Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold407
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: 4418299
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 127125 characters in sequence are not A, C, G, or T
File 28 of 28
Found at i:4348634 original size:21 final size:24
Alignment explanation
Indices: 4348594--4348655 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 24
4348584 TCTATTTATA
*
4348594 TAAAAAATGAATAAAATAAA-A-T
1 TAAAAAATAAATAAAATAAAGATT
**
4348616 T-AAAAATAAATAATTTAAAGATT
1 TAAAAAATAAATAAAATAAAGATT
*
4348639 TAAAAAATAAATTAAAT
1 TAAAAAATAAATAAAAT
4348656 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 15 0.48
22 2 0.06
23 2 0.06
24 12 0.39
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (24 bp):
TAAAAAATAAATAAAATAAAGATT
Found at i:4348648 original size:20 final size:19
Alignment explanation
Indices: 4348603--4348664 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 19
4348593 ATAAAAAATG
* *
4348603 AATAAAATAAAATTAAAAATA
1 AATAAATTAAAATT-TAAA-A
*
4348624 AATAATTTAAAGATTTAAAA
1 AATAAATTAAA-ATTTAAAA
*
4348644 AATAAATTAAATTTTAAAA
1 AATAAATTAAAATTTAAAA
4348663 AA
1 AA
4348665 AATGTTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 9 0.26
20 11 0.31
21 12 0.34
22 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATAAATTAAAATTTAAAA
Found at i:4348664 original size:21 final size:22
Alignment explanation
Indices: 4348594--4348667 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 22
4348584 TCTATTTATA
*
4348594 TAAAAAATGAATAAAATAAA-ATT
1 TAAAAAA--AATAAATTAAAGATT
* * *
4348617 AAAAATAAATAATTTAAAGATT
1 TAAAAAAAATAAATTAAAGATT
*
4348639 T--AAAAAATAAATTAAA-TTT
1 TAAAAAAAATAAATTAAAGATT
4348658 TAAAAAAAAT
1 TAAAAAAAAT
4348668 GTTGAAAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
19 3 0.08
20 13 0.32
21 16 0.40
22 3 0.08
23 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAAAAAAATAAATTAAAGATT
Found at i:4348665 original size:20 final size:20
Alignment explanation
Indices: 4348603--4348665 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
4348593 ATAAAAAATG
* *
4348603 AATAAAATAAAATTAAAAATA
1 AATAAATTAAAATTTAAAA-A
*
4348624 AATAATTTAAAGATTT-AAAA
1 AATAAATTAAA-ATTTAAAAA
*
4348644 AATAAATTAAATTTTAAAAA
1 AATAAATTAAAATTTAAAAA
4348664 AA
1 AA
4348666 ATGTTGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.09
20 17 0.49
21 12 0.34
22 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAATTAAAATTTAAAAA
Found at i:4348830 original size:15 final size:15
Alignment explanation
Indices: 4348810--4348860 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 15
4348800 TATTTAAAAT
4348810 ATTTTATATATATAA
1 ATTTTATATATATAA
4348825 ATTTTAATATATTAATAA
1 ATTTT-ATATA-T-ATAA
*
4348843 TTTTTAT-TATATAA
1 ATTTTATATATATAA
4348857 ATTT
1 ATTT
4348861 AAAATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 7 0.23
15 6 0.19
16 7 0.23
17 3 0.10
18 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTATATATATAA
Found at i:4348835 original size:18 final size:18
Alignment explanation
Indices: 4348814--4348875 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 18
4348804 TAAAATATTT
4348814 TATATATATAAATTTTAA
1 TATATATATAAATTTTAA
4348832 TATAT-TA-ATAATTTT--
1 TATATATATA-AATTTTAA
*
4348847 TAT-TATATAAATTTAAAA
1 TATATATATAAATTT-TAA
*
4348865 TATTTATATAA
1 TATATATATAA
4348876 TTATATTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
14 1 0.03
15 10 0.28
16 2 0.06
17 8 0.22
18 8 0.22
19 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATATATATAAATTTTAA
Found at i:4348895 original size:33 final size:31
Alignment explanation
Indices: 4348807--4348895 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
4348797 TCGTATTTAA
* *
4348807 AATATTTTATA-TATATAAATTTTAATATATT
1 AATAATTTATATTATAT-AATTTTAAAATATT
* *
4348838 AATAATTTTTATTATATAAATTTAAAATATTT
1 AATAATTTATATTATATAATTTTAAAATA-TT
*
4348870 ATATAA-TTATATTATATCTATTTTAA
1 A-ATAATTTATATTATAT-AATTTTAA
4348896 TTATTTTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
31 19 0.40
32 18 0.38
33 10 0.21
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
AATAATTTATATTATATAATTTTAAAATATT
Found at i:4348901 original size:32 final size:31
Alignment explanation
Indices: 4348807--4348901 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 31
4348797 TCGTATTTAA
*
4348807 AATATTTTATA-TATATAAATTTTAATATATT
1 AATAATTTATATTATATAAATTTTAATAT-TT
* *
4348838 AATAATTTTTATTATATAAATTTAAAATATTT
1 AATAATTTATATTATATAAATTT-TAATATTT
**
4348870 ATATAA-TTATATTATATCTATTTTAATTATTT
1 A-ATAATTTATATTATATAAATTTTAA-TATTT
4348902 TTTAATATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
31 11 0.21
32 33 0.62
33 9 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (31 bp):
AATAATTTATATTATATAAATTTTAATATTT
Found at i:4349978 original size:22 final size:22
Alignment explanation
Indices: 4349953--4350003 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
4349943 GGATTCGAAC
4349953 ATTGTTTTAACACTTTTTTGAA
1 ATTGTTTTAACACTTTTTTGAA
* * *
4349975 ATTG-TTTGAGATTTTTTTGAA
1 ATTGTTTTAACACTTTTTTGAA
*
4349996 ATTATTTT
1 ATTGTTTT
4350004 TTAATTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.59
Consensus pattern (22 bp):
ATTGTTTTAACACTTTTTTGAA
Found at i:4350054 original size:75 final size:75
Alignment explanation
Indices: 4349931--4350087 Score: 235
Period size: 75 Copynumber: 2.1 Consensus size: 75
4349921 TCGATTCGAA
* **
4349931 AATTTTGAATTCGGATTCGAACATTGTTTTAACACTTTTTTGAAATTGTTTGAGATTTTTTTGAA
1 AATTTTGAATTCGGATTCGAACATTGTTTTAAAACTTTTTTGAAATTGTTTGAGATTTTTTCAAA
*
4349996 ATTATTTTTT
66 ATTATTTTCT
* *
4350006 AATTTTGAGTTTGGATTCGAACATT-TTTTCAAAACTTTTTTGAAATTGTTTGAGATTTTTTCAA
1 AATTTTGAATTCGGATTCGAACATTGTTTT-AAAACTTTTTTGAAATTGTTTGAGATTTTTTCAA
*
