Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 153 of 187
Found at i:45501057 original size:49 final size:48
Alignment explanation
Indices: 45501000--45501105 Score: 133
Period size: 49 Copynumber: 2.2 Consensus size: 48
45500990 CACATGGCCT
* * *
45501000 ACCACACGGTCTGCAATG-TTTCACATGGTCATGTGCTCTACACGGCCA
1 ACCACACGGGCTGCAA-GATTTCACACGGTCATGTGCTCTACACGACCA
* *
45501048 AGCCACACGGGCTGCAAGATTTCACACGGTCTTGTGCTTTACACGACCA
1 A-CCACACGGGCTGCAAGATTTCACACGGTCATGTGCTCTACACGACCA
45501097 ACCAACACG
1 ACC-ACACG
45501106 ACCTGCAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
48 4 0.08
49 46 0.92
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.22
Consensus pattern (48 bp):
ACCACACGGGCTGCAAGATTTCACACGGTCATGTGCTCTACACGACCA
Found at i:45504787 original size:5 final size:5
Alignment explanation
Indices: 45504771--45504807 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
45504761 AATACTTATT
45504771 TTTTA -TTT- TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
45504808 GTTGATATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.20
5 24 0.80
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTA
Found at i:45508296 original size:34 final size:34
Alignment explanation
Indices: 45508253--45508326 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
45508243 CACAATTGCA
*
45508253 AAGGAAGCATGGAAAATACTTCAAACTGCTGACC
1 AAGGAAGCATGGAAAATACTTCAAACTGCTCACC
45508287 AAGGAAGCATGGAAAATACTTCAAACTGCTCACC
1 AAGGAAGCATGGAAAATACTTCAAACTGCTCACC
45508321 AAGGAA
1 AAGGAA
45508327 CTAATATGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (34 bp):
AAGGAAGCATGGAAAATACTTCAAACTGCTCACC
Found at i:45517857 original size:13 final size:13
Alignment explanation
Indices: 45517839--45517868 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45517829 TCCAGCAACT
45517839 ATGAATTTATTTC
1 ATGAATTTATTTC
*
45517852 ATGAATTTATTTG
1 ATGAATTTATTTC
45517865 ATGA
1 ATGA
45517869 TGATCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:45518022 original size:50 final size:50
Alignment explanation
Indices: 45517963--45518305 Score: 461
Period size: 50 Copynumber: 6.8 Consensus size: 50
45517953 ATTTGGGTAA
* *
45517963 AGAGGTCCCATGTAAGACCTTGTCTGGGACATGGCATTAGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
45518013 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
45518063 ACAGGTCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCTAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
45518113 AGAGGTCCTATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
45518163 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGCCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * * * *
45518213 GGAGGTCCCCCGAAAGACCATGTCTGGGATATGGCATGGGCACCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
45518263 AGTACATCCCACGTAAGATCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45518306 TGTTATTATC
Statistics
Matches: 256, Mismatches: 36, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
50 224 0.88
51 32 0.12
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:45525688 original size:50 final size:50
Alignment explanation
Indices: 45525609--45525900 Score: 390
Period size: 50 Copynumber: 5.8 Consensus size: 50
45525599 TTTGGGTAAG
* *
45525609 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAACGAGATTA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
* * * *
45525659 GAGCTCCCATGTAAGACCATATCTGGGACATGACGTTGGCACCGAGATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
* *
45525709 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGG
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
45525759 GAGGTCCCATGTAAGACCATGTCTAGGG-CATGGCATTGGCACCGAGATGA
1 GAGGTCCCATGTAAGACCATGTCT-GGGACATGGCATTGGCACCGAGATGA
** *
45525809 GAGGTCCCCCGTAAGACCATGTCTGGGACATGGCA-TGGACACCGACATGA
1 GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATGA
** ** * *
45525859 GTACATCTTATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 G-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
45525901 TGTTATTATC
Statistics
Matches: 214, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
49 6 0.03
50 174 0.81
51 31 0.14
52 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
GAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA
Found at i:45546180 original size:24 final size:24
Alignment explanation
Indices: 45546152--45546203 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
45546142 TTTCTAGAAG
* * *
45546152 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATAAGCATAATAT
*
45546176 ATTTAGAATTTATAAGCATAATTT
1 ATTTAGAATTTATAAGCATAATAT
45546200 ATTT
1 ATTT
45546204 GACCTACGAA
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:0.02, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGAATTTATAAGCATAATAT
Found at i:45550511 original size:20 final size:19
Alignment explanation
Indices: 45550488--45550543 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 19
45550478 GGTGAGAAGT
45550488 AAAAGTTTAGGGGGAAAATA
1 AAAAGTTT-GGGGGAAAATA
*
45550508 AAAAGTTTTGGGG---A-A
1 AAAAGTTTGGGGGAAAATA
*
45550523 AAAAGTTTGAGGGAAAATA
1 AAAAGTTTGGGGGAAAATA
45550542 AA
1 AA
45550544 TAGGTGGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
15 12 0.41
16 1 0.03
18 1 0.03
19 7 0.24
20 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (19 bp):
AAAAGTTTGGGGGAAAATA
Found at i:45550657 original size:31 final size:30
Alignment explanation
