Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 20 of 130
Found at i:5425574 original size:23 final size:23
Alignment explanation
Indices: 5425548--5425899 Score: 151
Period size: 23 Copynumber: 14.9 Consensus size: 23
5425538 TTTATAAATA
5425548 ATATTATATTAATAAA-AAGTATT
1 ATATTATATTAATAAATAA-TATT
* *
5425571 ATATTA-ATAAAATAATATTATATT
1 ATATTATAT-TAATAA-ATAATATT
* *
5425595 GTAATATATTAATAAATAATATT
1 ATATTATATTAATAAATAATATT
* * *
5425618 ATATGA-ATAAATAATATACA-ATCA
1 ATATTATATTAATAA-ATA-ATAT-T
*
5425642 ATATGATATATTAATGAA-AATATT
1 ATAT--TATATTAATAAATAATATT
*
5425666 ATAATATATTAATAAATAATATT
1 ATATTATATTAATAAATAATATT
5425689 AT-TATATATTAATAAATAATA-T
1 ATAT-TATATTAATAAATAATATT
*
5425711 ATTATTA-A-TAAT-ACT-ATATT
1 A-TATTATATTAATAAATAATATT
* *
5425731 A-ATAAATAATAATAAAATAATATT
1 ATAT-TATATTAAT-AAATAATATT
* *
5425755 ATAATATATTAATAAATAATATA
1 ATATTATATTAATAAATAATATT
* *
5425778 ATAATAATTATTAATTTAATTAATCA--
1 AT-ATTA-TATTAA--TAAATAAT-ATT
* * * *
5425804 ATATTACAATAATATATGAATA-A
1 ATATTATATTAATAAAT-AATATT
5425827 ATAATATACTATTAATATAAT-ATATT
1 AT-AT-TA-TATTAATA-AATAATATT
* *
5425853 AATAAATATTATTAATTAATAATATT
1 -AT-ATTA-TATTAATAAATAATATT
**
5425879 ATAACATATTAATAAATAATA
1 ATATTATATTAATAAATAATA
5425900 AAAAGAACAA
Statistics
Matches: 250, Mismatches: 42, Indels: 74
0.68 0.11 0.20
Matches are distributed among these distances:
18 2 0.01
19 4 0.02
20 5 0.02
21 8 0.03
22 27 0.11
23 86 0.34
24 48 0.19
25 26 0.10
26 24 0.10
27 19 0.08
28 1 0.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATATTAATAAATAATATT
Found at i:5425610 original size:65 final size:63
Alignment explanation
Indices: 5425536--5425881 Score: 180
Period size: 65 Copynumber: 5.3 Consensus size: 63
5425526 AGTATAGTTT
* * *
5425536 TATTTATAAATAATATTATATTAATAAAAAGTATTATATTAATAAAATAATATTATATTGTAATA
1 TATTAATAAATAATATTATATTAATAAAAA-TA-TATATTAATAAAATAATAATATATTATAATA
* * * *
5425601 TATTAATAAATAATATTATATGAATAAATAATATACAATCAATATGATATATTAATGAAAATATT
1 TATTAATAAATAATATTATATTAATAAA-AATATA-TATTAATA--A-A-A-TAAT-AATATATT
5425666 ATAATA
58 ATAATA
* * *
5425672 TATTAATAAATAATATTATTATATATTAATAAATAATATATT-AT-TAATAATACTATATTAATA
1 TATTAATAAATAATATTA-TAT-TAATAA-AAAT-ATATATTAATAAAATAATAATATATT-ATA
5425735 A-A
61 ATA
* * *
5425737 TAATAATAAAATAATATTATAATATATTAATAAATA-ATA-TAAT--AATAATTAT-TAATT-TA
1 TATTAAT-AAATAATATTAT-AT-TAATAA-AAATATATATTAATAAAATAATAATAT-ATTATA
5425796 AT-
61 ATA
* * * * * * *
5425798 TAATCAATATTACAATAATATATGAATAAATAATATACTATTAATATAAT-AT-AT-TAATA-AA
1 T-ATTAATA-AATAATATTATATTAATAAA-AATATA-TATTAATAAAATAATAATATATTATAA
5425859 TA
62 TA
*
5425861 TTATTAATTAATAATATTATA
1 -TATTAATAAATAATATTATA
5425882 ACATATTAAT
Statistics
Matches: 222, Mismatches: 30, Indels: 61
0.71 0.10 0.19
Matches are distributed among these distances:
59 1 0.00
60 8 0.04
61 8 0.04
62 29 0.13
63 23 0.10
64 10 0.05
65 52 0.23
66 35 0.16
67 2 0.01
68 2 0.01
69 1 0.00
70 4 0.02
71 29 0.13
72 5 0.02
73 9 0.04
74 4 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (63 bp):
TATTAATAAATAATATTATATTAATAAAAATATATATTAATAAAATAATAATATATTATAATA
Found at i:5425709 original size:3 final size:3
Alignment explanation
Indices: 5425666--5425785 Score: 56
Period size: 3 Copynumber: 40.7 Consensus size: 3
5425656 TGAAAATATT
* * * *
5425666 ATA AT- ATA TTA ATAA ATA ATA TTA TTA TATA TTA ATAA ATA AT- ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA ATA AT-A ATA ATA ATA
* * * * *
5425712 TTA TTA ATA ATA CT- ATA TTA ATAA ATA ATA ATA A-A ATA AT- ATT
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA
*
5425755 ATA AT- ATA TTA ATAA ATA AT- ATA ATA ATA AT
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA AT
5425786 TATTAATTTA
Statistics
Matches: 90, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
2 13 0.14
3 63 0.70
4 14 0.16
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:5425709 original size:26 final size:26
Alignment explanation
Indices: 5425660--5425900 Score: 92
Period size: 26 Copynumber: 9.1 Consensus size: 26
5425650 TATTAATGAA
*
5425660 AATATTATAATATATTAAT--A-AAT
1 AATATTATTATATATTAATAAATAAT
5425683 AATATTATTATATATTAATAAATAAT
1 AATATTATTATATATTAATAAATAAT
5425709 ATATTATTAATAATACTATATTAATAAATAAT
1 A-A-TATT-AT--TA-TATATTAATAAATAAT
* * *
5425741 AATA-AAATA-ATATT-ATAATATATT
1 AATATTATTATATATTAATAA-ATAAT
* * * * *
5425765 AATA-AATAATATAATAATAATTATT
1 AATATTATTATATATTAATAAATAAT
5425790 AAT-TTAATTAATCAATATTACA-ATAATATAT
1 AATATT-ATT-AT--ATATTA-ATA-AATA-AT
* *
5425821 GAATAAATAATATACTATTAAT--ATAAT
1 -AAT-ATTATTATA-TATTAATAAATAAT
* * * *
5425848 -ATATTAATAAATATTATTAATTAAT
1 AATATTATTATATATTAATAAATAAT
* *
5425873 AATATTATAACATATTAATAAATAAT
1 AATATTATTATATATTAATAAATAAT
5425899 AA
1 AA
5425901 AAAGAACAAT
Statistics
Matches: 166, Mismatches: 24, Indels: 53
0.68 0.10 0.22
Matches are distributed among these distances:
23 28 0.17
24 23 0.14
25 18 0.11
26 34 0.20
27 5 0.03
28 8 0.05
29 8 0.05
30 8 0.05
31 9 0.05
32 22 0.13
33 2 0.01
34 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATTATTATATATTAATAAATAAT
Found at i:5425729 original size:34 final size:33
Alignment explanation
Indices: 5425536--5425877 Score: 60
Period size: 31 Copynumber: 10.5 Consensus size: 33
5425526 AGTATAGTTT
* *
5425536 TATTTATAAATAATAT-TATATTAATAAAAAGTATTA
1 TATTAATAAATAATATAT-TATTAAT-AATA-TA-TA
* *
5425572 TATTAAT-AA-AATA-A-TATT-ATATTGTAATA
1 TATTAATAAATAATATATTATTAATAATAT-ATA
*
5425601 TATTAATAAATAATAT-TATATGAATAA-ATA-A
1 TATTAATAAATAATATAT-TATTAATAATATATA
* * * *
5425632 TATACAATCAATATGATATATTAATGAAAATATTATAATA
1 TAT-TAAT-AA-ATAATATATT-AT--TAATAATAT-ATA
*
5425672 TATTAATAAATAATATTATTATATATTAATAAATAATA
1 TATTAATAAATAATA-TATTAT-TAATAAT--AT-ATA
*
5425710 TATT-ATTAATAATACTA-TATTAATAA-ATA-A
1 TATTAATAAATAATA-TATTATTAATAATATATA
* * *
5425740 TAATAAAATAATATTATAATATATTAATAA-ATA-A
1 TATTAATA-AATAATAT-AT-TATTAATAATATATA
*
5425774 TA-TAAT-AATAAT-TATTAATTTAATTAAT-CA-A
1 TATTAATAAATAATATATT-A-TTAA-TAATATATA
* * * *
5425805 TATT-A-CAATAATATATGAATAAATAATATA-C
1 TATTAATAAATAATATAT-TATTAATAATATATA
5425836 TATTAAT--AT-A-ATA-TATTAATAA-ATAT-
1 TATTAATAAATAATATATTATTAATAATATATA
*
5425862 TATTAATTAATAATAT
1 TATTAATAAATAATAT
5425878 TATAACATAT
Statistics
Matches: 232, Mismatches: 32, Indels: 90
0.66 0.09 0.25
Matches are distributed among these distances:
26 10 0.04
27 7 0.03
28 3 0.01
29 17 0.07
30 20 0.09
31 42 0.18
32 23 0.10
33 9 0.04
34 29 0.12
35 10 0.04
36 14 0.06
37 22 0.09
38 18 0.08
39 4 0.02
40 4 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (33 bp):
TATTAATAAATAATATATTATTAATAATATATA
Found at i:5425973 original size:21 final size:18
Alignment explanation
Indices: 5425938--5426022 Score: 83
Period size: 18 Copynumber: 4.9 Consensus size: 18
5425928 GTATTTTTAT
5425938 AATAATATTTTAATATTA
1 AATAATATTTTAATATTA
*
5425956 AATAATATTATTAA-AATA
1 AATAATATT-TTAATATTA
*
5425974 TAATTA-ATTTTAATATT-
1 -AATAATATTTTAATATTA
*
5425991 AAT-A-ATTTTAATAATA
1 AATAATATTTTAATATTA
5426007 AATAAT-TTTTAATATT
1 AATAATATTTTAATATT
5426023 TTAATAGTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
15 11 0.20
16 6 0.11
17 14 0.25
18 17 0.30
19 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAATATTTTAATATTA
Found at i:5425993 original size:16 final size:16
Alignment explanation
Indices: 5425944--5426022 Score: 70
Period size: 17 Copynumber: 4.7 Consensus size: 16
5425934 TTATAATAAT
*
5425944 ATTTTAATATTAAATAA
1 ATTTTAATATT-AATTA
*
5425961 TATTATTAAAATATAATTA
1 -ATT-TTAATAT-TAATTA
5425980 ATTTTAATATTAA-TA
1 ATTTTAATATTAATTA
* *
5425995 ATTTTAATAATAAATA
1 ATTTTAATATTAATTA
5426011 ATTTTTAATATT
1 A-TTTTAATATT
5426023 TTAATAGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
15 14 0.27
16 6 0.12
17 15 0.29
18 6 0.12
19 10 0.19
20 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTTAATATTAATTA
Found at i:5426017 original size:32 final size:36
Alignment explanation
Indices: 5425935--5426022 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 36
5425925 TAAGTATTTT
5425935 TATAATAATATTTTAATATTAAATAATATTATTAAAA
1 TATAATAAT-TTTTAATATTAAATAATATTATTAAAA
5425972 TATAATTAA-TTTTAATATT-AAT-A-ATT-TTAATAA
1 TATAA-TAATTTTTAATATTAAATAATATTATTAA-AA
5426005 TA-AATAATTTTTAATATT
1 TATAATAATTTTTAATATT
5426023 TTAATAGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
31 3 0.06
32 16 0.33
33 7 0.15
34 1 0.02
35 3 0.06
36 10 0.21
37 5 0.10
38 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
TATAATAATTTTTAATATTAAATAATATTATTAAAA
Found at i:5426067 original size:16 final size:15
Alignment explanation
Indices: 5426048--5426082 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
5426038 ATATTATTTG
5426048 AAAAAAATAAATTAAA
1 AAAAAAATAAA-TAAA
*
5426064 AAAAAACTAAATAAA
1 AAAAAAATAAATAAA
5426079 AAAA
1 AAAA
5426083 TATTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAAATAAATAAA
Found at i:5426068 original size:15 final size:15
Alignment explanation
Indices: 5426048--5426082 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5426038 ATATTATTTG
5426048 AAAAAAA-TAAATTAA
1 AAAAAAACTAAA-TAA
5426063 AAAAAAACTAAATAA
1 AAAAAAACTAAATAA
5426078 AAAAA
1 AAAAA
5426083 TATTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAAAACTAAATAA
Found at i:5426163 original size:25 final size:25
Alignment explanation
Indices: 5426135--5426207 Score: 101
Period size: 25 Copynumber: 2.8 Consensus size: 25
5426125 ATTCAAAAAA
**
5426135 AAAAATTTTTTTTTAAATATTTTTC
