Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 16 of 195
Found at i:3661539 original size:31 final size:30
Alignment explanation
Indices: 3661501--3661558 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
3661491 ATGAATACAC
**
3661501 ATGATTAATATTAATATATATATAAATAAAT
1 ATGATTAATACAAATATATATA-AAATAAAT
3661532 ATGATTAATACAAATATATATAAAATA
1 ATGATTAATACAAATATATATAAAATA
3661559 TGATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (30 bp):
ATGATTAATACAAATATATATAAAATAAAT
Found at i:3661572 original size:25 final size:27
Alignment explanation
Indices: 3661512--3661572 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
3661502 TGATTAATAT
3661512 TAATATATATATAAATAAATATGATTAA
1 TAATA-ATATATAAATAAATATGATTAA
*
3661540 TACA-AATATATATA-AAATATGATTAA
1 TA-ATAATATATAAATAAATATGATTAA
3661566 -AATAATA
1 TAATAATA
3661573 AATGACTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 1 0.03
25 5 0.17
26 12 0.40
27 8 0.27
28 3 0.10
29 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (27 bp):
TAATAATATATAAATAAATATGATTAA
Found at i:3661925 original size:21 final size:22
Alignment explanation
Indices: 3661899--3661943 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3661889 ATTAATAGCT
* *
3661899 AATTAAATATT-ATAATTAAAA
1 AATTAAAAATTAAAAATTAAAA
3661920 AATTAAAAATTAAAAATTAAAA
1 AATTAAAAATTAAAAATTAAAA
3661942 AA
1 AA
3661944 ATCTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTAAAAATTAAAAATTAAAA
Found at i:3661943 original size:8 final size:7
Alignment explanation
Indices: 3661899--3661942 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
3661889 ATTAATAGCT
3661899 AATTAAA
1 AATTAAA
* *
3661906 TATT-AT
1 AATTAAA
3661912 AATTAAAA
1 AATT-AAA
3661920 AATTAAA
1 AATTAAA
3661927 AATTAAA
1 AATTAAA
3661934 AATTAAA
1 AATTAAA
3661941 AA
1 AA
3661943 AATCTTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 4 0.13
7 22 0.71
8 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:3662018 original size:18 final size:18
Alignment explanation
Indices: 3661997--3662031 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3661987 TGTTAATGAG
3661997 TTAAACATGTTAAATGTT
1 TTAAACATGTTAAATGTT
*
3662015 TTAAATATGTTAAATGT
1 TTAAACATGTTAAATGT
3662032 ATACTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (18 bp):
TTAAACATGTTAAATGTT
Found at i:3663763 original size:13 final size:14
Alignment explanation
Indices: 3663741--3663768 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3663731 GTTGCTTCTC
3663741 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
3663755 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
3663769 AATCCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:3665484 original size:21 final size:19
Alignment explanation
Indices: 3665447--3665489 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3665437 AATTTGTGAG
*
3665447 TTTAATTAAATTTTTATAT
1 TTTAATTAAATTATTATAT
*
3665466 TTTAATTAAA-AATTATTAT
1 TTTAATTAAATTATTA-TAT
3665485 TTTAA
1 TTTAA
3665490 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTAAATTATTATAT
Found at i:3665539 original size:18 final size:17
Alignment explanation
Indices: 3665507--3665540 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3665497 TATATATATA
3665507 TGAATTGAATTTGAATT
1 TGAATTGAATTTGAATT
*
3665524 TGAATTCGAGTTTGAAT
1 TGAATT-GAATTTGAAT
3665541 ATAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATTGAATTTGAATT
Found at i:3666920 original size:15 final size:15
Alignment explanation
Indices: 3666901--3666942 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3666891 GAAAAAGTCC
3666901 AAAATTAAAA-AGAA
1 AAAATTAAAAGAGAA
3666915 ATAAA-TAAAAGAGAA
1 A-AAATTAAAAGAGAA
*
3666930 AAGATTAAAAGAG
1 AAAATTAAAAGAG
3666943 GAGATTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAATTAAAAGAGAA
Found at i:3679184 original size:21 final size:20
Alignment explanation
Indices: 3679160--3679200 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3679150 CCAAGATGAT
*
3679160 GCAGACTGAGCAGCAACAACC
1 GCAGACTCAGCAGCAA-AACC
*
3679181 GCAGCCTCAGCAGCAAAACC
1 GCAGACTCAGCAGCAAAACC
3679201 AGTTAACGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.37, G:0.22, T:0.05
Consensus pattern (20 bp):
GCAGACTCAGCAGCAAAACC
Found at i:3680827 original size:13 final size:14
Alignment explanation
Indices: 3680802--3680828 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3680792 AATGCTCATC
3680802 TTTTGTACTTTTTT
1 TTTTGTACTTTTTT
3680816 TTTTGTACTTTTT
1 TTTTGTACTTTTT
3680829 AAGTTTTTGT
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:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTGTACTTTTTT
Found at i:3684990 original size:14 final size:14
Alignment explanation
Indices: 3684963--3685001 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
3684953 CCCAAAATGT
*
3684963 ATTTT-TTTTGAAA
1 ATTTTATTTTAAAA
3684976 ATTTTATTTTAAAA
1 ATTTTATTTTAAAA
3684990 ATTTTATTTTAA
1 ATTTTATTTTAA
3685002 GAAAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
ATTTTATTTTAAAA
Found at i:3685160 original size:119 final size:116
Alignment explanation
Indices: 3684973--3685296 Score: 409
Period size: 120 Copynumber: 2.7 Consensus size: 116
3684963 ATTTTTTTTG
* * *
3684973 AAAATTTTATTTTAAAAATTTTATTTT-AAGAAAAATTGATACTTTCAACTTTTCCTCAAAATAC
1 AAAATATT-TTTTAAAAATTTTATTTTCAAGAAAAATTGAAACTTTCAACTTTTCCTAAAAATA-
*
3685037 TTTTTTCTTGAAATTTTATTTTTAAAAAAAATCGATACTTTCAACTTTTTCCTCA
64 TTTTTT-TTGAAATTTTATTTTCAAAAAAAATCGATACTTTCAACTTTTTCC-CA
* * * *
3685092 AAAATATTTTTTAGAAATTTTATTTTCAAGGAAAATTGAAACTTTCAATTTTTTCCTGAAAATAT
1 AAAATATTTTTTAAAAATTTTATTTTCAAGAAAAATTGAAACTTTCAA-CTTTTCCTAAAAATAT
* ** *
3685157 TTTTTTTAAACATTTTTATTTTCAAAGGAAATTGATACTTTCAACTTTTTCCCA
65 TTTTTTTGAA-A-TTTTATTTTCAAAAAAAATCGATACTTTCAACTTTTTCCCA
*
3685211 AAAATATTTTTTAAAAAATTTTATTTTCAAGAAAAATT-AATATTTTCAACTTTTCCTTAAAAAT
1 AAAATATTTTTT-AAAAATTTTATTTTCAAGAAAAATTGAA-ACTTTCAACTTTTCC-TAAAAAT
* *
3685275 ATATTTTTTGAGATTTTATTTT
63 ATTTTTTTTGAAATTTTATTTT
3685297 AGGAAAATCA
Statistics
Matches: 179, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
118 30 0.17
119 56 0.31
120 93 0.52
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (116 bp):
AAAATATTTTTTAAAAATTTTATTTTCAAGAAAAATTGAAACTTTCAACTTTTCCTAAAAATATT
TTTTTTGAAATTTTATTTTCAAAAAAAATCGATACTTTCAACTTTTTCCCA
Found at i:3685279 original size:61 final size:59
Alignment explanation
Indices: 3684982--3685296 Score: 338
Period size: 59 Copynumber: 5.3 Consensus size: 59
3684972 GAAAATTTTA
3684982 TTTTAAAAATTTTATTTT-AAGAAAAATTGATACTTTCAACTTTTCCTCAAAATACT-TT
1 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATA-TATT
** * * *
3685040 TTTCTTGAAATTTTATTTTTAAAAAAAATCGATACTTTCAACTTTTTCCTCAAAA-ATATT
1 TTT-TAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAAC-TTTTCCTCAAAATATATT
* * * * * *
3685100 TTTTAGAAATTTTATTTTCAAGGAAAATTGAAACTTTCAATTTTTTCCTGAAAATATTTT
1 TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAA-CTTTTCCTCAAAATATATT
* *
3685160 TTTTAAACATTTTTATTTTCAA-AGGAAATTGATACTTTCAACTTTTTCC-CAAAA-ATATT
1 TTTTAAA-AATTTTATTTTCAAGA-AAAATTGATACTTTCAAC-TTTTCCTCAAAATATATT
* * *
3685219 TTTTAAAAAATTTTATTTTCAAGAAAAATTAATATTTTCAACTTTTCCTTAAAAATATATT
1 TTTT-AAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCC-TCAAAATATATT
* *
3685280 TTTT-GAGATTTTATTTT
1 TTTTAAAAATTTTATTTT
3685297 AGGAAAATCA
Statistics
Matches: 215, Mismatches: 28, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
58 9 0.04
59 103 0.48
60 48 0.22
61 55 0.26
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (59 bp):
TTTTAAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAATATATT
Found at i:3685932 original size:12 final size:12
Alignment explanation
Indices: 3685915--3685946 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3685905 TCGAAATCTG
*
3685915 AAAATTTTCCAA
1 AAAATTTTCAAA
3685927 AAAATTTTCAAA
1 AAAATTTTCAAA
3685939 AAAATTTT
1 AAAATTTT
3685947 TCTTCTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTTTCAAA
Found at i:3686301 original size:6 final size:5
Alignment explanation
Indices: 3686273--3686337 Score: 51
Period size: 5 Copynumber: 11.8 Consensus size: 5
3686263 CTATTATCTA
*
3686273 AAAAT AAAAT -AAAT AATAAT AAAATT AAAAATT AAAAATT AGAAT AAAACT
1 AAAAT AAAAT AAAAT AA-AAT AAAA-T -AAAA-T -AAAA-T AAAAT AAAA-T
3686324 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
3686338 AAATAAACAG
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 4 0.08
5 22 0.42
6 14 0.26
7 13 0.25
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:3688086 original size:24 final size:24
Alignment explanation
Indices: 3688044--3688089 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3688034 ATTTAACATT
* * *
3688044 AAAAAAAAATTTAAGAAAAGAAAG
1 AAAAAAAAAATAAAAAAAAGAAAG
3688068 AAAAAAAAAATAAAAAAAAGAA
1 AAAAAAAAAATAAAAAAAAGAA
3688090 TAATGATTCA
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:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (24 bp):
AAAAAAAAAATAAAAAAAAGAAAG
Found at i:3688364 original size:59 final size:58
Alignment explanation