4350070 AATTGTTTTCT
65 AATTATTTTCT
4350081 AATTTTG
1 AATTTTG
4350088 GTTGTGAAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
74 4 0.05
75 70 0.95
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (75 bp):
AATTTTGAATTCGGATTCGAACATTGTTTTAAAACTTTTTTGAAATTGTTTGAGATTTTTTCAAA
ATTATTTTCT
Found at i:4352303 original size:23 final size:23
Alignment explanation
Indices: 4352264--4352320 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
4352254 TCTAAGATAA
*
4352264 TCTCTCC-TTTT-ATAAAACAACT
1 TCTCTCCTTTTTCA-AAAAAAACT
*
4352286 TCT-TCCATTTTTCAAAAAAAATT
1 TCTCTCC-TTTTTCAAAAAAAACT
4352309 TCTCTCCTTTTT
1 TCTCTCCTTTTT
4352321 GTTATAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
23 19 0.66
24 4 0.14
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (23 bp):
TCTCTCCTTTTTCAAAAAAAACT
Found at i:4363565 original size:20 final size:20
Alignment explanation
Indices: 4363536--4363612 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
4363526 GTAAAAAGAT
4363536 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* * * *
4363556 AGAATTTATCAATTCATTCA
1 AGAATGTATCGATACATTGA
*
4363576 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
4363596 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
4363613 CTAGGTAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.02
20 43 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:4364571 original size:28 final size:28
Alignment explanation
Indices: 4364442--4365241 Score: 954
Period size: 28 Copynumber: 27.9 Consensus size: 28
4364432 TTTAAAAAAA
*
4364442 GGTGCCACTAACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* *
4364473 AGTTGCCACCGACTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
* * *
4364505 AGTTACCACTGGCTTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACTTGTGGGCTTTG-AAAG
**
4364535 AATGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
4364563 GGTTCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
** *
4364591 AATGCCACTGACTTATGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
4364620 AGTGCCATTGACTTGTGTGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
4364648 GGTACCATTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
4364677 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
4364705 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
4364733 AGTGCCACTGACTTGTGGGCTTTGAATG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
4364761 GGTGCCACTGACTCGTGGGATTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
4364788 GGTGCCACTGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
4364816 GATGCCATTGACTTGTGGGCTTTAAAAAG
1 GGTGCCACTGACTTGTGGGCTTT-GAAAG
* * *
4364845 AGTTGCCACCGACTCGTGGGCTTTGAAAG
1 -GGTGCCACTGACTTGTGGGCTTTGAAAG
*
4364874 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
4364903 AGTTGCCACCGACTCGTGTAGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
*
4364935 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
4364963 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
4364991 GATGCCATTGACTTGTAGGCTTTCACAAG
1 GGTGCCACTGACTTGTGGGCTTTGA-AAG
* *
4365020 AGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
4365048 GGTGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
4365076 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
4365105 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
4365133 GGTGCCATTGACTTCTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
4365162 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
**
4365190 GAAGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
4365218 GATGCCACTGACTTGTGGGCTTTG
1 GGTGCCACTGACTTGTGGGCTTTG
4365242 GAGAGATGAA
Statistics
Matches: 671, Mismatches: 84, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
27 25 0.04
28 373 0.56
29 164 0.24
30 46 0.07
31 11 0.02
32 52 0.08
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:4364585 original size:57 final size:56
Alignment explanation
Indices: 4364439--4365241 Score: 966
Period size: 57 Copynumber: 14.0 Consensus size: 56
4364429 TTTTTTAAAA
* * *
4364439 AAAG-GTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAGAGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTG
* * **
4364500 AAAAGAGTTACCACTGGCTTGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTG
1 -AAAGAG-TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
* * * ** *
4364559 AAAGGGTTCCACTAACTTGTGGGCTTTGAAAGAATGCCACTGACTTATGGGCTTTG
1 AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
4364615 AAAAGAGTGCCATTGACTTGTGTGCTTTGAAAGGGTACCATTGACTTGTGGGCTTTG
1 -AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
4364672 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 -AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
4364729 AAAGAGTGCCACTGACTTGTGGGCTTTGAATGGGTGCCACTGACTCGTGGGATTT-
1 AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * * *
4364784 AAAGGGTGCCACTGACTCGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTAA
1 AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-G
* * *
4364841 AAAGAGTTGCCACCGACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
4364898 AAAAGAGTTGCCACCGACTCGTGTAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 -AAAGAG-TGCCACTGACT--TGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
* * * * *
4364959 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTAGGCTTTC
1 AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
4365015 ACAAGAGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTG
1 A-AAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
*
4365072 AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGAG-TGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
4365129 AAAGGGTGCCATTGACTTCTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
* *