1 AAAAATTTTTTTAAAAATATTTTTC
5426160 AAAAATTTTTTTAAAAATATTTTTC
1 AAAAATTTTTTTAAAAATATTTTTC
5426185 AAAAATTAATTTTTACAAAATAT
1 AAAAATT--TTTTTA-AAAATAT
5426208 ACGAACCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 30 0.70
27 6 0.14
28 7 0.16
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAAATTTTTTTAAAAATATTTTTC
Found at i:5426165 original size:13 final size:13
Alignment explanation
Indices: 5426149--5426204 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
5426139 ATTTTTTTTT
5426149 AAATATTTTTCAA
1 AAATATTTTTCAA
*
5426162 AAAT-TTTTTTAA
1 AAATATTTTTCAA
5426174 AAATATTTTTCAA
1 AAATATTTTTCAA
5426187 AAATTAATTTTTACAA
1 AAA-T-ATTTTT-CAA
5426203 AA
1 AA
5426205 TATACGAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
12 11 0.30
13 14 0.38
14 1 0.03
15 6 0.16
16 5 0.14
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATTTTTCAA
Found at i:5426436 original size:16 final size:16
Alignment explanation
Indices: 5426415--5426466 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5426405 TTTAATTAAT
5426415 TATTTATATATATATA
1 TATTTATATATATATA
5426431 TATTTATATA-ATGATA
1 TATTTATATATAT-ATA
* *
5426447 T-TTT-TAAATATTTA
1 TATTTATATATATATA
5426461 TATTTA
1 TATTTA
5426467 AAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.20
15 10 0.33
16 14 0.47
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTTATATATATATA
Found at i:5426449 original size:30 final size:29
Alignment explanation
Indices: 5426415--5426484 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
5426405 TTTAATTAAT
* * *
5426415 TATTTATATATATATATATTTATATAATGA
1 TATTT-TATATATATATATTTAAAAAATAA
* *
5426445 TATTTTTAAATATTTATATTTAAAAAATAA
1 TA-TTTTATATATATATATTTAAAAAATAA
5426475 TATTTTATAT
1 TATTTTATAT
5426485 TTTAAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 7 0.21
30 23 0.70
31 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TATTTTATATATATATATTTAAAAAATAA
Found at i:5426483 original size:21 final size:22
Alignment explanation
Indices: 5426453--5426504 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5426443 GATATTTTTA
5426453 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
5426473 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
5426495 AATATTTTAT
1 AATATTTTAT
5426505 TAATTTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:5432992 original size:14 final size:14
Alignment explanation
Indices: 5432973--5432999 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5432963 TGTGATTTAA
5432973 AATTTTCAAAAATG
1 AATTTTCAAAAATG
5432987 AATTTTCAAAAAT
1 AATTTTCAAAAAT
5433000 TTTTAAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (14 bp):
AATTTTCAAAAATG
Found at i:5433019 original size:34 final size:33
Alignment explanation
Indices: 5432968--5433034 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
5432958 TTTGATGTGA
* *
5432968 TTTAAAATTTTCAAAAATGAATTTTCAAAAATT
1 TTTAAAATTTTCAAAAATAAACTTTCAAAAATT
** *
5433001 TTTAAGAATTTTTGAAAATAAACTTTCTAAAATT
1 TTTAA-AATTTTCAAAAATAAACTTTCAAAAATT
5433035 CATTTTCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (33 bp):
TTTAAAATTTTCAAAAATAAACTTTCAAAAATT
Found at i:5433079 original size:14 final size:14
Alignment explanation
Indices: 5433057--5433100 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5433047 TCTTTAAAAC
*
5433057 TTTTTAAAAATTAA
1 TTTTAAAAAATTAA
*
5433071 TTTTAAAAAATTTA
1 TTTTAAAAAATTAA
* *
5433085 TTTGAAAAAAATAA
1 TTTTAAAAAATTAA
5433099 TT
1 TT
5433101 AATTAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TTTTAAAAAATTAA
Found at i:5433081 original size:48 final size:48
Alignment explanation
Indices: 5432972--5433087 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 48
5432962 ATGTGATTTA
* * *
5432972 AAATTTTCAAAAATGAATTTTCAAAAATTTTTAAGAATTTTTGAAAAT
1 AAATTTTCAAAAATTAATTTTCAAAAATCTTTAAGAATTTTTAAAAAT
* * *
5433020 AAACTTTCTAAAATTCATTTTCAAAAATCTTTAA-AACTTTTTAAAAAT
1 AAATTTTCAAAAATTAATTTTCAAAAATCTTTAAGAA-TTTTTAAAAAT
* * *
5433068 TAATTTTAAAAAATTTATTT
1 AAATTTTCAAAAATTAATTT
5433088 GAAAAAAATA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 2 0.04
48 54 0.96
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.44
Consensus pattern (48 bp):
AAATTTTCAAAAATTAATTTTCAAAAATCTTTAAGAATTTTTAAAAAT
Found at i:5435645 original size:3 final size:3
Alignment explanation
Indices: 5435631--5435679 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
5435621 TTTAGTCTCT
* * *
5435631 TTC TTC TAC TTC TTC TTC TTC TTC TTC TTC TCC TTC TTC TCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5435679 T
1 T
5435680 CTATCATCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (3 bp):
TTC
Found at i:5443497 original size:43 final size:42
Alignment explanation
Indices: 5443436--5443521 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 42
5443426 TGAATTGTGA
*
5443436 CAAATACAATTCATACTAAACCTAACCGTGTCCTGTCATGGGC
1 CAAATACAATTCATACTAAACCT-ACCATGTCCTGTCATGGGC
*
5443479 CAAATACAATTCATACTAAACCTACCATGTCTTGTCATGGGC
1 CAAATACAATTCATACTAAACCTACCATGTCCTGTCATGGGC
5443521 C
1 C
5443522 GGCAGCCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 18 0.44
43 23 0.56
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (42 bp):
CAAATACAATTCATACTAAACCTACCATGTCCTGTCATGGGC
Found at i:5444888 original size:167 final size:167
Alignment explanation
Indices: 5444612--5444948 Score: 674
Period size: 167 Copynumber: 2.0 Consensus size: 167
5444602 GCATTTGAAC
5444612 TCAAGGCTATCATCCATTTCCGTGGATCGCCCCTCAATCATTTTAAAAGCATTACATAGTTTTTG
1 TCAAGGCTATCATCCATTTCCGTGGATCGCCCCTCAATCATTTTAAAAGCATTACATAGTTTTTG
5444677 AAGTTTGCAGCGTCTCAAAAAAGCCCTGTTCATTTGGTTTGTTTTGCGAATTGTGATTTGGTGCA
66 AAGTTTGCAGCGTCTCAAAAAAGCCCTGTTCATTTGGTTTGTTTTGCGAATTGTGATTTGGTGCA
5444742 TCTTTATGTATGTGTTTATAGGAATGGAATACAGAAT
131 TCTTTATGTATGTGTTTATAGGAATGGAATACAGAAT
5444779 TCAAGGCTATCATCCATTTCCGTGGATCGCCCCTCAATCATTTTAAAAGCATTACATAGTTTTTG
1 TCAAGGCTATCATCCATTTCCGTGGATCGCCCCTCAATCATTTTAAAAGCATTACATAGTTTTTG
5444844 AAGTTTGCAGCGTCTCAAAAAAGCCCTGTTCATTTGGTTTGTTTTGCGAATTGTGATTTGGTGCA
66 AAGTTTGCAGCGTCTCAAAAAAGCCCTGTTCATTTGGTTTGTTTTGCGAATTGTGATTTGGTGCA
5444909 TCTTTATGTATGTGTTTATAGGAATGGAATACAGAAT
131 TCTTTATGTATGTGTTTATAGGAATGGAATACAGAAT
5444946 TCA
1 TCA
5444949 CGGTTCTCTT
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 170 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (167 bp):
TCAAGGCTATCATCCATTTCCGTGGATCGCCCCTCAATCATTTTAAAAGCATTACATAGTTTTTG
AAGTTTGCAGCGTCTCAAAAAAGCCCTGTTCATTTGGTTTGTTTTGCGAATTGTGATTTGGTGCA
TCTTTATGTATGTGTTTATAGGAATGGAATACAGAAT
Found at i:5457589 original size:20 final size:20
Alignment explanation
Indices: 5457545--5457588 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
5457535 CTAATTATCG
*
5457545 ATTTTCTCGTAAAATCACAA
1 ATTTTCTCATAAAATCACAA
5457565 ATTTTCTCATAAAATCAC-A
1 ATTTTCTCATAAAATCACAA
5457584 ATTTT
1 ATTTT
5457589 TTTGCTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTTCTCATAAAATCACAA
Found at i:5463713 original size:19 final size:18
Alignment explanation
Indices: 5463681--5463731 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
5463671 TATAATAAAA
* *
5463681 AATTTGATTTTGATTTTT
1 AATTTGAATTTGATATTT
5463699 AACTTGTG-ATTTGATATTT
1 AA-TT-TGAATTTGATATTT
5463718 AATTTGAATTTGAT
1 AATTTGAATTTGAT
5463732 CAAATTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 13 0.46
20 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (18 bp):
AATTTGAATTTGATATTT
Found at i:5464205 original size:6 final size:6
Alignment explanation
Indices: 5464194--5464226 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5464184 TCACTTTTCA
*
5464194 AAAAAT AAAAAT AAAAAT AAAAAT -GAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
5464227 CCCTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:5465370 original size:19 final size:20
Alignment explanation
Indices: 5465343--5465396 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
5465333 TAATTTTTAT
* *
5465343 ATATCTATTTTAA-AAATTG
1 ATATTTATTTTAATAAAATG
5465362 ATATTTATTTATTAATAAAATG
1 ATATTTA-TT-TTAATAAAATG
5465384 ATATTT-TTTTAAT
1 ATATTTATTTTAAT
5465397 TTATTGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 11 0.37
20 4 0.13
21 4 0.13
22 11 0.37
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
ATATTTATTTTAATAAAATG
Found at i:5465374 original size:23 final size:23
Alignment explanation
Indices: 5465351--5465399 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5465341 ATATATCTAT
*
5465351 TTTAA-AAATTGATATTTATTTA
1 TTTAATAAAATGATATTTATTTA
*
5465373 -TTAATAAAATGATATTTTTTTAA
1 TTTAATAAAATGATATTTATTT-A
5465396 TTTA
1 TTTA
5465400 TTGATAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 1 0.05
24 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTAATAAAATGATATTTATTTA
Found at i:5470551 original size:15 final size:14
Alignment explanation
Indices: 5470524--5470553 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5470514 TAATTAGGTT
5470524 ATTTAATTTAAAAA
1 ATTTAATTTAAAAA
*
5470538 ATTTTATTTAAAAA
1 ATTTAATTTAAAAA
5470552 AT
1 AT
5470554 AAGACTTCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTAATTTAAAAA
Found at i:5472133 original size:14 final size:14
Alignment explanation
Indices: 5472114--5472151 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
5472104 AAAGCCTAAA
5472114 TTTATTT-ATTTTT
1 TTTATTTAATTTTT
5472127 TTATATTTAATTTTT
1 TT-TATTTAATTTTT
5472142 TTTA-TTAATT
1 TTTATTTAATT