Indices: 45550622--45550681 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
45550612 GGAGATGGGA
45550622 TGGGA-AGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAGAGAGAA-AAAA-TTTTAGGGGAAAAG
* *
45550653 TGGGAGGGAGAAAAAATTTTGGGGGAAAA
1 TGGGAGAGAGAAAAAATTTTAGGGGAAAA
45550682 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 9 0.35
32 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.18
Consensus pattern (30 bp):
TGGGAGAGAGAAAAAATTTTAGGGGAAAAG
Found at i:45550984 original size:9 final size:9
Alignment explanation
Indices: 45550967--45550997 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
45550957 TCAAGTTGAT
45550967 TCGAATAAC
1 TCGAATAAC
*
45550976 TCGATTAAC
1 TCGAATAAC
45550985 TCGAATAAC
1 TCGAATAAC
45550994 TCGA
1 TCGA
45550998 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:45551515 original size:18 final size:16
Alignment explanation
Indices: 45551481--45551539 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
45551471 TTTATAATTT
* *
45551481 TTTTTTACTTTT-GAA
1 TTTTTTATTTTTAAAA
45551496 TTTTTTATTTCTTGAAAA
1 TTTTTTATTT-TT-AAAA
45551514 TTTTTATATTTTTAAAA
1 TTTTT-TATTTTTAAAA
*
45551531 TTATTTATT
1 TTTTTTATT
45551540 GACATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.24
16 6 0.16
17 8 0.22
18 9 0.24
19 5 0.14
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTTTATTTTTAAAA
Found at i:45551517 original size:17 final size:16
Alignment explanation
Indices: 45551482--45551539 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
45551472 TTATAATTTT
* *
45551482 TTTTTACTTTTG-AAT
1 TTTTTATTTTTGAAAA
45551497 TTTTTATTTCTTGAAAA
1 TTTTTATTT-TTGAAAA
*
45551514 TTTTTATATTTTTAAAA
1 TTTTTAT-TTTTGAAAA
45551531 TTATTTATT
1 TT-TTTATT
45551540 GACATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 8 0.22
16 3 0.08
17 18 0.50
18 7 0.19
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTTATTTTTGAAAA
Found at i:45551518 original size:19 final size:17
Alignment explanation
Indices: 45551494--45551538 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
45551484 TTTACTTTTG
45551494 AATTTTT-TATTTCTTGAA
1 AATTTTTATATTT-TT-AA
45551512 AATTTTTATATTTTTAA
1 AATTTTTATATTTTTAA
45551529 AATTATTTAT
1 AATT-TTTAT
45551539 TGACATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.24
18 14 0.56
19 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTTATATTTTTAA
Found at i:45552314 original size:20 final size:20
Alignment explanation
Indices: 45552286--45552323 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45552276 CAAAGGGGCG
45552286 TCAAACTTTTTAATGTATAC
1 TCAAACTTTTTAATGTATAC
* *
45552306 TCAATCTTTTTCATGTAT
1 TCAAACTTTTTAATGTAT
45552324 TTGGAATATC
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:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (20 bp):
TCAAACTTTTTAATGTATAC
Found at i:45568964 original size:5 final size:5
Alignment explanation
Indices: 45568954--45569004 Score: 68
Period size: 5 Copynumber: 10.2 Consensus size: 5
45568944 ATATATTAAT
* *
45568954 TTCAA TTCAA TTCAA TTCAA TTCAA TTCAA -TCAA TTTTAA ATCAA TTCAA
1 TTCAA TTCAA TTCAA TTCAA TTCAA TTCAA TTCAA -TTCAA TTCAA TTCAA
45569004 T
1 T
45569005 AATCAAAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
4 4 0.10
5 33 0.82
6 3 0.08
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCAA
Found at i:45570653 original size:2 final size:2
Alignment explanation
Indices: 45570646--45570679 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
45570636 TGAGTTTTTG
45570646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45570680 TTGCATCGTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45573795 original size:16 final size:16
Alignment explanation
Indices: 45573772--45573816 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
45573762 ATTTCTAAAT
45573772 AAATAATTATTTTA-A
1 AAATAATTATTTTATA
**
45573787 AAATAAATTAAATTATA
1 AAAT-AATTATTTTATA
45573804 AAATAATTATTTT
1 AAATAATTATTTT
45573817 TAATTGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATAATTATTTTATA
Found at i:45580092 original size:44 final size:44
Alignment explanation
Indices: 45580013--45580582 Score: 203
Period size: 44 Copynumber: 12.6 Consensus size: 44
45580003 CATAGCAAAC
* * * * *
45580013 CTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTTACTAGT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATACAAGT
*
45580057 CTTATCTCCTTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAA-T
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AAGT
* * * *
45580102 CTTATTTTCC-TGAAGTTGTAGTGGAACAGATTGAAGCTATAAATTGCAGAT
1 CTTA-TCTCCTTGAAGTTGCAGTGGAGCAGATTGAAG--ATACA----AG-T
* * **
45580153 CTTATCT-CTCTGAAGTTGCAGTAGAGCAGA-T---CATAGCAAAC
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAGT
* *
45580194 CTTATCT-CTCTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGT
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGATACAAGT
* *
45580238 CTTATCTCTTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-T
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATA-C-AAGT
* * * * *
45580283 CTTAAT-TCCCTGAAGTTGTAGTGGAACTGATTGAAGCTATAAATTGTAGAT
1 CTT-ATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAG--ATACA----AG-T
** * * * *
45580334 CTTATCT-CTCTGAAGTTGCAGCAGAACAGA-T-CATAT-CAAAT
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGATACAAGT
* * * * **
45580375 CTTATCT-CTCTGAAGTTGCAGTAGAGTAGA-T-CATAT-CAAAC
