*
2217096 TTAAAAAACTATTCACTTTTTTAC
1 TTAAAAAACTACT-A-TTTTTTAC
2217120 TTAAAAAA-TAACTATTTTTTA
1 TTAAAAAACT-ACTATTTTTTA
2217141 TATTTCTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 7 0.17
23 14 0.35
24 13 0.32
25 6 0.15
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAAAACTACTATTTTTTAC
Found at i:2217115 original size:24 final size:23
Alignment explanation
Indices: 2217073--2217127 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
2217063 TATCCATTTT
*
2217073 TTAAAAAACTACTATTTTTTCAC
1 TTAAAAAACTACTACTTTTTCAC
* *
2217096 TTAAAAAACTATTCACTTTTTTAC
1 TTAAAAAACTACT-ACTTTTTCAC
2217120 TTAAAAAA
1 TTAAAAAA
2217128 TAACTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAAAAAACTACTACTTTTTCAC
Found at i:2217456 original size:21 final size:22
Alignment explanation
Indices: 2217424--2217467 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2217414 CATATTTATA
*
2217424 TATTTATATTTTTTTTATTTTT
1 TATTTATATTTTATTTATTTTT
2217446 TATTT-TATTTTATTTATTTTT
1 TATTTATATTTTATTTATTTTT
2217467 T
1 T
2217468 GCCTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (22 bp):
TATTTATATTTTATTTATTTTT
Found at i:2217458 original size:17 final size:17
Alignment explanation
Indices: 2217416--2217460 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2217406 AATTCTAGCA
2217416 TATTTATATATTTATATTT
1 TATTT-TAT-TTTATATTT
*
2217435 T-TTTTATTTTTTATTT
1 TATTTTATTTTATATTT
2217451 TATTTTATTT
1 TATTTTATTT
2217461 ATTTTTTGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 11 0.46
18 3 0.12
19 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTTTATTTTATATTT
Found at i:2218799 original size:21 final size:23
Alignment explanation
Indices: 2218774--2218817 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2218764 TGATAAATGT
2218774 TTTTAATA-TA-AAATATTAATA
1 TTTTAATAGTATAAATATTAATA
2218795 TTTTAATAGTATAAATATTAATA
1 TTTTAATAGTATAAATATTAATA
2218818 GAAATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTAATAGTATAAATATTAATA
Found at i:2218813 original size:17 final size:17
Alignment explanation
Indices: 2218790--2218834 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
2218780 TATAAAATAT
*
2218790 TAATATTTTAATAG-TA
1 TAATATTTTAATAGAAA
*
2218806 TAA-ATATTAATAGAAA
1 TAATATTTTAATAGAAA
2218822 TAATATTTTAATA
1 TAATATTTTAATA
2218835 ATTATTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 9 0.38
16 7 0.29
17 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
TAATATTTTAATAGAAA
Found at i:2219204 original size:13 final size:14
Alignment explanation
Indices: 2219190--2219225 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2219180 TTTTAATTTT
2219190 AAATATTTTTATTA
1 AAATATTTTTATTA
*
2219204 AAATGTTTTTATTTA
1 AAATATTTTTA-TTA
2219219 AAATATT
1 AAATATT
2219226 AATATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (14 bp):
AAATATTTTTATTA
Found at i:2219212 original size:14 final size:15
Alignment explanation
Indices: 2219180--2219225 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2219170 TAACGTAGTG
* *
2219180 TTTTAATTTTAAATA
1 TTTTTATTTAAAATA
*
2219195 TTTTTA-TTAAAATG
1 TTTTTATTTAAAATA
2219209 TTTTTATTTAAAATA
1 TTTTTATTTAAAATA
2219224 TT
1 TT
2219226 AATATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTTTATTTAAAATA
Found at i:2219331 original size:35 final size:35
Alignment explanation
Indices: 2219292--2219370 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
2219282 TTTTTGTTTA
2219292 AAAAAAGT-TAATTTTTTAAAATATAACTGAATAAT
1 AAAAAA-TATAATTTTTTAAAATATAACTGAATAAT
*
2219327 AAAAAATATAATTTTTTAAAATATAATTGAATAAT
1 AAAAAATATAATTTTTTAAAATATAACTGAATAAT
2219362 AAAAAATAT
1 AAAAAATAT
2219371 TAAATCATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 1 0.02
35 41 0.98
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (35 bp):
AAAAAATATAATTTTTTAAAATATAACTGAATAAT
Found at i:2219369 original size:20 final size:20
Alignment explanation
Indices: 2219309--2219370 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
2219299 TTAATTTTTT
*
2219309 AAAATATAACTGAATAATAA
1 AAAATATAATTGAATAATAA
**
2219329 AAAATATAATT---T--TTT
1 AAAATATAATTGAATAATAA
2219344 AAAATATAATTGAATAATAA
1 AAAATATAATTGAATAATAA
2219364 AAAATAT
1 AAAATAT
2219371 TAAATCATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
15 12 0.38
17 1 0.03
18 1 0.03
20 18 0.56
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATATAATTGAATAATAA
Found at i:2219843 original size:14 final size:14
Alignment explanation
Indices: 2219824--2219850 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2219814 ATATTTTAAA
2219824 AAAATTTAAATTTT
1 AAAATTTAAATTTT
2219838 AAAATTTAAATTT
1 AAAATTTAAATTT
2219851 AAATTTAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATTTAAATTTT
Found at i:2219939 original size:40 final size:40
Alignment explanation
Indices: 2219887--2219962 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
2219877 CTCGAATTTA
*
2219887 TTATTTATTTTATAA-TAAAATAAAAAAATTATATTAAAAT
1 TTATATATTTTATAATTAAAATAAAAAAA-TATATTAAAAT
* *
2219927 TTATATATTTTATAATTAAATTTAAAAAATATATTA
1 TTATATATTTTATAATTAAAATAAAAAAATATATTA
2219963 TTTTAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 21 0.66
41 11 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (40 bp):
TTATATATTTTATAATTAAAATAAAAAAATATATTAAAAT
Found at i:2222384 original size:22 final size:21
Alignment explanation
Indices: 2222344--2222400 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
2222334 ATTTAAAAAT
2222344 TTTA-AAAAAAT-TATATATA
1 TTTATAAAAAATATATATATA
*
2222363 TTTATAAAAAATATATTTTATA
1 TTTATAAAAAATATA-TATATA
*
2222385 TTTATATATAAATATA
1 TTTATA-AAAAATATA