5472152 GCTAAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.35
14 7 0.30
15 8 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTAATTTTT
Found at i:5474422 original size:16 final size:16
Alignment explanation
Indices: 5474401--5474486 Score: 61
Period size: 16 Copynumber: 5.5 Consensus size: 16
5474391 TTTTCAAAAC
5474401 CCTAAAACCTCGAAAT
1 CCTAAAACCTCGAAAT
* * *
5474417 CCTAAAACC-CTAGAC
1 CCTAAAACCTCGAAAT
* * *
5474432 CCTGAATCCTTGAAA-
1 CCTAAAACCTCGAAAT
*
5474447 CTCTAAAACC-CAAAAT
1 C-CTAAAACCTCGAAAT
* *
5474463 CCTAAAATCTTGAAAT
1 CCTAAAACCTCGAAAT
5474479 CCTAAAAC
1 CCTAAAAC
5474487 GAGATCCTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
15 21 0.42
16 29 0.58
ACGTcount: A:0.43, C:0.30, G:0.06, T:0.21
Consensus pattern (16 bp):
CCTAAAACCTCGAAAT
Found at i:5476330 original size:18 final size:18
Alignment explanation
Indices: 5476294--5476332 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5476284 TCTAACACAA
* *
5476294 TTTTAAAAGTTTTAAATT
1 TTTTAAAAATATTAAATT
*
5476312 TTTTAAAAATATTAGATT
1 TTTTAAAAATATTAAATT
5476330 TTT
1 TTT
5476333 CATTAACTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTTAAAAATATTAAATT
Found at i:5479690 original size:13 final size:12
Alignment explanation
Indices: 5479659--5479705 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
5479649 GACTAAGTCT
5479659 TTCTCTTCAC-TC
1 TTCTCTT-ACTTC
5479671 TTCTCTTACTTC
1 TTCTCTTACTTC
5479683 TTCTTCTT-CGTTC
1 TTC-TCTTAC-TTC
5479696 TTCTCTTACT
1 TTCTCTTACT
5479706 AGAAACACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.06
12 18 0.58
13 11 0.35
ACGTcount: A:0.06, C:0.34, G:0.02, T:0.57
Consensus pattern (12 bp):
TTCTCTTACTTC
Found at i:5481899 original size:18 final size:20
Alignment explanation
Indices: 5481868--5481904 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
5481858 TAAAAATCAC
5481868 ATTAGAAAACAAATATTAGA
1 ATTAGAAAACAAATATTAGA
5481888 ATTA-AAAA-AAATATTAG
1 ATTAGAAAACAAATATTAG
5481905 TTTTTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (20 bp):
ATTAGAAAACAAATATTAGA
Found at i:5487751 original size:2 final size:2
Alignment explanation
Indices: 5487744--5487774 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5487734 TTATGTTTAT
5487744 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
5487775 GCCCCATAAC
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:5491163 original size:2 final size:2
Alignment explanation
Indices: 5491158--5491186 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5491148 AAAATAAAAG
5491158 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5491187 AGCTAGCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5493362 original size:19 final size:19
Alignment explanation
Indices: 5493312--5493368 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
5493302 ATGAGTGATT
*
5493312 TATTTTTTTAAAAA-ATTA
1 TATTTTTATAAAAATATTA
* *
5493330 TAATTATA-ATAAAATATTA
1 TATTTTTATA-AAAATATTA
5493349 TATTTTTATAAAAATTATTA
1 TATTTTTATAAAAA-TATTA
5493369 AATTCAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 1 0.03
18 9 0.30
19 14 0.47
20 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTTATAAAAATATTA
Found at i:5493456 original size:7 final size:7
Alignment explanation
Indices: 5493440--5493468 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5493430 AATAATGAGG
5493440 CTTG-AA
1 CTTGAAA
5493446 CTTGAAA
1 CTTGAAA
5493453 CTTGAAA
1 CTTGAAA
5493460 CTTGAAA
1 CTTGAAA
5493467 CT
1 CT
5493469 ATCAAGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (7 bp):
CTTGAAA
Found at i:5499101 original size:27 final size:27
Alignment explanation
Indices: 5499070--5499124 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
5499060 AGATACTGTA
5499070 AGCCTTTATGTTTTTTATATCTATTCT
1 AGCCTTTATGTTTTTTATATCTATTCT
5499097 AGCCTTTATGTTTTTTATATCTATTCT
1 AGCCTTTATGTTTTTTATATCTATTCT
5499124 A
1 A
5499125 TGTAAAACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (27 bp):
AGCCTTTATGTTTTTTATATCTATTCT
Found at i:5499412 original size:18 final size:18
Alignment explanation
Indices: 5499389--5499425 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5499379 GAGCTGGTGA
5499389 GCTATTCATTTAATACTT
1 GCTATTCATTTAATACTT
5499407 GCTATTCATTTAATACTT
1 GCTATTCATTTAATACTT
5499425 G
1 G
5499426 GTTATCTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (18 bp):
GCTATTCATTTAATACTT
Found at i:5500934 original size:20 final size:20
Alignment explanation
Indices: 5500911--5500950 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5500901 GAAAATGTTA
5500911 ATTTG-TTCAATTGAAGAATT
1 ATTTGCTTC-ATTGAAGAATT
*
5500931 ATTTGCTTCTTTGAAGAATT
1 ATTTGCTTCATTGAAGAATT
5500951 TCCAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.47
Consensus pattern (20 bp):
ATTTGCTTCATTGAAGAATT
Found at i:5511907 original size:16 final size:16
Alignment explanation
Indices: 5511886--5511934 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
5511876 AATTTTACTT
*
5511886 TTATTTTGTATTTTTA
1 TTATTTTATATTTTTA
5511902 TTATTTTATATTTTTAA
1 TTATTTTATATTTTT-A
5511919 TTTTATTTTATATTTT
1 --TTATTTTATATTTT
5511935 ATGTATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 14 0.48
17 1 0.03
19 14 0.48
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (16 bp):
TTATTTTATATTTTTA
Found at i:5511926 original size:19 final size:19
Alignment explanation
Indices: 5511878--5511934 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
5511868 GTAAGCCCAA
* *
5511878 TTTTACTTTTATTTTGTAT
1 TTTTAATTTTATTTTATAT
5511897 TTTT-A--TTATTTTATAT
1 TTTTAATTTTATTTTATAT
5511913 TTTTAATTTTATTTTATAT
1 TTTTAATTTTATTTTATAT
5511932 TTT
1 TTT
5511935 ATGTATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 14 0.42
17 1 0.03
19 18 0.55
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTAATTTTATTTTATAT
Found at i:5511935 original size:7 final size:7
Alignment explanation
Indices: 5511884--5511936 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
5511874 CCAATTTTAC
5511884 TTTTAT-
1 TTTTATA
5511890 TTTGTAT-
1 TTT-TATA
5511897 TTTTATTA
1 TTTTA-TA
5511905 TTTTATA
1 TTTTATA
5511912 TTTT-TA
1 TTTTATA
*
5511918 ATTT-TA
1 TTTTATA
5511924 TTTTATA
1 TTTTATA
5511931 TTTTAT
1 TTTTAT
5511937 GTATATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 15 0.37
7 21 0.51
8 5 0.12
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (7 bp):
TTTTATA
Found at i:5512082 original size:4 final size:4
Alignment explanation
Indices: 5512042--5512168 Score: 54
Period size: 4 Copynumber: 32.2 Consensus size: 4
5512032 TTTCTATTAA
* * * * *
5512042 TATT TATA TATG TATTT TATT TATC TAGT TATA TATT TA-T TA-T TATT
1 TATT TATT TATT TA-TT TATT TATT TATT TATT TATT TATT TATT TATT
* * *
5512089 TATT CATT TATA TATT ATAATT TATC TA-T TA-T TA-T TATT T-TT TATT
1 TATT TATT TATT TATT -T-ATT TATT TATT TATT TATT TATT TATT TATT
* *
5512135 TATCT TGTAA TATT T-TT TATT TATCT TA-T TATT T
1 TAT-T TAT-T TATT TATT TATT TAT-T TATT TATT T
5512169 TTTTCTAATT
Statistics
Matches: 93, Mismatches: 20, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
3 23 0.25
4 54 0.58
5 13 0.14
6 3 0.03
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:5512099 original size:26 final size:25
Alignment explanation
Indices: 5512042--5512209 Score: 109
Period size: 22 Copynumber: 7.2 Consensus size: 25
5512032 TTTCTATTAA
*
5512042 TATTTATATATGTATTTTATTTATC
1 TATTTATATATTTATTTTATTTATC
*
5512067 TAGTTATATATTTATTATTATTTAT-
1 TATTTATATATTTATT-TTATTTATC
*
5512092 TCATTTATATA-TTA--TAATTTATC
1 T-ATTTATATATTTATTTTATTTATC
*
5512115 TA-TTAT-TATTATTTTTTATTTATC
1 TATTTATATATT-TATTTTATTTATC
*
5512139 T-TGTA-ATA-TT-TTTTATTTATC
1 TATTTATATATTTATTTTATTTATC
* *
5512160 T-TATTAT-T-TTT-TTCTAATTATC
1 TAT-TTATATATTTATTTTATTTATC
5512182 TA-TTA-ATATTT-TTTTATTTATC
1 TATTTATATATTTATTTTATTTATC
5512204 TGATTT
1 T-ATTT
5512210 TTTTTTAGGC
Statistics
Matches: 114, Mismatches: 12, Indels: 35
0.71 0.07 0.22
Matches are distributed among these distances:
20 2 0.02
21 22 0.19
22 38 0.33
23 3 0.03
24 15 0.13
25 18 0.16
26 16 0.14
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (25 bp):
TATTTATATATTTATTTTATTTATC
Found at i:5512150 original size:21 final size:20
Alignment explanation
Indices: 5512124--5512204 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 20
5512114 CTATTATTAT
5512124 TATTTTTTATTTATCTTGTAA
1 TATTTTTTATTTATCTT-TAA
*
5512145 TATTTTTTATTTATCTTATTA
1 TATTTTTTATTTATCTT-TAA
* *
5512166 TTTTTTTCTAATTATCTATTAA
1 TATTTTT-TATTTATCT-TTAA
5512188 TATTTTTTTATTTATCT
1 TA-TTTTTTATTTATCT
5512205 GATTTTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 25 0.50
22 19 0.38
23 6 0.12
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.69
Consensus pattern (20 bp):
TATTTTTTATTTATCTTTAA
Found at i:5512181 original size:43 final size:43
Alignment explanation
Indices: 5512108--5512215 Score: 132
Period size: 43 Copynumber: 2.5 Consensus size: 43
5512098 ATATATTATA
*
5512108 ATTTATCTATTATTATTATTTTTTATTTATCT-TGTAATA-TTTTTT
1 ATTTATC--TTATTATT-TTTTTTAATTATCTAT-TAATATTTTTTT
5512153 ATTTATCTTATTATTTTTTTCTAATTATCTATTAATATTTTTTT
1 ATTTATCTTATTATTTTTTT-TAATTATCTATTAATATTTTTTT
*
5512197 ATTTATCTGATT-TTTTTTT
1 ATTTATCTTATTATTTTTTT
5512216 AGGCTGAGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
42 5 0.09
43 28 0.48
44 18 0.31
45 7 0.12
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (43 bp):
ATTTATCTTATTATTTTTTTTAATTATCTATTAATATTTTTTT
Found at i:5512593 original size:5 final size:5
