Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 109 of 127
Found at i:20289650 original size:3 final size:3
Alignment explanation
Indices: 20289644--20289830 Score: 104
Period size: 3 Copynumber: 68.0 Consensus size: 3
20289634 AATAAAGAGA
* *
20289644 AAT AAT AAT AAT AAT AAT -AT ACT -TT AAT -AT AAT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
20289688 ACT -TT AAT -AT AAT AAT -AT TAT AAT AAT -AT AAT AAT AGT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
20289731 -GT AAT AAT -AT AAT AGT -GT AAT AAT AAT -AT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
20289773 -AT ACT -AT ATT AAT AAT AAT AAC AAT AAT AA- AAT AAT AAC AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* *
20289816 AAT ACT AAT ATT AAT
1 AAT AAT AAT AAT AAT
20289831 GACAAAAATA
Statistics
Matches: 140, Mismatches: 25, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
2 31 0.22
3 107 0.76
4 2 0.01
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:20289696 original size:40 final size:39
Alignment explanation
Indices: 20289646--20289809 Score: 123
Period size: 40 Copynumber: 4.3 Consensus size: 39
20289636 TAAAGAGAAA
20289646 TAATAATAATAATAAT-ATACTTTAATATAATAATAATAATA
1 TAAT-ATAAT-ATAATAATA-TTTAATATAATAATAATAATA
* * *
20289687 TACTTTAATATAATAATATTATAATA-ATATAATAATAGTA
1 TAATATAATATAATAATATT-TAATATA-ATAATAATAATA
* *
20289727 TAATGTAATA-ATATAATAGTGT-A-ATAATAAT-ATAATA
1 TAATATAATATA-ATAATA-TTTAATATAATAATAATAATA
* *
20289764 TAATATAATATACT-ATA-TTAATAATAATAACAATAATA
1 TAATATAATATAATAATATTTAAT-ATAATAATAATAATA
20289802 -AA-ATAATA
1 TAATATAATA
20289810 ACAACTAATA
Statistics
Matches: 101, Mismatches: 11, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 9 0.09
37 24 0.24
38 13 0.13
39 11 0.11
40 38 0.38
41 4 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (39 bp):
TAATATAATATAATAATATTTAATATAATAATAATAATA
Found at i:20289705 original size:8 final size:8
Alignment explanation
Indices: 20289645--20289810 Score: 99
Period size: 8 Copynumber: 19.9 Consensus size: 8
20289635 ATAAAGAGAA
20289645 ATAATAAT
1 ATAATAAT
20289653 AATAATAAT
1 -ATAATAAT
*
20289662 ATACTTTAAT
1 ATA--ATAAT
20289672 ATAATAAT
1 ATAATAAT
20289680 AATAATATACT
1 -ATAATA-A-T
*
20289691 TTAAT-AT
1 ATAATAAT
*
20289698 AATAATATT
1 -ATAATAAT
20289707 ATAATAAT
1 ATAATAAT
20289715 ATAATAAT
1 ATAATAAT
20289723 AGT-ATAAT
1 A-TAATAAT
*
20289731 GTAATAAT
1 ATAATAAT
*
20289739 ATAATAGT
1 ATAATAAT
*
20289747 GTAATAAT
1 ATAATAAT
20289755 A-ATATAAT
1 ATA-ATAAT
20289763 ATAAT-AT
1 ATAATAAT
*
20289770 A-ATATACT
1 ATA-ATAAT
*
20289778 ATATTAAT
1 ATAATAAT
*
20289786 AATAATAACA
1 -ATAATAA-T
*
20289796 ATAATAAA
1 ATAATAAT
20289804 ATAATAA
1 ATAATAA
20289811 CAACTAATAC
Statistics
Matches: 124, Mismatches: 17, Indels: 33
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.01
7 8 0.06
8 71 0.57
9 31 0.25
10 12 0.10
11 1 0.01
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (8 bp):
ATAATAAT
Found at i:20293628 original size:26 final size:26
Alignment explanation
Indices: 20293599--20293648 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
20293589 AAAGATGATA
20293599 ATTACATTAATCATTGAA-ATATTGTT
1 ATTACATTAATCATT-AATATATTGTT
20293625 ATTACATTAATCATTAATATATTG
1 ATTACATTAATCATTAATATATTG
20293649 ATAAACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (26 bp):
ATTACATTAATCATTAATATATTGTT
Found at i:20298158 original size:24 final size:23
Alignment explanation
Indices: 20298064--20298205 Score: 113
Period size: 24 Copynumber: 6.0 Consensus size: 23
20298054 TAATGTAAAT
* * *
20298064 TTTTTCGTTTATACAATTTCAAA
1 TTTTTCATTTATACAAGTCCAAA
* * * *
20298087 TTTTGTAATTAATACAAGTCGAACT
1 TTTT-TCATTTATACAAGTCCAA-A
* * * * *
20298112 TTTTTTAATTAAACACGTTCAAA
1 TTTTTCATTTATACAAGTCCAAA
*
20298135 TTTTACGATTTATACAAGTCCAAA
1 TTTTTC-ATTTATACAAGTCCAAA
*
20298159 GTTTTTCATATATACAAGTCCAAAA
1 -TTTTTCATTTATACAAGTCC-AAA
20298184 TTTTTCATTTATACAAGTCCAA
1 TTTTTCATTTATACAAGTCCAA
20298206 CTGTTATCAA
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
23 10 0.11
24 68 0.76
25 12 0.13
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (23 bp):
TTTTTCATTTATACAAGTCCAAA
Found at i:20299692 original size:11 final size:11
Alignment explanation
Indices: 20299678--20299703 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20299668 AAAAAGATGG
20299678 AAAACAAATAT
1 AAAACAAATAT
20299689 AAAACAAATAT
1 AAAACAAATAT
20299700 AAAA
1 AAAA
20299704 AATAAATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAACAAATAT
Found at i:20301082 original size:20 final size:18
Alignment explanation
Indices: 20301058--20301102 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
20301048 TTGCAAGGTC
20301058 TTTATTTTTACATGACTAA
1 TTTATTTTTACATGA-TAA
* *
20301077 TATTATATTTGCATGATAA
1 T-TTATTTTTACATGATAA
20301096 TTTATTT
1 TTTATTT
20301103 GCTAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 12 0.55
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTATTTTTACATGATAA
Found at i:20301103 original size:16 final size:16
Alignment explanation
Indices: 20301082--20301135 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
20301072 ACTAATATTA
20301082 TATTTGCATGATAATT
1 TATTTGCATGATAATT
*
20301098 TATTTGC-TAATATATT
1 TATTTGCATGATA-ATT
* *
20301114 TGTTTGCATGATTAATA
1 TATTTGCATGA-TAATT
20301131 TATTT
1 TATTT
20301136 ATTTGTGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 4 0.13
16 16 0.53
17 8 0.27
18 2 0.07
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.54
Consensus pattern (16 bp):
TATTTGCATGATAATT
Found at i:20301190 original size:24 final size:24
Alignment explanation
Indices: 20301110--20301265 Score: 110
Period size: 24 Copynumber: 6.6 Consensus size: 24
20301100 TTTGCTAATA
* *
20301110 TATTTGTTTGCATGATTAATATATT
1 TATTTGTATG-ATTATTAATATATT
*
20301135 TATTTGTGTGATTTATT-A-ATA--
1 TATTTGTATGA-TTATTAATATATT
* *
20301156 TGTTTGCATGATTATTAATATATT
1 TATTTGTATGATTATTAATATATT
*
20301180 TATTTGTATGATTA-T-ATTTAATT
1 TATTTGTATGATTATTAATAT-ATT
** *
20301203 TGA-TTACATGAGTATTAATATATT
1 T-ATTTGTATGATTATTAATATATT
* * *
20301227 TAATTGTTTGATTAATAATATATT
1 TATTTGTATGATTATTAATATATT
*
20301251 TATTTGCATGATTAT
1 TATTTGTATGATTAT
20301266 ATATTTAATT
Statistics
Matches: 100, Mismatches: 21, Indels: 21
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.05
21 9 0.09
22 6 0.06
23 17 0.17
24 47 0.47
25 16 0.16
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (24 bp):
TATTTGTATGATTATTAATATATT
Found at i:20301219 original size:47 final size:46
Alignment explanation
Indices: 20301124--20301247 Score: 155
Period size: 47 Copynumber: 2.7 Consensus size: 46
20301114 TGTTTGCATG
* * * *
20301124 ATTAATATATTTATTTGTGTGATT-TATTAATATGTTTGCATGATT
1 ATTAATATATTTATTTGTATGATTATATTAATATGATTACATGAGT
*
20301169 ATTAATATATTTATTTGTATGATTATATTTAATTTGATTACATGAGT
1 ATTAATATATTTATTTGTATGATTATA-TTAATATGATTACATGAGT
* *
20301216 ATTAATATATTTAATTGTTTGATTA-A-TAATAT
1 ATTAATATATTTATTTGTATGATTATATTAATAT
20301248 ATTTATTTGC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 5 0.07
45 23 0.33
46 3 0.04
47 38 0.55
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (46 bp):
ATTAATATATTTATTTGTATGATTATATTAATATGATTACATGAGT
Found at i:20301274 original size:32 final size:32
Alignment explanation
Indices: 20301238--20301349 Score: 107
Period size: 32 Copynumber: 3.8 Consensus size: 32
20301228 AATTGTTTGA
*
20301238 TTAATAATATATTTATTTGCATGATTATATAT
1 TTAATAACATATTTATTTGCATGATTATATAT
* * *
20301270 TTAATTACATATTTATTTGCATAACT-TATA-
1 TTAATAACATATTTATTTGCATGATTATATAT
*
20301300 -T-AT----T-TTTATTTGCACGATTATATAT
1 TTAATAACATATTTATTTGCATGATTATATAT
*
20301325 TTAATAACATGTTTATTTGCATGAT
1 TTAATAACATATTTATTTGCATGAT
20301350 ATACATTGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
23 12 0.19
24 5 0.08
26 1 0.02
27 2 0.03
28 2 0.03
29 1 0.02
31 5 0.08
32 35 0.56
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (32 bp):
TTAATAACATATTTATTTGCATGATTATATAT
Found at i:20301323 original size:22 final size:23
Alignment explanation
Indices: 20301281--20301326 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20301271 TAATTACATA
*
20301281 TTTATTTGCATAACTTATATATT
1 TTTATTTGCACAACTTATATATT
*
20301304 TTTATTTGCACGA-TTATATATT
1 TTTATTTGCACAACTTATATATT