Indices: 3688278--3688518 Score: 258
Period size: 59 Copynumber: 4.1 Consensus size: 58
3688268 GGAAATTGTG
* *
3688278 TTTTAGAAATTTTATCTT-AAGAAAAATTGATACATTCAACTTTTCCTCAAAATATTTTT
1 TTTTA-AAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTCAAAA-ATTTTT
* * *
3688337 TTTTGAAATTTTATTTTAAAGAAAAATTGATACTTTCAA-TTTTTCTCTAAAAATATTT
1 TTTTAAAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAAATTTTT
*
3688395 TTTTAAAACCTTTTTATTTTCAAAG-GAAATTGATACTTTCAACTTTCTCCT-AAAAATATTTT
1 TTTTAAAA---TTTTATTTT-AAAGAAAAATTGATACTTTCAACTTT-TCCTCAAAAAT-TTTT
** * * *
3688457 TTAAAAAAATTTTATTTTTAA-AAAAATTGATATTTTCAACTTTTCCTTAAAAATTTTT
1 TT-TTAAAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTT
3688515 TTTT
1 TTTT
3688519 TGGATTTTAT
Statistics
Matches: 154, Mismatches: 16, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
58 40 0.26
59 55 0.36
60 9 0.06
61 31 0.20
62 12 0.08
63 7 0.05
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (58 bp):
TTTTAAAATTTTATTTTAAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTT
Found at i:3688436 original size:120 final size:120
Alignment explanation
Indices: 3688301--3688518 Score: 314
Period size: 120 Copynumber: 1.8 Consensus size: 120
3688291 ATCTTAAGAA
* ****
3688301 AAATTGATACATTCAACTTT-TCCTCAAAATATTTTTTTTTGAAATTTTATTTTAAAGAAAAATT
1 AAATTGATACATTCAACTTTCTCCTAAAAATATTTTTTAAAAAAATTTTATTTTAAA-AAAAATT
*
3688365 GATACTTTCAA-TTTTTCTCTAAAAATATTTTTTTAAAACCTTTTTATTTTCAAAGG
65 GATACTTTCAACTTTTCCT-TAAAAATATTTTTTTAAAACCTTTTTATTTTCAAAGG
* *
3688421 AAATTGATACTTTCAACTTTCTCCTAAAAATATTTTTTAAAAAAATTTTATTTTTAAAAAAATTG
1 AAATTGATACATTCAACTTTCTCCTAAAAATATTTTTTAAAAAAATTTTATTTTAAAAAAAATTG
* *
3688486 ATATTTTCAACTTTTCCTTAAAAATTTTTTTTT
66 ATACTTTCAACTTTTCCTTAAAAATATTTTTTT
3688519 TGGATTTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
120 50 0.58
121 36 0.42
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (120 bp):
AAATTGATACATTCAACTTTCTCCTAAAAATATTTTTTAAAAAAATTTTATTTTAAAAAAAATTG
ATACTTTCAACTTTTCCTTAAAAATATTTTTTTAAAACCTTTTTATTTTCAAAGG
Found at i:3688492 original size:17 final size:17
Alignment explanation
Indices: 3688446--3688492 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3688436 ACTTTCTCCT
3688446 AAAAA-TAT-TTTTTAA
1 AAAAATTATATTTTTAA
*
3688461 AAAAATTTTATTTTTAA
1 AAAAATTATATTTTTAA
3688478 AAAAATTGATATTTT
1 AAAAATT-ATATTTT
3688493 CAACTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 5 0.19
16 2 0.07
17 14 0.52
18 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AAAAATTATATTTTTAA
Found at i:3688640 original size:18 final size:18
Alignment explanation
Indices: 3688591--3688641 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
3688581 CCAAATAATT
3688591 CAAATTAAA-AAATAATAA
1 CAAA-TAAATAAATAATAA
3688609 C-AAT-AATAATAATAATAA
1 CAAATAAAT-A-AATAATAA
3688627 CAAATAAATAAATAA
1 CAAATAAATAAATAA
3688642 CCTTGAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 2 0.07
16 1 0.04
17 3 0.11
18 15 0.54
19 4 0.14
20 3 0.11
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
CAAATAAATAAATAATAA
Found at i:3689454 original size:6 final size:6
Alignment explanation
Indices: 3689385--3689454 Score: 63
Period size: 6 Copynumber: 11.5 Consensus size: 6
3689375 TCTAAAAATG
* * **
3689385 AAATAA ATATAA TAA-AA AAATCAA AAATAA AAACCA AAATAA AAAT-A
1 AAATAA AAATAA AAATAA AAAT-AA AAATAA AAATAA AAATAA AAATAA
3689432 AAATAAA ATAATAA AAATAA AAA
1 AAAT-AA A-AATAA AAATAA AAA
3689455 ACAAACAGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 9 0.18
6 28 0.55
7 11 0.22
8 3 0.06
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:3689925 original size:31 final size:31
Alignment explanation
Indices: 3689890--3689949 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3689880 TTGAAAAGTC
* *
3689890 TGTCAAAAAGTTCAA-CTGGCGTTGGAAAACT
1 TGTCAAAAAATTCAATC-GACGTTGGAAAACT
3689921 TGTCAAAAAATTCAATCGACGTTGGAAAA
1 TGTCAAAAAATTCAATCGACGTTGGAAAA
3689950 TTTTACCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (31 bp):
TGTCAAAAAATTCAATCGACGTTGGAAAACT
Found at i:3690343 original size:18 final size:17
Alignment explanation
Indices: 3690318--3690400 Score: 71
Period size: 18 Copynumber: 4.8 Consensus size: 17
3690308 TCTTATTATC
3690318 TAAAAATAAAATAAATAA
1 TAAAAATAAAA-AAATAA
* *
3690336 TAATAATAAAAACAT--
1 TAAAAATAAAAAAATAA
* * *
3690351 CAAAAATAAAAACCAGAA
1 TAAAAATAAAAA-AATAA
3690369 TAAAAATAAAATAAAATAA
1 TAAAAAT-AAA-AAAATAA
3690388 TAAAAATAAAAAA
1 TAAAAATAAAAAA
3690401 CAAACAATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
15 10 0.19
16 2 0.04
17 6 0.12
18 19 0.37
19 13 0.25
20 2 0.04
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.18
Consensus pattern (17 bp):
TAAAAATAAAAAAATAA
Found at i:3690361 original size:6 final size:6
Alignment explanation
Indices: 3690318--3690399 Score: 60
Period size: 6 Copynumber: 13.0 Consensus size: 6
3690308 TCTTATTATC
* ** *
3690318 TAAAAA T-AAAA TAAATAA TAATAA TAAAAACA TCAAAAA TAAAAA CCAGAA
1 TAAAAA TAAAAA TAAA-AA TAAAAA T-AAAA-A T-AAAAA TAAAAA TAAAAA
3690369 TAAAAA T-AAAA TAAAATAA TAAAAA TAAAAA
1 TAAAAA TAAAAA T-AAA-AA TAAAAA TAAAAA
3690400 ACAAACAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
5 10 0.17
6 26 0.43
7 15 0.25
8 9 0.15
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:3690661 original size:2 final size:2
Alignment explanation
Indices: 3690654--3690699 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
3690644 CCTTTGCTCC
*
3690654 CT CT CT CT CT ACT -T CT -T CT -T TT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3690694 CT CT CT
1 CT CT CT
3690700 ATCTACCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
1 3 0.08
2 34 0.87
3 2 0.05
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.54
Consensus pattern (2 bp):
CT
Found at i:3690661 original size:946 final size:945
Alignment explanation
Indices: 3688806--3691237 Score: 3144
Period size: 924 Copynumber: 2.6 Consensus size: 945
3688796 CTTCTTTTCC
* * * * * *
3688806 CTCTCTCTCTCTATCCACCCAAGAATACCAATTGAATTTAATC-AGATTCTGAAAATTTTTATCA
1 CTCTCTCTCTCTATCCACCCAAGAACACCAATCGAATTTAACCGA-ATTCTGAAAATTCTTGTCG
* * *** * * * * ** ****
3688870 AAAT-TTGAGTTATTCATTGGAAGTTTACCAGAAAGCTCGTCGGTTTCTCAAAAGTTG-TTGTTA
65 AAATCTAG-GTTATTCGTCAAAAGTTCACCAGAAAGCTCATCGATTTTTGGAAAGTTGCTACCGA
* * * *** ** **
3688933 GAAACTGGAAAGCTAACCGAAATCTGAAAAGTCTGTTGAAAAGTTCAACCGGCACTGGAAAACTC
129 -AAACTGAAAAGCTAACCGAAATTTGAAAAGTATGCCAAAAAGTTCAACCAACGTTGG-AAACTC
* * * * * * **
3688998 ATCAAAAAATTTAACCAAC-ATCGAAAAATTTTACCGAAATAT-GAAA-ATTTT--CCAA-----
192 GTCAAAAAATTCAACCGACGCT-GAAAAATTTTACCGAAATCTAGAAATTTTTTAAAAAATTTTC
* * *
3689053 AAAAAA-TGTTCTTCTCTTTAACAAAACTTCATA-ATTTTTTTTCTTCTGCTTGCTGTGTTTCTG
256 AAAAAATTTTTCTTCTCTTTAACAAAACTTAAAATATTTTTTTTCTTCTGCTTGCTGTGTTTCTG
* * * *
3689116 ATCTATCTATTCTCTTTTCTACTTCTGATTTTGTCTTTGTGTTTTTACG-TT-TTTTTTTTTGTT
321 ATCTATCTATTCTCTTTTCTGCTTTTGATTTTCTCTTTGTGTTTCTACGTTTCTTTTTTTTTGTT
* * * *
3689179 ATGTGTTGTGTCTAAGGCTGTATTTGTAGAATCAGATCAGAAGAGTTTCTGATTACTTAGAAAT-
386 CTGTGTTGTGTCTAAGGTTGTATTTATAGAATCAGATCAGAAGAGTTTCTGATTAATTAGAAATC
*
3689243 TCCCCTTTGATTGGGTTTTCACATTATCAAAAAATTTAGGAATTATCCTAGGAGATTGAAATCAA
451 T-CCCTTCGATTGGGTTTTCACATTATCAAAAAATTTAGGAATTATCCTAGGAGATTGAAATCAA
* *
3689308 TTGTAATTCTGCCAGTGCCTATGCACGGTAGAATTTGTAATTTTTTTTTTTTAGTAATATCCTAT
515 TTGTAATTCTGCCAGTGCCTATGCACAGCAGAATTTGTAATTTTTTTTTTTTAGTAATATCCTAT
*
3689373 TATCTAAAAATGAAATAAATATAATAAAAAAATCAAAAATAAAAACCAAAATAAAAATAAAATAA
580 TATCTAAAAATAAAATAAATATAATAAAAAAATCAAAAATAAAAACCAAAATAAAAATAAAATAA
* * *
3689438 AATAATAAAAATAAAAAACAAACAGTTGGGCTTATCACTTGGACCCCATTTAATCGAGCCAAATG
645 AATAATAAAAATAAAAAACAAACAATTGGGCCTATCACTTGGACCCCATTGAATCGAGCCAAATG
* *
3689503 GGCTTCGACCCAGGCCCTATTGAACCAGCCCAATGGGTTTATAAACGCGCGGATCCTGGGTTTAT
710 GGCTTAGACCCAGGCCCTATTGAACCAGCCCAATGGGTTTATAAACACGCGGATCCTGGGTTTAT
*
3689568 TGGAATTGAGAAAATAAGCAAAAAAATTTGACTTGACAAAACGCGCGAATTCTAGGCTTATTAAC
775 TGGAATTGAGAAAATAAGCAAAAAAATTTGACTTGACAAAACGCGCGAATCCTAGGCTTATTAAC
* * * *
3689633 GCCCAAAACAACGTCATTTTGCGAAGGCTATAAAAGCCTGAGTTTCAGTCTATTTTGTCAAAATT
840 ACCCAAAACAACATCATTTTGCGAAGGCTATAAAAGCCTGAGTTTCAGCCTATTTCGTCAAAATT
*
3689698 CCTCTGCTTCCTCTCTCTCTA-ATTC-TTCT-T-T-TCTCT
905 CCTCTGCTCCCTCTCTCTCTATATTCTTTCTCTCTCTCTCT
* *
3689734 -T-TCTCT-T-TATCCACCGAAGAACATCAATCGAATTTAACCGAATTCTGAAAATTCTTGTCGA
1 CTCTCTCTCTCTATCCACCCAAGAACACCAATCGAATTTAACCGAATTCTGAAAATTCTTGTCGA
* * * *
3689795 AATCTGGGTTATTCGTCGAAAGTTCACCAGAAAGCTCGTTGATTTTTGGAAAGTTGCTACCGAAA
66 AATCTAGGTTATTCGTCAAAAGTTCACCAGAAAGCTCATCGATTTTTGGAAAGTTGCTACCGAAA
* * * * *** *
3689860 ATTGGAAAGCTAACCGAAATTTGAAAAGTCTGTCAAAAAGTTCAACTGGCGTTGGAAAACTTGTC
131 ACTGAAAAGCTAACCGAAATTTGAAAAGTATGCCAAAAAGTTCAACCAACGTTGG-AAACTCGTC
* * * * *
3689925 AAAAAATTCAATCGACGTTGGAAAATTTTACCGGAATCTAGAAATTTTTTTAAAAATTTTCAAAA
195 AAAAAATTCAACCGACGCTGAAAAATTTTACCGAAATCTAGAAATTTTTTAAAAAATTTTCAAAA
*
3689990 AATTTTTCTTCTCTTTAACAAAACTTAAAATATTTTTTTTTCTTCTACTTGCTGTGTTTCTGATC
260 AATTTTTCTTCTCTTTAACAAAACTTAAAATA-TTTTTTTTCTTCTGCTTGCTGTGTTTCTGATC
* * *