2222401 CTTAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.12
20 7 0.22
21 2 0.06
22 11 0.34
23 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATAAAAAATATATATATA
Found at i:2223237 original size:31 final size:28
Alignment explanation
Indices: 2223137--2223235 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 28
2223127 TGTGTTGAAT
*
2223137 AATAATAAAAAATTATATTTATATTAAA
1 AATAATAAAAATTTATATTTATATTAAA
* *
2223165 AATAAATTATTAAAA-TTATGTTTATA-T-CA
1 AAT-AA-TA--AAAATTTATATTTATATTAAA
2223194 AATAATAAAATATTTATATTTATATTAAA
1 AATAATAAAA-ATTTATATTTATATTAAA
*
2223223 TAATAATTAAAAT
1 -AATAATAAAAAT
2223236 ATATTAACAT
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 12 0.21
28 6 0.11
29 9 0.16
30 12 0.21
31 10 0.18
32 4 0.07
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
AATAATAAAAATTTATATTTATATTAAA
Found at i:2227510 original size:18 final size:19
Alignment explanation
Indices: 2227473--2227512 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2227463 CTTAACTTAA
*
2227473 TTTTTAAATAAGTTTCATT
1 TTTTTAAATAAATTTCATT
*
2227492 TTTTTATATAAATTT-ATT
1 TTTTTAAATAAATTTCATT
2227510 TTT
1 TTT
2227513 CAAACATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTTAAATAAATTTCATT
Found at i:2232958 original size:13 final size:13
Alignment explanation
Indices: 2232929--2232980 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2232919 TAATATATAT
**
2232929 TAAATATAAATGT
1 TAAATATAAATAC
2232942 TAAATATAAATAC
1 TAAATATAAATAC
*
2232955 TAAATATGAATAC
1 TAAATATAAATAC
*
2232968 TTAAAAATAAATA
1 -TAAATATAAATA
2232981 ATTTGGATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
13 23 0.70
14 10 0.30
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (13 bp):
TAAATATAAATAC
Found at i:2233416 original size:2 final size:2
Alignment explanation
Indices: 2233409--2233436 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2233399 AGTTTTAATT
2233409 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
2233437 AATTGTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2236145 original size:2 final size:2
Alignment explanation
Indices: 2236138--2236179 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2236128 AAGATTTAAG
*
2236138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2236180 CTTCGCTTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2237313 original size:22 final size:22
Alignment explanation
Indices: 2237288--2237330 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2237278 TTATATTTTT
2237288 ATTATATTATAATTATATATAA
1 ATTATATTATAATTATATATAA
* * *
2237310 ATTATTTTTTATTTATATATA
1 ATTATATTATAATTATATATA
2237331 TTTAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATATTATAATTATATATAA
Found at i:2237314 original size:33 final size:33
Alignment explanation
Indices: 2237277--2237445 Score: 99
Period size: 33 Copynumber: 5.2 Consensus size: 33
2237267 TTATACTTAT
2237277 ATTATATTTTTATTATATTATAATTATATATAA
1 ATTATATTTTTATTATATTATAATTATATATAA
* *
2237310 ATTAT-TTTTTATT-TATATATATTTAATATATTA
1 ATTATATTTTTATTATAT-TATAATT-ATATATAA
*
2237343 A-TA-ATTTATATTATA-TA-AATT-T-TA-AA
1 ATTATATTTTTATTATATTATAATTATATATAA
* *
2237369 ATATATATTTATT-TTGTATTATAA-TATATTATAT
1 AT-TATATTT-TTATTATATTATAATTATA-TATAA
* * *
2237403 GTTATATATTTTATTTATCATATGTAATTATATTTAAA
1 ATTATAT-TTTTA-TTAT-AT-TATAATTATATAT-AA
2237441 ATTAT
1 ATTAT
2237446 TATGTAAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 37
0.66 0.09 0.24
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 3 0.03
29 8 0.08
30 7 0.07
31 8 0.08
32 23 0.23
33 24 0.24
34 4 0.04
35 3 0.03
36 2 0.02
37 6 0.06
38 9 0.09
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATATTTTTATTATATTATAATTATATATAA
Found at i:2237322 original size:27 final size:27
Alignment explanation
Indices: 2237267--2237326 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2237257 ACGATAATTT
* *
2237267 TTATACTTATATTATATTTTTATTATA
1 TTATAATTATATTAAATTTTTATTATA
*
2237294 TTATAATTATATATAAATTATTTTTTAT-
1 TTATAATTATAT-TAAATT-TTTATTATA
2237322 TTATA
1 TTATA
2237327 TATATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.39
28 10 0.36
29 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATAATTATATTAAATTTTTATTATA
Found at i:2237330 original size:26 final size:26
Alignment explanation
Indices: 2237301--2237376 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
2237291 ATATTATAAT
** *
2237301 TATATATAAATTATTTTTTATTTATA
1 TATATATAAATTATTAATAATTTATA
*
2237327 TATAT-TTAATATATTAATAATTTATA
1 TATATATAAAT-TATTAATAATTTATA
*
2237353 T-TATATAAATT-TTAA-AATATATA
1 TATATATAAATTATTAATAATTTATA
2237376 T
1 T
2237377 TTATTTTGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.19
24 4 0.10
25 8 0.19
26 22 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATATATAAATTATTAATAATTTATA
Found at i:2237357 original size:31 final size:30
Alignment explanation
Indices: 2237274--2237364 Score: 87
Period size: 32 Copynumber: 3.0 Consensus size: 30
2237264 TTTTTATACT
*
2237274 TATATT-AT-ATTTTTATTATATTATAATTA
1 TATATTAATAATTTTTATTATA-TATATTTA
* *
2237303 TATATAAATTATTTTTTATTTATATATATTTAA
1 TATATTAA-TAATTTTTA-TTATATATATTT-A
* *
2237336 TATATTAATAATTTATATTATATAAATTT
1 TATATTAATAATTTTTATTATATATATTT
2237365 TAAAATATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 5 0.10
30 1 0.02
31 12 0.24
32 19 0.38
33 13 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATATTAATAATTTTTATTATATATATTTA
Found at i:2237411 original size:14 final size:13
Alignment explanation
Indices: 2237274--2237425 Score: 61
Period size: 14 Copynumber: 11.4 Consensus size: 13
2237264 TTTTTATACT
2237274 TATATTATATTT-
1 TATATTATATTTA