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGATACAAGT
* * * * * *
45580416 CTTATCT-CTCTAAAGTTGTAGTGGAACAGGTTAAAAATAAACCAA-T
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGAT--A-CAAGT
* * *
45580462 CTTATCTCCCTGAAGGTGCAGTGGAGCAGATTGAAGACAGGATACAAAT
1 CTTATCTCCTTGAAGTTGCAGTGGAGCAGATT---GA-A-GATACAAGT
* * * **
45580511 CTTATCT-CTCTGAAGTTGTAGTGGAGCAGATTAAAGACACAAAC
1 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGATTGAAGATACAAGT
* *
45580555 CTTATCTTCC-TGAAGTTGTAGTAGAGCA
1 CTTATC-TCCTTGAAGTTGCAGTGGAGCA
45580583 AATTAAAGCT
Statistics
Matches: 407, Mismatches: 71, Indels: 96
0.71 0.12 0.17
Matches are distributed among these distances:
41 91 0.22
42 4 0.01
43 3 0.01
44 100 0.25
45 69 0.17
46 37 0.09
47 12 0.03
48 4 0.01
49 34 0.08
50 8 0.02
51 45 0.11
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (44 bp):
CTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATACAAGT
Found at i:45580125 original size:89 final size:88
Alignment explanation
Indices: 45580021--45580307 Score: 287
Period size: 89 Copynumber: 3.2 Consensus size: 88
45580011 ACCTTATCTC
*
45580021 CCTGAAGTTGCAGTGGAGTAGGTTGAAGTTACTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAG
1 CCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAG
45580086 AATGAAGATAGCGAATCTTATTTT
66 AATGAAGATAGCGAATCTTA-TTT
* * * *
45580110 CCTGAAGTTGTAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCT-CTCTGAAGTTGCAG
1 CCTGAAGTTGCAGTGGAGCAGGTTGAAG-T-T--ACT--AG-TCTTATCTCCT-TGAAGTTGCAG
* * * * *
45580174 TAGAGCAG-AT---CATAGCAAACCTTATCT
58 TGGAGCAGAATGAAGATAGCGAATCTTATTT
* * * *
45580201 CTCTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATCTCTTTGAAGTTGCAGTGGAGCA
1 C-CTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCA
* *
45580266 GACTGAAGATAGCGAATCTTAATTC
65 GAATGAAGATAGCGAATCTT-ATTT
*
45580291 CCTGAAGTTGTAGTGGA
1 CCTGAAGTTGCAGTGGA
45580308 ACTGATTGAA
Statistics
Matches: 156, Mismatches: 27, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
85 26 0.17
86 4 0.03
88 1 0.01
89 48 0.31
90 5 0.03
91 4 0.03
92 34 0.22
93 2 0.01
95 6 0.04
96 26 0.17
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (88 bp):
CCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAG
AATGAAGATAGCGAATCTTATTT
Found at i:45580183 original size:51 final size:47
Alignment explanation
Indices: 45580056--45580399 Score: 180
Period size: 45 Copynumber: 7.6 Consensus size: 47
45580046 AAGTTACTAG
* * *
45580056 TCTTATCTC-CTTGAAGTTGCAGTGGAGCAGAATGAAG-AT-AGC-GAA
1 TCTTATCTCTC-TGAAGTTGCAGTAGAACAGATTGAAGCATAAGCAG-A
* * *
45580101 TCTTAT-TTTCCTGAAGTTGTAGTGGAACAGATTGAAGCTATAAATTGCAGA
1 TCTTATCTCT-CTGAAGTTGCAGTAGAACAGATTGAAGC-AT-AA--GCAGA
* *
45580152 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T----CAT-AGCAAA
1 TCTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGCATAAGCAGA
* * *
45580193 CCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAG-AT-A-CA-A
1 TCTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGCATAAGCAGA
* * * *
45580236 GTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACTGAAG-AT-AGC-GAA
1 -TCTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGCATAAGCAG-A
* * * * *
45580282 TCTTAAT-TCCCTGAAGTTGTAGTGGAACTGATTGAAGCTATAAATTGTAGA
1 TCTT-ATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGC-AT-AA--GCAGA
* * *
45580333 TCTTATCTCTCTGAAGTTGCAGCAGAACAGA-T----CAT-ATCAAA
1 TCTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGCATAAGCAGA
45580374 TCTTATCTCTCTGAAGTTGCAGTAGA
1 TCTTATCTCTCTGAAGTTGCAGTAGA
45580400 GTAGATCATA
Statistics
Matches: 239, Mismatches: 32, Indels: 60
0.72 0.10 0.18
Matches are distributed among these distances:
41 60 0.25
42 1 0.00
43 3 0.01
44 38 0.16
45 65 0.27
46 6 0.03
47 4 0.02
49 2 0.01
50 4 0.02
51 52 0.22
52 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (47 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAACAGATTGAAGCATAAGCAGA
Found at i:45580210 original size:41 final size:41
Alignment explanation
Indices: 45580151--45580433 Score: 183
Period size: 41 Copynumber: 6.5 Consensus size: 41
45580141 TAAATTGCAG
45580151 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAA
* * *
45580192 ACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGA-AGATACAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCA-GATCATAG---CAA
* * * * *
45580236 GTCTTATCTCTTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATAGCAA
* * * * * * *
45580281 ATCTTAAT-TCCCTGAAGTTGTAGTGGAACTGATTGAAGCTATAAATTGTAG
1 ATCTT-ATCTCTCTGAAGTTGCAGT---A--GA--GCAG--AT-CATAGCAA
* * *
45580332 ATCTTATCTCTCTGAAGTTGCAGCAGAACAGATCATATCAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAA
* *
45580373 ATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCATATCAA
1 ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAA
* *
45580414 ACCTTATCTCTCTAAAGTTG
1 ATCTTATCTCTCTGAAGTTG
45580434 TAGTGGAACA
Statistics
Matches: 187, Mismatches: 35, Indels: 40
0.71 0.13 0.15
Matches are distributed among these distances:
41 90 0.48
42 5 0.03
43 1 0.01
44 32 0.17
45 19 0.10
46 4 0.02
47 2 0.01
48 3 0.02
50 4 0.02
51 22 0.12
52 3 0.02
53 1 0.01
54 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (41 bp):
ATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAGCAA
Found at i:45580303 original size:181 final size:181
Alignment explanation
Indices: 45579999--45580400 Score: 669
Period size: 181 Copynumber: 2.2 Consensus size: 181
45579989 GATGGATTGA