Alignment explanation
Indices: 5512572--5512657 Score: 79
Period size: 5 Copynumber: 16.8 Consensus size: 5
5512562 TTTAATATTC
* * *
5512572 TTTTA TTTTTA TCTTTA TTTTA TTTTT TTTTA TTTTA CTTT- TTTAA TTTTTA
1 TTTTA -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
5512624 TTTTCA CTTTTA TTTTA TTTTA --TTA TTTTA TTTT
1 TTTT-A -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
5512658 CTTTAAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
3 3 0.04
4 2 0.03
5 42 0.63
6 16 0.24
7 4 0.06
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5512634 original size:13 final size:12
Alignment explanation
Indices: 5512572--5512657 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 12
5512562 TTTAATATTC
5512572 TTTTA-TTTTTA
1 TTTTACTTTTTA
5512583 TCTTTA--TTTTA
1 T-TTTACTTTTTA
5512594 TTTT--TTTTTA
1 TTTTACTTTTTA
5512604 TTTTAC---TT-
1 TTTTACTTTTTA
*
5512612 TTTTAATTTTTA
1 TTTTACTTTTTA
5512624 TTTTCAC-TTTTA
1 TTTT-ACTTTTTA
*
5512636 TTTTATTTTATTA
1 TTTTACTTT-TTA
5512649 TTTTA-TTTT
1 TTTTACTTTT
5512658 CTTTAAATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 22
0.71 0.03 0.26
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 12 0.20
11 11 0.18
12 22 0.36
13 9 0.15
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTACTTTTTA
Found at i:5512821 original size:57 final size:57
Alignment explanation
Indices: 5512654--5513120 Score: 475
Period size: 57 Copynumber: 8.1 Consensus size: 57
5512644 TATTATTTTA
* * *
5512654 TTTTCTT-TAAATAAA-ATTCAAAAACAATATTTTTGGGGAAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAATTTTCAAAAA-AATA-TTTTGAGGAAAAGTTGAAAGTATCAAT
* ** * * *
5512710 TTTTCTTTGAAAATAAGCTTTCGAAAAAATATTTTCAAGGAATAGTTGAAAGTATCAAT
1 TTTTC-TTAAAAATAAATTTTCAAAAAAATATTTT-GAGGAAAAGTTGAAAGTATCAAT
** * *
5512769 TTTTCTTAAAAATAAATTTTCAAAAAAAGGTTTTAAGAAAAAGTTGAAAGTATCAA-
1 TTTTCTTAAAAATAAATTTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAAT
*
5512825 TTTTCTTTAAAAATAAATTTTCAAAAAAAATTTTTTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTC-TTAAAAATAAATTTTC-AAAAAAA--TATTTTGAGGAAAAGTTGAAAGTATCAAT
** * * *
5512886 TTTTCTCGAAATTAAAGTTTTCTAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAA-TTTTCAAAAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAAT
** *
5512945 TTTTCTTAAAAATAAATTTTC-AAAAAAGGTTTTGAGGAAAAGTTTAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAAT
** * *
5513001 TTTTCTCGAAATTAAAGTTTTC--AAAAATATTTTG-GGAAAAAGTTGAAAGTATCAAC
1 TTTTCTTAAAAATAAA-TTTTCAAAAAAATATTTTGAGG-AAAAGTTGAAAGTATCAAT
* * * * *
5513057 TTTCCTCAAAATTAAAATTTCTAAAAAATATTTTG-GGAAAAAGTTGAAAGTATCAAT
1 TTTTCTTAAAAATAAATTTTCAAAAAAATATTTTGAGG-AAAAGTTGAAAGTATCAAT
5513114 TTTTCTT
1 TTTTCTT
5513121 GCACAAAAGC
Statistics
Matches: 350, Mismatches: 45, Indels: 31
0.82 0.11 0.07
Matches are distributed among these distances:
55 6 0.02
56 89 0.25
57 91 0.26
58 65 0.19
59 51 0.15
60 38 0.11
61 10 0.03
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (57 bp):
TTTTCTTAAAAATAAATTTTCAAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:5512834 original size:30 final size:30
Alignment explanation
Indices: 5512800--5512888 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 30
5512790 AAAAAAAGGT
5512800 TTTAAGAAAAAGTTGAAAGTATCAATTTTC
1 TTTAAGAAAAAGTTGAAAGTATCAATTTTC
* * * ** *
5512830 TTTAAAAATAAATTTTCAAA--AAAAATTTTT
1 TTTAAGAA-AAA-GTTGAAAGTATCAATTTTC
* *
5512860 TTTGAGGAAAAGTTGAAAGTATCAATTTT
1 TTTAAGAAAAAGTTGAAAGTATCAATTTT
5512889 TCTCGAAATT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
28 5 0.12
29 3 0.07
30 26 0.62
31 3 0.07
32 5 0.12
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTAAGAAAAAGTTGAAAGTATCAATTTTC
Found at i:5515183 original size:14 final size:14
Alignment explanation
Indices: 5515161--5515194 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5515151 GCTAATTCTG
*
5515161 ATAAATTTAATTTT
1 ATAATTTTAATTTT
5515175 ATAATTTTAATTTT
1 ATAATTTTAATTTT
*
5515189 AAAATT
1 ATAATT
5515195 AATATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATAATTTTAATTTT
Found at i:5518892 original size:13 final size:13
Alignment explanation
Indices: 5518851--5518894 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5518841 AATTTGAATC
5518851 TAAAAAATAT-ATT
1 TAAAAAATATGA-T
5518864 TAAAAAATATGA-
1 TAAAAAATATGAT
*
5518876 TAAAAAATGTGAT
1 TAAAAAATATGAT
5518889 TAAAAA
1 TAAAAA
5518895 TTTTAAGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 11 0.39
13 16 0.57
14 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
TAAAAAATATGAT
Found at i:5519207 original size:22 final size:22
Alignment explanation
Indices: 5519181--5519234 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
5519171 AATTAAGTAT
5519181 ATAAAATTTGATAAAATTTTT-A
1 ATAAAATTTGAT-AAATTTTTAA
* *
5519203 ATAAATTTTGATATATTTTTAA
1 ATAAAATTTGATAAATTTTTAA
5519225 ATAAATATTT
1 ATAAA-ATTT
5519235 TTACTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.26
22 17 0.63
23 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATAAAATTTGATAAATTTTTAA
Found at i:5521520 original size:2 final size:2
Alignment explanation
Indices: 5521513--5521538 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5521503 AGTTGATGGG
5521513 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
5521539 GCATATCATT
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:5522185 original size:22 final size:21
Alignment explanation
Indices: 5522160--5522214 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5522150 TTAATTTCGA
*
5522160 TAACTTTTGATACAAATTTTGG
1 TAACTTTTGATA-AAAGTTTGG
* *
5522182 TAACATTTGATAATAGTTTGG
1 TAACTTTTGATAAAAGTTTGG
*
5522203 TAACTTATGATA
1 TAACTTTTGATA
5522215 TAATTGTGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.44
Consensus pattern (21 bp):
TAACTTTTGATAAAAGTTTGG
Found at i:5522203 original size:21 final size:20
Alignment explanation
Indices: 5522177--5522239 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
5522167 TGATACAAAT
5522177 TTTGGTAACATTTGATAATAG
1 TTTGGTAACATTTGAT-ATAG
*
5522198 TTTGGTAAC-TTATGATATAA
1 TTTGGTAACATT-TGATATAG
5522218 TTGTGGTAATCA-TTGATATAG
1 TT-TGGTAA-CATTTGATATAG
5522239 T
1 T
5522240 CTTGATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 7 0.19
21 27 0.75
22 2 0.06
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTGGTAACATTTGATATAG
Found at i:5522234 original size:42 final size:42
Alignment explanation
Indices: 5522160--5522239 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
5522150 TTAATTTCGA
* *
5522160 TAACTTTTGATACAAATTTTGGTAACATTTGATAATAGTTTGG
1 TAACTTATGATACAAATTGTGGTAACATTTGAT-ATAGTTTGG
*
5522203 TAACTTATGATA-TAATTGTGGTAATCA-TTGATATAGT
1 TAACTTATGATACAAATTGTGGTAA-CATTTGATATAGT
5522240 CTTGATAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 5 0.15
42 15 0.45
43 13 0.39
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.44
Consensus pattern (42 bp):
TAACTTATGATACAAATTGTGGTAACATTTGATATAGTTTGG
Found at i:5522735 original size:22 final size:22
Alignment explanation
Indices: 5522710--5522870 Score: 73
Period size: 22 Copynumber: 7.3 Consensus size: 22
5522700 AGTATTGAAG
* *
5522710 TACTACTAATTTATGAATAATT
1 TACTAATAAATTATGAATAATT
* * *
5522732 TACTATTAAGTTATGAATTATT
1 TACTAATAAATTATGAATAATT
*
5522754 TACTAATAAATTATTG-ATGATT
1 TACTAATAAATTA-TGAATAATT
* * **
5522776 TATTATTAAATTATTG-ATGTTT
1 TACTAATAAATTA-TGAATAATT
*
5522798 TA-TTATAAAGTTAT-AACTAATT
1 TACTAATAAA-TTATGAA-TAATT
* * *
5522820 TATTATTAATTTATTG-ATAATT
1 TACTAATAAATTA-TGAATAATT
* *
5522842 TACTACA-AAATTATCAATGATT
1 TACTA-ATAAATTATGAATAATT
*
5522864 AACTAAT
1 TACTAAT
5522871 TTACTATAAA
Statistics
Matches: 107, Mismatches: 22, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
21 9 0.08
22 90 0.84
23 8 0.07
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (22 bp):
TACTAATAAATTATGAATAATT
Found at i:5522834 original size:11 final size:11
Alignment explanation
Indices: 5522716--5522843 Score: 50
Period size: 11 Copynumber: 11.6 Consensus size: 11
5522706 GAAGTACTAC
* *
5522716 TAATTTATGAA
1 TAATTTATTAT
*
5522727 TAATTTACTAT
1 TAATTTATTAT
* *
5522738 TAAGTTATGAAT
1 TAATTTAT-TAT
* *
5522750 T-ATTTACTAA
1 TAATTTATTAT
*
5522760 TAAATTATTGA-
1 TAATTTATT-AT
*
5522771 TGATTTATTAT
1 TAATTTATTAT
*
5522782 TAAATTATTGAT
1 TAATTTATT-AT
5522794 GT--TTTATTAT
1 -TAATTTATTAT
* * * *
5522804 AAAGTTATAAC
1 TAATTTATTAT
5522815 TAATTTATTAT
1 TAATTTATTAT
5522826 TAATTTATTGA-
1 TAATTTATT-AT
5522837 TAATTTA
1 TAATTTA
5522844 CTACAAAATT
Statistics
Matches: 83, Mismatches: 25, Indels: 18
0.66 0.20 0.14
Matches are distributed among these distances:
10 5 0.06
11 70 0.84
12 7 0.08
13 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (11 bp):
TAATTTATTAT
Found at i:5522871 original size:30 final size:30
Alignment explanation
Indices: 5522837--5522893 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5522827 AATTTATTGA
5522837 TAATTTACTACAAAATTATCAA-TGATTAAC
1 TAATTTACTACAAAATTAT-AACTGATTAAC
*
5522867 TAATTTACTATAAAATTATAACTGATT
1 TAATTTACTACAAAATTATAACTGATT
5522894 TACAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (30 bp):
TAATTTACTACAAAATTATAACTGATTAAC
Found at i:5522912 original size:22 final size:22
Alignment explanation
Indices: 5522863--5522916 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
5522853 TATCAATGAT
* *
5522863 TAACTAATTTACTATAAAATTA
1 TAACTGATTTACAATAAAATTA
*
5522885 TAACTGATTTACAATTAAATTA
1 TAACTGATTTACAATAAAATTA