2237286 T-TATTATA-TTA
1 TATATTATATTTA
2237297 TA-ATTATA--TA
1 TATATTATATTTA
* *
2237307 TAAATTATTTTTTA
1 TATATTA-TATTTA
*
2237321 TTTATATATATTTAA
1 TATAT-TATATTT-A
2237336 TATATTAATAATTTA
1 TATATT-AT-ATTTA
*
2237351 TATTATATAAATTT-
1 TA-TAT-TATATTTA
*
2237365 TAAAATATATATTTA
1 T-ATAT-TATATTTA
*
2237380 T-T-TTGTATTATAA
1 TATATTATATT-T-A
2237393 TATATTATATGTTA
1 TATATTATAT-TTA
*
2237407 TATATTTTATTTA
1 TATATTATATTTA
2237420 TCATAT
1 T-ATAT
2237426 GTAATTATAT
Statistics
Matches: 108, Mismatches: 12, Indels: 38
0.68 0.08 0.24
Matches are distributed among these distances:
10 6 0.06
11 23 0.21
12 4 0.04
13 6 0.06
14 35 0.32
15 24 0.22
16 9 0.08
17 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:2237701 original size:4 final size:4
Alignment explanation
Indices: 2237692--2237731 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
2237682 TAGATCAAGC
* * *
2237692 AAAT AAAT AAAT TAAT AAAT TAAT AAAT AATT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2237732 TTAACATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (4 bp):
AAAT
Found at i:2239452 original size:10 final size:10
Alignment explanation
Indices: 2239423--2239468 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
2239413 TTCATAAATA
2239423 AATTTATTATT
1 AATTTA-TATT
*
2239434 ATGTTTATATT
1 A-ATTTATATT
2239445 AATTTATATT
1 AATTTATATT
2239455 AATTTATATGT
1 AATTTATAT-T
2239466 AAT
1 AAT
2239469 AATTTTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 17 0.55
11 10 0.32
12 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (10 bp):
AATTTATATT
Found at i:2239480 original size:24 final size:24
Alignment explanation
Indices: 2239439--2239499 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
2239429 TTATTATGTT
* **
2239439 TATATTAATTTATATTAATTTA-TA
1 TATAATAATTT-TATTAAAGTATTA
*
2239463 TGTAATAATTTTACTTAAAGTATTA
1 TATAATAATTTTA-TTAAAGTATTA
2239488 TATAATAATTTT
1 TATAATAATTTT
2239500 GACATATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 13 0.43
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (24 bp):
TATAATAATTTTATTAAAGTATTA
Found at i:2239620 original size:20 final size:19
Alignment explanation
Indices: 2239562--2239621 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
2239552 TCACGTTCAA
*
2239562 ATTTTAT-ATTATGTTT-T
1 ATTTTATAATTATATTTAT
* *
2239579 AATTTTTTACATAATATTTAT
1 -ATTTTATA-ATTATATTTAT
2239600 ATTTTATAATTATATTATAT
1 ATTTTATAATTATATT-TAT
2239620 AT
1 AT
2239622 AAAATAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 6 0.18
19 7 0.21
20 19 0.58
21 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTATAATTATATTTAT
Found at i:2239735 original size:19 final size:20
Alignment explanation
Indices: 2239699--2239747 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2239689 ATTTTACTTT
*
2239699 ATTTTAATTTGATCAAAAAA
1 ATTTTAATTTGATAAAAAAA
*
2239719 ATTTT-ATTTTATAAAAAAA
1 ATTTTAATTTGATAAAAAAA
*
2239738 ATTATAATTT
1 ATTTTAATTT
2239748 AAAAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTTTAATTTGATAAAAAAA
Found at i:2239763 original size:23 final size:25
Alignment explanation
Indices: 2239733--2239783 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
2239723 TATTTTATAA
2239733 AAAAAATTAT-AAT-TTAAAAATAT
1 AAAAAATTATAAATATTAAAAATAT
*
2239756 AAAAAATTATAAATATTAAAAATTT
1 AAAAAATTATAAATATTAAAAATAT
2239781 AAA
1 AAA
2239784 TTTTAAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 10 0.40
24 3 0.12
25 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAAATTATAAATATTAAAAATAT
Found at i:2239783 original size:15 final size:16
Alignment explanation
Indices: 2239750--2239789 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2239740 TATAATTTAA
*
2239750 AAATATAAAAAATTAT
1 AAATATTAAAAATTAT
2239766 AAATATTAAAAATT-T
1 AAATATTAAAAATTAT
*
2239781 AAATTTTAA
1 AAATATTAA
2239790 GATGAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTAAAAATTAT
Found at i:2240559 original size:7 final size:7
Alignment explanation
Indices: 2240547--2240578 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
2240537 CCACATGGAT
2240547 GCCTATG
1 GCCTATG
2240554 GCCTATG
1 GCCTATG
2240561 GCCTATG
1 GCCTATG
2240568 GCCTAT-
1 GCCTATG
2240574 GCCTA
1 GCCTA
2240579 CCCTATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.16, C:0.31, G:0.25, T:0.28
Consensus pattern (7 bp):
GCCTATG
Found at i:2251869 original size:21 final size:20
Alignment explanation
Indices: 2251845--2251910 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
2251835 ATGCCAGACG
*
2251845 AAACAAGTTTAATAAACATGA
1 AAACAAGTTTAATAAACA-AA
*
2251866 AAACAA-TATAATAAATACAAA
1 AAACAAGTTTAAT-AA-ACAAA
2251887 AAACAAGTTTAATAAACACAA
1 AAACAAGTTTAATAAACA-AA
2251908 AAA
1 AAA
2251911 TAATATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.21
21 22 0.58
22 8 0.21
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.20
Consensus pattern (20 bp):
AAACAAGTTTAATAAACAAA
Found at i:2251877 original size:20 final size:19
Alignment explanation
Indices: 2251854--2251922 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
2251844 GAAACAAGTT
*
2251854 TAATAAACATGAAAACAATA
1 TAATAAACA-AAAAACAATA
*
2251874 TAATAAATACAAAAAACAAGTT
1 TAAT-AA-ACAAAAAACAA-TA
*
2251896 TAATAAACACAAAAATAATA
1 TAATAAACA-AAAAACAATA
2251916 TAATAAA
1 TAATAAA
2251923 TATAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 15 0.37
21 18 0.44
22 8 0.20
ACGTcount: A:0.67, C:0.09, G:0.03, T:0.22
Consensus pattern (19 bp):
TAATAAACAAAAAACAATA
Found at i:2251904 original size:42 final size:42
Alignment explanation
Indices: 2251845--2251940 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