* * * * *
45579999 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTTACTAGTCTTATCT
1 AGATCATAGCAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATCT
* *
45580064 CCTTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATCTTATTTTCCTGAAGTTGTAGTGGAAC
66 CCTTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATCTTAATTCCCTGAAGTTGTAGTGGAAC
* *
45580129 AGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
131 AGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGCAGAAC
45580180 AGATCATAGCAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATCT
1 AGATCATAGCAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATCT
* *
45580245 CTTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTAATTCCCTGAAGTTGTAGTGGAAC
66 CCTTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATCTTAATTCCCTGAAGTTGTAGTGGAAC
* *
45580310 TGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTGCAGCAGAAC
131 AGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGCAGAAC
* *
45580361 AGATCATATCAAATCTTATCTCTCTGAAGTTGCAGTAGAG
1 AGATCATAGCAAACCTTATCTCTCTGAAGTTGCAGTAGAG
45580401 TAGATCATAT
Statistics
Matches: 206, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
181 206 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (181 bp):
AGATCATAGCAAACCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTTGAAGATACAAGTCTTATCT
CCTTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATCTTAATTCCCTGAAGTTGTAGTGGAAC
AGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGCAGAAC
Found at i:45580353 original size:96 final size:94
Alignment explanation
Indices: 45580056--45580354 Score: 341
Period size: 96 Copynumber: 3.2 Consensus size: 94
45580046 AAGTTACTAG
* *
45580056 TCTTATCTC-CTTGAAGTTGCAGTGGAGCAGAATGAAGATAGCGAATCTTATTTTCCTGAAGTTG
1 TCTTATCTCTC-TGAAGTTGCAGTGGAGCAG-ATGAAGATAGCGAATCTTAATTCCCTGAAGTTG
45580120 TAGTGGAACAGATTGAAGCTATAAATTGCAGA
64 TAGTGGAACAGATTGAAGCTATAAATTG-AGA
* * * * * *
45580152 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT---CATAGCAAACCTT-ATCTCTCTGAAGTTGC
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATGAAGATAGCGAATCTTAAT-TCCCTGAAGTTGT
* * * *
45580213 AGTAGAGCAGGTTGAAG--ATACA---AG-
65 AGTGGAACAGATTGAAGCTATAAATTGAGA
*
45580237 TCTTATCTCTTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTAATTCCCTGAAGTTGT
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGA-TGAAGATAGCGAATCTTAATTCCCTGAAGTTGT
*
45580302 AGTGGAACTGATTGAAGCTATAAATTGTAGA
65 AGTGGAACAGATTGAAGCTATAAATTG-AGA
45580333 TCTTATCTCTCTGAAGTTGCAG
1 TCTTATCTCTCTGAAGTTGCAG
45580355 CAGAACAGAT
Statistics
Matches: 164, Mismatches: 25, Indels: 28
0.76 0.12 0.13
Matches are distributed among these distances:
85 29 0.18
86 3 0.02
89 34 0.21
90 6 0.04
91 5 0.03
92 34 0.21
95 4 0.02
96 48 0.29
97 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (94 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATGAAGATAGCGAATCTTAATTCCCTGAAGTTGTA
GTGGAACAGATTGAAGCTATAAATTGAGA
Found at i:45580562 original size:49 final size:48
Alignment explanation
Indices: 45580416--45580590 Score: 166
Period size: 49 Copynumber: 3.8 Consensus size: 48
45580406 CATATCAAAC
* * * *
45580416 CTTATCTCTCTAAAGTTGTAGTGGAACAGGTTAAA-A-ATAAACCAAT
1 CTTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGACACAAACCAAT
* * * * * * *
45580462 CTTATCTCCCTGAAGGTGCAGTGGAGCAGATTGAAGACAGGATACAAAT
1 CTTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGACA-CAAACCAAT
45580511 CTTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGACACAAA-C---
1 CTTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGACACAAACCAAT
* *
45580555 CTTATCT-TCCTGAAGTTGTAGTAGAGCAAATTAAAG
1 CTTATCTCT-CTGAAGTTGTAGTGGAGCAGATTAAAG
45580591 CTATTAATCT
Statistics
Matches: 106, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.01
44 32 0.30
46 28 0.26
47 1 0.01
48 3 0.03
49 41 0.39
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (48 bp):
CTTATCTCTCTGAAGTTGTAGTGGAGCAGATTAAAGACACAAACCAAT
Found at i:45580603 original size:44 final size:44
Alignment explanation
Indices: 45580505--45580612 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
45580495 AAGACAGGAT
* *
45580505 ACAAATCTTATC-TCTCTGAAGTTGTAGTGGAGCAGATTAAAGAC
1 ACAAATCTTATCTTC-CTGAAGTTGTAGTAGAGCAAATTAAAGAC
*
45580549 ACAAACCTTATCTTCCTGAAGTTGTAGTAGAGCAAATTAAAG-C
1 ACAAATCTTATCTTCCTGAAGTTGTAGTAGAGCAAATTAAAGAC
** *
45580592 TATTAATCTTATCTCCCTGAA
1 -ACAAATCTTATCTTCCTGAA
45580613 ATTACAATGG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.02
44 52 0.95
45 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (44 bp):
ACAAATCTTATCTTCCTGAAGTTGTAGTAGAGCAAATTAAAGAC
Found at i:45580762 original size:44 final size:44
Alignment explanation
Indices: 45580694--45580816 Score: 138
Period size: 45 Copynumber: 2.8 Consensus size: 44
45580684 ATAGTAAGTT
* *
45580694 TTATCTCCCTGAAATTGTAGTGGAGCAGATTAAAACCACAAATC
1 TTATCTCCTTGAAATTGCAGTGGAGCAGATTAAAACCACAAATC
* * * **
45580738 TTATCTCCTTAAAATTGCAATGGAGCAGATTGCAAACCATTAATC
1 TTATCTCCTTGAAATTGCAGTGGAGCAGATT-AAAACCACAAATC
* * * *
45580783 TTATCTCTTTGAAGTTACAGTAGAGCAGATTAAA
1 TTATCTCCTTGAAATTGCAGTGGAGCAGATTAAA
45580817 GCTACAAGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
44 29 0.45
45 35 0.55
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (44 bp):
TTATCTCCTTGAAATTGCAGTGGAGCAGATTAAAACCACAAATC
Found at i:45580789 original size:45 final size:44
Alignment explanation
