Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 74 of 93
Found at i:10719665 original size:3 final size:3
Alignment explanation
Indices: 10719657--10719691 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10719647 AAAAAGAATG
10719657 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10719692 CCAGTTAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10727834 original size:20 final size:20
Alignment explanation
Indices: 10727809--10727914 Score: 149
Period size: 20 Copynumber: 5.3 Consensus size: 20
10727799 ATAACAAATT
*
10727809 ATGCAAATATATTAGTAATC
1 ATGCAAATATATTAATAATC
10727829 ATGCAAATATATTAATAATC
1 ATGCAAATATATTAATAATC
* *
10727849 ATGCAAAAATATAAATAATC
1 ATGCAAATATATTAATAATC
* * *
10727869 ATGCAAAAATATAAATAACC
1 ATGCAAATATATTAATAATC
*
10727889 ATGCAAATATAATAATAATC
1 ATGCAAATATATTAATAATC
10727909 ATGCAA
1 ATGCAA
10727915 GAATACAATG
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (20 bp):
ATGCAAATATATTAATAATC
Found at i:10728235 original size:21 final size:20
Alignment explanation
Indices: 10728211--10728261 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
10728201 AACAGAAAGG
10728211 AAAAA-AAAGAAGGAAAAAATC
1 AAAAATAAA-AAGG-AAAAATC
*
10728232 AAAAATAAAATGGAAAAATC
1 AAAAATAAAAAGGAAAAATC
*
10728252 AAAAAGAAAA
1 AAAAATAAAA
10728262 TCAAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 16 0.59
21 8 0.30
22 3 0.11
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.08
Consensus pattern (20 bp):
AAAAATAAAAAGGAAAAATC
Found at i:10728248 original size:20 final size:20
Alignment explanation
Indices: 10728225--10728262 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10728215 AAAAGAAGGA
*
10728225 AAAAATCAAAAATAAAATGG
1 AAAAATCAAAAAGAAAATGG
10728245 AAAAATCAAAAAGAAAAT
1 AAAAATCAAAAAGAAAAT
10728263 CAAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAATCAAAAAGAAAATGG
Found at i:10728273 original size:18 final size:18
Alignment explanation
Indices: 10728252--10728286 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10728242 TGGAAAAATC
*
10728252 AAAAAGAAAATCAAAAGA
1 AAAAAGAAAAGCAAAAGA
10728270 AAAAAGAAAAGCAAAAG
1 AAAAAGAAAAGCAAAAG
10728287 CCTACGATCA
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:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAAGCAAAAGA
Found at i:10729774 original size:15 final size:15
Alignment explanation
Indices: 10729751--10729872 Score: 82
Period size: 15 Copynumber: 8.6 Consensus size: 15
10729741 AATAAAAAAT
*
10729751 AATATTATATTAATA
1 AATAATATATTAATA
10729766 AATAATATATTAATA
1 AATAATATATTAATA
* *
10729781 ATTATTATATTAAT-
1 AATAATATATTAATA
*
10729795 --TAAT-TAATAATA
1 AATAATATATTAATA
*
10729807 TATTAATATATTAATA
1 -AATAATATATTAATA
*
10729823 AA-AA-ATA-TGAT-
1 AATAATATATTAATA
* *
10729834 ATTAATA-AATAATA
1 AATAATATATTAATA
*
10729848 ATATAATATATTCATA
1 A-ATAATATATTAATA
10729864 AATAATATA
1 AATAATATA
10729873 AAAATCATAA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
11 7 0.08
12 9 0.11
13 7 0.08
14 3 0.04
15 44 0.53
16 13 0.16
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:10729792 original size:8 final size:8
Alignment explanation
Indices: 10729756--10729822 Score: 66
Period size: 8 Copynumber: 8.2 Consensus size: 8
10729746 AAAATAATAT
10729756 TATATTAA
1 TATATTAA
*
10729764 TA-AATAA
1 TATATTAA
10729771 TATATTAA
1 TATATTAA
*
10729779 TA-ATTAT
1 TATATTAA
10729786 TATATTAA
1 TATATTAA
*
10729794 TTAATTAATAA
1 -T-A-TATTAA
10729805 TATATTAA
1 TATATTAA
10729813 TATATTAA
1 TATATTAA
10729821 TA
1 TA
10729823 AAAAATATGA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
7 12 0.25
8 27 0.56
9 2 0.04
10 2 0.04
11 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TATATTAA
Found at i:10729800 original size:23 final size:24
Alignment explanation
Indices: 10729709--10729859 Score: 56
Period size: 23 Copynumber: 6.4 Consensus size: 24
10729699 CTTATAAATA
* *
10729709 ATATTATATTAA-TAAATAATTA-
1 ATATTATATTAATTAATTAATAAT
*
10729731 ATATCATATTAA-TAA--AA-AAT
1 ATATTATATTAATTAATTAATAAT
*
10729751 AATATTATATTAA-TAAATAAT-AT
1 -ATATTATATTAATTAATTAATAAT
*
10729774 ATTAATAATTATTATATTAATTAATTAAT
1 A-T-ATTA-TATTA-ATTAATTAA-TAAT
*
10729803 A-A-TATATTAA-TATATTAATAAAAA
1 ATATTATATTAATTA-ATTAAT--AAT
* *
10729827 ATATGATATTAA-TAAATAATAAT
1 ATATTATATTAATTAATTAATAAT
*
10729850 ATAATATATT
1 ATATTATATT
10729860 CATAAATAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 33
0.69 0.08 0.23
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 14 0.14
22 18 0.18
23 21 0.21
24 11 0.11
25 12 0.12
26 11 0.11
27 6 0.06
28 1 0.01
29 3 0.03
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (24 bp):
ATATTATATTAATTAATTAATAAT
Found at i:10729826 original size:78 final size:82
Alignment explanation
Indices: 10729709--10729864 Score: 207
Period size: 78 Copynumber: 1.9 Consensus size: 82
10729699 CTTATAAATA
*
10729709 ATATTATATTAATAAATAATTAATATCATATTAATAAAAAATA-ATATT-AT-ATTAATAA-ATA
1 ATATTATATTAATAAATAATTAATATCATATTAATAAAAAATAGATATTAATAAATAATAATATA
10729770 ATATATTAATAATTATT
66 ATATATTAATAATTATT
* *
10729787 ATATTA-ATTAATTAATAATATATTAAT-ATATTAATAAAAAATATGATATTAATAAATAATAAT
1 ATATTATATTAATAAATAAT-TAAT-ATCATATTAATAAAAAATA-GATATTAATAAATAATAAT
*
10729850 ATAATATATTCATAA
63 ATAATATATTAATAA
10729865 ATAATATAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
77 12 0.18
78 25 0.37
79 2 0.03
80 5 0.07
81 2 0.03
82 7 0.10
83 14 0.21
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (82 bp):
ATATTATATTAATAAATAATTAATATCATATTAATAAAAAATAGATATTAATAAATAATAATATA
ATATATTAATAATTATT
Found at i:10729882 original size:18 final size:20
Alignment explanation
Indices: 10729844--10729885 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
10729834 ATTAATAAAT
*
10729844 AATAATATAATATATTCATA
1 AATAATATAATATAATCATA
10729864 AATAATATAA-A-AATCATA
1 AATAATATAATATAATCATA
10729882 AATA
1 AATA
10729886 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATATAATATAATCATA
Found at i:10729883 original size:41 final size:41
Alignment explanation
Indices: 10729768--10729885 Score: 103
Period size: 41 Copynumber: 2.9 Consensus size: 41
10729758 TATTAATAAA
** * * * *
10729768 TAATATATTAATAATTATTATATTAATTAATTAATAATATAT
1 TAATATATTAATAAAAAATATA-AAAATAATAAATAATATAT
* * *
10729810 TAATATATTAATAAAAAATATGATATTAATAAATAATA-AT
1 TAATATATTAATAAAAAATATAAAAATAATAAATAATATAT
* * *
10729850 ATAATATATTCATAAATAATATAAAAATCATAAATA
1 -TAATATATTAATAAAAAATATAAAAATAATAAATA
10729886 TTTTTATTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
40 2 0.03
41 42 0.68
42 18 0.29
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (41 bp):
TAATATATTAATAAAAAATATAAAAATAATAAATAATATAT
Found at i:10729929 original size:19 final size:18
Alignment explanation
Indices: 10729902--10729989 Score: 58
Period size: 19 Copynumber: 4.9 Consensus size: 18
10729892 TTTTTAGTAT
*
10729902 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
10729921 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
* * *
10729939 TTATTAA-AATATAATTATT
1 TT-TTAATATTA-AATAATA
*
10729958 TTTTAATATT-AAT--CA
1 TTTTAATATTAAATAATA
*
10729973 TTTTAATAATAAATAAT
1 TTTTAATATTAAATAAT
10729990 TTCAATATAC
Statistics
Matches: 52, Mismatches: 11, Indels: 13
0.68 0.14 0.17
Matches are distributed among these distances:
15 9 0.17
16 3 0.06
17 3 0.06
18 14 0.27
19 23 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:10729970 original size:17 final size:17
Alignment explanation
Indices: 10729899--10729976 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 17
10729889 TTATTTTTAG
10729899 TATTTTTT-ATATTAACAT
1 TATTTTTTAATATT-A-AT
* * *
10729917 AATATTTTAATATTAAA
1 TATTTTTTAATATTAAT
*
10729934 TATTATTATTAAAATATAAT
1 TATT-TT-TTAATAT-TAAT
10729954 TATTTTTTAATATTAAT
1 TATTTTTTAATATTAAT
*
10729971 CATTTT
1 TATTTT
10729977 AATAATAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
17 12 0.26
18 15 0.32
19 13 0.28
20 7 0.15
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTTTTAATATTAAT
Found at i:10730064 original size:15 final size:15
Alignment explanation
Indices: 10730046--10730074 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10730036 TATTAATATT
10730046 ATTTAAAAAAATAAA
1 ATTTAAAAAAATAAA
10730061 ATTTAAAAAAATAA
1 ATTTAAAAAAATAA
10730075 TTAATAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTTAAAAAAATAAA
Found at i:10735091 original size:9 final size:10
Alignment explanation
Indices: 10735072--10735189 Score: 77
Period size: 9 Copynumber: 11.8 Consensus size: 10
10735062 AATAGACCCA
*
10735072 TATTTTTTAT
1 TATTATTTAT
10735082 T-TTATTTAT
1 TATTATTTAT
10735091 TATTA-TTAT
1 TATTATTTAT
**
10735100 TAGCA-TTAT
1 TATTATTTAT
*
10735109 TATTCTTT-T
1 TATTATTTAT
* *
10735118 TTTTCGTTTAT
1 TATT-ATTTAT
10735129 TATTTATTTTTAT
1 TA-TTA--TTTAT
10735142 TATTATTTAT
1 TATTATTTAT
10735152 TATTA-TTAT
1 TATTATTTAT
*
10735161 CATTATTTATTT
1 TATTATTTA--T
10735173 TATTATTTAT
1 TATTATTTAT
10735183 T-TTATTT
1 TATTATTT
10735190 TATCTTTTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
9 39 0.45
10 24 0.28
11 2 0.02
12 14 0.16
13 7 0.08
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (10 bp):
TATTATTTAT
Found at i:10735095 original size:3 final size:3
Alignment explanation
Indices: 10735078--10735192 Score: 69
Period size: 3 Copynumber: 38.3 Consensus size: 3
10735068 CCCATATTTT
** * * * *
10735078 TTA TT- TTA TTTA TTA TTA TTA TTA GCA TTA TTA TTC TTT TTT TTC