2251835 ATGCCAGACG
**
2251845 AAACAAGTTTAATAAACATGAAAACAATATAATAAATACAAA
1 AAACAAGTTTAATAAACACAAAAACAATATAATAAATACAAA
* *
2251887 AAACAAGTTTAATAAACACAAAAATAATATAATAAATATAAA
1 AAACAAGTTTAATAAACACAAAAACAATATAATAAATACAAA
* *
2251929 AAATACGTTTAA
1 AAACAAGTTTAA
2251941 ATATAATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (42 bp):
AAACAAGTTTAATAAACACAAAAACAATATAATAAATACAAA
Found at i:2251929 original size:20 final size:20
Alignment explanation
Indices: 2251854--2251930 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
2251844 GAAACAAGTT
*
2251854 TAATAAACATGAAAACAATA
1 TAATAAACATAAAAACAATA
*
2251874 TAATAAATACA-AAAAACAAGTT
1 TAAT-AA-ACATAAAAACAA-TA
* *
2251896 TAATAAACACAAAAATAATA
1 TAATAAACATAAAAACAATA
*
2251916 TAATAAATATAAAAA
1 TAATAAACATAAAAA
2251931 ATACGTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 21 0.45
21 18 0.38
22 8 0.17
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (20 bp):
TAATAAACATAAAAACAATA
Found at i:2251933 original size:21 final size:20
Alignment explanation
Indices: 2251865--2251931 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
2251855 AATAAACATG
2251865 AAAACAATATAATAAATACAA
1 AAAACAATATAATAAATA-AA
* * *
2251886 AAAACAAGTTTAATAAACACA
1 AAAACAA-TATAATAAATAAA
*
2251907 AAAATAATATAATAAATATAA
1 AAAACAATATAATAAATA-AA
2251928 AAAA
1 AAAA
2251932 TACGTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 9 0.24
21 19 0.51
22 9 0.24
ACGTcount: A:0.70, C:0.07, G:0.01, T:0.21
Consensus pattern (20 bp):
AAAACAATATAATAAATAAA
Found at i:2252891 original size:20 final size:20
Alignment explanation
Indices: 2252866--2252908 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2252856 TAATATTTTT
2252866 ATATAAAAATAATTTTAAAA
1 ATATAAAAATAATTTTAAAA
* *
2252886 ATATAATAATAATTTTAATA
1 ATATAAAAATAATTTTAAAA
2252906 ATA
1 ATA
2252909 ATGTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAAAATAATTTTAAAA
Found at i:2252979 original size:15 final size:16
Alignment explanation
Indices: 2252959--2252997 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2252949 TGTGTTGTTG
2252959 TATAAATAAATT-TTT
1 TATAAATAAATTCTTT
*
2252974 TATAAATAATTTCTTT
1 TATAAATAAATTCTTT
*
2252990 TAAAAATA
1 TATAAATA
2252998 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TATAAATAAATTCTTT
Found at i:2253695 original size:23 final size:25
Alignment explanation
Indices: 2253651--2253702 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
2253641 ATTGGCTTGA
2253651 ATATAAGATAAAAAATTAAAATATG
1 ATATAAGATAAAAAATTAAAATATG
*
2253676 ATATAATATAAAAAA-T-AAATATG
1 ATATAAGATAAAAAATTAAAATATG
2253699 ATAT
1 ATAT
2253703 GAATTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 11 0.42
24 1 0.04
25 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (25 bp):
ATATAAGATAAAAAATTAAAATATG
Found at i:2254468 original size:22 final size:22
Alignment explanation
Indices: 2254443--2254485 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2254433 ACCTGTCAAC
2254443 AAATAAAAGAT-AACAACTAAAT
1 AAATAAAA-ATAAACAACTAAAT
*
2254465 AAATAATAATAAACAACTAAA
1 AAATAAAAATAAACAACTAAA
2254486 AAAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAAATAAACAACTAAAT
Found at i:2254496 original size:18 final size:21
Alignment explanation
Indices: 2254443--2254496 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2254433 ACCTGTCAAC
2254443 AAATAAAAGATAACAACTAAAT
1 AAATAAAAGA-AACAACTAAAT
*
2254465 AAATAATAATAAACAACT-AA-
1 AAATAA-AAGAAACAACTAAAT
2254485 AAA-AAAAGAAAC
1 AAATAAAAGAAAC
2254497 GAAGAGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 3 0.10
21 2 0.07
22 13 0.45
23 3 0.10
ACGTcount: A:0.72, C:0.09, G:0.04, T:0.15
Consensus pattern (21 bp):
AAATAAAAGAAACAACTAAAT
Found at i:2258514 original size:13 final size:13
Alignment explanation
Indices: 2258496--2258520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2258486 ATTATTCAAA
2258496 TGTATCGATACAT
1 TGTATCGATACAT
2258509 TGTATCGATACA
1 TGTATCGATACA
2258521 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2258585 original size:52 final size:52
Alignment explanation
Indices: 2258529--2258653 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
2258519 CACTGATCTT
*
2258529 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
2258581 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2258633 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2258654 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2263941 original size:24 final size:25
Alignment explanation
Indices: 2263893--2263941 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
2263883 AGCCACCATT
*
2263893 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAA--GTGGTAATTTTG
2263920 TGTTTGTCAAAAA-TGGTAATTT
1 TGTTTGTCAAAAAGTGGTAATTT
2263942 CTTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
27 13 0.62
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (25 bp):
TGTTTGTCAAAAAGTGGTAATTTTG
Found at i:2269200 original size:34 final size:34
Alignment explanation
Indices: 2269120--2269337 Score: 192
Period size: 34 Copynumber: 6.4 Consensus size: 34
2269110 TTATGTATGT
* *
2269120 ATTGTTGATTAAATG-GTA-ATTTAGTAGTTTACC
1 ATTGTTGATTAAATGAG-AGATTTGGTGGTTTACC
* * * *
2269153 ATTGTTAATTAAATGAGTGATTTGGTGGTTTGCT
1 ATTGTTGATTAAATGAGAGATTTGGTGGTTTACC
* * * *
2269187 ATTGTTGACTAAAT-AGGAGATTTGGTAGCTTATC
1 ATTGTTGATTAAATGA-GAGATTTGGTGGTTTACC
* * * *
2269221 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGAGAGATTTGGTGGTTTACC
* * *
2269255 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGAGAGATTTGGTGGTTTACC
* * * *
2269289 ATTATTGACTAAATGAGAGATTTGCTAGG-TTGCC
1 ATTGTTGATTAAATGAGAGATTTGGT-GGTTTACC