3690055 TATCTATTCTTTTTTTTGCTTTTGATTTTCTCTTTGTGTTTCTGCGTTTCTTTTTTTTTGTTCTG
324 TATCTATTCTCTTTTCTGCTTTTGATTTTCTCTTTGTGTTTCTACGTTTCTTTTTTTTTGTTCTG
*
3690120 TGTTGTGTCTAAGGTTGTATTTATAGAATCAGATCAGAAGAGTTTCTAATTAATTA-AGAATCTC
389 TGTTGTGTCTAAGGTTGTATTTATAGAATCAGATCAGAAGAGTTTCTGATTAATTAGA-AATCTC
* *
3690184 CCTTCGATTGGGTTTTCACACTATCAAAAAATTTAAGAATTATCCTAGGAGATTGAAATCAATTG
453 CCTTCGATTGGGTTTTCACATTATCAAAAAATTTAGGAATTATCCTAGGAGATTGAAATCAATTG
* * * *
3690249 CAATCCTGCCAGTGCCTATGCACAGCAGAATTTGTAATTTTTTCTTTTTTTTATTAATATCTTAT
518 TAATTCTGCCAGTGCCTATGCACAGCAGAATTTGTAA--TTTT-TTTTTTTTAGTAATATCCTAT
*
3690314 TATCTAAAAATAAAATAAATAATAATAATAAAAACATCAAAAATAAAAACCAGAATAAAAATAAA
580 TATCTAAAAATAAAATAAAT-ATAAT-A-AAAAA-ATCAAAAATAAAAACCAAAATAAAAATAAA
* * **
3690379 ATAAAATAATAAAAATAAAAAACAAACAATTGGGCCTATCACTTGGACCCCATTGAATTGGGCTT
641 ATAAAATAATAAAAATAAAAAACAAACAATTGGGCCTATCACTTGGACCCCATTGAATCGAGCCA
* *** *
3690444 AATGGGCTTAGGCTTGGGCCCTATTGAACCATGCCTAATGGGTTTATAAACACGCGGATCCTGGG
706 AATGGGCTTAGACCCAGGCCCTATTGAACCA-GCCCAATGGGTTTATAAACACGCGGATCCTGGG
* * *
3690509 TTTATTGGAATTGAGAAAATAAGCAAAAAAATTTGACTTGGCAAAACGCGCGGATCCTAGGTTTA
770 TTTATTGGAATTGAGAAAATAAGCAAAAAAATTTGACTTGACAAAACGCGCGAATCCTAGGCTTA
* *
3690574 TTAACACCCAAAACAACATCGTTTTGCGGAGGCTATAAAAGCCTGAGTTTCAGCCTATTTCG-CT
835 TTAACACCCAAAACAACATCATTTTGCGAAGGCTATAAAAGCCTGAGTTTCAGCCTATTTCGTC-
* * *
3690638 AGAATTCCTTTGCTCCCTCTCTCTCTACTTCTTCTTTTCTCTCTCTCTCT
899 AAAATTCCTCTGCTCCCTCTCTCTCTA--TATTC-TTTCTCTCTCTCTCT
* * * *
3690688 CTCTCTCTCTCTATCTACCCAAGAACACCGATCGAATTTAATCGGATTCTGAAAATTCTTGTCGA
1 CTCTCTCTCTCTATCCACCCAAGAACACCAATCGAATTTAACCGAATTCTGAAAATTCTTGTCGA
*
3690753 AATCTAGGTTATTCGTCAAAAGTTCACTAGAAAGCTCATCGATTTTTGGAAAGTTGCTACCGAAA
66 AATCTAGGTTATTCGTCAAAAGTTCACCAGAAAGCTCATCGATTTTTGGAAAGTTGCTACCGAAA
* *
3690818 ACTGAAAAGCTAATCGAAATTTGAAAAGTATGCCGAAAAGTTCAACCAACGTTGGAAACTCGTCA
131 ACTGAAAAGCTAACCGAAATTTGAAAAGTATGCCAAAAAGTTCAACCAACGTTGGAAACTCGTCA
* * * *
3690883 AAAAATTCAACCGGCGCTGAAAAATTTTGCCGAAATCTATAAATTTTTTAAAAAATTTCCAAAAA
196 AAAAATTCAACCGACGCTGAAAAATTTTACCGAAATCTAGAAATTTTTTAAAAAATTTTCAAAAA
* *** *
3690948 ATTTTTCTTCTATTTAACAAAACTTCAAAA-AAAATTTTCCTTCTGCTTGCTGTGTTTCTGATCT
261 ATTTTTCTTCTCTTTAACAAAACTT-AAAATATTTTTTTTCTTCTGCTTGCTGTGTTTCTGATCT
*
3691012 ATCTATTCTCTTTTCTGCTTTTGATTTTCTCTTTGTGTTTCTACGTTTCTTTTTTTTTATTCTGT
325 ATCTATTCTCTTTTCTGCTTTTGATTTTCTCTTTGTGTTTCTACGTTTCTTTTTTTTTGTTCTGT
* * * * * *
3691077 GTTGTGTC-AAGGTTGTATTTATAAAATCATATCAGAAGAGCTTCTGATCAATTAGTAATCCCCC
390 GTTGTGTCTAAGGTTGTATTTATAGAATCAGATCAGAAGAGTTTCTGATTAATTAGAAATCTCCC
* * * *
3691141 TTCGATTAGGTTTCCACATTATCAGAAAATCTAGGAATTATCCTAGGGAGATTGAAATCAATTGT
455 TTCGATTGGGTTTTCACATTATCAAAAAATTTAGGAATTATCCTA-GGAGATTGAAATCAATTGT
* * **
3691206 AATTTTGTCAGTGCCTATGCATTGCAGAATTT
519 AATTCTGCCAGTGCCTATGCACAGCAGAATTT
3691238 ATAAAATCAT
Statistics
Matches: 1305, Mismatches: 155, Indels: 60
0.86 0.10 0.04
Matches are distributed among these distances:
924 175 0.13
925 11 0.01
926 9 0.01
927 1 0.00
928 2 0.00
933 6 0.00
934 24 0.02
935 1 0.00
936 70 0.05
937 3 0.00
938 165 0.13
939 1 0.00
940 4 0.00
941 38 0.03
942 5 0.00
943 1 0.00
944 5 0.00
945 114 0.09
946 172 0.13
949 3 0.00
951 4 0.00
952 1 0.00
953 1 0.00
954 5 0.00
955 88 0.07
956 147 0.11
957 91 0.07
958 158 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (945 bp):
CTCTCTCTCTCTATCCACCCAAGAACACCAATCGAATTTAACCGAATTCTGAAAATTCTTGTCGA
AATCTAGGTTATTCGTCAAAAGTTCACCAGAAAGCTCATCGATTTTTGGAAAGTTGCTACCGAAA
ACTGAAAAGCTAACCGAAATTTGAAAAGTATGCCAAAAAGTTCAACCAACGTTGGAAACTCGTCA
AAAAATTCAACCGACGCTGAAAAATTTTACCGAAATCTAGAAATTTTTTAAAAAATTTTCAAAAA
ATTTTTCTTCTCTTTAACAAAACTTAAAATATTTTTTTTCTTCTGCTTGCTGTGTTTCTGATCTA
TCTATTCTCTTTTCTGCTTTTGATTTTCTCTTTGTGTTTCTACGTTTCTTTTTTTTTGTTCTGTG
TTGTGTCTAAGGTTGTATTTATAGAATCAGATCAGAAGAGTTTCTGATTAATTAGAAATCTCCCT
TCGATTGGGTTTTCACATTATCAAAAAATTTAGGAATTATCCTAGGAGATTGAAATCAATTGTAA
TTCTGCCAGTGCCTATGCACAGCAGAATTTGTAATTTTTTTTTTTTAGTAATATCCTATTATCTA
AAAATAAAATAAATATAATAAAAAAATCAAAAATAAAAACCAAAATAAAAATAAAATAAAATAAT
AAAAATAAAAAACAAACAATTGGGCCTATCACTTGGACCCCATTGAATCGAGCCAAATGGGCTTA
GACCCAGGCCCTATTGAACCAGCCCAATGGGTTTATAAACACGCGGATCCTGGGTTTATTGGAAT
TGAGAAAATAAGCAAAAAAATTTGACTTGACAAAACGCGCGAATCCTAGGCTTATTAACACCCAA
AACAACATCATTTTGCGAAGGCTATAAAAGCCTGAGTTTCAGCCTATTTCGTCAAAATTCCTCTG
CTCCCTCTCTCTCTATATTCTTTCTCTCTCTCTCT
Found at i:3690986 original size:32 final size:32
Alignment explanation
Indices: 3690929--3690991 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
3690919 CTATAAATTT
* * *
3690929 TTTAAAAAATTTC-CAAAAAATTTTTCTTCTA
1 TTTAAAAAACTTCAAAAAAAATTTTCCTTCTA
3690960 TTTAACAAAACTTCAAAAAAAATTTTCCTTCT
1 TTTAA-AAAACTTCAAAAAAAATTTTCCTTCT
3690992 GCTTGCTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 5 0.19
32 7 0.26
33 15 0.56
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (32 bp):
TTTAAAAAACTTCAAAAAAAATTTTCCTTCTA
Found at i:3691351 original size:141 final size:141
Alignment explanation
Indices: 3691093--3691379 Score: 511
Period size: 141 Copynumber: 2.0 Consensus size: 141
3691083 TCAAGGTTGT
3691093 ATTTATAAAATCATATCAGAAGAGCTTCTGATCAATTAGTAATCCCCCTTCGATTAGGTTTCCAC
1 ATTTATAAAATCATATCAGAAGAGCTTCTGATCAATTAGTAATCCCCCTTCGATTAGGTTTCCAC
* * **
3691158 ATTATCAGAAAATCTAGGAATTATCCTAGGGAGATTGAAATCAATTGTAATTTTGTCAGTGCCTA
66 ATTATCAAAAAATCTAGGAATTATCCTAGGGAGATTGAAATCAATTGCAATTTTACCAGTGCCTA
* *
3691223 TGCATTGCAGA
131 TACATGGCAGA
*
3691234 ATTTATAAAATCATATCAGAAGAGTTTCTGATCAATTAGTAATCCCCCTTCGATTAGGTTTCCAC
1 ATTTATAAAATCATATCAGAAGAGCTTCTGATCAATTAGTAATCCCCCTTCGATTAGGTTTCCAC
3691299 ATTATCAAAAAATCTAGGAATTATCCTAGGGAGATTGAAATCAATTGCAATTTTACCAGTGCCTA
66 ATTATCAAAAAATCTAGGAATTATCCTAGGGAGATTGAAATCAATTGCAATTTTACCAGTGCCTA
3691364 TACATGGCAGA
131 TACATGGCAGA
3691375 ATTTA
1 ATTTA
3691380 CAATTTTTTC
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
141 139 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (141 bp):
ATTTATAAAATCATATCAGAAGAGCTTCTGATCAATTAGTAATCCCCCTTCGATTAGGTTTCCAC
ATTATCAAAAAATCTAGGAATTATCCTAGGGAGATTGAAATCAATTGCAATTTTACCAGTGCCTA
TACATGGCAGA
Found at i:3691461 original size:16 final size:16
Alignment explanation
Indices: 3691442--3691485 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3691432 TAATAATAAT
* *
3691442 AATAAATAAAAACCGA
1 AATAAATAAAAAACAA
3691458 AATAAA-AATAAAACAA
1 AATAAATAA-AAAACAA
3691474 AATAAATAAAAA
1 AATAAATAAAAA
3691486 TAAAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 2 0.08
16 20 0.83
17 2 0.08
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (16 bp):
AATAAATAAAAAACAA
Found at i:3691468 original size:6 final size:6
Alignment explanation
Indices: 3691418--3691491 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
3691408 TCCTATTATC
* * * ***
3691418 TAAAAA T-ATAA TAATAA TAATAA TAATAAA TAAAAA CCGAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAA-AAA TAAAAA TAAAAA TAAAAA
*
3691466 TAAAACA AAATAAA TAAAAA TAAAAA
1 TAAAA-A TAA-AAA TAAAAA TAAAAA
3691492 ACAAACCGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 4 0.07
6 37 0.69
7 11 0.20
8 2 0.04
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:3691475 original size:22 final size:21
Alignment explanation
Indices: 3691436--3691492 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
3691426 TAATAATAAT
*
3691436 AATAATAATAAATAAAAACCGA
1 AATAAAAATAAA-AAAAACCGA
*
3691458 AATAAAAATAAAACAAAA--TA
1 AATAAAAATAAAA-AAAACCGA
3691478 AATAAAAATAAAAAA
1 AATAAAAATAAAAAA
3691493 CAAACCGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 14 0.44
21 1 0.03
22 15 0.47
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (21 bp):
AATAAAAATAAAAAAAACCGA
Found at i:3691482 original size:42 final size:43
Alignment explanation
Indices: 3691418--3691499 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
3691408 TCCTATTATC
* * * *
3691418 TAAAAATATAATAATAATAATAATAATAAATAA-AAACCGAAA
1 TAAAAATAAAACAATAATAATAAAAATAAAAAACAAACCGAAA
3691460 TAAAAATAAAACAA-AATAAATAAAAATAAAAAACAAACCG
1 TAAAAATAAAACAATAAT-AATAAAAATAAAAAACAAACCG
3691500 TTGGGCCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 3 0.09
42 25 0.74
43 6 0.18
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.18
Consensus pattern (43 bp):
TAAAAATAAAACAATAATAATAAAAATAAAAAACAAACCGAAA
Found at i:3694523 original size:2 final size:2
Alignment explanation
Indices: 3694518--3694560 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3694508 ATATATATAT
3694518 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3694560 G
1 G
3694561 GCAAGTTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3699478 original size:19 final size:20
Alignment explanation
Indices: 3699440--3699481 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3699430 AAAGTTTTAA
*
3699440 ATTTAAATATTATATTAAAT
1 ATTTAAATATAATATTAAAT
*
3699460 ATTTTAATATAAT-TTAAAT
1 ATTTAAATATAATATTAAAT
3699479 ATT
1 ATT
3699482 ATTCATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAAATATAATATTAAAT
Found at i:3699947 original size:10 final size:11
Alignment explanation
Indices: 3699927--3699951 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3699917 TATGGGTATC
