Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold39
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: 4724573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 178835 characters in sequence are not A, C, G, or T
File 21 of 27
Found at i:3517261 original size:13 final size:13
Alignment explanation
Indices: 3517243--3517268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3517233 TACACCAAGT
3517243 ATGTATCGATACA
1 ATGTATCGATACA
3517256 ATGTATCGATACA
1 ATGTATCGATACA
3517269 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3519534 original size:21 final size:22
Alignment explanation
Indices: 3519488--3519532 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3519478 TTGCAAGATG
3519488 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
3519510 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
3519530 AAA
1 AAA
3519533 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:3521356 original size:15 final size:15
Alignment explanation
Indices: 3521336--3521366 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3521326 TAAAAATGTC
*
3521336 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3521351 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3521366 C
1 C
3521367 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3523461 original size:13 final size:13
Alignment explanation
Indices: 3523443--3523468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3523433 ACATTTTTCT
3523443 TTGTATCGATACA
1 TTGTATCGATACA
3523456 TTGTATCGATACA
1 TTGTATCGATACA
3523469 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:3523632 original size:20 final size:20
Alignment explanation
Indices: 3523589--3523634 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3523579 AAATCTTTTG
3523589 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3523610 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3523630 CAAAA
1 CAAAA
3523635 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3530087 original size:20 final size:20
Alignment explanation
Indices: 3530062--3530133 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
3530052 TGCCACTTTC
3530062 ATGTATCGATACAATTGAGT
1 ATGTATCGATACAATTGAGT
*
3530082 ATGTATCGATACAA-AGCA-T
1 ATGTATCGATACAATTG-AGT
3530101 GATGTATCGATAC-ATCT-AGAT
1 -ATGTATCGATACAAT-TGAG-T
3530122 ATGTATCGATAC
1 ATGTATCGATAC
3530134 TTTCAAGGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.09
20 39 0.89
21 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTGAGT
Found at i:3531047 original size:2 final size:2
Alignment explanation
Indices: 3531040--3531064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3531030 TTAAAGGCAT
3531040 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 T
3531065 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3534260 original size:14 final size:14
Alignment explanation
Indices: 3534241--3534270 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3534231 TTAATTAAAT
3534241 GAGTCCAAAATTCA
1 GAGTCCAAAATTCA
3534255 GAGTCCAAAATTCA
1 GAGTCCAAAATTCA
3534269 GA
1 GA
3534271 TTTCAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (14 bp):
GAGTCCAAAATTCA
Found at i:3536521 original size:31 final size:30
Alignment explanation
Indices: 3536486--3536546 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
3536476 CATTTAGGAC
*
3536486 ATTATCT-ATATTTAATTTATATATAAATAAA
1 ATTATCTAATATTTAAATTA-AT-TAAATAAA
3536517 ATTATCTAGATATTTAAATTAATTAAATAA
1 ATTATCTA-ATATTTAAATTAATTAAATAA
3536547 TTGACTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 14 0.52
32 2 0.07
33 11 0.41
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (30 bp):
ATTATCTAATATTTAAATTAATTAAATAAA
Found at i:3539968 original size:48 final size:48
Alignment explanation
Indices: 3539897--3539996 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
3539887 TTCTCCTTCA
3539897 ACTCCTATGAACTTCTCTCATACATTTCTAT-CCTCAAACAACGCTCTC
1 ACTCCTATGAACTTCTCTCATACATTTCT-TCCCTCAAACAACGCTCTC
*
3539945 ACTCCTATGAACTTCTCTCATACATTTCTTCCCTCAAACAACGCTCTT
1 ACTCCTATGAACTTCTCTCATACATTTCTTCCCTCAAACAACGCTCTC
3539993 ACTC
1 ACTC
3539997 TTCGAGGTCC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.26, C:0.36, G:0.04, T:0.34
Consensus pattern (48 bp):
ACTCCTATGAACTTCTCTCATACATTTCTTCCCTCAAACAACGCTCTC
Found at i:3543610 original size:18 final size:17
Alignment explanation
Indices: 3543568--3543610 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
3543558 AAGACACTTT
*
3543568 AAGCAGCAAACACACTA
1 AAGCAACAAACACACTA
* *
3543585 ATGCAACAAACATCATTA
1 AAGCAACAAACA-CACTA
3543603 AAGCAACA
1 AAGCAACA
3543611 TCCACATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.53, C:0.26, G:0.09, T:0.12
Consensus pattern (17 bp):
AAGCAACAAACACACTA
Found at i:3544064 original size:12 final size:12
Alignment explanation
Indices: 3544047--3544111 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
3544037 AAATATTTTA
3544047 TATTTTAAAATT
1 TATTTTAAAATT
3544059 TATTTT--AATT
1 TATTTTAAAATT
* *
3544069 TCA-TATATAATT
1 T-ATTTTAAAATT
*
3544081 T-TTTT-AAATA
1 TATTTTAAAATT
3544091 TATTTTAAAATT
1 TATTTTAAAATT
3544103 ATATTTTAA
1 -TATTTTAA
3544112 GAAAATTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
10 11 0.27
11 7 0.17
12 15 0.37
13 8 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:3544240 original size:21 final size:19
Alignment explanation
Indices: 3544198--3544259 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
3544188 AATGCAAAAA
*
3544198 AAATTAAAATTATATATTTT
1 AAATTAATATT-TATATTTT
3544218 AAATTAATATTTATATTAATT
1 AAATTAATATTTATATT--TT
* *
3544239 AAAAT-ATATTTAAATTTT
1 AAATTAATATTTATATTTT
3544257 AAA
1 AAA
3544260 ATTACACTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.14
19 6 0.16
20 20 0.54
21 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AAATTAATATTTATATTTT
Found at i:3546542 original size:16 final size:17
Alignment explanation
Indices: 3546521--3546553 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3546511 AAATTAAGAC
3546521 CCAAATTTGAGA-AAAT
1 CCAAATTTGAGATAAAT
3546537 CCAAATTTGAGATAAAT
1 CCAAATTTGAGATAAAT
3546554 AAAACTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (17 bp):
CCAAATTTGAGATAAAT
Found at i:3547027 original size:13 final size:14
Alignment explanation
Indices: 3547002--3547030 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3546992 TTGAAAACAA
3547002 TTTTCAAGTTAATT
1 TTTTCAAGTTAATT
3547016 TTTTCAAG-TAATT
1 TTTTCAAGTTAATT
3547029 TT
1 TT
3547031 AAATTTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTCAAGTTAATT
Found at i:3547910 original size:19 final size:19
Alignment explanation
Indices: 3547886--3547927 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3547876 AATAGCACTT
3547886 ACAACAGCAACTTGGCAAA
1 ACAACAGCAACTTGGCAAA
*
3547905 ACAACAGCAACTTGGCGAA
1 ACAACAGCAACTTGGCAAA
3547924 ACAA
1 ACAA
3547928 AGGATGGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.10
Consensus pattern (19 bp):
ACAACAGCAACTTGGCAAA
Found at i:3548843 original size:13 final size:15
Alignment explanation
Indices: 3548825--3548856 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3548815 TAAAATTTAT
3548825 TTAAAA-TAATA-TA
1 TTAAAAGTAATAGTA
3548838 TTAAAAGTAATAGTA
1 TTAAAAGTAATAGTA
3548853 TTAA
1 TTAA
3548857 CTAATAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
TTAAAAGTAATAGTA
Found at i:3554530 original size:2 final size:2
Alignment explanation
Indices: 3554523--3554556 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3554513 ACTCCCACCC
3554523 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3554557 CACATGATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3555612 original size:6 final size:6
Alignment explanation
Indices: 3555603--3555631 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3555593 AAAAATAAAC
3555603 TGAGCT TGAGCT TGAGCT TGAGCT TGAGC
1 TGAGCT TGAGCT TGAGCT TGAGCT TGAGC
3555632 AATGAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (6 bp):
TGAGCT
Found at i:3555876 original size:13 final size:13
Alignment explanation
Indices: 3555858--3555883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3555848 CAGATATTAA
3555858 AATTTATTTTTAT
1 AATTTATTTTTAT
3555871 AATTTATTTTTAT
1 AATTTATTTTTAT
3555884 TTATATTTAT
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:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTTATTTTTAT
Found at i:3555885 original size:23 final size:24
Alignment explanation
Indices: 3555859--3555903 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3555849 AGATATTAAA
*
3555859 ATTTATTTTTATAATT-TATTTTT
1 ATTTATATTTATAATTATATTTTT
*
3555882 ATTTATATTTATTATTATATTT
1 ATTTATATTTATAATTATATTT
3555904 AGAGATTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
ATTTATATTTATAATTATATTTTT
Found at i:3556654 original size:18 final size:19
Alignment explanation
Indices: 3556611--3556655 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
3556601 AATTAAGTGA
*
3556611 CAAAATTCAATTAAAAATT
1 CAAAATTTAATTAAAAATT
3556630 -AAAATTTAATT-AAAATT
1 CAAAATTTAATTAAAAATT
3556647 CAAAATTTA
1 CAAAATTTA
3556656 GTGATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (19 bp):