2269323 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
2269338 GTGGTTTTTA
Statistics
Matches: 151, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
33 15 0.10
34 134 0.89
35 2 0.01
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGAGAGATTTGGTGGTTTACC
Found at i:2269234 original size:68 final size:66
Alignment explanation
Indices: 2269120--2269338 Score: 233
Period size: 68 Copynumber: 3.2 Consensus size: 66
2269110 TTATGTATGT
* * * *
2269120 ATTGTTGATTAAATGGTA-ATTTAGTAGTTTACCATTGTTAATTAAATGAGTGATTTGGTGGTTT
1 ATTGTTGATTAAATGG-AGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGTGG-TT
*
2269184 GCT
64 GCC
* * * * *
2269187 ATTGTTGACTAAATAGGAGATTTGGTAGCTTATCATTGTTGATTAAATGGGAAATTTGGTAGCTT
1 ATTGTTGATTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGT-GGTT
*
2269252 ACC
64 GCC
* * * * *
2269255 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTATTGACTAAATGAGAGATTTGCTAGGTT
1 ATTGTTGATTAAAT-GGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGT-GGTT
2269320 GCC
64 GCC
2269323 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2269339 TGGTTTTTAC
Statistics
Matches: 126, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
67 16 0.13
68 109 0.87
69 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (66 bp):
ATTGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGAGAGATTTGGTGGTTGC
C
Found at i:2269297 original size:102 final size:102
Alignment explanation
Indices: 2269120--2269338 Score: 298
Period size: 102 Copynumber: 2.2 Consensus size: 102
2269110 TTATGTATGT
* * *
2269120 ATTGTTGATTAAAT-GGTAATTTAGTAGTTTACCATTGTTAATTAAATGAGTGATTTGGTGGTTT
1 ATTGTTGATTAAATGGGAAATTTAGTAGCTTACCATTGTTAATTAAATGAGTGATTTGGTGGCTT
* * * * *
2269184 GCTATTGTTGACTAAAT-AGGAGATTTGGTAGCTTATC
66 ACCATTATTGACTAAATGA-GAGATTTGCTAGCTTACC
* * *
2269221 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGGGAAATTTAGTAGCTTACCATTGTTAATTAAATGAGTGATTTGGTGGCTT
* *
2269286 ACCATTATTGACTAAATGAGAGATTTGCTAGGTTGCC
66 ACCATTATTGACTAAATGAGAGATTTGCTAGCTTACC
2269323 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2269339 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
101 14 0.14
102 88 0.85
103 1 0.01
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (102 bp):
ATTGTTGATTAAATGGGAAATTTAGTAGCTTACCATTGTTAATTAAATGAGTGATTTGGTGGCTT
ACCATTATTGACTAAATGAGAGATTTGCTAGCTTACC
Found at i:2273673 original size:34 final size:34
Alignment explanation
Indices: 2273604--2273821 Score: 260
Period size: 34 Copynumber: 6.5 Consensus size: 34
2273594 AAGTGGGAGA
* * * *
2273604 ATTGTTGATTAAAT-TGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2273637 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2273671 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2273705 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2273739 ATTGTTGATTAAATGGGTGATTTGGTGGCTTA-C
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
2273772 ATTATTGACTAAATGAGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2273806 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2273822 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
33 40 0.25
34 117 0.75
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2273795 original size:101 final size:100
Alignment explanation
Indices: 2273604--2273820 Score: 319
Period size: 101 Copynumber: 2.1 Consensus size: 100
2273594 AAGTGGGAGA
* * *
2273604 ATTGTTGATTAAATTGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAA-TGAGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTG
* * *
2273669 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
65 ACATTATTGACTAAATGAGAGATTTGGTAGCTTACC
*
2273705 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGAG--ATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
* *
2273770 -ACATTATTGACTAAATGAGAGATTTGGTAGGTTGCC
64 GACATTATTGACTAAATGAGAGATTTGGTAGCTTACC
2273806 ATTGTTGATTAAATG
1 ATTGTTGATTAAATG
2273821 GTGGTTTTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 3 0.03
101 59 0.56
102 43 0.41
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.41
Consensus pattern (100 bp):
ATTGTTGATTAAATGAGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTGA
CATTATTGACTAAATGAGAGATTTGGTAGCTTACC
Found at i:2274110 original size:4 final size:4
Alignment explanation
Indices: 2274101--2274130 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2274091 ATGCTCTAAC
2274101 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2274131 ACACACCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2276686 original size:24 final size:24
Alignment explanation
Indices: 2276658--2276703 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2276648 ATAGTTATTT
2276658 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
2276682 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
2276704 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:2281093 original size:28 final size:29
Alignment explanation
Indices: 2281061--2281122 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
2281051 AAATGCCACC
2281061 CTTTGTATTTGTCAAATATAGTGGTT-TT
1 CTTTGTATTTGTCAAATATAGTGGTTATT
*
2281089 CTTTGTATTTGTCAAATATGGTGGTTATT
1 CTTTGTATTTGTCAAATATAGTGGTTATT
2281118 -TTTGT
1 CTTTGT
2281123 TTGTAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.55
Consensus pattern (29 bp):
CTTTGTATTTGTCAAATATAGTGGTTATT
Found at i:2281155 original size:24 final size:24
Alignment explanation
Indices: 2281096--2281164 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2281086 TTTCTTTGTA
* * *
2281096 TTTGTCAAATATGGTGGTTATTTTTG
1 TTTGTCAAAAATGGTGG--CTTGTTG
*
2281122 TTTGTAAAAAATGGTGGCTTGTTG