3699927 TTTCTTTTTTT
1 TTTCTTTTTTT
3699938 TTTCTTTTTTT
1 TTTCTTTTTTT
3699949 TTT
1 TTT
3699952 TGTTTGGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:3705383 original size:34 final size:34
Alignment explanation
Indices: 3705340--3705408 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
3705330 TGTACAATTC
3705340 CTGGCTCTTTATATATGTTTATTAACATATTTTA
1 CTGGCTCTTTATATATGTTTATTAACATATTTTA
3705374 CTGGCTCTTTATATATGTTTATTAACATATTTTA
1 CTGGCTCTTTATATATGTTTATTAACATATTTTA
3705408 C
1 C
3705409 AACATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (34 bp):
CTGGCTCTTTATATATGTTTATTAACATATTTTA
Found at i:3711072 original size:20 final size:20
Alignment explanation
Indices: 3711027--3711070 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
3711017 TATTTAAATA
3711027 TATTTAATAAATTAATTTTT
1 TATTTAATAAATTAATTTTT
3711047 TATTTAA-AAATATAA-TTTT
1 TATTTAATAAAT-TAATTTTT
3711066 TATTT
1 TATTT
3711071 TAGATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTAATAAATTAATTTTT
Found at i:3711115 original size:21 final size:20
Alignment explanation
Indices: 3711079--3711118 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3711069 TTTAGATTAA
3711079 TTAAAATTAAATATTTATAC
1 TTAAAATTAAATATTTATAC
*
3711099 TTAAAATATATATATTTATA
1 TTAAAAT-TAAATATTTATA
3711119 AAAAATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAATTAAATATTTATAC
Found at i:3718874 original size:2 final size:2
Alignment explanation
Indices: 3718867--3718911 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
3718857 TAAGTGTTGA
3718867 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
3718907 A- AT AT
1 AT AT AT
3718912 TGTAACATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 37 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3719255 original size:22 final size:23
Alignment explanation
Indices: 3719225--3719268 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3719215 AAAAATAATG
* *
3719225 ATATTATTTTATTTTAT-TTATA
1 ATATCATTTTATCTTATCTTATA
3719247 ATATCATTTTATCTTATCTTAT
1 ATATCATTTTATCTTATCTTAT
3719269 TATAATCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATCATTTTATCTTATCTTATA
Found at i:3724237 original size:24 final size:25
Alignment explanation
Indices: 3724191--3724254 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
3724181 ATTATGAAAA
*
3724191 AAATATCATAATAAATCAAGCAAAT
1 AAATATAATAATAAATCAAGCAAAT
*
3724216 AAATATAATAA-AAATCACGCAAAT
1 AAATATAATAATAAATCAAGCAAAT
3724240 AAATATAATAATAAA
1 AAATATAATAATAAA
3724255 AATCCTACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 23 0.64
25 13 0.36
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.23
Consensus pattern (25 bp):
AAATATAATAATAAATCAAGCAAAT
Found at i:3726656 original size:241 final size:241
Alignment explanation
Indices: 3726184--3726811 Score: 897
Period size: 241 Copynumber: 2.6 Consensus size: 241
3726174 GGAAAAAAAA
* ** *
3726184 AGTGATGACTTTCCTATTTGATTTTAAAATTTCATCTACCAGTCACAAAATCATTATGACACTA-
1 AGTGATGACTTTCCGATTTGATTTTAAAATTTCATCTAATAGTCTCAAAATCATTATGACACTAT
* * * *
3726248 TTTTGTTTTCAAGTCATCAAATGCTTAATGAAACAATGTGCCAAATAATTATTGACTGAACATTC
66 TTTTTTTTTCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACATTC
* * *
3726313 TTATCAAAAATAAAATAAAATATAATAAAATAAATTAGTTCAGGAACAATAATTAATTATTAGTA
131 TTATCAAAAAT-AAATAAAATATAATAAAATAAATTAATTCAGGAACAAGAATTAATTATTAGGA
* *
3726378 TTAAAAATTTATGAGATATCATATATAGATGGAGTATCTAAAAATTT
195 TTAAAAATTTATGAGATATCATATATAAATAGAGTATCTAAAAATTT
* **
3726425 AGTGATGATTTTTTGATTTGATTTTAAAATTTCATCTAATAGTCTCAAAATCATTATGACACTAT
1 AGTGATGACTTTCCGATTTGATTTTAAAATTTCATCTAATAGTCTCAAAATCATTATGACACTAT
* * * ** *
3726490 TTTTTTTTTCAAATCTTCAAATGCTTGATGAAACAATATGCTAAATAATTCTTGGTTGAACATTT
66 TTTTTTTTTCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACATTC
* *
3726555 TTATCAACAATAAATAAAATATAAT-AAATAAATTAATTCTGGAACAAGAATTAATTATTAGGAT
131 TTATCAAAAATAAATAAAATATAATAAAATAAATTAATTCAGGAACAAGAATTAATTATTAGGAT
* *
3726619 TAAAAATTTATGAGATATTCTTGTATAAATAGAGTATCTAAAAATTT
196 TAAAAATTTATGAGATA-TCATATATAAATAGAGTATCTAAAAATTT
* * * *
3726666 AGTGATGACTTTCCGATTTGATTTTAAAATTTTAT-TTATCAG-ATAAAAATC-TTATGACACTA
1 AGTGATGACTTTCCGATTTGATTTTAAAATTTCATCTAAT-AGTCTCAAAATCATTATGACACTA
3726728 TTTTTTTTTTTTCCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAAC
65 --TTTTTTTTTT-CAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAAC
3726793 ATTCTTATCAAAAATAAAT
127 ATTCTTATCAAAAATAAAT
3726812 TAGTTCGGGA
Statistics
Matches: 341, Mismatches: 40, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
239 11 0.03
240 62 0.18
241 139 0.41
242 129 0.38
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (241 bp):
AGTGATGACTTTCCGATTTGATTTTAAAATTTCATCTAATAGTCTCAAAATCATTATGACACTAT
TTTTTTTTTCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACATTC
TTATCAAAAATAAATAAAATATAATAAAATAAATTAATTCAGGAACAAGAATTAATTATTAGGAT
TAAAAATTTATGAGATATCATATATAAATAGAGTATCTAAAAATTT
Found at i:3726834 original size:242 final size:236
Alignment explanation
Indices: 3726184--3726811 Score: 830
Period size: 242 Copynumber: 2.6 Consensus size: 236
3726174 GGAAAAAAAA
* * *
3726184 AGTGATGACTTTCCTATTTGATTTTAAAATTTCATCTACCAGTCACAAAATCATTATGACACTA-
1 AGTGATGACTTTCCGATTTGATTTTAAAATTTCATTTATCAGT-A-AAAATCATTATGACACTAT
* * * *
3726248 TTTTGTTTTCAAGTCATCAAATGCTTAATGAAACAATGTGCCAAATAATTATTGACTGAACATTC
64 TTTTTTTTTCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACATTC
* * *
3726313 TTATCAAAAATAAAATAAAATATAATAAAATAAATTAGTTCAGGAACAATAATTAATTATTAGTA
129 TTATCAAAAAT-AAAT-AAAT-T-ATAAAATAAATTAATTCAGGAACAAGAATTAATTATTAGGA
* *
3726378 TTAAAAATTTATGAGATATCATATATAGATGGAGTATCTAAAAATTT
190 TTAAAAATTTATGAGATATCATATATAAATAGAGTATCTAAAAATTT
* ** * *
3726425 AGTGATGATTTTTTGATTTGATTTTAAAATTTCATCTAAT-AGTCTCAAAATCATTATGACACTA
1 AGTGATGACTTTCCGATTTGATTTTAAAATTTCAT-TTATCAG--TAAAAATCATTATGACACTA
* * * **
3726489 TTTTTTTTTTCAAATCTTCAAATGCTTGATGAAACAATATGCTAAATAATTCTTGGTTGAACATT
63 TTTTTTTTTTCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACATT
* * * *
3726554 TTTATCAACAATAAATAAAATATAATAAATAAATTAATTCTGGAACAAGAATTAATTATTAGGAT
128 CTTATCAAAAATAAATAAATTAT-A-AAATAAATTAATTCAGGAACAAGAATTAATTATTAGGAT
* *
3726619 TAAAAATTTATGAGATATTCTTGTATAAATAGAGTATCTAAAAATTT
191 TAAAAATTTATGAGATA-TCATATATAAATAGAGTATCTAAAAATTT
*
3726666 AGTGATGACTTTCCGATTTGATTTTAAAATTTTATTTATCAGATAAAAATC-TTATGACACTATT
1 AGTGATGACTTTCCGATTTGATTTTAAAATTTCATTTATCAG-TAAAAATCATTATGACACTA--
3726730 TTTTTTTTTTCCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACAT
63 TTTTTTTTTT-CAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACAT
3726795 TCTTATCAAAAATAAAT
127 TCTTATCAAAAATAAAT
3726812 TAGTTCGGGA
Statistics
Matches: 334, Mismatches: 42, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
238 2 0.01
239 13 0.04
240 65 0.19
241 123 0.37
242 130 0.39
243 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (236 bp):
AGTGATGACTTTCCGATTTGATTTTAAAATTTCATTTATCAGTAAAAATCATTATGACACTATTT
TTTTTTTCAAATCATCAAATGCTTGATGAAACAATGTGCCAAATAATTCTTGACTGAACATTCTT
ATCAAAAATAAATAAATTATAAAATAAATTAATTCAGGAACAAGAATTAATTATTAGGATTAAAA
ATTTATGAGATATCATATATAAATAGAGTATCTAAAAATTT
Found at i:3727069 original size:24 final size:23
Alignment explanation
Indices: 3727042--3727086 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
3727032 TAACTTTTCA
3727042 TTTAAG-TTTAATTCAAATTTAAGT
1 TTTAAGATTT-ATTC-AATTTAAGT
*
3727066 TTTACGATTTATTCAATTTAA
1 TTTAAGATTTATTCAATTTAA
3727087 ATTAACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 9 0.47
25 3 0.16
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (23 bp):
TTTAAGATTTATTCAATTTAAGT
Found at i:3728781 original size:23 final size:23
Alignment explanation
Indices: 3728749--3728793 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3728739 TTAGTTAAAG
* *
3728749 TAATAGTTTATTAAATAATTATT
1 TAATAATTTAATAAATAATTATT
*
3728772 TAATAATTTAATAATTAATTAT
1 TAATAATTTAATAAATAATTAT
3728794 ACGAATGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAATAATTTAATAAATAATTATT
Found at i:3729446 original size:24 final size:24
Alignment explanation
Indices: 3729409--3729464 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
3729399 TAAGAATTTA
*
3729409 ATAAGATAAAAAATAATTATA-ATAG
1 ATAA-ATAAAAAAT-ATTAGAGATAG
*
3729434 ATAAATAACAAATATTAGAGATAG
1 ATAAATAAAAAATATTAGAGATAG
*
3729458 AAAAATA
1 ATAAATA
3729465 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.19
24 18 0.67
25 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (24 bp):
ATAAATAAAAAATATTAGAGATAG
Found at i:3730700 original size:18 final size:18
Alignment explanation
Indices: 3730664--3730712 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
3730654 ATAAAATATT
3730664 ATTTTT-AAAAATATAAA
1 ATTTTTAAAAAATATAAA
3730681 ATTTTTTAAAAAATAT-AA
1 A-TTTTTAAAAAATATAAA
*
3730699 A-TATTAAAAAATAT
1 ATTTTTAAAAAATAT
3730713 TATTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.41
17 1 0.03
18 8 0.28
19 8 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTTAAAAAATATAAA
Found at i:3730707 original size:16 final size:16