CAAAATTTAATTAAAAATT
Found at i:3556956 original size:14 final size:14
Alignment explanation
Indices: 3556916--3556956 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
3556906 ATTTGATCAA
3556916 TAGTGAATTAAATTT
1 TAGT-AATTAAATTT
*
3556931 AAGTAA--AAATTT
1 TAGTAATTAAATTT
3556943 TAGTAATTAAATTT
1 TAGTAATTAAATTT
3556957 AATTTAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.50
14 8 0.36
15 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (14 bp):
TAGTAATTAAATTT
Found at i:3558393 original size:13 final size:13
Alignment explanation
Indices: 3558375--3558400 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3558365 TACACCAAGT
3558375 ATGTATCGATACA
1 ATGTATCGATACA
3558388 ATGTATCGATACA
1 ATGTATCGATACA
3558401 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3560651 original size:21 final size:21
Alignment explanation
Indices: 3560618--3560667 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
3560608 TTGCAAGTTG
*
3560618 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3560640 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
3560661 AAATAAA
1 AAATAAA
3560668 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3562485 original size:15 final size:15
Alignment explanation
Indices: 3562465--3562495 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3562455 TAAAAATGTC
*
3562465 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3562480 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3562495 C
1 C
3562496 CGAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3564593 original size:13 final size:13
Alignment explanation
Indices: 3564575--3564599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3564565 CATTTTTCTC
3564575 TGTATCGATACAT
1 TGTATCGATACAT
3564588 TGTATCGATACA
1 TGTATCGATACA
3564600 GGGTGATTAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3564763 original size:20 final size:20
Alignment explanation
Indices: 3564720--3564765 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3564710 AAATCTTTTG
3564720 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3564741 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3564761 CAAAA
1 CAAAA
3564766 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3567069 original size:13 final size:13
Alignment explanation
Indices: 3567051--3567076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3567041 TACACCAAGT
3567051 ATGTATCGATACA
1 ATGTATCGATACA
3567064 ATGTATCGATACA
1 ATGTATCGATACA
3567077 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3569224 original size:13 final size:13
Alignment explanation
Indices: 3569206--3569230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3569196 CATTATGCTT
3569206 TGTATCGATACAA
1 TGTATCGATACAA
3569219 TGTATCGATACA
1 TGTATCGATACA
3569231 TGTTCATTAT
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:3569325 original size:20 final size:20
Alignment explanation
Indices: 3569299--3569352 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3569289 CTATCACTAT
*
3569299 TTGTATCGATACATGACATAA
1 TTGTATCGATACATGA-AGAA
3569320 -TGTATCGATACATGAAGAA
1 TTGTATCGATACATGAAGAA
*
3569339 TTGTATCAATACAT
1 TTGTATCGATACAT
3569353 TGCCTCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAAGAA
Found at i:3575513 original size:13 final size:13
Alignment explanation
Indices: 3575495--3575519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3575485 CAATGTTTTT
3575495 TGTATCGATACAA
1 TGTATCGATACAA
3575508 TGTATCGATACA
1 TGTATCGATACA
3575520 TGGGTTACTA
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:3577039 original size:33 final size:33
Alignment explanation
Indices: 3576997--3577063 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3576987 CGAGAGTTGA
*
3576997 TCACTTCACTTTCGCAGCACATGAATGAGCACT
1 TCACTTCACTCTCGCAGCACATGAATGAGCACT
* *
3577030 TCACTTCACTCTCGCAGCGCATGGATGAGCACT
1 TCACTTCACTCTCGCAGCACATGAATGAGCACT
3577063 T
1 T
3577064 TAGTTCTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (33 bp):
TCACTTCACTCTCGCAGCACATGAATGAGCACT
Found at i:3577440 original size:3 final size:3
Alignment explanation
Indices: 3577434--3577459 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3577424 CGATGAAGAA
3577434 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
3577460 CTCAGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3581365 original size:20 final size:19
Alignment explanation
Indices: 3581340--3581463 Score: 100
Period size: 20 Copynumber: 6.6 Consensus size: 19
3581330 TTTTCACAAT
3581340 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATT-TTCA
3581360 TTGTATCGATACATTTTGCA
1 TTGTATCGATACATTTT-CA
* *
3581380 TTGTATAGATACATTGCTCA
1 TTGTATCGATACATT-TTCA
* *
3581400 TTGTGTTGAT--A----CA
1 TTGTATCGATACATTTTCA
3581413 TTGTATCGATACATTGCTT-A
1 TTGTATCGATACATT--TTCA
3581433 TTGTATCGATACATTTTACA
1 TTGTATCGATACATTTT-CA
*
3581453 ATGTATCGATA
1 TTGTATCGATA
3581464 TATTCAGGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
13 10 0.12
15 1 0.01
18 3 0.04
19 2 0.02
20 68 0.80
21 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (19 bp):
TTGTATCGATACATTTTCA
Found at i:3581415 original size:33 final size:33
Alignment explanation
Indices: 3581378--3581447 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
3581368 ATACATTTTG
* *
3581378 CATTGTATAGATACATTGCTCATTGTGTTGATA
1 CATTGTATAGATACATTGCTCATTGTATCGATA
* *
3581411 CATTGTATCGATACATTGCTTATTGTATCGATA
1 CATTGTATAGATACATTGCTCATTGTATCGATA
3581444 CATT
1 CATT
3581448 TTACAATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (33 bp):
CATTGTATAGATACATTGCTCATTGTATCGATA
Found at i:3583884 original size:80 final size:78
Alignment explanation
Indices: 3583720--3583885 Score: 174
Period size: 80 Copynumber: 2.1 Consensus size: 78
3583710 AAATTTCTAG
* *
3583720 ATTTTTCATCTCGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGCTTTAT
1 ATTTTTCATATCGAGGATACTCCAACCCCGTTATTATC-AGGGGATACTCCAACCCCAGCTTTAT
* *
3583785 ATCTAAAATATTGA
65 ATCCAAAATATTAA
* * * *
3583799 TTTTTTCATAATCGGGGGTACTCCAACCCCGTTATGTCATC-GGGGATACTCCAACCCC-GTTGT
1 ATTTTTCAT-ATCGAGGATACTCCAACCCCGTTAT-T-ATCAGGGGATACTCCAACCCCAGCT-T
* * *
3583862 TGTCTCCAAAGTATTAA
62 TATATCCAAAATATTAA
3583879 ATTTTTC
1 ATTTTTC
3583886 GTCAGGAGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
79 10 0.14
80 58 0.82
81 1 0.01
82 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (78 bp):
ATTTTTCATATCGAGGATACTCCAACCCCGTTATTATCAGGGGATACTCCAACCCCAGCTTTATA
TCCAAAATATTAA
Found at i:3585913 original size:20 final size:20
Alignment explanation
Indices: 3585875--3585914 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
3585865 TTTCAAATTT
3585875 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
3585896 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
3585915 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:3587286 original size:33 final size:33
Alignment explanation
Indices: 3587230--3587296 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
3587220 CGAGAGTTGA
* *
3587230 TCACTTCACTTTCACAACACATGAGTGAACACT
1 TCACTTCACTCTCACAACACATGAATGAACACT
* * * *
3587263 TCACTTCACTCTCGCAGCGCATGAATGAGCACT
1 TCACTTCACTCTCACAACACATGAATGAACACT
3587296 T
1 T
3587297 TGGTGCACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.27
Consensus pattern (33 bp):
TCACTTCACTCTCACAACACATGAATGAACACT
Found at i:3587511 original size:16 final size:16
Alignment explanation
Indices: 3587492--3587522 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3587482 ATATGCGATG
3587492 TTTGCTTTCTTATCTA
1 TTTGCTTTCTTATCTA
3587508 TTTGCTTTCTTATCT
1 TTTGCTTTCTTATCT
3587523 GTTATATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TTTGCTTTCTTATCTA
Found at i:3587684 original size:20 final size:21
Alignment explanation
Indices: 3587640--3587689 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3587630 AAAATTTTTT
*
3587640 AAATGTTTATCAAGGGGGAGA
1 AAATTTTTATCAAGGGGGAGA
3587661 AAATTTTTATCAAGGGGGAG-
1 AAATTTTTATCAAGGGGGAGA
3587681 AAATTTTTA
1 AAATTTTTA
3587690 AAAGAGAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (21 bp):
AAATTTTTATCAAGGGGGAGA
Found at i:3588286 original size:13 final size:13
Alignment explanation
Indices: 3588268--3588292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3588258 CATTATGCTT
3588268 TGTATCGATACAA
1 TGTATCGATACAA
3588281 TGTATCGATACA
1 TGTATCGATACA
3588293 TGCACAATTA
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:3594076 original size:17 final size:17
Alignment explanation
Indices: 3594054--3594096 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
3594044 ACTCAAGGTT
3594054 AAACAAAGAAATTATAC
1 AAACAAAGAAATTATAC
3594071 AAACAAAGAAATTATAC
1 AAACAAAGAAATTATAC
3594088 AAACAAAGA
1 AAACAAAGA
3594097 TTGCCTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (17 bp):
AAACAAAGAAATTATAC
Found at i:3594481 original size:20 final size:21
Alignment explanation
Indices: 3594456--3594509 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
3594446 GTTTGAGGCA
*
3594456 ATGTATCGATACAATTCT-TC
1 ATGTATCGATACAATTCTGCC
*
3594476 ATGTATCGATAC-ATTGTGCC
1 ATGTATCGATACAATTCTGCC
3594496 ATGTATCGATACAA
1 ATGTATCGATACAA