1 TTTGTCAAAAATGGTGGCTTGTTG
* *
2281146 TTTGTCAAAATTAGTGGCT
1 TTTGTCAAAAATGGTGGCT
2281165 AATTTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 21 0.58
26 15 0.42
ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAAATGGTGGCTTGTTG
Found at i:2283043 original size:19 final size:18
Alignment explanation
Indices: 2283012--2283082 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
2283002 TCACAAATTA
2283012 TAAGAATCATAGATTTTT
1 TAAGAATCATAGATTTTT
*
2283030 TAAGAAATCTTAGATTTTT
1 TAAG-AATCATAGATTTTT
* * *
2283049 TAAAAATTACAGATTTTT
1 TAAGAATCATAGATTTTT
2283067 TAAGAATCATAGATTT
1 TAAGAATCATAGATTT
2283083 CTGTAATCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 28 0.64
19 16 0.36
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.44
Consensus pattern (18 bp):
TAAGAATCATAGATTTTT
Found at i:2285725 original size:18 final size:18
Alignment explanation
Indices: 2285698--2285769 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 18
2285688 CAATAATAGA
* *
2285698 TTTTAGGAATCATATATT
1 TTTTAAGAATCATAAATT
* *
2285716 TTTTAAGAATCTTAGA-T
1 TTTTAAGAATCATAAATT
* *
2285733 TTTTAGGAATCACAAATT
1 TTTTAAGAATCATAAATT
* *
2285751 TTCTAAAAATCATAAATT
1 TTTTAAGAATCATAAATT
2285769 T
1 T
2285770 CTATAATCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.31
18 29 0.69
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
TTTTAAGAATCATAAATT
Found at i:2285752 original size:35 final size:35
Alignment explanation
Indices: 2285693--2285787 Score: 95
Period size: 35 Copynumber: 2.8 Consensus size: 35
2285683 AACATCAATA
* * *
2285693 ATAGA-TTTTAGGAATCATATATTTTTTAAGAATC
1 ATAGATTTTTAGGAATCACAAATTTTTTAAAAATC
* *
2285727 TTAGATTTTTAGGAATCACAAATTTTCTAAAAATC
1 ATAGATTTTTAGGAATCACAAATTTTTTAAAAATC
* * * *
2285762 ATAAATTTCTA-TAATCACAAAATTTT
1 ATAGATTTTTAGGAATCACAAATTTTT
2285788 AACCCAATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
34 16 0.33
35 33 0.67
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.42
Consensus pattern (35 bp):
ATAGATTTTTAGGAATCACAAATTTTTTAAAAATC
Found at i:2285784 original size:17 final size:18
Alignment explanation
Indices: 2285740--2285786 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2285730 GATTTTTAGG
*
2285740 AATCACAAATTTTCTAAA
1 AATCACAAAATTTCTAAA
* *
2285758 AATCA-TAAATTTCT-AT
1 AATCACAAAATTTCTAAA
2285774 AATCACAAAATTT
1 AATCACAAAATTT
2285787 TAACCCAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.25
17 13 0.54
18 5 0.21
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (18 bp):
AATCACAAAATTTCTAAA
Found at i:2286366 original size:14 final size:15
Alignment explanation
Indices: 2286349--2286381 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2286339 TAAAAAAATT
2286349 TATTTAA-ATATAAA
1 TATTTAATATATAAA
2286363 TA-TTAATATATAAA
1 TATTTAATATATAAA
2286377 TATTT
1 TATTT
2286382 TTTAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 11 0.65
15 2 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTAATATATAAA
Found at i:2286816 original size:6 final size:6
Alignment explanation
Indices: 2286805--2286841 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2286795 CGACACCTCT
2286805 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC T
1 TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC TTTCTC T
2286842 CCATGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTCTC
Found at i:2290024 original size:2 final size:2
Alignment explanation
Indices: 2290019--2290049 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2290009 ATAAAAGATC
*
2290019 AT AT AT GT 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 A
2290050 ATAGTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2290207 original size:21 final size:21
Alignment explanation
Indices: 2290173--2290214 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2290163 GCAACTTCCC
2290173 TATTCAAATGCATACAATTTT
1 TATTCAAATGCATACAATTTT
2290194 TATTCCAAAT-CATACAATTTT
1 TATT-CAAATGCATACAATTTT
2290215 GAACCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTCAAATGCATACAATTTT
Found at i:2291352 original size:11 final size:11
Alignment explanation
Indices: 2291336--2291399 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
2291326 CAAGGTTCGT
2291336 TTTATTATTTA
1 TTTATTATTTA
2291347 TTTATTATTTA
1 TTTATTATTTA
*
2291358 TTATATTATTAA
1 TT-TATTATTTA
**
2291370 AATATTATTTTA
1 TTTATTA-TTTA
*
2291382 TATTAATATTTA
1 T-TTATTATTTA
*
2291394 TATATT
1 TTTATT
2291400 TTATAATTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
11 21 0.51
12 16 0.39
13 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:2291399 original size:21 final size:21
Alignment explanation
Indices: 2291375--2291414 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2291365 ATTAAAATAT
2291375 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
2291396 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
2291415 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:2291680 original size:29 final size:30
Alignment explanation
Indices: 2291632--2291693 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2291622 GTCCACACAT
* *
2291632 AATTATATAAAAAATTATTTTTAAT-TTTA
1 AATTATATAAAAAATAATTTGTAATATTTA
* *
2291661 AATTATATTAAGAATAATTTGTAATATTTA
1 AATTATATAAAAAATAATTTGTAATATTTA
2291691 AAT
1 AAT
2291694 AATAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AATTATATAAAAAATAATTTGTAATATTTA
Found at i:2296888 original size:16 final size:16
Alignment explanation
Indices: 2296867--2296903 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2296857 TATGTTAACA
* *
2296867 TATTTTAGATTTAGAT
1 TATTTTAAATTTAAAT