4365186 AAAG-GAAGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
4365242 GAGAGATGAA
Statistics
Matches: 660, Mismatches: 66, Indels: 36
0.87 0.09 0.05
Matches are distributed among these distances:
55 49 0.07
56 154 0.23
57 286 0.43
58 71 0.11
59 21 0.03
60 14 0.02
61 36 0.05
62 20 0.03
63 2 0.00
64 7 0.01
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (56 bp):
AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:4364613 original size:85 final size:84
Alignment explanation
Indices: 4364442--4365241 Score: 1001
Period size: 85 Copynumber: 9.3 Consensus size: 84
4364432 TTTAAAAAAA
* * *
4364442 GGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTG-AAAGAG
* *
4364507 TTACCACTGGCTTGTGGGCTTTGAAAAG
59 -TGCCACTGACTTGTGGGCTTTG-AAAG
** * * *
4364535 AATGCCACTGACTTGTGGGCTTTGAAAGGGTTCCACTAACTTGTGGGCTTTGAAAGAATGCCACT
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACT
*
4364600 GACTTATGGGCTTTGAAAAG
66 GACTTGTGGGCTTTG-AAAG
* * * * *
4364620 AGTGCCATTGACTTGTGTGCTTTGAAAGGGTACCATTGACTTGTGGGCTTTGAAAAGAGTGCCAC
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCAC
4364685 TGACTTGTGGGCTTTGAAAG
65 TGACTTGTGGGCTTTGAAAG
* * *
4364705 GGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAATGGGTGCCACT
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACT
* *
4364770 GACTCGTGGGATTT-AAAG
66 GACTTGTGGGCTTTGAAAG
* * * *
4364788 GGTGCCACTGACTCGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTAAAAAGAGTTGCCA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGAG-TGCCA
* *
4364853 CCGACTCGTGGGCTTTGAAAG
64 CTGACTTGTGGGCTTTGAAAG
* * * *
4364874 GATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTAGGCTTTGAAAAGAGTG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACT--TGTGGGCTTTG-AAAGAGTG
4364939 CCACTGACTTGTGGGCTTTGAAAG
61 CCACTGACTTGTGGGCTTTGAAAG
* * * *
4364963 GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCATTGACTTGTAGGCTTTCACAAGAGTGCCAC
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGA-AAGAGTGCCAC
*
4365028 TGACTTATGGGCTTTGAAAG
65 TGACTTGTGGGCTTTGAAAG
* *
4365048 GGTGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCAC
4365113 TGACTTGTGGGCTTTGAAAG
65 TGACTTGTGGGCTTTGAAAG
* * * *
4365133 GGTGCCATTGACTTCTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-GAAGCCA
1 GGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCA
4365197 CTGACTTGTGGGCTTTGAAAG
64 CTGACTTGTGGGCTTTGAAAG
*
4365218 GATGCCACTGACTTGTGGGCTTTG
1 GGTGCCACTGACTTGTGGGCTTTG
4365242 GAGAGATGAA
Statistics
Matches: 629, Mismatches: 65, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
83 51 0.08
84 29 0.05
85 330 0.52
86 84 0.13
87 25 0.04
88 14 0.02
89 56 0.09
90 19 0.03
91 11 0.02
92 1 0.00
93 9 0.01
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (84 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACT
GACTTGTGGGCTTTGAAAG
Found at i:4371328 original size:32 final size:33
Alignment explanation
Indices: 4371270--4371331 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
4371260 TAAGCCAATG
*
4371270 TATCGATACATTTTATGGTGTATCGATACATTA
1 TATCGATACATCTTATGGTGTATCGATACATTA
4371303 TATCGATACATACTT-T-GTGTATCGATACA
1 TATCGATACAT-CTTATGGTGTATCGATACA
4371332 AGTTTGGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 12 0.44
34 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (33 bp):
TATCGATACATCTTATGGTGTATCGATACATTA
Found at i:4371422 original size:13 final size:13
Alignment explanation
Indices: 4371404--4371428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4371394 ACAATGCAAC
4371404 ATGTATCGATACA
1 ATGTATCGATACA
4371417 ATGTATCGATAC
1 ATGTATCGATAC
4371429 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4371423 original size:33 final size:33
Alignment explanation
Indices: 4371386--4371451 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
4371376 TCTTTTTTAA
4371386 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
4371419 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
4371452 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:4372044 original size:17 final size:17
Alignment explanation
Indices: 4372022--4372056 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4372012 CCTTAATAAG
4372022 GTAATTTTAACAAATTC
1 GTAATTTTAACAAATTC
4372039 GTAATTTTAACAAATTC
1 GTAATTTTAACAAATTC
4372056 G
1 G
4372057 CATTCTCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
GTAATTTTAACAAATTC
Found at i:4372110 original size:75 final size:75
Alignment explanation
Indices: 4371987--4372149 Score: 299
Period size: 75 Copynumber: 2.2 Consensus size: 75
4371977 TTCTTTTGTT
* *
4371987 TCCCCCTTAATCAAATATTTCTCCCCCTTAATAAGGTAATTTTAACAAATTCGTAATTTTAACAA
1 TCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGTAATTTTAACAAATTCATAATTTTAACAA
4372052 ATTCGCATTC
66 ATTCGCATTC
4372062 TCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGTAATTTTAACAAATTCATAATTTTAACAA
1 TCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGTAATTTTAACAAATTCATAATTTTAACAA
4372127 ATTCGCATTC
66 ATTCGCATTC
*
4372137 TTCCCCTTAATCA
1 TCCCCCTTAATCA
4372150 TAAGCACTTA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 85 1.00
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (75 bp):
TCCCCCTTAATCAAACATTTCTCCCCCTTAATAAGGTAATTTTAACAAATTCATAATTTTAACAA
ATTCGCATTC
Found at i:4372120 original size:17 final size:17
Alignment explanation
Indices: 4372098--4372130 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4372088 CTTAATAAGG
4372098 TAATTTTAACAAATTCA
1 TAATTTTAACAAATTCA
4372115 TAATTTTAACAAATTC
1 TAATTTTAACAAATTC
4372131 GCATTCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTTTAACAAATTCA
Found at i:4374002 original size:13 final size:12
Alignment explanation
Indices: 4373984--4374021 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