20301326 T
1 T
20301327 AATAACATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.57
Consensus pattern (23 bp):
TTTATTTGCACAACTTATATATT
Found at i:20301497 original size:24 final size:25
Alignment explanation
Indices: 20301442--20301497 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
20301432 ATTTATCTGT
*
20301442 TATTAT-TATTATTGCATGATATGA
1 TATTATATATTATTGCATGATATAA
*
20301466 TATTATATGTTATTGCATGAT-TAA
1 TATTATATATTATTGCATGATATAA
20301490 TATTATAT
1 TATTATAT
20301498 TTGAATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (25 bp):
TATTATATATTATTGCATGATATAA
Found at i:20302426 original size:12 final size:13
Alignment explanation
Indices: 20302404--20302436 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
20302394 TTTAAAAAAA
20302404 ATTATTTTATTTAT
1 ATTA-TTTATTTAT
20302418 -TTATTTATTTAT
1 ATTATTTATTTAT
20302430 ATTATTT
1 ATTATTT
20302437 TCCAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
ATTATTTATTTAT
Found at i:20302510 original size:9 final size:9
Alignment explanation
Indices: 20302496--20302570 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 9
20302486 ACTACTCAAT
20302496 AAAAATAAA
1 AAAAATAAA
*
20302505 AAAAATCAA
1 AAAAATAAA
*
20302514 TAAAATAAA
1 AAAAATAAA
* **
20302523 ATAAATACT
1 AAAAATAAA
*
20302532 TAAAAT--A
1 AAAAATAAA
*
20302539 TAAAATAAA
1 AAAAATAAA
20302548 TAAAAATAAA
1 -AAAAATAAA
20302558 ATAAAATAAA
1 A-AAAATAAA
20302568 AAA
1 AAA
20302571 GGAACATTTT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
7 6 0.12
9 28 0.55
10 17 0.33
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATAAA
Found at i:20302520 original size:5 final size:5
Alignment explanation
Indices: 20302497--20302568 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
20302487 CTACTCAATA
*
20302497 AAAAT AAAA- AAAAT -CAAT AAAAT AAAAT AAATACTT AAAAT ATAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-A--T AAAAT A-AAAT
20302543 ATAAAT AAAAAT AAAAT AAAAT AAAA
1 A-AAAT -AAAAT AAAAT AAAAT AAAA
20302569 AAGGAACATT
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 7 0.12
5 36 0.63
6 8 0.14
7 2 0.04
8 4 0.07
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:20302561 original size:20 final size:20
Alignment explanation
Indices: 20302493--20302567 Score: 74
Period size: 18 Copynumber: 4.1 Consensus size: 20
20302483 TAAACTACTC
*
20302493 AATAAAAATAAAA-AAAATC
1 AATAAAAATAAAATAAAATA
20302512 AAT-AAAATAAAAT-AAAT-
1 AATAAAAATAAAATAAAATA
* *
20302529 ACTTAAAAT---ATAAAATA
1 AATAAAAATAAAATAAAATA
20302546 AATAAAAATAAAATAAAATA
1 AATAAAAATAAAATAAAATA
20302566 AA
1 AA
20302568 AAAGGAACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.04
16 4 0.09
17 9 0.20
18 18 0.39
19 3 0.07
20 10 0.22
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
AATAAAAATAAAATAAAATA
Found at i:20305637 original size:18 final size:18
Alignment explanation
Indices: 20305614--20305652 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20305604 AAAAAACTAC
20305614 ATTTTTAAGTATTATAT-A
1 ATTTTTAA-TATTATATCA
*
20305632 ATTTTTTATATTATATCA
1 ATTTTTAATATTATATCA
20305650 ATT
1 ATT
20305653 ACGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTTTAATATTATATCA
Found at i:20314969 original size:3 final size:3
Alignment explanation
Indices: 20314961--20314991 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20314951 TCACTCACTC
20314961 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20314992 TCAATGAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20315344 original size:15 final size:15
Alignment explanation
Indices: 20315301--20315346 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
20315291 GAACTCAAAA
20315301 TTAATATTTACCAA-T
1 TTAATATTTA-CAATT
* *
20315316 GTAAAATTTA-AATT
1 TTAATATTTACAATT
20315330 TTAATATTTACAATT
1 TTAATATTTACAATT
20315345 TT
1 TT
20315347 TTTTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 14 0.56
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (15 bp):
TTAATATTTACAATT
Found at i:20320035 original size:70 final size:70
Alignment explanation
Indices: 20319922--20320054 Score: 241
Period size: 70 Copynumber: 1.9 Consensus size: 70
20319912 CGTGCAGCCA
20319922 ACTTTGCGTGATTCTGGGTATAAAAGGAGTTCTGAAATGAAGAAAAACGGCATCGTTCTTTTTAA
1 ACTTTGCGTGATTCTGGGTATAAAAGGAGTTCTGAAATGAAGAAAAACGGCATCGTTCTTTTTAA
20319987 AGTTC
66 AGTTC
*
20319992 ACTTTGCGTGATTCTGTGTATAAAA-GAGGTTCTGAAATGAAGAAAAACGGCATCGTTCTTTTT
1 ACTTTGCGTGATTCTGGGTATAAAAGGA-GTTCTGAAATGAAGAAAAACGGCATCGTTCTTTTT
20320055 TAATGCTAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
69 2 0.03
70 59 0.97
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (70 bp):
ACTTTGCGTGATTCTGGGTATAAAAGGAGTTCTGAAATGAAGAAAAACGGCATCGTTCTTTTTAA
AGTTC
Found at i:20320599 original size:15 final size:15
Alignment explanation
Indices: 20320576--20320616 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20320566 ATTTTACTTT
20320576 ATTTAAAATATGAAA
1 ATTTAAAATATGAAA
* * *
20320591 ATTTTAAATTTTAAA
1 ATTTAAAATATGAAA
20320606 ATTTAAAATAT
1 ATTTAAAATAT
20320617 AATTTAATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
ATTTAAAATATGAAA
Found at i:20326855 original size:13 final size:13
Alignment explanation
Indices: 20326837--20326875 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20326827 TTTGATTTAG
20326837 ATTAAATTTAAAT
1 ATTAAATTTAAAT
** *
20326850 ATTAAAAATATAT
1 ATTAAATTTAAAT
20326863 ATTAAATTTAAAT
1 ATTAAATTTAAAT
20326876 TGAATTTTAG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTAAATTTAAAT
Found at i:20326966 original size:19 final size:19
Alignment explanation
Indices: 20326926--20326964 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
20326916 ATTGAATTAA
20326926 TTATATATATTTTAAATTT
1 TTATATATATTTTAAATTT
20326945 TTATATAT-TTTTAAATTT
1 TTATATATATTTTAAATTT
20326963 TT
1 TT
20326965 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATATATTTTAAATTT
Found at i:20327000 original size:10 final size:10
Alignment explanation
Indices: 20326985--20327014 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20326975 ATAATAATTT
20326985 TATATTAAAA
1 TATATTAAAA
20326995 TATATT-AAA
1 TATATTAAAA
20327004 TATATTAAAA
1 TATATTAAAA
20327014 T
1 T
20327015 TTTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATTAAAA
Found at i:20327439 original size:20 final size:22
Alignment explanation
Indices: 20327402--20327443 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
20327392 ATATATTATT
20327402 TTAAAATAAAATTTTTAATATA
1 TTAAAATAAAATTTTTAATATA
20327424 TTAAAAT-AAA-TTTTAATATA
1 TTAAAATAAAATTTTTAATATA
20327444 AAATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAAATAAAATTTTTAATATA
Found at i:20329043 original size:18 final size:18
Alignment explanation
Indices: 20329020--20329070 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
20329010 TCATATAAAT
20329020 TATTATATTTATATTATA
1 TATTATATTTATATTATA
* ** *
20329038 TTTTATATAAAAATTATA
1 TATTATATTTATATTATA
20329056 TATTATCATTTATAT
1 TATTAT-ATTTATAT
20329071 CAATGTAAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATTTATATTATA
Found at i:20329061 original size:25 final size:28
Alignment explanation
Indices: 20329029--20329098 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 28
20329019 TTATTATATT
20329029 TATATTAT-ATTTTAT-A-TAAAAATTA
1 TATATTATAATTTTATAAGTAAAAATTA
*
20329054 TATATTATCATTTATATCAATGTAAAAATTA
1 TATATTATAATTT-TAT-AA-GTAAAAATTA
*
20329085 TAAATTATAATTTT
1 TATATTATAATTTT
20329099 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 8 0.22
26 4 0.11
27 3 0.08
29 1 0.03
30 1 0.03
31 20 0.54
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (28 bp):
TATATTATAATTTTATAAGTAAAAATTA
Found at i:20329163 original size:15 final size:16
Alignment explanation
Indices: 20329145--20329177 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20329135 TTTTAAATAA
*
20329145 TTTATTTTTA-TATTT
1 TTTATTTATATTATTT
20329160 TTTATTTATATTATTT
1 TTTATTTATATTATTT
20329176 TT
1 TT
20329178 ATATCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTATATTATTT
Found at i:20330044 original size:24 final size:24
Alignment explanation
Indices: 20330012--20330062 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
20330002 ACGTTTACAT
*
20330012 TATTATCACATGTAATTATGTATA