Alignment explanation
Indices: 3730686--3730735 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
3730676 ATAAAATTTT
3730686 TTAAAAAATATAAATA
1 TTAAAAAATATAAATA
* *
3730702 TTAAAAAATATTATTA
1 TTAAAAAATATAAATA
*
3730718 TATAAATATATATAAATA
1 T-TAAA-AAATATAAATA
3730736 AAAAATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 15 0.56
17 4 0.15
18 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAAATATAAATA
Found at i:3730723 original size:17 final size:17
Alignment explanation
Indices: 3730651--3730723 Score: 60
Period size: 17 Copynumber: 4.3 Consensus size: 17
3730641 CGATCCGAAA
*
3730651 TTAATAAAATATTATT-T
1 TTAA-AAAATATAATTAT
* *
3730668 TTAAAAATATAAAATTTT
1 TTAAAAA-ATATAATTAT
*
3730686 TTAAAAAATATAAATA-
1 TTAAAAAATATAATTAT
*
3730702 TTAAAAAATATTATTAT
1 TTAAAAAATATAATTAT
*
3730719 ATAAA
1 TTAAA
3730724 TATATATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 17 0.38
17 20 0.44
18 8 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAAATATAATTAT
Found at i:3735297 original size:23 final size:23
Alignment explanation
Indices: 3735249--3735298 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3735239 AATATATTTT
*
3735249 TATTTTAAAAATATATTAATATA
1 TATTTTAAAAATATATTAATAAA
3735272 TATTTATAAAAA-A-ATTACATAAA
1 TATTT-TAAAAATATATTA-ATAAA
3735295 TATT
1 TATT
3735299 AAAGATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTTAAAAATATATTAATAAA
Found at i:3751693 original size:19 final size:20
Alignment explanation
Indices: 3751657--3751702 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
3751647 TTTGAAAATA
*
3751657 AAAAAATCTAAATTTTTTTT
1 AAAAAATCTAAATATTTTTT
*
3751677 AAAAGATCTAAA-ATTTTTT
1 AAAAAATCTAAATATTTTTT
3751696 AAAAAAT
1 AAAAAAT
3751703 TATAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAAATCTAAATATTTTTT
Found at i:3751708 original size:20 final size:19
Alignment explanation
Indices: 3751657--3751709 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
3751647 TTTGAAAATA
* *
3751657 AAAAAATCTAAATTTTTTTT
1 AAAAAATATAAA-ATTTTTT
* *
3751677 AAAAGATCTAAAATTTTTT
1 AAAAAATATAAAATTTTTT
3751696 AAAAAATTATAAAA
1 AAAAAA-TATAAAA
3751710 AAATTGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAAAATATAAAATTTTTT
Found at i:3751866 original size:25 final size:25
Alignment explanation
Indices: 3751829--3751887 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3751819 AAATTTATAT
*
3751829 ATTTTTAAATTTTATTATCTTAAAA
1 ATTTTTTAATTTTATTATCTTAAAA
* * * *
3751854 ATTTTTTATTTTTTTTATTTTTAAA
1 ATTTTTTAATTTTATTATCTTAAAA
3751879 ATTTTTTAA
1 ATTTTTTAA
3751888 AAAAATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTTTTTAATTTTATTATCTTAAAA
Found at i:3751926 original size:21 final size:20
Alignment explanation
Indices: 3751879--3751925 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3751869 TATTTTTAAA
3751879 ATTTTTTAAAAAAATTTTAG
1 ATTTTTTAAAAAAATTTTAG
* *
3751899 ATTTTTTCAAAAGATTTTAG
1 ATTTTTTAAAAAAATTTTAG
3751919 ATTTTTT
1 ATTTTTT
3751926 TAATTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (20 bp):
ATTTTTTAAAAAAATTTTAG
Found at i:3751938 original size:16 final size:16
Alignment explanation
Indices: 3751912--3751973 Score: 88
Period size: 16 Copynumber: 3.9 Consensus size: 16
3751902 TTTTCAAAAG
* *
3751912 ATTTTAGATTTTTTTA
1 ATTTTAAATTTTTTAA
* *
3751928 ATTTTCAATTTTTAAA
1 ATTTTAAATTTTTTAA
3751944 ATTTTAAATTTTTTAA
1 ATTTTAAATTTTTTAA
3751960 ATTTTAAATTTTTT
1 ATTTTAAATTTTTT
3751974 TAAGTTACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTTTAAATTTTTTAA
Found at i:3751946 original size:9 final size:8
Alignment explanation
Indices: 3751929--3751972 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
3751919 ATTTTTTTAA
*
3751929 TTTTCAAT
1 TTTTAAAT
*
3751937 TTTTAAAA
1 TTTTAAAT
3751945 TTTTAAATT
1 TTTTAAA-T
3751954 TTTTAAA-
1 TTTTAAAT
3751961 TTTTAAAT
1 TTTTAAAT
3751969 TTTT
1 TTTT
3751973 TTAAGTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 7 0.23
8 17 0.55
9 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAAAT
Found at i:3754932 original size:17 final size:18
Alignment explanation
Indices: 3754907--3754950 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
3754897 TTTTTTTTTT
*
3754907 TTTAATTTTAAGAAAA-A
1 TTTATTTTTAAGAAAATA
**
3754924 TTTATTTTTATTAAAATA
1 TTTATTTTTAAGAAAATA
3754942 TTTATTTTT
1 TTTATTTTT
3754951 TGGAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTATTTTTAAGAAAATA
Found at i:3755020 original size:17 final size:17
Alignment explanation
Indices: 3754996--3755039 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3754986 TATTGTATTA
*
3754996 AAAT-TTTTAGTTTTTT
1 AAATATTTTAATTTTTT
3755012 AAATATTTTAATTTTTT
1 AAATATTTTAATTTTTT
3755029 ATAA-ATTTTAA
1 A-AATATTTTAA
3755040 AAATATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 19 0.76
18 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
AAATATTTTAATTTTTT
Found at i:3755076 original size:28 final size:28
Alignment explanation
Indices: 3755006--3755080 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
3754996 AAATTTTTAG
*
3755006 TTTTTTAAATATTTTAATTTTTTATAAA
1 TTTTATAAATATTTTAATTTTTTATAAA
*
3755034 TTTTAAAAATATTTTAGATTTTTT-T-AA
1 TTTTATAAATATTTTA-ATTTTTTATAAA
*
3755061 TGTTTGATAAATTTTTTAAT
1 T-TTT-ATAAATATTTTAAT
3755081 ACCAATTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.08
28 20 0.50
29 17 0.43
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (28 bp):
TTTTATAAATATTTTAATTTTTTATAAA
Found at i:3758331 original size:75 final size:74
Alignment explanation
Indices: 3758148--3758339 Score: 215
Period size: 75 Copynumber: 2.6 Consensus size: 74
3758138 CATAAATCTC
* * * * *
3758148 TTTTGAAAACTTATAAATTGATTATCAATAAAGATCGTTAACAGAGAAAATTGAAGCTAAATCTT
1 TTTTGAGAACTTATAAATTGATTATAAATAAAAATTGTTAACAGAGAAAATTAAAGCTAAATCTT
***
3758213 TTTTTTTTT
66 TTAAATTTT
* * *
3758222 TTTTGAGAACTCATAAACTGATTATAAATGAAAAATTGTTAACAGAGAAAATTAAATCTAAATTC
1 TTTTGAGAACTTATAAATTGATTATAAAT-AAAAATTGTTAACAGAGAAAATTAAAGCTAAA-TC
3758287 TTTTAAATTTT
64 TTTTAAATTTT
* * *
3758298 TTTT-AGAACTTATAAATTTATTTTTAATAAAAAAATTGTTAA
1 TTTTGAGAACTTATAAATTGA-TTATAA-ATAAAAATTGTTAA
3758340 AAGACGCTCC
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
74 25 0.26
75 41 0.42
76 31 0.32
77 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (74 bp):
TTTTGAGAACTTATAAATTGATTATAAATAAAAATTGTTAACAGAGAAAATTAAAGCTAAATCTT
TTAAATTTT
Found at i:3769219 original size:26 final size:26
Alignment explanation
Indices: 3769190--3769239 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
3769180 AGGAAAAATG
3769190 TATTATGTTTCTTTCTATTAAAGATT
1 TATTATGTTTCTTTCTATTAAAGATT
3769216 TATTATGTTTCTTTCTATTAAAGA
1 TATTATGTTTCTTTCTATTAAAGA
3769240 GAACGGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (26 bp):
TATTATGTTTCTTTCTATTAAAGATT
Found at i:3770913 original size:32 final size:33
Alignment explanation
Indices: 3770847--3770913 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
3770837 ATCTGTTTTT
* *
3770847 ATTTTATATGTAAAATTATTTAAATATATTAAA
1 ATTTTATATGTAAAATTATATAAATATATAAAA
3770880 ATTTTATAT-TAAAATAATATATAAAT-TA-AAAA
1 ATTTTATATGTAAAAT--TATATAAATATATAAAA
3770912 AT
1 AT
3770914 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
32 11 0.37
33 11 0.37
34 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
ATTTTATATGTAAAATTATATAAATATATAAAA
Found at i:3772424 original size:18 final size:20
Alignment explanation
Indices: 3772401--3772439 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
3772391 AGATTTAAAT
3772401 TAAAAAT-ATTTTT-ATTAA
1 TAAAAATAATTTTTAATTAA
3772419 TAAAAATAATTTTTAATTAA
1 TAAAAATAATTTTTAATTAA
3772439 T
1 T
3772440 TAAATCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAAATAATTTTTAATTAA
Found at i:3772444 original size:19 final size:20
Alignment explanation
Indices: 3772398--3772444 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
3772388 GTAAGATTTA
*
3772398 AATTAAA-AATATTTTTATT
1 AATTAAATAATATTTTAATT
*
3772417 AATAAAAATAAT-TTTTAATT
1 AAT-TAAATAATATTTTAATT
3772437 AATTAAAT
1 AATTAAAT
3772445 CAATCACTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 13 0.57
21 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAAATAATATTTTAATT
Found at i:3775301 original size:32 final size:32
Alignment explanation
Indices: 3775265--3775328 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
3775255 TATATAAAAA
* *
3775265 TATATAGAAAAATTAAACAATTAAAAACAATT
1 TATATAGAAAAATCAAACAATGAAAAACAATT
3775297 TATATAGAAAAATCAAACAATGAAAAACAATT
1 TATATAGAAAAATCAAACAATGAAAAACAATT
3775329 AAGATATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (32 bp):
TATATAGAAAAATCAAACAATGAAAAACAATT
Found at i:3780420 original size:18 final size:18
Alignment explanation
Indices: 3780397--3780435 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3780387 GTTGATTGCT
3780397 AGCCATAAAGAGAAGGAA
1 AGCCATAAAGAGAAGGAA
3780415 AGCCATAAAGAGAAGGAA
1 AGCCATAAAGAGAAGGAA
3780433 AGC
1 AGC
3780436 AACTTCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.13, G:0.28, T:0.05