5522907 -ACACTGATTT
1 TA-ACTGATTT
5522917 GCAACTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (22 bp):
TAACTGATTTACAATAAAATTA
Found at i:5523221 original size:21 final size:21
Alignment explanation
Indices: 5523161--5523231 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
5523151 TTATTAATTG
5523161 TTAAGTTATCAATAATTTACTAT
1 TTAAGTTA-CAATAATTTACT-T
* *
5523184 TACTAAGTTATATTAATTTACTT
1 T--TAAGTTACAATAATTTACTT
* * *
5523207 TTAAGTTCCAATAATTAACTA
1 TTAAGTTACAATAATTTACTT
5523228 TTAA
1 TTAA
5523232 ATTATCATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
21 19 0.49
23 3 0.08
24 10 0.26
25 7 0.18
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAAGTTACAATAATTTACTT
Found at i:5523356 original size:22 final size:22
Alignment explanation
Indices: 5522869--5523363 Score: 138
Period size: 22 Copynumber: 22.5 Consensus size: 22
5522859 TGATTAACTA
* * *
5522869 ATTTACTATAAAATTATAACTG
1 ATTTACTATTAAATTATCATTG
* * *
5522891 ATTTACAATTAAATTAACACTG
1 ATTTACTATTAAATTATCATTG
* * * ** *
5522913 ATTTGCAACTATTTTATTATTG
1 ATTTACTATTAAATTATCATTG
* * *
5522935 ATTTACTACTAAATTATCAATA
1 ATTTACTATTAAATTATCATTG
5522957 ATTTAC-ATATAAATTATCAATT-
1 ATTTACTAT-TAAATTATC-ATTG
* * *
5522979 ATTTACTATTATACTATTA-TG
1 ATTTACTATTAAATTATCATTG
*
5523000 CATTTACTATTATATTATCATTG
1 -ATTTACTATTAAATTATCATTG
** * *
5523023 ATTTACTACTTAGTTTTTGATT-
1 ATTTACTA-TTAAATTATCATTG
** **
5523045 ATTTACTA-TACAATCGTCACAG
1 ATTTACTATTA-AATTATCATTG
* * * *
5523067 ATTTATTACTAATTTAAC-TATG
1 ATTTACTATTAAATTATCAT-TG
* * *
5523089 ATTTA-T-TTCCAAGTTATCACTA
1 ATTTACTATT--AAATTATCATTG
* *
5523111 ATTTA-TATTCAATTTTCA-TG
1 ATTTACTATTAAATTATCATTG
* **
5523131 ATTTATTATTAGGTTATCACTT-
1 ATTTACTATTAAATTATCA-TTG
* * * * * *
5523153 ATTAATTGTTAAGTTATCAATA
1 ATTTACTATTAAATTATCATTG
*
5523175 ATTTACTATTACTAAGTTAT-ATTA
1 ATTTACTATTA--AA-TTATCATTG
* * * * *
5523199 ATTTACTTTTAAGTT-CCAATA
1 ATTTACTATTAAATTATCATTG
*
5523220 ATTAACTATTAAATTATCATTG
1 ATTTACTATTAAATTATCATTG
* * *
5523242 ATTTATTACTAAGTTATTCA-TG
1 ATTTACTATTAAATTA-TCATTG
* * *
5523264 CTTTACTATGAAGTTTATCAATT-
1 ATTTACTATTAA-ATTATC-ATTG
* * ** *
5523287 AATTACTATTAGATTAAAACTG
1 ATTTACTATTAAATTATCATTG
* * * *
5523309 ATTTTCTATTAAGTTATCACTA
1 ATTTACTATTAAATTATCATTG
5523331 ATTTACTATTAAATTATCATTG
1 ATTTACTATTAAATTATCATTG
*
5523353 ATTTATTATTA
1 ATTTACTATTA
5523364 TTAATGATTA
Statistics
Matches: 340, Mismatches: 104, Indels: 58
0.68 0.21 0.12
Matches are distributed among these distances:
20 10 0.03
21 41 0.12
22 235 0.69
23 35 0.10
24 15 0.04
25 4 0.01
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATCATTG
Found at i:5523707 original size:22 final size:22
Alignment explanation
Indices: 5523679--5523804 Score: 112
Period size: 22 Copynumber: 5.8 Consensus size: 22
5523669 AGATTATTAG
* *
5523679 TAATTTACTACTAAGTTATCAA
1 TAATTTACTATTAAATTATCAA
** *
5523701 TGTTTTATTATTAAATTATCAA
1 TAATTTACTATTAAATTATCAA
* *
5523723 TAATTTACTATTAATTTATGAA
1 TAATTTACTATTAAATTATCAA
* *
5523745 TAATTTA-TCATTAAGTTATGAA
1 TAATTTACT-ATTAAATTATCAA
* * *
5523767 TGATTTACCATTAAATTATGAA
1 TAATTTACTATTAAATTATCAA
*
5523789 TGATTT-CTATTAAATT
1 TAATTTACTATTAAATT
5523805 GTTGTTGATC
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
21 10 0.11
22 77 0.89
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCAA
Found at i:5523752 original size:44 final size:44
Alignment explanation
Indices: 5523679--5523804 Score: 137
Period size: 44 Copynumber: 2.9 Consensus size: 44
5523669 AGATTATTAG
* * * *
5523679 TAATTTACTACTAAGTTATCAATGTTTTATTATTAAATTATCAA
1 TAATTTACTATTAAATTATGAATGATTTATTATTAAATTATCAA
* * * * *
5523723 TAATTTACTATTAATTTATGAATAATTTATCATTAAGTTATGAA
1 TAATTTACTATTAAATTATGAATGATTTATTATTAAATTATCAA
* * *
5523767 TGATTTACCATTAAATTATGAATGATTT-CTATTAAATT
1 TAATTTACTATTAAATTATGAATGATTTATTATTAAATT
5523805 GTTGTTGATC
Statistics
Matches: 67, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 7 0.10
44 60 0.90
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.48
Consensus pattern (44 bp):
TAATTTACTATTAAATTATGAATGATTTATTATTAAATTATCAA
Found at i:5523846 original size:22 final size:22
Alignment explanation
Indices: 5523821--5523889 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
5523811 GATCACTAAG
* *
5523821 TTATTGATGATTTATTATAAAT
1 TTATTGATGATTTACTACAAAT
* *
5523843 TTA-TAACCGATTTACTACAAAT
1 TTATTGA-TGATTTACTACAAAT
* *
5523865 TTTTTGATGATTTACTA-AAAG
1 TTATTGATGATTTACTACAAAT
5523886 TTAT
1 TTAT
5523890 CAACGATTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
21 8 0.22
22 26 0.72
23 2 0.06
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (22 bp):
TTATTGATGATTTACTACAAAT
Found at i:5524025 original size:8 final size:8
Alignment explanation
Indices: 5524012--5524050 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
5524002 ATTAATGATT
5524012 TATTATTA
1 TATTATTA
5524020 TATTATTA
1 TATTATTA
5524028 TA-TATT-
1 TATTATTA
5524034 TATTATTA
1 TATTATTA
*
5524042 TGTTATTA
1 TATTATTA
5524050 T
1 T
5524051 TGATTTACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 8 0.29
8 18 0.64
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TATTATTA
Found at i:5524027 original size:22 final size:22
Alignment explanation
Indices: 5523903--5524322 Score: 171
Period size: 22 Copynumber: 19.4 Consensus size: 22
5523893 CGATTAATTA
* * *
5523903 ATTTATTACTAAATTATCATTG
1 ATTTATTATTAAATTATTAATG
** * *
5523925 ATTTACAATTAAATTTTTGAT-
1 ATTTATTATTAAATTATTAATG
* *
5523946 ATTTTATTATT-AGTTATTAGTG
1 A-TTTATTATTAAATTATTAATG
* * * *
5523968 ATTTACTACTAACTT-TTCA--
1 ATTTATTATTAAATTATTAATG
* * *
5523987 ATTTACTAATAAATCATTAATG
1 ATTTATTATTAAATTATTAATG
*
5524009 ATTTATTATTATATTATTATAT-
1 ATTTATTATTAAATTATTA-ATG
** *
5524031 ATTTATTATTATGTTATTATTG
1 ATTTATTATTAAATTATTAATG
** * * *
5524053 ATTTACTGCTT-AATTTTTTATT
1 ATTTA-TTATTAAATTATTAATG
* * * *
5524075 ATTTACTATGAAATTATCATTG
1 ATTTATTATTAAATTATTAATG
***
5524097 ATTTATCGCTAAATTATCT-ATG
1 ATTTATTATTAAATTAT-TAATG
* * * * *
5524119 ATTCACTATCAAATTGTTACTG
1 ATTTATTATTAAATTATTAATG
* *
5524141 ATTTA-TATTAAATTATTCATA
1 ATTTATTATTAAATTATTAATG
* * *
5524162 ATTTACTATTAAATTATTATTA
1 ATTTATTATTAAATTATTAATG
* * *
5524184 ATTAACTATTAAATTATCAATG
1 ATTTATTATTAAATTATTAATG
* *
5524206 ATTTATTACTAAATTA-TATTG
1 ATTTATTATTAAATTATTAATG
*
5524227 ATATACTT-TTAAATT-TTCAATG
1 ATTTA-TTATTAAATTATT-AATG
* * * *
5524249 ATTAATTACTAAATTATCAATT
1 ATTTATTATTAAATTATTAATG
** *
5524271 ATTTACAATTAAATTATTATTG
1 ATTTATTATTAAATTATTAATG
* * * *
5524293 ATTTACTAATAAATTATTTATA
1 ATTTATTATTAAATTATTAATG
5524315 ATTTATTA
1 ATTTATTA
5524323 CTATTAATTA
Statistics
Matches: 282, Mismatches: 98, Indels: 36
0.68 0.24 0.09
Matches are distributed among these distances:
19 12 0.04
20 3 0.01
21 51 0.18
22 210 0.74
23 6 0.02
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (22 bp):
ATTTATTATTAAATTATTAATG
Found at i:5524170 original size:43 final size:45
Alignment explanation
Indices: 5524106--5524200 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 45
5524096 GATTTATCGC
* * * *
5524106 TAAATTA-TCTATGATTCACTATCAAATTGTTACTGATTTA-TAT
1 TAAATTATTCTATAATTCACTATCAAATTATTACTAATTAACTAT
* * *
5524149 TAAATTATTC-ATAATTTACTATTAAATTATTATTAATTAACTAT
1 TAAATTATTCTATAATTCACTATCAAATTATTACTAATTAACTAT
5524193 TAAATTAT
1 TAAATTAT
5524201 CAATGATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
43 30 0.70
44 13 0.30
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (45 bp):
TAAATTATTCTATAATTCACTATCAAATTATTACTAATTAACTAT
Found at i:5524184 original size:11 final size:11
Alignment explanation
Indices: 5524146--5524200 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
5524136 TACTGATTTA
5524146 TATTAAATTAT
1 TATTAAATTAT
* *
5524157 TCA-TAATTTAC
1 T-ATTAAATTAT
5524168 TATTAAATTAT
1 TATTAAATTAT
*
5524179 TATT-AATTAAC
1 TATTAAATT-AT
5524190 TATTAAATTAT
1 TATTAAATTAT
5524201 CAATGATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
10 5 0.15
11 24 0.71
12 5 0.15
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTAAATTAT
Found at i:5524239 original size:65 final size:67
Alignment explanation
Indices: 5524165--5524310 Score: 172
Period size: 65 Copynumber: 2.2 Consensus size: 67
5524155 ATTCATAATT
* * **
5524165 TACTATTAAATTATT-ATTAATTAACTATTAAATTATCAATGATTTATTACTAAATTA-TATTGA
1 TACTATTAAATTATTCAATAATTAACTACTAAATTATCAATGATTTACAACTAAATTATTATTGA
5524228 TA
66 TA
* * * * *
5524230 TACTTTTAAATT-TTCAATGATTAATTACTAAATTATCAATTATTTACAATTAAATTATTATTGA
1 TACTATTAAATTATTCAATAATTAACTACTAAATTATCAATGATTTACAACTAAATTATTATTGA
*
5524294 TT
66 TA
*
5524296 TACTAATAAATTATT
1 TACTATTAAATTATT
5524311 TATAATTTAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
64 2 0.03
65 45 0.68
66 17 0.26
67 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (67 bp):
TACTATTAAATTATTCAATAATTAACTACTAAATTATCAATGATTTACAACTAAATTATTATTGA
TA
Found at i:5524239 original size:87 final size:87
Alignment explanation
Indices: 5524148--5524309 Score: 193
Period size: 87 Copynumber: 1.9 Consensus size: 87
5524138 CTGATTTATA
* * * *
5524148 TTAAATTATTC-ATAATTTACTATTAAATTAT-TATTAATTAACTATTAAATTATCAATGATTTA
1 TTAAATT-TTCAATAATTAACTACTAAATTATCAATT-ATTAACAATTAAATTATCAATGATTTA
* *
5524211 TTACTAAATTATATTGATATACTT
64 CTAATAAATTATATTGATATACTT
* * * * *
5524235 TTAAATTTTCAATGATTAATTACTAAATTATCAATTATTTACAATTAAATTATTATTGATTTACT
1 TTAAATTTTCAATAATTAACTACTAAATTATCAATTATTAACAATTAAATTATCAATGATTTACT
5524300 AATAAATTAT
