Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 162 of 204
Found at i:48515150 original size:38 final size:36
Alignment explanation
Indices: 48515091--48515162 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 36
48515081 AGTAGTAGTT
* *
48515091 TTTAAATTTTATAACATTTAATACTTTTTAATAACA
1 TTTAAATTTTATAACATTTAATAATTTCTAATAACA
* *
48515127 TTTATAATTTTCTAATATTTTAATAATTTCTAATAA
1 TTTA-AATTTTATAACA-TTTAATAATTTCTAATAA
48515163 TTTTTAAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 4 0.13
37 10 0.33
38 16 0.53
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (36 bp):
TTTAAATTTTATAACATTTAATAATTTCTAATAACA
Found at i:48519983 original size:41 final size:41
Alignment explanation
Indices: 48519900--48520045 Score: 193
Period size: 41 Copynumber: 3.5 Consensus size: 41
48519890 TTTAACATAT
** *
48519900 TCACCGGCACTTAGCCTGCTAAACTTTATAGCCTGATCCAGA
1 TCACCGGCACTTAGCCTGCT-AGGTTTATAGCCTGATTCAGA
** * *
48519942 TCACCAACACTTAGTCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
* *
48519983 TCACCGGCACTTAGCCTGCTGGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
*
48520024 TCACCGGCACTTAGCCTACTAG
1 TCACCGGCACTTAGCCTGCTAG
48520046 ACTTAAAGTC
Statistics
Matches: 89, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 72 0.81
42 17 0.19
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAGCCTGATTCAGA
Found at i:48520548 original size:110 final size:110
Alignment explanation
Indices: 48520391--48520934 Score: 908
Period size: 110 Copynumber: 4.8 Consensus size: 110
48520381 CACACATTTA
48520391 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
1 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
48520456 ATACAATAGATATACATATATATACATATTCGAACTTCATTTATG
66 ATACAATAGATATACATATATATACATATTCGAACTTCATTTATG
*
48520501 TATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
1 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
48520566 ATACAATAGATATACATATATATATATATATATATACATATTCGAACTTCATTTATG
66 ATACAATAGATATAC------------ATATATATACATATTCGAACTTCATTTATG
48520623 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
1 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
48520688 ATACAATAGATATACATATATATACATATTCGAACTTCATTTATG
66 ATACAATAGATATACATATATATACATATTCGAACTTCATTTATG
* *
48520733 TATATATATAACATTCATACTTAACTAATTTCAATTTATATACTTTTAATTATAGCTCATCAAAT
1 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
48520798 ATACAATAGATATACATATATATGTATACATATTCGAACTTCATTTATG
66 ATACAATAGATATAC--ATATA--TATACATATTCGAACTTCATTTATG
*
48520847 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAACTCATCAAAT
1 CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
48520912 ATACAATAGATATACATATATAT
66 ATACAATAGATATACATATATAT
48520935 GTATATACTG
Statistics
Matches: 411, Mismatches: 7, Indels: 32
0.91 0.02 0.07
Matches are distributed among these distances:
110 190 0.46
112 10 0.02
114 102 0.25
122 109 0.27
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (110 bp):
CATATATATAACATTCATACTTAACTAATTTCAATTCATATACTTTTAATTATAGCTCATCAAAT
ATACAATAGATATACATATATATACATATTCGAACTTCATTTATG
Found at i:48520878 original size:114 final size:114
Alignment explanation
Indices: 48520583--48520939 Score: 641
Period size: 114 Copynumber: 3.2 Consensus size: 114
48520573 AGATATACAT
* *
48520583 ATATATATATATATATATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
1 ATATACATATATATGTATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
48520648 TAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAG
66 TAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAG
*
48520697 ATATAC--ATATA--TATACATATTCGAACTTCATTTATGTATATATATAACATTCATACTTAAC
1 ATATACATATATATGTATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
*
48520758 TAATTTCAATTTATATACTTTTAATTATAGCTCATCAAATATACAATAG
66 TAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAG
48520807 ATATACATATATATGTATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
1 ATATACATATATATGTATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
*
48520872 TAATTTCAATTCATATACTTTTAATTATAACTCATCAAATATACAATAG
66 TAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAG
48520921 ATATACATATATATGTATA
1 ATATACATATATATGTATA
48520940 TACTGATTTA
Statistics
Matches: 233, Mismatches: 6, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
110 103 0.44
112 10 0.04
114 120 0.52
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (114 bp):
ATATACATATATATGTATACATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
TAATTTCAATTCATATACTTTTAATTATAGCTCATCAAATATACAATAG
Found at i:48522996 original size:52 final size:52
Alignment explanation
Indices: 48522916--48523019 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
48522906 GAGCTTGAAG
48522916 ATAGTGGAGAAGACCACTAAGCCAAAGCGTTCATCCTAAACAAATAAAAAAT
1 ATAGTGGAGAAGACCACTAAGCCAAAGCGTTCATCCTAAACAAATAAAAAAT
** * *
48522968 ATAGTGGAGAAGACCACTCGGCCGAAGCGTTCATCCTAGACAAATAAAAAAT
1 ATAGTGGAGAAGACCACTAAGCCAAAGCGTTCATCCTAAACAAATAAAAAAT
48523020 GTATGAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.17
Consensus pattern (52 bp):
ATAGTGGAGAAGACCACTAAGCCAAAGCGTTCATCCTAAACAAATAAAAAAT
Found at i:48523642 original size:22 final size:22
Alignment explanation
Indices: 48523612--48523655 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
48523602 ATAGTTTATC
48523612 TTTTATTTGCTTGATGAGAAAA
1 TTTTATTTGCTTGATGAGAAAA
* *
48523634 TTTTGTTTGTTTGATGAGAAAA
1 TTTTATTTGCTTGATGAGAAAA
48523656 ATTGGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (22 bp):
TTTTATTTGCTTGATGAGAAAA
Found at i:48524229 original size:17 final size:18
Alignment explanation
Indices: 48524207--48524240 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48524197 GCTAAGCATA
*
48524207 CCAAAA-CACATTTCCAG
1 CCAAAAGCACATCTCCAG
48524224 CCAAAAGCACATCTCCA
1 CCAAAAGCACATCTCCA
48524241 ATAGGTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.38, G:0.06, T:0.15
Consensus pattern (18 bp):
CCAAAAGCACATCTCCAG
Found at i:48533552 original size:22 final size:20
Alignment explanation
Indices: 48533524--48533570 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
48533514 TTGTTAAGAT
48533524 TAATATTAAAAAATTATATTTA
1 TAATATTAAAAAA-TATA-TTA
* *
48533546 TAATATTATAACATATATTA
1 TAATATTAAAAAATATATTA
48533566 TAATA
1 TAATA
48533571 AAAGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 11 0.48
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATTAAAAAATATATTA
Found at i:48542473 original size:35 final size:35
Alignment explanation
Indices: 48542411--48542496 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
48542401 TTTTATTTGT
*
48542411 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
48542444 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
48542480 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
48542497 ATAAATCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:48542482 original size:25 final size:23
Alignment explanation
Indices: 48542438--48542498 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
48542428 TGATATTTAA
*
48542438 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
48542462 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
48542487 ATATTATTAAAT
1 ATATAATTAAAT
48542499 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:48542919 original size:15 final size:14
Alignment explanation
Indices: 48542899--48542932 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
48542889 TAAAAGATAT
48542899 TTATTAATTAAATTA
1 TTATTAA-TAAATTA
48542914 TTATTAATAAATTA
1 TTATTAATAAATTA
48542928 -TATTA
1 TTATTA
48542933 TTACAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATTAATAAATTA
Found at i:48544116 original size:2 final size:2
Alignment explanation
Indices: 48544103--48544134 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
48544093 NNNNNNNNAC
*
48544103 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48544135 GTCATGACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48545016 original size:37 final size:38
Alignment explanation
Indices: 48544962--48545034 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
48544952 TTTTCATAAT
* **
48544962 TTCACTTTTTCACTTTCAA-TCCCTATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAAGTCAATATTCAATTCAAAA
*
48544999 TTCACTTTTCCATTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTCAAGTCAATATTCAATTCAA
48545035 TTCCACACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 17 0.55
38 14 0.45
ACGTcount: A:0.30, C:0.25, G:0.01, T:0.44
Consensus pattern (38 bp):
TTCACTTTTCCACTTTCAAGTCAATATTCAATTCAAAA
Found at i:48545065 original size:23 final size:22
Alignment explanation
Indices: 48545022--48545065 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
48545012 TTTCAAGTCA
48545022 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
48545045 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
48545066 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:48545190 original size:23 final size:23
Alignment explanation
Indices: 48545164--48545239 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
48545154 ATAAGTGCCA
48545164 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48545187 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
48545210 CACTGAAATATAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
48545233 CACTGAT
1 CACTGAT
48545240 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:48547104 original size:45 final size:45
Alignment explanation
Indices: 48547036--48547132 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
48547026 GCCGACTACT
* *
48547036 GTTACTGTTACCGAATCGACACTTTGTGTGTCGGATACTGTTACC
1 GTTACTGTTACAGAATCGACACTTTGTGTGTCGAATACTGTTACC
* * * *
48547081 GTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATATTGTTACT
1 GTTACTGTTACAGAATCGA-CACTTTGTGTGTCGAATACTGTTACC
48547126 GTTACTG
1 GTTACTG
48547133 CTACTGTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 1 0.02
45 44 0.98
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (45 bp):
GTTACTGTTACAGAATCGACACTTTGTGTGTCGAATACTGTTACC
Found at i:48552145 original size:2 final size:2
Alignment explanation
Indices: 48552138--48552172 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48552128 AAGACTTAGA
48552138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48552173 AAACATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48552551 original size:41 final size:41
Alignment explanation
Indices: 48552506--48552670 Score: 190
Period size: 41 Copynumber: 4.0 Consensus size: 41
48552496 ACAAATCCAA
* *
48552506 ATATGATACACCGA-CACAAAGCCTGCTAGGCATAATGCCTG
1 ATATGATACA-CGAGCATAAAGCCTGCTAGGCATAAAGCCTG
* *
48552547 ATATGGTACACCG-GCATGAAGCCTGCTAGGCATAAAGCCTG
1 ATATGATACA-CGAGCATAAAGCCTGCTAGGCATAAAGCCTG
* * * *
48552588 ATATGGTACACAAGCATGAAGCATGCTAGGCATAAAGCCTG
1 ATATGATACACGAGCATAAAGCCTGCTAGGCATAAAGCCTG
* * * *
48552629 ATATAATTCACTAGCATAAAGCCTGCTAGACATAAAGCCTG
1 ATATGATACACGAGCATAAAGCCTGCTAGGCATAAAGCCTG
48552670 A
1 A
48552671 ATATCACTGA
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 1 0.01
41 108 0.99
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (41 bp):
ATATGATACACGAGCATAAAGCCTGCTAGGCATAAAGCCTG
Found at i:48552664 original size:16 final size:15
Alignment explanation
Indices: 48552639--48552669 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
48552629 ATATAATTCA
48552639 CTAGCATAAAGCCTG
1 CTAGCATAAAGCCTG
48552654 CTAGACATAAAGCCTG
1 CTAG-CATAAAGCCTG
48552670 AATATCACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (15 bp):
CTAGCATAAAGCCTG
Found at i:48553643 original size:24 final size:24
Alignment explanation
Indices: 48553585--48553644 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
48553575 TATTATAACA
*
48553585 TAATAATATATTATACCTTATTAT
1 TAATAATATATTATACATTATTAT
* *
48553609 AACATATATATATATATATATTA-TAT
1 TA-ATA-ATATAT-TATACATTATTAT
48553635 TAATAATATA
1 TAATAATATA
48553645 AGAAAACCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
24 6 0.21
25 6 0.21
26 10 0.34
27 7 0.24
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATAATATATTATACATTATTAT
Found at i:48554844 original size:8 final size:8
Alignment explanation
Indices: 48554831--48554860 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
48554821 GGTATGGGAA
48554831 AAAAATTT
1 AAAAATTT
48554839 AAAAATTT
1 AAAAATTT
48554847 AAAAATTT
1 AAAAATTT
48554855 AAAAAT
1 AAAAAT
48554861 ATATAAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAAATTT
Found at i:48558480 original size:3 final size:3
Alignment explanation
Indices: 48558474--48558499 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48558464 AGGAGGAGAA
48558474 GGT GGT GGT GGT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GG
48558500 AGGGGGTGGG
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:0.00, C:0.00, G:0.69, T:0.31
Consensus pattern (3 bp):
GGT
Found at i:48562895 original size:21 final size:21
Alignment explanation
Indices: 48562852--48562906 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
48562842 TTGCATATTT
* * *
48562852 ATTTATTTTT-AAATATTCTA
1 ATTTATTTTTAAAAAAATCAA
48562872 ATTTATTTTTAAAAAAATCAA
1 ATTTATTTTTAAAAAAATCAA
48562893 ATTTATTTTTAAAA
1 ATTTATTTTTAAAA
48562907 TGATTAGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTATTTTTAAAAAAATCAA
Found at i:48563213 original size:2 final size:2
Alignment explanation
Indices: 48563201--48563236 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
48563191 AGACCTTCCC
48563201 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48563237 AAAGATGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48564425 original size:18 final size:20
Alignment explanation
Indices: 48564399--48564436 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
48564389 TTTTCTATTA
48564399 TTTATTTCT-TTTTAATTTT
1 TTTATTTCTCTTTTAATTTT
*
48564418 TTTA-TTCTCTTTTACTTTT
1 TTTATTTCTCTTTTAATTTT
48564437 CTAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTCTCTTTTAATTTT
Found at i:48574242 original size:2 final size:2
Alignment explanation
Indices: 48574235--48574260 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48574225 GCAGATGATT
48574235 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
48574261 CACATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48582678 original size:41 final size:41
Alignment explanation
Indices: 48582622--48582734 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
48582612 TGATTCGATA
* * *
48582622 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGT-A-T
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCG-AAT-TAATT
* *
48582663 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAATTAATT
* *
48582704 CACCGGCATCAAGCCTGCTAGACGTAAAGTC
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTC
48582735 TGTATTACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
39 1 0.02
40 4 0.06
41 59 0.92
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAATTAATT
Found at i:48582735 original size:41 final size:42
Alignment explanation
Indices: 48582662--48582746 Score: 145
Period size: 41 Copynumber: 2.0 Consensus size: 42
48582652 CCGAAATGTA
*
48582662 TCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTA-AT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTACAT
*
48582703 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGTATTACAT
1 TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTACAT
48582745 TC
1 TC
48582747 GATCACTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 37 0.90
42 4 0.10
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (42 bp):
TCACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAATTACAT
Found at i:48584455 original size:13 final size:13
Alignment explanation
Indices: 48584437--48584461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48584427 CAATCACATG
48584437 CACACAAAATAAA
1 CACACAAAATAAA
48584450 CACACAAAATAA
1 CACACAAAATAA
48584462 TATTAATAAT
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:48586898 original size:22 final size:21
Alignment explanation
Indices: 48586857--48586903 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
48586847 ATTTTAATGC
48586857 AAATTTTTCTTAGATTTTTTA
1 AAATTTTTCTTAGATTTTTTA
*
48586878 AAATTCTTTACTTA-ATTTTTTT
1 AAATT-TTT-CTTAGATTTTTTA
48586900 AAAT
1 AAAT
48586904 AATAAATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 14 0.61
23 4 0.17
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (21 bp):
AAATTTTTCTTAGATTTTTTA
Found at i:48588417 original size:4 final size:4
Alignment explanation
Indices: 48588408--48588434 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
48588398 ACATTTTCTC
48588408 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
48588435 TGAAATACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:48599514 original size:23 final size:22
Alignment explanation
Indices: 48599488--48599539 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
48599478 AATTAAAAAT
*
48599488 AAAATAA-TAAATATTTTAATATGA
1 AAAATAATTAAA-ATTATAAT-T-A
48599512 AAAA-AATTAAAATTATAATTA
1 AAAATAATTAAAATTATAATTA
48599533 AAAATAA
1 AAAATAA
48599540 AATCTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.20
22 3 0.12
23 9 0.36
24 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATAATTAAAATTATAATTA
Found at i:48599550 original size:19 final size:19
Alignment explanation
Indices: 48599513--48599550 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
48599503 TTAATATGAA
*
48599513 AAAAATTAAAATTATAATT
1 AAAAATTAAAATTAAAATT
48599532 AAAAA-TAAAATCTAAAATT
1 AAAAATTAAAAT-TAAAATT
48599551 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTAAAATTAAAATT
Found at i:48599572 original size:25 final size:25
Alignment explanation
Indices: 48599478--48599583 Score: 67
Period size: 24 Copynumber: 4.2 Consensus size: 25
48599468 ATATAGTAAA
* *
48599478 AATTAAAAATAAAATAATAAATATTTT
1 AATTAAAAATAAAAT-TTAAA-ATTAT
*
48599505 AA-TATGAAA-AAAA-TTAAAATTAT
1 AATTA-AAAATAAAATTTAAAATTAT
*
48599528 AATTAAAAATAAAATCTAAAATT-T
1 AATTAAAAATAAAATTTAAAATTAT
* * * * *
48599552 TATTTAAAATAACATTTTAAATAAAT
1 AATTAAAAATAAAATTTAAAAT-TAT
48599578 AATTAA
1 AATTAA
48599584 CAGAATAATA
Statistics
Matches: 60, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
23 9 0.15
24 28 0.47
25 7 0.12
26 11 0.18
27 5 0.08
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (25 bp):
AATTAAAAATAAAATTTAAAATTAT
Found at i:48614648 original size:22 final size:22
Alignment explanation
Indices: 48614623--48614680 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
48614613 AAATTTATTG
*
48614623 TTTTGATGTTATTTTTCCACTA
1 TTTTGTTGTTATTTTTCCACTA
* *
48614645 TTTTGTTGTTGTTTTTCCACTG
1 TTTTGTTGTTATTTTTCCACTA
*
48614667 TTTTGTTGTCATTT
1 TTTTGTTGTTATTT
48614681 CACTATTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (22 bp):
TTTTGTTGTTATTTTTCCACTA
Found at i:48619670 original size:24 final size:24
Alignment explanation
Indices: 48619641--48619694 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
48619631 TCTTTCTAGA
** *
48619641 ATATTTAGTATTAATGAGTATAAT
1 ATATTTAACATTAATGAGCATAAT
* *
48619665 ATATTTAACATTTATTAGCATAAT
1 ATATTTAACATTAATGAGCATAAT
48619689 ATATTT
1 ATATTT
48619695 GACTTTGATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
ATATTTAACATTAATGAGCATAAT
Found at i:48624041 original size:24 final size:24
Alignment explanation
Indices: 48624007--48624058 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
48623997 TTTCTAAAAG
* **
48624007 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