1 TATTATCACACGTAATTATGTATA
* *
20330036 TATTGTCACGCGTAATTATGTATA
1 TATTATCACACGTAATTATGTATA
20330060 TAT
1 TAT
20330063 GTTAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (24 bp):
TATTATCACACGTAATTATGTATA
Found at i:20331000 original size:26 final size:25
Alignment explanation
Indices: 20330943--20331001 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
20330933 TGCTTGATAT
*
20330943 AAAAGATTATGATAGAATATAATAA
1 AAAATATTATGATAGAATATAATAA
*
20330968 AATAATATTATGATTAGAAT-TAAATTA
1 AA-AATATTATGA-TAGAATAT-AATAA
20330995 AAAATAT
1 AAAATAT
20331002 CATCTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 2 0.07
26 15 0.52
27 12 0.41
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (25 bp):
AAAATATTATGATAGAATATAATAA
Found at i:20334021 original size:13 final size:13
Alignment explanation
Indices: 20334003--20334027 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20333993 TTAAACATAA
20334003 TAAATTTAATTTT
1 TAAATTTAATTTT
20334016 TAAATTTAATTT
1 TAAATTTAATTT
20334028 ATTTAATATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATTTAATTTT
Found at i:20334270 original size:33 final size:31
Alignment explanation
Indices: 20334224--20334296 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 31
20334214 AAATATTGTT
*
20334224 TTAAAATAGATGAAGTGTGTAATAAATAAAAATA
1 TTAAAA-A-ATGAAGGGTGTAATAAATAAAAA-A
20334258 TTCAAAAAATGAAGGGTGTAATAAATAAAAAA
1 TT-AAAAAATGAAGGGTGTAATAAATAAAAAA
20334290 TTAAAAA
1 TTAAAAA
20334297 CGTGTGTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 5 0.14
32 3 0.08
33 22 0.59
34 3 0.08
35 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.14, T:0.26
Consensus pattern (31 bp):
TTAAAAAATGAAGGGTGTAATAAATAAAAAA
Found at i:20336227 original size:17 final size:17
Alignment explanation
Indices: 20336193--20336226 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20336183 AAAAATTATT
*
20336193 ATTTGAAAATTCATAAA
1 ATTTGAAAATTAATAAA
20336210 ATTT-AAAATTAATAAA
1 ATTTGAAAATTAATAAA
20336226 A
1 A
20336227 AATTGCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
ATTTGAAAATTAATAAA
Found at i:20339422 original size:18 final size:18
Alignment explanation
Indices: 20339401--20339449 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
20339391 GATACTGGGG
* *
20339401 ATGATGTTGTAGCTGGTA
1 ATGATGTAGTAGCTGGCA
*
20339419 ATGATGCAGTAGCTGGCA
1 ATGATGTAGTAGCTGGCA
*
20339437 ATGATGTGGTAGC
1 ATGATGTAGTAGC
20339450 GGCTGAGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.35, T:0.31
Consensus pattern (18 bp):
ATGATGTAGTAGCTGGCA
Found at i:20346342 original size:10 final size:10
Alignment explanation
Indices: 20346327--20346378 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
20346317 TCTTCTTTAT
20346327 ATAATAATAA
1 ATAATAATAA
20346337 ATAATAAATAAA
1 ATAAT-AAT-AA
20346349 ATAA-AATAA
1 ATAATAATAA
*
20346358 ATAA-AAGAGA
1 ATAATAATA-A
20346368 ATAATAATAA
1 ATAATAATAA
20346378 A
1 A
20346379 AAAATGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 9 0.25
10 15 0.42
11 6 0.17
12 6 0.17
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (10 bp):
ATAATAATAA
Found at i:20346733 original size:15 final size:14
Alignment explanation
Indices: 20346709--20346743 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
20346699 ATCAAAATCT
20346709 TAAAATTTAAACTC
1 TAAAATTTAAACTC
20346723 TAAACATTTAAACTC
1 TAAA-ATTTAAACTC
*
20346738 CAAAAT
1 TAAAAT
20346744 CGAAAGCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAATTTAAACTC
Found at i:20346881 original size:31 final size:31
Alignment explanation
Indices: 20346831--20346900 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
20346821 GAAAAACTTT
*
20346831 TAAACCTTTAAAACTCTAAAA-TCTAAAACCC
1 TAAACCTTTAAAACACTAAAATTC-AAAACCC
* *
20346862 TAAATCTTTCAAACACTAAAATTCAAAACCC
1 TAAACCTTTAAAACACTAAAATTCAAAACCC
20346893 TAAACCTT
1 TAAACCTT
20346901 AAATTTCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 32 0.94
32 2 0.06
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (31 bp):
TAAACCTTTAAAACACTAAAATTCAAAACCC
Found at i:20346903 original size:22 final size:22
Alignment explanation
Indices: 20346878--20346919 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20346868 TTTCAAACAC
20346878 TAAAATTCAAAACCCTAAACCT
1 TAAAATTCAAAACCCTAAACCT
* *
20346900 TAAATTTCGAAACCCTAAAC
1 TAAAATTCAAAACCCTAAAC
20346920 ATCGAACCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAATTCAAAACCCTAAACCT
Found at i:20346929 original size:14 final size:14
Alignment explanation
Indices: 20346909--20346946 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
20346899 TTAAATTTCG
20346909 AAACCCTAAACATC
1 AAACCCTAAACATC
*
20346923 GAACCCTAAACATC
1 AAACCCTAAACATC
*
20346937 AAACCTTAAA
1 AAACCCTAAA
20346947 TATTGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.32, G:0.03, T:0.16
Consensus pattern (14 bp):
AAACCCTAAACATC
Found at i:20346994 original size:29 final size:30
Alignment explanation
Indices: 20346956--20347031 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
20346946 ATATTGAAAT
**
20346956 CCTTTCAATCATAAAAT-TTAAACCCTAAAC
1 CCTTT-AATCATAAAATCCAAAACCCTAAAC
*
20346986 CCTTTAATCATAAAATCCAAAACCCTAAAT
1 CCTTTAATCATAAAATCCAAAACCCTAAAC
*
20347016 CCTTTAAACTATAAAA
1 CCTTTAATC-ATAAAA
20347032 CCTCTAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.28
30 23 0.57
31 6 0.15
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (30 bp):
CCTTTAATCATAAAATCCAAAACCCTAAAC
Found at i:20347122 original size:19 final size:19
Alignment explanation
Indices: 20347100--20347138 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
20347090 TAAATAAAAA
* *
20347100 TTAATCAAAATCTTAAATT
1 TTAACCAAAACCTTAAATT
*
20347119 TTAACCTAAACCTTAAATT
1 TTAACCAAAACCTTAAATT
20347138 T
1 T
20347139 GGCACACAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAACCAAAACCTTAAATT
Found at i:20352912 original size:2 final size:2
Alignment explanation
Indices: 20352905--20352944 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
20352895 ATACTTAAAA
*
20352905 AT AT AT AT AT AT AT AT AA 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
20352945 TTAATTTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:20356490 original size:2 final size:2
Alignment explanation
Indices: 20356483--20356508 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20356473 ATGAAATAAA
20356483 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
20356509 GAAAATTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20361935 original size:21 final size:21
Alignment explanation
Indices: 20361902--20361948 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
20361892 GAAAAATGAA
*
20361902 TTTTATCTTGATAATTTTAATT
1 TTTTATCTAGATAATTTT-ATT
20361924 TTTTAT-TAGATAATTTTATT
1 TTTTATCTAGATAATTTTATT
20361944 TTTTA
1 TTTTA
20361949 AAATTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
21 10 0.42
22 6 0.25
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATCTAGATAATTTTATT
Found at i:20363369 original size:16 final size:16
Alignment explanation
Indices: 20363342--20363375 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
20363332 TTTATTATTC
20363342 AAAATTAT-AAAATTT
1 AAAATTATAAAAATTT
20363357 AAAATTAATAAAAATTT
1 AAAATT-ATAAAAATTT
20363374 AA
1 AA
20363376 TTTTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 2 0.12
17 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTATAAAAATTT
Found at i:20364453 original size:34 final size:34
Alignment explanation
Indices: 20364397--20364487 Score: 91
Period size: 33 Copynumber: 2.7 Consensus size: 34
20364387 TATATTTTTT
* *
20364397 AAATATT-TATAAAATAAAATTAATATTTTTATATAA
1 AAATATTATAT-AAAT-ATATTAA-AATTTTATATAA
* *
20364433 AAAT-TTATTTAAATATATTAAAATTTTATATTA
1 AAATATTATATAAATATATTAAAATTTTATATAA
20364466 AAATATTATATAAA-A-ATTAAAA
1 AAATATTATATAAATATATTAAAA
20364488 ATCAATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 7 0.15
33 15 0.31
34 14 0.29
35 6 0.12
36 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAATATTATATAAATATATTAAAATTTTATATAA
Found at i:20364460 original size:21 final size:22
Alignment explanation
Indices: 20364426--20364483 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
20364416 TTAATATTTT
20364426 TATA-TAAAAATTTAT-TTAAA