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
10735123 GT- TTA TTA TTTA TTT TTA TTA TTA TTTA TTA TTA TTA TCA TTA TTTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA
10735170 TT- TTA TTA TTTA TT- TTA TT- TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA T
10735193 CTTTTATTTT
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
2 9 0.10
3 65 0.73
4 15 0.17
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:10735975 original size:7 final size:8
Alignment explanation
Indices: 10735964--10736031 Score: 57
Period size: 8 Copynumber: 8.2 Consensus size: 8
10735954 CATTTTAGAT
10735964 TTTTTTTA
1 TTTTTTTA
10735972 TTTTTTTA
1 TTTTTTTA
10735980 TTTATTTTA
1 TTT-TTTTA
****
10735989 TTTAAGCA
1 TTTTTTTA
10735997 TTTTATTTA
1 TTTT-TTTA
*
10736006 TTTGTTT-
1 TTTTTTTA
10736013 TTTTTTTA
1 TTTTTTTA
10736021 GTTTTTTTA
1 -TTTTTTTA
10736030 TT
1 TT
10736032 ATTAAATTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
7 6 0.13
8 20 0.43
9 20 0.43
ACGTcount: A:0.16, C:0.01, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTTTTTA
Found at i:10737287 original size:22 final size:22
Alignment explanation
Indices: 10737244--10737287 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
10737234 AAATAACCTC
* *
10737244 ATTTTCCATTGACTAGTAAGTT
1 ATTTTCCATTGACCAATAAGTT
* *
10737266 ATTTTCTATTGACCAATCAGTT
1 ATTTTCCATTGACCAATAAGTT
10737288 TTCTACCAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (22 bp):
ATTTTCCATTGACCAATAAGTT
Found at i:10741162 original size:26 final size:26
Alignment explanation
Indices: 10741126--10741178 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
10741116 TTTCAGTACT
10741126 TATAATAATAATGAAGCATGATGTAA
1 TATAATAATAATGAAGCATGATGTAA
10741152 TATAATAATAATGAAGCATGATGTAA
1 TATAATAATAATGAAGCATGATGTAA
10741178 T
1 T
10741179 TTCTAAAGTT
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:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (26 bp):
TATAATAATAATGAAGCATGATGTAA
Found at i:10749648 original size:15 final size:16
Alignment explanation
Indices: 10749623--10749657 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
10749613 CTTTTGTTTC
*
10749623 TGGAGAAAAACTTTGT
1 TGGAGAAAAACTTTAT
10749639 TGGA-AAAAACTTTAT
1 TGGAGAAAAACTTTAT
10749654 TGGA
1 TGGA
10749658 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (16 bp):
TGGAGAAAAACTTTAT
Found at i:10757678 original size:29 final size:29
Alignment explanation
Indices: 10757636--10757720 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
10757626 TATTGTAGAA
*
10757636 ATCTGATTCTCCTACATTAGTGCAGCTTG
1 ATCTGATTCTCCTACATTAATGCAGCTTG
10757665 ATCTGATTCTCCTACATTAATGCA----G
1 ATCTGATTCTCCTACATTAATGCAGCTTG
*
10757690 ATCTGATTCTCCTACATTACTGCAGCTTG
1 ATCTGATTCTCCTACATTAATGCAGCTTG
10757719 AT
1 AT
10757721 TTCCTAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
25 24 0.48
29 26 0.52
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.38
Consensus pattern (29 bp):
ATCTGATTCTCCTACATTAATGCAGCTTG
Found at i:10757698 original size:25 final size:25
Alignment explanation
Indices: 10757636--10757726 Score: 105
Period size: 25 Copynumber: 3.6 Consensus size: 25
10757626 TATTGTAGAA
*
10757636 ATCTGATTCTCCTACATTAGTGCAGCTTG
1 ATCTGATTCTCCTACATTAATGCA----G
10757665 ATCTGATTCTCCTACATTAATGCAG
1 ATCTGATTCTCCTACATTAATGCAG
*
10757690 ATCTGATTCTCCTACATTACTGCAG
1 ATCTGATTCTCCTACATTAATGCAG
*
10757715 CT-TGATT-TCCTA
1 ATCTGATTCTCCTA
10757727 ATTTATTTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.08
24 5 0.08
25 26 0.44
29 23 0.39
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (25 bp):
ATCTGATTCTCCTACATTAATGCAG
Found at i:10768262 original size:2 final size:2
Alignment explanation
Indices: 10768257--10768315 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
10768247 AAAATTAATC
* * *
10768257 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT GT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
10768298 CT GT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT
10768316 GTAATCTGGC
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10768270 original size:8 final size:8
Alignment explanation
Indices: 10768257--10768318 Score: 90
Period size: 8 Copynumber: 7.9 Consensus size: 8
10768247 AAAATTAATC
*
10768257 ATATATAT
1 ATATGTAT
*
10768265 ATATATAT
1 ATATGTAT
10768273 ATATGTAT
1 ATATGTAT
10768281 ATATGTAT
1 ATATGTAT
10768289 ATATGTA-
1 ATATGTAT
*
10768296 ATCTGTAT
1 ATATGTAT
10768304 ATATGTAT
1 ATATGTAT
10768312 ATATGTA
1 ATATGTA
10768319 ATCTGGCAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
7 6 0.12
8 44 0.88
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (8 bp):
ATATGTAT
Found at i:10769034 original size:82 final size:82
Alignment explanation
Indices: 10768934--10769094 Score: 268
Period size: 82 Copynumber: 2.0 Consensus size: 82
10768924 AATTTATTCT
* *
10768934 AACCAAGAAGCATCTAGTCAGGGAATGGATAAAACTCAAAACGCCCAGCACAAATTCTAACGAGA
1 AACCAAGAAGCATCTAGTCAGGGAATGGATAAAACTCAAAACACCCAGCACAAATTCCAACGAGA
10768999 TGAAAAAATAATCATGA
66 TGAAAAAATAATCATGA
* * * *
10769016 AACCAAGAAGCATCTAGTCAGGGAATGGTTAAAACTCAAAACACCCTGCACGAATTCCAATGAGA
1 AACCAAGAAGCATCTAGTCAGGGAATGGATAAAACTCAAAACACCCAGCACAAATTCCAACGAGA
10769081 TGAAAAAATAATCA
66 TGAAAAAATAATCA
10769095 CGAAGCTTTG
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.17
Consensus pattern (82 bp):
AACCAAGAAGCATCTAGTCAGGGAATGGATAAAACTCAAAACACCCAGCACAAATTCCAACGAGA
TGAAAAAATAATCATGA
Found at i:10770293 original size:2 final size:2
Alignment explanation
Indices: 10770286--10770322 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
10770276 GTTTTAAAGC
*
10770286 AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10770323 AGTTTAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10775701 original size:26 final size:26
Alignment explanation
Indices: 10775672--10775736 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
10775662 CTCTCTCATC
*
10775672 TTTTCCTCAATTTGGACTACCCCTAA
1 TTTTCCTCAATTCGGACTACCCCTAA
10775698 TTTTCCTCAATTCGGACTACCCCTAA
1 TTTTCCTCAATTCGGACTACCCCTAA
10775724 TTTTCCTCAATTC
1 TTTTCCTCAATTC
10775737 ACATGTCCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.22, C:0.32, G:0.06, T:0.40
Consensus pattern (26 bp):
TTTTCCTCAATTCGGACTACCCCTAA
Found at i:10782025 original size:29 final size:29
Alignment explanation
Indices: 10781983--10782047 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
10781973 TTAGATTATT
*
10781983 TATTTTTTAGTAACTATCTTCCTTCTATA
1 TATTTTTTAGTAACTATCTCCCTTCTATA
10782012 TATTTTTTAGTAACTATCTCCCTTCTATA
1 TATTTTTTAGTAACTATCTCCCTTCTATA
10782041 TATTTTT
1 TATTTTT
10782048 AGAAGATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.03, T:0.57
Consensus pattern (29 bp):
TATTTTTTAGTAACTATCTCCCTTCTATA
Found at i:10790796 original size:16 final size:16
Alignment explanation
Indices: 10790773--10790814 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
10790763 CATGGAACCA
10790773 TAAATTCATGAAT-GAT
1 TAAATTCATGAATAG-T
*
10790789 TAACTTCATGAATAGT
1 TAAATTCATGAATAGT
10790805 TAAATTCATG
1 TAAATTCATG
10790815 CAATTTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (16 bp):
TAAATTCATGAATAGT
Found at i:10790967 original size:16 final size:15
Alignment explanation
Indices: 10790946--10791013 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
10790936 ATGGATACTA
10790946 TAAATTCATAAATGAT
1 TAAATTCATAAAT-AT
* *
10790962 TAAATTTATGAATAGT
1 TAAATTCATAAATA-T
*
10790978 TAAAATTTATAAATAAT
1 T-AAATTCATAAAT-AT
10790995 TAAATTCATATAAT-T
1 TAAATTCATA-AATAT
10791010 TAAA
1 TAAA
10791014 ATAAAAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
15 6 0.14
16 21 0.48
17 16 0.36
18 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (15 bp):
TAAATTCATAAATAT
Found at i:10790985 original size:17 final size:17
Alignment explanation
Indices: 10790947--10790998 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
10790937 TGGATACTAT
* *
10790947 AAATTCATAAATGATT-
1 AAATTTATAAATAATTA
* *
10790963 AAATTTATGAATAGTTA
1 AAATTTATAAATAATTA
10790980 AAATTTATAAATAATTA
1 AAATTTATAAATAATTA
10790997 AA
1 AA
10790999 TTCATATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (17 bp):
AAATTTATAAATAATTA
Found at i:10792412 original size:4 final size:4
Alignment explanation
Indices: 10792403--10792432 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
10792393 TATTTTTATT
10792403 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
10792433 ATTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:10792443 original size:16 final size:16
Alignment explanation
Indices: 10792393--10792444 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
10792383 AAGATGGGTC
* *
10792393 TATTTTTATTTTTATT
1 TATTATTATTATTATT
10792409 TATTTATTTATTTATTTATT
1 TA-TTA-TTA-TTA-TTATT
10792429 TATTATTATTATTATT
1 TATTATTATTATTATT
10792445 GTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 7 0.23
17 5 0.17
18 6 0.20
19 5 0.17
20 7 0.23
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TATTATTATTATTATT
Found at i:10793266 original size:21 final size:21
Alignment explanation
Indices: 10793230--10793281 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
10793220 CCGATTCAAT
* *
10793230 TTTTTTTTGGTATTTTTTGTTTA
1 TTTTCTTTGGT-TTTTTTG-GTA
10793253 TTTTCTTTGGTTTTTTTGGTA
1 TTTTCTTTGGTTTTTTTGGTA
10793274 TTTTCTTT
1 TTTTCTTT
10793282 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 10 0.37
22 7 0.26
23 10 0.37