3594510 ACAGTGATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 25 0.83
21 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTCTGCC
Found at i:3594576 original size:13 final size:13
Alignment explanation
Indices: 3594558--3594584 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3594548 TACAATGAAC
3594558 ATATATCGATACA
1 ATATATCGATACA
3594571 ATATATCGATACA
1 ATATATCGATACA
3594584 A
1 A
3594585 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ATATATCGATACA
Found at i:3595492 original size:2 final size:2
Alignment explanation
Indices: 3595485--3595515 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3595475 TCTTTCAATT
3595485 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
3595516 TTAAAGAATT
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:3596390 original size:16 final size:16
Alignment explanation
Indices: 3596371--3596419 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
3596361 ACTTGAATTT
*
3596371 AAAATAACTCGAACCC
1 AAAATGACTCGAACCC
*
3596387 AAAATGATTCGAACCC
1 AAAATGACTCGAACCC
*
3596403 GAAATGACTCGAACCC
1 AAAATGACTCGAACCC
3596419 A
1 A
3596420 GAATTACGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.45, C:0.29, G:0.12, T:0.14
Consensus pattern (16 bp):
AAAATGACTCGAACCC
Found at i:3598064 original size:148 final size:148
Alignment explanation
Indices: 3597884--3598181 Score: 578
Period size: 148 Copynumber: 2.0 Consensus size: 148
3597874 ATGTATCATC
3597884 ATGCTCTCTCCTATCCCATCATCGTGCTGCTGTTTGTTTGTTTCAAGGCCAAGAGCAAAATTAAT
1 ATGCTCTCTCCTATCCCATCATCGTGCTGCTGTTTGTTTGTTTCAAGGCCAAGAGCAAAATTAAT
*
3597949 GTGTAACTGCAAATTGCATTTTATCAGGTAACTGCATGTTCGATAAATGCCAGAAACACTACCAG
66 GTGTAACTGCAAATTGCATTTTATCAAGTAACTGCATGTTCGATAAATGCCAGAAACACTACCAG
3598014 AATGTAAAAGAACAGAAA
131 AATGTAAAAGAACAGAAA
3598032 ATGCTCTCTCCTATCCCATCATCGTGCTGCTGTTTGTTTGTTTCAAGGCCAAGAGCAAAATTAAT
1 ATGCTCTCTCCTATCCCATCATCGTGCTGCTGTTTGTTTGTTTCAAGGCCAAGAGCAAAATTAAT
*
3598097 GTGTAACTGCAAATTGCATTTTATCAAGTAACTGCATGTTCGATAAATGCCAGAAACACTACCGG
66 GTGTAACTGCAAATTGCATTTTATCAAGTAACTGCATGTTCGATAAATGCCAGAAACACTACCAG
3598162 AATGTAAAAGAACAGAAA
131 AATGTAAAAGAACAGAAA
3598180 AT
1 AT
3598182 AAAAACAGGC
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 148 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (148 bp):
ATGCTCTCTCCTATCCCATCATCGTGCTGCTGTTTGTTTGTTTCAAGGCCAAGAGCAAAATTAAT
GTGTAACTGCAAATTGCATTTTATCAAGTAACTGCATGTTCGATAAATGCCAGAAACACTACCAG
AATGTAAAAGAACAGAAA
Found at i:3609370 original size:13 final size:13
Alignment explanation
Indices: 3609352--3609377 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3609342 CAATTTTTTG
3609352 TGTATCGATACAT
1 TGTATCGATACAT
3609365 TGTATCGATACAT
1 TGTATCGATACAT
3609378 ACTTGCTGTA
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:3611799 original size:21 final size:20
Alignment explanation
Indices: 3611753--3611799 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
3611743 TTTGATGTTG
3611753 ATTTTGATGAAAAACGAAGT
1 ATTTTGATGAAAAACGAAGT
3611773 -TGTTTGAAGTGAAAAAC-AAGT
1 AT-TTTG-A-TGAAAAACGAAGT
3611794 ATTTTG
1 ATTTTG
3611800 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:3611941 original size:13 final size:13
Alignment explanation
Indices: 3611923--3611961 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3611913 ATAATCACCC
*
3611923 TGTATCGATACAG
1 TGTATCGATACAA
3611936 TGTATCGATACAA
1 TGTATCGATACAA
3611949 TGTATCGATACAA
1 TGTATCGATACAA
3611962 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3611972 original size:20 final size:20
Alignment explanation
Indices: 3611947--3612025 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
3611937 GTATCGATAC
3611947 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3611967 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
3611992 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
3612012 CATGTATCGATACA
1 AATGTATCGATACA
3612026 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3614062 original size:15 final size:15
Alignment explanation
Indices: 3614042--3614072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3614032 ATTTCGTTTG
*
3614042 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3614057 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3614072 G
1 G
3614073 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3615905 original size:21 final size:21
Alignment explanation
Indices: 3615876--3615920 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3615866 AAGTTTTCAT
*
3615876 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3615896 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3615918 TTT
1 TTT
3615921 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3618157 original size:13 final size:13
Alignment explanation
Indices: 3618139--3618164 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3618129 CAATTTTTTG
3618139 TGTATCGATACAT
1 TGTATCGATACAT
3618152 TGTATCGATACAT
1 TGTATCGATACAT
3618165 ACTTGCTGTA
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:3619700 original size:26 final size:26
Alignment explanation
Indices: 3619669--3619718 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
3619659 ATCTAGCTTC
3619669 TTGAATTCATTTGGTGACTTCTCTTA
1 TTGAATTCATTTGGTGACTTCTCTTA
3619695 TTGAATTCATTTGGTGACTTCTCT
1 TTGAATTCATTTGGTGACTTCTCT
3619719 CTTCTCCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (26 bp):
TTGAATTCATTTGGTGACTTCTCTTA
Found at i:3620027 original size:20 final size:21
Alignment explanation
Indices: 3619979--3620030 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
3619969 ATAAGGAAAG
3619979 TAAATAAAAATAATTTAAAAA
1 TAAATAAAAATAATTTAAAAA
* * **
3620000 TAACTAAAATTAA-TTAAATC
1 TAAATAAAAATAATTTAAAAA
3620020 TAAATAAAAAT
1 TAAATAAAAAT
3620031 CTCTAAGACT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAATAAAAATAATTTAAAAA
Found at i:3624173 original size:23 final size:22
Alignment explanation
Indices: 3624134--3624186 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 22
3624124 CACCATTTCG
*
3624134 GAAAAGAAATTTGTAAAAATTTTT
1 GAAAA-AAATTTGTAAAAA-ATTT
3624158 GAAAAAAATATT-TAAAAAATTT
1 GAAAAAAAT-TTGTAAAAAATTT
3624180 GAAAAAA
1 GAAAAAA
3624187 TCGTTTGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (22 bp):
GAAAAAAATTTGTAAAAAATTT
Found at i:3627669 original size:10 final size:11
Alignment explanation
Indices: 3627640--3627678 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 11
3627630 TCTTCTTCAC
3627640 TTTTTTGTTTTAT
1 TTTTTTG-TTT-T
3627653 GTTTTTTGTTTT
1 -TTTTTTGTTTT
3627665 TTTTTTGTTTT
1 TTTTTTGTTTT
3627676 TTT
1 TTT
3627679 ATTTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 14 0.56
12 1 0.04
13 3 0.12
14 7 0.28
ACGTcount: A:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:3627673 original size:18 final size:18
Alignment explanation
Indices: 3627640--3627687 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
3627630 TCTTCTTCAC
*
3627640 TTTTTTGTTTTATGTTTT
1 TTTTTTTTTTTATGTTTT
3627658 TTGTTTTTTTTT-TGTTTT
1 TT-TTTTTTTTTATGTTTT
*
3627676 TTTATTTTTTTA
1 TTTTTTTTTTTA
3627688 GAGTGGTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 8 0.31
18 10 0.38
19 8 0.31
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTTATGTTTT
Found at i:3627677 original size:7 final size:7
Alignment explanation
Indices: 3627640--3627685 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
3627630 TCTTCTTCAC
3627640 TTTTTTG
1 TTTTTTG
*
3627647 TTTTATG
1 TTTTTTG
3627654 TTTTTTG
1 TTTTTTG
3627661 TTTTTT-
1 TTTTTTG
*
3627667 TTTTGT-
1 TTTTTTG
*
3627673 TTTTTTA
1 TTTTTTG
3627680 TTTTTT
1 TTTTTT
3627686 TAGAGTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 10 0.29
7 24 0.71
ACGTcount: A:0.04, C:0.00, G:0.09, T:0.87
Consensus pattern (7 bp):
TTTTTTG
Found at i:3631871 original size:27 final size:27
Alignment explanation
Indices: 3631841--3631909 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
3631831 TTGAAAAACA
*
3631841 GGGTTGGAGTATCCCCACGAAAGAATG
1 GGGTTGGAGTGTCCCCACGAAAGAATG
*
3631868 GGGTTGGAGTGTCCCCACGAAGGAATG
1 GGGTTGGAGTGTCCCCACGAAAGAATG
3631895 GGGTTGGAGTGTCCC
1 GGGTTGGAGTGTCCC
3631910 TGATAATGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.20
Consensus pattern (27 bp):
GGGTTGGAGTGTCCCCACGAAAGAATG
Found at i:3633709 original size:19 final size:20
Alignment explanation
Indices: 3633687--3633729 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3633677 TGATAGATTC
*
3633687 ACTTATGTAT-GATGCATTT
1 ACTTATGTATCGATGCATTA
*
3633706 ACTTTTGTATCGATGCATTA
1 ACTTATGTATCGATGCATTA
3633726 ACTT
1 ACTT
3633730 GTTATATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (20 bp):
ACTTATGTATCGATGCATTA
Found at i:3640393 original size:22 final size:23
Alignment explanation
Indices: 3640368--3640416 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
3640358 ATTATTTCAT
* *
3640368 AAAATTAGACAT-AAAACATATC
1 AAAATTAAACATGAAAACATACC
*
3640390 AAAATTAAACTTGAAAACATACC
1 AAAATTAAACATGAAAACATACC
3640413 AAAA
1 AAAA
3640417 ACCATTCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.20
Consensus pattern (23 bp):
AAAATTAAACATGAAAACATACC
Found at i:3641344 original size:13 final size:13