Consensus pattern (18 bp):
AGCCATAAAGAGAAGGAA
Found at i:3785519 original size:22 final size:22
Alignment explanation
Indices: 3785489--3785539 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3785479 TTTAAAATTA
*
3785489 TAATATTTTATTTGGTTTGAAT
1 TAATATTTTATTTGATTTGAAT
* *
3785511 TAATTTTTTATTTGATTTGACT
1 TAATATTTTATTTGATTTGAAT
3785533 TAA-ATTT
1 TAATATTT
3785540 AAATATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (22 bp):
TAATATTTTATTTGATTTGAAT
Found at i:3787713 original size:27 final size:28
Alignment explanation
Indices: 3787670--3787723 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
3787660 TGTGCATAAT
*
3787670 TCAATTTTAATCAAATTAATTGATCGAA
1 TCAATTTTAATCAAATTAATTAATCGAA
3787698 TCAA-TTTAATTC-AATTAATTAATCGA
1 TCAATTTTAA-TCAAATTAATTAATCGA
3787724 TTATCGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (28 bp):
TCAATTTTAATCAAATTAATTAATCGAA
Found at i:3794195 original size:2 final size:2
Alignment explanation
Indices: 3794188--3794240 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3794178 TTTCCAAATT
3794188 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3794230 TC TC TC TC TC T
1 TC TC TC TC TC T
3794241 TTGCTTTCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3796204 original size:22 final size:22
Alignment explanation
Indices: 3796168--3796224 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
3796158 GGGGTTATCA
3796168 GAATTTT-GGGTTTTA-AAGTTTT
1 GAATTTTAGGG-TTTAGAA-TTTT
3796190 GAATTTTAGGGTTTAGAATTTT
1 GAATTTTAGGGTTTAGAATTTT
* *
3796212 GGATTTTAAGGTT
1 GAATTTTAGGGTT
3796225 AATGTTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (22 bp):
GAATTTTAGGGTTTAGAATTTT
Found at i:3797949 original size:15 final size:14
Alignment explanation
Indices: 3797931--3797963 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3797921 CAGTCTGTTA
3797931 TTTTTTT-TTTTGT
1 TTTTTTTGTTTTGT
*
3797944 TGTTTTTGTTTTGT
1 TTTTTTTGTTTTGT
3797958 TTTTTT
1 TTTTTT
3797964 AAATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTTTGTTTTGT
Found at i:3797955 original size:14 final size:13
Alignment explanation
Indices: 3797931--3797963 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3797921 CAGTCTGTTA
3797931 TTTTTTT-TTTTG
1 TTTTTTTGTTTTG
3797943 TTGTTTTTGTTTTG
1 TT-TTTTTGTTTTG
3797957 TTTTTTT
1 TTTTTTT
3797964 AAATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:3798267 original size:37 final size:37
Alignment explanation
Indices: 3798226--3798325 Score: 121
Period size: 37 Copynumber: 2.7 Consensus size: 37
3798216 GCGAGTCGAG
3798226 AAGTAAGAAAACGATCAGGACAACACCACAAGTCAAA
1 AAGTAAGAAAACGATCAGGACAACACCACAAGTCAAA
* * * * *
3798263 AAGTAA-AGAATCGATCGGGACAACACCGCGAGTCGAA
1 AAGTAAGA-AAACGATCAGGACAACACCACAAGTCAAA
* *
3798300 AAGTAAGAAAATGACCAGGACAACAC
1 AAGTAAGAAAACGATCAGGACAACAC
3798326 GTCAGTGGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 1 0.02
37 50 0.96
38 1 0.02
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (37 bp):
AAGTAAGAAAACGATCAGGACAACACCACAAGTCAAA
Found at i:3798308 original size:74 final size:73
Alignment explanation
Indices: 3798215--3798360 Score: 204
Period size: 74 Copynumber: 2.0 Consensus size: 73
3798205 AAGACGATAT
* *
3798215 CGCGAGTCGAGAAGTAAGAAAACGATCAGGACAACACCACAAGT-CAAAAAGTAAAGAATCGATC
1 CGCGAGTCGAAAAGTAAGAAAACGACCAGGACAACACCAC-AGTGCAAAAA-TAAAGAATCGATC
3798279 GGGACAACAC
64 GGGACAACAC
* ** * *
3798289 CGCGAGTCGAAAAGTAAGAAAATGACCAGGACAACACGTCAGTGGAAAAATAAAGAATTGATCGG
1 CGCGAGTCGAAAAGTAAGAAAACGACCAGGACAACACCACAGTGCAAAAATAAAGAATCGATCGG
3798354 GACAACA
66 GACAACA
3798361 TCACGAATCA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
73 24 0.38
74 40 0.62
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (73 bp):
CGCGAGTCGAAAAGTAAGAAAACGACCAGGACAACACCACAGTGCAAAAATAAAGAATCGATCGG
GACAACAC
Found at i:3798357 original size:36 final size:37
Alignment explanation
Indices: 3798238--3798360 Score: 110
Period size: 37 Copynumber: 3.4 Consensus size: 37
3798228 GTAAGAAAAC
* * * *
3798238 GATCAGGACAACACCACAAGTC-AAAAAGTAAAGAATC
1 GATCGGGACAACACCGCGAGTCGAAAAA-TAAAGAATT
* *
3798275 GATCGGGACAACACCGCGAGTCGAAAAGT-AAGAAAAT
1 GATCGGGACAACACCGCGAGTCGAAAAATAAAG-AATT
* * *
3798312 GACCAGGACAACA-CGTC-AGTGGAAAAATAAAGAATT
1 GATCGGGACAACACCG-CGAGTCGAAAAATAAAGAATT
3798348 GATCGGGACAACA
1 GATCGGGACAACA
3798361 TCACGAATCA
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
36 28 0.41
37 37 0.54
38 4 0.06
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (37 bp):
GATCGGGACAACACCGCGAGTCGAAAAATAAAGAATT
Found at i:3798401 original size:22 final size:22
Alignment explanation
Indices: 3798373--3798415 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3798363 ACGAATCAAA
* *
3798373 ATTATGTTCGGAGGTTTTAAAG
1 ATTATGTCCGGAGGTCTTAAAG
3798395 ATTATGTCCGGAGGTCTTAAA
1 ATTATGTCCGGAGGTCTTAAA
3798416 AATCATGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (22 bp):
ATTATGTCCGGAGGTCTTAAAG
Found at i:3798542 original size:22 final size:22
Alignment explanation
Indices: 3798502--3798572 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
3798492 TTGTGAATCG
* *
3798502 AAATGATGCCCAGAAGTCTTAA
1 AAATTATGCCCAGAGGTCTTAA
* *
3798524 AGATTATGCCTAGAGGTCTTAA
1 AAATTATGCCCAGAGGTCTTAA
* *
3798546 AAATTATACCCGGAGGTCTTACA
1 AAATTATGCCCAGAGGTCTTA-A
3798569 AAAT
1 AAAT
3798573 CGATTGGTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 35 0.88
23 5 0.12
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (22 bp):
AAATTATGCCCAGAGGTCTTAA
Found at i:3798631 original size:131 final size:131
Alignment explanation
Indices: 3798389--3798653 Score: 286
Period size: 131 Copynumber: 2.0 Consensus size: 131
3798379 TTCGGAGGTT
* * *
3798389 TTAAAGATTATGTCCGGAGGTCTTAAAAATCATGCCCAGAGGTATTACAGAATCGACTGGGATAA
1 TTAAAGATTATGTCCAGAGGTCTTAAAAATCATACCCAGAGGTATTACAAAATCGACTGGGATAA
* * ** * * *
3798454 TACCGTAAGTAGAAATTAAAGAATCAATCAGGATAACATTGTGAATCGAAATGATGCCCAGAAGT
66 CACCGCAAGTAGAAATTAAAGAATCAATCAGGATAACACCGCGAATCAAAATGATACCCAGAAGT
3798519 C
131 C
* * * * *
3798520 TTAAAGATTATG-CCTAGAGGTCTTAAAAATTATACCCGGAGGTCTTACAAAATCGATTGGTATA
1 TTAAAGATTATGTCC-AGAGGTCTTAAAAATCATACCCAGAGGTATTACAAAATCGACTGGGATA
* * * *
3798584 ACATCGCAAGTCA-AAATTAAA-AAGTCGATC-GATATAACACCGCGAATCAAAATTATACCCAG
65 ACACCGCAAGT-AGAAATTAAAGAA-TCAATCAG-GATAACACCGCGAATCAAAATGATACCCAG
*
3798646 AGGTC
127 AAGTC
3798651 TTA
1 TTA
3798654 CAGAATCGAC
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
130 5 0.05
131 104 0.95
132 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (131 bp):
TTAAAGATTATGTCCAGAGGTCTTAAAAATCATACCCAGAGGTATTACAAAATCGACTGGGATAA
CACCGCAAGTAGAAATTAAAGAATCAATCAGGATAACACCGCGAATCAAAATGATACCCAGAAGT
C
Found at i:3798691 original size:87 final size:87
Alignment explanation
Indices: 3798545--3798726 Score: 217
Period size: 87 Copynumber: 2.1 Consensus size: 87
3798535 AGAGGTCTTA
* * * *
3798545 AAAATTATACCCGGAGGTCTTACAAAATCGATTGGTATAACATCGCAAGTCAAAATTAAA-AAGT
1 AAAATTATACCCAGAGGTCTTACAAAATCGACTGGGACAACATCGCAAGTCAAAATTAAAGAA-T
*
3798609 CGATCGA-TATAACACCGCGAATC
65 CGAT-GAGGATAACACCGCGAATC
* * *
3798632 AAAATTATACCCAGAGGTCTTACAGAATCGACTGGGACAACATC-CTAGGTCAATATTAAAGAAT
1 AAAATTATACCCAGAGGTCTTACAAAATCGACTGGGACAACATCGC-AAGTCAAAATTAAAGAAT
* * *
3798696 CGATTAGGATAACATCGTGAATC
65 CGATGAGGATAACACCGCGAATC
3798719 AAAATTAT
1 AAAATTAT
3798727 GCTTAGAGGT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
86 2 0.02
87 77 0.95
88 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (87 bp):
AAAATTATACCCAGAGGTCTTACAAAATCGACTGGGACAACATCGCAAGTCAAAATTAAAGAATC
GATGAGGATAACACCGCGAATC
Found at i:3798871 original size:88 final size:88
Alignment explanation
Indices: 3798739--3798993 Score: 305
Period size: 88 Copynumber: 2.9 Consensus size: 88
3798729 TTAGAGGTCC
* * *
3798739 TAAAAATCATGCCCGAAGGTCTTACAGAATCGACTGAGACAACATCGCAAGTTGAAAAGA-AAAT
1 TAAAAATTATGCCCGAAGGTCTTACAGAATCGATTGAGACAACATCGCAAGTTGAAAA-ATAAAG
* *
3798803 AATCAATTGGGATAATATCGCAAA
65 AATCAATCGAGATAATATCGCAAA
* * *
3798827 TAAAAATTATGCCCGAAGGTCTTACAGAATCGATTGGGATAACATTGCAAGTTGAAAAATAAAGA
1 TAAAAATTATGCCCGAAGGTCTTACAGAATCGATTGAGACAACATCGCAAGTTGAAAAATAAAGA
* *
3798892 ATCAATCGAGATAATATTGCGAA
66 ATCAATCGAGATAATATCGCAAA
** * * * * * **
3798915 TCGAAATTATGCCTGAAGGTCTTACAGAATCGATCGTGACAATAACGCAAGTCAAAAAATAAAGA
1 TAAAAATTATGCCCGAAGGTCTTACAGAATCGATTGAGACAACATCGCAAGTTGAAAAATAAAGA
* *
3798980 ATCGATTGAGATAA
66 ATCAATCGAGATAA
3798994 CACCGTGAAT
Statistics
Matches: 143, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
87 1 0.01
88 142 0.99
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.23
Consensus pattern (88 bp):
TAAAAATTATGCCCGAAGGTCTTACAGAATCGATTGAGACAACATCGCAAGTTGAAAAATAAAGA
ATCAATCGAGATAATATCGCAAA
Found at i:3799004 original size:88 final size:88
Alignment explanation
Indices: 3798741--3799026 Score: 299
Period size: 88 Copynumber: 3.2 Consensus size: 88
3798731 AGAGGTCCTA
* * * *
3798741 AAAATCATGCCCGAAGGTCTTACAGAATCGA-CTGAGACAACATCGCAAGTTGAAAAGA-AAATA
1 AAAATTATGCCCGAAGGTCTTACAGAATCGATC-GAGACAACATCGCAAG-TCAAAAAATAAAGA