4373974 ATAATCCCCT
4373984 TGTATCGATACA
1 TGTATCGATACA
4373996 GTGTATCGATACTA
1 -TGTATCGATAC-A
4374010 TGTATCGATACA
1 TGTATCGATACA
4374022 AAGAATGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:4380223 original size:13 final size:13
Alignment explanation
Indices: 4380205--4380230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4380195 CATTTTATGG
4380205 TGTATCGATACAT
1 TGTATCGATACAT
4380218 TGTATCGATACAT
1 TGTATCGATACAT
4380231 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4380227 original size:33 final size:32
Alignment explanation
Indices: 4380185--4380248 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
4380175 TATAAGCCAA
*
4380185 TGTATCGATACAT-TTTATGGTGTATCGATACAT
1 TGTATCGATACATACTT-T-GTGTATCGATACAT
4380218 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
4380249 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 14 0.48
34 2 0.07
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:4380339 original size:13 final size:12
Alignment explanation
Indices: 4380319--4380399 Score: 61
Period size: 13 Copynumber: 7.2 Consensus size: 12
4380309 ATACAATGCA
4380319 ACATGTATCGAT
1 ACATGTATCGAT
4380331 ACAATGTATCGAT
1 AC-ATGTATCGAT
*
4380344 AC-TGT-GC-A-
1 ACATGTATCGAT
4380352 ACATGTATCGAT
1 ACATGTATCGAT
*
4380364 ACAATGTATTGAT
1 AC-ATGTATCGAT
*
4380377 AC-TGT-GC-A-
1 ACATGTATCGAT
4380385 ACATGTATCGAT
1 ACATGTATCGAT
4380397 ACA
1 ACA
4380400 ATTAAATGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
8 4 0.08
9 8 0.15
10 3 0.06
11 8 0.15
12 7 0.13
13 23 0.43
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (12 bp):
ACATGTATCGAT
Found at i:4380340 original size:33 final size:33
Alignment explanation
Indices: 4380303--4380401 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
4380293 TCTTTTTCAA
**
4380303 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACTGTGCAACATGTATCGATACAAT
4380336 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACTGTGCAACATGTATCGATACAAT
*
4380369 GTATTGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACTGTGCAACATGTATCGATACAAT
4380402 TAAATGTGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (33 bp):
GTATCGATACTGTGCAACATGTATCGATACAAT
Found at i:4380359 original size:20 final size:20
Alignment explanation
Indices: 4380334--4380398 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
4380324 TATCGATACA
4380334 ATGTATCGATACTGTGCAAC
1 ATGTATCGATACTGTGCAAC
4380354 ATGTATCGATA-----C-A-
1 ATGTATCGATACTGTGCAAC
*
4380367 ATGTATTGATACTGTGCAAC
1 ATGTATCGATACTGTGCAAC
4380387 ATGTATCGATAC
1 ATGTATCGATAC
4380399 AATTAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
15 1 0.03
18 1 0.03
19 1 0.03
20 22 0.61
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACTGTGCAAC
Found at i:4385558 original size:19 final size:19
Alignment explanation
Indices: 4385534--4385595 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
4385524 TTTTGAACTT
4385534 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
4385553 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
* *
4385574 CATA-AGTGTTGTATCAATA
1 CAAACAGT-TTGTATCGATA
4385593 CAA
1 CAA
4385596 TGTATCGATA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:4385603 original size:32 final size:32
Alignment explanation
Indices: 4385562--4385634 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
4385552 ACAAACAGAA
4385562 AATGTATCGATACATAAGTGTTGTATCAATAC
1 AATGTATCGATACATAAGTGTTGTATCAATAC
* *
4385594 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCAATAC
4385626 AATGTATCG
1 AATGTATCG
4385635 CTACGAAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCAATAC
Found at i:4385620 original size:19 final size:18
Alignment explanation
Indices: 4385564--4385626 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
4385554 AAACAGAAAA
4385564 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
*
4385583 TGTATCAATAC--AA---
1 TGTATCGATACATAAGTT
4385596 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
4385615 TGTATCGATACA
1 TGTATCGATACA
4385627 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:4385676 original size:13 final size:13
Alignment explanation
Indices: 4385658--4385683 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4385648 GCCAAGGAAA
4385658 TGTATCGATACAT
1 TGTATCGATACAT
4385671 TGTATCGATACAT
1 TGTATCGATACAT
4385684 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4386041 original size:27 final size:27
Alignment explanation
Indices: 4386011--4386191 Score: 123
Period size: 27 Copynumber: 6.1 Consensus size: 27
4386001 ACACGGAATG
4386011 ATGGGCATGGAATAAAAAAATGAAAGC
1 ATGGGCATGGAATAAAAAAATGAAAGC
* *
4386038 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
1 ATGGGCATGGAATAAAAAAATG-A---A---AG-C
*
4386073 ATGGGCATGGAAT-AAAAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAAGC
*
4386099 ATGGGCATGGAATAAAAAAATTGAAGGCATGGGATG
1 ATGGGCATGGAATAAAAAAA-TGAA---A---G--C
*
4386135 ATGGGCATGGAATAAAAAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAAGC
* * *
4386162 ATGGCCATGGAAT-AAGAAATGAAGGC
1 ATGGGCATGGAATAAAAAAATGAAAGC
4386188 ATGG
1 ATGG
4386192 AATGATGAAA
Statistics
Matches: 125, Mismatches: 11, Indels: 37
0.72 0.06 0.21
Matches are distributed among these distances:
26 29 0.23
27 40 0.32
28 5 0.04
29 1 0.01
30 1 0.01
31 1 0.01
33 1 0.01
34 10 0.08
35 17 0.14
36 20 0.16
ACGTcount: A:0.44, C:0.07, G:0.31, T:0.17
Consensus pattern (27 bp):
ATGGGCATGGAATAAAAAAATGAAAGC
Found at i:4386084 original size:35 final size:34
Alignment explanation
Indices: 4386038--4386165 Score: 164
Period size: 35 Copynumber: 3.9 Consensus size: 34
4386028 AAATGAAAGC
4386038 ATGGGCATGGAATAAAAAATTGAAGGCATGGAGTG
1 ATGGGCATGGAATAAAAAATTGAAGGCATGG-GTG