Indices: 45580694--45580789 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 44
45580684 ATAGTAAGTT
* * *
45580694 TTATCTCCCTGAAATTGTAGTGGAGCAGATTAAAACCACAAATC
1 TTATCTCCCTAAAATTGCAATGGAGCAGATTAAAACCACAAATC
* * **
45580738 TTATCTCCTTAAAATTGCAATGGAGCAGATTGCAAACCATTAATC
1 TTATCTCCCTAAAATTGCAATGGAGCAGATT-AAAACCACAAATC
45580783 TTATCTC
1 TTATCTC
45580790 TTTGAAGTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 27 0.61
45 17 0.39
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (44 bp):
TTATCTCCCTAAAATTGCAATGGAGCAGATTAAAACCACAAATC
Found at i:45582426 original size:60 final size:60
Alignment explanation
Indices: 45582307--45582418 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
45582297 TATCATTCTC
* * * * *
45582307 TTACTTTTAAAATATTCAAATTTAATATTAGGTATTATTTTATCTATCTATTTATTTTTT
1 TTACTCTTAAAATATTCAAACTTAACATTAGGTATCATATTATCTATCTATTTATTTTTT
* *
45582367 TTACTCTTAAAATATTTAAACTTAACATTATGTATACATATT-T-TATCTATTT
1 TTACTCTTAAAATATTCAAACTTAACATTAGGTAT-CATATTATCTATCTATTT
45582419 CGTTTTTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
59 9 0.20
60 31 0.70
61 4 0.09
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (60 bp):
TTACTCTTAAAATATTCAAACTTAACATTAGGTATCATATTATCTATCTATTTATTTTTT
Found at i:45586260 original size:21 final size:20
Alignment explanation
Indices: 45586222--45586261 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
45586212 AATATTTTAC
*
45586222 ATTTTACCCCAAACCTTTTT
1 ATTTTACCCCAAAACTTTTT
*
45586242 ATTTTCCCCCAAAAACTTTT
1 ATTTTACCCC-AAAACTTTT
45586262 ACTTTCTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTTACCCCAAAACTTTTT
Found at i:45598830 original size:21 final size:21
Alignment explanation
Indices: 45598804--45598844 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45598794 TTTTTAATTT
45598804 TTTTTAAAAAT-TAATATAATA
1 TTTTTAAAAATCTAAT-TAATA
*
45598825 TTTTTAAGAATCTAATTAAT
1 TTTTTAAAAATCTAATTAAT
45598845 TAGATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTTAAAAATCTAATTAATA
Found at i:45606048 original size:4 final size:4
Alignment explanation
Indices: 45606041--45606071 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
45606031 CTACACATAT
*
45606041 ATAG ATAG ATAG ATAG ACAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
45606072 TTAATGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.23
Consensus pattern (4 bp):
ATAG
Found at i:45618076 original size:372 final size:372
Alignment explanation
Indices: 45617386--45618121 Score: 1289
Period size: 372 Copynumber: 2.0 Consensus size: 372
45617376 AAGGGAAGTG
*
45617386 GGAAATGTACCATGCAATTCACAACCCTCAAGAGAGAGATATGTTAAAGCAGATAAATTTGCCAA
1 GGAAATGAACCATGCAATTCACAACCCTCAAGAGAGAGATATGTTAAAGCAGATAAATTTGCCAA
* *
45617451 ACTCTGAGGGATTGTTGAAGATACATTTACCATGTCAAGATCAAGAATCTTGAGGTTCAATAACC
66 ACTCTGAGGGATTGTCGAAGATACATTTACCATGTAAAGATCAAGAATCTTGAGGTTCAATAACC
*
45617516 TCTCGGATAAACTTTTCAAACTTGGGTTTCGGAGCTCTAATGGATTCCCAGAGAGATCAAGTATC
131 TCTCGGATAAACTTTTCAAACTTGGGTTTCGGAGCTCTAATCGATTCCCAGAGAGATCAAGTATC
** *
45617581 ACCAGGTTTGAAAGCTGTAGAACTTCATATGGAATTTGACCTGTAAAGCCAGACGAGGAGAGGTC
196 ACCAGGTTTGAAAGCAATAGAACTTCATATGGAATTTGACCTGTAAAGCCAGACCAGGAGAGGTC
*
45617646 CAACCGTGATAGCCTTGTAAGGTTAGCAATTGCAGAAGGGATTTCAGAGCCGTTGAAGTCATTGT
261 CAACCGTGATAGCCTTGTAAGGTTACCAATTGCAGAAGGGATTTCAGAGCCGTTGAAGTCATTGT
45617711 CAC-AAAGGCTGAGCCTTCTAAGGTGATGGAGCTGGAAAACTTCAATA
326 C-CGAAAGGCTGAGCCTTCTAAGGTGATGGAGCTGGAAAACTTCAATA
* *
45617758 GGAAATGAACCATGCAATTCACAAGCGTCAAGAGAGAGATATGTTAAAGCAGATAAATTTGCCAA
1 GGAAATGAACCATGCAATTCACAACCCTCAAGAGAGAGATATGTTAAAGCAGATAAATTTGCCAA
*
45617823 ACTCTGAGGGATTGTCGACGATACATTTACCATGTAAAGATCAAG-ATGCTTGAGGTTCAATAAC
66 ACTCTGAGGGATTGTCGAAGATACATTTACCATGTAAAGATCAAGAAT-CTTGAGGTTCAATAAC
* *
45617887 CTCTCGGATAAACTTTTCAAGCTTGGGTTTCGGAGCTCTAATCGATTCCTAGAGAGATCAAGTAT
130 CTCTCGGATAAACTTTTCAAACTTGGGTTTCGGAGCTCTAATCGATTCCCAGAGAGATCAAGTAT
45617952 CACCAGGTTTGAAAGCAATAGAACTTCATATGGAATTTGACCTGTAAAGCCAGACCAGGAGAGGT
195 CACCAGGTTTGAAAGCAATAGAACTTCATATGGAATTTGACCTGTAAAGCCAGACCAGGAGAGGT
*
45618017 CCAACCGTGATAGCCTTGTAAGGTTACCAATTGCAGAAGGGATTTCAGAG-CGATTGAAGTTATT
260 CCAACCGTGATAGCCTTGTAAGGTTACCAATTGCAGAAGGGATTTCAGAGCCG-TTGAAGTCATT
*
45618081 GTCCGAAAGGTTGAGCCTTCTAAGGTGATGGAGCTGGAAAA
324 GTCCGAAAGGCTGAGCCTTCTAAGGTGATGGAGCTGGAAAA
45618122 GGCTGTTGTT
Statistics
Matches: 346, Mismatches: 15, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
371 5 0.01
372 341 0.99
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (372 bp):
GGAAATGAACCATGCAATTCACAACCCTCAAGAGAGAGATATGTTAAAGCAGATAAATTTGCCAA
ACTCTGAGGGATTGTCGAAGATACATTTACCATGTAAAGATCAAGAATCTTGAGGTTCAATAACC
TCTCGGATAAACTTTTCAAACTTGGGTTTCGGAGCTCTAATCGATTCCCAGAGAGATCAAGTATC
ACCAGGTTTGAAAGCAATAGAACTTCATATGGAATTTGACCTGTAAAGCCAGACCAGGAGAGGTC
CAACCGTGATAGCCTTGTAAGGTTACCAATTGCAGAAGGGATTTCAGAGCCGTTGAAGTCATTGT
CCGAAAGGCTGAGCCTTCTAAGGTGATGGAGCTGGAAAACTTCAATA
Found at i:45618548 original size:12 final size:12
Alignment explanation
Indices: 45618531--45618559 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
45618521 AATCAAGTTG
45618531 TGTATATGCGTA
1 TGTATATGCGTA
45618543 TGTATATGCGTA
1 TGTATATGCGTA
45618555 TGTAT
1 TGTAT
45618560 GCATCATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (12 bp):
TGTATATGCGTA
Found at i:45620932 original size:79 final size:79
Alignment explanation
Indices: 45620840--45620990 Score: 203
Period size: 79 Copynumber: 1.9 Consensus size: 79
45620830 ATGCATAGTT