48624031 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
48624055 ATTT
1 ATTT
48624059 GACTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:48624233 original size:14 final size:14
Alignment explanation
Indices: 48624182--48624239 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
48624172 AAATGTACCA
*
48624182 TTTTAATACATATT
1 TTTTAATATATATT
* * * *
48624196 TTTTAAAAGATGTCA
1 TTTTAATATATAT-T
48624211 TTTTAATATATATT
1 TTTTAATATATATT
48624225 TTTTAATAT-TATT
1 TTTTAATATATATT
48624238 TT
1 TT
48624240 AGTAAAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
13 6 0.17
14 19 0.54
15 10 0.29
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTTAATATATATT
Found at i:48625689 original size:3 final size:3
Alignment explanation
Indices: 48625681--48625707 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48625671 AGATACCTCC
48625681 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
48625708 AATTGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:48628247 original size:27 final size:27
Alignment explanation
Indices: 48628196--48628247 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
48628186 TTGCTTCTTC
*
48628196 TTCTTCTCCTCCTCCTTGTTGTTGTTA
1 TTCTTCTCCTCCTCCTTGTTATTGTTA
*
48628223 TTCTTCTCCTCTTTCCTTG-TATTGT
1 TTCTTCTCCTC-CTCCTTGTTATTGT
48628248 AAGCAGTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 16 0.73
28 6 0.27
ACGTcount: A:0.04, C:0.29, G:0.10, T:0.58
Consensus pattern (27 bp):
TTCTTCTCCTCCTCCTTGTTATTGTTA
Found at i:48645832 original size:27 final size:27
Alignment explanation
Indices: 48645802--48645859 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
48645792 CAACACGAAA
*
48645802 CTAACATAATTAACAATACTTTAAGAC
1 CTAACATAATAAACAATACTTTAAGAC
*
48645829 CTAACATAATAAACAATACTTTAATAC
1 CTAACATAATAAACAATACTTTAAGAC
48645856 CTAA
1 CTAA
48645860 ATTCTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (27 bp):
CTAACATAATAAACAATACTTTAAGAC
Found at i:48646279 original size:23 final size:25
Alignment explanation
Indices: 48646245--48646299 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
48646235 AATATATATT
*
48646245 AAATATA-TTTTTTA-TTTTTAAAC
1 AAATATACTTTTTAACTTTTTAAAC
*
48646268 AAATATACTTTTTAACTTTTTAATC
1 AAATATACTTTTTAACTTTTTAAAC
48646293 AAATATA
1 AAATATA
48646300 TATATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 6 0.21
25 15 0.54
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (25 bp):
AAATATACTTTTTAACTTTTTAAAC
Found at i:48647793 original size:11 final size:11
Alignment explanation
Indices: 48647777--48647967 Score: 95
Period size: 11 Copynumber: 18.2 Consensus size: 11
48647767 TTATTTTTTT
*
48647777 TATTTTTCAAA
1 TATTTTTTAAA
*
48647788 TATTTTTTACA
1 TATTTTTTAAA
48647799 TACTTTTTTAAA
1 TA-TTTTTTAAA
*
48647811 TTTTTTTTAAA
1 TATTTTTTAAA
* *
48647822 -AATTTTAAAA
1 TATTTTTTAAA
*
48647832 TATTTTTAAAA
1 TATTTTTTAAA
*
48647843 TACTTTTTTTTAA
1 TA--TTTTTTAAA
48647856 T-TTTTTT---
1 TATTTTTTAAA
* *
48647863 TAATTTTAAAA
1 TATTTTTTAAA
*
48647874 TATTTTTAAAA
1 TATTTTTTAAA
*
48647885 TATATTTTTTAA
1 TAT-TTTTTAAA
48647897 T-TTTTTT--A
1 TATTTTTTAAA
**
48647905 -ATTTTAAAAA
1 TATTTTTTAAA
*
48647915 TATTTTTAAAA
1 TATTTTTTAAA
*
48647926 TACTTTTTT-TA
1 TA-TTTTTTAAA
48647937 -ATTTTTTAAA
1 TATTTTTTAAA
48647947 -A-TTTTTAAA
1 TATTTTTTAAA
*
48647956 -ATTTTTAAAA
1 TATTTTTTAAA
48647966 TA
1 TA
48647968 AAAATGGGCC
Statistics
Matches: 141, Mismatches: 22, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
7 1 0.01
8 9 0.06
9 15 0.11
10 29 0.21
11 58 0.41
12 21 0.15
13 8 0.06
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTTAAA
Found at i:48647827 original size:20 final size:20
Alignment explanation
Indices: 48647804--48647965 Score: 61
Period size: 18 Copynumber: 8.0 Consensus size: 20
48647794 TTACATACTT
* *
48647804 TTTTAAATTTTTTTTAAAAA
1 TTTTAAAATATTTTTAAAAA
48647824 TTTTAAAATATTTTTAAAATA
1 TTTTAAAATATTTTTAAAA-A
** **
48647845 CTTTTTTTTAAT-TTTTT-TTAA
1 ---TTTTAAAATATTTTTAAAAA
48647866 TTTTAAAATATTTTTAAAATATA
1 TTTTAAAATATTTTT-AAA-A-A
** *
48647889 TTTTTTAAT-TTTTT--TAA
1 TTTTAAAATATTTTTAAAAA
48647906 TTTTAAAAATATTTTTAAAATA
1 TTTT-AAAATATTTTTAAAA-A
**
48647928 CTTTTTTTAAT-TTTTT-AAAA
1 --TTTTAAAATATTTTTAAAAA
*
48647948 TTTTTAAA-ATTTTTAAAA
1 TTTTAAAATATTTTTAAAA
48647966 TAAAAATGGG
Statistics
Matches: 105, Mismatches: 19, Indels: 37
0.65 0.12 0.23
Matches are distributed among these distances:
17 5 0.05
18 23 0.22
19 13 0.12
20 18 0.17
21 6 0.06
22 13 0.12
23 16 0.15
24 11 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAAATATTTTTAAAAA
Found at i:48647873 original size:42 final size:41
Alignment explanation
Indices: 48647769--48647967 Score: 251
Period size: 41 Copynumber: 4.8 Consensus size: 41
48647759 AAATATATTT
* * * * *
48647769 ATTTTTTTTATTTTTCAAATATTTTTTACATACTTTTTTAA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
48647810 ATTTTTTTTAAAAATTTTAAAATATTTTTAAAATACTTTTTTTTA
1 ATTTTTTTT---AATTTTAAAATATTTTTAAAATAC-TTTTTTTA
48647855 ATTTTTTTTAATTTTAAAATATTTTTAAAATA-TATTTTTTA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATACT-TTTTTTA
48647896 A-TTTTTTTAATTTTAAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTTAATTTT-AAAATATTTTTAAAATACTTTTTTTA
** *
48647937 ATTTTTTAAAATTTTTAAA-ATTTTTAAAATA
1 ATTTTTTTTAATTTTAAAATATTTTTAAAATA
48647968 AAAATGGGCC
Statistics
Matches: 142, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
40 26 0.18
41 45 0.32
42 35 0.25
44 20 0.14
45 16 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (41 bp):
ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:48647932 original size:29 final size:29
Alignment explanation
Indices: 48647877--48647932 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
48647867 TTTAAAATAT
* **
48647877 TTTTAAAATATATTTTTTAATTTTTTTAA
1 TTTTAAAATATATTTTTAAATACTTTTAA
48647906 TTTTAAAA-ATATTTTTAAAATACTTTT
1 TTTTAAAATATATTTTT-AAATACTTTT
48647933 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTAAAATATATTTTTAAATACTTTTAA
Found at i:48647938 original size:32 final size:31
Alignment explanation
Indices: 48647897--48647957 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
48647887 TATTTTTTAA
48647897 TTTTTTTAATTTTAAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAAAA-ATTTTTAAAATAC
**
48647929 TTTTTTTAATTTTTTAAAATTTTTAAAAT
1 TTTTTTTAATTTTAAAAAATTTTTAAAAT
48647958 TTTTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAAAATTTTTAAAATAC
Found at i:48647951 original size:9 final size:9
Alignment explanation
Indices: 48647939--48647966 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48647929 TTTTTTTAAT
48647939 TTTTTAAAA
1 TTTTTAAAA
48647948 TTTTTAAAA
1 TTTTTAAAA
48647957 TTTTTAAAA
1 TTTTTAAAA
48647966 T
1 T
48647967 AAAAATGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:48653187 original size:22 final size:22
Alignment explanation
Indices: 48653159--48653216 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
48653149 TTTATTGTTC
48653159 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
48653181 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
48653203 AGCCATGAGAGCTT
1 AAACATGAGAGCTT
48653217 TTTCTAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:48655638 original size:9 final size:9
Alignment explanation
Indices: 48655624--48655651 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48655614 CTCACTCAAA
48655624 TCTTATTCT
1 TCTTATTCT
48655633 TCTTATTCT
1 TCTTATTCT
48655642 TCTTATTCT
1 TCTTATTCT
48655651 T
1 T
48655652 TTTTGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (9 bp):
TCTTATTCT
Found at i:48655689 original size:17 final size:17
Alignment explanation
Indices: 48655667--48655716 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
48655657 TTGAAGAATA
48655667 TGTTTGGATTTTGCATC
1 TGTTTGGATTTTGCATC
*
48655684 TGTTT-G--TTT-AATC
1 TGTTTGGATTTTGCATC
48655697 TGTTTGGATTTTGCATC
1 TGTTTGGATTTTGCATC
48655714 TGT
1 TGT
48655717 CTGTTGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
16 4 0.15
17 11 0.41
ACGTcount: A:0.12, C:0.10, G:0.22, T:0.56
Consensus pattern (17 bp):
TGTTTGGATTTTGCATC
Found at i:48658999 original size:32 final size:32
Alignment explanation
Indices: 48658957--48659081 Score: 232
Period size: 32 Copynumber: 3.9 Consensus size: 32
48658947 TTAGATATTG
* *
48658957 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATATTTTAAGCTTGTTGGATATTGAATTT
48658989 ATTATATTTTAAGCTTGTTGGATATTGAATTT
1 ATTATATTTTAAGCTTGTTGGATATTGAATTT
48659021 ATTATATTTTAAGCTTGTTGGATATTGAATTT
1 ATTATATTTTAAGCTTGTTGGATATTGAATTT
48659053 ATTATATTTTAAGCTTGTTGGATATTGAA
1 ATTATATTTTAAGCTTGTTGGATATTGAA
48659082 ATGATTGACA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 91 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATATTTTAAGCTTGTTGGATATTGAATTT
Found at i:48660282 original size:9 final size:9
Alignment explanation
Indices: 48660268--48660304 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
48660258 NNNNNNNNGA
48660268 TATTCGAAT
1 TATTCGAAT
48660277 TATTCGAAT
1 TATTCGAAT
*
48660286 TATTCGAGT
1 TATTCGAAT
48660295 TATTCGAAT
1 TATTCGAAT
48660304 T
1 T
48660305 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:48667749 original size:18 final size:20
Alignment explanation
Indices: 48667728--48667769 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
48667718 ACAATTTAAA
48667728 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
48667748 ATATAAAAATTTATTAATATAT
1 ATAT--AAATTTATTAATATAT
48667770 GTAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATAAATTTATTAATATAT
Found at i:48667874 original size:19 final size:20
Alignment explanation
Indices: 48667850--48667896 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
48667840 CATCCAAACA