66 AATAAATTAT
5524310 TTATAATTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 3 0.05
87 56 0.90
88 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (87 bp):
TTAAATTTTCAATAATTAACTACTAAATTATCAATTATTAACAATTAAATTATCAATGATTTACT
AATAAATTATATTGATATACTT
Found at i:5524330 original size:14 final size:14
Alignment explanation
Indices: 5524313--5524343 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5524303 AAATTATTTA
*
5524313 TAATTTATTACTAT
1 TAATTAATTACTAT
5524327 TAATTAATTACTAT
1 TAATTAATTACTAT
5524341 TAA
1 TAA
5524344 GTTGAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTAATTACTAT
Found at i:5524380 original size:22 final size:22
Alignment explanation
Indices: 5524352--5524422 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
5524342 AAGTTGAAAC
*
5524352 TAATTTACTACTAAATTATCAA
1 TAATTTACTATTAAATTATCAA
* * *
5524374 TAATTTATTATTAAGTTATCAT
1 TAATTTACTATTAAATTATCAA
* * *
5524396 TCATTTATTATTAAGTTATCAA
1 TAATTTACTATTAAATTATCAA
5524418 TAATT
1 TAATT
5524423 AACAACTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.49
Consensus pattern (22 bp):
TAATTTACTATTAAATTATCAA
Found at i:5524433 original size:44 final size:44
Alignment explanation
Indices: 5524367--5524456 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 44
5524357 TACTACTAAA
* ** *
5524367 TTATCAATAATTTATTATTAAGTTATCA-TTCATTTATTATTAAG
1 TTATCAATAATTAACAACTAAGTTATCACTT-ATTTATTATTAAG
* *
5524411 TTATCAATAATTAACAACTAAGTTATCACTTATTTTTTGTTAAG
1 TTATCAATAATTAACAACTAAGTTATCACTTATTTATTATTAAG
5524455 TT
1 TT
5524457 GCCCTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.50
Consensus pattern (44 bp):
TTATCAATAATTAACAACTAAGTTATCACTTATTTATTATTAAG
Found at i:5524535 original size:19 final size:19
Alignment explanation
Indices: 5524511--5524564 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5524501 ATAATTGTTG
5524511 TTATTAAAATATTA-TGTAT
1 TTATTAAAATATTATTG-AT
* *
5524530 TTATTATATTATTATTGAT
1 TTATTAAAATATTATTGAT
* *
5524549 TTACTAAAAAATTATT
1 TTATTAAAATATTATT
5524565 AATCATTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
TTATTAAAATATTATTGAT
Found at i:5524598 original size:22 final size:22
Alignment explanation
Indices: 5524515--5524623 Score: 80
Period size: 22 Copynumber: 5.1 Consensus size: 22
5524505 TTGTTGTTAT
* *
5524515 TAAAATATTATGTATTTATTA-
1 TAAATTATTATTTATTTATTAC
* * *
5524536 T--ATTATTATTGATTTACTAA
1 TAAATTATTATTTATTTATTAC
* * * *
5524556 AAAATTATTAATCATTAATTAC
1 TAAATTATTATTTATTTATTAC
*
5524578 TAAATTATTATTTATTTATTAT
1 TAAATTATTATTTATTTATTAC
* **
5524600 TAAGTTATTATAAATTTATTAC
1 TAAATTATTATTTATTTATTAC
5524622 TA
1 TA
5524624 TGTTTCGATA
Statistics
Matches: 66, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
19 14 0.21
21 1 0.02
22 51 0.77
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (22 bp):
TAAATTATTATTTATTTATTAC
Found at i:5534556 original size:28 final size:30
Alignment explanation
Indices: 5534524--5534585 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
5534514 ACTATCAGTG
*
5534524 AATTAAATGATAATATTTTAAT-A-AAATA
1 AATTAAATAATAATATTTTAATAATAAATA
* *
5534552 AATTAAATAATTATATTTTATTAATAAATA
1 AATTAAATAATAATATTTTAATAATAAATA
5534582 AATT
1 AATT
5534586 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.66
29 1 0.03
30 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
AATTAAATAATAATATTTTAATAATAAATA
Found at i:5547963 original size:16 final size:16
Alignment explanation
Indices: 5547942--5547974 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5547932 GATAAAACCC
*
5547942 TCTCTCTCTCTCTCTT
1 TCTCTCACTCTCTCTT
5547958 TCTCTCACTCTCTCTT
1 TCTCTCACTCTCTCTT
5547974 T
1 T
5547975 TTGATTGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTCTCACTCTCTCTT
Found at i:5555197 original size:21 final size:21
Alignment explanation
Indices: 5555166--5555220 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
5555156 ACTTTAAGAA
5555166 AATAA-AAAATAATTAA-AGA-
1 AATAATAAAATAATTAATA-AT
*
5555185 AATAATTAAAATAAATAATAAT
1 AATAA-TAAAATAATTAATAAT
5555207 AATAATAAAATAAT
1 AATAATAAAATAAT
5555221 AACAACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 5 0.17
21 19 0.63
22 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AATAATAAAATAATTAATAAT
Found at i:5555363 original size:19 final size:17
Alignment explanation
Indices: 5555330--5555381 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 17
5555320 ATATTTATTT
5555330 TAAAACAAAATAAAAAA
1 TAAAACAAAATAAAAAA
5555347 TAAAACAAATGATAAAAAA
1 TAAAACAAA--ATAAAAAA
5555366 TAAATA-AAAATAAAAA
1 TAAA-ACAAAATAAAAA
5555382 CTAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 16 0.50
19 15 0.47
20 1 0.03
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.15
Consensus pattern (17 bp):
TAAAACAAAATAAAAAA
Found at i:5555395 original size:29 final size:30
Alignment explanation
Indices: 5555337--5555394 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
5555327 TTTTAAAACA
*
5555337 AAATAAAAAATAAAACAAATGATAAAAAAT
1 AAATAAAAAATAAAACAAATAATAAAAAAT
*
5555367 AAAT-AAAAATAAAAACTAATAATAAAAA
1 AAATAAAAAAT-AAAACAAATAATAAAAA
5555395 TCTAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (30 bp):
AAATAAAAAATAAAACAAATAATAAAAAAT
Found at i:5555675 original size:3 final size:3
Alignment explanation
Indices: 5555667--5555707 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5555657 TTCCTAAGTA
5555667 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5555708 AAATTATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5556598 original size:17 final size:17
Alignment explanation
Indices: 5556576--5556610 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5556566 TTAAATAGTC
* *
5556576 TAGTTTTCTTTATTCAT
1 TAGTTTTATTGATTCAT
5556593 TAGTTTTATTGATTCAT
1 TAGTTTTATTGATTCAT
5556610 T
1 T
5556611 TGACTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (17 bp):
TAGTTTTATTGATTCAT
Found at i:5556923 original size:33 final size:33
Alignment explanation
Indices: 5556881--5556943 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
5556871 TGATAGTAAG
*
5556881 GAACAATTTGGAAACTTTAGCTTGTTATCTAAA
1 GAACAATTTGGAAACTTTAGCTTCTTATCTAAA
5556914 GAACAATTTGGAAACTTTAGCTTCTTATCT
1 GAACAATTTGGAAACTTTAGCTTCTTATCT
5556944 TAACCCAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (33 bp):
GAACAATTTGGAAACTTTAGCTTCTTATCTAAA
Found at i:5558178 original size:29 final size:29
Alignment explanation
Indices: 5558115--5558281 Score: 92
Period size: 29 Copynumber: 5.7 Consensus size: 29
5558105 AAGATTCATA
* * *
5558115 TTTTAAGGGTTTGGATTTAAGTTTTGAGGG
1 TTTT-AGGGTTTGGATTTAAGGTGTGAAGG
*
5558145 TTTTAGGGTTTGGTTTTAAGGTGTGAAAGG
1 TTTTAGGGTTTGGATTTAAGGTGTG-AAGG
* * * *
5558175 -TTTAGGGTTTTGATTTTAGAGTTTGAAGA
1 TTTTAGGGTTTGGATTTAAG-GTGTGAAGG
* * ** *
5558204 TTTTACGGTTTTGATTTTAAAATTTG-AGG
1 TTTTAGGGTTTGGA-TTTAAGGTGTGAAGG
* * *
5558233 -TTTGGGGTTTTGATTTAAAGGTTTGAA--
1 TTTTAGGGTTTGGATTT-AAGGTGTGAAGG
5558260 TTTTAAAGGGTTTGGATTTAAG
1 TTTT--AGGGTTTGGATTTAAG
5558282 AGTTAAAGGT
Statistics
Matches: 108, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
27 3 0.03
28 20 0.19
29 43 0.40
30 38 0.35
31 4 0.04
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (29 bp):
TTTTAGGGTTTGGATTTAAGGTGTGAAGG
Found at i:5558264 original size:15 final size:16
Alignment explanation
Indices: 5558246--5558278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5558236 GGGGTTTTGA
5558246 TTTAAA-GGTTTGAAT
1 TTTAAAGGGTTTGAAT
*
5558261 TTTAAAGGGTTTGGAT
1 TTTAAAGGGTTTGAAT
5558277 TT
1 TT
5558279 AAGAGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (16 bp):
TTTAAAGGGTTTGAAT
Found at i:5558279 original size:15 final size:15
Alignment explanation
Indices: 5558237--5558280 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5558227 TTGAGGTTTG
*
5558237 GGGTTTTGATTTAAA
1 GGGTTTGGATTTAAA
*
5558252 -GGTTTGAATTTTAAA
1 GGGTTTGGA-TTTAAA
5558267 GGGTTTGGATTTAA
1 GGGTTTGGATTTAA
5558281 GAGTTAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (15 bp):
GGGTTTGGATTTAAA
Found at i:5558292 original size:58 final size:58
Alignment explanation
Indices: 5558121--5558296 Score: 148
Period size: 58 Copynumber: 3.0 Consensus size: 58
5558111 CATATTTTAA
* * * * * *
5558121 GGGTTTGGATTTAAG-TTTTGAGGGTTTTAGGGTTTGGTTTTAAG-GTGTGAAAGGTTTA
1 GGGTTTTGATTTAAGAGTTTGAAGATTTTAGGGTTTGGATTTAAGAGT-T-AAAGGTTTG
* * * * **
5558179 GGGTTTTGATTTTAGAGTTTGAAGATTTTACGGTTTTGATTTTAA-AATTTGAGGTTTG
1 GGGTTTTGATTTAAGAGTTTGAAGATTTTAGGGTTTGGA-TTTAAGAGTTAAAGGTTTG
5558237 GGGTTTTGATTTAA-AGGTTTG-A-ATTTTAAAGGGTTTGGATTTAAGAGTTAAAGGTTTG
1 GGGTTTTGATTTAAGA-GTTTGAAGATTTT--AGGGTTTGGATTTAAGAGTTAAAGGTTTG
5558295 GG
1 GG
5558297 ATTTCGGATT
Statistics
Matches: 93, Mismatches: 18, Indels: 14
0.74 0.14 0.11
Matches are distributed among these distances:
56 5 0.05
57 7 0.08
58 57 0.61
59 18 0.19
60 6 0.06
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.45
Consensus pattern (58 bp):
GGGTTTTGATTTAAGAGTTTGAAGATTTTAGGGTTTGGATTTAAGAGTTAAAGGTTTG
Found at i:5558323 original size:16 final size:16
Alignment explanation
Indices: 5558302--5558349 Score: 80
Period size: 15 Copynumber: 3.0 Consensus size: 16
5558292 TTGGGATTTC
5558302 GGATTTTAGGAGTTTT
1 GGATTTTAGGAGTTTT
5558318 GGATTTTAGGA-TTTT
1 GGATTTTAGGAGTTTT
5558333 GGATTTTAGGAGATTTT
1 GGATTTTAGGAG-TTTT
5558350 TTATTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.50
16 11 0.37
17 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (16 bp):