1 TATATTAAAAATTTATATTAAA
*
20364446 TATATTAAAATTTTATATTAAAA
1 TATATTAAAAATTTATATT-AAA
20364469 TATTATATAAAAATT
1 TA-TAT-TAAAAATT
20364484 AAAAATCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
22 2 0.06
23 5 0.16
24 3 0.10
25 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TATATTAAAAATTTATATTAAA
Found at i:20364464 original size:13 final size:13
Alignment explanation
Indices: 20364446--20364483 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
20364436 TTTATTTAAA
20364446 TATATTAAAATTT
1 TATATTAAAATTT
*
20364459 TATATTAAAATAT
1 TATATTAAAATTT
*
20364472 TATATAAAAATT
1 TATATTAAAATT
20364484 AAAAATCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATTAAAATTT
Found at i:20364567 original size:28 final size:27
Alignment explanation
Indices: 20364515--20364568 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
20364505 ATGAACTAAT
*
20364515 AAAATTTGATTCAATTTAGATTAAATA
1 AAAATTTAATTCAATTTAGATTAAATA
20364542 AAAATTTAATTCAGATTTAGATTAAAT
1 AAAATTTAATTCA-ATTTAGATTAAAT
20364569 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (27 bp):
AAAATTTAATTCAATTTAGATTAAATA
Found at i:20366705 original size:61 final size:61
Alignment explanation
Indices: 20366635--20366759 Score: 207
Period size: 61 Copynumber: 2.0 Consensus size: 61
20366625 TTAACGTCGA
*
20366635 GCAGACAAATAAAAAAAATTAAAATGATGTCATC-GCGAGAAAAAGCTTCGCGAGAAAACTT
1 GCAGACAAATAAAAAAAATTAAAATGATATCATCGGC-AGAAAAAGCTTCGCGAGAAAACTT
* *
20366696 GCAGACAAATAAAAAAAATTAAAATGATATTATCGGCAGAAAAAGCTTTGCGAGAAAACTT
1 GCAGACAAATAAAAAAAATTAAAATGATATCATCGGCAGAAAAAGCTTCGCGAGAAAACTT
20366757 GCA
1 GCA
20366760 AACTTGCGTG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.19
Consensus pattern (61 bp):
GCAGACAAATAAAAAAAATTAAAATGATATCATCGGCAGAAAAAGCTTCGCGAGAAAACTT
Found at i:20367067 original size:61 final size:61
Alignment explanation
Indices: 20366972--20367137 Score: 289
Period size: 61 Copynumber: 2.7 Consensus size: 61
20366962 TAACGTCGAG
*
20366972 AAAATGATGTCATCGCGAGAAAAAGCTTCGCGAGAAAACTTGCAGACAAATAAAAAAAATT
1 AAAATGATGTCATCGCGAGAAAAAGCTTTGCGAGAAAACTTGCAGACAAATAAAAAAAATT
20367033 AAAATGATGTCATCGCGAGAAAAAGCTTTGCGAGAAAACTTGCAGACAAATAAAAAAAATT
1 AAAATGATGTCATCGCGAGAAAAAGCTTTGCGAGAAAACTTGCAGACAAATAAAAAAAATT
* *
20367094 AAAATGATATTATCG-GCAGAAAAAGCTTTGCGAGAAAACTTGCA
1 AAAATGATGTCATCGCG-AGAAAAAGCTTTGCGAGAAAACTTGCA
20367138 AACTTGTGTG
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
60 1 0.01
61 100 0.99
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.20
Consensus pattern (61 bp):
AAAATGATGTCATCGCGAGAAAAAGCTTTGCGAGAAAACTTGCAGACAAATAAAAAAAATT
Found at i:20386215 original size:2 final size:2
Alignment explanation
Indices: 20386210--20386241 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
20386200 TGTTCCGGCT
20386210 TA TA TA TA TA TA TA TA TA TA TA TGA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T
20386242 GTGCCAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20386472 original size:10 final size:10
Alignment explanation
Indices: 20386451--20386482 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
20386441 CATTTTTTTC
20386451 AAAA-AAAA-
1 AAAAGAAAAT
20386459 AAAAGAAAAT
1 AAAAGAAAAT
20386469 AAAAGAAAAT
1 AAAAGAAAAT
20386479 AAAA
1 AAAA
20386483 TATCAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 4 0.18
9 4 0.18
10 14 0.64
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:20388243 original size:19 final size:19
Alignment explanation
Indices: 20388204--20388255 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
20388194 AAAAAATAAA
*
20388204 AAAATCATAAAATATAATTTT
1 AAAAT-ATAAAA-AGAATTTT
20388225 AAAATATAAAAAGAATTTT
1 AAAATATAAAAAGAATTTT
20388244 -AAATATTAAAAA
1 AAAATA-TAAAAA
20388256 ATAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.17
19 13 0.45
20 6 0.21
21 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATATAAAAAGAATTTT
Found at i:20388300 original size:46 final size:46
Alignment explanation
Indices: 20388210--20388300 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 46
20388200 TAAAAAAATC
* * *
20388210 ATAAAATATAATTTTAAAATATAAAAAGAATTTTAAATATTAAAAA
1 ATAAAATATAATTTTAAAATATAAAAAGAATATTAAAAAATAAAAA
* *
20388256 ATAAAATATAATTTTAGGACATCTAAAAA-AA-ATTAAAAAATAAAA
1 ATAAAATATAATTTTA--AAATATAAAAAGAATATTAAAAAATAAAA
20388301 CATAGGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
46 27 0.71
47 2 0.05
48 9 0.24
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (46 bp):
ATAAAATATAATTTTAAAATATAAAAAGAATATTAAAAAATAAAAA
Found at i:20389747 original size:18 final size:19
Alignment explanation
Indices: 20389724--20389759 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20389714 TCTTCCCCTG
20389724 AAAAATTAATAA-ACAAAT
1 AAAAATTAATAACACAAAT
*
20389742 AAAAATTACTAACACAAA
1 AAAAATTAATAACACAAA
20389760 AAATAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAATTAATAACACAAAT
Found at i:20391871 original size:40 final size:40
Alignment explanation
Indices: 20391813--20391891 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
20391803 TTAAAAGGAT
* *
20391813 TATAAGTTGCTCCTTACATGCATGGATGTTAGTTCCATGA
1 TATAAGTTGCTCCCTACATGCATGGATATTAGTTCCATGA
*
20391853 TATAAGTTGTTCCCTACATGCATGGATATTAGTTCCATG
1 TATAAGTTGCTCCCTACATGCATGGATATTAGTTCCATG
20391892 GTTTTAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
TATAAGTTGCTCCCTACATGCATGGATATTAGTTCCATGA
Found at i:20393214 original size:12 final size:12
Alignment explanation
Indices: 20393194--20393236 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
20393184 TATTATGTTG
20393194 TTGGAATATCAA
1 TTGGAATATCAA
*
20393206 TTGGCATATCAA
1 TTGGAATATCAA
20393218 TT-G-ATATCAA
1 TTGGAATATCAA
20393228 TTGGAATAT
1 TTGGAATAT
20393237 ATTTTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.32
11 2 0.07
12 17 0.61
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (12 bp):
TTGGAATATCAA
Found at i:20394429 original size:2 final size:2
Alignment explanation
Indices: 20394413--20394447 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20394403 TATCAACAGT
* *
20394413 TA TA TA GA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20394448 CATAAATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:20395484 original size:2 final size:2
Alignment explanation
Indices: 20395477--20395511 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20395467 TCCATTTATG
* *
20395477 AT AT AT AT AT AT AT AT AT AT AT AT GT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20395512 ACTGTTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20409239 original size:24 final size:23
Alignment explanation
Indices: 20409195--20409241 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
20409185 ATTTTTATAT
*
20409195 ATTTAATTTATAAATTTATAAAA
1 ATTTAATTTATAAATTAATAAAA
**
20409218 ATTTATATTTATTTATTAATAAAA
1 ATTTA-ATTTATAAATTAATAAAA
20409242 TAATATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAATTTATAAATTAATAAAA
Found at i:20413623 original size:3 final size:3
Alignment explanation
Indices: 20413615--20413666 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
20413605 TATTTTTATG
20413615 ATA ATA ATA ATA ATA ATA ATA ATA 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
20413663 ATA A
1 ATA A
20413667 CCGTCAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20414084 original size:2 final size:2
Alignment explanation
Indices: 20414071--20414156 Score: 84
Period size: 2 Copynumber: 42.5 Consensus size: 2
20414061 TATATTATTA
* * * * *
20414071 AT AT AA AT AT AT AT AT AT AT ACT A- AA AA AT CT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* *
20414113 AT AC ACT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20414156 A
1 A
20414157 CTGGAGTTCG
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
1 1 0.01
2 66 0.94
3 3 0.04
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:20420390 original size:19 final size:19
Alignment explanation
Indices: 20420366--20420413 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
20420356 ACCTTGTAGC
*
20420366 AATAAAGGCTTTTATCAAT
1 AATAAAAGCTTTTATCAAT
20420385 AATAAAAGCTTTTATCAAT
1 AATAAAAGCTTTTATCAAT
20420404 AATAAAAGCT
1 AATAAAAGCT
20420414 ATTTTATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (19 bp):
AATAAAAGCTTTTATCAAT