2296883 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
2296899 TATTT
1 TATTT
2296904 AATTTTAATT
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:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (16 bp):
TATTTTAAATTTAAAT
Found at i:2297198 original size:33 final size:33
Alignment explanation
Indices: 2297138--2297228 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
2297128 TTTTAGGGAT
* * *
2297138 TATTATAAAA-AAATTTTATCTTAAATTTAATAA
1 TATTA-AAAATAAATATTATTTTTAATTTAATAA
2297171 TATTAAAAATAAATATTATTTTTAATTTAATAA
1 TATTAAAAATAAATATTATTTTTAATTTAATAA
*
2297204 TATTAAGAATAAATATTATTTTTAA
1 TATTAAAAATAAATATTATTTTTAA
2297229 AATTTTTAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 4 0.08
33 49 0.92
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (33 bp):
TATTAAAAATAAATATTATTTTTAATTTAATAA
Found at i:2297267 original size:21 final size:22
Alignment explanation
Indices: 2297223--2297269 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2297213 TAAATATTAT
* *
2297223 TTTTAAAATTTTTAAGAGATAA
1 TTTTAAAACTTTTAAGAAATAA
2297245 TTTTAAAACTTTTAA-AAATAA
1 TTTTAAAACTTTTAAGAAATAA
2297266 TTTT
1 TTTT
2297270 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTAAAACTTTTAAGAAATAA
Found at i:2299828 original size:16 final size:16
Alignment explanation
Indices: 2299806--2299861 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
2299796 TTTGTTTGGA
2299806 TTTGAATTCATTCAGG
1 TTTGAATTCATTCAGG
* ** * *
2299822 TTCGAATTTTTTTAAG
1 TTTGAATTCATTCAGG
*
2299838 TTTGAACTCATTCAGG
1 TTTGAATTCATTCAGG
2299854 TTTGAATT
1 TTTGAATT
2299862 TTTTCGAGTT
Statistics
Matches: 28, Mismatches: 12, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (16 bp):
TTTGAATTCATTCAGG
Found at i:2304801 original size:2 final size:2
Alignment explanation
Indices: 2304796--2304826 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2304786 ATATATATAT
*
2304796 AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2304827 ATCAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2306480 original size:41 final size:41
Alignment explanation
Indices: 2306426--2306608 Score: 113
Period size: 41 Copynumber: 4.4 Consensus size: 41
2306416 AATTAGCAAG
*
2306426 AAAATAATAAATAAAGATTAGTTAATATTTTAATTTAATAA
1 AAAATAATTAATAAAGATTAGTTAATATTTTAATTTAATAA
* * * * *
2306467 AAAATCATTAATAAAAACTTGAATTAAAAATTATTAA-ATAATAA
1 AAAATAATTAATAAAGA-TT-AGTT-AATATT-TTAATTTAATAA
* ** * *
2306511 AAAATATATCAATCAAA-AAAAGTT--TATTCTAAGATTAATAA
1 AAAATA-ATTAAT-AAAGATTAGTTAATATTTTAA-TTTAATAA
* * * *
2306552 GAAAATAATAAATAATGATTAGTCAATATTTAAATTTAATAA
1 -AAAATAATTAATAAAGATTAGTTAATATTTTAATTTAATAA
* *
2306594 AAATTTATTAATAAA
1 AAAATAATTAATAAA
2306609 AAATTACTCA
Statistics
Matches: 104, Mismatches: 26, Indels: 24
0.68 0.17 0.16
Matches are distributed among these distances:
39 3 0.03
40 5 0.05
41 40 0.38
42 15 0.14
43 12 0.12
44 16 0.15
45 10 0.10
46 3 0.03
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (41 bp):
AAAATAATTAATAAAGATTAGTTAATATTTTAATTTAATAA
Found at i:2307073 original size:21 final size:21
Alignment explanation
Indices: 2307047--2307091 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2307037 TTAATTTAAA
2307047 AAAATAATAAT-GTACAAAATT
1 AAAAT-ATAATAGTACAAAATT
* *
2307068 AAAATATATTAGTATAAAATT
1 AAAATATAATAGTACAAAATT
2307089 AAA
1 AAA
2307092 CTTCTAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAATATAATAGTACAAAATT
Found at i:2308509 original size:27 final size:27
Alignment explanation
Indices: 2308474--2308538 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
2308464 AGCCTCCATA
*
2308474 TTTGACAAATACAAAATAACCACAATT
1 TTTGACAAACACAAAATAACCACAATT
*
2308501 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAACACAAAATAACCACAATT
2308528 TTTGACAAACA
1 TTTGACAAACA
2308539 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.25
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACAATT
Found at i:2310448 original size:21 final size:22
Alignment explanation
Indices: 2310422--2310467 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2310412 ATCTGTTGAA
* *
2310422 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
2310443 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
2310465 ACT
1 ACT
2310468 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:2311992 original size:27 final size:27
Alignment explanation
Indices: 2311957--2312021 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
2311947 AGCTTTCATA
*
2311957 TTTGACAAATACAAAATAACCACTATT
1 TTTGACAAACACAAAATAACCACTATT
2311984 TTTGACAAACACAAAATAACCACTATT
1 TTTGACAAACACAAAATAACCACTATT
*
2312011 TTTTACAAACA
1 TTTGACAAACA
2312022 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.29
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACTATT
Found at i:2315322 original size:24 final size:26
Alignment explanation
Indices: 2315292--2315381 Score: 105
Period size: 27 Copynumber: 3.5 Consensus size: 26
2315282 TAGCCACTAA
2315292 TTTTGACAAACAACAA-G-TCACCAT
1 TTTTGACAAACAACAAGGATCACCAT
*
2315316 TTTTGACAAACAAAAAGGAATCACCAT
1 TTTTGACAAACAACAAGG-ATCACCAT
* *
2315343 TTTTTACAAAC-ACAAAGGAACCACCAT
1 TTTTGACAAACAAC-AAGG-ATCACCAT
2315370 TTTTGACAAACA
1 TTTTGACAAACA
2315382 CAAAGGGTGG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
24 15 0.27
25 1 0.02
26 1 0.02
27 39 0.70
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.24
Consensus pattern (26 bp):
TTTTGACAAACAACAAGGATCACCAT
Found at i:2315351 original size:27 final size:27
Alignment explanation
Indices: 2315309--2315387 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
2315299 AAACAACAAG
*
2315309 TCACCATTTTTGACAAACAAAAAGGAA