* * * * ** *
45620840 ATAAATCAAAATCAGTAACAATTAGTCTAACATATTCAGATATTGTGTATTCCTCATCAACAAAG
1 ATAAATCAAAATCAGTAACAATCAATCTAACATAATCAAATATCATATATTCCTCATCAACAAAG
45620905 TAACGTAAAGGGTC
66 TAACGTAAAGGGTC
* * * *
45620919 ATAAATCAGAATCAGTAACAATCAATTTAACATAATCAAATGTCATATATTCTTCATCAACAAAG
1 ATAAATCAAAATCAGTAACAATCAATCTAACATAATCAAATATCATATATTCCTCATCAACAAAG
45620984 TAACGTA
66 TAACGTA
45620991 GAGATGTATC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (79 bp):
ATAAATCAAAATCAGTAACAATCAATCTAACATAATCAAATATCATATATTCCTCATCAACAAAG
TAACGTAAAGGGTC
Found at i:45626761 original size:19 final size:19
Alignment explanation
Indices: 45626739--45626784 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
45626729 ACAAGCCCAT
45626739 GTGTGAGCTACACACACCC
1 GTGTGAGCTACACACACCC
*
45626758 GTGTCTGAGCTACACACATCC
1 GTG--TGAGCTACACACACCC
45626779 GTGTGA
1 GTGTGA
45626785 AGGGGATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
21 18 0.75
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (19 bp):
GTGTGAGCTACACACACCC
Found at i:45626768 original size:21 final size:21
Alignment explanation
Indices: 45626742--45626782 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45626732 AGCCCATGTG
45626742 TGAGCTACACACACCCGTGTC
1 TGAGCTACACACACCCGTGTC
*
45626763 TGAGCTACACACATCCGTGT
1 TGAGCTACACACACCCGTGT
45626783 GAAGGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
TGAGCTACACACACCCGTGTC
Found at i:45628295 original size:13 final size:13
Alignment explanation
Indices: 45628277--45628327 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
45628267 AGTTCTTCAT
45628277 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
45628290 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
45628303 TGCTGTGGAGAAG
1 TGCTTTTGAAAAG
45628316 TGCTTTTGAAAA
1 TGCTTTTGAAAA
45628328 TTTTGAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:45633497 original size:86 final size:87
Alignment explanation
Indices: 45633352--45633525 Score: 341
Period size: 86 Copynumber: 2.0 Consensus size: 87
45633342 TCTATGACCA
45633352 TATTTTACCACAATTAATACATAAGTTACTTTAATATTAATTCCTTATATATAGAAAAGT-AAAA
1 TATTTTACCACAATTAATACATAAGTTACTTTAATATTAATTCCTTATATATAGAAAAGTAAAAA
45633416 GGGAAAAGTGAAAATGTGAGAT
66 GGGAAAAGTGAAAATGTGAGAT
45633438 TATTTTACCACAATTAATACATAAGTTACTTTAATATTAATTCCTTATATATAGAAAAGTAAAAA
1 TATTTTACCACAATTAATACATAAGTTACTTTAATATTAATTCCTTATATATAGAAAAGTAAAAA
45633503 GGGAAAAGTGAAAATGTGAGAT
66 GGGAAAAGTGAAAATGTGAGAT
45633525 T
1 T
45633526 TGAACCTTGG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 60 0.69
87 27 0.31
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTTACCACAATTAATACATAAGTTACTTTAATATTAATTCCTTATATATAGAAAAGTAAAAA
GGGAAAAGTGAAAATGTGAGAT
Found at i:45636109 original size:20 final size:18
Alignment explanation
Indices: 45636068--45636110 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
45636058 TCGATGTGAT
* *
45636068 ATCTGTTAATTGAGTATT
1 ATCTGTTAATTGAATATG
45636086 ATCTGCTTAATTTGAATATG
1 ATCTG-TTAA-TTGAATATG
45636106 ATCTG
1 ATCTG
45636111 AATCTAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 12 0.57
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (18 bp):
ATCTGTTAATTGAATATG
Found at i:45639740 original size:30 final size:30
Alignment explanation
Indices: 45639704--45639764 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
45639694 ACGGGCACGG
*
45639704 ACACGATCGTGTGTCCCTATTTTGAATGTT
1 ACACGATCGTGTGTCCCTATTTCGAATGTT
*
45639734 ACACGATCGTGTTTCCCTATTTCGAATGTT
1 ACACGATCGTGTGTCCCTATTTCGAATGTT
45639764 A
1 A
45639765 TACGGCTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (30 bp):
ACACGATCGTGTGTCCCTATTTCGAATGTT
Found at i:45641018 original size:21 final size:21
Alignment explanation
Indices: 45640992--45641046 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
45640982 AACAGCGGTG
*
45640992 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
45641013 GCGGTGAGATTGGGTACTGTA
1 GCGGTGAGATTAGGTACTGTA
*
45641034 GTGGTGAGATTAG
1 GCGGTGAGATTAG
45641047 AAACAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.40, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:45641360 original size:22 final size:22
Alignment explanation
Indices: 45641309--45641360 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
45641299 TTTTATAGTT
*
45641309 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
45641332 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
45641354 ATAATAA
1 ATAATAA
45641361 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:45650767 original size:21 final size:22
Alignment explanation
Indices: 45650717--45650767 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
45650707 ATATATATAT
* *
45650717 ATATTAATTATTTTTTTAAGAA
1 ATATTATTTATTTTTGTAAGAA
* *
45650739 A-ATAATTTCTTTTTGTAA-AA
1 ATATTATTTATTTTTGTAAGAA
45650759 ATATTATTT
1 ATATTATTT
45650768 TTATTTCCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.13
21 19 0.83
22 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATATTATTTATTTTTGTAAGAA
Found at i:45651210 original size:26 final size:27
Alignment explanation
Indices: 45651166--45651226 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
45651156 ATTATATATT
45651166 AAATATATTTTTTTAATTTTTAATCAA
1 AAATATATTTTTTTAATTTTTAATCAA
45651193 AAATATATTTTTTT-ATTTTTAATCAA
1 AAATATATTTTTTTAATTTTTAATCAA
*
45651219 ATATATAT
1 AAATATAT
45651227 ATATAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.58