Found at i:20427125 original size:29 final size:29
Alignment explanation
Indices: 20427092--20427150 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
20427082 GTTAAATTAT
*
20427092 TAGCAGCATCATTTTATTTCCAACAAACA
1 TAGCAGCATAATTTTATTTCCAACAAACA
*
20427121 TAGCAGCATAATTTTATTTTCAACAAACA
1 TAGCAGCATAATTTTATTTCCAACAAACA
20427150 T
1 T
20427151 GGTGCATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (29 bp):
TAGCAGCATAATTTTATTTCCAACAAACA
Found at i:20428053 original size:66 final size:66
Alignment explanation
Indices: 20427947--20428074 Score: 211
Period size: 66 Copynumber: 1.9 Consensus size: 66
20427937 AACTTCCTTG
**
20427947 TGGGTGAGGTTAAGAGATGGAAAATTTCCATTGTTTGATTTCTGATACCTGCAGTAAGTTCATCC
1 TGGGTGAGGTTAAGAGATGGAAAATTTCCATTGTTTGATTTCTGATACCTGCAACAAGTTCATCC
20428012 A
66 A
* * *
20428013 TGGGTGAGTTTAAGAGATGGAAATTTTCTATTGTTTGATTTCTGATACCTGCAACAAGTTCA
1 TGGGTGAGGTTAAGAGATGGAAAATTTCCATTGTTTGATTTCTGATACCTGCAACAAGTTCA
20428075 CCAAATAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.37
Consensus pattern (66 bp):
TGGGTGAGGTTAAGAGATGGAAAATTTCCATTGTTTGATTTCTGATACCTGCAACAAGTTCATCC
A
Found at i:20433453 original size:35 final size:35
Alignment explanation
Indices: 20433407--20433480 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
20433397 TTACTATATA
20433407 TACTTTTTATATTATTGCATAGATTGTGTATCTCT
1 TACTTTTTATATTATTGCATAGATTGTGTATCTCT
20433442 TACTTTTTATATTATTGCATAGATTGTGTATCTCT
1 TACTTTTTATATTATTGCATAGATTGTGTATCTCT
20433477 TACT
1 TACT
20433481 CAACCATGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (35 bp):
TACTTTTTATATTATTGCATAGATTGTGTATCTCT
Found at i:20433751 original size:2 final size:2
Alignment explanation
Indices: 20433746--20433773 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20433736 TTAAAAAAAT
20433746 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
20433774 ATGAGCAGTA
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:20438368 original size:17 final size:17
Alignment explanation
Indices: 20438331--20438368 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20438321 CGCCGTGAAA
*
20438331 TTAAAAAAATATTTTTT
1 TTAAAAAAATATTTTTG
20438348 TTAAAAAAA-ATTTTCTG
1 TTAAAAAAATATTTT-TG
20438365 TTAA
1 TTAA
20438369 TATTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAAAAAATATTTTTG
Found at i:20446809 original size:187 final size:186
Alignment explanation
Indices: 20446436--20447098 Score: 696
Period size: 187 Copynumber: 3.5 Consensus size: 186
20446426 AAGAGCATTC
* * * * *
20446436 AATAATTTCTTTGAAATTTTGTACATAAATATTGAA-GCATTTTTTAATAA-AATCACCTTTAAT
1 AATAATTCCTTTGAAATTTTGTACATAATTATTGAAGGCATTTTTTGATAACAAACACCTTCAAT
* * * * *
20446499 AATTTTTTTCTAAAAATTTTTGAGATTATTAAAGGCGTCTTCAAGTG-AAAACGCCTTCAATATA
66 AATTTTTTT-AAAAAAATTTTGAGATTATTAAAGGCGTCTTCTACTGAAAAATGCCTTCAATATA
* ** *
20446563 TCGGTACACAAATTTTAAGATGG-TAATTGAAAGCGTTTATTTCCA-AAAAAAAGCCTTT
130 TCAGTACTTAAATTTTAAGATGGTTAA-TGAAAGCATTTA-TTCCAGAAAAAAA-CCTTT
* * * * *
20446621 AATAATTCCTTTGAAATTTTGTACATAATTATCGAAGGTATTTCTTGATAATAACCACCTTCAAT
1 AATAATTCCTTTGAAATTTTGTACATAATTATTGAAGGCATTTTTTGATAACAAACACCTTCAAT
* * * *
20446686 AATTTTCTTTTAAAAAATTTTGAGATTATTAAAAGTGTCTTCTACTGAAAAATACCTTCAATATA
66 AATTTT-TTTAAAAAAATTTTGAGATTATTAAAGGCGTCTTCTACTGAAAAATGCCTTCAATATA
** * * *
20446751 -CTAGTACTTAAATTTTAAGACAGTTAGTGAATGCATTTATTCCAGAAAAACACCTTT
130 TC-AGTACTTAAATTTTAAGATGGTTAATGAAAGCATTTATTCCAGAAAAAAACCTTT
** * ***
20446808 AATAATTTTTTTTAAATTTTGTACATAATTATTGAAGGCATTTTTTGATAACAAATGTCTTCAAT
1 AATAATTCCTTTGAAATTTTGTACATAATTATTGAAGGCATTTTTTGATAACAAACACCTTCAAT
** * *
20446873 AATTTTTAAAAAAAAAATATTGAGATTATTAAAGGCGTCTTCTACTGAAAAATGCCTTTAATATA
66 AATTTTT-TTAAAAAAATTTTGAGATTATTAAAGGCGTCTTCTACTGAAAAATGCCTTCAATATA
* * ** * *
20446938 TCAGTACTTAAATTTTTAAGATGGTTAAT-AAAGGTATTTATTCTAGAAAAATGCATTC
130 TCAGTACTTAAA-TTTTAAGATGGTTAATGAAA-GCATTTATTCCAGAAAAAAACCTTT
* * * * * * *
20446996 ACTAATTCGTTT-TAATATTTGTACATAATTATTGAAGGTAATTTTTT-AGAACAAAAACCTACA
1 AATAATTCCTTTGAAAT-TTTGTACATAATTATTGAAGG-CATTTTTTGATAACAAACACCTTCA
20447059 ATAATTTTTTTAAAAAAATTTTTGAGATTATTAAAGGCGT
64 ATAATTTTTTTAAAAAAA-TTTTGAGATTATTAAAGGCGT
20447099 TTTTTAGTAT
Statistics
Matches: 398, Mismatches: 66, Indels: 25
0.81 0.13 0.05
Matches are distributed among these distances:
185 33 0.08
186 12 0.03
187 191 0.48
188 153 0.38
189 9 0.02
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (186 bp):
AATAATTCCTTTGAAATTTTGTACATAATTATTGAAGGCATTTTTTGATAACAAACACCTTCAAT
AATTTTTTTAAAAAAATTTTGAGATTATTAAAGGCGTCTTCTACTGAAAAATGCCTTCAATATAT
CAGTACTTAAATTTTAAGATGGTTAATGAAAGCATTTATTCCAGAAAAAAACCTTT
Found at i:20447899 original size:12 final size:12
Alignment explanation
Indices: 20447857--20447908 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
20447847 TTTATGATAT
20447857 TGGTATGCTGAA
1 TGGTATGCTGAA
**
20447869 TCATATGCTGAA
1 TGGTATGCTGAA
**
20447881 TTATATGCTGAA
1 TGGTATGCTGAA
*
20447893 TGGTATGTTGAA
1 TGGTATGCTGAA
20447905 TGGT
1 TGGT
20447909 TTACTAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.38
Consensus pattern (12 bp):
TGGTATGCTGAA
Found at i:20447931 original size:25 final size:25
Alignment explanation
Indices: 20447901--20447953 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
20447891 AATGGTATGT
*
20447901 TGAATGGTTTACTAAATGGTGTTTC
1 TGAATGATTTACTAAATGGTGTTTC
*
20447926 TGAATGATTTGCTAAATGGTGTTTC
1 TGAATGATTTACTAAATGGTGTTTC
20447951 TGA
1 TGA
20447954 GCACATTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.43
Consensus pattern (25 bp):
TGAATGATTTACTAAATGGTGTTTC
Found at i:20451822 original size:307 final size:306
Alignment explanation
Indices: 20451212--20451841 Score: 716
Period size: 307 Copynumber: 2.1 Consensus size: 306
20451202 TTTTTAGTAA
* *
20451212 GAAAATGCCTTGAATCATCCATAACAAAATGTTATTGAAGGCATTTTTAACGAAAAATCACCTTC
1 GAAAATGCCTTAAATAATCCATAACAAAATGTTATTGAAGGCATTTTTAAC-AAAAATCACCTTC
* *
20451277 AATAATCCCACCTAAAAAAATATTGTGTGAAACATTAAAGGCGTTTTGGGCAAAAAATGCCTTTA
65 AATAATCCAACCTAAAAAAATATTGTGTGAAACATTAAAGGCGTTTTGAGCAAAAAATGCCTTTA
* * * * * * *
20451342 AGAATCTGTTTCAATTTTTTTGTATGGATTATTGAAGGCGTTTTAAAAAAAAAATTGCCTTTAAT
130 AAAATCTATTCCAACTTTTGTGTATGGATTATTGAAGGCATTTTAAAAAAAAAACTGCCTTTAAT
* * * * *
20451407 AATATCAACTAAAAATTAATTGAATAGATTATTGAAGGCGCTTTCGACAAAAAAACGTCTTCAAT
195 AATACCAACCAAAAATTAATTGAATAGATTATTAAAGGCGCTTTCGACAAAAAAACGCCTTCAAG
* *
20451472 AATCCGTTTCATATTTTGGTATGGATTATTAAAGGCATTTTTCTGCC
260 AATCCGTTTCATATTTTGCTATAGATTATTAAAGGCATTTTTCTGCC
* * *
20451519 GAAAATGCCTTAAATAATCCATAACAAAATTTTATTGAAGTCGTTTTTTAA-AAAAATCACCTTC
1 GAAAATGCCTTAAATAATCCATAACAAAATGTTATTGAAGGC-ATTTTTAACAAAAATCACCTTC
* ** ** * *
20451583 AATAATTCAACCATTCAAATTTATTGTGTGAAATATTAAAGGCGTTTTGAGCCAAAAATG-CTTT
65 AATAATCCAACC-TAAAAAAATATTGTGTGAAACATTAAAGGCGTTTTGAGCAAAAAATGCCTTT
* ** *
20451647 CAAAAATCTATTCCAACTTTTGTGTATGGATTATTGAAGGTATTTT-TGATAAAAACTGCCTTTA
129 -AAAAATCTATTCCAACTTTTGTGTATGGATTATTGAAGGCATTTTAAAAAAAAAACTGCCTTTA
* * * * * * *
20451711 ATAAT-CCATACCAAAAATTTATTGATTGGATTATTAAAGGTGAGTTT-GGC-AAAAAATGCCTT
193 ATAATACCA-ACCAAAAATTAATTGAATAGATTATTAAAGGCG-CTTTCGACAAAAAAACGCCTT
* * * **
20451773 CAAGAAT-CGGTTCTATATTTTTTCTATAGATTATTAAGGGTGTTTTTTCTGCC
256 CAAGAATCCGTTTC-ATA-TTTTGCTATAGATTATTAAAGG-CATTTTTCTGCC
* *
20451826 AAAAATGCCTTCAATA
1 GAAAATGCCTTAAATA
20451842 TTCTCTCCAT
Statistics
Matches: 269, Mismatches: 46, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
304 5 0.02
305 21 0.08
306 93 0.35
307 143 0.53
308 7 0.03
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (306 bp):
GAAAATGCCTTAAATAATCCATAACAAAATGTTATTGAAGGCATTTTTAACAAAAATCACCTTCA
ATAATCCAACCTAAAAAAATATTGTGTGAAACATTAAAGGCGTTTTGAGCAAAAAATGCCTTTAA
AAATCTATTCCAACTTTTGTGTATGGATTATTGAAGGCATTTTAAAAAAAAAACTGCCTTTAATA
ATACCAACCAAAAATTAATTGAATAGATTATTAAAGGCGCTTTCGACAAAAAAACGCCTTCAAGA
ATCCGTTTCATATTTTGCTATAGATTATTAAAGGCATTTTTCTGCC
Found at i:20454988 original size:52 final size:53
Alignment explanation
Indices: 20454898--20455054 Score: 167
Period size: 52 Copynumber: 3.0 Consensus size: 53
20454888 TATAACCATA
* * * * * * *
20454898 CAAATTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTTTTC-TGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTTCTCTTAAAATTCTTTCTCTTGCAAGT
* *