48667850 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
48667869 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
48667889 CCAGAAAA
1 CCAGAAAA
48667897 TATTTTACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:48669403 original size:17 final size:16
Alignment explanation
Indices: 48669377--48669416 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
48669367 AATCAATTAA
48669377 ATTAACTAAATTAATTT
1 ATTAACTAAA-TAATTT
*
48669394 ATTAATTAAATAATTT
1 ATTAACTAAATAATTT
*
48669410 TTTAACT
1 ATTAACT
48669417 CAATTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAACTAAATAATTT
Found at i:48670098 original size:30 final size:30
Alignment explanation
Indices: 48670062--48670124 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
48670052 ACTTAACAAG
*
48670062 CAAATGTCTCTAAAATAGTAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
48670092 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
48670122 CAA
1 CAA
48670125 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:48672436 original size:25 final size:26
Alignment explanation
Indices: 48672397--48672446 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
48672387 GATAGATTTA
*
48672397 AATTATATATTTTTACATATTTTAAT
1 AATTATATATTTTTACAAATTTTAAT
*
48672423 AATT-TATATTTTTATAAATTTTAA
1 AATTATATATTTTTACAAATTTTAA
48672447 AAGTGTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
AATTATATATTTTTACAAATTTTAAT
Found at i:48673766 original size:90 final size:90
Alignment explanation
Indices: 48673611--48673909 Score: 347
Period size: 90 Copynumber: 3.3 Consensus size: 90
48673601 ACTACTATTC
* * * **
48673611 AAAATGTTCGTATTATTTTTGTATCCGTAAATCAATTTTAGTCTGTATAATTTATTGGTAAAATT
1 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTATTGGTCGAATT
*
48673676 TTATATTTTCTTATATCAGTTTTGT
66 TTATATTTTCATATATCAGTTTTGT
* * * *
48673701 AAAATGTTTGCATTATTTTTAG-ATCTGTAAA-AATATTTTAGTTTGTATTATTTGTTGGTCGAA
1 AAAATGTTCGTATTATTTTT-GTATCTGTAAATAA-ATTTTAGTCTGTATTATTTATTGGTCGAA
* *
48673764 TTTTATATTTTCGTATATCAAG-TTTCT
64 TTTTATATTTTCATATATC-AGTTTTGT
* * *
48673791 AAAATGTTCGTATTATTTTTGTATATGTAAATAAAATTTAGTCGGTATTATTTATTGGTCGAATT
1 AAAATGTTCGTATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTATTGGTCGAATT
* *
48673856 ATATATTTTCATATATTAGTTTTGT
66 TTATATTTTCATATATCAGTTTTGT
* * *
48673881 AGAATGCTT-GTATT-TTCTTGTATATGTAA
1 AAAATG-TTCGTATTATTTTTGTATCTGTAA
48673910 TTTTTTTTGT
Statistics
Matches: 178, Mismatches: 24, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
89 18 0.10
90 153 0.86
91 7 0.04
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (90 bp):
AAAATGTTCGTATTATTTTTGTATCTGTAAATAAATTTTAGTCTGTATTATTTATTGGTCGAATT
TTATATTTTCATATATCAGTTTTGT
Found at i:48677979 original size:42 final size:42
Alignment explanation
Indices: 48677933--48678014 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
48677923 ACACACCCCA
*
48677933 ATGTCCTTGCTTGTGTAGCTCACACGGTATGGGCACACGCTC
1 ATGTCCTTGCTTGTGTAGCTCACACGGCATGGGCACACGCTC
* *
48677975 ATGTCCTTGCTTGTGTGGCTCACACGGCCTGGGCACACGC
1 ATGTCCTTGCTTGTGTAGCTCACACGGCATGGGCACACGC
48678015 CCATATCTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (42 bp):
ATGTCCTTGCTTGTGTAGCTCACACGGCATGGGCACACGCTC
Found at i:48678033 original size:42 final size:42
Alignment explanation
Indices: 48677912--48678035 Score: 108
Period size: 42 Copynumber: 3.0 Consensus size: 42
48677902 ACAATGAGTT
* * * * * *
48677912 ACACGGCCTGGACACAC-CCCAATGTCCTTGCTTGTGTAGCTC
1 ACACGGCATGGGCACACGCCC-ATATCCTAGCTCGTGTGGCTC
* * * * *
48677954 ACACGGTATGGGCACACGCTCATGTCCTTGCTTGTGTGGCTC
1 ACACGGCATGGGCACACGCCCATATCCTAGCTCGTGTGGCTC
*
48677996 ACACGGCCTGGGCACACGCCCATATCTCTAGC-CGTGTGGC
1 ACACGGCATGGGCACACGCCCATATC-CTAGCTCGTGTGGC
48678036 GTAAACAATC
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 63 0.91
43 6 0.09
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.23
Consensus pattern (42 bp):
ACACGGCATGGGCACACGCCCATATCCTAGCTCGTGTGGCTC
Found at i:48684158 original size:37 final size:38
Alignment explanation
Indices: 48684115--48684201 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 38
48684105 TTTTACATTA
* **
48684115 TATTATTGTTAG-T-TATTATTTTTAGTAAAACCCTAAT
1 TATTATTGTTAGTTATATTATTTTGAGTAAAAAACT-AT
48684152 TATTATTGTTAGTTAGTATTATTTTGAGTAAAAAACTAT
1 TATTATTGTTAGTTA-TATTATTTTGAGTAAAAAACTAT
48684191 TATTATTGTTA
1 TATTATTGTTA
48684202 TTGTGTTAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 12 0.27
38 1 0.02
39 13 0.30
40 18 0.41
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (38 bp):
TATTATTGTTAGTTATATTATTTTGAGTAAAAAACTAT
Found at i:48684195 original size:76 final size:76
Alignment explanation
Indices: 48683994--48684201 Score: 215
Period size: 76 Copynumber: 2.6 Consensus size: 76
48683984 TAGTTATTAA
*
48683994 TATTATTTTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGATTAGTTATTAGG
1 TATTA-TTTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-TG-TTAGTTATTAGG
48684059 ATTAGTAAAAACCCTAAT
59 ATTAGTAAAAACCCTAAT
* *** * * ***
48684077 TATTATTTTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATTGTTAGTTATTATTTTTAGT
1 TATTATTTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGTTAGTTATTAGGATTAGT
48684141 -AAAACCCTAAT
65 AAAAACCCTAAT
48684152 TATTATTGTTAGTTAGTATTATT-TTGAGTAAAAAACTATTATTATTGTTA
1 TATTATT-TTAGTTAGTATTATTGTT-AGTAAAAAACTATTATTATTGTTA
48684202 TTGTGTTAGT
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
75 25 0.24
76 42 0.40
77 2 0.02
78 1 0.01
79 5 0.05
80 2 0.02
82 20 0.19
83 8 0.08
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (76 bp):
TATTATTTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTAGTTATTAGGATTAGTA
AAAACCCTAAT
Found at i:48687373 original size:17 final size:18
Alignment explanation
Indices: 48687351--48687384 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48687341 TAAAAATATA
48687351 TTATTTT-TTTTATTTTT
1 TTATTTTATTTTATTTTT
48687368 TTATTTTATTTTATTTT
1 TTATTTTATTTTATTTT
48687385 AGTACATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTATTTTATTTTATTTTT
Found at i:48687385 original size:10 final size:9
Alignment explanation
Indices: 48687351--48687384 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
48687341 TAAAAATATA
48687351 TTATTTTTT
1 TTATTTTTT
48687360 TTA-TTTTT
1 TTATTTTTT
48687368 TTATTTTATT
1 TTATTTT-TT
48687378 TTATTTT
1 TTATTTT
48687385 AGTACATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (9 bp):
TTATTTTTT
Found at i:48687552 original size:154 final size:155
Alignment explanation
Indices: 48687124--48687694 Score: 728
Period size: 154 Copynumber: 3.7 Consensus size: 155
48687114 CAAAAAAAAA
* * * *
48687124 TTAGTAAAAAACCCTTATTTTGACCATTTGTTCGTATTTTTTCCCCGGATTTTATTACTTT-A-A
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGCTCGTATTTTTTCCTCGGATTTTATTACTTTAATA
*
48687187 AAAA-ATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATT
66 AAAATATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATT
48687251 AATTTAGTGTGTTTTTTAAATAAAT
131 AATTTAGTGTGTTTTTTAAATAAAT
* * * *
48687276 TTAGAAAAATAACCCTTATTTTGGCCCTTTGCTCGTATTTTTTTCCT-GGATTTAATTACTTTCA
1 TTAGTAAAA-AACCCTTATTTCGGCCATTTGCTCGTA-TTTTTTCCTCGGATTTTATTACTTT-A
* * * ** *
48687340 ATAAAAATATATTATTTTTTTTATTTTTTTATTTTATTTTATTTTAGTACATTATGTTTGAAATA
63 ATAAAAATATACTA-TTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
* * * *
48687405 GATTAATTAATTCTGTTTTTTAAA-AATAT
127 CATTAATTTAGTGTGTTTTTTAAATAA-AT
* * * * *
48687434 TTAGTAAAAAATCCTTATTTCGCCCCTTTGTTCGTATTTTCTCCTCGGATTTTATTACTTTAA-A
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGCTCGTATTTTTTCCTCGGATTTTATTACTTTAATA
*
48687498 AAAATATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATT
66 AAAATATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATT
*
48687563 AATTTAGTGTG-GTTTTAAATAAAT
131 AATTTAGTGTGTTTTTTAAATAAAT
* * * *
48687587 TTAATAAAAAACCCTTATTTCGGTCATTTGCTCGTATTTTTTCC-CGAATTTTATTACTGTCAAT
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGCTCGTATTTTTTCCTCGGATTTTATTACT-TTAAT
* *
48687651 AAAAATATATTATTTTCGT-ATTTTATTATTTTACATTATTTTAG
65 AAAAATATACTATTTT-TTAATTTTATTATTTTACATTATTTTAG
48687695 GTTTTTTGTG
Statistics
Matches: 360, Mismatches: 46, Indels: 24
0.84 0.11 0.06
Matches are distributed among these distances:
152 21 0.06
153 87 0.24
154 106 0.29
155 13 0.04
156 15 0.04
157 44 0.12
158 74 0.21
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.51
Consensus pattern (155 bp):
TTAGTAAAAAACCCTTATTTCGGCCATTTGCTCGTATTTTTTCCTCGGATTTTATTACTTTAATA
AAAATATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATT
AATTTAGTGTGTTTTTTAAATAAAT
Found at i:48687628 original size:310 final size:308
Alignment explanation
Indices: 48687124--48687694 Score: 887
Period size: 310 Copynumber: 1.8 Consensus size: 308
48687114 CAAAAAAAAA
* *
48687124 TTAGTAAAAAACCCTTATTTTGACCATTTGTTCGTATTTTTTCCCCGGATTTTATTACTTTAAAA
1 TTAGTAAAAAACCCTTATTTCGACCATTTGTTCGTATTTTCTCCCCGGATTTTATTACTTTAAAA
48687189 AAATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATTAAT
66 AAATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATTAAT
* * *
48687254 TTAGTGTGTTTTTTAAATAAATTTAGAAAAATAACCCTTATTTTGGCCCTTTGCTCGTATTTTTT
131 TTAGTGTGTGTTTTAAATAAATTTAGAAAAATAACCCTTATTTCGGCCATTTGCTCGTA-TTTTT
* * * ** * **
48687319 TCCTGGATTTAATTACTTTCAATAAAAATATATTATTTTTTTTATTTTTTTATTTTATTTTATTT
195 TCCCGAATTTAATTACTGTCAATAAAAATATATTA-TTTTCGTATTTTATTATTTTACATTATTT
48687384 TAGTACATTATGTTTGAAATAGATTAATTAATTCTGTTTTTTAAAAATAT
259 TAGTACATTATGTTTGAAATAGATTAATTAATTCTGTTTTTTAAAAATAT
* * * *
48687434 TTAGTAAAAAATCCTTATTTCGCCCCTTTGTTCGTATTTTCTCCTCGGATTTTATTACTTTAAAA
1 TTAGTAAAAAACCCTTATTTCGACCATTTGTTCGTATTTTCTCCCCGGATTTTATTACTTT-AAA
* *
48687499 AAATATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTA
65 AAA-ATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATTA
*
48687564 ATTTAGTGTG-GTTTTAAATAAATTTA-ATAAAA-AACCCTTATTTCGGTCATTTGCTCGTATTT
129 ATTTAGTGTGTGTTTTAAATAAATTTAGA-AAAATAACCCTTATTTCGGCCATTTGCTCGTATTT
*
48687626 TTTCCCGAATTTTATTACTGTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATT
193 TTTCCCGAATTTAATTACTGTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATT
48687691 TTAG
258 TTAG
48687695 GTTTTTTGTG
Statistics
Matches: 237, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
308 27 0.11
309 36 0.15
310 80 0.34
311 25 0.11
312 69 0.29
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.51
Consensus pattern (308 bp):
TTAGTAAAAAACCCTTATTTCGACCATTTGTTCGTATTTTCTCCCCGGATTTTATTACTTTAAAA
AAATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTCATTAAT
TTAGTGTGTGTTTTAAATAAATTTAGAAAAATAACCCTTATTTCGGCCATTTGCTCGTATTTTTT
CCCGAATTTAATTACTGTCAATAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTA
GTACATTATGTTTGAAATAGATTAATTAATTCTGTTTTTTAAAAATAT
Found at i:48687843 original size:9 final size:9
Alignment explanation
Indices: 48687829--48688043 Score: 132
Period size: 9 Copynumber: 25.9 Consensus size: 9
48687819 TGGTGTAGTG
48687829 TTACATAAC
1 TTACATAAC
*
48687838 TTACATAAA
1 TTACATAAC
*
48687847 TTAAATAAC
1 TTACATAAC
*
48687856 TTACTTAAC
1 TTACATAAC
*
48687865 TTAAATAAC
1 TTACATAAC
48687874 TTACATAA-
1 TTACATAAC
48687882 -TACATAACC
1 TTACATAA-C
*
48687891 TT-CTTAAC
1 TTACATAAC
*
48687899 TTACATTA-
1 TTACATAAC
*
48687907 -TACACAAC
1 TTACATAAC
48687915 TTACATAA-
1 TTACATAAC
*
48687923 TTA-AT-AT
1 TTACATAAC
*
48687930 TATACACAAC
1 T-TACATAAC
48687940 TTACATAA-
1 TTACATAAC
* *
48687948 -TGCATTAC
1 TTACATAAC
48687956 TTACATAAC
1 TTACATAAC
*
48687965 TTACATTAC
1 TTACATAAC
48687974 TTACAGT-AC
1 TTACA-TAAC
48687983 TT---T-AC
1 TTACATAAC
48687988 TTACAGT-AC
1 TTACA-TAAC
48687997 TTACATAA-
1 TTACATAAC
48688005 -TACATAA-
1 TTACATAAC
48688012 -TACATAA-
1 TTACATAAC
48688019 -TACATAAC
1 TTACATAAC
48688027 TTACATAAC
1 TTACATAAC
48688036 TTACATAA
1 TTACATAA
48688044 TACATAAAAA
Statistics
Matches: 164, Mismatches: 22, Indels: 40
0.73 0.10 0.18
Matches are distributed among these distances:
5 5 0.03
6 1 0.01
7 41 0.25
8 9 0.05
9 104 0.63
10 4 0.02
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.35
Consensus pattern (9 bp):
TTACATAAC
Found at i:48687960 original size:25 final size:25
Alignment explanation
Indices: 48687905--48687970 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
48687895 TAACTTACAT
* *
48687905 TATACACAACTTACATAATTAATAT
1 TATACACAACTTACATAATCAATAC
*
48687930 TATACACAACTTACATAATGCATTAC
1 TATACACAACTTACATAAT-CAATAC
*
48687956 T-TACATAACTTACAT
1 TATACACAACTTACAT
48687971 TACTTACAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.35
Consensus pattern (25 bp):
TATACACAACTTACATAATCAATAC
Found at i:48687987 original size:14 final size:14
Alignment explanation
Indices: 48687970--48687998 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
48687960 ATAACTTACA
48687970 TTACTTACAGTACT
1 TTACTTACAGTACT
48687984 TTACTTACAGTACT
1 TTACTTACAGTACT
48687998 T
1 T
48687999 ACATAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (14 bp):
TTACTTACAGTACT
Found at i:48688010 original size:7 final size:7
Alignment explanation
Indices: 48687998--48688050 Score: 70
Period size: 7 Copynumber: 7.0 Consensus size: 7
48687988 TTACAGTACT
48687998 TACATAA
1 TACATAA
48688005 TACATAA
1 TACATAA
48688012 TACATAA
1 TACATAA
48688019 TACATAA
1 TACATAA
48688026 CTTACATAA
1 --TACATAA
48688035 CTTACATAA
1 --TACATAA
48688044 TACATAA
1 TACATAA
48688051 AAATATATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 28 0.64
9 16 0.36
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:48688043 original size:25 final size:22
Alignment explanation
Indices: 48687999--48688050 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 22
48687989 TACAGTACTT
48687999 ACATAATACATAATACATAA-T
1 ACATAATACATAATACATAACT
48688020 ACATAACTTACATAACTTACATAA-T
1 ACATAA--TACATAA--TACATAACT
48688045 ACATAA
1 ACATAA
48688051 AAATATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.22
23 7 0.26
25 14 0.52
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
ACATAATACATAATACATAACT
Found at i:48690997 original size:229 final size:222
Alignment explanation
Indices: 48690666--48691508 Score: 732
Period size: 229 Copynumber: 3.8 Consensus size: 222
48690656 CGTGAATGAT
* * * * * *
48690666 AAACGCCGC-AGAGATATTAAAGC-AGAACGCAGGGTTCGGTGTTGATCAATTGTTGCTTTAGCG
1 AAACGCCGCAAAAGATGTTAAAACTA-AACGCAGCGTTCGGTGTTGATCAATTGTGGATTTAGCG
* ** * * *
48690729 GCACTAATCTAGAAAA-GCCGCCAAAGATCAG-TATTAACGGCACTTATA-TAGTAAACGCCACA
65 GCGC-AAAATA-AAAACACCGCTAAAGATCAGATATTAACGGCACTTA-ACTAGTAAACGCCGCA
* * * *
48690791 GAAAGTTAACCAAAATGCATCGTTTGACCTCGAGGTATAGTGGCATTTAGCAGCGCTTTAGTTAC
127 GAAAGTTAACCAAAACGCATCGTTTGGCCTTGAGGTATAGTGGCATTTAGC-GCGCTTTA-TAAC
48690856 -AACGCCACTAAAGATCTTCATTAGCGGCGATTTC
190 GAACGCCACTAAAGATCTTCATTA-C-GCGATTTC
* *
48690890 ACCATAGCGCCGCAAAAGATGTTAAAACTAAACGCAGCGTTCGGTGTTCATCAATTGTGGCTTTA
1 A--A-A-CGCCGCAAAAGATGTTAAAACTAAACGCAGCGTTCGGTGTTGATCAATTGTGGATTTA
* * **
48690955 GCGGCGCAAACATAAAAACACCGCTAAAAATC-GATATTAACGGCGCTT-ACCGGATAAACGCCG
62 GCGGCGCAAA-ATAAAAACACCGCTAAAGATCAGATATTAACGGCACTTAACTAG-TAAACGCCG
* * * *
48691018 CAGAAAGCTAACCAAAACGCATCGTTTGGCCTTGATGTATGGTGGCATTCAGCGACGCTTT-TAA
125 CAGAAAGTTAACCAAAACGCATCGTTTGGCCTTGAGGTATAGTGGCATTTAGCG-CGCTTTATAA
*
48691082 CTGAACGCCACTAAAGATCTTCATTAACAGCGTTTTC
189 C-GAACGCCACTAAAGATCTTCATT-AC-GCGATTTC
** * * * * * *
48691119 GTTAAAACGCCGC-CGAGTCTGTTAAAACTAAATGCAGCGTTTGGTTTTAATCAATTG-CGATTC
1 ----AAACGCCGCAAAAG-ATGTTAAAACTAAACGCAGCGTTCGGTGTTGATCAATTGTGGATT-
* * * * *
48691182 TAGCGGCGC-TAATAAAAATCACCGCGAAAGATCAGA-ATTAACGGCGCTTAACGAATAAACGCC
60 TAGCGGCGCAAAATAAAAA-CACCGCTAAAGATCAGATATTAACGGCACTTAACTAGTAAACGCC
** *
48691245 GCAGAAAGTTAACCAAAACGCATCGTTTGGCCTTGATTTATGGTGGCATTTAGCGGCGCTTTA-A
124 GCAGAAAGTTAACCAAAACGCATCGTTTGGCCTTGAGGTATAGTGGCATTTAGC-GCGCTTTATA
48691309 ACCGAACGCCACTAAAGA---TC-TT----GA----
188 A-CGAACGCCACTAAAGATCTTCATTACGCGATTTC
* * * *
48691333 AAACGCCGCAAAATATGTTAAAACTAAACGCAGCGTTCGGTTTTGATCAATTCTGGATTTCGCGG
1 AAACGCCGCAAAAGATGTTAAAACTAAACGCAGCGTTCGGTGTTGATCAATTGTGGATTTAGCGG
* * * * * * ** *
48691398 CGCTAATTGAAAAACGCCGCTAAAGATCTG-TATTAACGACATTTAACTAGTAAACGCTTCAAAA
66 CGCAAAAT-AAAAACACCGCTAAAGATCAGATATTAACGGCACTTAACTAGTAAACGCCGCAGAA
*
48691462 AGTTAACCAAAACGCATCGTTTGGCCGTGAGGTATAGTGGCATTTAG
130 AGTTAACCAAAACGCATCGTTTGGCCTTGAGGTATAGTGGCATTTAG
48691509 TGGTGCTTTG
Statistics
Matches: 515, Mismatches: 72, Indels: 77
0.78 0.11 0.12
Matches are distributed among these distances:
210 51 0.10
211 88 0.17
212 5 0.01
218 1 0.00
224 3 0.01
225 2 0.00
226 1 0.00
227 12 0.02
228 128 0.25
229 219 0.43
230 3 0.01
231 1 0.00
233 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (222 bp):
AAACGCCGCAAAAGATGTTAAAACTAAACGCAGCGTTCGGTGTTGATCAATTGTGGATTTAGCGG
CGCAAAATAAAAACACCGCTAAAGATCAGATATTAACGGCACTTAACTAGTAAACGCCGCAGAAA
GTTAACCAAAACGCATCGTTTGGCCTTGAGGTATAGTGGCATTTAGCGCGCTTTATAACGAACGC
CACTAAAGATCTTCATTACGCGATTTC
Found at i:48691326 original size:114 final size:112
Alignment explanation
Indices: 48690751--48691328 Score: 273
Period size: 114 Copynumber: 5.1 Consensus size: 112
48690741 AAAAGCCGCC
* * * * *
48690751 AAAGATCAGTATTAACGGCACTTATA-TAGTAAACGCCACAGAAAGTTAACCAAAATGCATCGTT
1 AAAGATCAGAATTAACGGCGCTTA-ACGA-TAAACGCCGCAGAAAGTTAACCAAAACGCATCGTT
* * ** * * *
48690815 TGACCTCGAGGTATAGTGGCATTTAGCAGCGCTTTAGTTAC-AACGCCACT
64 TGGCCTTGATCTATGGTGGCATTTAGCGGCGCTTTA--AACGAACGCCACT
*** * * * * * * * * *
48690865 AAAGATCTTCATTAGCGGCGATTTCACCAT-AGCGCCGCAAAAGATGTTAAAACTAAACGCAGCG
1 AAAGATCAGAATTAACGGCG-CTTAACGATAAACGCCGCAGAA-A-GTT-AACCAAAACGCATCG
* ** * * * ** * *
48690929 TTCGGTGTTCATCAATTGTGGC-TTTAGCGGCGCAAACATAAA--AACACCGCT
62 TTTGGCCTTGATCTATGGTGGCATTTAGCGGCGC---TTTAAACGAACGCCACT
* * *
48690980 AAAAATC-GATATTAACGGCGCTTACCGGATAAACGCCGCAGAAAGCTAACCAAAACGCATCGTT
1 AAAGATCAGA-ATTAACGGCGCTTAAC-GATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTT
* * * *
48691044 TGGCCTTGATGTATGGTGGCATTCAGCGACGCTTTTAACTGAACGCCACT
64 TGGCCTTGATCTATGGTGGCATTTAGCGGCGCTTTAAAC-GAACGCCACT
*** * ** * *** * * * *
48691094 AAAGATCTTCATTAACAGCG-TTTTCGTTAAAACGCCGCCGAGTCTGTTAAAACTAAATGCAGCG
1 AAAGATCAGAATTAACGGCGCTTAACGAT-AAACGCCG-C-AGAAAGTT-AACCAAAACGCATCG
** * * * * * *
48691158 TTTGGTTTTAATCAAT--T-GCGATTCTAGCGGCGCTAATAAA--AATCACCGCG
62 TTTGGCCTTGATCTATGGTGGC-ATT-TAGCGGCGCT-TTAAACGAA-CGCCACT
48691208 AAAGATCAGAATTAACGGCGCTTAACGAATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTT
1 AAAGATCAGAATTAACGGCGCTTAACG-ATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTT
*
48691273 GGCCTTGATTTATGGTGGCATTTAGCGGCGCTTTAAACCGAACGCCACT
65 GGCCTTGATCTATGGTGGCATTTAGCGGCGCTTTAAA-CGAACGCCACT
48691322 AAAGATC
1 AAAGATC
48691329 TTGAAAACGC
Statistics
Matches: 323, Mismatches: 109, Indels: 64
0.65 0.22 0.13
Matches are distributed among these distances:
111 3 0.01
112 28 0.09
113 66 0.20
114 95 0.29
115 69 0.21
116 60 0.19
118 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (112 bp):
AAAGATCAGAATTAACGGCGCTTAACGATAAACGCCGCAGAAAGTTAACCAAAACGCATCGTTTG
GCCTTGATCTATGGTGGCATTTAGCGGCGCTTTAAACGAACGCCACT
Found at i:48691487 original size:211 final size:210
Alignment explanation
Indices: 48691138--48691517 Score: 505
Period size: 211 Copynumber: 1.8 Consensus size: 210
48691128 CCGCCGAGTC
* *
48691138 TGTTAAAACTAAATGCAGCGTTTGGTTTTAATCAATTGCGATTCTAGCGGCGCTAATAAAAATCA
1 TGTTAAAACTAAACGCAGCGTTCGGTTTTAATCAATTGCGATTCTAGCGGCGCTAATAAAAATCA
* * *
48691203 CCGCGAAAGATCAGAATTAACGGCGCTTAACGAATAAACGCCGCAGAAAGTTAACCAAAACGCAT
66 CCGCGAAAGATCAGAATTAACGACACTTAACGAATAAACGCCGCAAAAAGTTAACCAAAACGCAT