ACGTcount: A:0.06, C:0.04, G:0.13, T:0.77
Consensus pattern (21 bp):
TTTTCTTTGGTTTTTTTGGTA
Found at i:10793430 original size:16 final size:17
Alignment explanation
Indices: 10793403--10793444 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
10793393 AGCATCAATT
*
10793403 TTTCTTAAAAAT-AAAA
1 TTTCTAAAAAATAAAAA
*
10793419 TTTTTAAAAAATAAAAA
1 TTTCTAAAAAATAAAAA
10793436 TTTCTAAAA
1 TTTCTAAAA
10793445 GATATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTCTAAAAAATAAAAA
Found at i:10793481 original size:75 final size:75
Alignment explanation
Indices: 10793347--10793564 Score: 257
Period size: 75 Copynumber: 2.9 Consensus size: 75
10793337 AAAATAGAAA
* * * * * * *
10793347 AAAAAATAAAATTTTCAAGAAAAAATATTTTTAAGGAAAAGTTAAAAGCATCAATTTTTCTTAAA
1 AAAAAATAAAAATTTC--TAAAAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAA
10793412 AATAAAATTTTT
64 AATAAAATTTTT
10793424 AAAAAATAAAAATTTCTAAAAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
1 AAAAAATAAAAATTTCTAAAAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
10793489 TAAAATTTTT
66 TAAAATTTTT
* * * *
10793499 -AACAATAAAAATTT-TCAAAAG-T-GTTTTGAAGAAAAA-TTGACAGTATCAATTTTTCTTGAA
1 AAAAAATAAAAATTTCT-AAAAGATATTTTTG-AGAAAAAGTTGAAAGTATCAATTTTTCTTAAA
*
10793559 ATTAAA
64 AATAAA
10793565 TAAAAAAAAT
Statistics
Matches: 127, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
72 32 0.25
73 9 0.07
74 18 0.14
75 53 0.42
77 15 0.12
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (75 bp):
AAAAAATAAAAATTTCTAAAAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
TAAAATTTTT
Found at i:10793490 original size:59 final size:57
Alignment explanation
Indices: 10793425--10793843 Score: 282
Period size: 60 Copynumber: 7.0 Consensus size: 57
10793415 AAAATTTTTA
*
10793425 AAAAATAAAAATTTCTAAAAGATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAAAATTTC-AAAAAATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* * *
10793484 AAAAATAAAATTTTTAACAATAAAAATTTTCAAAAGTGTTTTGA-AGAAAAATTGACAGTATCAA
1 AAAAATAAAA-ATTT--C-A-AAAAA---T----A---TTTTGAGA-AAAAGTTGAAAGTATCAA
10793548 TTTTTCTT
50 TTTTTCTT
* * *
10793556 GAAATTAAATAA----AAAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTT
1 AAAAATAAA-AATTTCAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
*
10793610 AAAAATAAAAATTATCAAGAAAAGTATTTTGAGAAAAAGTTGAAAGTATC-AGTTTTCTT
1 AAAAATAAAAATT-TCAA-AAAA-TATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* * * * * * * *
10793669 TAAAATTAAAACTTCAAAAAAAAACATTTTGAGGAAAAGCTGGAAGTACCAATTTTTCTT
1 AAAAATAAAAATTTC---AAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* * * *
10793729 AAAAATAAAAATTATCAAGAAAAATATTTTAAGAAAAAGTTGAAAGTGTTAA-TTTTGTT
1 AAAAATAAAAATT-TC-A-AAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
* * ** *
10793788 AAAAATAAAAATCTC--CAAATGCTTTAACG-AAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAAAATTTCAAAAAATATTTTGA-GAAAAAGTTGAAAGTATCAATTTTTCTT
10793843 A
1 A
10793844 TACAAAAGCA
Statistics
Matches: 285, Mismatches: 44, Indels: 66
0.72 0.11 0.17
Matches are distributed among these distances:
53 2 0.01
54 61 0.21
55 9 0.03
57 1 0.00
58 6 0.02
59 73 0.26
60 75 0.26
61 5 0.02
62 2 0.01
63 4 0.01
64 5 0.02
65 1 0.00
66 1 0.00
70 1 0.00
71 1 0.00
72 37 0.13
73 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (57 bp):
AAAAATAAAAATTTCAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT
Found at i:10793641 original size:60 final size:60
Alignment explanation
Indices: 10793569--10793799 Score: 288
Period size: 60 Copynumber: 3.9 Consensus size: 60
10793559 ATTAAATAAA
10793569 AAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAG
1 AAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAG
* * * * * * *
10793629 AAAAGTATTTTGAGAAAAAGTTGAAAGTATC-AGTTTTCTTTAAAATTAAAACT-TCAAAA
1 AAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATC-AAG
* * * *
10793688 AAAAACATTTTGAGGAAAAGCTGGAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAG
1 AAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAG
* *** *
10793748 AAAAATATTTTAAGAAAAAGTTGAAAGTGTTAA-TTTTGTTAAAAATAAAAAT
1 AAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAAT
10793800 CTCCAAATGC
Statistics
Matches: 141, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
58 2 0.01
59 63 0.45
60 74 0.52
61 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (60 bp):
AAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAG
Found at i:10793793 original size:119 final size:119
Alignment explanation
Indices: 10793566--10793798 Score: 358
Period size: 119 Copynumber: 2.0 Consensus size: 119
10793556 GAAATTAAAT
* *
10793566 AAAAAAAATATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAA
1 AAAAAAAACATTTTGAGAAAAAGCTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAA
* * * * *
10793631 AAGTATTTTGAGAAAAAGTTGAAAGTATCAGTTTTCTTTAAAATTAAAACTTCA
66 AAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAAAACTTCA
* *
10793685 AAAAAAAACATTTTGAGGAAAAGCTGGAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAA
1 AAAAAAAACATTTTGAGAAAAAGCTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAA
* * *
10793750 AAATATTTTAAGAAAAAGTTGAAAGTGTTAATTTTGTTAAAAATAAAAA
66 AAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAAAA
10793799 TCTCCAAATG
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (119 bp):
AAAAAAAACATTTTGAGAAAAAGCTGAAAGTACCAATTTTTCTTAAAAATAAAAATTATCAAGAA
AAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTAAAAATAAAAACTTCA
Found at i:10797965 original size:14 final size:13
Alignment explanation
Indices: 10797945--10797989 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
10797935 ATGAAAGAAG
10797945 AAAAAAAAATGAA
1 AAAAAAAAATGAA
*
10797958 AGAAAAAAATGAA
1 AAAAAAAAATGAA
*
10797971 AAAATAAAAAGGAA
1 AAAA-AAAAATGAA
10797985 AAAAA
1 AAAAA
10797990 TGAGAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (13 bp):
AAAAAAAAATGAA
Found at i:10798005 original size:15 final size:15
Alignment explanation
Indices: 10797987--10798019 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
10797977 AAAAGGAAAA
10797987 AAATGAGA-AAAATGG
1 AAATGAGAGAAAA-GG
10798002 AAATGAGAGAAAAGG
1 AAATGAGAGAAAAGG
10798017 AAA
1 AAA
10798020 ACTCAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (15 bp):
AAATGAGAGAAAAGG
Found at i:10799577 original size:41 final size:43
Alignment explanation
Indices: 10799407--10799596 Score: 234
Period size: 42 Copynumber: 4.6 Consensus size: 43
10799397 TGGTCTCCAA
* * *
10799407 GAGCA-TTTATTTTTCAAAAG-CGTGGTTGCCTCTATTTAGAT
1 GAGCATTTTATTTTTCAAAAGTCGTGGTTACCTCTGTTTAGAG
*
10799448 AAGCATTTTATTTTTC-AAAGTCGTGGTTACCTCTGTTTAGAG
1 GAGCATTTTATTTTTCAAAAGTCGTGGTTACCTCTGTTTAGAG
* * *
10799490 GAGCATTTTATTTTT-TAAAGTCGTGATTACCTCTGTTTAGAA
1 GAGCATTTTATTTTTCAAAAGTCGTGGTTACCTCTGTTTAGAG
* *
10799532 GAGCATTTTA-TTTTCAAAAGTTGTGG-TGCCTCTGTTTA-AGG
1 GAGCATTTTATTTTTCAAAAGTCGTGGTTACCTCTGTTTAGA-G
10799573 GAGCA-TTTATTTTTCAAAAGTCGT
1 GAGCATTTTATTTTTCAAAAGTCGT
10799597 TGAGCCTCTG
Statistics
Matches: 130, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
40 5 0.04
41 41 0.32
42 84 0.65
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (43 bp):
GAGCATTTTATTTTTCAAAAGTCGTGGTTACCTCTGTTTAGAG
Found at i:10799604 original size:41 final size:41
Alignment explanation
Indices: 10799407--10799801 Score: 229
Period size: 44 Copynumber: 9.4 Consensus size: 41
10799397 TGGTCTCCAA
* * * *
10799407 GAGCATTTATTTTTCAAAAG-CGTGGTTGCCTCTATTTAGAT
1 GAGCATTTATTTTTCAAAAGTCGTTG-AGCCTCTGTTTAGAG
* *
10799448 AAGCATTTTATTTTTC-AAAGTCGTGGTTA-CCTCTGTTTAGAG
1 GAGCA-TTTATTTTTCAAAAGTCGT--TGAGCCTCTGTTTAGAG
* * *
10799490 GAGCATTTTATTTTT-TAAAGTCG-TGATTACCTCTGTTTAGAA
1 GAGCA-TTTATTTTTCAAAAGTCGTTGA--GCCTCTGTTTAGAG
* * *
10799532 GAGCATTT-TATTTTCAAAAGTTGTGGTGCCTCTGTTTA-AGG
1 GAGCATTTAT-TTTTCAAAAGTCGTTGAGCCTCTGTTTAGA-G
* *
10799573 GAGCATTTATTTTTCAAAAGTCGTTGAGCCTCTGATTATAG
1 GAGCATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTTAGAG
* *** * * * * *
10799614 GAGCTTTGTTTATTTTTTTGAAGTAGTTAAGCCTTTGATTAGAA
1 GAGC---ATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTTAGAG
* *
10799658 GAGCTTTATTTATTTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAA
1 GAGC---ATTTA-TTTTTCAAAAGTCGTTGAGCCTCTGTTTAGAG
* *
10799702 GAGCTTCATTTATTTTTTC-AAAGTTCTGTT--GCCTTTATTTAGAG
1 GAG---CATTTA-TTTTTCAAAAG-TC-GTTGAGCCTCTGTTTAGAG
* *
10799746 GAGCAATTTA-TTTTCCAAAGTCATTGAGCCTCTGTTTAGAG
1 GAGC-ATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTTAGAG
*
10799787 GAGCATTTATGTTTC
1 GAGCATTTATTTTTC
10799802 TTGAAGTCGT
Statistics
Matches: 283, Mismatches: 43, Indels: 56
0.74 0.11 0.15
Matches are distributed among these distances:
39 4 0.01
40 14 0.05
41 87 0.31
42 75 0.27
43 1 0.00
44 92 0.33
45 6 0.02
46 3 0.01
47 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (41 bp):
GAGCATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTTAGAG
Found at i:10799818 original size:42 final size:41
Alignment explanation
Indices: 10799434--10799832 Score: 201
Period size: 42 Copynumber: 9.4 Consensus size: 41
10799424 AAGCGTGGTT
* ** * *
10799434 GCCTCTATTTAGATAAGCATTTTATTTT-TCAAAGTCGTGGTTA
1 GCCTCTGTTTAGAGGAGCA-TTTATTTTCTTAAAGTCGT--TGA
10799477 -CCTCTGTTTAGAGGAGCATTTTATTTT-TTAAAGTCG-TGA
1 GCCTCTGTTTAGAGGAGCA-TTTATTTTCTTAAAGTCGTTGA
* * * * * *
10799516 TTACCTCTGTTTAGAAGAGCATTTTATTTTC-AAAAGTTGTGGT
1 --GCCTCTGTTTAGAGGAGCA-TTTATTTTCTTAAAGTCGTTGA
*
10799559 GCCTCTGTTTA-AGGGAGCATTTATTTT-TCAAAAGTCGTTGA