20454950 CAAACTTGCCTATTAACAATCCCTTTTCTTTTAAAATTC-TTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTTCTCTTAAAATTCTTTCTCTTGCAAGT
* ** * *
20455002 CAAACTTACCTATTAAGAATCTTTTTTCTCTTGAAATTC-TTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTTCTCTTAAAATTCTTTCTCTTGCAAGT
20455054 C
1 C
20455055 TTCTTGTCCA
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 4 0.05
52 84 0.95
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.43
Consensus pattern (53 bp):
CAAACTTGCCTATTAAGAATCCCTTTTCTCTTAAAATTCTTTCTCTTGCAAGT
Found at i:20455110 original size:11 final size:11
Alignment explanation
Indices: 20455079--20455110 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20455069 GTAATATCTG
*
20455079 ACAAATCTCAA
1 ACAAATCTCTA
20455090 ACAAATCTCTA
1 ACAAATCTCTA
20455101 ACAAATCTCT
1 ACAAATCTCT
20455111 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:20455229 original size:32 final size:32
Alignment explanation
Indices: 20455169--20455231 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
20455159 TGCTACGCAC
* * * * *
20455169 TTGTTTATTTTTTTCTTTTTTTTTTTGAAAAT
1 TTGTTTATTCTTTTCTTGTATATATTGAAAAT
20455201 TTGTTTATTCTTTTCTTGTATATATTGAAAA
1 TTGTTTATTCTTTTCTTGTATATATTGAAAA
20455232 AGTATAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.05, G:0.08, T:0.67
Consensus pattern (32 bp):
TTGTTTATTCTTTTCTTGTATATATTGAAAAT
Found at i:20463294 original size:14 final size:16
Alignment explanation
Indices: 20463271--20463303 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
20463261 AAATTACTAA
20463271 TTTATGAAAAAAT-AT
1 TTTATGAAAAAATAAT
20463286 TTTAT-AAAAAATAAT
1 TTTATGAAAAAATAAT
20463301 TTT
1 TTT
20463304 TAATGATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TTTATGAAAAAATAAT
Found at i:20465850 original size:22 final size:21
Alignment explanation
Indices: 20465816--20465857 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
20465806 AATTTTTAAG
*
20465816 CTTTTATTTCTTTTCTATATT
1 CTTTTATCTCTTTTCTATATT
*
20465837 CTTTTCATCTCTTTTTTATAT
1 CTTTT-ATCTCTTTTCTATAT
20465858 CAGATATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (21 bp):
CTTTTATCTCTTTTCTATATT
Found at i:20471813 original size:66 final size:66
Alignment explanation
Indices: 20471707--20471834 Score: 213
Period size: 66 Copynumber: 1.9 Consensus size: 66
20471697 AACTTCCTTG
*
20471707 TGGGTGAGGTTAAGAGATGGAAAATTTTCATTGTTTGATTTCTGATACCTGCAATAAGTTCATCC
1 TGGGTGAGGTTAAGAGATGGAAAATTTTCATTGTTTGATTTCTGATACCTGCAACAAGTTCATCC
20471772 A
66 A
* *
20471773 TGGGTGAGTTTAAGAGATGG-AAATTTTCCATTGTTTGATTTGTGATACCTGCAACAAGTTCA
1 TGGGTGAGGTTAAGAGATGGAAAATTTT-CATTGTTTGATTTCTGATACCTGCAACAAGTTCA
20471835 CCAAATAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 7 0.12
66 51 0.88
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (66 bp):
TGGGTGAGGTTAAGAGATGGAAAATTTTCATTGTTTGATTTCTGATACCTGCAACAAGTTCATCC
A
Found at i:20471863 original size:24 final size:24
Alignment explanation
Indices: 20471836--20471886 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
20471826 ACAAGTTCAC
20471836 CAAATAAATGGTACAAAAAGATAG
1 CAAATAAATGGTACAAAAAGATAG
*
20471860 CAAATAAATGGTACAGAAAGATAG
1 CAAATAAATGGTACAAAAAGATAG
20471884 CAA
1 CAA
20471887 TCACTTCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.18, T:0.16
Consensus pattern (24 bp):
CAAATAAATGGTACAAAAAGATAG
Found at i:20474739 original size:22 final size:22
Alignment explanation
Indices: 20474713--20474756 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20474703 TGTATATTTA
*
20474713 TATTTGTATCTCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
20474735 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
20474757 GAAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:20478888 original size:24 final size:26
Alignment explanation
Indices: 20478848--20478898 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
20478838 TCAGTTTTAC
20478848 TCTTAGTTTTTCACACAATTT-TATT
1 TCTTAGTTTTTCACACAATTTCTATT
* *
20478873 TCTTAGTTTTT-TCACATTTTCTATT
1 TCTTAGTTTTTCACACAATTTCTATT
20478898 T
1 T
20478899 GCATTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.61
Consensus pattern (26 bp):
TCTTAGTTTTTCACACAATTTCTATT
Found at i:20479110 original size:1 final size:1
Alignment explanation
Indices: 20479104--20479134 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
20479094 TTTCTATTCC
20479104 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20479135 CAAGAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20479564 original size:2 final size:2
Alignment explanation
Indices: 20479557--20479583 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20479547 CTTTAAGCTA
20479557 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
20479584 AACCCAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20486163 original size:2 final size:2
Alignment explanation
Indices: 20486146--20486181 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
20486136 TATCTAAAAC
* *
20486146 AT AT AT AC AT AC 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
20486182 GATGCACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:20497808 original size:17 final size:17
Alignment explanation
Indices: 20497782--20497818 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20497772 TATTTGTTTA
*
20497782 AATTATTTTTAATTTTT
1 AATTAATTTTAATTTTT
*
20497799 AATTAATTTTTATTTTT
1 AATTAATTTTAATTTTT
20497816 AAT
1 AAT
20497819 ATTTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTAATTTTAATTTTT
Found at i:20506289 original size:13 final size:13
Alignment explanation
Indices: 20506271--20506298 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
20506261 TTCTGCTATG
20506271 ATAAACCATGGAA
1 ATAAACCATGGAA
20506284 ATAAACCATGGAA
1 ATAAACCATGGAA
20506297 AT
1 AT
20506299 TGAGCTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (13 bp):
ATAAACCATGGAA
Found at i:20506317 original size:2 final size:2
Alignment explanation
Indices: 20506310--20506338 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20506300 GAGCTCTTAA
20506310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20506339 AAGCTGTTCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20506434 original size:23 final size:23
Alignment explanation
Indices: 20506408--20506454 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
20506398 GAAAATTAAT
20506408 ACTATAGGAATTTGACATTTGCA
1 ACTATAGGAATTTGACATTTGCA
*
20506431 ACTATAGGAATTTTACATTTGCA
1 ACTATAGGAATTTGACATTTGCA
20506454 A
1 A
20506455 ACAGGCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (23 bp):
ACTATAGGAATTTGACATTTGCA
Found at i:20507957 original size:13 final size:13
Alignment explanation
Indices: 20507939--20507963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20507929 TAATAAATTT
20507939 GATAGATATTTTA
1 GATAGATATTTTA
20507952 GATAGATATTTT
1 GATAGATATTTT
20507964 TAATAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
GATAGATATTTTA
Found at i:20514262 original size:2 final size:2
Alignment explanation
Indices: 20514255--20514287 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20514245 AGTTAAACAA
20514255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20514288 AAGCTCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20516284 original size:11 final size:10
Alignment explanation
Indices: 20516262--20516300 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 10
20516252 TAAAACATTT
20516262 ATAACATAATA
1 ATAA-ATAATA
20516273 ATAAATACATA
1 ATAAATA-ATA
20516284 ATAATATAATA
1 ATAA-ATAATA
20516295 ATAAAT
1 ATAAAT
20516301 TATTGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 18 0.69
12 3 0.12
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAATAATA
Found at i:20516284 original size:14 final size:15
Alignment explanation
Indices: 20516265--20516298 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
20516255 AACATTTATA
20516265 ACATAATAATA-AAT
1 ACATAATAATATAAT
20516279 ACATAATAATATAAT
1 ACATAATAATATAAT
20516294 A-ATAA
1 ACATAA
20516299 ATTATTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (15 bp):
ACATAATAATATAAT
Found at i:20516511 original size:18 final size:19
Alignment explanation
Indices: 20516474--20516510 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20516464 ATAAATTCAT
*