4386073 ATGGGCATGGAATAAAAAA-TGAAGGC-------
1 ATGGGCATGGAATAAAAAATTGAAGGCATGGGTG
4386099 ATGGGCATGGAATAAAAAAATTGAAGGCATGGGATG
1 ATGGGCATGGAAT-AAAAAATTGAAGGCATGGG-TG
*
4386135 ATGGGCATGGAATAAAAAAATGAAGGCATGG
1 ATGGGCATGGAATAAAAAATTGAAGGCATGG
4386166 CCATGGAATA
Statistics
Matches: 82, Mismatches: 1, Indels: 20
0.80 0.01 0.19
Matches are distributed among these distances:
26 13 0.16
27 6 0.07
28 7 0.09
34 7 0.09
35 36 0.44
36 13 0.16
ACGTcount: A:0.43, C:0.06, G:0.33, T:0.18
Consensus pattern (34 bp):
ATGGGCATGGAATAAAAAATTGAAGGCATGGGTG
Found at i:4386102 original size:26 final size:26
Alignment explanation
Indices: 4386073--4386191 Score: 121
Period size: 26 Copynumber: 4.2 Consensus size: 26
4386063 GCATGGAGTG
4386073 ATGGGCATGGAATAAAAAATGAAGGC
1 ATGGGCATGGAATAAAAAATGAAGGC
4386099 ATGGGCATGGAATAAAAAAATTGAAGGC
1 ATGGGCATGGAAT-AAAAAA-TGAAGGC
4386127 ATGGGATGATGGGCATGGAATAAAAAAATGAAGGC
1 --------ATGGGCATGGAATAAA-AAATGAAGGC
* *
4386162 ATGGCCATGGAATAAGAAATGAAGGC
1 ATGGGCATGGAATAAAAAATGAAGGC
4386188 ATGG
1 ATGG
4386192 AATGATGAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 22
0.77 0.02 0.21
Matches are distributed among these distances:
26 27 0.34
27 20 0.25
28 7 0.09
35 10 0.12
36 16 0.20
ACGTcount: A:0.44, C:0.08, G:0.32, T:0.17
Consensus pattern (26 bp):
ATGGGCATGGAATAAAAAATGAAGGC
Found at i:4386107 original size:61 final size:62
Alignment explanation
Indices: 4386009--4386198 Score: 305
Period size: 62 Copynumber: 3.1 Consensus size: 62
4385999 AAACACGGAA
*
4386009 TGATGGGCATGGAATAAAAAAATGAAAGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
4386071 TGATGGGCATGGAAT-AAAAAATGAAGGCATGGGCATGGAATAAAAAAATTGAAGGCATGG-G
1 TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAAT-AAAAAATTGAAGGCATGGAG
* * *
4386132 ATGATGGGCATGGAATAAAAAAATGAAGGCATGGCCATGGAATAAGAAA-TGAAGGCATGGAA
1 -TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
4386194 TGATG
1 TGATG
4386199 AAAAAAGGAA
Statistics
Matches: 120, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
61 42 0.35
62 53 0.44
63 25 0.21
ACGTcount: A:0.44, C:0.07, G:0.32, T:0.18
Consensus pattern (62 bp):
TGATGGGCATGGAATAAAAAAATGAAGGCATGGGCATGGAATAAAAAATTGAAGGCATGGAG
Found at i:4387462 original size:28 final size:28
Alignment explanation
Indices: 4387422--4387602 Score: 159
Period size: 28 Copynumber: 6.6 Consensus size: 28
4387412 TTTCACAATC
4387422 GGGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
4387450 GGGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
* *
4387478 GGGGATACTCCAACCCCGGTTTTATTTCTA
1 GGGGATACTCCAACCCC-GTTAT-TTTCGA
* * *
4387508 ----AAACATCC-A-----TT-TTTCACAA
1 GGGGATAC-TCCAACCCCGTTATTT-TCGA
*
4387527 TCGGGGATACTCCAACCCCGTTATTTCCGA
1 --GGGGATACTCCAACCCCGTTATTTTCGA
*
4387557 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
*
4387585 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
4387603 GCTTTATTTC
Statistics
Matches: 127, Mismatches: 9, Indels: 34
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.02
19 3 0.02
20 2 0.02
24 3 0.02
25 4 0.03
26 4 0.03
27 3 0.02
28 90 0.71
29 4 0.03
30 9 0.07
31 3 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:4387595 original size:107 final size:107
Alignment explanation
Indices: 4387409--4387681 Score: 492
Period size: 107 Copynumber: 2.6 Consensus size: 107
4387399 AAGTTTCTCA
*
4387409 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGTTATTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTATTT
* * *
4387474 TCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCC
66 CCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACATCC
4387516 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTATTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTATTT
4387581 CCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACATCC
66 CCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACATCC
**
4387623 ATTTTTCGTAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG
4387682 GTTTTATTTC
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 160 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (107 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTATTT
CCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACATCC
Found at i:4387640 original size:79 final size:79
Alignment explanation
Indices: 4387557--4387969 Score: 718
Period size: 79 Copynumber: 5.2 Consensus size: 79
4387547 TTATTTCCGA
* *
4387557 GGGGATACTCCAACCCCGTTATTTCCGAGAGGATACTCCAACCCCGGCTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
* *
4387622 CATTTTTCGTAATC
66 AATTTTTCATAATC
4387636 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
4387701 AATTTTTCATAATC
66 AATTTTTCATAATC
* * *
4387715 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAATATT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
*
4387780 AATTTTTCACAATC
66 AATTTTTCATAATC
*
4387794 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
*
4387859 AAATTTTCATAATC
66 AATTTTTCATAATC
*
4387873 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
4387938 AATTTTTCATAATC
66 AATTTTTCATAATC
*
4387952 GGGGATACTCTAACCCCG
1 GGGGATACTCCAACCCCG
4387970 ATTTTATTTT
Statistics
Matches: 316, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 316 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATC
AATTTTTCATAATC
Found at i:4388021 original size:52 final size:51
Alignment explanation
Indices: 4387901--4388035 Score: 175
Period size: 51 Copynumber: 2.6 Consensus size: 51
4387891 TTATTTCCGA
*
4387901 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATC
1 GGGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATC
* * *
4387952 GGGGATACTCTAACCCCGATTTTATTTTTTAGAACA-CCATTTTTCCATAATC
1 GGGGATACTCTAACCCCGATTTTA-TTTCTAAAACATCAATTTTT-CATAATC
* *