1 GCCTCTGTTTAGA-GGAGCATTTATTTTCT-TAAAGTCGTTGA
* * * * * * *
10799600 GCCTCTGATTATAGGAGCTTTGTTTATTTTTTTGAAGTAGTTAA
1 GCCTCTGTTTAGAGGAGC---ATTTATTTTCTTAAAGTCGTTGA
* * * *
10799644 GCCTTTGATTAGAAGAGCTTTATTTATTTT-TTCAAAGTTGTTGA
1 GCCTCTGTTTAGAGGAGC---ATTTATTTTCTT-AAAGTCGTTGA
*
10799688 GCCTCTGTTTAGAAGAGCTTCATTTATTTT-TTCAAAGTTCTGTT--
1 GCCTCTGTTTAGAGGAG---CATTTATTTTCTT-AAAG-TC-GTTGA
* * * *
10799732 GCCTTTATTTAGAGGAGCAATTTATTTTC-CAAAGTCATTGA
1 GCCTCTGTTTAGAGGAGC-ATTTATTTTCTTAAAGTCGTTGA
* *
10799773 GCCTCTGTTTAGAGGAGCATTTATGTTTCTTGAAGTCGTTAA
1 GCCTCTGTTTAGAGGAGCATTTAT-TTTCTTAAAGTCGTTGA
* * *
10799815 GCCTTTGGTCAGAGGAGC
1 GCCTCTGTTTAGAGGAGC
10799833 TTTGATCAAA
Statistics
Matches: 286, Mismatches: 45, Indels: 51
0.75 0.12 0.13
Matches are distributed among these distances:
39 4 0.01
40 17 0.06
41 64 0.22
42 97 0.34
43 3 0.01
44 95 0.33
45 2 0.01
46 3 0.01
47 1 0.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (41 bp):
GCCTCTGTTTAGAGGAGCATTTATTTTCTTAAAGTCGTTGA
Found at i:10800044 original size:4 final size:4
Alignment explanation
Indices: 10800035--10800061 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10800025 TTTTATTTTC
10800035 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
10800062 GGATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:10800432 original size:19 final size:19
Alignment explanation
Indices: 10800374--10800433 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
10800364 ATTCTGGCGA
*
10800374 AATTTTTCGGCATCGATTG
1 AATTTTTTGGCATCGATTG
10800393 AATTTTTTGG--T-GA--G
1 AATTTTTTGGCATCGATTG
*
10800407 -TTTTTTTGGCATCGATTG
1 AATTTTTTGGCATCGATTG
10800425 AATTTTTTG
1 AATTTTTTG
10800434 ACAAGGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
13 8 0.25
14 1 0.03
15 1 0.03
16 4 0.12
17 1 0.03
18 1 0.03
19 16 0.50
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.52
Consensus pattern (19 bp):
AATTTTTTGGCATCGATTG
Found at i:10800925 original size:7 final size:8
Alignment explanation
Indices: 10800874--10800951 Score: 63
Period size: 8 Copynumber: 9.6 Consensus size: 8
10800864 TTCAATTTTT
10800874 TTTTTGTA
1 TTTTTGTA
10800882 TTTTTGTA
1 TTTTTGTA
10800890 TTTATT-T-
1 TTT-TTGTA
* *
10800897 TCTTTGGTT
1 T-TTTTGTA
10800906 TTTTTGTA
1 TTTTTGTA
10800914 TTTTTGTA
1 TTTTTGTA
10800922 TTTTTTGTA
1 -TTTTTGTA
* *
10800931 TTTATGTG
1 TTTTTGTA
10800939 TTTGTT-TA
1 TTT-TTGTA
10800947 TTTTT
1 TTTTT
10800952 TTAGAGTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
7 4 0.07
8 41 0.72
9 12 0.21
ACGTcount: A:0.10, C:0.01, G:0.13, T:0.76
Consensus pattern (8 bp):
TTTTTGTA
Found at i:10800925 original size:17 final size:17
Alignment explanation
Indices: 10800873--10800951 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
10800863 TTTCAATTTT
10800873 TTTTTTGTATTTTTGTA
1 TTTTTTGTATTTTTGTA
* *
10800890 TTTATTT-T-CTTTGGT-
1 TTT-TTTGTATTTTTGTA
10800905 TTTTTTGTATTTTTGTA
1 TTTTTTGTATTTTTGTA
* *
10800922 TTTTTTGTATTTATGTG
1 TTTTTTGTATTTTTGTA
*
10800939 TTTGTT-TATTTTT
1 TTTTTTGTATTTTT
10800952 TTAGAGTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
14 3 0.06
15 4 0.08
16 16 0.32
17 24 0.48
18 3 0.06
ACGTcount: A:0.10, C:0.01, G:0.13, T:0.76
Consensus pattern (17 bp):
TTTTTTGTATTTTTGTA
Found at i:10801098 original size:74 final size:71
Alignment explanation
Indices: 10801015--10801213 Score: 213
Period size: 74 Copynumber: 2.7 Consensus size: 71
10801005 TTTAAAGAAA
* *
10801015 AAAATATTTTTAAGGAAAAGTTGAAAGCATCAATTTTTCTTAAAATAAAATTTTTAAAAAATAAA
1 AAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAATTTCT-AAAAATAAA
10801080 AATTTCTTC
65 AATTTC--C
* * **** *
10801089 AAGATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTAAAAAAAAAAGAACATTTCTAAAAATAA
1 AAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATA-AA-ATTTCTAAAAATAA
10801153 AAATTTCC
64 AAATTTCC
* * *
10801161 AAAAGTA-TTTTAAGGAAAAGTTAAAAGTATCATTTTTTCTTTAAATTAAAATT
1 AAAA-TATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAATAAAATT
10801214 AAAAAAAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
72 30 0.30
73 15 0.15
74 51 0.50
75 5 0.05
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (71 bp):
AAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAATAAAATTTCTAAAAATAAAA
ATTTCC
Found at i:10801301 original size:60 final size:60
Alignment explanation
Indices: 10801140--10801495 Score: 326
Period size: 59 Copynumber: 6.1 Consensus size: 60
10801130 AAAAAGAACA
* * * *
10801140 TTTC-TAAAAATAAAAATT-TC--CAAAAGTATTTTAAGGAAAAGTTAAAAGTATCATTT
1 TTTCTTAAAAATAAAAATTATCAAAAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATT
* * ** * ** * *
10801196 TTTCTT-TAAATTAAAATTAAAAAAAAAAACATTTCGAGGACAAGTTGGAAGTATCAATT
1 TTTCTTAAAAATAAAAATTATCAAAAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATT
* * *
10801255 TTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAATTATCAAAAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATT
* * * * ** *
10801315 TTCCTTTAAATTAAAATTTCAGAAAAAAAAATATTTTGAA-GAAAAGTTGAAAGTACCAA-T
1 TTTCTTAAAAATAAAAATT-ATCAAAAAAAATATTTT-AAGGAAAAGTTGAAAGTATCAATT
* * *
10801375 TTTCTTAAAAATAAAAATTATCAAGAAAAATATTTTAAGGAAAAGTTTAAAGTGTCAA-T
1 TTTCTTAAAAATAAAAATTATCAAAAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATT
* * *
10801434 TTTCTTTAAAATAAAAA-TCTC----CAAATGA-TTTAAGGAAAAGTTGAAAGTATCAATT
1 TTTCTTAAAAATAAAAATTATCAAAAAAAAT-ATTTTAAGGAAAAGTTGAAAGTATCAATT
10801489 TTTCTTA
1 TTTCTTA
10801496 TACAAAAGTA
Statistics
Matches: 241, Mismatches: 49, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
54 27 0.11
55 8 0.03
56 14 0.06
57 1 0.00
58 5 0.02
59 80 0.33
60 74 0.31
61 31 0.13
62 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (60 bp):
TTTCTTAAAAATAAAAATTATCAAAAAAAATATTTTAAGGAAAAGTTGAAAGTATCAATT
Found at i:10801451 original size:120 final size:119
Alignment explanation
Indices: 10801140--10801449 Score: 416
Period size: 120 Copynumber: 2.6 Consensus size: 119
10801130 AAAAAGAACA
* *
10801140 TTTC-TAAAAATAAAAATT-TC--CAAAAGTATTTTAAGGAAAAGTTAAAAGTATCATTTTTTCT
1 TTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTAAGGAAAAGTTAAAAGTATCA-ATTTTCT
* * * *
10801201 TTAAATTAAAA-TTAAAAAAAAAAACATTTCGAGGACAAGTTGGAAGTATCAATT
65 TTAAATTAAAATTTAAAAAAAAAAACATTTCGAAGAAAAGTTGAAAGTACCAATT
* *
10801255 TTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCT
1 TTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTAAGGAAAAGTTAAAAGTATCAATTTT-CT
* * *
10801320 TTAAATTAAAATTTCAGAAAAAAAAATATTTTGAAGAAAAGTTGAAAGTACCAA-T
65 TTAAATTAAAATTT-AAAAAAAAAAACATTTCGAAGAAAAGTTGAAAGTACCAATT
* * *
10801375 TTTCTTAAAAATAAAAATTATCAAGAAAAATATTTTAAGGAAAAGTTTAAAGTGTCAATTTTCTT
1 TTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTAAGGAAAAGTTAAAAGTATCAATTTTCTT
*
10801440 TAAAATAAAA
66 TAAATTAAAA
10801450 ATCTCCAAAT
Statistics
Matches: 172, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
115 4 0.02
116 14 0.08
117 2 0.01
118 4 0.02
119 55 0.32
120 61 0.35
121 32 0.19
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (119 bp):
TTTCTTAAAAATAAAAATTATCAAGAAAAGTATTTTAAGGAAAAGTTAAAAGTATCAATTTTCTT
TAAATTAAAATTTAAAAAAAAAAACATTTCGAAGAAAAGTTGAAAGTACCAATT
Found at i:10803234 original size:86 final size:88
Alignment explanation
Indices: 10803107--10803276 Score: 215
Period size: 86 Copynumber: 2.0 Consensus size: 88
10803097 AAATTATTAT
10803107 AATGCCCCTTCTTACCATAATTATAAAAATACCTCTCATATTATAATTTGCCAAAAATTACTATA
1 AATGCCCCTTCTTACCATAATTATAAAAATACCTCTCATATTATAATTTG-CAAAAATTACTATA
*
10803172 A-ATCCTT-TAACCATAATTAAGAA
65 ATA-CCTTCTAACCACAATTAAGAA
* * * ** *
10803195 AATG-CCC-TCTTATCATAATTATGAAAATACC-CTTGATATTATAATTTGTTAAAATTATTATA
1 AATGCCCCTTCTTACCATAATTATAAAAATACCTC-TCATATTATAATTTGCAAAAATTACTATA
10803257 ATACCTTCTAACCACAATTA
65 ATACCTTCTAACCACAATTA
10803277 CCTAGAAAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
85 17 0.24
86 48 0.67
87 3 0.04
88 4 0.06
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (88 bp):
AATGCCCCTTCTTACCATAATTATAAAAATACCTCTCATATTATAATTTGCAAAAATTACTATAA
TACCTTCTAACCACAATTAAGAA
Found at i:10803885 original size:584 final size:583
Alignment explanation
Indices: 10802627--10804219 Score: 1560
Period size: 585 Copynumber: 2.7 Consensus size: 583
10802617 CTCTCTTACT
** * * * * * * * * *
10802627 ATAATTACAAAAATACCTTTTATATTATATTTGGCTGAAATTACTATGATACTTTC-CACTCACA
1 ATAATTATGAAAATACCCTTCATATTATAATTAGCTAAAATTATTATAATACCTTCTAAC-CACA
* * * * * ** *
10802691 ATTA-C-AAAAAAATCCTTTTTTAATTACTTCATATAATGCATCTCCTGCC-TAATTACGAAAAT
65 ATTACCTAAAAAAAT--TTTGTTAATTGCTTCACATAATACTTCTCCAACCATAATTACAAAAAT
* * * * ** * ** * **
10802753 AT-TCATCATATTATAATTAATC-AAAATTACCATAACGCTC-CTAAGCATAATTACAAAAATAC
128 ATCCCTTTATATTATCATTAGCCAAAAATTACTATAATACTCTCTAAACATAATTATGAAAATAC
* * * **
10802815 GTTTTTGATTGCTTCATAATTACGTATTAAATTTTAACATTTATACAATAATATGAAATTAATCC
193 CTTTTTGATTGCTTCATAATTATGCATTAAATTTTAACATACATACAATAATATGAAATTAATCC
** * ** *
10802880 TTTTAGAAATT-ATCATAATGCCTTTTTAATTACTTA-ATGATTGAATTATATGTATCCAAATTG
258 ACTTAGAAATTGATTATAATGCC-TTTTAATTAC-TAGACAATTG-ATTATATGCATCCAAATTG
** * * * *
10802943 ACTATGACACCCATGTTTCTATGATTAACTAAAATTACTTTATTGCTTCTCTTAACATAATTACT
320 ACTATGATTCCCATTTTTCAATGATTAACTAAAATTACTATAATGC-TCTCTTAACATAATTACT
* * * * * * * * *
10803008 AAAATGCCCCTCTTATCATAATTGGTCAAAATGACTATAATACCCCTAAAACTATAATTATGCAA
384 AAAATACCCATCTTATCATAATTGGTCAAAGTTACTATAAT-GCACTAAAACCATAATAACGCAA
** * * ** *
10803073 ATGCCCTTCCACCATCGTTTGCTAAAATTATTATAATGCCCCTTCTTACCATAATTATAAAAATA