27 14 0.42
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATATATTTTTTTAATTTTTAATCAA
Found at i:45652440 original size:4 final size:4
Alignment explanation
Indices: 45652431--45652464 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
45652421 TGAGGTCTCT
45652431 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
45652465 CACATACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:45661028 original size:22 final size:21
Alignment explanation
Indices: 45660948--45661068 Score: 54
Period size: 25 Copynumber: 5.3 Consensus size: 21
45660938 AGATATTGTG
45660948 ATAATTATACATTTAAAAATAATT
1 ATAATT-TA-ATTT-AAAATAATT
45660972 ATAATTTAA--TAAAAT--TT
1 ATAATTTAATTTAAAATAATT
*
45660989 GTAATAATTACACGTTTAGAAATAATT
1 ATAAT--TTA-A--TTTA-AAATAATT
45661016 ATAATTTAATTTACAAATATTACTT
1 ATAATTTAATTTA-AAATA--A-TT
*
45661041 AAAATTTTTAA-TTAAAATAATT
1 ATAA--TTTAATTTAAAATAATT
45661063 ATAATT
1 ATAATT
45661069 GAAGTAAAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 34
0.66 0.04 0.29
Matches are distributed among these distances:
17 6 0.08
19 8 0.10
20 4 0.05
22 15 0.19
23 3 0.04
24 10 0.13
25 17 0.22
26 3 0.04
27 11 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAATTTAATTTAAAATAATT
Found at i:45661531 original size:31 final size:29
Alignment explanation
Indices: 45661493--45661562 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
45661483 ACTATTAAAA
* *
45661493 TAGTCACTTTTGTTTGTCTAAGGTTACATTT
1 TAGTCACTTATGTTTGAC--AGGTTACATTT
* *
45661524 TAGTCACTTATGTTTGACATGTTACGTTT
1 TAGTCACTTATGTTTGACAGGTTACATTT
45661553 TAGTCACTTA
1 TAGTCACTTA
45661563 CGCTATCCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATGTTTGACAGGTTACATTT
Found at i:45661869 original size:20 final size:20
Alignment explanation
Indices: 45661848--45661884 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
45661838 TTCTTTTTCT
45661848 TTTTCTTTTTCT-TCTTCCC
1 TTTTCTTTTTCTCTCTTCCC
*
45661867 TTTTGTTTTTCTCTCTTC
1 TTTTCTTTTTCTCTCTTC
45661885 TCATATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTCTTTTTCTCTCTTCCC
Found at i:45663026 original size:15 final size:15
Alignment explanation
Indices: 45663006--45663034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
45662996 TACTCTAATA
45663006 AAAATTCGTTCAAAT
1 AAAATTCGTTCAAAT
45663021 AAAATTCGTTCAAA
1 AAAATTCGTTCAAA
45663035 GTACACATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (15 bp):
AAAATTCGTTCAAAT
Found at i:45665810 original size:23 final size:23
Alignment explanation
Indices: 45665766--45665810 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
45665756 TATTTAAGTA
*
45665766 TCAAAATAAAATTGAAGTCAAAT
1 TCAAAATAAAATTGAAGACAAAT
*
45665789 TCAAATATTAAATTG-AGACAAA
1 TCAAA-ATAAAATTGAAGACAAA
45665811 AAAAAAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (23 bp):
TCAAAATAAAATTGAAGACAAAT
Found at i:45668277 original size:20 final size:20
Alignment explanation
Indices: 45668241--45668278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45668231 ATGAGATTTG
*
45668241 TAAAATAATATAAATATGTT
1 TAAAATAATAAAAATATGTT
45668261 TAAAA-AATAAAATATATG
1 TAAAATAATAAAA-ATATG
45668279 CCATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAATAATAAAAATATGTT
Found at i:45668681 original size:14 final size:14
Alignment explanation
Indices: 45668658--45668692 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
45668648 ATTAAAAGAT
45668658 TTAATTATGTT-AA
1 TTAATTATGTTAAA
45668671 TTAACTTATGTTAAA
1 TTAA-TTATGTTAAA
45668686 TTAATTA
1 TTAATTA
45668693 ATATAAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 10 0.50
15 6 0.30
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (14 bp):
TTAATTATGTTAAA
Found at i:45669430 original size:4 final size:4
Alignment explanation
Indices: 45669421--45669517 Score: 167
Period size: 4 Copynumber: 24.2 Consensus size: 4
45669411 TGATTTCTTT
* * *
45669421 TGTA TGTA TGTA TGTA TGTG TGTG TGTG TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
45669469 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
45669517 T
1 T
45669518 TGGCATGAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 91 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:45670095 original size:58 final size:56
Alignment explanation
Indices: 45670026--45670171 Score: 161
Period size: 58 Copynumber: 2.5 Consensus size: 56
45670016 TTTTTATAAT
* * *
45670026 ATTATATATTATAATTT-TTTAATTCATA-TAATAATAATTATATTAAGAATGTTATTAA
1 ATTATATATTAT--TTTATTAAATT-ATATTAATAATAATTATATTAA-AATATGATTAA
45670084 ATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGATTAA
1 ATTATATATTATTTTATTAAATTATA-TTAATAATAATTATATTAAAATATGATTAA
* *
45670141 ATTATTTATTTTTATTTTATTAAAATATATT
1 ATTA--TA-TATTATTTTATTAAATTATATT
45670172 TCACCATAAT
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
56 6 0.08
57 19 0.25
58 30 0.39
59 4 0.05
60 18 0.23
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (56 bp):
ATTATATATTATTTTATTAAATTATATTAATAATAATTATATTAAAATATGATTAA
Found at i:45670129 original size:15 final size:15
Alignment explanation
Indices: 45670045--45670133 Score: 55
Period size: 15 Copynumber: 6.1 Consensus size: 15
45670035 TATAATTTTT
45670045 TAATTCATA-TAATAA
1 TAATT-ATATTAATAA
*
45670060 TAATTATATTAAGAA
1 TAATTATATTAATAA
* * *
45670075 T-GTTAT-TAAATTA
1 TAATTATATTAATAA
* *
45670088 TATATTAT-TTTATTA
1 TA-ATTATATTAATAA
45670103 -AATTATATTTAATAA
1 TAATTATA-TTAATAA
45670118 TAATTATATTAA-AA