4388004 GGGGATACTCTAGCCCCG-TTGTTATCTCTAAA
1 GGGGATACTCTAACCCCGATT-TTATTTCTAAA
4388036 CTACTAATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
51 37 0.51
52 36 0.49
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (51 bp):
GGGGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATC
Found at i:4389590 original size:24 final size:24
Alignment explanation
Indices: 4389560--4389618 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
4389550 CTATTCCCGT
4389560 AGCTCCAAAAACCACCACCAAAGA
1 AGCTCCAAAAACCACCACCAAAGA
*
4389584 AGCTCCAAAAACCACCACCAAGGA
1 AGCTCCAAAAACCACCACCAAAGA
*
4389608 ACCTCCAAAAA
1 AGCTCCAAAAA
4389619 GCTACCTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.49, C:0.37, G:0.08, T:0.05
Consensus pattern (24 bp):
AGCTCCAAAAACCACCACCAAAGA
Found at i:4391406 original size:52 final size:52
Alignment explanation
Indices: 4391340--4391469 Score: 176
Period size: 52 Copynumber: 2.5 Consensus size: 52
4391330 GTTTCTCAAT
*
4391340 TTTTC-TTAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACCAA
1 TTTTCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA
* *
4391390 TTTTCCTTTAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACTAA
1 TTTT-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA
*
4391443 TTTT-TTCACAATCGGGGATACTCCAAC
1 TTTTCTT--TAATCGGGGATACTCCAAC
4391470 CCCGTTAATC
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
50 4 0.06
51 3 0.04
52 33 0.46
53 31 0.44
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (52 bp):
TTTTCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA
Found at i:4391523 original size:28 final size:27
Alignment explanation
Indices: 4391453--4391527 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 27
4391443 TTTTTTCACA
4391453 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
4391480 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
4391506 GTCGAGGGGATACTCCAACCCC
1 ATC--GGGGATACTCCAACCCC
4391528 CGATTTTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 23 0.52
28 17 0.39
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.21
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:4391652 original size:79 final size:78
Alignment explanation
Indices: 4391480--4391798 Score: 363
Period size: 79 Copynumber: 4.0 Consensus size: 78
4391470 CCCGTTAATC
* * *
4391480 ATCGGGGATACTCCAACCCCGTTATTGTCGAGGGGATACTCCAACCCCCGATTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA--CCCGGTTTTATTTCTAAAA
*
4391545 TATTGATTTCTCATA
64 TATTAATTTCTCATA
** * *
4391560 ATCAAGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACTCCGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAAC-CCGGTTTTATTTCTAAAAT
4391625 ATTAATTTCTCATA
65 ATTAATTTCTCATA
* * *
4391639 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCTGGTTTTATTTC-CAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC-GGTTTTATTTCTAAAAT
* * *
4391703 CATCAATTTTTTTCACA
65 -ATTAA--TTTCTCATA
* * * * *
4391720 ATCGGGGATACTCCAACCCCGTTATTTTC-ATGGGGATACTTCAACCCCGTTACTATCTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCCAACCCGGTT-TTATTTCTAAAA
4391784 TATTAAATTTCTCAT
64 TATT-AATTTCTCAT
4391799 CGGGAAATAT
Statistics
Matches: 202, Mismatches: 28, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
78 7 0.03
79 83 0.41
80 50 0.25
81 56 0.28
82 6 0.03
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCGGTTTTATTTCTAAAATA
TTAATTTCTCATA
Found at i:4405362 original size:54 final size:53
Alignment explanation
Indices: 4405282--4405475 Score: 228
Period size: 54 Copynumber: 3.5 Consensus size: 53
4405272 CCTTTCACCT
*
4405282 TTTAGTCTTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-C
* * * *
4405336 TTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCTACACGAGTTGGTGGCAC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCAC
* *
4405389 TTCAGTCCTCAAAGAG-AGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 TTTAGTCCTCAAAGAGCAGGA---C---GCCTTTTAAAGCCCACACAAGTTGGTGGCAC
*
4405447 TTCTCAGTCCTCAAAGAACAGGACGCCTT
1 TT-T-AGTCCTCAAAGAGCAGGACGCCTT
4405476 CTCCCTTCAC
Statistics
Matches: 117, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
52 4 0.03
53 16 0.14
54 47 0.40
55 4 0.03
58 30 0.26
60 12 0.10
61 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (53 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCAC
Found at i:4405439 original size:58 final size:58
Alignment explanation
Indices: 4405305--4405475 Score: 219
Period size: 58 Copynumber: 3.0 Consensus size: 58
4405295 GAGCAGGACG
*
4405305 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCCTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCAGTCCTCAAAGAGCAGGATGCCTTT
* *
4405364 -C----AAAGCCTACACGAGTTGGTGGCACTTCAGTCCTCAAAGAG-AGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCAGTCCTCAAAGAGCAGGATGCC-TTT
* *
4405417 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAACAGGACGCCTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-T-TCAGTCCTCAAAGAGCAGGATGCCTT
4405476 CTCCCTTCAC
Statistics
Matches: 96, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
52 8 0.08
53 19 0.20
54 22 0.23
58 23 0.24
59 1 0.01
60 16 0.17
61 7 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (58 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCAGTCCTCAAAGAGCAGGATGCCTTT
Found at i:4405514 original size:152 final size:149
Alignment explanation
Indices: 4405334--4405624 Score: 401
Period size: 152 Copynumber: 1.9 Consensus size: 149
4405324 GTTGGTGGCA
* * *
4405334 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCTACACGAGTTGGTGGCA-CTTCAGT-CC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCC
*
4405397 TCAAAGAG-AGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTC-AGTCCTCA
66 TCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCA-TTCTCTAGTCCTCA