* ** *
48691268 CGTTTGGCCTTGATTTATGGTGGCATTTAGCGGCGCTTTAAACCGAACGCCACTAAAGATCTTGA
131 CGTTTGGCCGTGAGGTATAGTGGCATTTAGCGGCGCTTTAAACCGAACGCCACTAAAGATCTTGA
48691333 AAACGCCGCAAAATA
196 AAACGCCGCAAAATA
* *
48691348 TGTTAAAACTAAACGCAGCGTTCGGTTTTGATCAATT-CTGGATT-TCGCGGCGCTAATTGAAAA
1 TGTTAAAACTAAACGCAGCGTTCGGTTTTAATCAATTGC--GATTCTAGCGGCGCTAA-T-AAAA
* * * * * * * **
48691411 A-CGCCGCTAAAGATCTGTATTAACGACATTTAACTAGTAAACGCTTCAAAAAGTTAACCAAAAC
62 ATCACCGCGAAAGATCAGAATTAACGACACTTAACGAATAAACGCCGCAAAAAGTTAACCAAAAC
* *
48691475 GCATCGTTTGGCCGTGAGGTATAGTGGCATTTAGTGGTGCTTT
127 GCATCGTTTGGCCGTGAGGTATAGTGGCATTTAGCGGCGCTTT
48691518 GCCTAAAAAC
Statistics
Matches: 144, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
209 1 0.01
210 45 0.31
211 93 0.65
212 5 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (210 bp):
TGTTAAAACTAAACGCAGCGTTCGGTTTTAATCAATTGCGATTCTAGCGGCGCTAATAAAAATCA
CCGCGAAAGATCAGAATTAACGACACTTAACGAATAAACGCCGCAAAAAGTTAACCAAAACGCAT
CGTTTGGCCGTGAGGTATAGTGGCATTTAGCGGCGCTTTAAACCGAACGCCACTAAAGATCTTGA
AAACGCCGCAAAATA
Found at i:48692203 original size:15 final size:16
Alignment explanation
Indices: 48692169--48692205 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
48692159 AAGGATTTAG
48692169 GGTATATTTGGGGATT
1 GGTATATTTGGGGATT
*
48692185 -GTAT-TTTGGGGTTT
1 GGTATATTTGGGGATT
48692199 GGTATAT
1 GGTATAT
48692206 ATTGTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 9 0.50
15 8 0.44
16 1 0.06
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (16 bp):
GGTATATTTGGGGATT
Found at i:48692330 original size:15 final size:15
Alignment explanation
Indices: 48692312--48692361 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
48692302 GGGTTTAGTA
48692312 GTTTAGTGTTTTATG
1 GTTTAGTGTTTTATG
*
48692327 GTTTATGAGTTTTAT-
1 GTTTA-GTGTTTTATG
* *
48692342 GTTTA-TGGTTTAGG
1 GTTTAGTGTTTTATG
48692356 GTTTAG
1 GTTTAG
48692362 AGCTTACGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 5 0.18
14 5 0.18
15 10 0.36
16 8 0.29
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (15 bp):
GTTTAGTGTTTTATG
Found at i:48694497 original size:15 final size:15
Alignment explanation
Indices: 48694477--48694512 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
48694467 ACCACCAATT
*
48694477 TGTTTTCATTTGTAC
1 TGTTTTCATTTCTAC
48694492 TGTTTTCATTTCTAC
1 TGTTTTCATTTCTAC
48694507 T-TTTTC
1 TGTTTTC
48694513 CTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (15 bp):
TGTTTTCATTTCTAC
Found at i:48695234 original size:93 final size:93
Alignment explanation
Indices: 48695127--48695536 Score: 639
Period size: 93 Copynumber: 4.4 Consensus size: 93
48695117 TACATACATT
*
48695127 ACATAACTTATTAATATATTTATGGATAAATGATACATAACTTACATAACTTATTAATACATATC
1 ACATAACTTATTAATATATTTATGGATAAATGATACATAACTTACATAACTTATTAATACATAAC
* *
48695192 ATT-TTTAATACATAACTTATATAATACG
66 -TTATATAATACATAACTTACATAATACG
* * **
48695220 ACATAACTTGTTAATATATATAT-TTTAAAATGATACATAACTTACATAACTTATTAATACATAA
1 ACATAACTTATTAATATATTTATGGAT-AAATGATACATAACTTACATAACTTATTAATACATAA
48695284 CTTATATAATACATAACTTACATAATACG
65 CTTATATAATACATAACTTACATAATACG
* *
48695313 ACATAACTTATTAATATATTTATGGATAAATGATACAAAACTTACATAACTTATTAATACTTAAC
1 ACATAACTTATTAATATATTTATGGATAAATGATACATAACTTACATAACTTATTAATACATAAC
*
48695378 ATT-TTTAATACATAACTTACATAATACG
66 -TTATATAATACATAACTTACATAATACG
* **
48695406 ACATAACTTATTAATATATATAT-TTTAAAATGATACATAACTTACATAACTTATTAATACATAA
1 ACATAACTTATTAATATATTTATGGAT-AAATGATACATAACTTACATAACTTATTAATACATAA
48695470 CTTATATAATACATAACTTACATAATACG
65 CTTATATAATACATAACTTACATAATACG
48695499 ACATAACTTATTAATATATTTATGGATAAATGATACAT
1 ACATAACTTATTAATATATTTATGGATAAATGATACAT
48695537 NNNNNNNNNN
Statistics
Matches: 287, Mismatches: 23, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
92 6 0.02
93 277 0.97
94 4 0.01
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (93 bp):
ACATAACTTATTAATATATTTATGGATAAATGATACATAACTTACATAACTTATTAATACATAAC
TTATATAATACATAACTTACATAATACG
Found at i:48695267 original size:9 final size:9
Alignment explanation
Indices: 48695253--48695308 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
48695243 TTTAAAATGA
48695253 TACATAACT
1 TACATAACT
48695262 TACATAACT
1 TACATAACT
*
48695271 TA-TTAA--
1 TACATAACT
48695277 TACATAACT
1 TACATAACT
*
48695286 TATATAA--
1 TACATAACT
48695293 TACATAACT
1 TACATAACT
48695302 TACATAA
1 TACATAA
48695309 TACGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.05
7 9 0.24
8 3 0.08
9 24 0.63
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:48695317 original size:50 final size:49
Alignment explanation
Indices: 48695170--48695514 Score: 288
Period size: 50 Copynumber: 7.3 Consensus size: 49
48695160 TACATAACTT
* * *
48695170 ACATAACTTATTAATACATATCATTTTTAATACATAACTTATATAATACG
1 ACATAACTTATTAATACATAAC-TTTATAATACATAACTTACATAATACG
* * * *
48695220 ACATAACTTGTTAATATATATA-TTT-TAA-A-ATGA--TACAT-A-ACTT
1 ACATAACTTATTAATACATA-ACTTTATAATACATAACTTACATAATAC-G
48695263 ACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
1 ACATAACTTATTAATACATAACTT-TATAATACATAACTTACATAATACG
* * * *
48695313 ACATAACTTATTAAT--AT-A-TTTATGGATAAATGA--TACA-AA-ACTT
1 ACATAACTTATTAATACATAACTTTAT-AATACATAACTTACATAATAC-G
* *
48695356 ACATAACTTATTAATACTTAACATTTTTAATACATAACTTACATAATACG
1 ACATAACTTATTAATACATAAC-TTTATAATACATAACTTACATAATACG
* * *
48695406 ACATAACTTATTAATATATATA-TTT-TAA-A-ATGA--TACAT-A-ACTT
1 ACATAACTTATTAATACATA-ACTTTATAATACATAACTTACATAATAC-G
48695449 ACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
1 ACATAACTTATTAATACATAACTT-TATAATACATAACTTACATAATACG
48695499 ACATAACTTATTAATA
1 ACATAACTTATTAATA
48695515 TATTTATGGA
Statistics
Matches: 235, Mismatches: 27, Indels: 66
0.72 0.08 0.20
Matches are distributed among these distances:
42 8 0.03
43 60 0.26
44 15 0.06
45 10 0.04
46 17 0.07
47 15 0.06
48 12 0.05
49 20 0.09
50 71 0.30
51 7 0.03
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (49 bp):
ACATAACTTATTAATACATAACTTTATAATACATAACTTACATAATACG
Found at i:48695322 original size:19 final size:16
Alignment explanation
Indices: 48695262--48695311 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
48695252 ATACATAACT
*
48695262 TACATAACTTA-TTAA
1 TACATAACTTACATAA
*
48695277 TACATAACTTATATAA
1 TACATAACTTACATAA
48695293 TACATAACTTACATAA
1 TACATAACTTACATAA
48695309 TAC
1 TAC
48695312 GACATAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:48695370 original size:186 final size:186
Alignment explanation
Indices: 48695127--48695535 Score: 773
Period size: 186 Copynumber: 2.2 Consensus size: 186
48695117 TACATACATT
* *
48695127 ACATAACTTATTAATATATTTATGGATAAATGATACATAACTTACATAACTTATTAATACATATC
1 ACATAACTTATTAATATATTTATGGATAAATGATACAAAACTTACATAACTTATTAATACATAAC
* *
48695192 ATTTTTAATACATAACTTATATAATACGACATAACTTGTTAATATATATATTTTAAAATGATACA
66 ATTTTTAATACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACA
48695257 TAACTTACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
131 TAACTTACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
*
48695313 ACATAACTTATTAATATATTTATGGATAAATGATACAAAACTTACATAACTTATTAATACTTAAC
1 ACATAACTTATTAATATATTTATGGATAAATGATACAAAACTTACATAACTTATTAATACATAAC
48695378 ATTTTTAATACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACA
66 ATTTTTAATACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACA
48695443 TAACTTACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
131 TAACTTACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
48695499 ACATAACTTATTAATATATTTATGGATAAATGATACA
1 ACATAACTTATTAATATATTTATGGATAAATGATACA
48695536 TNNNNNNNNN
Statistics
Matches: 218, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 218 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (186 bp):
ACATAACTTATTAATATATTTATGGATAAATGATACAAAACTTACATAACTTATTAATACATAAC
ATTTTTAATACATAACTTACATAATACGACATAACTTATTAATATATATATTTTAAAATGATACA
TAACTTACATAACTTATTAATACATAACTTATATAATACATAACTTACATAATACG
Found at i:48695453 original size:9 final size:9
Alignment explanation
Indices: 48695439--48695494 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
48695429 TTTAAAATGA
48695439 TACATAACT
1 TACATAACT
48695448 TACATAACT
1 TACATAACT
*
48695457 TA-TTAA--
1 TACATAACT
48695463 TACATAACT
1 TACATAACT
*
48695472 TATATAA--
1 TACATAACT
48695479 TACATAACT
1 TACATAACT
48695488 TACATAA
1 TACATAA
48695495 TACGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.05
7 9 0.24
8 3 0.08
9 24 0.63
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:48695484 original size:40 final size:43
Alignment explanation
Indices: 48695220--48695494 Score: 161
Period size: 43 Copynumber: 6.1 Consensus size: 43
48695210 ATATAATACG
* * * *
48695220 ACATAACTTGTTAATATATATATTTTAAAATGATACATAACTT
1 ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
*
48695263 ACATAACTTATTAATACATA-A-CTT-ATATAATACATAACTT
1 ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
* * * * *
48695303 ACATAATACGACATAACTTATTA-ATATATTTATGGATAAATGATACAAAACTT
1 AC---ATA--AC-TTA-TTAATACATATATCT-T--A-AAATAATACATAACTT
* * * *
48695356 ACATAACTTATTAATACTTAACATTTTTAATACATAACTTACATAA-TACG
1 ACATAACTTATTAATACAT-ATA-TCTTAA-A-ATAA--TACATAACT--T
* * *
48695406 ACATAACTTATTAATATATATATTTTAAAATGATACATAACTT
1 ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
*
48695449 ACATAACTTATTAATACATA-A-CTT-ATATAATACATAACTT
1 ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
48695489 ACATAA
1 ACATAA
48695495 TACGACATAA
Statistics
Matches: 181, Mismatches: 27, Indels: 51
0.70 0.10 0.20
Matches are distributed among these distances:
40 36 0.20
41 4 0.02
42 2 0.01
43 40 0.22
44 7 0.04
45 4 0.02
46 15 0.08
47 13 0.07
48 13 0.07
49 12 0.07
50 20 0.11
53 15 0.08
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.38