Alignment explanation
Indices: 3641326--3641351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3641316 CTAGTTATGA
3641326 TGTATCGATACAC
1 TGTATCGATACAC
3641339 TGTATCGATACAC
1 TGTATCGATACAC
3641352 ACAAATATGT
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:3641471 original size:21 final size:22
Alignment explanation
Indices: 3641441--3641492 Score: 97
Period size: 21 Copynumber: 2.4 Consensus size: 22
3641431 ACAGTGACCT
3641441 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
3641463 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
3641484 ATGAACAGT
1 ATGAACAGT
3641493 TATGAATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:3641602 original size:53 final size:53
Alignment explanation
Indices: 3641538--3641674 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
3641528 CTACTTTCAA
3641538 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
3641591 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
3641644 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
3641675 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:3641707 original size:20 final size:20
Alignment explanation
Indices: 3641644--3641714 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3641634 GCCAATGTCC
**
3641644 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
3641664 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
3641684 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
3641704 TGTATCGATAC
1 TGTATCGATAC
3641715 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:3641778 original size:21 final size:21
Alignment explanation
Indices: 3641754--3641794 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3641744 GTCAACCTTG
3641754 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
3641775 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
3641795 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:3642634 original size:20 final size:19
Alignment explanation
Indices: 3642588--3642645 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
3642578 CTTTTTCTTT
*
3642588 TTTCTTTGC-TTGTTGCT-
1 TTTCTTTGCTTTCTTGCTA
3642605 TTTC-TT-CTTTCCTTGCTA
1 TTTCTTTGCTTT-CTTGCTA
*
3642623 TTTCTTTGCTTTGCTTGTTA
1 TTTCTTTGCTTT-CTTGCTA
3642643 TTT
1 TTT
3642646 GGATTGATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 1 0.03
16 4 0.12
17 9 0.27
18 4 0.12
19 2 0.06
20 13 0.39
ACGTcount: A:0.03, C:0.19, G:0.12, T:0.66
Consensus pattern (19 bp):
TTTCTTTGCTTTCTTGCTA
Found at i:3642718 original size:19 final size:19
Alignment explanation
Indices: 3642664--3642719 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
3642654 GCTTTGTTTC
*
3642664 CTTTTTTTTGGTGTTTCGATT
1 CTTTTTTTT-GT-TTTCTATT
* *
3642685 CTAGTTTTCTG-TTTCTATT
1 CT-TTTTTTTGTTTTCTATT
3642704 CTTTTTTTTGTTTTCT
1 CTTTTTTTTGTTTTCT
3642720 TTTGTTGTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.21
19 14 0.50
21 3 0.11
22 5 0.18
ACGTcount: A:0.05, C:0.12, G:0.12, T:0.70
Consensus pattern (19 bp):
CTTTTTTTTGTTTTCTATT
Found at i:3643021 original size:31 final size:31
Alignment explanation
Indices: 3642976--3643051 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
3642966 GCTATAGCTA
* * *
3642976 TTTCTTCTTTTTTTCATTGCAGCATCGGTTT
1 TTTCTTGTTGTTTTCATTGCAGCATCAGTTT
3643007 TTTCTTGTTGTTTTCATTGCAGCATCAGTTT
1 TTTCTTGTTGTTTTCATTGCAGCATCAGTTT
* *
3643038 CTTCTAGTTGTTTT
1 TTTCTTGTTGTTTT
3643052 GTTGCGGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.11, C:0.17, G:0.14, T:0.58
Consensus pattern (31 bp):
TTTCTTGTTGTTTTCATTGCAGCATCAGTTT
Found at i:3643197 original size:12 final size:12
Alignment explanation
Indices: 3643177--3643206 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3643167 TGCTTTATGT
3643177 ATGAAAGCATGC
1 ATGAAAGCATGC
*
3643189 ATGATAGCATGC
1 ATGAAAGCATGC
3643201 ATGAAA
1 ATGAAA
3643207 TGCCACCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (12 bp):
ATGAAAGCATGC
Found at i:3643895 original size:42 final size:42
Alignment explanation
Indices: 3643834--3644147 Score: 210
Period size: 42 Copynumber: 7.5 Consensus size: 42
3643824 GCCAATGGGT
* * * *
3643834 AGAC-AAAGGGTAAAGAAGTCTCTCGAGTCAAAGTCAATAAGC
1 AGACTAAAGGTTAAA-AAGTCTCTCGAGTCAAAGCCGACAAGC
3643876 AGACTAAAGGTTAAAAAGTCTC-CAGAGTCAAAGCCGACAAGC
1 AGACTAAAGGTTAAAAAGTCTCTC-GAGTCAAAGCCGACAAGC
** * *
3643918 AGACTAAAGGCAAAAAAGTCTCT-AAGATCAAAGCCGACAAGT
1 AGACTAAAGGTTAAAAAGTCTCTCGAG-TCAAAGCCGACAAGC
* * * * *
3643960 AGACTAAAGGTGAAGAAGTCTCT-TAGATCAAAACCGACAGGC
1 AGACTAAAGGTTAAAAAGTCTCTCGAG-TCAAAGCCGACAAGC
* * * * * * * *
3644002 AGACTAAAAGTGAGAAAGTCT-TCCAAGGTTAAAGCTGATAGGC
1 AGACTAAAGGTTAAAAAGTCTCT-CGA-GTCAAAGCCGACAAGC
* * * **
3644045 AGACTAAAGGTGAGAAAGTCTCT-AAGGTCAAAGTTGACAAGC
1 AGACTAAAGGTTAAAAAGTCTCTCGA-GTCAAAGCCGACAAGC
* ** * * *
3644087 AGACTAAAGGTGAGGAAGTCTCTAGGGTCAAAGCCGACAGGC
1 AGACTAAAGGTTAAAAAGTCTCTCGAGTCAAAGCCGACAAGC
*
3644129 AAACTAAAGG-TAAGAAAGT
1 AGACTAAAGGTTAA-AAAGT
3644148 TTTTAGGGTC
Statistics
Matches: 224, Mismatches: 38, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
41 5 0.02
42 176 0.79
43 41 0.18
44 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
AGACTAAAGGTTAAAAAGTCTCTCGAGTCAAAGCCGACAAGC
Found at i:3644084 original size:127 final size:127
Alignment explanation
Indices: 3643916--3644147 Score: 331
Period size: 127 Copynumber: 1.8 Consensus size: 127
3643906 AAGCCGACAA
*
3643916 GCAGACTAAAGGCAAAAAAGTCTCTAAGATCAAAGCCGACAAGTAGACTAAAGGTGAAGAAGTCT
1 GCAGACTAAAGGCAAAAAAGTCTCTAAGATCAAAGCCGACAAGCAGACTAAAGGTGAAGAAGTCT
* *
3643981 CTTA-GATCAAAACCGACAGGCAGACTAAAAGTGAGAAAGTCTTCCAAGGTTAAAGCTGATAG
66 C-TAGGATCAAAACCGACAGGCAAACTAAAAGTAAGAAAGTCTTCCAAGGTTAAAGCTGATAG
** * * ** *
3644043 GCAGACTAAAGGTGAGAAAGTCTCTAAGGTCAAAGTTGACAAGCAGACTAAAGGTGAGGAAGTCT
1 GCAGACTAAAGGCAAAAAAGTCTCTAAGATCAAAGCCGACAAGCAGACTAAAGGTGAAGAAGTCT
* * *
3644108 CTAGGGTCAAAGCCGACAGGCAAACTAAAGGTAAGAAAGT
66 CTAGGATCAAAACCGACAGGCAAACTAAAAGTAAGAAAGT
3644148 TTTTAGGGTC
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
126 2 0.02
127 89 0.98
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.17
Consensus pattern (127 bp):
GCAGACTAAAGGCAAAAAAGTCTCTAAGATCAAAGCCGACAAGCAGACTAAAGGTGAAGAAGTCT
CTAGGATCAAAACCGACAGGCAAACTAAAAGTAAGAAAGTCTTCCAAGGTTAAAGCTGATAG
Found at i:3644155 original size:42 final size:42
Alignment explanation
Indices: 3643874--3644315 Score: 363
Period size: 42 Copynumber: 10.5 Consensus size: 42
3643864 AAGTCAATAA
* *
3643874 GCAGACTAAAGGTTAA-AAAGTCTC-CAGAGTCAAAGCCGACAA
1 GCAGACTAAAGG-TAAGAAAGTCTCTAAG-GTCAAAGCCGACAG
* * * *
3643916 GCAGACTAAAGGCAAAAAAGTCTCTAAGATCAAAGCCGACAA
1 GCAGACTAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAG
* * * *
3643958 GTAGACTAAAGGTGAAG-AAGTCTCTTAGATCAAAACCGACAG
1 GCAGACTAAAGGT-AAGAAAGTCTCTAAGGTCAAAGCCGACAG
* * * * * *
3644000 GCAGACTAAAAGTGAGAAAGTCTTCCAAGGTTAAAGCTGATAG
1 GCAGACTAAAGGTAAGAAAGTC-TCTAAGGTCAAAGCCGACAG
* ** *
3644043 GCAGACTAAAGGTGAGAAAGTCTCTAAGGTCAAAGTTGACAA
1 GCAGACTAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAG
* * *
3644085 GCAGACTAAAGGTGAGGAAGTCTCTAGGGTCAAAGCCGACAG
1 GCAGACTAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAG
* * * * * **
3644127 GCAAACTAAAGGTAAGAAAGTTTTTAGGGTCTAAGTTGACAG
1 GCAGACTAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAG
* * * * *
3644169 GTAGACTAAAAGTCAAG-AAGTCTCTAGGGTTAAAGCCGATAG
1 GCAGACTAAAGGT-AAGAAAGTCTCTAAGGTCAAAGCCGACAG
** * * * *
3644211 GCAGACTAAAAATCAGGAAA-TCTCCAAGGTCAAAGTCGATAG
1 GCAGACTAAAGGT-AAGAAAGTCTCTAAGGTCAAAGCCGACAG
* * * * * *
3644253 GGAGACTAAAGGTAAGGAAGTCTCTAGGGTTAAAGCCAATAG
1 GCAGACTAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAG
*
3644295 GCAGACTAAAGGTAAGGAAGT
1 GCAGACTAAAGGTAAGAAAGT
3644316 TAAAAAAGTT
Statistics
Matches: 326, Mismatches: 66, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
41 8 0.02
42 275 0.84
43 43 0.13
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (42 bp):
GCAGACTAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAG
Found at i:3644538 original size:44 final size:44
Alignment explanation
Indices: 3644489--3644715 Score: 210
Period size: 44 Copynumber: 5.2 Consensus size: 44
3644479 GGCAAAACTG
* *
3644489 TATGTCAAATCAGAATGAGAAGAATCTGACTAGAGTGGTAACCA
1 TATGTCAAATCAAAATGAGAAGAATCTGACTAGGGTGGTAACCA
* *
3644533 TATGTCAAATCAAAATGAGACGAATCTGACTAGGGTGGTAACCG
1 TATGTCAAATCAAAATGAGAAGAATCTGACTAGGGTGGTAACCA
* * * * *
3644577 TACT-TCAGACCAAAATAAGAA-AAGTTTGACCAGGGTGGTAACCA
1 TA-TGTCAAATCAAAATGAGAAGAA-TCTGACTAGGGTGGTAACCA
* * * * *
3644621 TATGTCAAA-CATAAAGGA-AATAGATTTAACTAGGGTGGTAACCT
1 TATGTCAAATCA-AAATGAGAAGA-ATCTGACTAGGGTGGTAACCA
* * * * * *
3644665 TACGTCAAATTAGAATAAAAAGAATCTGACTAGGGTAGTAACCA
1 TATGTCAAATCAAAATGAGAAGAATCTGACTAGGGTGGTAACCA
3644709 TATGTCA
1 TATGTCA
3644716 GACTAAAATA
Statistics
Matches: 147, Mismatches: 28, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
43 7 0.05
44 134 0.91
45 6 0.04
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (44 bp):
TATGTCAAATCAAAATGAGAAGAATCTGACTAGGGTGGTAACCA
Found at i:3644682 original size:88 final size:87
Alignment explanation
Indices: 3644492--3644715 Score: 236