448 ATGCCCTTCCACCATAATATGCTAAAATTACTATAACACCCCTTCTCACCATAATTATAAAAATA
* * ** *
10803138 CCTCTCATATTATAATTTGCCAAAAATTACTATAAATCCTTTAACCATAATTAAGAAAATGCCCT
513 CCTCTCACATTATAATTTGCCAAAAATTACTATAAACCCACTAACCATAATTAAGAAAATGCCAT
10803203 CTTATC
578 CTTATC
* * *
10803209 ATAATTATGAAAATACCCTTGATATTATAATTTGTTAAAATTATTATAATACCTTCTAACCACAA
1 ATAATTATGAAAATACCCTTCATATTATAATTAGCTAAAATTATTATAATACCTTCTAACCACAA
* * * *
10803274 TTACCTAGAAAAGTTTTGTTAATTGCTTCACATAATGGCTT-TCCAACCATACTTACAAAAATAT
66 TTACCTAAAAAAATTTTGTTAATTGCTTCACATAAT-ACTTCTCCAACCATAATTACAAAAATAT
* * * * *
10803338 CCCTTTATATTATGATTGGTC-AAAATTATTATAATACAT-TCTAAACATAATTATGAGAATACC
130 CCCTTTATATTATCATTAGCCAAAAATTACTATAATAC-TCTCTAAACATAATTATGAAAATACC
* *
10803401 TTTTTGATTGCTTCATAATTATGCATTAAATTTTAACATACATATAATAATATTAAATTAAT-CA
194 TTTTTGATTGCTTCATAATTATGCATTAAATTTTAACATACATACAATAATATGAAATTAATCCA
* *
10803465 CCTTA-AAATTGATTATAATATCCTTTTAATTACTAGACAATTGATCTATATGCATCTAAATTGA
259 -CTTAGAAATTGATTATAAT-GCCTTTTAATTACTAGACAATTGAT-TATATGCATCCAAATTGA
* ** *
10803529 -TAATGATTCCCCTTTTTCAATTTTTAACTAAAATTACTATAATGCTCTCTAAACATAATTACTA
321 CT-ATGATTCCCATTTTTCAATGATTAACTAAAATTACTATAATGCTCTCTTAACATAATTACTA
* * * * * * *
10803593 AAATACTCTTCTTACCATAATTGGTCAATGTTTCTATAATGCATTACAACCATAATAACGCAAAT
385 AAATACCCATCTTATCATAATTGGTCAAAGTTACTATAATGCACTAAAACCATAATAACGCAAAT
*
10803658 GCCC-TCCTACCATAATATGCTAAAATTACTATAACACCCCATTC-CACCATAATTATGAAAATA
450 GCCCTTCC-ACCATAATATGCTAAAATTACTATAACACCCC-TTCTCACCATAATTATAAAAATA
** ** * **
10803721 TTTCTCACATTATAATTTTTCAAAAATTACTATAATACCCACTAATCATAATTAAGAAAATGTTA
513 CCTCTCACATTATAATTTGCCAAAAATTACTATAA-ACCCACTAACCATAATTAAGAAAATGCCA
10803786 TCTTATC
577 TCTTATC
* * *
10803793 ATAATTATGAAAATA-CCTCTCATATTATAATTAGCTAGAATTATTATGATACCTTCTAA-CATA
1 ATAATTATGAAAATACCCT-TCATATTATAATTAGCTAAAATTATTATAATACCTTCTAACCACA
* ** * **
10803856 ATTACCTAAAAAAATCCTTT-TTGATTGCTTCGTATAATATTTCTCCAACCATAATTATGAAAAT
65 ATTACCTAAAAAAAT--TTTGTTAATTGCTTCACATAATACTTCTCCAACCATAATTACAAAAAT
* * * * * *
10803920 TTTCCTTTATATTGTCTTTAGCCAAAAATTACTATAATACTCTCTAAGCATAATTATGAAAATGC
128 ATCCCTTTATATTATCATTAGCCAAAAATTACTATAATACTCTCTAAACATAATTATGAAAATAC
** * * * *
10803985 CTTTTTGATTATTTCATAATTGTGCGTTAAATTTTAATAGACATACAATAATATGAAATTAATCC
193 CTTTTTGATTGCTTCATAATTATGCATTAAATTTTAACATACATACAATAATATGAAATTAATCC
* * ** * *
10804050 ACTTAGAAA-TGATTATAGTGCATTTCTAGCTA-TTGACAATTGATTTACATGCATCCAAATTGA
258 ACTTAGAAATTGATTATAATGCCTTT-TAATTACTAGACAATTGA-TTATATGCATCCAAATTGA
* * *
10804113 CTATGATAT--CATTCTTTCAATGATTAACTAAAATTATTATAGTACCTCTCTTAACATAATTAC
321 CTATGAT-TCCCATT-TTTCAATGATTAACTAAAATTACTATAAT-GCTCTCTTAACATAATTAC
* * *
10804176 TAAAATACCCATATTTTCATAATTGGCCAAAGTTACTATAATGC
383 TAAAATACCCATCTTATCATAATTGGTCAAAGTTACTATAATGC
10804220 GCCTTCAACC
Statistics
Matches: 826, Mismatches: 154, Indels: 59
0.79 0.15 0.06
Matches are distributed among these distances:
582 80 0.10
583 138 0.17
584 285 0.35
585 316 0.38
586 7 0.01
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (583 bp):
ATAATTATGAAAATACCCTTCATATTATAATTAGCTAAAATTATTATAATACCTTCTAACCACAA
TTACCTAAAAAAATTTTGTTAATTGCTTCACATAATACTTCTCCAACCATAATTACAAAAATATC
CCTTTATATTATCATTAGCCAAAAATTACTATAATACTCTCTAAACATAATTATGAAAATACCTT
TTTGATTGCTTCATAATTATGCATTAAATTTTAACATACATACAATAATATGAAATTAATCCACT
TAGAAATTGATTATAATGCCTTTTAATTACTAGACAATTGATTATATGCATCCAAATTGACTATG
ATTCCCATTTTTCAATGATTAACTAAAATTACTATAATGCTCTCTTAACATAATTACTAAAATAC
CCATCTTATCATAATTGGTCAAAGTTACTATAATGCACTAAAACCATAATAACGCAAATGCCCTT
CCACCATAATATGCTAAAATTACTATAACACCCCTTCTCACCATAATTATAAAAATACCTCTCAC
ATTATAATTTGCCAAAAATTACTATAAACCCACTAACCATAATTAAGAAAATGCCATCTTATC
Found at i:10804811 original size:26 final size:25
Alignment explanation
Indices: 10804766--10804815 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
10804756 CTACTATCAT
* *
10804766 TTACCAAAATTATTATAATATCCTTC
1 TTACCAAAATTATAAAAATA-CCTTC
*
10804792 TTACCATAATTATAAAAATACCTT
1 TTACCAAAATTATAAAAATACCTT
10804816 TCATATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (25 bp):
TTACCAAAATTATAAAAATACCTTC
Found at i:10807712 original size:3 final size:3
Alignment explanation
Indices: 10807704--10807762 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
10807694 CAAAATATCA
*
10807704 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TC ATT ATT ATT -TT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
10807749 ATT TTT A-T ATT ATT
1 ATT ATT ATT ATT ATT
10807763 TAAATAAACC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 7 0.15
3 41 0.85
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:10807718 original size:9 final size:9
Alignment explanation
Indices: 10807704--10807762 Score: 72
Period size: 8 Copynumber: 7.0 Consensus size: 9
10807694 CAAAATATCA
10807704 ATTATTATT
1 ATTATTATT
10807713 ATTATTATT
1 ATTATTATT
10807722 ATTATTATT
1 ATTATTATT
*
10807731 -TCATTATT
1 ATTATTATT
10807739 ATT-TTATT
1 ATTATTATT
*
10807747 -TTATTTTT
1 ATTATTATT
10807755 A-TATTATT
1 ATTATTATT
10807763 TAAATAAACC
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
7 2 0.05
8 22 0.51
9 19 0.44
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTATTATT
Found at i:10807754 original size:11 final size:12
Alignment explanation
Indices: 10807705--10807763 Score: 70
Period size: 11 Copynumber: 5.0 Consensus size: 12
10807695 AAAATATCAA
*
10807705 TTATTATTATTA
1 TTATTATTATTT
10807717 TTATTATTATTAT
1 TTATTATTATT-T
10807730 TTCATTATTA-TT
1 TT-ATTATTATTT
10807742 TTATT-TTATTT
1 TTATTATTATTT
10807753 TTA-TATTATTT
1 TTATTATTATTT
10807764 AAATAAACCT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
10 4 0.10
11 14 0.33
12 14 0.33
13 3 0.07
14 7 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:10808234 original size:20 final size:23
Alignment explanation
Indices: 10808206--10808259 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
10808196 TAATACCAAT
*
10808206 AATATCATAAAATAT-AA-A-AA
1 AATAACATAAAATATCAATATAA
10808226 AATAACATAAAA-ATCAATATAA
1 AATAACATAAAATATCAATATAA
10808248 AATAA-ATAAAAT
1 AATAACATAAAAT
10808260 CAAAATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 2 0.07
20 13 0.45
21 7 0.24
22 7 0.24
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (23 bp):
AATAACATAAAATATCAATATAA
Found at i:10808239 original size:11 final size:10
Alignment explanation
Indices: 10808178--10808258 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 10
10808168 TAATAATATA
10808178 AAATAAAAAT
1 AAATAAAAAT
*
10808188 -AATAAGAAT
1 AAATAAAAAT
**
10808197 -AATACCAAT
1 AAATAAAAAT
10808206 AATATCATAAAAT
1 AA-AT-A-AAAAT
10808219 ATAA-AAAAAT
1 A-AATAAAAAT
10808229 AACATAAAAAT
1 AA-ATAAAAAT
*
10808240 CAATATAAAAT
1 AAATA-AAAAT
10808251 AAATAAAA
1 AAATAAAA
10808259 TCAAAATCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
9 16 0.29
10 14 0.25
11 19 0.34
12 1 0.02
13 5 0.09
14 1 0.02
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.22
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:10808264 original size:26 final size:25
Alignment explanation
Indices: 10808216--10808277 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 25
10808206 AATATCATAA
*
10808216 AATATAAAAAAATAACATAAAAATC
1 AATATAAAAAAATAAAATAAAAATC
*
10808241 AATATAAAATAAATAAAATCAAAATC
1 AATATAAAA-AAATAAAATAAAAATC
* *
10808267 AAAACAAAAAA
1 AATATAAAAAA
10808278 GAAAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (25 bp):
AATATAAAAAAATAAAATAAAAATC
Found at i:10809523 original size:34 final size:34
Alignment explanation
Indices: 10809462--10809562 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
10809452 AAATTCAAAG
* *
10809462 GCTCATCTAACCAGAGGTAATGAAACTTTAAATA
1 GCTCATCTGACCAGAGGTAACGAAACTTTAAATA
* * *
10809496 GCTTATCTGACCAGAGGCAACGGAACTTTAAATA
1 GCTCATCTGACCAGAGGTAACGAAACTTTAAATA
* *
10809530 GCTCATCTGACCAAAGGTAACGAAATTTTAAAT
1 GCTCATCTGACCAGAGGTAACGAAACTTTAAAT
10809563 TAAAAATCTG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (34 bp):
GCTCATCTGACCAGAGGTAACGAAACTTTAAATA
Found at i:10809731 original size:40 final size:40
Alignment explanation
Indices: 10809687--10809888 Score: 170
Period size: 40 Copynumber: 5.0 Consensus size: 40
10809677 GCTATGAAAT
* * *
10809687 TTTAAATGGCTTCTTTGACCAAAGGCAATGAAACTTTAAA
1 TTTAAAAGGCTTCTCTAACCAAAGGCAATGAAACTTTAAA
** * * *
10809727 TTTAAAAACCCTCATCTAACCGAAGGCAATGATACTTTAAA
1 TTTAAAAGGCTTC-TCTAACCAAAGGCAATGAAACTTTAAA
* * * * *
10809768 TTTAAAAGGTTTCTCTATCTAGAGGTAATGAAACTTTAAA
1 TTTAAAAGGCTTCTCTAACCAAAGGCAATGAAACTTTAAA
* * * **
10809808 TTCAAAAGGCTCCTCTAACTAAAGAAAATGAAACTTTAAA
1 TTTAAAAGGCTTCTCTAACCAAAGGCAATGAAACTTTAAA
* * * * * **
10809848 TTCAAAAAGCTTATTTGACCAAAGGCAACAAAACTTTAAA
1 TTTAAAAGGCTTCTCTAACCAAAGGCAATGAAACTTTAAA
10809888 T
1 T
10809889 GGTTCTTCTG
Statistics
Matches: 126, Mismatches: 35, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
40 94 0.75
41 32 0.25
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (40 bp):
TTTAAAAGGCTTCTCTAACCAAAGGCAATGAAACTTTAAA
Found at i:10816096 original size:69 final size:69
Alignment explanation
Indices: 10815985--10816123 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 69
10815975 GGCATAATTG
** * *
10815985 TACAAACTAGTTCATCAATTTTAACATTCAATTTCTCATCATAAAAGATGGTGACAAGCTCAAAA
1 TACAAACTAGTTCATCAACCTTAACATTCAATTTCTCATCATAAAAAATGGTAACAAGCTCAAAA
10816050 TTCA
66 TTCA
* *
10816054 TACAAACTAGCTT-ATCAACCTTAACACTT-GATTTCTCTTCATAAAAAATGGTAACAAGCTCAA