20516474 TTAAATTTTTACTAAAAAA
1 TTAAATTTTTAATAAAAAA
20516493 TTAAATTTTTAATAAAAA
1 TTAAATTTTTAATAAAAA
20516511 TATGTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATTTTTAATAAAAAA
Found at i:20516822 original size:2 final size:2
Alignment explanation
Indices: 20516817--20516847 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20516807 TGTGTGTGTG
20516817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20516848 TATTGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20517533 original size:32 final size:31
Alignment explanation
Indices: 20517469--20517533 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
20517459 TTATTTTACA
** *
20517469 ATTTTATGTGTTTGGTTATTTTTATCAGTAT
1 ATTTTATGTACTTGGTTATTTTTATCAATAT
*
20517500 ATTTTATGTACTTGGTTAATTTTTATTAATAT
1 ATTTTATGTACTTGGTT-ATTTTTATCAATAT
20517532 AT
1 AT
20517534 ATGCATGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (31 bp):
ATTTTATGTACTTGGTTATTTTTATCAATAT
Found at i:20517705 original size:22 final size:23
Alignment explanation
Indices: 20517643--20517709 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 23
20517633 GTTATCGAAG
*
20517643 ATTTACTACTAAGTTATATCAATA
1 ATTTATTACTAAGTTATA-CAATA
* *
20517667 ATTTATTATTAAATTATA-AATA
1 ATTTATTACTAAGTTATACAATA
*
20517689 ATTTATTACTGAGTTAT-CAAT
1 ATTTATTACTAAGTTATACAAT
20517710 GATTAACTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 21 0.58
24 15 0.42
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (23 bp):
ATTTATTACTAAGTTATACAATA
Found at i:20517780 original size:22 final size:22
Alignment explanation
Indices: 20517755--20517825 Score: 101
Period size: 22 Copynumber: 3.2 Consensus size: 22
20517745 ATTATCTATA
20517755 ATTTACTATTAAGTTATCCA-TG
1 ATTTACTATTAAGTTAT-CATTG
20517777 ATTTACTATTAAGTTAAT-ATTG
1 ATTTACTATTAAGTT-ATCATTG
*
20517799 ATTTACTAATAAGTTATCATTG
1 ATTTACTATTAAGTTATCATTG
20517821 ATTTA
1 ATTTA
20517826 TTGTTATCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
21 3 0.07
22 40 0.89
23 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCATTG
Found at i:20518383 original size:3 final size:3
Alignment explanation
Indices: 20518375--20518430 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
20518365 AAAATTTTGT
* * *
20518375 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TCA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
20518423 TTT TTA TT
1 TTA TTA TT
20518431 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:20518440 original size:7 final size:8
Alignment explanation
Indices: 20518423--20518451 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
20518413 ATCATCATTA
20518423 TTTTTATT
1 TTTTTATT
20518431 TTTTTATT
1 TTTTTATT
20518439 TTTTTATT
1 TTTTTATT
20518447 TTTTT
1 TTTTT
20518452 TGGTTTCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTATT
Found at i:20519745 original size:48 final size:49
Alignment explanation
Indices: 20519688--20519802 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 49
20519678 CTTTTCTTCC
*
20519688 AAAAA-AAATAAAATACAAGAA-AAATTAATAAAAAAAATTTTCT-AAAA
1 AAAAATAAATAAAATA-AAAAAGAAATTAATAAAAAAAATTTTCTCAAAA
* * **
20519735 AAAAATAAATAAAAGTAAAAAAGGAAATTAATGAATAATTTTTTCTCAAAA
1 AAAAATAAATAAAA-TAAAAAA-GAAATTAATAAAAAAAATTTTCTCAAAA
*
20519786 AAAGGATAAATAAAATA
1 AAA-AATAAATAAAATA
20519803 TACACACTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
47 5 0.09
48 12 0.21
49 2 0.04
50 18 0.32
51 9 0.16
52 10 0.18
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.23
Consensus pattern (49 bp):
AAAAATAAATAAAATAAAAAAGAAATTAATAAAAAAAATTTTCTCAAAA
Found at i:20520038 original size:19 final size:18
Alignment explanation
Indices: 20520013--20520047 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20520003 TATTTTTCTA
20520013 AAAAAAAAAGAAAAAAAT
1 AAAAAAAAAGAAAAAAAT
*
20520031 AAATAAAAAGAAAAAAA
1 AAAAAAAAAGAAAAAAA
20520048 AATCCCGATA
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:0.89, C:0.00, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAAT
Found at i:20520885 original size:22 final size:22
Alignment explanation
Indices: 20520831--20520979 Score: 140
Period size: 22 Copynumber: 6.8 Consensus size: 22
20520821 TGCTACTATA
20520831 TTATCAATGATTTATTATTAA-
1 TTATCAATGATTTATTATTAAG
*
20520852 TTA-CTAATGATTTACTATTAAG
1 TTATC-AATGATTTATTATTAAG
* *
20520874 TTATGAATGATTTATCATTAAG
1 TTATCAATGATTTATTATTAAG
* * *
20520896 TTATAAATGATTTATTGTTAAA
1 TTATCAATGATTTATTATTAAG
** * *
20520918 TTATTGATAATTTATTATAAAG
1 TTATCAATGATTTATTATTAAG
* * **
20520940 TTATCACTGATTTACTACGAAG
1 TTATCAATGATTTATTATTAAG
*
20520962 TTATTAATGATTTATTAT
1 TTATCAATGATTTATTAT
20520980 AAAATTATAT
Statistics
Matches: 100, Mismatches: 25, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.01
21 18 0.18
22 81 0.81
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (22 bp):
TTATCAATGATTTATTATTAAG
Found at i:20520942 original size:66 final size:66
Alignment explanation
Indices: 20520831--20521022 Score: 192
Period size: 66 Copynumber: 2.9 Consensus size: 66
20520821 TGCTACTATA
* * * * * **
20520831 TTATCAATGATTTATTATT-AATTACTAATGATTTACTATTAAGTTATGAATGATTTA-TCATTA
1 TTATAAATGATTTATTATTAAATTATTAATAATTTACTATAAAGTTATCAATGATTTACT-ACGA
20520894 AG
65 AG
* * * *
20520896 TTATAAATGATTTATTGTTAAATTATTGATAATTTATTATAAAGTTATCACTGATTTACTACGAA
1 TTATAAATGATTTATTATTAAATTATTAATAATTTACTATAAAGTTATCAATGATTTACTACGAA
20520961 G
66 G
* * * *
20520962 TTATTAATGATTTATTATAAAATTATATAACTAATTTACTACTAAA-TTATCATTAATTTAC
1 TTATAAATGATTTATTATTAAATTAT-TAA-TAATTTACTA-TAAAGTTATCAATGATTTAC
20521023 AATTATTACT
Statistics
Matches: 104, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
65 17 0.16
66 58 0.56
67 3 0.03
68 22 0.21
69 4 0.04
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (66 bp):
TTATAAATGATTTATTATTAAATTATTAATAATTTACTATAAAGTTATCAATGATTTACTACGAA
G
Found at i:20520987 original size:22 final size:22
Alignment explanation
Indices: 20520830--20521011 Score: 134
Period size: 22 Copynumber: 8.2 Consensus size: 22
20520820 TTGCTACTAT
*
20520830 ATTATCAATGATTTATTATT-A
1 ATTATTAATGATTTATTATTAA
* *
20520851 ATTACTAATGATTTACTATTAA
1 ATTATTAATGATTTATTATTAA
* * *
20520873 GTTATGAATGATTTATCATTAA
1 ATTATTAATGATTTATTATTAA
* * *
20520895 GTTATAAATGATTTATTGTTAA
1 ATTATTAATGATTTATTATTAA
* *
20520917 ATTATTGATAATTTATTA-TAA
1 ATTATTAATGATTTATTATTAA
* * * **
20520938 AGTTATCACTGATTTACTACGAA
1 A-TTATTAATGATTTATTATTAA
* *
20520961 GTTATTAATGATTTATTATAAA
1 ATTATTAATGATTTATTATTAA
* * *
20520983 ATTATATAACTAATTTACTACTAA
1 ATTAT-TAA-TGATTTATTATTAA
20521007 ATTAT
1 ATTAT
20521012 CATTAATTTA
Statistics
Matches: 123, Mismatches: 33, Indels: 7
0.75 0.20 0.04
Matches are distributed among these distances:
21 21 0.17
22 82 0.67
23 5 0.04
24 15 0.12
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTATTAATGATTTATTATTAA
Found at i:20521021 original size:46 final size:44
Alignment explanation
Indices: 20520807--20521021 Score: 110
Period size: 44 Copynumber: 4.9 Consensus size: 44
20520797 TTGACAACTT
* * * * * * *
20520807 AGTTATCACCAATTTGCTACTATATTATCAATGATTTATTATTA
1 AGTTATAACTAATTTACTACGAAATTATCAATAATTTATTATAA
* ** * * * * *
20520851 A-TTACTAA-TGATTTACTATTAAGTTATGAATGATTTATCATTA
1 AGTTA-TAACTAATTTACTACGAAATTATCAATAATTTATTATAA
* * * *** **
20520894 AGTTATAAATGATTTATTGTTAAATTATTGATAATTTATTATAA
1 AGTTATAACTAATTTACTACGAAATTATCAATAATTTATTATAA
* * * * *
20520938 AGTTATCACTGATTTACTACGAAGTTATTAATGATTTATTATAAA
1 AGTTATAACTAATTTACTACGAAATTATCAATAATTTATTAT-AA
* * *
20520983 ATTATATAACTAATTTACTACTAAATTATCATTAATTTA
1 AGT-TATAACTAATTTACTACGAAATTATCAATAATTTA
20521022 CAATTATTAC
Statistics
Matches: 132, Mismatches: 34, Indels: 8
0.76 0.20 0.05
Matches are distributed among these distances:
43 34 0.26
44 66 0.50
45 4 0.03
46 28 0.21
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (44 bp):
AGTTATAACTAATTTACTACGAAATTATCAATAATTTATTATAA
Found at i:20521066 original size:22 final size:22
Alignment explanation
Indices: 20521023--20521082 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
20521013 ATTAATTTAC
*
20521023 AATTATTACTGATTTAGAACTA
1 AATTATTAGTGATTTAGAACTA
* **
20521045 AATTATGAGTGATTTATTACTA
1 AATTATTAGTGATTTAGAACTA
**
20521067 CGTTATTAGTGATTTA
1 AATTATTAGTGATTTA
20521083 CTGCTAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (22 bp):