* * *
3798804 ATCAATTGGGATAATATCGCAAATA
64 ATCAATTGAGATAATATCGCGAATC
* * * * **
3798829 AAAATTATGCCCGAAGGTCTTACAGAATCGATTGGGATAACATTGCAAGTTGAAAAATAAAGAAT
1 AAAATTATGCCCGAAGGTCTTACAGAATCGATCGAGACAACATCGCAAGTCAAAAAATAAAGAAT
* *
3798894 CAATCGAGATAATATTGCGAATC
66 CAATTGAGATAATATCGCGAATC
* * * * *
3798917 GAAATTATGCCTGAAGGTCTTACAGAATCGATCGTGACAATAACGCAAGTCAAAAAATAAAGAAT
1 AAAATTATGCCCGAAGGTCTTACAGAATCGATCGAGACAACATCGCAAGTCAAAAAATAAAGAAT
* * * *
3798982 CGATTGAGATAACACCGTGAATC
66 CAATTGAGATAATATCGCGAATC
*
3799005 AAAATTATGTCC-AGAGGTCTTA
1 AAAATTATGCCCGA-AGGTCTTA
3799027 AAGATTATGC
Statistics
Matches: 162, Mismatches: 33, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
87 6 0.04
88 156 0.96
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (88 bp):
AAAATTATGCCCGAAGGTCTTACAGAATCGATCGAGACAACATCGCAAGTCAAAAAATAAAGAAT
CAATTGAGATAATATCGCGAATC
Found at i:3799058 original size:22 final size:21
Alignment explanation
Indices: 3799005--3799058 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
3798995 ACCGTGAATC
*
3799005 AAAATTATGTCCAGAGGTCTT
1 AAAATTATGCCCAGAGGTCTT
3799026 AAAGATTATGCCCAGAGGTCTT
1 AAA-ATTATGCCCAGAGGTCTT
*
3799048 AGAAATCATGC
1 A-AAATTATGC
3799059 TCGAAGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAATTATGCCCAGAGGTCTT
Found at i:3799765 original size:15 final size:15
Alignment explanation
Indices: 3799745--3799774 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3799735 TGTCTTTCTT
*
3799745 GTGATGCAGATGCAA
1 GTGATGCAAATGCAA
3799760 GTGATGCAAATGCAA
1 GTGATGCAAATGCAA
3799775 ATGTCCCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (15 bp):
GTGATGCAAATGCAA
Found at i:3799767 original size:41 final size:41
Alignment explanation
Indices: 3799713--3799809 Score: 133
Period size: 41 Copynumber: 2.4 Consensus size: 41
3799703 ACAAGTGTAA
* * * *
3799713 ATGCAAGTGATGCAAATGCGAATGT-CTTTCTTGTGATGCAG
1 ATGCAAGTGATGCAAATGCAAATGTCCCTT-TAGTGATGCAC
3799754 ATGCAAGTGATGCAAATGCAAATGTCCCTTTAGTGATGCAC
1 ATGCAAGTGATGCAAATGCAAATGTCCCTTTAGTGATGCAC
*
3799795 AGGCAAGTGATGCAA
1 ATGCAAGTGATGCAA
3799810 CTACGAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 47 0.94
42 3 0.06
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (41 bp):
ATGCAAGTGATGCAAATGCAAATGTCCCTTTAGTGATGCAC
Found at i:3800757 original size:5 final size:5
Alignment explanation
Indices: 3800739--3800767 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3800729 CATTCTCTGG
3800739 CTTTT CTTTT -TTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3800768 TTGTTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
CTTTT
Found at i:3800758 original size:14 final size:15
Alignment explanation
Indices: 3800739--3800767 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3800729 CATTCTCTGG
3800739 CTTTTCTTTT-TTTT
1 CTTTTCTTTTCTTTT
3800753 CTTTTCTTTTCTTTT
1 CTTTTCTTTTCTTTT
3800768 TTGTTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTCTTTTCTTTT
Found at i:3804762 original size:17 final size:17
Alignment explanation
Indices: 3804740--3804773 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3804730 AACTTTGGGT
3804740 CGAAGATTAGGTTGAAA
1 CGAAGATTAGGTTGAAA
*
3804757 CGAAGATTGGGTTGAAA
1 CGAAGATTAGGTTGAAA
3804774 AAATAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.24
Consensus pattern (17 bp):
CGAAGATTAGGTTGAAA
Found at i:3805923 original size:38 final size:37
Alignment explanation
Indices: 3805881--3805952 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
3805871 ATTAATACGA
3805881 ATGGGATGAAATGC-TCATATTATCTTATTATGATGCAC
1 ATGGGATGAAATGCAT-ATATTAT-TTATTATGATGCAC
* *
3805919 ATGGGATGAGATGCATGTATTATTTATTATGATG
1 ATGGGATGAAATGCATATATTATTTATTATGATG
3805953 TATAGAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 11 0.35
38 19 0.61
39 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (37 bp):
ATGGGATGAAATGCATATATTATTTATTATGATGCAC
Found at i:3806104 original size:20 final size:20
Alignment explanation
Indices: 3806065--3806104 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3806055 AAACAAAGAA
3806065 TTTAAGAAAATCTTTATTTT
1 TTTAAGAAAATCTTTATTTT
3806085 TTTAA-AAAATCTTT-TTTT
1 TTTAAGAAAATCTTTATTTT
3806103 TT
1 TT
3806105 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 9 0.45
20 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTAAGAAAATCTTTATTTT
Found at i:3807962 original size:22 final size:22
Alignment explanation
Indices: 3807944--3808013 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
3807934 GGTTTTAAAG
* *
3807944 TTTTGGATTTTATGGTTTAGGA
1 TTTTGGATTTTAAGGTTTAAGA
3807966 TTTTGGATTTTAAGG-TTAAG-
1 TTTTGGATTTTAAGGTTTAAGA
* * * *
3807986 GTTTCGAGTTTTTAGGTTTAAGC
1 TTTTGGA-TTTTAAGGTTTAAGA
3808009 TTTTG
1 TTTTG
3808014 CTCTTAGAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 5 0.13
21 11 0.29
22 19 0.50
23 3 0.08
ACGTcount: A:0.19, C:0.03, G:0.26, T:0.53
Consensus pattern (22 bp):
TTTTGGATTTTAAGGTTTAAGA
Found at i:3808088 original size:16 final size:16
Alignment explanation
Indices: 3808066--3808103 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3808056 TGGGGTTTGG
*
3808066 ATTTTAGGGTTTTAAA
1 ATTTTAGGGTCTTAAA
*
3808082 TTTTTAGGGTCTTAAA
1 ATTTTAGGGTCTTAAA
3808098 ATTTTA
1 ATTTTA
3808104 CGTTTTGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (16 bp):
ATTTTAGGGTCTTAAA
Found at i:3808409 original size:13 final size:13
Alignment explanation
Indices: 3808386--3808419 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3808376 TTTGTTATTC
3808386 TATTA-TTATTAT
1 TATTATTTATTAT
3808398 TATTATTTATTAT
1 TATTATTTATTAT
*
3808411 TATTTTTTA
1 TATTATTTA
3808420 AAGCATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:3810067 original size:21 final size:20
Alignment explanation
Indices: 3810034--3810073 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3810024 TATTTTCAAA
*
3810034 ATAATATTAAATTCTAATTAT
1 ATAAAATTAAATTC-AATTAT
*
3810055 ATAAAATTTAATTCAATTA
1 ATAAAATTAAATTCAATTA
3810074 ATTAATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAATTAAATTCAATTAT
Found at i:3810651 original size:2 final size:2
Alignment explanation
Indices: 3810644--3810672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3810634 CTATTTCCCC
3810644 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3810673 AAGTTCTGTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3822554 original size:42 final size:42
Alignment explanation
Indices: 3822495--3822579 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
3822485 TTAACTTATG
*
3822495 ATTGAAATTACCAAGCTTTGCAATCAAAATTCAAATATAAAA
1 ATTGAAATTACCAAGCTTTCCAATCAAAATTCAAATATAAAA
3822537 ATTGAAATTACCAAGCTTTCCAATCAAAATTCAAATATAAAA
1 ATTGAAATTACCAAGCTTTCCAATCAAAATTCAAATATAAAA
3822579 A
1 A
3822580 AGAAACCTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (42 bp):
ATTGAAATTACCAAGCTTTCCAATCAAAATTCAAATATAAAA
Found at i:3833828 original size:63 final size:62
Alignment explanation
Indices: 3833706--3833829 Score: 155
Period size: 62 Copynumber: 2.0 Consensus size: 62
3833696 AAATGATCAA
* * *
3833706 TTTATATTTTAGTAAAAGGATTATTTAAGATGTTTGTATATGAAAACACCTTAAATAATTTT
1 TTTATATTTTAGTAAAAGGATTATTTAAGACGCTTCTATATGAAAACACCTTAAATAATTTT
*
3833768 TTTATATTTTTA-TAAATGGATTATTTAAGACGCTTCTCA-ATGAAAA-ACGTCTTAAATAATTT
1 TTTATA-TTTTAGTAAAAGGATTATTTAAGACGCTTCT-ATATGAAAACAC--CTTAAATAATTT
3833830 CATTTAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
61 2 0.04
62 34 0.63
63 18 0.33
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (62 bp):
TTTATATTTTAGTAAAAGGATTATTTAAGACGCTTCTATATGAAAACACCTTAAATAATTTT
Found at i:3834046 original size:65 final size:66
Alignment explanation
Indices: 3833969--3834091 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 66
3833959 TCAATATAAC
* * * *
3833969 AAGATTTTTTAAAGCATTTTTTAACGAAAAACACCTTAAATAATCTTCA-ATAAAAAAATTAGAA
1 AAGATTATTTAAAACATTTTTGAACGAAAAACACCTTAAATAATCTCCATATAAAAAAATTAGAA
3834033 T
66 T
* *** **
3834034 AAGATTATTTAAAATATTTTTGGTTGAAAAACGGCTTAAATAATCTCCATATAAAAAA
1 AAGATTATTTAAAACATTTTTGAACGAAAAACACCTTAAATAATCTCCATATAAAAAA
3834092 TAGCTCATGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
65 39 0.83
66 8 0.17
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (66 bp):
AAGATTATTTAAAACATTTTTGAACGAAAAACACCTTAAATAATCTCCATATAAAAAAATTAGAA
T
Found at i:3834741 original size:26 final size:26
Alignment explanation
Indices: 3834712--3834764 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3834702 ATTAATATAC
3834712 ATAAAATTTTCTAAATCAAATAAGTA
1 ATAAAATTTTCTAAATCAAATAAGTA
3834738 ATAAAATTTTCTAAATCAAATAAGTA
1 ATAAAATTTTCTAAATCAAATAAGTA
3834764 A
1 A
3834765 ATTTAAACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.34
Consensus pattern (26 bp):
ATAAAATTTTCTAAATCAAATAAGTA
Found at i:3835614 original size:58 final size:58
Alignment explanation
Indices: 3835552--3835668 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
3835542 ACAATGCAGT
* *
3835552 TAAAATGATGATTCTCAAAAATAATGAAAGAGAAAATTCATATGCAACAACAGAACCG
1 TAAAATGATAATTCTCAAAAACAATGAAAGAGAAAATTCATATGCAACAACAGAACCG
* *