1 TACAAACTAG-TTCATCAACCTTAACA-TTCAATTTCTCATCATAAAAAATGGTAACAAGCTCAA
10816117 AATTCA
64 AATTCA
10816123 T
1 T
10816124 TTGGTAAGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 58 0.94
70 4 0.06
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (69 bp):
TACAAACTAGTTCATCAACCTTAACATTCAATTTCTCATCATAAAAAATGGTAACAAGCTCAAAA
TTCA
Found at i:10821454 original size:13 final size:13
Alignment explanation
Indices: 10821436--10821465 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10821426 TTAATTACTT
10821436 TTTATTGTGATTA
1 TTTATTGTGATTA
*
10821449 TTTATTGTTATTA
1 TTTATTGTGATTA
10821462 TTTA
1 TTTA
10821466 CTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (13 bp):
TTTATTGTGATTA
Found at i:10821475 original size:14 final size:14
Alignment explanation
Indices: 10821445--10821500 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 14
10821435 TTTTATTGTG
*
10821445 ATTATTTAT-TGTT
1 ATTATTTATATATT
10821458 ATTATTTACTAT-TT
1 ATTATTTA-TATATT
10821472 ATTATTTATATATT
1 ATTATTTATATATT
10821486 -TTATTT-TATATT
1 ATTATTTATATATT
10821498 ATT
1 ATT
10821501 TAAAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.15
13 19 0.49
14 13 0.33
15 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (14 bp):
ATTATTTATATATT
Found at i:10821480 original size:7 final size:7
Alignment explanation
Indices: 10821445--10821502 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
10821435 TTTTATTGTG
10821445 ATTATTT
1 ATTATTT
*
10821452 ATT-GTT
1 ATTATTT
10821458 ATTATTT
1 ATTATTT
*
10821465 ACTATTT
1 ATTATTT
10821472 ATTATTT
1 ATTATTT
10821479 ATATATTTT
1 AT-TA-TTT
10821488 ATT-TTAT
1 ATTATT-T
10821495 ATTATTT
1 ATTATTT
10821502 A
1 A
10821503 AAAAAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 7 0.17
7 25 0.60
8 5 0.12
9 5 0.12
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (7 bp):
ATTATTT
Found at i:10822134 original size:20 final size:21
Alignment explanation
Indices: 10822098--10822138 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10822088 ACAATAATAT
10822098 CATAAAAAACATAAAAATCAA
1 CATAAAAAACATAAAAATCAA
10822119 CATAAAATAA-AT-AAAATCAA
1 CATAAAA-AACATAAAAATCAA
10822139 AATCAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 9 0.47
22 2 0.11
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (21 bp):
CATAAAAAACATAAAAATCAA
Found at i:10822681 original size:21 final size:23
Alignment explanation
Indices: 10822655--10822701 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
10822645 ATCGAGAAAA
*
10822655 TTTTTTG-TTTCT-AGAAATTTT
1 TTTTTTGCTTTCTGAAAAATTTT
*
10822676 TTTTTTGCTTTTTGAAAAATTTT
1 TTTTTTGCTTTCTGAAAAATTTT
10822699 TTT
1 TTT
10822702 GTTTTGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 4 0.18
23 11 0.50
ACGTcount: A:0.19, C:0.04, G:0.09, T:0.68
Consensus pattern (23 bp):
TTTTTTGCTTTCTGAAAAATTTT
Found at i:10823583 original size:22 final size:22
Alignment explanation
Indices: 10823556--10823636 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 22
10823546 TTTTTATTTG
*
10823556 ATATATTATTAATATATAAATT
1 ATATATTATTAATAAATAAATT
10823578 ATATATTATTAATAAATAAAATGAT
1 ATATATTATTAATAAAT-AAAT--T
* *
10823603 GTATTTTATTAATAAATTAAATT
1 ATATATTATTAATAAA-TAAATT
* *
10823626 AAATAATATTA
1 ATATATTATTA
10823637 TTTTATTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 16 0.33
23 12 0.25
25 19 0.40
26 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATATATTATTAATAAATAAATT
Found at i:10823651 original size:21 final size:21
Alignment explanation
Indices: 10823625--10823741 Score: 64
Period size: 21 Copynumber: 5.5 Consensus size: 21
10823615 TAAATTAAAT
10823625 TAAATAATATTATTTTATTAA
1 TAAATAATATTATTTTATTAA
10823646 TAAATAA-A-T-TTTT-TTAA
1 TAAATAATATTATTTTATTAA
* *
10823663 AAAATAATTTTTATATATTTATTATA
1 TAAATAA--TAT-TAT-TTTATTA-A
* * *
10823689 AAAATTAATATTA-ATCATTAA
1 TAAA-TAATATTATTTTATTAA
* *
10823710 TAAAATAATATTATTTAATTTA
1 T-AAATAATATTATTTTATTAA
*
10823732 TTAATAATAT
1 TAAATAATAT
10823742 ATAAAATTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
17 10 0.14
18 4 0.05
19 1 0.01
20 1 0.01
21 24 0.32
22 15 0.20
23 1 0.01
24 5 0.07
25 5 0.07
26 5 0.07
27 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATAATATTATTTTATTAA
Found at i:10823656 original size:17 final size:17
Alignment explanation
Indices: 10823613--10823676 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
10823603 GTATTTTATT
** *
10823613 AATAAATTAAATTAAAT
1 AATAAATTTTATTAAAA
* *
10823630 AATATTATTTTATTAATA
1 AATA-AATTTTATTAAAA
*
10823648 AATAAATTTTTTTAAAA
1 AATAAATTTTATTAAAA
*
10823665 AATAATTTTTAT
1 AATAAATTTTAT
10823677 ATATTTATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
17 24 0.67
18 12 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATAAATTTTATTAAAA
Found at i:10826007 original size:20 final size:19
Alignment explanation
Indices: 10825973--10826013 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
10825963 GAGCACTTTG
*
10825973 TTCTTTTGGGGGGTTTCCT
1 TTCTCTTGGGGGGTTTCCT
*
10825992 TTCTCTTGGTGGGGTTTTCT
1 TTCTCTTGG-GGGGTTTCCT
10826012 TT
1 TT
10826014 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.00, C:0.15, G:0.29, T:0.56
Consensus pattern (19 bp):
TTCTCTTGGGGGGTTTCCT
Found at i:10839033 original size:18 final size:17
Alignment explanation
Indices: 10838991--10839034 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
10838981 GCTGCTGCCG
*
10838991 CTGCCACCGCTACCCCA
1 CTGCCACCGCCACCCCA
*
10839008 CATACCACCGCCACCCCAA
1 C-TGCCACCGCCACCCC-A
10839027 CTGCCACC
1 CTGCCACC
10839035 TTCCCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.23, C:0.59, G:0.09, T:0.09
Consensus pattern (17 bp):
CTGCCACCGCCACCCCA
Found at i:10839231 original size:20 final size:20
Alignment explanation
Indices: 10839203--10839240 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10839193 TTGTGCGAGA
10839203 AAATAAAAA-TAAATCAAATC
1 AAATAAAAAGTAAA-CAAATC
*
10839223 AAATCAAAAGTAAACAAA
1 AAATAAAAAGTAAACAAA
10839241 AAGCAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.16
Consensus pattern (20 bp):
AAATAAAAAGTAAACAAATC
Found at i:10841502 original size:49 final size:49
Alignment explanation
Indices: 10841425--10841523 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
10841415 AACCTGAGAT
* * *
10841425 TCACGTAATGCCCAACATGTATTTCATATACCAGTCAGAACATTGTAAA
1 TCACATAATGCCCAACATGTAGTTCATATACCAGTCAGAAAATTGTAAA
*
10841474 TCACATAATGCCCAACATGTAGTTCATATTCCAGTCAGAAAATTGTAAA
1 TCACATAATGCCCAACATGTAGTTCATATACCAGTCAGAAAATTGTAAA
10841523 T
1 T
10841524 AATCTCTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.29
Consensus pattern (49 bp):
TCACATAATGCCCAACATGTAGTTCATATACCAGTCAGAAAATTGTAAA
Found at i:10847488 original size:14 final size:14
Alignment explanation
Indices: 10847463--10847503 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
10847453 ACCTACCACT
*
10847463 AACAACGGACAATG
1 AACAACGAACAATG
* *
10847477 AACAATGAACAACG
1 AACAACGAACAATG
10847491 AACAACGAACAAT
1 AACAACGAACAAT
10847504 CTTAAGTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.22, G:0.15, T:0.07
Consensus pattern (14 bp):
AACAACGAACAATG
Found at i:10847489 original size:21 final size:21
Alignment explanation
Indices: 10847463--10847503 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10847453 ACCTACCACT
* *
10847463 AACAACGGACAATGAACAATG
1 AACAACGAACAACGAACAATG
10847484 AACAACGAACAACGAACAAT
1 AACAACGAACAACGAACAAT
10847504 CTTAAGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.15, T:0.07
Consensus pattern (21 bp):
AACAACGAACAACGAACAATG
Found at i:10848713 original size:28 final size:29
Alignment explanation
Indices: 10848666--10848720 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
10848656 TAATAAAATA
* *
10848666 TTTAATATGATATCTAAAATTAAAAATTT
1 TTTAATATAATACCTAAAATTAAAAATTT
*
10848695 TTTAATATAATACCT-AAATTATAAAT
1 TTTAATATAATACCTAAAATTAAAAAT
10848721 ACATTAAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
TTTAATATAATACCTAAAATTAAAAATTT
Found at i:10849234 original size:19 final size:19
Alignment explanation
Indices: 10849190--10849236 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
10849180 ATTTTTTTTA
10849190 TAAAAAAAGAAGCAAGTAT
1 TAAAAAAAGAAGCAAGTAT
10849209 TATAAAAAAG-AGCTAA-TAAT
1 TA-AAAAAAGAAGC-AAGT-AT
10849229 TAAAAAAA
1 TAAAAAAA
10849237 TAATATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.66, C:0.04, G:0.11, T:0.19
Consensus pattern (19 bp):
TAAAAAAAGAAGCAAGTAT
Found at i:10849676 original size:2 final size:2
Alignment explanation
Indices: 10849669--10849698 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10849659 ATGAAAACTA
10849669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10849699 TGAGTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10853591 original size:15 final size:15
Alignment explanation
Indices: 10853513--10853591 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 15
10853503 AAATTTTAAT
10853513 ATAATAT-TTAAATT-
1 ATAATATATT-AATTA
*
10853527 ATAAATTTATTAATTA
1 AT-AATATATTAATTA
10853543 AT-ATAGTATTAATTA
1 ATAATA-TATTAATTA
** *
10853558 AT-ATATTAAAAATAA
1 ATAATA-TATTAATTA
10853573 ATAATATATTAATTA
1 ATAATATATTAATTA
10853588 ATAA
1 ATAA
10853592 ATTTATAATT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.08
15 40 0.78
16 7 0.14
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (15 bp):
ATAATATATTAATTA
Found at i:10853600 original size:15 final size:16
Alignment explanation