Consensus pattern (43 bp):
ACATAACTTATTAATACATATATCTTAAAATAATACATAACTT
Found at i:48695508 original size:19 final size:16
Alignment explanation
Indices: 48695448--48695497 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
48695438 ATACATAACT
*
48695448 TACATAACTTA-TTAA
1 TACATAACTTACATAA
*
48695463 TACATAACTTATATAA
1 TACATAACTTACATAA
48695479 TACATAACTTACATAA
1 TACATAACTTACATAA
48695495 TAC
1 TAC
48695498 GACATAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:48695798 original size:9 final size:9
Alignment explanation
Indices: 48695786--48695832 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
48695776 AATAAATTAA
48695786 ATAACTTAC
1 ATAACTTAC
48695795 ATAACTTAC
1 ATAACTTAC
* *
48695804 ATAAATTAA
1 ATAACTTAC
*
48695813 ATAAATTAC
1 ATAACTTAC
48695822 ATAACTTAC
1 ATAACTTAC
48695831 AT
1 AT
48695833 TACATAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:48695807 original size:18 final size:18
Alignment explanation
Indices: 48695777--48695832 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
48695767 TTGCATTTCA
*
48695777 ATAAATTAAATAACTTAC
1 ATAAATTACATAACTTAC
* * *
48695795 ATAACTTACATAAATTAA
1 ATAAATTACATAACTTAC
48695813 ATAAATTACATAACTTAC
1 ATAAATTACATAACTTAC
48695831 AT
1 AT
48695833 TACATAATAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATTACATAACTTAC
Found at i:48695815 original size:27 final size:27
Alignment explanation
Indices: 48695777--48695832 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
48695767 TTGCATTTCA
*
48695777 ATAAATTAAATAACTTACATAACTTAC
1 ATAAATTAAATAAATTACATAACTTAC
48695804 ATAAATTAAATAAATTACATAACTTAC
1 ATAAATTAAATAAATTACATAACTTAC
48695831 AT
1 AT
48695833 TACATAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAAATTAAATAAATTACATAACTTAC
Found at i:48695851 original size:36 final size:36
Alignment explanation
Indices: 48695776--48695848 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
48695766 TTTGCATTTC
* *
48695776 AATAAATTAAATAACTTACATAACTTACATAAATTA
1 AATAAATTAAATAACTTACATAACATACATAAATAA
* * *
48695812 AATAAATTACATAACTTACATTACATA-ATACATAA
1 AATAAATTAAATAACTTACATAACATACATAAATAA
48695847 AA
1 AA
48695849 ATATATCATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
35 8 0.25
36 24 0.75
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (36 bp):
AATAAATTAAATAACTTACATAACATACATAAATAA
Found at i:48701306 original size:2 final size:2
Alignment explanation
Indices: 48701293--48701327 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
48701283 TAATTAACCT
* *
48701293 TA TA TA TG TA TA TA TA TA TA TA TA GA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48701328 TTTAAGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48701628 original size:2 final size:2
Alignment explanation
Indices: 48701610--48701666 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
48701600 GAGCAAGCAG
* *
48701610 AT AT AT AG AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48701652 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
48701667 CTTTTTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48702296 original size:2 final size:2
Alignment explanation
Indices: 48702291--48702321 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48702281 ACACACACAC
48702291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48702322 AAAGTTCCAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48709495 original size:5 final size:6
Alignment explanation
Indices: 48709478--48709502 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48709468 CAATATTCCC
48709478 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
48709503 GAAATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:48714625 original size:14 final size:15
Alignment explanation
Indices: 48714601--48714630 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
48714591 AAGTTCTAAT
48714601 TTTATTTTTTTTAAA
1 TTTATTTTTTTTAAA
48714616 TTTA-TTTTTTTAAA
1 TTTATTTTTTTTAAA
48714630 T
1 T
48714631 AAAAAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTTTTTAAA
Found at i:48715733 original size:7 final size:7
Alignment explanation
Indices: 48715721--48715746 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48715711 TAGTCGATTC
48715721 GTATTTA
1 GTATTTA
48715728 GTATTTA
1 GTATTTA
48715735 GTATTTA
1 GTATTTA
48715742 GTATT
1 GTATT
48715747 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:48716462 original size:96 final size:95
Alignment explanation
Indices: 48716282--48716715 Score: 476
Period size: 96 Copynumber: 4.4 Consensus size: 95
48716272 AGTAACCCTA
* * * * * * *
48716282 AACCCTAAACCTTAGTTTATTTGATTTTTCTTTAAAAACCCTAAACCCTAAATCTTAATCTATTT
1 AACCCTAAACCCTAATTTATTTGATTTTTCTTTAAAAACCATAAACACTAAACCCTAATCTA-AT
*
48716347 TTTTTTAAATTTATAATTAATTTACTCAAGT
65 TTTTTAAAATTTATAATTAATTTACTCAAGT
* * *
48716378 AACCCTAAGCTCTAATTTATTTGACTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTCTTTAAAAACCATAAACACTAAACCCTAATCTAAT
48716443 TTTTTAAAATTTATAATTAATTTACTCAAGT
65 TTTTTAAAATTTATAATTAATTTACTCAAGT
*
48716474 AACCCTAAATCCTAATTTATTTGATTTTTCTTTAAAAACCTTAAACCTTAAACCTTAAACCCTAA
1 AACCCTAAACCCTAATTTATTTGATTTTTCTTTAAAAACC----A---TAAA-C----A--CTAA
* *
48716539 ACCCTAATCT-ATTTTTTAAAAAAAATTATAATTAATTTACTCAAAT
52 ACCCTAATCTAATTTTTT---AAAATTTATAATTAATTTACTCAAGT
** *
48716585 AACTTTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAA-T
1 AACCCTAAACCCTAATTTATTTGATTTTTCTTTAAAAACCATAAACACTAAACCCTAATCTAATT
* * * *
48716649 TTTTAAAATTTATAACTAATTTAATTAAGA
66 TTTTAAAATTTATAATTAATTTACTCAAGT
* *
48716679 AACCCTAAACCCTTATTTATTTAATTTTTCTTTAAAA
1 AACCCTAAACCCTAATTTATTTGATTTTTCTTTAAAA
48716716 CCCTAAAATT
Statistics
Matches: 287, Mismatches: 32, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
94 52 0.18
95 15 0.05
96 72 0.25
97 52 0.18
98 1 0.00
99 2 0.01
102 4 0.01
103 2 0.01
104 4 0.01
107 2 0.01
108 7 0.02
109 14 0.05
111 60 0.21
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTGATTTTTCTTTAAAAACCATAAACACTAAACCCTAATCTAATT
TTTTAAAATTTATAATTAATTTACTCAAGT
Found at i:48716545 original size:7 final size:7
Alignment explanation
Indices: 48716509--48716541 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
48716499 TTTTCTTTAA
48716509 AAACCTT
1 AAACCTT
48716516 AAACCTT
1 AAACCTT
48716523 AAACCTT
1 AAACCTT
*
48716530 AAACCCT
1 AAACCTT
48716537 AAACC
1 AAACC
48716542 CTAATCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCTT
Found at i:48716599 original size:111 final size:109
Alignment explanation
Indices: 48716414--48716638 Score: 319
Period size: 111 Copynumber: 2.0 Consensus size: 109
48716404 TTTTCCTTAA
* *
48716414 AAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAATTAATTTACTCAAGTAACCC
1 AAACCATAAACACTAAACCCTAATCTAATTTTTTAAAAATTATAATTAATTTACTCAAATAACCC
* * *
48716479 TAAATCCTAATTTATTTGATTTTTCTTTAAAAACCTTAAAC-CTT
66 TAAACCCTAATTTATTTGATTTTTCCTTAAAAACCATAAACAC-T
* *
48716523 AAACCTTAAACCCTAAACCCTAATCT-ATTTTTTAAAAAAAATTATAATTAATTTACTCAAATAA
1 AAACCATAAACACTAAACCCTAATCTAATTTTTT---AAAAATTATAATTAATTTACTCAAATAA
**
48716587 CTTTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCATAAACACT
63 CCCTAAACCCTAATTTATTTGATTTTTCCTTAAAAACCATAAACACT
48716634 AAACC
1 AAACC
48716639 CTAATCTAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
108 7 0.07
109 24 0.23
111 71 0.69
112 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.37
Consensus pattern (109 bp):
AAACCATAAACACTAAACCCTAATCTAATTTTTTAAAAATTATAATTAATTTACTCAAATAACCC
TAAACCCTAATTTATTTGATTTTTCCTTAAAAACCATAAACACT
Found at i:48716616 original size:206 final size:205
Alignment explanation
Indices: 48716317--48716715 Score: 602
Period size: 206 Copynumber: 1.9 Consensus size: 205
48716307 TTTTCTTTAA
* * *** * *
48716317 AAACCCTAAACCCTAAATCTTAATCTATTTTTTTTTAAATTTATAATTAATTTACTCAAGTAACC
1 AAACCCTAAACCCTAAACCCTAATCTATTTTTTAAAAAAATTATAATTAATTTACTCAAATAACC
* *
48716382 CTAAGCTCTAATTTATTTGACTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTT
66 CTAAACCCTAATTTATTTGACTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAA-TTTT
* * * * *
48716447 TAAAATTTATAATTAATTTACTCAAGTAACCCTAAATCCTAATTTATTTGATTTTTCTTTAAAAA
130 TAAAATTTATAACTAATTTAATCAAGAAACCCTAAACCCTAATTTATTTAATTTTTCTTTAAAAA
48716512 CCTTAAACCTT
195 CCTTAAACCTT
*
48716523 AAACCTTAAACCCTAAACCCTAATCTATTTTTTAAAAAAAATTATAATTAATTTACTCAAATAAC
1 AAACCCTAAACCCTAAACCCTAATCTATTTTTT-AAAAAAATTATAATTAATTTACTCAAATAAC
**
48716588 TTTAAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTT
65 CCTAAACCCTAATTTATTTGACTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTT
* *
48716652 TAAAATTTATAACTAATTTAATTAAGAAACCCTAAACCCTTATTTATTTAATTTTTCTTTAAAA
130 TAAAATTTATAACTAATTTAATCAAGAAACCCTAAACCCTAATTTATTTAATTTTTCTTTAAAA
48716716 CCCTAAAATT
Statistics
Matches: 173, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
205 61 0.35
206 69 0.40
207 43 0.25
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.41
Consensus pattern (205 bp):
AAACCCTAAACCCTAAACCCTAATCTATTTTTTAAAAAAATTATAATTAATTTACTCAAATAACC
CTAAACCCTAATTTATTTGACTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTT
AAAATTTATAACTAATTTAATCAAGAAACCCTAAACCCTAATTTATTTAATTTTTCTTTAAAAAC
CTTAAACCTT
Found at i:48716727 original size:15 final size:15
Alignment explanation
Indices: 48716709--48716738 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48716699 TTAATTTTTC
*
48716709 TTTAAAACCCTAAAA
1 TTTAAAAACCTAAAA
48716724 TTTAAAAACCTAAAA
1 TTTAAAAACCTAAAA
48716739 ACCCTAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (15 bp):
TTTAAAAACCTAAAA
Found at i:48720390 original size:2 final size:2
Alignment explanation
Indices: 48720379--48720421 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
48720369 CAATTGTGTG
* *
48720379 TA TA TG TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48720421 T