Period size: 88 Copynumber: 2.5 Consensus size: 87
3644482 AAAACTGTAT
* * * * *
3644492 GTCAAATCAGAATGAGAAGAATCTGACTAGAGTGGTAACCATATGTCAAATCAAAATGAGACGAA
1 GTCAAATCAGAATAAGAA-AATCTGACTAGGGTGGTAACCATATGTCAAATCAAAAGGAAAAGAA
*
3644557 TCTGACTAGGGTGGTAACCGTAC
65 TCTAACTAGGGTGGTAACCGTAC
* * * * * *
3644580 TTCAGACCAAAATAAGAAAAGTTTGACCAGGGTGGTAACCATATGTCAAA-CATAAAGGAAATAG
1 GTCAAATCAGAATAAGAAAA-TCTGACTAGGGTGGTAACCATATGTCAAATCA-AAAGGAAA-AG
* *
3644644 -ATTTAACTAGGGTGGTAACCTTAC
63 AATCTAACTAGGGTGGTAACCGTAC
* * *
3644668 GTCAAATTAGAATAAAAAGAATCTGACTAGGGTAGTAACCATATGTCA
1 GTCAAATCAGAATAAGAA-AATCTGACTAGGGTGGTAACCATATGTCA
3644716 GACTAAAATA
Statistics
Matches: 109, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
87 4 0.04
88 102 0.94
89 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (87 bp):
GTCAAATCAGAATAAGAAAATCTGACTAGGGTGGTAACCATATGTCAAATCAAAAGGAAAAGAAT
CTAACTAGGGTGGTAACCGTAC
Found at i:3659017 original size:22 final size:22
Alignment explanation
Indices: 3658989--3659043 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3658979 TTACTTCGAA
**
3658989 TGCTGCTGCTTGCTGGTGTTGC
1 TGCTGCTGCTTGCTGACGTTGC
*
3659011 TGCTGCTTG-TTGTTGACGTTGC
1 TGCTGC-TGCTTGCTGACGTTGC
*
3659033 TGCTGGTGCTT
1 TGCTGCTGCTT
3659044 TTGTTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.02, C:0.20, G:0.35, T:0.44
Consensus pattern (22 bp):
TGCTGCTGCTTGCTGACGTTGC
Found at i:3659075 original size:20 final size:19
Alignment explanation
Indices: 3659045--3659104 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
3659035 CTGGTGCTTT
*
3659045 TGTTTTTTTCTTCGCTTGC
1 TGTTTTCTTCTTCGCTTGC
3659064 TGCTTTTCTTCTTTC-CTTGC
1 TG-TTTTCTTC-TTCGCTTGC
* *
3659084 TGTTTGCTTGCTTTGCTTGC
1 TGTTTTCTT-CTTCGCTTGC
3659104 T
1 T
3659105 ATTTCGATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 10 0.29
20 21 0.62
21 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.17, T:0.60
Consensus pattern (19 bp):
TGTTTTCTTCTTCGCTTGC
Found at i:3659458 original size:28 final size:31
Alignment explanation
Indices: 3659425--3659516 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 31
3659415 TGTTGGTGTC
* * *
3659425 TTCATTGCAGCAGCTGTTTCTT-TT-T-TTT
1 TTCATTGCAGCATCAGTTTCTTCTTGTCGTT
* *
3659453 TTCATTGCAACATCGGTTTCTTCTTGTCGTT
1 TTCATTGCAGCATCAGTTTCTTCTTGTCGTT
*
3659484 TTCATTGCAGCATCAGTTTCTTCTTGTTGTT
1 TTCATTGCAGCATCAGTTTCTTCTTGTCGTT
3659515 TT
1 TT
3659517 GCTGCAGCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 19 0.35
29 2 0.04
30 1 0.02
31 32 0.59
ACGTcount: A:0.12, C:0.20, G:0.15, T:0.53
Consensus pattern (31 bp):
TTCATTGCAGCATCAGTTTCTTCTTGTCGTT
Found at i:3659739 original size:3 final size:3
Alignment explanation
Indices: 3659733--3659773 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3659723 TTTTTTTAAT
3659733 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3659774 TATTTAATTT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3663166 original size:20 final size:20
Alignment explanation
Indices: 3663143--3663180 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3663133 TGAAGTTGGA
*
3663143 AGCTAACTAGATTAGTTTTC
1 AGCTAACTAGACTAGTTTTC
3663163 AGCTAACTAGACTAGTTT
1 AGCTAACTAGACTAGTTT
3663181 CTAACAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
AGCTAACTAGACTAGTTTTC
Found at i:3665201 original size:72 final size:72
Alignment explanation
Indices: 3665084--3665228 Score: 218
Period size: 72 Copynumber: 2.0 Consensus size: 72
3665074 AGAAATTATG
* * * * * *
3665084 AAAATGCCTCTATGGATATACCTTCGACATGAAAGTATCCTGATAACTTTAAAGGATTTAAAAAG
1 AAAATGCCCCTATAGATATACCTTCAACATAAAAGTATCCTGATAACCTTAAAGGACTTAAAAAG
3665149 GTTCTAA
66 GTTCTAA
**
3665156 AAAATGCCCCTATAGATATACCTTCAACATAAAAGTATTTTGATAACCTTAAAGGACTTAAAAAG
1 AAAATGCCCCTATAGATATACCTTCAACATAAAAGTATCCTGATAACCTTAAAGGACTTAAAAAG
3665221 GTTCTAA
66 GTTCTAA
3665228 A
1 A
3665229 TATACCTTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (72 bp):
AAAATGCCCCTATAGATATACCTTCAACATAAAAGTATCCTGATAACCTTAAAGGACTTAAAAAG
GTTCTAA
Found at i:3665582 original size:155 final size:156
Alignment explanation
Indices: 3665257--3665664 Score: 360
Period size: 155 Copynumber: 2.6 Consensus size: 156
3665247 GCGGACTCAG
* * * * * * * * * * *
3665257 TGACAACTTAGGAGTTGGTTCTAAAAAATTATGAACAT-GCCCGAAGGATATACCTTCGACATAA
1 TGACAACCTAGGAGTTAGTTCTGAAAAATTACGAAAATACCCCTAAAGA-ATATCTTCAACGT-A
** * * * *
3665321 AAAGTACTCGACACCCCTAAAGGACTTCAA-AAGGATTTTAAATGGGATGAACCTATCCTAAATA
64 AAAGTACTTAATACCCCTAAAGGACTTAAAGAATGATTTTAAATAGGATGAACCTATCCTAAATA
*
3665385 CCTAGCTTTAGCATAAAAGTGAACCCCA
129 CCCAGCTTTAGCATAAAAGTGAACCCCA
** * *
3665413 TGACAACCTAGGAGTTAGTTCTGAAAAATTACGAAAATGTCCCTAAAGGATA-CTTTCAACGTTA
1 TGACAACCTAGGAGTTAGTTCTGAAAAATTACGAAAATACCCCTAAAGAATATC-TTCAACGTAA
* * *
3665477 AAGTA-TCTAATACCCCTAAAAGACTT-AAGAATGATTTTAACTAGGATGAACCTATCTTAAATA
65 AAGTACT-TAATACCCCTAAAGGACTTAAAGAATGATTTTAAATAGGATGAACCTATCCTAAATA
* * * ***
3665540 CCCA-CTTTCGACATAAAATTGGACCTGG
129 CCCAGCTTTAG-CATAAAAGTGAACCCCA
*** * * * * * *
3665568 TGGTGACCTCGGAGTTGGTTTTGGAAAATTATGAAAATACCCCTAAAGAATATCTTCGACGTAAA
1 TGACAACCTAGGAGTTAGTTCTGAAAAATTACGAAAATACCCCTAAAGAATATCTTCAACGTAAA
*
3665633 AGTACTTGATACCCCTAAAGGACTTAAAGAAT
66 AGTACTTAATACCCCTAAAGGACTTAAAGAAT
3665665 AAAAACAAAC
Statistics
Matches: 202, Mismatches: 42, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
154 8 0.04
155 138 0.68
156 50 0.25
157 6 0.03
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (156 bp):
TGACAACCTAGGAGTTAGTTCTGAAAAATTACGAAAATACCCCTAAAGAATATCTTCAACGTAAA
AGTACTTAATACCCCTAAAGGACTTAAAGAATGATTTTAAATAGGATGAACCTATCCTAAATACC
CAGCTTTAGCATAAAAGTGAACCCCA
Found at i:3666202 original size:3 final size:3
Alignment explanation
Indices: 3666194--3666237 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3666184 CTAATTTCAT
3666194 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3666238 TAAAATACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3667132 original size:20 final size:20
Alignment explanation
Indices: 3667107--3667147 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3667097 AAGCTCTAGC
3667107 TATTTTT-CTATTTTCTTCTT
1 TATTTTTCCTATTTT-TTCTT
*
3667127 TATTTTTCCTCTTTTTTCTT
1 TATTTTTCCTATTTTTTCTT
3667147 T
1 T
3667148 CCTTTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTCCTATTTTTTCTT
Found at i:3667153 original size:11 final size:11
Alignment explanation
Indices: 3667139--3667168 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
3667129 TTTTTCCTCT
3667139 TTTTTCTTTCC
1 TTTTTCTTTCC
3667150 TTTTTCTTTCC
1 TTTTTCTTTCC
3667161 TTTTTCTT
1 TTTTTCTT
3667169 CTCTCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTCC
Found at i:3669063 original size:84 final size:81
Alignment explanation
Indices: 3668860--3669107 Score: 277
Period size: 84 Copynumber: 3.0 Consensus size: 81
3668850 TTGACAGGTA
* * * *
3668860 AACAATGGATGAAAGGTTGACTAGGGCTGAATCGATAAGTCAACAAAGGGT-AAGGAGTTTACCA
1 AACAAGGGATAAAAGGTTGACTAGGGCTAAAT-GATAAGTCAACAAA-GGTAAAAGAGTTTACCA
* * *
3668924 AGGATTAAGCTATCAAGT
64 GGGATTGAGCTAACAAGT
* *
3668942 AA-ATAGAGATGAAAA-GTTGACTAGGGCTAAACTGATAAGTCAACAAAGGATAAAAGAGTTCAC
1 AACA-AGGGAT-AAAAGGTTGACTAGGGCTAAA-TGATAAGTCAACAAAGG-TAAAAGAGTTTAC
*
3669005 CAGGGACTGAGCTAACAAGT
62 CAGGGATTGAGCTAACAAGT
* *
3669025 AAGCAAGGGATAAAAGGTTGACTAGGGCTAAAGTGATAAGTCAATAAAAGGCAAAAGAGTTTACC
1 AA-CAAGGGATAAAAGGTTGACTAGGGCTAAA-TGATAAGTCAA-CAAAGGTAAAAGAGTTTACC
*
3669090 AGGGATTGAGCTGACAAG
63 AGGGATTGAGCTAACAAG
3669108 CAAATGGGGA
Statistics
Matches: 140, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
81 3 0.02
82 36 0.26
83 35 0.25
84 60 0.43
85 6 0.04
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (81 bp):
AACAAGGGATAAAAGGTTGACTAGGGCTAAATGATAAGTCAACAAAGGTAAAAGAGTTTACCAGG
GATTGAGCTAACAAGT
Found at i:3669423 original size:44 final size:43
Alignment explanation
Indices: 3669329--3669818 Score: 334
Period size: 44 Copynumber: 11.2 Consensus size: 43
3669319 ATAAGAAACA
* * * * *
3669329 TTTGTCTAGAGTGGTAATCATACGTTAAATGGGAATGAAAA-AGG
1 TTTGACTAGGGTGGTAACCATACGTCAAAT-AGAATGAAAAGA-G
* * * *
3669373 CTTGACTAGGGTGGTAACCACACGTCAAGTAGGAATGAAAGGAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATA-GAATGAAAAGAG
* * * * * *
3669417 TCTGACTA-GG-GGTATCCATATGTC-AATCCGACTTAAAAAGAG
1 TTTGACTAGGGTGGTAACCATACGTCAAAT-AGA-ATGAAAAGAG
* * * * **
3669459 TCTGACCAGGGTGGTAACCATACGTCAAACGAAAAATGAGGTAGA-
1 TTTGACTAGGGTGGTAACCATACGTCAAA--TAGAATGA-AAAGAG
* *
3669504 TTTGACTAGGGTGGTAACCATACGTCAAATTAGAATGAAAATAA
1 TTTGACTAGGGTGGTAACCATACGTCAAA-TAGAATGAAAAGAG
* * * *
3669548 TTTGACTAAGGTGGTAACCATACATCAAATCAAAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAAT-AGAATGAAAAGAG
* * * *
3669592 TCTGACCAGGGTGGTAACCATACGTCAAATCAAAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAAT-AGAATGAAAAGAG
* * * *
3669636 TTTGACAAGGGTGGTAACCATA--T-AGATCGAAATGAGAAGAG
1 TTTGACTAGGGTGGTAACCATACGTCAAATAG-AATGAAAAGAG
* * * **
3669677 TTTGACCAGGGTGGTAACCTTACGTCAAATAGGAAGGAGGCAGA-
1 TTTGACTAGGGTGGTAACCATACGTCAAATA-GAATGA-AAAGAG
* * *
3669721 TTTGACCAGGGTGGTAACCATTCGTCAAATTAGAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTCAAA-TAGAATGAAAAGAG
* ** *