GGATTTTAGGAGTTTT
Found at i:5558324 original size:7 final size:7
Alignment explanation
Indices: 5558295--5558339 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
5558285 TAAAGGTTTG
*
5558295 GGATTTC
1 GGATTTT
5558302 GGATTTT
1 GGATTTT
5558309 AGGAGTTTT
1 -GGA-TTTT
5558318 GGATTTT
1 GGATTTT
5558325 AGGATTTT
1 -GGATTTT
5558333 GGATTTT
1 GGATTTT
5558340 AGGAGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 17 0.50
8 13 0.38
9 4 0.12
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.51
Consensus pattern (7 bp):
GGATTTT
Found at i:5558331 original size:8 final size:8
Alignment explanation
Indices: 5558302--5558343 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
5558292 TTGGGATTTC
5558302 GGATTTTA
1 GGATTTTA
5558310 GGAGTTTT-
1 GGA-TTTTA
5558318 GGATTTTA
1 GGATTTTA
5558326 GGATTTT-
1 GGATTTTA
5558333 GGATTTTA
1 GGATTTTA
5558341 GGA
1 GGA
5558344 GATTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 11 0.35
8 16 0.52
9 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (8 bp):
GGATTTTA
Found at i:5558331 original size:31 final size:32
Alignment explanation
Indices: 5558295--5558358 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
5558285 TAAAGGTTTG
5558295 GGATTTCGGATTTTAGGAG-TTTTGGATTTTA
1 GGATTTCGGATTTTAGGAGATTTTGGATTTTA
* **
5558326 GGATTTTGGATTTTAGGAGATTTTTTATTTTA
1 GGATTTCGGATTTTAGGAGATTTTGGATTTTA
5558358 G
1 G
5558359 AGGTTTTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.52
Consensus pattern (32 bp):
GGATTTCGGATTTTAGGAGATTTTGGATTTTA
Found at i:5558334 original size:15 final size:15
Alignment explanation
Indices: 5558295--5558343 Score: 80
Period size: 15 Copynumber: 3.2 Consensus size: 15
5558285 TAAAGGTTTG
*
5558295 GGATTTCGGATTTTA
1 GGATTTTGGATTTTA
5558310 GGAGTTTTGGATTTTA
1 GGA-TTTTGGATTTTA
5558326 GGATTTTGGATTTTA
1 GGATTTTGGATTTTA
5558341 GGA
1 GGA
5558344 GATTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 18 0.56
16 14 0.44
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.47
Consensus pattern (15 bp):
GGATTTTGGATTTTA
Found at i:5558592 original size:16 final size:16
Alignment explanation
Indices: 5558568--5558598 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5558558 ACATCTAGGT
*
5558568 GAAATTATTTTTTTAG
1 GAAAATATTTTTTTAG
5558584 GAAAATATTTTTTTA
1 GAAAATATTTTTTTA
5558599 TTCCCTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
GAAAATATTTTTTTAG
Found at i:5558819 original size:17 final size:18
Alignment explanation
Indices: 5558778--5558839 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
5558768 CATACATATA
*
5558778 TAAAAAAATATTTAAAA--
1 TAAAAAAA-ATTAAAAATG
*
5558795 TAACAAAAAA-TAATAATG
1 TAA-AAAAAATTAAAAATG
*
5558813 TAAAAAAAATTAAAAATT
1 TAAAAAAAATTAAAAATG
5558831 TAAAAAAAA
1 TAAAAAAAA
5558840 AATTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.11
17 10 0.27
18 23 0.62
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
TAAAAAAAATTAAAAATG
Found at i:5559835 original size:7 final size:7
Alignment explanation
Indices: 5559825--5559859 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
5559815 TACCCTTTTT
*
5559825 TTTTATT
1 TTTTATA
5559832 TTTTATA
1 TTTTATA
5559839 TTTTATA
1 TTTTATA
5559846 TTTTATA
1 TTTTATA
5559853 TTATTAT
1 TT-TTAT
5559860 TATTAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTATA
Found at i:5560245 original size:24 final size:24
Alignment explanation
Indices: 5560209--5560260 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5560199 ACCACGAATC
*
5560209 GAAATCACGTCCGAAGGTCTTACA
1 GAAATCACATCCGAAGGTCTTACA
* * *
5560233 GAAATCATATCCGGAGGTTTTACA
1 GAAATCACATCCGAAGGTCTTACA
5560257 -AAAT
1 GAAAT
5560261 TGACTGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
GAAATCACATCCGAAGGTCTTACA
Found at i:5560411 original size:87 final size:87
Alignment explanation
Indices: 5560246--5560417 Score: 200
Period size: 87 Copynumber: 2.0 Consensus size: 87
5560236 ATCATATCCG
* * * * * * * *
5560246 GAGGTTTTACAAAATTGACTGATATAACACCGCAAGTTGAGAATAATGAATCGATTGAGATAATA
1 GAGGTCTTACAAAATCGACTGAGATAACACCGCAAGTCGAGAATAATGAATCAATCGAGAGAACA
* * * *
5560311 TCGCTAATTGAAATTATGCCCA
66 CCACGAATCGAAATTATGCCCA
* * * *
5560333 GAGGTCTTACAGAATCGACTGGGATAACACCGTAAGTCGAGAATAATGAATCAATCGGGAGAACA
1 GAGGTCTTACAAAATCGACTGAGATAACACCGCAAGTCGAGAATAATGAATCAATCGAGAGAACA
5560398 CCACGAATCGAAATTATGCC
66 CCACGAATCGAAATTATGCC
5560418 TGAAGATCTT
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (87 bp):
GAGGTCTTACAAAATCGACTGAGATAACACCGCAAGTCGAGAATAATGAATCAATCGAGAGAACA
CCACGAATCGAAATTATGCCCA
Found at i:5560537 original size:109 final size:109
Alignment explanation
Indices: 5560336--5560537 Score: 244
Period size: 109 Copynumber: 1.9 Consensus size: 109
5560326 ATGCCCAGAG
* * * * * * *
5560336 GTCTTACAGAATCGACTGGGATAACACCGTAAGTCGAGAATAATGAATCAATCGGGAGAACACCA
1 GTCTTACAGAATCAACTAGGACAACACCGCAAGTCGAAAATAAAGAATCAATCAGGAGAACACCA
* * *
5560401 CGAATCGAAATTATGCCTGAAGATCTTAGAAATCATGCTCGAAA
66 CGAATCAAAATCATGCCCGAAGATCTTAGAAATCATGCTCGAAA
* * *
5560445 GTCTTACAGAATCAACTAGGACAACATCGCAAGTC-AAAATTAAAGAATCGATCAGGATAACACC
1 GTCTTACAGAATCAACTAGGACAACACCGCAAGTCGAAAA-TAAAGAATCAATCAGGAGAACACC
* * *
5560509 ATGAATCAAAATCATGCCCGGAGGTCTTA
65 ACGAATCAAAATCATGCCCGAAGATCTTA
5560538 TAGAATCGAC
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
108 3 0.04
109 73 0.96
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (109 bp):
GTCTTACAGAATCAACTAGGACAACACCGCAAGTCGAAAATAAAGAATCAATCAGGAGAACACCA
CGAATCAAAATCATGCCCGAAGATCTTAGAAATCATGCTCGAAA
Found at i:5560550 original size:87 final size:86
Alignment explanation
Indices: 5560430--5560692 Score: 305
Period size: 87 Copynumber: 3.0 Consensus size: 86
5560420 AAGATCTTAG
* * * * *
5560430 AAATCATGCTCGAAAGTCTTACAGAATCAACTAGGACAACATCGCAAGTCAAAATTAAAGAATCG
1 AAATCATGCCCGAAAGTCTTATAGAATCGACTAGGACAACATCGTAAGTCAAAA-TAATGAATCG
* *
5560495 ATCAGGATAACACCATGAATCA
65 ATCGGGATAACACCGTGAATCA
* * *
5560517 AAATCATGCCCGGAGGTCTTATAGAATCGACTAGGATAACATCGTAAGTCAAGAATAATGAATCG
1 AAATCATGCCCGAAAGTCTTATAGAATCGACTAGGACAACATCGTAAGTCAA-AATAATGAATCG
* *
5560582 ATTGGGATAACATCGTGAATCA
65 ATCGGGATAACACCGTGAATCA
* * * * * * *
5560604 AAATTATACCCGAAAGTC-T-TAGAATCGACTAAGACAACACCATAAGTCGAGAATAATGAATCA
1 AAATCATGCCCGAAAGTCTTATAGAATCGACTAGGACAACATCGTAAGTC-AAAATAATGAATCG
*
5560667 ATCGGGATAACACCGCGAATCA
65 ATCGGGATAACACCGTGAATCA
5560689 AAAT
1 AAAT
5560693 TATACTCGAA
Statistics
Matches: 149, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
85 59 0.40
86 2 0.01
87 86 0.58
88 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (86 bp):
AAATCATGCCCGAAAGTCTTATAGAATCGACTAGGACAACATCGTAAGTCAAAATAATGAATCGA
TCGGGATAACACCGTGAATCA
Found at i:5560674 original size:85 final size:84
Alignment explanation
Indices: 5560440--5560712 Score: 303
Period size: 85 Copynumber: 3.2 Consensus size: 84
5560430 AAATCATGCT
* * * * *
5560440 CGAAAGTCTTACAGAATCAACTAGGACAACATCGCAAGTCAAAATTAAAGAATCGATCAGGATAA
1 CGAAAGTCTT--AGAATCGACTAGGACAACATCGTAAGTCAGAA-TAATGAATCGATCGGGATAA
* * *
5560505 CACCATGAATCAAAATCATGCC
63 CACCGTGAATCAAAATTATACC
* * * *
5560527 CGGAGGTCTTATAGAATCGACTAGGATAACATCGTAAGTCAAGAATAATGAATCGATTGGGATAA
1 CGAAAGTC-T-TAGAATCGACTAGGACAACATCGTAAGTC-AGAATAATGAATCGATCGGGATAA
*
5560592 CATCGTGAATCAAAATTATACC
63 CACCGTGAATCAAAATTATACC
* * * *
5560614 CGAAAGTCTTAGAATCGACTAAGACAACACCATAAGTCGAGAATAATGAATCAATCGGGATAACA
1 CGAAAGTCTTAGAATCGACTAGGACAACATCGTAAGTC-AGAATAATGAATCGATCGGGATAACA
* *
5560679 CCGCGAATCAAAATTATACT
65 CCGTGAATCAAAATTATACC
*
5560699 CGAAGGTCTTAGAA
1 CGAAAGTCTTAGAA
5560713 ATTAAGATCT
Statistics
Matches: 157, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
85 79 0.50
86 1 0.01
87 72 0.46
88 4 0.03
89 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (84 bp):
CGAAAGTCTTAGAATCGACTAGGACAACATCGTAAGTCAGAATAATGAATCGATCGGGATAACAC
CGTGAATCAAAATTATACC
Found at i:5561357 original size:65 final size:65
Alignment explanation
Indices: 5561283--5561597 Score: 341
Period size: 65 Copynumber: 4.8 Consensus size: 65
5561273 TTCTTTTAGA
* * * * * *
5561283 GCCAAATAAACTGGGCTTAAATTTTATTGAAGGCCAGCTAAACTGGGCTTAAAACCTCATTTGA-
1 GCCAGATAAACTGGGCTTAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAACTTCA-TTGAT
5561347 G
65 G
* * *
5561348 GCCAGATAAACTGAGCTTAAAACTTCATTGATGGCCAGATAAATTGGG-TTTAAA-TGTCATTGA
1 GCCAGATAAACTGGGCTT-AAACTTCATTGATGGCCAGATAAACTGGGCTTAAAACT-TCATTGA
5561411 TG
64 TG
* * * *
5561413 GTCAGATAAACTGGGCTTAAAGCTTCATTGATGGCCATATAAACTGGACTTAAAACTTCATTAAT
1 GCCAGATAAACTGGGCTTAAA-CTTCATTGATGGCCAGATAAACTGGGCTTAAAACTTCATTGAT
5561478 G
65 G
* * * **
5561479 GCCAGATAAATTGGGCTTAAA-TGTCATTGATGGCCAGATAAATTGGGTTTAAAGTTTCATTGAT
1 GCCAGATAAACTGGGCTTAAACT-TCATTGATGGCCAGATAAACTGGGCTTAAAACTTCATTGAT
5561543 G
65 G
* * * * *
5561544 GCCAGATAAACTGGGATTAAAGCTTCATTAATGGTCAGATAAATTAGGCTTAAA
1 GCCAGATAAACTGGGCTTAAA-CTTCATTGATGGCCAGATAAACTGGGCTTAAA
5561598 TTTTATTTAT
Statistics
Matches: 210, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
64 8 0.04
65 118 0.56
66 82 0.39
67 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (65 bp):
GCCAGATAAACTGGGCTTAAACTTCATTGATGGCCAGATAAACTGGGCTTAAAACTTCATTGATG
Found at i:5561358 original size:33 final size:33
Alignment explanation
Indices: 5561283--5561597 Score: 336
Period size: 33 Copynumber: 9.6 Consensus size: 33
5561273 TTCTTTTAGA
* * * *
5561283 GCCAAATAAACTGGGCTT-AAATTTTATTGAAG
1 GCCAGATAAACTGGGCTTAAAACTTCATTGATG