Indices: 10853523--10853601 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 16
10853513 ATAATATTTA
10853523 AATT-ATAAATTTATT
1 AATTAATAAATTTATT
* *
10853538 AATTAATATA-GTATT
1 AATTAATAAATTTATT
* **
10853553 AATTAATATA-TTAAA
1 AATTAATAAATTTATT
* *
10853568 AATAAAT-AATATATT
1 AATTAATAAATTTATT
10853583 AATTAATAAATTTA-T
1 AATTAATAAATTTATT
10853598 AATT
1 AATT
10853602 TAAATATTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
14 1 0.02
15 39 0.80
16 9 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
AATTAATAAATTTATT
Found at i:10853601 original size:45 final size:43
Alignment explanation
Indices: 10853499--10853610 Score: 101
Period size: 45 Copynumber: 2.6 Consensus size: 43
10853489 ATTTAAAATT
*
10853499 TTAA-AAATTT-TAATATAATAT-TTAAATTATAAATTTATTAA
1 TTAATAAATTTATAAT-TAATATATTAAATAATAAATTTATTAA
* *
10853540 TTAATATA-GTATTAATTAATATATTAAA-AATAAATAATATATTAA
1 TTAATAAATTTA-TAATTAATATATTAAATAATAAAT--T-TATTAA
10853585 TTAATAAATTTATAATTTAA-ATATTA
1 TTAATAAATTTATAA-TTAATATATTA
10853611 TATTAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
41 5 0.09
42 14 0.25
43 9 0.16
44 1 0.02
45 22 0.39
46 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (43 bp):
TTAATAAATTTATAATTAATATATTAAATAATAAATTTATTAA
Found at i:10854134 original size:5 final size:5
Alignment explanation
Indices: 10854124--10854148 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10854114 AACAGATAAT
10854124 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
10854149 AAAAAGATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:10854619 original size:2 final size:2
Alignment explanation
Indices: 10854612--10854647 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10854602 ACCATATCCC
10854612 CT CT CT CT CT CT CT CT CT 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
10854648 TATTTATTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10860380 original size:23 final size:24
Alignment explanation
Indices: 10860354--10860416 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
10860344 TATGTAATTT
10860354 TATTTAAATTTTTTAAATA-TTAA
1 TATTTAAATTTTTTAAATATTTAA
* * *
10860377 TATTAAAAGTTTTCAAATATTTTAA
1 TATTTAAATTTTTTAAATA-TTTAA
10860402 T-TTTAAATATTTTTA
1 TATTTAAAT-TTTTTA
10860417 TAGTCTTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
23 16 0.52
24 5 0.16
25 10 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TATTTAAATTTTTTAAATATTTAA
Found at i:10860997 original size:29 final size:30
Alignment explanation
Indices: 10860918--10860998 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 30
10860908 TTTTAATGTT
10860918 AAAAATTATTCTTAAATTACTTTAAAAAATG
1 AAAAATTATTCTTAAATTA-TTTAAAAAATG
* * *
10860949 AAAAAATCTTCTT-AAGTATTT-AAAAAT-
1 AAAAATTATTCTTAAATTATTTAAAAAATG
* *
10860976 AGGAAATTGTTCTTAAATTATTT
1 A-AAAATTATTCTTAAATTATTT
10860999 TAATAGCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.02
28 15 0.37
29 10 0.24
30 4 0.10
31 11 0.27
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (30 bp):
AAAAATTATTCTTAAATTATTTAAAAAATG
Found at i:10861350 original size:51 final size:51
Alignment explanation
Indices: 10861260--10861358 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
10861250 TTAATTTTAA
** *
10861260 AATTTTATTTTAAATTCATAAAAATTCTTCAATAATTTGATAAAATTTTTT
1 AATTTTATTTTAAATTCATAAAAAACCTTCAATAATTTGAAAAAATTTTTT
* *
10861311 AATTTTATTTTAAATTCATAAAAAACC-TCTATTAGTTTGAAAAAATTT
1 AATTTTATTTTAAATTCATAAAAAACCTTC-AATAATTTGAAAAAATTT
10861359 CATTTCTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (51 bp):
AATTTTATTTTAAATTCATAAAAAACCTTCAATAATTTGAAAAAATTTTTT
Found at i:10862707 original size:2 final size:2
Alignment explanation
Indices: 10862700--10862742 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10862690 TAAATCTTTC
10862700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10862742 A
1 A
10862743 AAAGACACCT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10863939 original size:18 final size:19
Alignment explanation
Indices: 10863918--10863962 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
10863908 AAATTTGTAC
*
10863918 TATTTTAATA-ATTAATAT
1 TATTTTAATATAATAATAT
10863936 TA-TTTAATATAATAATAT
1 TATTTTAATATAATAATAT
10863954 TATTTTAAT
1 TATTTTAAT
10863963 TATATGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
18 11 0.46
19 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTTAATATAATAATAT
Found at i:10864182 original size:13 final size:13
Alignment explanation
Indices: 10864138--10864185 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
10864128 AGTATAAATT
10864138 TTTTAAAATTTTAA
1 TTTTAAAATTTT-A
**
10864152 TAATAAATATTATTA
1 TTTTAAA-ATT-TTA
10864167 TTTTAAAATTTTA
1 TTTTAAAATTTTA
10864180 TTTTAA
1 TTTTAA
10864186 TAAAAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 9 0.32
14 8 0.29
15 9 0.32
16 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATTTTA
Found at i:10864292 original size:19 final size:19
Alignment explanation
Indices: 10864268--10864305 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10864258 TAAGTGTTTT
10864268 ATATTAATATAATAATTTA
1 ATATTAATATAATAATTTA
*
10864287 ATATTAATATAATATTTTA
1 ATATTAATATAATAATTTA
10864306 CTACTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATTAATATAATAATTTA
Found at i:10864410 original size:25 final size:26
Alignment explanation
Indices: 10864352--10864411 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
10864342 AATATTAAGA
10864352 ATTTTAATAATAAATAATTTCAATAT
1 ATTTTAATAATAAATAATTTCAATAT
10864378 ATTTTAATAATAAATAATTT--ATAAT
1 ATTTTAATAATAAATAATTTCAAT-AT
10864403 ATTTTAATA
1 ATTTTAATA
10864412 TTCTATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.06
25 11 0.33
26 20 0.61
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTTAATAATAAATAATTTCAATAT
Found at i:10865323 original size:13 final size:13
Alignment explanation
Indices: 10865305--10865330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10865295 TTTATTCAAC
10865305 ATAAATTTTTATT
1 ATAAATTTTTATT
10865318 ATAAATTTTTATT
1 ATAAATTTTTATT
10865331 TCATCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAAATTTTTATT
Found at i:10865734 original size:16 final size:16
Alignment explanation
Indices: 10865710--10865771 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
10865700 AATTATTTTT
10865710 TAATATATATATTTATA
1 TAAT-TATATATTTATA
*
10865727 TAATTATATATTTAAA
1 TAATTATATATTTATA
10865743 T-ATT-TATATTTA-A
1 TAATTATATATTTATA
*
10865756 -AAATA-ATATTTATA
1 TAATTATATATTTATA
10865770 TA
1 TA
10865772 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 10 0.26
14 9 0.23
15 4 0.10
16 12 0.31
17 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTATATATTTATA
Found at i:10865765 original size:19 final size:20
Alignment explanation
Indices: 10865741--10865793 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 20
10865731 TATATATTTA
10865741 AATATTTATATTT-AAAAAT
1 AATATTTATATTTAAAAAAT
10865760 AATATTTATATATTTTAAAAAAT
1 AATA-TT-TATA-TTTAAAAAAT
10865783 AATATTT-TATT
1 AATATTTATATT
10865794 AATTTCGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.20
20 4 0.13
21 5 0.17
22 5 0.17
23 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTTATATTTAAAAAAT
Found at i:10865774 original size:8 final size:8
Alignment explanation
Indices: 10865715--10865751 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
10865705 TTTTTTAATA
10865715 TATATATT
1 TATATATT
*
10865723 TATATAAT
1 TATATATT
10865731 TATATATT
1 TATATATT
*
10865739 TAAATATT
1 TATATATT
10865747 TATAT
1 TATAT
10865752 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:10865798 original size:24 final size:23
Alignment explanation
Indices: 10865747--10865789 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
10865737 TTTAAATATT
10865747 TATA-TTT-AAAAATAATATTTA
1 TATATTTTAAAAAATAATATTTA
10865768 TATATTTTAAAAAATAATATTT
1 TATATTTTAAAAAATAATATTT
10865790 TATTAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATTTTAAAAAATAATATTTA
Found at i:10873494 original size:12 final size:12
Alignment explanation
Indices: 10873477--10873501 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10873467 ATATTAGTTT
10873477 AATATTATTTCA
1 AATATTATTTCA
10873489 AATATTATTTCA
1 AATATTATTTCA
10873501 A
1 A
10873502 CGAGTGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (12 bp):
AATATTATTTCA
Found at i:10874068 original size:10 final size:10
Alignment explanation
Indices: 10874051--10874132 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 10
10874041 ATAAATTTTT
*
10874051 TTAAAATTAA
1 TTAAATTTAA
*
10874061 TTTGAATTTGAA
1 -TTAAATTT-AA
*
10874073 TTAAATTT-T
1 TTAAATTTAA
10874082 TATATAATTTAAA
1 T-TA-AATTT-AA
*
10874095 TTAAATTGAA
1 TTAAATTTAA
*
10874105 TTAAATTTTA
1 TTAAATTTAA
10874115 TT-AATTTAA
1 TTAAATTTAA
*
10874124 TTCAATTTA
1 TTAAATTTA
10874133 TTATTTTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
9 9 0.16
10 20 0.36
11 22 0.39
12 4 0.07
13 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (10 bp):
TTAAATTTAA
Found at i:10874104 original size:32 final size:33
Alignment explanation
Indices: 10874042--10874123 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 33
10874032 TATAATATTA
* * * *
10874042 TAAATTTTTTTA-AAATTAATTTGAATTTGAAT
1 TAAATTTTTATATAATTTAAATTGAAATTGAAT
10874074 TAAATTTTTATATAATTTAAATT-AAATTGAAT
1 TAAATTTTTATATAATTTAAATTGAAATTGAAT
10874106 TAAA-TTTTAT-TAATTTAA
1 TAAATTTTTATATAATTTAA