3669765 TCTGACTAGGGTGGTAACCATACGTCAGACCAAAATGAGAAA-AG
1 TTTGACTAGGGTGGTAACCATACGTCA-AATAGAATGA-AAAGAG
3669809 TTTGACTAGG
1 TTTGACTAGG
3669819 TCCTAATGTC
Statistics
Matches: 353, Mismatches: 71, Indels: 44
0.75 0.15 0.09
Matches are distributed among these distances:
41 36 0.10
42 26 0.07
43 11 0.03
44 233 0.66
45 43 0.12
46 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (43 bp):
TTTGACTAGGGTGGTAACCATACGTCAAATAGAATGAAAAGAG
Found at i:3670206 original size:88 final size:87
Alignment explanation
Indices: 3670020--3670334 Score: 302
Period size: 88 Copynumber: 3.6 Consensus size: 87
3670010 TGGTCATGTA
* ** * * * *
3670020 ATGCATCAATACCATCTAGTGGCTAAAAAAAGGAGATATGATTAGGAATG-AGTGGTCGGGATAT
1 ATGCATCAATACCATCTAGTGG-TTAATGAAGGGGATATGATT-GGAATGTAGAGGT--TG-CA-
* *
3670084 CCTTGCCCCAAGGAAATCTGATTTTGTG
60 CCTTACCCCAAGGAAATCTGGTTTTGTG
* *
3670112 ATGCATCAATACCATTTAGTGGTTGAATGAAGGGGATATGATTGGAATGT-GTCGGTTGCACCTT
1 ATGCATCAATACCATCTAGTGGTT-AATGAAGGGGATATGATTGGAATGTAG-AGGTTGCACCTT
* *
3670176 ACCTCAAGGAAATCTGGCTTTGTG
64 ACCCCAAGGAAATCTGGTTTTGTG
* * * *
3670200 ATGCATCAATACCATCTAATGG-T--T-AAGGGGATATGATAGGGAATTTAGAGGTTGCACCTTG
1 ATGCATCAATACCATCTAGTGGTTAATGAAGGGGATATGAT-TGGAATGTAGAGGTTGCACCTTA
**
3670261 CCCCAAGGAAATCCAGTTTTGTG
65 CCCCAAGGAAATCTGGTTTTGTG
*
3670284 ATGCATCAATACCATCTAGTGATTAAGTG-AGGGGATATGATTGGGAATGTA
1 ATGCATCAATACCATCTAGTGGTTAA-TGAAGGGGATATGATT-GGAATGTA
3670335 TGGTTTCCAC
Statistics
Matches: 186, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
83 13 0.07
84 57 0.31
85 2 0.01
87 1 0.01
88 64 0.34
89 1 0.01
90 1 0.01
91 8 0.04
92 39 0.21
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (87 bp):
ATGCATCAATACCATCTAGTGGTTAATGAAGGGGATATGATTGGAATGTAGAGGTTGCACCTTAC
CCCAAGGAAATCTGGTTTTGTG
Found at i:3670282 original size:84 final size:83
Alignment explanation
Indices: 3670084--3670333 Score: 261
Period size: 84 Copynumber: 2.9 Consensus size: 83
3670074 GTCGGGATAT
* *
3670084 CCTTGCCCCAAGGAAAT-CTGATTTTGTGATGCATCAATACCATTTAGTGGTTGAATGAAGGGGA
1 CCTTGCCCCAAGGAAATCCAG-TTTTGTGATGCATCAATACCATCTAGTGG-T---T-AAGGGGA
* *
3670148 TATGATTGGAATGTGTCGGTTGCA
60 TATGATGGGAATGTGTAGGTTGCA
* * ** * *
3670172 CCTTACCTCAAGGAAATCTGGCTTTGTGATGCATCAATACCATCTAATGGTTAAGGGGATATGAT
1 CCTTGCCCCAAGGAAATCCAGTTTTGTGATGCATCAATACCATCTAGTGGTTAAGGGGATATGAT
*
3670237 AGGGAATTTAG-AGGTTGCA
66 -GGGAATGT-GTAGGTTGCA
*
3670256 CCTTGCCCCAAGGAAATCCAGTTTTGTGATGCATCAATACCATCTAGTGATTAAGTGAGGGGATA
1 CCTTGCCCCAAGGAAATCCAGTTTTGTGATGCATCAATACCATCTAGTGGTT-A---AGGGGATA
3670321 TGATTGGGAATGT
62 TGA-TGGGAATGT
3670334 ATGGTTTCCA
Statistics
Matches: 136, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
83 13 0.10
84 59 0.43
85 2 0.01
87 1 0.01
88 59 0.43
89 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (83 bp):
CCTTGCCCCAAGGAAATCCAGTTTTGTGATGCATCAATACCATCTAGTGGTTAAGGGGATATGAT
GGGAATGTGTAGGTTGCA
Found at i:3673209 original size:21 final size:20
Alignment explanation
Indices: 3673185--3673228 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3673175 GAATTTTCCC
**
3673185 TTTTTCTTTGTTTCTTTTTGT
1 TTTTTCTTTCCTTCTTTTT-T
*
3673206 TTTTTTTTTCCTTCTTTTTT
1 TTTTTCTTTCCTTCTTTTTT
3673226 TTT
1 TTT
3673229 GGTTGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (20 bp):
TTTTTCTTTCCTTCTTTTTT
Found at i:3676562 original size:155 final size:153
Alignment explanation
Indices: 3676345--3676824 Score: 517
Period size: 155 Copynumber: 3.2 Consensus size: 153
3676335 CTTCTACATG
* * * ** * *
3676345 AAAGTATCTTGATAACCTTAAAGGACTTAAAAAGG-TTATAGTTGGGATGAACCTATCTTAAATA
1 AAAGTA-CCTGATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATGAAACTATCCTAAATA
* *
3676409 CCCATTTTCGGCATAAAAGCAGACTCAGTGACGACCTAAGAGTTGGTTTTAGAAAATTATGAAAA
65 CCCA-TTTCGGCATAAAAGCAGACTCGGTGACGACCTAAGAGTTGGTTTTA-AAAATTATAAAAA
3676474 TGCCTTTAGAGGATACCTTCGATGTA
128 TGCCTTTAGAGGATACCTTCGATGTA
*
3676500 AAAGTACCCGATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATGAAACTATCCTAAATAC
1 AAAGTACCTGATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATGAAACTATCCTAAATAC
* * * *
3676565 CCATCTTCGGCATAAAAGCGGACTCGGTTACGACCTAGGAGTTGGTTCTAAAAAATTATAAAAAT
66 CCAT-TTCGGCATAAAAGCAGACTCGGTGACGACCTAAGAGTTGGTT-TTAAAAATTATAAAAAT
* ** *
3676630 GCCTCT--A-G--ACCTTCGACATG
129 GCCTTTAGAGGATACCTTCGATGTA
* * *
3676650 AAAGTACCTAATACCCTTGAAGGACTTAAAAAGGATTTTAAATGGGATGAGAA-TA--CT---GA
1 AAAGTACCTGATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATGA-AACTATCCTAAATA
* * * *
3676709 -CC--TTCGACATAAAATCAGACTCGGTGATGACCTAAGAGTTAGTTTTAAAAATTATAAAAATG
65 CCCATTTCGGCATAAAAGCAGACTCGGTGACGACCTAAGAGTTGGTTTTAAAAATTATAAAAATG
* *
3676771 -CTCTTAGGGGATACCTTCAATGTA
130 CCT-TTAGAGGATACCTTCGATGTA
*
3676795 AAAGTACCTGATA-CCTCTATAGGACTTAAA
1 AAAGTACCTGATACCCT-TAAAGGACTTAAA
3676825 GGATAAATCG
Statistics
Matches: 275, Mismatches: 39, Indels: 32
0.79 0.11 0.09
Matches are distributed among these distances:
139 2 0.01
140 18 0.07
141 35 0.13
143 1 0.00
144 5 0.02
145 32 0.12
148 2 0.01
150 58 0.21
151 2 0.01
152 1 0.00
153 1 0.00
154 26 0.09
155 90 0.33
156 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (153 bp):
AAAGTACCTGATACCCTTAAAGGACTTAAAAAGGATTTTAAATGGGATGAAACTATCCTAAATAC
CCATTTCGGCATAAAAGCAGACTCGGTGACGACCTAAGAGTTGGTTTTAAAAATTATAAAAATGC
CTTTAGAGGATACCTTCGATGTA
Found at i:3678369 original size:19 final size:18
Alignment explanation
Indices: 3678340--3678387 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
3678330 TAGTTTTCTA
3678340 TTTTCTTCTTTATTTTTCCTC
1 TTTTC-TCTTTATTTTT--TC
3678361 TTTTC-CTTTATTTTTTC
1 TTTTCTCTTTATTTTTTC
3678378 TTTTCTCTTT
1 TTTTCTCTTT
3678388 TCTCTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 10 0.38
21 5 0.19
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTCTCTTTATTTTTTC
Found at i:3678400 original size:25 final size:25
Alignment explanation
Indices: 3678353--3678402 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3678343 TCTTCTTTAT
* *
3678353 TTTTCCTCTTTTCCTTTATTTTTTC
1 TTTTCCTCTTTTCCTCTAATTTTTC
3678378 TTTT-CTCTTTTCTCTCTAATTTTTC
1 TTTTCCTCTTTTC-CTCTAATTTTTC
3678403 CTACTAGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTCCTCTTTTCCTCTAATTTTTC
Found at i:3679065 original size:19 final size:21
Alignment explanation
Indices: 3679037--3679078 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3679027 TCCGTATTTT
*
3679037 AAAAATAATG-AAATTTCAAG
1 AAAAATAATGAAAAATTCAAG
3679057 AAAAA-AATGAAAAATTCAAG
1 AAAAATAATGAAAAATTCAAG
3679077 AA
1 AA
3679079 CGTGAATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAAATAATGAAAAATTCAAG
Found at i:3679117 original size:166 final size:165
Alignment explanation
Indices: 3678757--3679558 Score: 841
Period size: 166 Copynumber: 4.9 Consensus size: 165
3678747 TGAAATAATT
* * * **
3678757 TGAATTTTTCAAAACTG-ATTAATATGAATTTAATAACAATATTAGATGAATTTT-AAAATTAAA
1 TGAATTTTTGAAAA-TGAATTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAA
* * *
3678820 AACCAAGAAAAATCCTCC-AAAAATATTTACGAAGTAGAAAACTCCATATTTCGAAAAT-AGGAG
65 AACCAAGAAAAATCC-CCTAAAAATATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAATGAG
* * *
3678883 AATTTCAAAGAAAAAT-AAAAAATGAATGAAAATGAA
129 AATTTCAAAAAAAAATGAAAAATTCAATGAAAATGAA
* *
3678919 TGAATTTTT-AATAACTGACTTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATAAA
1 TGAATTTTTGAA-AA-TGAATTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAA
* * * *
3678983 AAACCAAGAAAAATCTCCCTAAAAACATTTATGGAGTAGAAAACTCCGTATTTTAAAAATAATGA
64 AAACCAAGAAAAATC-CCCTAAAAATATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAATGA
**
3679048 -AATTTCAAGAAAAAAATGAAAAATTCAA-GAACGTGAA
128 GAATTTCAA-AAAAAAATGAAAAATTCAATGAAAATGAA
*
3679085 TGAATTTTTGAAAATGAATTCAATATGAATTAAATAATGATATTTTATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAATGAATT-AATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAA
* * * * *
3679150 AACCAAAAAAAAATCCCCTTAAAATATTGACGAAGTAGAAAACTCCGTATTTCGAAAATAGT-AG
65 AACC-AAGAAAAATCCCCTAAAAATATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAATGAG
*
3679214 AATTTC-AAAAAAAATGAAACATTC-ATGAAAATGAA
129 AATTTCAAAAAAAAATGAAAAATTCAATGAAAATGAA
* * * *
3679249 T-AATTTTTTTAAATTGATTTAATATGAATTAAATCATAATA-TTTATGAATTTTAAAAATTAAA
1 TGAA-TTTTTGAAAATGAATTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAA
* * * * * * *
3679312 CACTAAGAAAAATCCCCCTGAAAATATTTACGGAGTAGAAAACTCCGTATTTTAGAAA-CA-GAA
65 AACCAAGAAAAAT-CCCCTAAAAATATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAATG-A
* * *
3679375 GAATTTCAAGGAAAAAATGAAAAA-TGAATGAAAATGAG
128 GAATTTCAA-AAAAAAATGAAAAATTCAATGAAAATGAA
* * * * *
3679413 TGCATTGTTGCAAACT-AATTTAATATGAATTAAATAATAACATTTTATGTATTTTAAAAATTAA
1 TGAATTTTTG-AAAATGAA-TTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAA
* * * * * *
3679477 AAATCCAA-AAAAATCCTCTCGAAAATATTTACGAAGTAGAAAATTTCATATTTCGAAAA-AATG
64 AAA-CCAAGAAAAATCCCCT-AAAAATATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAAT-
* *
3679540 GAGAATTTTAAAAGAAAAT
126 GAGAATTTCAAAAAAAAAT
3679559 CAATAACTCA
Statistics
Matches: 537, Mismatches: 75, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
161 10 0.02
162 84 0.16
163 56 0.10
164 89 0.17
165 80 0.15
166 186 0.35
167 31 0.06