* *
5561315 GCCAGCTAAACTGGGCTTAAAACCTCATTTGA-G
1 GCCAGATAAACTGGGCTTAAAACTTCA-TTGATG
*
5561348 GCCAGATAAACTGAGCTTAAAACTTCATTGATG
1 GCCAGATAAACTGGGCTTAAAACTTCATTGATG
* *
5561381 GCCAGATAAATTGGG-TTTAAA-TGTCATTGATG
1 GCCAGATAAACTGGGCTTAAAACT-TCATTGATG
* *
5561413 GTCAGATAAACTGGGCTTAAAGCTTCATTGATG
1 GCCAGATAAACTGGGCTTAAAACTTCATTGATG
* * *
5561446 GCCATATAAACTGGACTTAAAACTTCATTAATG
1 GCCAGATAAACTGGGCTTAAAACTTCATTGATG
*
5561479 GCCAGATAAATTGGGCTT-AAA-TGTCATTGATG
1 GCCAGATAAACTGGGCTTAAAACT-TCATTGATG
* * **
5561511 GCCAGATAAATTGGGTTTAAAGTTTCATTGATG
1 GCCAGATAAACTGGGCTTAAAACTTCATTGATG
* * *
5561544 GCCAGATAAACTGGGATTAAAGCTTCATTAATG
1 GCCAGATAAACTGGGCTTAAAACTTCATTGATG
* * *
5561577 GTCAGATAAATTAGGCTTAAA
1 GCCAGATAAACTGGGCTTAAA
5561598 TTTTATTTAT
Statistics
Matches: 240, Mismatches: 34, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.01
32 75 0.31
33 157 0.65
34 6 0.03
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (33 bp):
GCCAGATAAACTGGGCTTAAAACTTCATTGATG
Found at i:5561441 original size:98 final size:97
Alignment explanation
Indices: 5561283--5561598 Score: 418
Period size: 98 Copynumber: 3.2 Consensus size: 97
5561273 TTCTTTTAGA
* * * * * * * *
5561283 GCCAAATAAACTGGGCTTAAATTTTATTGAAGGCCAGCTAAACTGGGCTTAAAACCTCATTTGA-
1 GCCAGATAAATTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCA-TTGAT
*
5561347 GGCCAGATAAACTGAGCTTAAAACTTCATTGATG
65 GGCCAGATAAACTG-GCTTAAAACTTCATTAATG
* *
5561381 GCCAGATAAATTGGGTTTAAATGTCATTGATGGTCAGATAAACTGGGCTTAAAGCTTCATTGATG
1 GCCAGATAAATTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTGATG
*
5561446 GCCATATAAACTGGACTTAAAACTTCATTAATG
66 GCCAGATAAACTGG-CTTAAAACTTCATTAATG
* * *
5561479 GCCAGATAAATTGGGCTTAAATGTCATTGATGGCCAGATAAATTGGGTTTAAAGTTTCATTGATG
1 GCCAGATAAATTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTGATG
* *
5561544 GCCAGATAAACTGGGATTAAAGCTTCATTAATG
66 GCCAGATAAACT-GGCTTAAAACTTCATTAATG
* *
5561577 GTCAGATAAATTAGGCTTAAAT
1 GCCAGATAAATTGGGCTTAAAT
5561599 TTTATTTATT
Statistics
Matches: 193, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
97 5 0.03
98 186 0.96
99 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (97 bp):
GCCAGATAAATTGGGCTTAAATGTCATTGATGGCCAGATAAACTGGGCTTAAAGCTTCATTGATG
GCCAGATAAACTGGCTTAAAACTTCATTAATG
Found at i:5563570 original size:13 final size:12
Alignment explanation
Indices: 5563552--5563584 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5563542 AAAACTTCTT
5563552 TTTTTTTGTTACC
1 TTTTTTT-TTACC
5563565 -TTTTTTTTACC
1 TTTTTTTTTACC
5563576 TTTTTTTTT
1 TTTTTTTTT
5563585 GACATTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTTTTTACC
Found at i:5563579 original size:10 final size:11
Alignment explanation
Indices: 5563553--5563583 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5563543 AAACTTCTTT
5563553 TTTTTTGTTACC
1 TTTTTT-TTACC
5563565 TTTTTTTTACC
1 TTTTTTTTACC
5563576 TTTTTTTT
1 TTTTTTTT
5563584 TGACATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTTTTTACC
Found at i:5563886 original size:29 final size:28
Alignment explanation
Indices: 5563843--5564010 Score: 108
Period size: 30 Copynumber: 5.8 Consensus size: 28
5563833 ATCATCGTTA
*
5563843 GTTTTGAGGGTTTGGATTTAAGTTTTGAGG
1 GTTTT-AGGGTTTGGATTTAAGGTTTGA-G
* *
5563873 GTTTTAGGGTTTGGTTTTAAGGTGTGAAAG
1 GTTTTAGGGTTTGGATTTAAGGTTTG--AG
* *
5563903 G-TTTAGGGTTTTGATTTTAAAGTTTGAAG
1 GTTTTAGGGTTTGGA-TTTAAGGTTTG-AG
* * * **
5563932 ATTTTACGGTTTTGATTTTAAAATTTGAG
1 GTTTTAGGGTTTGGA-TTTAAGGTTTGAG
* *
5563961 G-TTTGGGGTTTTGATTTAAAGGTTTGA-
1 GTTTTAGGGTTTGGATTT-AAGGTTTGAG
*
5563988 ATTTTAAAGGGTTTGGATTTAAG
1 GTTTT--AGGGTTTGGATTTAAG
5564011 AGTTAAAGGT
Statistics
Matches: 112, Mismatches: 18, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
27 3 0.03
28 21 0.19
29 37 0.33
30 50 0.45
31 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.47
Consensus pattern (28 bp):
GTTTTAGGGTTTGGATTTAAGGTTTGAG
Found at i:5563953 original size:30 final size:29
Alignment explanation
Indices: 5563849--5563988 Score: 119
Period size: 30 Copynumber: 4.8 Consensus size: 29
5563839 GTTAGTTTTG
* *
5563849 AGGGTTTGGA-TTT-AAGTTTTGAGGGTTTT
1 AGGGTTTTGATTTTAAAG-TTTGAAGG-TTT
* * *
5563878 AGGG-TTTGGTTTTAAGGTGTGAAAGGTTT
1 AGGGTTTTGATTTTAAAGTTTG-AAGGTTT
*
5563907 AGGGTTTTGATTTTAAAGTTTGAAGATTTT
1 AGGGTTTTGATTTTAAAGTTTGAAG-GTTT
* *
5563937 ACGGTTTTGATTTTAAAATTTG-AGGTTT
1 AGGGTTTTGATTTTAAAGTTTGAAGGTTT
*
5563965 GGGGTTTTGA-TTTAAAGGTTTGAA
1 AGGGTTTTGATTTTAAA-GTTTGAA
5563989 TTTTAAAGGG
Statistics
Matches: 89, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
27 6 0.07
28 18 0.20
29 23 0.26
30 42 0.47
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (29 bp):
AGGGTTTTGATTTTAAAGTTTGAAGGTTT
Found at i:5563993 original size:15 final size:16
Alignment explanation
Indices: 5563975--5564007 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5563965 GGGGTTTTGA
5563975 TTTAAA-GGTTTGAAT
1 TTTAAAGGGTTTGAAT
*
5563990 TTTAAAGGGTTTGGAT
1 TTTAAAGGGTTTGAAT
5564006 TT
1 TT
5564008 AAGAGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (16 bp):
TTTAAAGGGTTTGAAT
Found at i:5564008 original size:15 final size:15
Alignment explanation
Indices: 5563966--5564009 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
5563956 TTGAGGTTTG
*
5563966 GGGTTTTGATTTAAA
1 GGGTTTGGATTTAAA
*
5563981 -GGTTTGAATTTTAAA
1 GGGTTTGGA-TTTAAA
5563996 GGGTTTGGATTTAA
1 GGGTTTGGATTTAA
5564010 GAGTTAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (15 bp):
GGGTTTGGATTTAAA
Found at i:5564021 original size:58 final size:58
Alignment explanation
Indices: 5563874--5564025 Score: 152
Period size: 58 Copynumber: 2.6 Consensus size: 58
5563864 GTTTTGAGGG
* *
5563874 TTTTAGGGTTTGGTTTTAAG-GTGTGAAAGGTTTAGGGTTTTGATTTTAAAGTTTGAAGA
1 TTTTAGGGTTTGGATTTAAGAGT-T-AAAGGTTTGGGGTTTTGATTTTAAAGTTTGAAGA
* * * **
5563933 TTTTACGGTTTTGATTTTAA-AATTTGAGGTTTGGGGTTTTGA-TTTAAAGGTTTG-A-A
1 TTTTAGGGTTTGGA-TTTAAGAGTTAAAGGTTTGGGGTTTTGATTTTAAA-GTTTGAAGA
5563989 TTTTAAAGGGTTTGGATTTAAGAGTTAAAGGTTTGGG
1 TTTT--AGGGTTTGGATTTAAGAGTTAAAGGTTTGGG
5564026 ATTTCGGATT
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
56 5 0.07
57 12 0.16
58 40 0.53
59 12 0.16
60 6 0.08
ACGTcount: A:0.24, C:0.01, G:0.29, T:0.46
Consensus pattern (58 bp):
TTTTAGGGTTTGGATTTAAGAGTTAAAGGTTTGGGGTTTTGATTTTAAAGTTTGAAGA
Found at i:5564053 original size:7 final size:7
Alignment explanation
Indices: 5564024--5564068 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
5564014 TAAAGGTTTG
*
5564024 GGATTTC
1 GGATTTT
5564031 GGATTTT
1 GGATTTT
5564038 AGGAGTTTT
1 -GGA-TTTT
5564047 GGATTTT
1 GGATTTT
5564054 AGGATTTT
1 -GGATTTT
5564062 GGATTTT
1 GGATTTT
5564069 AGGGGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 17 0.50
8 13 0.38
9 4 0.12
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.51
Consensus pattern (7 bp):
GGATTTT
Found at i:5564060 original size:8 final size:8
Alignment explanation
Indices: 5564031--5564071 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
5564021 TTGGGATTTC
5564031 GGATTTTA
1 GGATTTTA
5564039 GGAGTTTT-
1 GGA-TTTTA
5564047 GGATTTTA
1 GGATTTTA
5564055 GGATTTT-
1 GGATTTTA
5564062 GGATTTTA
1 GGATTTTA
5564070 GG
1 GG
5564072 GGATTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
7 11 0.37
8 15 0.50
9 4 0.13
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.49
Consensus pattern (8 bp):
GGATTTTA
Found at i:5564063 original size:15 final size:15
Alignment explanation
Indices: 5564024--5564071 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
5564014 TAAAGGTTTG
*
5564024 GGATTTCGGATTTTA
1 GGATTTTGGATTTTA
5564039 GGAGTTTTGGATTTTA
1 GGA-TTTTGGATTTTA
5564055 GGATTTTGGATTTTA
1 GGATTTTGGATTTTA
5564070 GG
1 GG
5564072 GGATTTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (15 bp):
GGATTTTGGATTTTA
Found at i:5564320 original size:16 final size:16
Alignment explanation
Indices: 5564296--5564326 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5564286 ACATCTAGGC
*
5564296 GAAATTATTTTTTTAG
1 GAAAATATTTTTTTAG
5564312 GAAAATATTTTTTTA
1 GAAAATATTTTTTTA
5564327 TTCCCTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
GAAAATATTTTTTTAG
Found at i:5564537 original size:16 final size:15
Alignment explanation
Indices: 5564504--5564553 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
5564494 GCATACATAT
5564504 ATAAAAAAATACTTAAA
1 ATAAAAAAA-A-TTAAA
5564521 ATAACAAAAAATTAAAA
1 ATAA-AAAAAATT-AAA
*
5564538 ATTAAAAAAATTAAA
1 ATAAAAAAAATTAAA
5564553 A
1 A
5564554 AATTAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 11 0.37
18 5 0.17
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (15 bp):
ATAAAAAAAATTAAA
Found at i:5564555 original size:17 final size:16
Alignment explanation
Indices: 5564526--5564566 Score: 73
Period size: 17 Copynumber: 2.5 Consensus size: 16
5564516 TTAAAATAAC
5564526 AAAAAATTAAAAATTA
1 AAAAAATTAAAAATTA
5564542 AAAAAATTAAAAAATTA
1 AAAAAATT-AAAAATTA
5564559 AAAAAATT
1 AAAAAATT
5564567 TTTACCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATTAAAAATTA
Found at i:5564566 original size:9 final size:8
Alignment explanation
Indices: 5564526--5564563 Score: 60
Period size: 8 Copynumber: 4.8 Consensus size: 8
5564516 TTAAAATAAC
5564526 AAAAAATT
1 AAAAAATT
5564534 -AAAAATT
1 AAAAAATT
5564541 AAAAAAATT
1 -AAAAAATT
5564550 AAAAAATT
1 AAAAAATT
5564558 AAAAAA
1 AAAAAA
5564564 ATTTTTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Done.