1 TCACCATTTTTGACAAACACAAAGGAA
*
2315336 TCACCATTTTTTACAAACACAAAGGAA
1 TCACCATTTTTGACAAACACAAAGGAA
*
2315363 CCACCATTTTTGACAAACACAAAGG
1 TCACCATTTTTGACAAACACAAAGG
2315388 GTGGCTTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.23
Consensus pattern (27 bp):
TCACCATTTTTGACAAACACAAAGGAA
Found at i:2317422 original size:21 final size:22
Alignment explanation
Indices: 2317396--2317441 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2317386 ATCTATTGAA
* *
2317396 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
2317417 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
2317439 ACT
1 ACT
2317442 TGTCTGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:2318096 original size:27 final size:27
Alignment explanation
Indices: 2318029--2318119 Score: 107
Period size: 27 Copynumber: 3.5 Consensus size: 27
2318019 TAAAAATTAG
* *
2318029 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
* *
2318053 CTACCATTTTTGGCAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
2318080 CCACCATTTTTGACAAACACAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
2318107 CCATCATTTTTGA
1 CCACCATTTTTGA
2318120 TAAATACAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
24 19 0.34
25 1 0.02
27 36 0.64
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:2318132 original size:28 final size:28
Alignment explanation
Indices: 2318055--2318132 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 28
2318045 ACAACAAGCT
*
2318055 ACCATTTTTGGCAAACA-AAAAGGAACC
1 ACCATTTTTGACAAACACAAAAGGAACC
2318082 ACCATTTTTGACAAACAC-AAAGGAACC
1 ACCATTTTTGACAAACACAAAAGGAACC
* * *
2318109 ATCATTTTTGATAAATACAAAAGG
1 ACCATTTTTGACAAACACAAAAGG
2318133 TAGCTTTTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
27 40 0.89
28 5 0.11
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (28 bp):
ACCATTTTTGACAAACACAAAAGGAACC
Found at i:2321905 original size:27 final size:27
Alignment explanation
Indices: 2321833--2321910 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
2321823 ACAAAAGTTA
*
2321833 CCTTTTATGTTTATCAAAAATGATGGTT
1 CCTTTT-TGTTTATCAAAAATGGTGGTT
* * * *
2321861 CCTTTGTATTTGTAAAAAATGGTGGTT
1 CCTTTTTGTTTATCAAAAATGGTGGTT
*
2321888 CCTTTTTGTTTATCAAAATTGGT
1 CCTTTTTGTTTATCAAAAATGGT
2321911 AGTAAATTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.26, C:0.10, G:0.17, T:0.47
Consensus pattern (27 bp):
CCTTTTTGTTTATCAAAAATGGTGGTT
Found at i:2326324 original size:27 final size:27
Alignment explanation
Indices: 2326293--2326369 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 27
2326283 CAAAAGCCAC
2326293 CCTTTGTGTTTGTCAAAAATGATGGTT
1 CCTTTGTGTTTGTCAAAAATGATGGTT
* * * *
2326320 CCTTTGTATTTATCAAAAAAGGTGGTT
1 CCTTTGTGTTTGTCAAAAATGATGGTT
* * *
2326347 CTTTTTTGTTTGTAAAAAATGAT
1 CCTTTGTGTTTGTCAAAAATGAT
2326370 AGCTTGTTGT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATGATGGTT
Found at i:2326379 original size:24 final size:24
Alignment explanation
Indices: 2326352--2326397 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2326342 TGGTTCTTTT
2326352 TTGTTTGTAAAAAATGATAGCTTG
1 TTGTTTGTAAAAAATGATAGCTTG
* * *
2326376 TTGTTTGTCAAAATTGGTAGCT
1 TTGTTTGTAAAAAATGATAGCT
2326398 AATTTTTATT
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:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGATAGCTTG
Found at i:2328120 original size:24 final size:26
Alignment explanation
Indices: 2328069--2328126 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
2328059 TGGGTGGCTA
*
2328069 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2328095 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2328119 GTCAACAA
1 GTCAACAA
2328127 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Found at i:2328155 original size:27 final size:27
Alignment explanation
Indices: 2328116--2328181 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
2328106 CCACCATGTG
*
2328116 TTTGTCAACAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
2328143 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
2328170 TTTGTCAAAAAT
1 TTTGTCAAAAAT
2328182 TATGGCTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:2328211 original size:24 final size:24
Alignment explanation
Indices: 2328143--2328212 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
2328133 TTACTTTGTA
* *
2328143 TTTGTCAAAAATGGTGGTTCCTTTTTG
1 TTTGTCAAAATTGGTGG---CTTGTTG
*
2328170 TTTGTCAAAAATT-ATGGCTTGTTG
1 TTTGTC-AAAATTGGTGGCTTGTTG
2328194 TTTGTCAAAATTGGTGGCT
1 TTTGTCAAAATTGGTGGCT
2328213 AATTTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 6 0.16
24 17 0.46
27 9 0.24
28 5 0.14
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTGTCAAAATTGGTGGCTTGTTG
Found at i:2330786 original size:21 final size:22
Alignment explanation
Indices: 2330757--2330802 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2330747 TGTTCAGACA
* *
2330757 AGTAGTACTCCACAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2330779 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2330800 AGT
1 AGT
2330803 TTCAACAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2332718 original size:24 final size:26
Alignment explanation
Indices: 2332667--2332724 Score: 93
Period size: 24 Copynumber: 2.3 Consensus size: 26
2332657 TGGGTGGCTA
*
2332667 GTCAACAAAAGCCACCCTTTGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2332693 GTCAACAAAAGCCA-CC-ATGTGTTT
1 GTCAACAAAAGCCACCCTATGTGTTT
2332717 GTCAACAA
1 GTCAACAA
2332725 TGGTGGTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 15 0.48
25 2 0.06
26 14 0.45
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (26 bp):
GTCAACAAAAGCCACCCTATGTGTTT
Done.