3835610 TAAAATGATAATTCTCATAAACAATGAAAGAGAAAATTCATATGCAACAGCAGAACCG
1 TAAAATGATAATTCTCAAAAACAATGAAAGAGAAAATTCATATGCAACAACAGAACCG
3835668 T
1 T
3835669 GTGTGTGTGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (58 bp):
TAAAATGATAATTCTCAAAAACAATGAAAGAGAAAATTCATATGCAACAACAGAACCG
Found at i:3840487 original size:10 final size:10
Alignment explanation
Indices: 3840472--3840501 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3840462 ATCAAGCTTT
3840472 TATATTTTAA
1 TATATTTTAA
3840482 TATATTTTAA
1 TATATTTTAA
3840492 T-TATTTTAA
1 TATATTTTAA
3840501 T
1 T
3840502 TGATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:3845244 original size:16 final size:16
Alignment explanation
Indices: 3845225--3845258 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
3845215 TCAATATTTA
3845225 TAAATT-TATTTATCTT
1 TAAATTATATTT-TCTT
3845241 TAAATTATATTTTCTT
1 TAAATTATATTTTCTT
3845257 TA
1 TA
3845259 TAAAATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAATTATATTTTCTT
Found at i:3846442 original size:17 final size:14
Alignment explanation
Indices: 3846400--3846447 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 14
3846390 ATAATAATTG
3846400 ATTAAAAATAAATA
1 ATTAAAAATAAATA
3846414 ATTAAAATATAACACTA
1 ATTAAAA-ATAA-A-TA
*
3846431 ATTATAAAATAATTA
1 ATTA-AAAATAAATA
3846446 AT
1 AT
3846448 CTATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 7 0.24
15 8 0.28
16 1 0.03
17 10 0.34
18 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAAAATAAATA
Found at i:3855150 original size:21 final size:21
Alignment explanation
Indices: 3855124--3855163 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3855114 AATGAAAAAT
*
3855124 CCACAGAGTTTTCAGATGAAA
1 CCACAGAATTTTCAGATGAAA
*
3855145 CCACAGAATTTTGAGATGA
1 CCACAGAATTTTCAGATGA
3855164 GAGGACATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (21 bp):
CCACAGAATTTTCAGATGAAA
Found at i:3855781 original size:2 final size:2
Alignment explanation
Indices: 3855774--3855817 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3855764 GTACTCTTAT
3855774 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3855816 GA
1 GA
3855818 ATGCCTTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3864063 original size:18 final size:17
Alignment explanation
Indices: 3864040--3864085 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
3864030 GTTTTGAGAA
3864040 ATAAATTTTCAAAATATC
1 ATAAATTTTCAAAA-ATC
*
3864058 ATAAATTTTTGAAAAATC
1 ATAAA-TTTTCAAAAATC
3864076 ATATAATTTT
1 ATA-AATTTT
3864086 TTAAAATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (17 bp):
ATAAATTTTCAAAAATC
Found at i:3864072 original size:19 final size:19
Alignment explanation
Indices: 3864040--3864092 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3864030 GTTTTGAGAA
3864040 ATAAA-TTTTCAAAATATC
1 ATAAATTTTTCAAAATATC
*
3864058 ATAAATTTTTGAAAA-ATC
1 ATAAATTTTTCAAAATATC
*
3864076 ATATAATTTTTTAAAAT
1 ATA-AATTTTTCAAAAT
3864093 GAATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAAATTTTTCAAAATATC
Found at i:3864209 original size:15 final size:15
Alignment explanation
Indices: 3864189--3864218 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3864179 AATTTTAAAG
*
3864189 ATTTTTCAAAATTTT
1 ATTTTTAAAAATTTT
3864204 ATTTTTAAAAATTTT
1 ATTTTTAAAAATTTT
3864219 GAATCATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTAAAAATTTT
Found at i:3865496 original size:16 final size:16
Alignment explanation
Indices: 3865475--3865506 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3865465 TAAGTGATAT
3865475 TTAAATTTTAGATTTA
1 TTAAATTTTAGATTTA
*
3865491 TTAAATTTTATATTTA
1 TTAAATTTTAGATTTA
3865507 AAAAATGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAAATTTTAGATTTA
Found at i:3869968 original size:29 final size:30
Alignment explanation
Indices: 3869931--3870000 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
3869921 ACAAAAAAAA
*
3869931 ATTATAATTTATATATCATATTAAAATTTT
1 ATTAAAATTTATATATCATATTAAAATTTT
* * *
3869961 -TTAAAATTAATATATTATATTAATATTTT
1 ATTAAAATTTATATATCATATTAAAATTTT
*
3869990 ATTATAATTTA
1 ATTAAAATTTA
3870001 AAAATAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
ATTAAAATTTATATATCATATTAAAATTTT
Found at i:3871119 original size:14 final size:14
Alignment explanation
Indices: 3871102--3871132 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3871092 ATTAATTTTT
*
3871102 TAAAATATATATTA
1 TAAAATATATATCA
3871116 TAAAATATATATCA
1 TAAAATATATATCA
3871130 TAA
1 TAA
3871133 TCTTAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAAATATATATCA
Found at i:3871486 original size:2 final size:2
Alignment explanation
Indices: 3871475--3871506 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3871465 TCAATGCCCA
3871475 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3871507 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3871511 original size:2 final size:2
Alignment explanation
Indices: 3871506--3871535 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3871496 TCTCTCTCTC
*
3871506 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3871536 GTGACTTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3874126 original size:89 final size:89
Alignment explanation
Indices: 3873975--3874152 Score: 329
Period size: 89 Copynumber: 2.0 Consensus size: 89
3873965 TATATTTCCA
3873975 CCATATGAACTATGTGATGTCTAAGACATTATGATGCCATCACTTACAGTCATCCCAACAAGGAT
1 CCATATGAACTATGTGATGTCTAAGACATTATGATGCCATCACTTACAGTCATCCCAACAAGGAT
3874040 TGGAAAATGAAGGCAATACTAGAG
66 TGGAAAATGAAGGCAATACTAGAG
**
3874064 CCATATGAACTATGTGATGTCTAAGACATTATTTTGCCATCACTTACAGTCATCCCAACAAGGAT
1 CCATATGAACTATGTGATGTCTAAGACATTATGATGCCATCACTTACAGTCATCCCAACAAGGAT
*
3874129 TGGAAAATGATGGCAATACTAGAG
66 TGGAAAATGAAGGCAATACTAGAG
3874153 TCTGCATTCC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (89 bp):
CCATATGAACTATGTGATGTCTAAGACATTATGATGCCATCACTTACAGTCATCCCAACAAGGAT
TGGAAAATGAAGGCAATACTAGAG
Found at i:3880393 original size:24 final size:24
Alignment explanation
Indices: 3880360--3880415 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
3880350 ACCAAAAAAA
* *
3880360 GATGAGGATGGTAGTGATGATGAG
1 GATGAAGATGATAGTGATGATGAG
**
3880384 GATGAAGATGATAGTTCTGATGAG
1 GATGAAGATGATAGTGATGATGAG
3880408 GATGAAGA
1 GATGAAGA
3880416 GTCTGGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.02, G:0.39, T:0.25
Consensus pattern (24 bp):
GATGAAGATGATAGTGATGATGAG
Found at i:3899899 original size:9 final size:9
Alignment explanation
Indices: 3899877--3899912 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
3899867 ATATGATAAT
*
3899877 TTTTATGTA
1 TTTTATATA
3899886 TTTTTATATA
1 -TTTTATATA
3899896 TTTTATATA
1 TTTTATATA
3899905 TTTTATAT
1 TTTTATAT
3899913 TCAACATACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTATATA
Found at i:3902366 original size:22 final size:21
Alignment explanation
Indices: 3902332--3902374 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3902322 TTTTTTGTAA
3902332 AAAAAATCATATTTA-TAAAAT
1 AAAAAATCATA-TTACTAAAAT
*
3902353 AAAAAATTATTATTACTAAAAT
1 AAAAAATCA-TATTACTAAAAT
3902375 TTAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATCATATTACTAAAAT
Found at i:3903036 original size:16 final size:15
Alignment explanation
Indices: 3902977--3903052 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 15
3902967 GAAGTAAATT
*
3902977 TTTATTTATTTTAAA
1 TTTATTTAATTTAAA
*
3902992 TTTAATTTAATTTTATA
1 TTT-ATTTAA-TTTAAA
*
3903009 TTTATTAAATTTAAA
1 TTTATTTAATTTAAA
*
3903024 TTTGATTTGATTTAAAA
1 TTT-ATTTAATTT-AAA
*
3903041 TTTTTTTAATTT
1 TTTATTTAATTT
3903053 TTTATTTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
15 11 0.22
16 24 0.49
17 14 0.29
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTATTTAATTTAAA
Found at i:3903042 original size:66 final size:65
Alignment explanation
Indices: 3902972--3903108 Score: 147
Period size: 66 Copynumber: 2.1 Consensus size: 65
3902962 GGACTGAAGT
*
3902972 AAATTTTTATTTATTTTAAATTTAATTTAATTT-TAT-AT-TTAT-TAAATTTAAATTTGATTTG
1 AAATTTTT-TTAATTTTAAA-TT--TTTAATTTATATGATGTTATATAAA-TTAAATTTGATTTG
3903033 ATTTA
61 ATTTA
** * *
3903038 AAATTTTTTTAATTTTTTATTTTTGATTTGATATGATGTTATATAAATTATATTTGATTTGATTT
1 AAATTTTTTTAATTTTAAATTTTTAATTT-ATATGATGTTATATAAATTAAATTTGATTTGATTT
3903103 A
65 A
3903104 AAATT
1 AAATT
3903109 AATAAAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
62 7 0.11
64 5 0.08
65 10 0.16
66 35 0.57
67 4 0.07
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (65 bp):
AAATTTTTTTAATTTTAAATTTTTAATTTATATGATGTTATATAAATTAAATTTGATTTGATTTA
Found at i:3903052 original size:32 final size:32
Alignment explanation
Indices: 3902971--3903052 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
3902961 AGGACTGAAG
* *
3902971 TAAATTTTTATTTATTTTAAATTTAATTTAATT
1 TAAAATTTT-TTTAATTTAAATTTAATTTAATT
* * * * * *
3903004 TTATATTTATTAAATTTAAATTTGATTTGATT
1 TAAAATTTTTTTAATTTAAATTTAATTTAATT
3903036 TAAAATTTTTTTAATTT
1 TAAAATTTTTTTAATTT
3903053 TTTATTTTTG
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (32 bp):
TAAAATTTTTTTAATTTAAATTTAATTTAATT
Done.