4405460 AAGAACAGGACGCCTTCTCCCTTCAC
124 AAGAACAGGACGCCTTCTCCCTTCAC
* *
4405486 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCC
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCC
* * * *
4405551 TCAAAGAGCAGGACGCCTTTCAAAGTCCACACGAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCA
66 TCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTCTCTAGTCCTCAAAGAACA
4405616 GGACGCCTT
131 GGACGCCTT
4405625 TCAAAGCCCA
Statistics
Matches: 125, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
148 4 0.03
149 44 0.35
152 50 0.40
153 7 0.06
154 13 0.10
155 7 0.06
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (149 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCC
TCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTCTCTAGTCCTCAAAGAACA
GGACGCCTTCTCCCTTCAC
Found at i:4405569 original size:55 final size:55
Alignment explanation
Indices: 4405486--4405735 Score: 335
Period size: 55 Copynumber: 4.5 Consensus size: 55
4405476 CTCCCTTCAC
*
4405486 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
4405540 CCTT-TAGTCCCTCAAAGAGCAGGACGCCTTTCAAAGTCCACACGAGTTGGTGGCA
1 CCTTCTAGT-CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
** *
4405595 TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
4405650 -CTTCTCAGTCCTCAAAGAGCATGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCT-AGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCA
4405711 CCTTCTAGTCCTCAAAGAGCAGGAC
1 CCTTCTAGTCCTCAAAGAGCAGGAC
4405736 ACACTTTATT
Statistics
Matches: 174, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
54 12 0.07
55 110 0.63
56 7 0.04
57 1 0.01
61 39 0.22
62 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (55 bp):
CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:4405776 original size:41 final size:43
Alignment explanation
Indices: 4405718--4405838 Score: 144
Period size: 42 Copynumber: 2.9 Consensus size: 43
4405708 GCACCTTCTA
4405718 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCT-TTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCTCTTT
* * *
4405760 GTCCTCAAA-AGTAGGACGCA-TTTCGTTTTCCT-TTTCTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTT-ATTTTCCTCTTTCT-CTTT
*
4405802 GTCCTCAAAGAGCAGGACACTCTTTA-TTTCCTTCTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTTCC-TCTTT
4405839 TCCCTACTAG
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
40 8 0.12
41 16 0.25
42 26 0.40
43 9 0.14
44 6 0.09
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.40
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTTCCTCTTTCTCTTT
Found at i:4406564 original size:19 final size:18
Alignment explanation
Indices: 4406540--4406602 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
4406530 AAACAGAAAA
4406540 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
4406559 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
4406572 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
4406591 TGTATCGATACA
1 TGTATCGATACA
4406603 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:4406577 original size:13 final size:13
Alignment explanation
Indices: 4406559--4406583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4406549 ACATAAGTGT
4406559 TGTATCGATACAA
1 TGTATCGATACAA
4406572 TGTATCGATACA
1 TGTATCGATACA
4406584 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4406579 original size:32 final size:32
Alignment explanation
Indices: 4406538--4406610 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
4406528 ACAAACAGAA
4406538 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
4406570 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
4406602 AATGTATCG
1 AATGTATCG
4406611 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:4406652 original size:13 final size:13
Alignment explanation
Indices: 4406634--4406659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4406624 GCTAAGGAAA
4406634 TGTATCGATACAT
1 TGTATCGATACAT
4406647 TGTATCGATACAT
1 TGTATCGATACAT
4406660 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4409074 original size:52 final size:51
Alignment explanation
Indices: 4409007--4409138 Score: 169
Period size: 53 Copynumber: 2.5 Consensus size: 51
4408997 ACCCAAAAGC
4409007 ATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTAATTT-C-AAAACACCA
1 ATTTTT-TTAATCGGGGATACTCCAACTCCGATTTT-ATTTCCAAAAACACCA
* *
4409058 ATTTTCCTTTAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACTA
1 ATTTT--TTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCA
*
4409111 ATTTTTTCACAATCGGGGATACTCCAAC
1 ATTTTTT--TAATCGGGGATACTCCAAC
4409139 CTCGTTATTG
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
51 11 0.15
52 29 0.40
53 32 0.44
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (51 bp):
ATTTTTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCA
Found at i:4409214 original size:80 final size:79
Alignment explanation
Indices: 4409111--4409330 Score: 275
Period size: 80 Copynumber: 2.7 Consensus size: 79
4409101 AAAAACACTA
* *
4409111 ATTTTTTCACAATCGGGGATACTCCAACCTCGTTATTGTCGAGGGGATACTCCAACCCCCAGCTT
1 ATTTTCTCACAATCGGGGATACTCCAACC-CGTTATTTTCGAGGGGATACTCCAACCCCCA-CTT
*
4409176 TA-TTCCTAAAAT-ATTG
64 TATTTCC--AAATCATCG
* * * *
4409192 A-TTTCTCATAATCGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCCCGATTTT
1 ATTTTCTCACAATCGGGGATACTCCAA-CCCGTTATTTTCGAGGGGATACTCCAACCCCCACTTT
4409256 ATTTCCAAATCATCG
65 ATTTCCAAATCATCG
* *
4409271 ATTTTTTTCACAATCGGGGATACTCCAACCCTGTTATTTTCAAGGGGATACTCCAACCCC
1 A-TTTTCTCACAATCGGGGATACTCCAACCC-GTTATTTTCGAGGGGATACTCCAACCCC
4409331 ATTACTATCT
Statistics
Matches: 122, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
78 4 0.03
79 8 0.07
80 58 0.48
81 52 0.43
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (79 bp):