168 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.30
Consensus pattern (165 bp):
TGAATTTTTGAAAATGAATTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAA
ACCAAGAAAAATCCCCTAAAAATATTTACGAAGTAGAAAACTCCGTATTTCAAAAATAATGAGAA
TTTCAAAAAAAAATGAAAAATTCAATGAAAATGAA
Found at i:3679354 original size:328 final size:328
Alignment explanation
Indices: 3678757--3679558 Score: 1005
Period size: 328 Copynumber: 2.4 Consensus size: 328
3678747 TGAAATAATT
* * * **
3678757 TGAATTTTTCAAAACTG-ATTAATATGAATTTAATAACAATATTAGATGAATTTT-AAAATTAAA
1 TGAATTTTTGAAAA-TGAATTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAA
*
3678820 AACCAAGAAAAATCCTCC-AAAAATATTTACGAAGTAGAAAACTCCATATTTCGAAAATAGGAGA
65 AACCAAAAAAAATCC-CCTAAAAATATTTACGAAGTAGAAAACTCCATATTTCGAAAATAGGAGA
3678884 ATTTCAAAGAAAAATAAAAAATGAATGAAAATGAATGAATTTTTAATAACTGACTTAATATGAAT
129 ATTTCAAA-AAAAATAAAAAATGAATGAAAATGAATGAATTTTTAATAACTGACTTAATATGAAT
*
3678949 TAAATAATAATATTTTATGAATTTTAAAAATAAAAAACCAAGAAAAATCTCCCTAAAAACATTTA
193 TAAATAATAATATTTTATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCTAAAAACATTTA
* *
3679014 TGGAGTAGAAAACTCCGTATTTTA-AAA-ATAATGAAATTTCAAGAAAAAAATGAAAAATTCAA-
258 CGGAGTAGAAAACTCCGTATTTTAGAAACAGAA-G-AATTTCAAGAAAAAAATGAAAAA-TCAAT
**
3679076 GAACGTGAA
320 GAAAATGAA
*
3679085 TGAATTTTTGAAAATGAATTCAATATGAATTAAATAATGATATTTTATGAATTTTAAAAATTAAA
1 TGAATTTTTGAAAATGAATT-AATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAA
* * * *
3679150 AACCAAAAAAAAATCCCCTTAAAATATTGACGAAGTAGAAAACTCCGTATTTCGAAAATAGTAGA
65 AACC-AAAAAAAATCCCCTAAAAATATTTACGAAGTAGAAAACTCCATATTTCGAAAATAGGAGA
* * ** * * *
3679215 ATTTCAAAAAAAATGAAACATTCATGAAAATGAAT-AATTTTT-TTAAATTGATTTAATATGAAT
129 ATTTCAAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTAAT-AACTGACTTAATATGAAT
* * * * * *
3679278 TAAATCATAATA-TTTATGAATTTTAAAAATTAAACACTAAGAAAAATCCCCCTGAAAATATTTA
193 TAAATAATAATATTTTATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCTAAAAACATTTA
* *
3679342 CGGAGTAGAAAACTCCGTATTTTAGAAACAGAAGAATTTCAAGGAAAAAATGAAAAATGAATGAA
258 CGGAGTAGAAAACTCCGTATTTTAGAAACAGAAGAATTTCAAGAAAAAAATGAAAAATCAATGAA
*
3679407 AATGAG
323 AATGAA
* * * * *
3679413 TGCATTGTTGCAAACT-AATTTAATATGAATTAAATAATAACATTTTATGTATTTTAAAAATTAA
1 TGAATTTTTG-AAAATGAA-TTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAA
* * * * *
3679477 AAATCC-AAAAAAATCCTCTCGAAAATATTTACGAAGTAGAAAATTTCATATTTCGAAAAAATGG
64 AAA-CCAAAAAAAATCCCCT-AAAAATATTTACGAAGTAGAAAACTCCATATTTCGAAAATA-GG
*
3679541 AGAATTTTAAAAGAAAAT
126 AGAATTTCAAAA-AAAAT
3679559 CAATAACTCA
Statistics
Matches: 412, Mismatches: 47, Indels: 28
0.85 0.10 0.06
Matches are distributed among these distances:
327 17 0.04
328 202 0.49
329 87 0.21
330 46 0.11
331 60 0.15
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.30
Consensus pattern (328 bp):
TGAATTTTTGAAAATGAATTAATATGAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAA
ACCAAAAAAAATCCCCTAAAAATATTTACGAAGTAGAAAACTCCATATTTCGAAAATAGGAGAAT
TTCAAAAAAAATAAAAAATGAATGAAAATGAATGAATTTTTAATAACTGACTTAATATGAATTAA
ATAATAATATTTTATGAATTTTAAAAATAAAAAACCAAGAAAAATCCCCCTAAAAACATTTACGG
AGTAGAAAACTCCGTATTTTAGAAACAGAAGAATTTCAAGAAAAAAATGAAAAATCAATGAAAAT
GAA
Found at i:3680985 original size:42 final size:40
Alignment explanation
Indices: 3680938--3681162 Score: 159
Period size: 42 Copynumber: 5.3 Consensus size: 40
3680928 ACAGGTAAAT
*
3680938 AAAGGATAAAAAGGTTGATCAGGATTAAACTAACAAGTCAAC
1 AAAGGAT-AAAAGGTTGA-CAGGATTAAACTGACAAGTCAAC
** * * *
3680980 AAAGGATAAAAAGAGTT-ACCTGATACTAAACTAACAGGTAAAC
1 AAAGGAT-AAAAG-GTTGACAGGAT--TAAACTGACAAGTCAAC
* *
3681023 AAGGGATAAAAGAGTTGATCAGGATTAAACTGACAAATCAAC
1 AAAGGATAAAAG-GTTGA-CAGGATTAAACTGACAAGTCAAC
* * * *
3681065 -AAGAGATAAAAGGATTTACCCGAGG-CTAAGCTGACAAGTAAAC
1 AAAG-GATAAAAGG-TTGA--C-AGGATTAAACTGACAAGTCAAC
* * *
3681108 AAAAGATAAAAGGATTGACTAGGATTGAATTGACAAGTCAAC
1 AAAGGATAAAAGG-TTGAC-AGGATTAAACTGACAAGTCAAC
3681150 AAAGGATAAAAGG
1 AAAGGATAAAAGG
3681163 ATTTACTTGA
Statistics
Matches: 145, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
41 11 0.08
42 72 0.50
43 53 0.37
44 9 0.06
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (40 bp):
AAAGGATAAAAGGTTGACAGGATTAAACTGACAAGTCAAC
Found at i:3681201 original size:43 final size:43
Alignment explanation
Indices: 3680887--3681203 Score: 168
Period size: 43 Copynumber: 7.4 Consensus size: 43
3680877 TTGAACCGAT
* ** * * * *
3680887 AAGTCAACAAAGGATAAAAAAAGTTACTTGGGACTAAGCCGAC
1 AAGTAAACAAAGGATAAAAGGATTTACTAGAGACTAAGCTGAC
* * * * * *
3680930 AGGTAAATAAAGGATAAAAAGG-TTGA-TCAG-GATTAAACTAAC
1 AAGTAAACAAAGGAT-AAAAGGATTTACT-AGAGACTAAGCTGAC
* * * * * *
3680972 AAGTCAACAAAGGATAAAAAGAGTTACCT-GATACTAAACTAAC
1 AAGTAAACAAAGGATAAAAGGATTTA-CTAGAGACTAAGCTGAC
* * * * *
3681015 AGGTAAACAAGGGATAAAA-GAGTTGA-TCAG-GATTAAACTGAC
1 AAGTAAACAAAGGATAAAAGGA-TTTACT-AGAGACTAAGCTGAC
* * ** *
3681057 AAATCAAC-AAGAGATAAAAGGATTTACCCGAGGCTAAGCTGAC
1 AAGTAAACAAAG-GATAAAAGGATTTACTAGAGACTAAGCTGAC
* * * *
3681100 AAGTAAACAAAAGATAAAAGGATTGACTAG-GATTGAA-TTGAC
1 AAGTAAACAAAGGATAAAAGGATTTACTAGAGACT-AAGCTGAC
* * *
3681142 AAGTCAACAAAGGATAAAAGGATTTACTTGAGACTAAGCTGAT
1 AAGTAAACAAAGGATAAAAGGATTTACTAGAGACTAAGCTGAC
*
3681185 AGGTAAACAAAGGATAAAA
1 AAGTAAACAAAGGATAAAA
3681204 AGGTTGACTG
Statistics
Matches: 201, Mismatches: 56, Indels: 34
0.69 0.19 0.12
Matches are distributed among these distances:
41 8 0.04
42 85 0.42
43 101 0.50
44 7 0.03
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (43 bp):
AAGTAAACAAAGGATAAAAGGATTTACTAGAGACTAAGCTGAC
Found at i:3681231 original size:85 final size:84
Alignment explanation
Indices: 3680740--3681210 Score: 387
Period size: 85 Copynumber: 5.5 Consensus size: 84
3680730 ATGAAAAGGG
* ** * * * * *
3680740 TTACTTGAGACTAAGTTGGTAGGTAGATAAAGGATACAAAGGTTGATCGGGGTTAAACCAACAA-
1 TTACTTGAGACTAAGCTGACAGGTAAACAAAGGATA-AAAGGTTGATCAGGATTAAACCGACAAG
*
3680804 TCCAATAAAGGATAAAAAGAT
65 T-CAACAAAGGATAAAAAGAT
* * * * * * * * * *
3680825 TTACTTGGGACTAAG-TCGATAAGTAAATAAGGGATGAAAGAGTT-AAC-CGATTTTGAACCGAT
1 TTACTTGAGACTAAGCT-GACAGGTAAACAAAGGATAAAAG-GTTGATCAGGA--TTAAACCGAC
* *
3680887 AAGTCAACAAAGGATAAAAAAAG
62 AAGTCAACAAAGGATAAAAAGAT
* * * **
3680910 TTACTTGGGACTAAGCCGACAGGTAAATAAAGGATAAAAAGGTTGATCAGGATTAAACTAACAAG
1 TTACTTGAGACTAAGCTGACAGGTAAACAAAGGAT-AAAAGGTTGATCAGGATTAAACCGACAAG
*
3680975 TCAACAAAGGATAAAAAGAG
65 TCAACAAAGGATAAAAAGAT
* * * * * * *
3680995 TTACCTGATACTAAACTAACAGGTAAACAAGGGATAAAAGAGTTGATCAGGATTAAACTGACAAA
1 TTACTTGAGACTAAGCTGACAGGTAAACAAAGGATAAAAG-GTTGATCAGGATTAAACCGACAAG
*
3681060 TCAAC-AAGAGATAAAAGGAT
65 TCAACAAAG-GATAAAAAGAT
** * * * * **
3681080 TTACCCGAGGCTAAGCTGACAAGTAAACAAAAGATAAAAGGATTGA-CTAGGATTGAATTGACAA
1 TTACTTGAGACTAAGCTGACAGGTAAACAAAGGATAAAAGG-TTGATC-AGGATTAAACCGACAA
*
3681144 GTCAACAAAGGATAAAAGGAT
64 GTCAACAAAGGATAAAAAGAT
*
3681165 TTACTTGAGACTAAGCTGATAGGTAAACAAAGGATAAAAAGGTTGA
1 TTACTTGAGACTAAGCTGACAGGTAAACAAAGGAT-AAAAGGTTGA
3681211 CTGGGAATGA
Statistics
Matches: 315, Mismatches: 56, Indels: 30
0.79 0.14 0.07
Matches are distributed among these distances:
83 1 0.00
84 17 0.05
85 279 0.89
86 16 0.05
87 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.21
Consensus pattern (84 bp):
TTACTTGAGACTAAGCTGACAGGTAAACAAAGGATAAAAGGTTGATCAGGATTAAACCGACAAGT
CAACAAAGGATAAAAAGAT
Found at i:3681304 original size:80 final size:79
Alignment explanation
Indices: 3681220--3681388 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 79
3681210 ACTGGGAATG
* * * * * *
3681220 AACCGATAAGTCGACTAATTAAAAAGTTTTCCAGGGCAAAACTGATAAAGCCAACAGGTTAAA-G
1 AACCGATAAGTCAACCAATT-AAAAGGTTGCCAGGACAAAACTGATAAAGCCAACAGATTAAACG
3681284 GGATTGACCAAGG-CAA
65 GG-TTGA-CAAGGACAA
** *
3681300 AACCGATAAAGTCAACCAATTGGAAGGTTGGCAGGACAAAACTGATAAAGCCAACAGATTAAACG
1 AACCGAT-AAGTCAACCAATTAAAAGGTTGCCAGGACAAAACTGATAAAGCCAACAGATTAAACG
*
3681365 GGTTGACTAGGACAA
65 GGTTGACAAGGACAA
*
3681380 AATCGATAA
1 AACCGATAA
3681389 AGTTAATAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
79 6 0.08
80 55 0.73
81 14 0.19
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (79 bp):
AACCGATAAGTCAACCAATTAAAAGGTTGCCAGGACAAAACTGATAAAGCCAACAGATTAAACGG
GTTGACAAGGACAA
Found at i:3681380 original size:41 final size:39
Alignment explanation
Indices: 3681251--3681390 Score: 126
Period size: 41 Copynumber: 3.5 Consensus size: 39
3681241 AAAAGTTTTC
* *
3681251 CAGGGCAAAACTGATAAAGCCAACAGGTTAAAGGGATTGA
1 CAGGACAAAACTGATAAAGCCAACAGATTAAAGGG-TTGA
* * * *
3681291 CCAAGG-CAAAACCGATAAAGTCAACCA-ATTGGAA-GGTTGG
1 -C-AGGACAAAACTGATAAAGCCAA-CAGATT-AAAGGGTTGA
3681331 CAGGACAAAACTGATAAAGCCAACAGATTAAACGGGTTGA
1 CAGGACAAAACTGATAAAGCCAACAGATTAAA-GGGTTGA
3681371 CTAGGACAAAA-TCGATAAAG
1 C-AGGACAAAACT-GATAAAG
3681391 TTAATAAGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
38 7 0.09
39 20 0.25
40 10 0.12
41 37 0.46
42 7 0.09
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (39 bp):
CAGGACAAAACTGATAAAGCCAACAGATTAAAGGGTTGA
Found at i:3682358 original size:90 final size:91
Alignment explanation
Indices: 3682128--3682731 Score: 684
Period size: 91 Copynumber: 6.6 Consensus size: 91
3682118 TATGGTCACG
* * * *