AATTATTAGTGATTTAGAACTA
Found at i:20521164 original size:22 final size:22
Alignment explanation
Indices: 20521139--20521205 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
20521129 TTTTATCATG
* *
20521139 AATTTATTACTAAGTTTTTAAT
1 AATTTAATACTAAGTTTTCAAT
* * *
20521161 AATTAAATATTAAGTTTTCATT
1 AATTTAATACTAAGTTTTCAAT
*
20521183 AATTTACTACTAAGTTTATCAAT
1 AATTTAATACTAAGTTT-TCAAT
20521206 TACATACTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTTAATACTAAGTTTTCAAT
Found at i:20521587 original size:22 final size:21
Alignment explanation
Indices: 20521461--20521600 Score: 77
Period size: 22 Copynumber: 6.4 Consensus size: 21
20521451 AATTTTAACG
20521461 ATTTACTATTAAATTATCATTA
1 ATTTACTA-TAAATTATCATTA
* *
20521483 ATCTACTACTAAATTATAAATT-
1 ATTTACTA-TAAATTAT-CATTA
* * * * *
20521505 ATTTACCACCAAATTGTGAATA
1 ATTTACTA-TAAATTATCATTA
* * *
20521527 ATTTACTATTAAATTGTTAATA
1 ATTTACTA-TAAATTATCATTA
* *
20521549 ATTTATTATAAAGTTATCATTC
1 ATTTACTATAAA-TTATCATTA
*
20521571 ATTTACTATGAAATTATTGATT-
1 ATTTACTAT-AAATTA-TCATTA
20521593 ATTTACTA
1 ATTTACTA
20521601 CAAAATATTC
Statistics
Matches: 93, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
21 6 0.06
22 77 0.83
23 10 0.11
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (21 bp):
ATTTACTATAAATTATCATTA
Found at i:20521710 original size:22 final size:22
Alignment explanation
Indices: 20521685--20522004 Score: 102
Period size: 22 Copynumber: 14.5 Consensus size: 22
20521675 ATTCTTAGTG
20521685 ATTTACTACTAAATTATCATTA
1 ATTTACTACTAAATTATCATTA
* * * *
20521707 ATTTATTACTAAATCATTAATA
1 ATTTACTACTAAATTATCATTA
** * *
20521729 ATTTACTACTTTATTTTTATGT-
1 ATTTACTACTAAATTATCAT-TA
* * * * *
20521751 AGTTCCTATTATATTATGATTA
1 ATTTACTACTAAATTATCATTA
* *
20521773 ATTTATTACTAAGTT-T--TTA
1 ATTTACTACTAAATTATCATTA
20521792 ATTTAACTACTAAATTATCAATT-
1 ATTT-ACTACTAAATTATC-ATTA
* *
20521815 ATTTATTACTAAGTTAT--TTA
1 ATTTACTACTAAATTATCATTA
20521835 TGATTTACTACTAAATTTATCAATTA
1 --ATTTACTACTAAA-TTATC-ATTA
* * * ** **
20521861 CTTAATTACTATTAAACTAGAAAAA
1 ---ATTTACTACTAAATTATCATTA
* * *
20521886 ATTTACTATTACATTATCACTA
1 ATTTACTACTAAATTATCATTA
* * *
20521908 ATTTGCTACTAAA-TATAATTG
1 ATTTACTACTAAATTATCATTA
* * * *
20521929 ATTAACTACTAAGTTATCAATG
1 ATTTACTACTAAATTATCATTA
* * *
20521951 ATTAATTATTAAATTATCACTT-
1 ATTTACTACTAAATTATCA-TTA
* * * *
20521973 ATTT-TTATTAAGTTATCCTTA
1 ATTTACTACTAAATTATCATTA
20521994 ATTTACTACTA
1 ATTTACTACTA
20522005 TGCATTTATG
Statistics
Matches: 216, Mismatches: 63, Indels: 38
0.68 0.20 0.12
Matches are distributed among these distances:
19 9 0.04
20 11 0.05
21 34 0.16
22 131 0.61
23 10 0.05
24 2 0.01
25 2 0.01
26 5 0.02
27 12 0.06
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (22 bp):
ATTTACTACTAAATTATCATTA
Found at i:20521733 original size:44 final size:44
Alignment explanation
Indices: 20521649--20521738 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
20521639 CACTGATATG
* * * * *
20521649 CTAAATTATCAATGATTTATTATTACATTCTTAGTGATTTACTA
1 CTAAATTATCAATAATTTATTACTACAATCTTAATAATTTACTA
*
20521693 CTAAATTATCATTAATTTATTACTA-AATCATTAATAATTTACTA
1 CTAAATTATCAATAATTTATTACTACAATC-TTAATAATTTACTA
20521737 CT
1 CT
20521739 TTATTTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 3 0.08
44 36 0.92
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (44 bp):
CTAAATTATCAATAATTTATTACTACAATCTTAATAATTTACTA
Found at i:20521821 original size:42 final size:44
Alignment explanation
Indices: 20521773--20521871 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 44
20521763 ATTATGATTA
20521773 ATTTATTACTAAGTT-TTTA-ATTTAACTACTAAA-TTATCAATT
1 ATTTATTACTAAGTTATTTAGATTT-ACTACTAAATTTATCAATT
20521815 ATTTATTACTAAGTTATTTATGATTTACTACTAAATTTATCAATT
1 ATTTATTACTAAGTTATTTA-GATTTACTACTAAATTTATCAATT
*
20521860 ACTTAATTACTA
1 A-TTTATTACTA
20521872 TTAAACTAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
42 15 0.29
43 4 0.08
44 9 0.18
45 14 0.27
46 9 0.18
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (44 bp):
ATTTATTACTAAGTTATTTAGATTTACTACTAAATTTATCAATT
Found at i:20522063 original size:22 final size:22
Alignment explanation
Indices: 20522036--20522100 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
20522026 ATATTATATT
20522036 TGATTTACTATTAAGTTATTA-
1 TGATTTACTATTAAGTTATTAC
* * *
20522057 TGTATTTATTATTATGTTGTTAC
1 TG-ATTTACTATTAAGTTATTAC
* *
20522080 TGATTTACTACTAAATTATTA
1 TGATTTACTATTAAGTTATTA
20522101 ACTATTTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.54
Consensus pattern (22 bp):
TGATTTACTATTAAGTTATTAC
Found at i:20522107 original size:22 final size:21
Alignment explanation
Indices: 20522076--20522143 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
20522066 TATTATGTTG
*
20522076 TTACTGATTTACTACTAAATTA
1 TTACT-ATTTATTACTAAATTA
* *
20522098 TTAACTATTTGTTGCTAAATTA
1 TT-ACTATTTATTACTAAATTA
**
20522120 TCTTTTATTTATTACTAAATTA
1 T-TACTATTTATTACTAAATTA
20522142 TT
1 TT
20522144 TATAATCTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.03
22 32 0.86
23 4 0.11
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.53
Consensus pattern (21 bp):
TTACTATTTATTACTAAATTA
Found at i:20522154 original size:22 final size:22
Alignment explanation
Indices: 20522112--20522162 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
20522102 CTATTTGTTG
* *
20522112 CTAAATTATCTTTTATTTATTA
1 CTAAATTATCTTTAATCTATTA
20522134 CTAAATTAT-TTATAATCTATTA
1 CTAAATTATCTT-TAATCTATTA
*
20522156 CGAAATT
1 CTAAATT
20522163 TATTATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (22 bp):
CTAAATTATCTTTAATCTATTA
Found at i:20522279 original size:22 final size:22
Alignment explanation
Indices: 20522254--20522301 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20522244 AGCTACTAAG
*
20522254 TTATCACTT-ATTTTTTATTAAA
1 TTATC-CTTAATTTATTATTAAA
*
20522276 TTATCCTTAATTTATTATTATA
1 TTATCCTTAATTTATTATTAAA
20522298 TTAT
1 TTAT
20522302 TATGCAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATCCTTAATTTATTATTAAA
Found at i:20522403 original size:22 final size:22
Alignment explanation
Indices: 20522285--20522464 Score: 93
Period size: 22 Copynumber: 8.2 Consensus size: 22
20522275 ATTATCCTTA
* * *
20522285 ATTTATTATTATATTATTATGC
1 ATTTACTACTATATTATTATGT
* * *
20522307 AGTTACAACTATATT-TTAATTT
1 ATTTACTACTATATTATT-ATGT
* *
20522329 ATTTACTACTAAAATATTCATG-
1 ATTTACTACTATATTATT-ATGT
* * * *
20522351 ATTTACGACAAAAATATTCATG-
1 ATTTACTACTATATTATT-ATGT
*
20522373 ATTTACTATTATATTATTATGT
1 ATTTACTACTATATTATTATGT
* * *
20522395 ATTTACTATTATGTTATTA-AT
1 ATTTACTACTATATTATTATGT
* *
20522416 AGTTTACTACTATTTTATCAAT-T
1 A-TTTACTACTATATTAT-TATGT
* *
20522439 A-TTACTACTAAATTATTATTT
1 ATTTACTACTATATTATTATGT
20522460 ATTTA
1 ATTTA
20522465 TTATTAAGTT
Statistics
Matches: 123, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.02
21 22 0.18
22 92 0.75
23 7 0.06
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTACTACTATATTATTATGT
Found at i:20522515 original size:65 final size:65
Alignment explanation
Indices: 20522375--20522500 Score: 153
Period size: 65 Copynumber: 1.9 Consensus size: 65
20522365 TATTCATGAT
* * * * * * * **
20522375 TTACTATTATATTATTATGTATTTACTATTATGTTATTAATAGTTTACTACTATTTTATCAATTA
1 TTACTACTAAATTATTATTTATTTACTATTAAGTTAGTAATAATTTACTACAAAATTATCAATTA
* *
20522440 TTACTACTAAATTATTATTTATTTATTATTAAGTTAGTCATAATTTACTACAAAATTATCA
1 TTACTACTAAATTATTATTTATTTACTATTAAGTTAGTAATAATTTACTACAAAATTATCA
20522501 TTGATTTAGT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.52
Consensus pattern (65 bp):
TTACTACTAAATTATTATTTATTTACTATTAAGTTAGTAATAATTTACTACAAAATTATCAATTA
Found at i:20522520 original size:22 final size:22
Alignment explanation
Indices: 20522495--20522574 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
20522485 TACTACAAAA
20522495 TTATCATTGATTTAGTCTAAAG
1 TTATCATTGATTTAGTCTAAAG
** * *
20522517 TTATTTTTAATTTTGTTCT-AAG
1 TTATCATTGATTTAG-TCTAAAG
* **
20522539 TTATTATTGATTTACAACTAAA-
1 TTATCATTGATTTA-GTCTAAAG
*
20522561 TTATCAATGATTTA
1 TTATCATTGATTTA
20522575 TTATGTATTT
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
22 39 0.89
23 5 0.11
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (22 bp):
TTATCATTGATTTAGTCTAAAG
Done.