ATTTTCTCACAATCGGGGATACTCCAACCCGTTATTTTCGAGGGGATACTCCAACCCCCACTTTA
TTTCCAAATCATCG
Found at i:4409308 original size:81 final size:81
Alignment explanation
Indices: 4409072--4409347 Score: 314
Period size: 81 Copynumber: 3.4 Consensus size: 81
4409062 TCCTTTAATC
* * * *
4409072 GGGGATACTCCAACTCTGATTTTATTTCCAAAAACA-CTAATTTTTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATCATC-GATTTTTTCACAATCGGGGATACTCC
*
4409136 AA-CCTCGTTATTGTCGA
65 AACCCT-GTTATTTTCGA
* * * * *
4409153 GGGGATACTCCAACCCCCAGCTTTA-TTCCTAAAAT-ATTGA-TTTCTCATAATCGGGGATACTC
1 GGGGATACTCCAACCCCGA-TTTTATTTCC-AAAATCATCGATTTTTTCACAATCGGGGATACTC
**
4409215 CAACCCCATTATTTTCGA
64 CAACCCTGTTATTTTCGA
4409233 GGGGATACTCCAACCCCGATTTTATTTCC-AAATCATCGATTTTTTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATCATCGA-TTTTTTCACAATCGGGGATACTCC
*
4409297 AACCCTGTTATTTTCAA
65 AACCCTGTTATTTTCGA
* *
4409314 GGGGATACTCCAACCCC-ATTACTATCTCCAAAAT
1 GGGGATACTCCAACCCCGATT-TTATTTCCAAAAT
4409348 ATTAAATTTC
Statistics
Matches: 163, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
78 4 0.02
79 8 0.05
80 57 0.35
81 82 0.50
82 12 0.07
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (81 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATCATCGATTTTTTCACAATCGGGGATACTCCA
ACCCTGTTATTTTCGA
Found at i:4409359 original size:161 final size:160
Alignment explanation
Indices: 4409072--4409361 Score: 410
Period size: 161 Copynumber: 1.8 Consensus size: 160
4409062 TCCTTTAATC
* * *
4409072 GGGGATACTCCAACTCTGATTTTATTTCCAAAAACACTAATTTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACGAATTTTTTCACAATCGGGGATACTCCA
* *
4409137 ACCTCGTTATTGTCGAGGGGATACTCCAACCCCCAGCTTTATTCCTAAAATATTGATTTCTCATA
66 ACCTCGTTATTGTCAAGGGGATACTCCAACCCCCA-CTTTATTCCTAAAATATTAATTTCTCATA
4409202 ATCGGGGATACTCCAACCCCATTATTTTCGA
130 ATCGGGGATACTCCAACCCCATTATTTTCGA
* *
4409233 GGGGATACTCCAACCCCGATTTTATTTCC-AAATCATCGATTTTTTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAACA-CGAATTTTTTCACAATCGGGGATACTCC
*
4409297 AACC-CTGTTATTTTCAAGGGGATACTCCAA-CCCCA-TTACTATCTCC-AAAATATTAAATTTC
65 AACCTC-GTTATTGTCAAGGGGATACTCCAACCCCCACTT--TAT-TCCTAAAATATT-AATTTC
4409358 TCAT
125 TCAT
4409362 CGGGAAATAT
Statistics
Matches: 115, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
158 2 0.02
160 22 0.19
161 91 0.79
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (160 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACGAATTTTTTCACAATCGGGGATACTCCA
ACCTCGTTATTGTCAAGGGGATACTCCAACCCCCACTTTATTCCTAAAATATTAATTTCTCATAA
TCGGGGATACTCCAACCCCATTATTTTCGA
Found at i:4411340 original size:1 final size:1
Alignment explanation
Indices: 4411326--4411414 Score: 70
Period size: 1 Copynumber: 89.0 Consensus size: 1
4411316 CCCCTTTCTG
* * * ** * * * * *
4411326 TTTTTTGTTATTTTTTTTCTTGGTTTTTTGTTTTTTTTTTTGTTTTTGTTTTTTTATTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
4411391 TTTTTATTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
4411415 GGGGTATGAA
Statistics
Matches: 66, Mismatches: 22, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.03, C:0.01, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:4411351 original size:23 final size:22
Alignment explanation
Indices: 4411320--4411415 Score: 82
Period size: 21 Copynumber: 4.6 Consensus size: 22
4411310 TCTGGACCCC
4411320 TTTC-TGTTTTTTGTTATTTTT
1 TTTCTTGTTTTTTGTTATTTTT
4411341 TTTCTTGGTTTTTTG-T-TTTTT
1 TTTCTT-GTTTTTTGTTATTTTT
*
4411362 TTT-TTG-TTTTTGTTTTTTTAT
1 TTTCTTGTTTTTTGTTATTTT-T
* *
4411383 TTTTTTGTTTTTTATT-TTTTT
1 TTTCTTGTTTTTTGTTATTTTT
*
4411404 GTT-TT-TTTTTTG
1 TTTCTTGTTTTTTG
4411416 GGGTATGAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
18 6 0.09
19 8 0.12
20 8 0.12
21 19 0.29
22 9 0.14
23 15 0.23
ACGTcount: A:0.03, C:0.02, G:0.10, T:0.84
Consensus pattern (22 bp):
TTTCTTGTTTTTTGTTATTTTT
Found at i:4411361 original size:18 final size:15
Alignment explanation
Indices: 4411349--4411414 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
4411339 TTTTTCTTGG
*
4411349 TTTTTTGTTT-TTTT
1 TTTTTTTTTTGTTTT
*
4411363 TTTTGTTTTTGTTTT
1 TTTTTTTTTTGTTTT
4411378 TTTATTTTTTTGTTTT
1 TTT-TTTTTTTGTTTT
*
4411394 TTATTTTTTTGTTTT
1 TTTTTTTTTTGTTTT
4411409 TTTTTT
1 TTTTTT
4411415 GGGGTATGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
14 8 0.18
15 24 0.53
16 13 0.29
ACGTcount: A:0.03, C:0.00, G:0.08, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTGTTTT
Found at i:4416890 original size:28 final size:28
Alignment explanation
Indices: 4416809--4416890 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
4416799 TTTTGGAGAT
*
4416809 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
4416837 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
4416865 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
4416891 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:4417033 original size:51 final size:51
Alignment explanation
Indices: 4416873--4417043 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
4416863 GAAATAACGA
* * *
4416873 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
4416925 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
4416978 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
4417029 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
4417044 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:4417089 original size:27 final size:28
Alignment explanation
Indices: 4417026--4417101 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
4417016 AAAATAAAGT
*
4417026 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
4417054 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
4417081 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
4417102 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Done.