3682128 TGATGCATCAGTATCATTTAGTGGTTGA--ATAAAAGAGATATGATTAGGAAATATGGTTAGGAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGA-AAAAG-GATATGATTAGGAAATGTGGTTGGGAT
*** * * * ** * *
3682191 ATCCTTGTTACAAGAAAACCAGGCTT-TG
64 ATCCTT-ACCCTAGAGATCTTGGATTATA
* * * * *
3682219 TGATGCA-CCGATATCATCTAGTAGTTGAGGAAGAAGGATATGATTAGGAAATGTGCTTGGGATA
1 TGATGCATCAG-TACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTGGGATA
* * *
3682283 TCCTTGCCTTGGAGATCTTGGATTATA
65 TCCTTACCCTAGAGATCTTGGATTATA
* *
3682310 TGATGCATCA-TACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAACGTGGTTAGGATAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTGGGATAT
*
3682374 CCTTGCCCTAGAGATCTTGGATTATA
66 CCTTACCCTAGAGATCTTGGATTATA
* * *
3682400 TGATGCATCAGTACCATCTAGTGGTTAAGGAAAAAAGATATGATTGGGAAATGTGGTTGGGATAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTGGGATAT
*
3682465 CCTTAACCT-GAAGATCTTGGATTATA
66 CCTTACCCTAG-AGATCTTGGATTATA
* * * *
3682491 TGATGCATCAGTACCATCTAGTGGTTGAGG-AATATGATATGATTGGGAAATGTGTTTGGGATAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTGGGATAT
*
3682555 CCTTACCCTAGAGATCTTGGACTATA
66 CCTTACCCTAGAGATCTTGGATTATA
* * * * *
3682581 TAATGCATCAGTACCATCAAGTGGTTGAGAAAAAAGTATATGATT-GGAAAATGTGTTTGGGATA
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGG-AAATGTGGTTGGGATA
*
3682645 TCCTTACCTTAGAGATCTTGGATTATA
65 TCCTTACCCTAGAGATCTTGGATTATA
* * * * *
3682672 TGATGCATTAATTCCATCTAGTGGTTGAGGAAAAAAGATATGATTAGAAATATGTGGTTG
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAA-ATGTGGTTG
3682732 ATGTTCCTTC
Statistics
Matches: 442, Mismatches: 59, Indels: 23
0.84 0.11 0.04
Matches are distributed among these distances:
90 175 0.40
91 252 0.57
92 14 0.03
93 1 0.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (91 bp):
TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTGGGATAT
CCTTACCCTAGAGATCTTGGATTATA
Found at i:3682452 original size:181 final size:182
Alignment explanation
Indices: 3682128--3682730 Score: 727
Period size: 181 Copynumber: 3.3 Consensus size: 182
3682118 TATGGTCACG
* * *
3682128 TGATGCATCAGTATCATTTAGTGGTTGA--ATAAAAGAGATATGATTAGGAAATATGGTTAGGAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGA-AAAAG-GATATGATTAGGAAATGTGGTTAGGAT
** * * * ** * * * * * *
3682191 ATCCTTGTTACAAGAAAACCAGGCTT-TGTGATGCA-CCGATATCATCTAGTAGTTGAGGAAGAA
64 ATCCTTG-CCCTAGAGATCTTGGATTATATGATGCATCAG-TACCATCTAGTGGTTGAGGAAAAA
* * *
3682254 GGATATGATTAGGAAATGTGCTTGGGATATCCTTGCCTTGGAGATCTTGGATTATA
127 AGATATGATTGGGAAATGTGCTTGGGATATCCTTACCTTGGAGATCTTGGATTATA
*
3682310 TGATGCATCA-TACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAACGTGGTTAGGATAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTAGGATAT
*
3682374 CCTTGCCCTAGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTAAGGAAAAAAGAT
66 CCTTGCCCTAGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAAGAT
* *
3682439 ATGATTGGGAAATGTGGTTGGGATATCCTTAACC-TGAAGATCTTGGATTATA
131 ATGATTGGGAAATGTGCTTGGGATATCCTT-ACCTTGGAGATCTTGGATTATA
* * * * *
3682491 TGATGCATCAGTACCATCTAGTGGTTGAGG-AATATGATATGATTGGGAAATGTGTTTGGGATAT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTAGGATAT
* * * *
3682555 CCTTACCCTAGAGATCTTGGACTATATAATGCATCAGTACCATCAAGTGGTTGA-GAAAAAAGTA
66 CCTTGCCCTAGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAAG-A
* * *
3682619 TATGATTGGAAAATGTGTTTGGGATATCCTTACCTTAGAGATCTTGGATTATA
130 TATGATTGGGAAATGTGCTTGGGATATCCTTACCTTGGAGATCTTGGATTATA
* * * * *
3682672 TGATGCATTAATTCCATCTAGTGGTTGAGGAAAAAAGATATGATTAGAAATATGTGGTT
1 TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAA-ATGTGGTT
3682731 GATGTTCCTT
Statistics
Matches: 365, Mismatches: 46, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
180 21 0.06
181 283 0.78
182 53 0.15
183 8 0.02
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (182 bp):
TGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAGGATATGATTAGGAAATGTGGTTAGGATAT
CCTTGCCCTAGAGATCTTGGATTATATGATGCATCAGTACCATCTAGTGGTTGAGGAAAAAAGAT
ATGATTGGGAAATGTGCTTGGGATATCCTTACCTTGGAGATCTTGGATTATA
Found at i:3690048 original size:13 final size:13
Alignment explanation
Indices: 3690030--3690055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3690020 TACAGCAAGT
3690030 ATGTATCGATACA
1 ATGTATCGATACA
3690043 ATGTATCGATACA
1 ATGTATCGATACA
3690056 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3694602 original size:13 final size:13
Alignment explanation
Indices: 3694584--3694609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3694574 TATAGCAAGT
3694584 ATGTATCGATACA
1 ATGTATCGATACA
3694597 ATGTATCGATACA
1 ATGTATCGATACA
3694610 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3701884 original size:10 final size:10
Alignment explanation
Indices: 3701861--3701895 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3701851 ATCTTTCCTA
*
3701861 TTTTCTTTATT
1 TTTTCTTT-CT
3701872 TTTTCTTTCT
1 TTTTCTTTCT
3701882 TTTTCTTTCT
1 TTTTCTTTCT
3701892 TTTT
1 TTTT
3701896 TTCCCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:3712633 original size:3 final size:3
Alignment explanation
Indices: 3712625--3712650 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3712615 TTGTCTTATT
3712625 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3712651 CCTAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3714268 original size:17 final size:19
Alignment explanation
Indices: 3714243--3714285 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3714233 TTAATATTTA
* *
3714243 AATATATATTTAAAACATC
1 AATATATGTTGAAAACATC
3714262 AATATATGTTGAAAACATC
1 AATATATGTTGAAAACATC
3714281 AATAT
1 AATAT
3714286 TCTTGATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (19 bp):
AATATATGTTGAAAACATC
Found at i:3716222 original size:18 final size:21
Alignment explanation
Indices: 3716196--3716233 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
3716186 TATGTGCTAA
3716196 AAATATTTTA-AT-TTAATAT
1 AAATATTTTACATATTAATAT
3716215 AAAT-TTTTACATATTAATA
1 AAATATTTTACATATTAATA
3716234 CTTTATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATTTTACATATTAATAT
Found at i:3716559 original size:15 final size:16
Alignment explanation
Indices: 3716539--3716572 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3716529 CTATCATATC
3716539 ATTTT-AATTTAAATA
1 ATTTTAAATTTAAATA
*
3716554 ATTTTAAATTTGAATA
1 ATTTTAAATTTAAATA
3716570 ATT
1 ATT
3716573 CTAACCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTTAAATTTAAATA
Found at i:3717066 original size:20 final size:21
Alignment explanation
Indices: 3717028--3717067 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3717018 ATGACATATT
3717028 AAAGTAAATATAACAATAATG
1 AAAGTAAATATAACAATAATG
3717049 AAAGTCAAATA-AAC-ATAAT
1 AAAGT-AAATATAACAATAAT
3717068 AATCACACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAGTAAATATAACAATAATG
Found at i:3717521 original size:20 final size:20
Alignment explanation
Indices: 3717496--3717549 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3717486 GTATCGATAC
**
3717496 AATGTATCGATACATGACTA
1 AATGTATCGATACATGAAAA
*
3717516 AATGTATCGATACTTGAAAA
1 AATGTATCGATACATGAAAA
3717536 AATGTATCGATACA
1 AATGTATCGATACA
3717550 AGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATGAAAA
Found at i:3717619 original size:13 final size:13
Alignment explanation
Indices: 3717601--3717626 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3717591 ACACACAATA
3717601 TGTATCGATACAT
1 TGTATCGATACAT
3717614 TGTATCGATACAT
1 TGTATCGATACAT
3717627 CACAAAATGT
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:3717637 original size:33 final size:32
Alignment explanation
Indices: 3717581--3717648 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
3717571 GTAGCTAAAT
*
3717581 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
3717613 TTGTATCGATACATCACAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
3717646 TTG
1 TTG
3717649 GCTTATAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:3718818 original size:21 final size:20
Alignment explanation
Indices: 3718785--3718824 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3718775 AAAGAGAGCC
3718785 AAAAAAAAGGAAAAAAAGAA
1 AAAAAAAAGGAAAAAAAGAA
*
3718805 AAAAAAAAGAGAAAGAAAGA
1 AAAAAAAAG-GAAAAAAAGA
3718825 GTGATAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGGAAAAAAAGAA
Found at i:3721841 original size:20 final size:20
Alignment explanation
Indices: 3721812--3721849 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3721802 TGAAACTAGT
*
3721812 TAAAAATAAAATAAAAATTC
1 TAAAAATAAAAGAAAAATTC
*
3721832 TAAAATTAAAAGAAAAAT
1 TAAAAATAAAAGAAAAAT
3721850 AAAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAAAATAAAAGAAAAATTC
Found at i:3722041 original size:23 final size:22
Alignment explanation
Indices: 3721985--3722047 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
3721975 TCATAAAATA
3721985 AATGAAATTTTAAAAAATGATTT
1 AATG-AATTTTAAAAAATGATTT
3722008 ACTATGAATTTTAATGAAAAT-ATTT
1 A--ATGAATTTTAA--AAAATGATTT
3722033 AATGAATTTTAAAAA
1 AATGAATTTTAAAAA
3722048 TTTTAAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
21 3 0.08
23 12 0.33
24 8 0.22
25 8 0.22
26 5 0.14
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (22 bp):
AATGAATTTTAAAAAATGATTT
Done.