1 T
48720422 TAATAATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48720817 original size:18 final size:19
Alignment explanation
Indices: 48720778--48720817 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
48720768 CCCAAAACCA
*
48720778 AAATAGTCTCAAATTGTCC
1 AAATAGTCTCAAATTGTAC
*
48720797 AAATAGTC-CAAATTTTAC
1 AAATAGTCTCAAATTGTAC
48720815 AAA
1 AAA
48720818 ACACTTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (19 bp):
AAATAGTCTCAAATTGTAC
Found at i:48723988 original size:19 final size:19
Alignment explanation
Indices: 48723960--48724003 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
48723950 AACATTATGT
*
48723960 AAAAATTTTAAA-TAAAACA
1 AAAAAATTTAAATTAAAA-A
48723979 AAAAAATTTAAATTAAAAA
1 AAAAAATTTAAATTAAAAA
48723998 AAAAAA
1 AAAAAA
48724004 CTAAACCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAATTTAAATTAAAAA
Found at i:48733551 original size:29 final size:29
Alignment explanation
Indices: 48733451--48733552 Score: 78
Period size: 29 Copynumber: 3.5 Consensus size: 29
48733441 TTAATTAGGC
* *
48733451 ACTATGTGTCGGTGATTATAGTTATCAAGT
1 ACTATGTGTCGGTG-TTATAATTATCAGGT
* * * * * *
48733481 ACTTTCTATTGGTGTTACAATTATCAGGC
1 ACTATGTGTCGGTGTTATAATTATCAGGT
** * * *
48733510 ACCCTATGCCGGTGTTATATTTATCAGGT
1 ACTATGTGTCGGTGTTATAATTATCAGGT
48733539 ACTATGTGTCGGTG
1 ACTATGTGTCGGTG
48733553 GTGGATATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 1
0.70 0.29 0.01
Matches are distributed among these distances:
29 41 0.80
30 10 0.20
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (29 bp):
ACTATGTGTCGGTGTTATAATTATCAGGT
Found at i:48739618 original size:17 final size:18
Alignment explanation
Indices: 48739593--48739626 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48739583 TTTAATTTCT
48739593 ATTTCTTATTTATTTATA
1 ATTTCTTATTTATTTATA
*
48739611 ATTT-TTATTTTTTTAT
1 ATTTCTTATTTATTTAT
48739627 TCTCAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTCTTATTTATTTATA
Found at i:48741916 original size:34 final size:34
Alignment explanation
Indices: 48741855--48741923 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
48741845 GAGCCCATAA
48741855 GACATGCGAACCCTATGCTATGCGAACCCCATGT
1 GACATGCGAACCCTATGCTATGCGAACCCCATGT
* * * * *
48741889 GACATGTGAACCCTATGTTGTGTGAACCCTATGT
1 GACATGCGAACCCTATGCTATGCGAACCCCATGT
48741923 G
1 G
48741924 TATTGGGAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (34 bp):
GACATGCGAACCCTATGCTATGCGAACCCCATGT
Found at i:48743816 original size:40 final size:41
Alignment explanation
Indices: 48743712--48743823 Score: 136
Period size: 43 Copynumber: 2.7 Consensus size: 41
48743702 GATAAAGCAG
**
48743712 GAAAACGCTTCCTTAAGGAAGCATTTTGTCCACGTGGACAAAA
1 GAAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGAC--AA
* **
48743755 AAAAACGCTTCCCCAAGGAAGCGCTTTGTCCACGTGGAC-A
1 GAAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGACAA
* *
48743795 GAAAATGCTTCCTTGAGGAAGCGCTTTGT
1 GAAAACGCTTCCTTAAGGAAGCGCTTTGT
48743824 GTCCACGTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 25 0.42
43 34 0.58
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (41 bp):
GAAAACGCTTCCTTAAGGAAGCGCTTTGTCCACGTGGACAA
Found at i:48743837 original size:19 final size:19
Alignment explanation
Indices: 48743813--48743850 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
48743803 TTCCTTGAGG
* *
48743813 AAGCGCTTTGTGTCCACGT
1 AAGCGCCTTCTGTCCACGT
48743832 AAGCGCCTTCTGTCCACGT
1 AAGCGCCTTCTGTCCACGT
48743851 GGACAAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.32, G:0.24, T:0.29
Consensus pattern (19 bp):
AAGCGCCTTCTGTCCACGT
Found at i:48744131 original size:97 final size:94
Alignment explanation
Indices: 48743987--48744276 Score: 402
Period size: 97 Copynumber: 3.0 Consensus size: 94
48743977 AAATAAGGGT
* * * * *
48743987 TTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTAAAAAAAATTAGATTAGAGTTTAGA
1 TTAGGGTTTA-GGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAGA
*
48744052 GTTTATGGTTTTTAAGGAAAAAATTAAATAAA
65 GTTTA-GGTTTTTAAGG-AAAAATCAAATAAA
*
48744084 TTCGGGTTTAGGATTACTTGAGTAAATTAATTATAAATTTTTAAAAAAATTAGATTAGGGTTTAG
1 TTAGGGTTTAGG-TTACTTGAGTAAATTAATTATAAA-TTTTAAAAAAATTAGATTAGGGTTTAG
*
48744149 TGTTTAAGGTTTTTAAGGAAAAATCAAATAAA
64 AGTTT-AGGTTTTTAAGGAAAAATCAAATAAA
* *
48744181 TTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTGAAAAAATTAGATTGGGGTTTAGT
1 TTAGGGTTT-AGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAG-
48744246 A-TTTAGAGTTTTTAAGGAAAAATCAAATAAA
64 AGTTTAG-GTTTTTAAGGAAAAATCAAATAAA
48744277 ACTAGTTGTT
Statistics
Matches: 175, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
95 2 0.01
96 54 0.31
97 75 0.43
98 43 0.25
99 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (94 bp):
TTAGGGTTTAGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAGAG
TTTAGGTTTTTAAGGAAAAATCAAATAAA
Found at i:48744969 original size:11 final size:11
Alignment explanation
Indices: 48744919--48744944 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48744909 GTTAGACTTA
48744919 ATAAATAATTT
1 ATAAATAATTT
48744930 ATAAATAATTT
1 ATAAATAATTT
48744941 ATAA
1 ATAA
48744945 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:48745585 original size:2 final size:2
Alignment explanation
Indices: 48745578--48745604 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48745568 TAAGAAAAAT
48745578 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 T
48745605 TCAAATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48747002 original size:34 final size:33
Alignment explanation
Indices: 48746959--48747074 Score: 160
Period size: 34 Copynumber: 3.4 Consensus size: 33
48746949 CGAATCTCAG
*
48746959 ATCAGAATGTCACATTACCAGAAACATATATCAT
1 ATCAGAATGTCATATT-CCAGAAACATATATCAT
* *
48746993 ATCAGAATGTCATATTTCCAGAAACATATACCAA
1 ATCAGAATGTCATA-TTCCAGAAACATATATCAT
* *
48747027 ATCAGAATGTCATAGTTTCATAAACATATATCAT
1 ATCAGAATGTCATA-TTCCAGAAACATATATCAT
48747061 ATCAGAATGTCATA
1 ATCAGAATGTCATA
48747075 CCATATCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
34 71 0.97
35 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (33 bp):
ATCAGAATGTCATATTCCAGAAACATATATCAT
Found at i:48748387 original size:32 final size:35
Alignment explanation
Indices: 48748341--48748412 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 35
48748331 GTTTTCTAAA
48748341 CGGGCCTCATTTTTTAGCCC-AAT-C-C-CATATTT
1 CGGGCCTCATTTTTTA-CCCAAATCCTCTCATATTT
48748373 CGGGCCT-ATATTTTTACCCAAATCCTCTCATATTT
1 CGGGCCTCAT-TTTTTACCCAAATCCTCTCATATTT
48748408 CGGGC
1 CGGGC
48748413 AGGCCATGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
31 5 0.14
32 16 0.46
33 1 0.03
34 1 0.03
35 12 0.34
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (35 bp):
CGGGCCTCATTTTTTACCCAAATCCTCTCATATTT
Found at i:48749335 original size:41 final size:39
Alignment explanation
Indices: 48749233--48749336 Score: 111
Period size: 41 Copynumber: 2.6 Consensus size: 39
48749223 CGATAATATT
* * *
48749233 CAGGCTTTGTGCCGGTGATAT-TCAGGCTTCGTGCCTAG
1 CAGGCTTTGTGCCGGTGTTATATCAAGCTCCGTGCCTAG
* *
48749271 CAAGCTTTATGCCGGTGTATTATATCAAGCTCCGTGCCTAG
1 CAGGCTTTGTGCCGGTG--TTATATCAAGCTCCGTGCCTAG
*
48749312 CAGGCTTTGTTCCGACGTGTTATAT
1 CAGGCTTTGTGCCG--GTGTTATAT
48749337 TAGCCTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
38 15 0.28
40 3 0.06
41 32 0.60
43 3 0.06
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (39 bp):
CAGGCTTTGTGCCGGTGTTATATCAAGCTCCGTGCCTAG
Found at i:48751105 original size:22 final size:22
Alignment explanation
Indices: 48751071--48751119 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
48751061 AAAAAATGGG
48751071 CTCACATGGCCTAC-CTGACCTA
1 CTCACATGGCCTACAC-GACCTA
* *
48751093 CTCATATGTCCTACACGACCTA
1 CTCACATGGCCTACACGACCTA
48751115 C-CACA
1 CTCACA
48751120 ATTGCTCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.13
22 19 0.83
23 1 0.04
ACGTcount: A:0.27, C:0.41, G:0.10, T:0.22
Consensus pattern (22 bp):
CTCACATGGCCTACACGACCTA
Found at i:48751170 original size:24 final size:24
Alignment explanation
Indices: 48751143--48751188 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
48751133 TCGTACACGG
48751143 CTTGGCACACGG-TCGACCACACAC
1 CTTGGCACACGGCT-GACCACACAC
*
48751167 CTTGGCACATGGCTGACCACAC
1 CTTGGCACACGGCTGACCACAC
48751189 GCCCGTGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.24, C:0.39, G:0.22, T:0.15
Consensus pattern (24 bp):
CTTGGCACACGGCTGACCACACAC
Found at i:48751214 original size:29 final size:29
Alignment explanation
Indices: 48751182--48751247 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
48751172 CACATGGCTG
* *
48751182 ACCACACGCCCGTGTGGTGCACACTGCCA
1 ACCACACGACCGTGTGGTGCACACGGCCA
48751211 ACCACACGACCGTGTGGTGCACACGGCCA
1 ACCACACGACCGTGTGGTGCACACGGCCA
48751240 ACCACACG
1 ACCACACG
48751248 GCCATTTGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.11
Consensus pattern (29 bp):
ACCACACGACCGTGTGGTGCACACGGCCA
Found at i:48755752 original size:18 final size:19
Alignment explanation
Indices: 48755708--48755745 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
48755698 ATATACCATG
*
48755708 TTAACAAATAATTTAAAAA
1 TTAAAAAATAATTTAAAAA
*
48755727 TTATAAAAT-ATTTAAAAA
1 TTAAAAAATAATTTAAAAA
48755745 T
1 T
48755746 ACAAAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAAAAATAATTTAAAAA
Found at i:48756743 original size:4 final size:4
Alignment explanation
Indices: 48756736--48756793 Score: 98
Period size: 4 Copynumber: 14.5 Consensus size: 4
48756726 ACATATATTA
* *
48756736 ATGT ATGT ATGT ATGT ATGT ATGC ATGT ATGT ATTT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
48756784 ATGT ATGT AT
1 ATGT ATGT AT
48756794 AGAGGAATGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (4 bp):
ATGT
Done.