10874124 TTCAATTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 8 0.18
31 6 0.13
32 23 0.51
33 8 0.18
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (33 bp):
TAAATTTTTATATAATTTAAATTGAAATTGAAT
Found at i:10874125 original size:19 final size:18
Alignment explanation
Indices: 10874098--10874154 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
10874088 ATTTAAATTA
*
10874098 AATTGAATTAAATTTTATT
1 AATTTAATT-AATTTTATT
10874117 AATTTAATTCAA-TTTATT
1 AATTTAATT-AATTTTATT
10874135 -ATTT--TTAATTTTATT
1 AATTTAATTAATTTTATT
10874150 AATTT
1 AATTT
10874155 TTATATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 2 0.06
15 8 0.24
16 4 0.12
17 4 0.12
18 6 0.18
19 10 0.29
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
AATTTAATTAATTTTATT
Found at i:10874151 original size:9 final size:9
Alignment explanation
Indices: 10874108--10874155 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
10874098 AATTGAATTA
10874108 AATTTTATT
1 AATTTTATT
*
10874117 AATTTAATT
1 AATTTTATT
10874126 CAA-TTTATT
1 -AATTTTATT
10874135 -A-TTT-TT
1 AATTTTATT
10874141 AATTTTATT
1 AATTTTATT
10874150 AATTTT
1 AATTTT
10874156 TATATATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 2 0.06
7 5 0.15
8 3 0.09
9 21 0.64
10 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
AATTTTATT
Found at i:10874234 original size:17 final size:16
Alignment explanation
Indices: 10874212--10874255 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
10874202 AATTTTATTT
10874212 TATATAAATTTAAGAAA
1 TATATAAATTTAA-AAA
*
10874229 TATATAAAAATTAAAAA
1 TATAT-AAATTTAAAAA
*
10874246 AATATAAATT
1 TATATAAATT
10874256 ATTTTCATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TATATAAATTTAAAAA
Found at i:10874239 original size:19 final size:19
Alignment explanation
Indices: 10874212--10874251 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10874202 AATTTTATTT
* * *
10874212 TATATAAATTTAAGAAATA
1 TATAAAAATTAAAAAAATA
10874231 TATAAAAATTAAAAAAATA
1 TATAAAAATTAAAAAAATA
10874250 TA
1 TA
10874252 AATTATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
TATAAAAATTAAAAAAATA
Found at i:10874256 original size:15 final size:18
Alignment explanation
Indices: 10874212--10874256 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 18
10874202 AATTTTATTT
10874212 TATATAAATTTAAGAAATA
1 TATATAAA-TTAAGAAATA
*
10874231 TATAAAAATTAA-AAA-A
1 TATATAAATTAAGAAATA
10874247 -ATATAAATTA
1 TATATAAATTA
10874257 TTTTCATTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.38
16 1 0.04
17 3 0.12
18 4 0.17
19 7 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TATATAAATTAAGAAATA
Found at i:10874298 original size:11 final size:12
Alignment explanation
Indices: 10874272--10874330 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
10874262 ATTGGATTTT
10874272 TTTAATTTAAAA
1 TTTAATTTAAAA
*
10874284 TTTAATTT-CAA
1 TTTAATTTAAAA
*
10874295 TTTAA-TTATATA
1 TTTAATTTA-AAA
*
10874307 TTTAATATTTAAA
1 TTTAAT-TTAAAA
*
10874320 TTTGATTTAAA
1 TTTAATTTAAA
10874331 TCGGATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
10 2 0.06
11 7 0.19
12 18 0.50
13 7 0.19
14 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (12 bp):
TTTAATTTAAAA
Found at i:10880390 original size:35 final size:35
Alignment explanation
Indices: 10880323--10880390 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
10880313 TATATGTCAA
* * *
10880323 GTTAGTTGTAGGTTTATACCTAGAAAACATTTGAT
1 GTTAGTTGTAGATTTATACCAAAAAAACATTTGAT
* * *
10880358 GTTAGTTGTATATTTATGCCAAAAAAATATTTG
1 GTTAGTTGTAGATTTATACCAAAAAAACATTTG
10880391 GTTTATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (35 bp):
GTTAGTTGTAGATTTATACCAAAAAAACATTTGAT
Found at i:10889274 original size:23 final size:25
Alignment explanation
Indices: 10889228--10889275 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
10889218 GGTTAACGTT
*
10889228 TTAATAATTCTCACCAAGTTGATTAA
1 TTAATAATTCTCA-CAAGTAGATTAA
10889254 TTAATAATTCTCA-AAG-AGATTA
1 TTAATAATTCTCACAAGTAGATTA
10889276 TCATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
26 13 0.62
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (25 bp):
TTAATAATTCTCACAAGTAGATTAA
Found at i:10890710 original size:71 final size:71
Alignment explanation
Indices: 10890627--10890758 Score: 192
Period size: 71 Copynumber: 1.9 Consensus size: 71
10890617 TTTAAATTTA
* *
10890627 ATCAAACAAATAAAAATATTGAAAAATTATTAGTTATCCAAAATTAATTTTCTAATAATTTTATG
1 ATCAAACAAATAAAAATATTGAAAAATGATTAGCTATCCAAAATTAATTTTCTAATAATTTTATG
10890692 GTAATT
66 GTAATT
* * * * * *
10890698 ATCAAATAAATAAAAGTCTTTAAAAATGATTAGCTATCCAAAATTATTTTTCTAGTAATTT
1 ATCAAACAAATAAAAATATTGAAAAATGATTAGCTATCCAAAATTAATTTTCTAATAATTT
10890759 AGATATATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.39
Consensus pattern (71 bp):
ATCAAACAAATAAAAATATTGAAAAATGATTAGCTATCCAAAATTAATTTTCTAATAATTTTATG
GTAATT
Found at i:10891657 original size:20 final size:21
Alignment explanation
Indices: 10891618--10891658 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10891608 ACAATTAATT
* *
10891618 TTTTAATAATTTAGATATATC
1 TTTTAATAATTTAAAAATATC
10891639 TTTTAA-AATTTAAAAATATC
1 TTTTAATAATTTAAAAATATC
10891659 AAATGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTAATAATTTAAAAATATC
Found at i:10892614 original size:19 final size:18
Alignment explanation
Indices: 10892590--10892640 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
10892580 TTAAATTTTA
10892590 TTAATTTTTAATTAAAATT
1 TTAATTTTTAATTAAAA-T
*
10892609 TTAATTTTT-ATTATAAT
1 TTAATTTTTAATTAAAAT
*
10892626 TTGATATTTTAATTA
1 TTAAT-TTTTAATTA
10892641 TATTATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 10 0.36
19 13 0.46
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAATTTTTAATTAAAAT
Found at i:10892641 original size:19 final size:18
Alignment explanation
Indices: 10892595--10892642 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
10892585 TTTTATTAAT
* *
10892595 TTTTAATTAAAATTTTAA
1 TTTTAATTATAATTTGAA
*
10892613 TTTTTATTATAATTTGATA
1 TTTTAATTATAATTTGA-A
10892632 TTTTAATTATA
1 TTTTAATTATA
10892643 TTATGTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTAATTATAATTTGAA
Found at i:10892816 original size:22 final size:23
Alignment explanation
Indices: 10892773--10892816 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
10892763 ATCTTTTAAA
*
10892773 ATTAATTATATATCATATATAAT
1 ATTAATTATATATCATACATAAT
10892796 ATTATATTATA-AT-ATACATAA
1 ATTA-ATTATATATCATACATAA
10892817 AAATTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAATTATATATCATACATAAT
Found at i:10894974 original size:2 final size:2
Alignment explanation
Indices: 10894967--10895004 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
10894957 CTTCTTTACA
10894967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10895005 TAAACATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10895824 original size:101 final size:99
Alignment explanation
Indices: 10895704--10895888 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 99
10895694 ATGGTATTTA
* * *
10895704 TCAAATAATTTAAAATATTTAAAAATTATTACTTATCCAAAATTA-ATTTGCTAATAATTTATAT
1 TCAAATAAATAAAAATATTTAAAAATTATAACTTATCCAAAATTAGATTTG-TAATAATTTATAT
10895768 AGAAGTTAAATATATATCTTTTATGTTTTAAAATTAC
65 --AAGTTAAATATATATCTTTTATGTTTTAAAATTAC
* * *
10895805 TCAAATAAATAAAAATATTTAAAAATTATAAGTTATCCAAAATTAGTTTTGTAATAATTTATCTA
1 TCAAATAAATAAAAATATTTAAAAATTATAACTTATCCAAAATTAGATTTGTAATAATTTATATA
*
10895870 ATTTAAATATATATCTTTT
66 AGTTAAATATATATCTTTT
10895889 TATTTTCTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
99 19 0.25
101 53 0.70
102 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (99 bp):
TCAAATAAATAAAAATATTTAAAAATTATAACTTATCCAAAATTAGATTTGTAATAATTTATATA
AGTTAAATATATATCTTTTATGTTTTAAAATTAC
Found at i:10897162 original size:12 final size:12
Alignment explanation
Indices: 10897147--10897176 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
10897137 AAAAAAATAC
10897147 AAAAACAAAGAA
1 AAAAACAAAGAA
10897159 AAAAACAAAGAA
1 AAAAACAAAGAA
10897171 ACAAAA
1 A-AAAA
10897177 AAGTGACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAACAAAGAA
Found at i:10898371 original size:3 final size:3
Alignment explanation
Indices: 10898357--10898404 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
10898347 ATGTTGCTTT
*
10898357 ATA ATA ATTA ATA ATA ATA ACA ATA ATA A-A AT- ATA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10898401 ATA A
1 ATA A
10898405 AAAGTTATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:10898383 original size:19 final size:17
Alignment explanation
Indices: 10898359--10898404 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
10898349 GTTGCTTTAT
10898359 AATAATTAATAATAATAAC
1 AATAA-TAATAAT-ATAAC
*
10898378 AATAATAA-AATATAAT
1 AATAATAATAATATAAC
10898394 AATAATAATAA
1 AATAATAATAA
10898405 AAAGTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 12 0.48
17 5 0.20
18 3 0.12
19 5 0.20
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATATAAC
Found at i:10898405 original size:19 final size:20
Alignment explanation
Indices: 10898357--10898406 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
10898347 ATGTTGCTTT
*
10898357 ATAATAAT-TAATAATAATA
1 ATAATAATAAAATAATAATA
*
10898376 ACAATAATAAAAT-ATAATA
1 ATAATAATAAAATAATAATA
10898395 ATAATAATAAAA
1 ATAATAATAAAA
10898407 AGTTATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 24 0.89
20 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAATAATAAAATAATAATA
Done.