1 TAATTATATTAATAA
45670132 TA
1 TA
45670134 TGATTAAATT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.17
14 12 0.21
15 29 0.50
16 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (15 bp):
TAATTATATTAATAA
Found at i:45670170 original size:60 final size:57
Alignment explanation
Indices: 45670054--45670192 Score: 170
Period size: 60 Copynumber: 2.4 Consensus size: 57
45670044 TTAATTCATA
* * *
45670054 TAATAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTATATT
1 TAATAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAAATATATT
*
45670112 TAATAATAATTATATTAAAATATGATTAAATTATTTATTTTTATTTTATTAAAATATATT
1 TAATAATAATTATATTAAAATATGATTAAATTA--TA-TATTATTTTATTAAAATATATT
* ** *
45670172 TCACCATAATTTTATTAAAAT
1 TAATAATAATTATATTAAAAT
45670193 TTAATAACCA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
57 13 0.19
58 18 0.26
59 2 0.03
60 37 0.53
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (57 bp):
TAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATT
Found at i:45670381 original size:16 final size:16
Alignment explanation
Indices: 45670360--45670398 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
45670350 GAAATTACTG
45670360 ATTACAGCTCTA-TTC
1 ATTACAGCTCTATTTC
45670375 AATTACAGCTCTATTTC
1 -ATTACAGCTCTATTTC
45670392 ATTACAG
1 ATTACAG
45670399 TGAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:45671776 original size:96 final size:95
Alignment explanation
Indices: 45671581--45671857 Score: 366
Period size: 97 Copynumber: 2.9 Consensus size: 95
45671571 GCTTCTTAAT
* * *
45671581 TAAATTAATTATAAATTTTTCAAAATTAGATTAGGGTTTCGTGTTTATGGTTTTTAAGGAAAAAT
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGGAAAAAT
* *
45671646 TAAATAAATT-AGAGTTTAGGATTACTTGAG
66 AAAATAAATTAAG-GTTTAGGGTTACTTGAG
* * * *
45671676 TAAATTGATTATAAATTTTTTTAAAAATTAGATTAAGGTTTAGTGTTAAGGGTTTTAAAGGAAAA
1 TAAATTAATTATAAA--TTTTTAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGGAAAA
45671741 ATAAAAT-AATTAAGGTTTAGGGTTACTTGAG
64 ATAAAATAAATTAAGGTTTAGGGTTACTTGAG
* *
45671772 TAAATTAATTATAAA---TTAAAAAATAGATTAGGGTTTAGTATTTAGGGTTTTTAAGGAAAAAA
1 TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGG-AAAAA
* *
45671834 TCAAATAAATTAAGGTTTGGGGTT
65 TAAAATAAATTAAGGTTTAGGGTT
45671858 TAGGGTTACT
Statistics
Matches: 160, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
91 36 0.22
92 10 0.06
93 16 0.10
95 14 0.09
96 34 0.21
97 50 0.31
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (95 bp):
TAAATTAATTATAAATTTTTAAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGGAAAAAT
AAAATAAATTAAGGTTTAGGGTTACTTGAG
Found at i:45672135 original size:126 final size:126
Alignment explanation
Indices: 45671910--45672184 Score: 433
Period size: 126 Copynumber: 2.2 Consensus size: 126
45671900 TCACGTGAAA
* *
45671910 GCTCTTTTGCTATAGTAGCTCCTCAAAAAATAATTTTAAGAAGACGTTCCTGAGCAAATAGTGTC
1 GCTCTTTTGCTACAGTAGTTCCTCAAAAAATAATTTTAAGAAGACGTTCCTGAGCAAATAGTGTC
* *
45671975 AAAAATGCTTTAAGCAGGATGTTTTATCAGCAAAAGTACTGAAAGAAGCTCCCACATGGAC
66 AAAAATGCTTTAAGCAGGATGCTTTATCAGCAAAAGTACTGAAAGAAACTCCCACATGGAC
* * * * *
45672036 GCTCTTTTGCTACAGTAGTTCCTGAAAAGATAATTTTGAGAAGATGTTTCTGAGCAAATAGTGTC
1 GCTCTTTTGCTACAGTAGTTCCTCAAAAAATAATTTTAAGAAGACGTTCCTGAGCAAATAGTGTC
* * *
45672101 AAAAATGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAACTCCCACGTGGAT
66 AAAAATGCTTTAAGCAGGATGCTTTATCAGCAAAAGTACTGAAAGAAACTCCCACATGGAC
*
45672162 GCTCTTTTGTTACAGTAGTTCCT
1 GCTCTTTTGCTACAGTAGTTCCT
45672185 ATTTGGCCTG
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
126 136 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (126 bp):
GCTCTTTTGCTACAGTAGTTCCTCAAAAAATAATTTTAAGAAGACGTTCCTGAGCAAATAGTGTC
AAAAATGCTTTAAGCAGGATGCTTTATCAGCAAAAGTACTGAAAGAAACTCCCACATGGAC
Found at i:45676684 original size:15 final size:16
Alignment explanation
Indices: 45676654--45676685 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45676644 TTATATTATA
45676654 AAAATATTATTAAATT
1 AAAATATTATTAAATT
45676670 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
45676685 A
1 A
45676686 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:45676689 original size:25 final size:26
Alignment explanation
Indices: 45676646--45676697 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 26
45676636 TTCTTGATTT
45676646 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATT-AATTAAA
*
45676673 ATATTAT-AAATTA-TATTAATTAAA
1 ATATTATAAAAATATTATTAATTAAA
45676697 A
1 A
45676698 GTAAGATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 4 0.17
26 5 0.21
27 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAATTAAA
Found at i:45676706 original size:25 final size:22
Alignment explanation
Indices: 45676656--45676713 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
45676646 ATATTATAAA
**
45676656 AATATTATTAAATTAAAATATTAT
1 AATA-TATT-AATTAAAATAAGAT
45676680 AAATTATATTAATTAAAAGTAAGAT
1 -AA-TATATTAATTAAAA-TAAGAT
45676705 AATATATTA
1 AATATATTA
45676714 TAGGAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.24
24 10 0.34
25 10 0.34
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
AATATATTAATTAAAATAAGAT
Found at i:45677457 original size:21 final size:20
Alignment explanation
Indices: 45677431--45677486 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
45677421 TTTGCCGATT
*
45677431 AGGCACTTTATGTGTCGTTTC
1 AGGCAC-TTATGTGTCGTTAC
**
45677452 AGGCACCTCGTGTGTCGTTAC
1 AGGCA-CTTATGTGTCGTTAC
45677473 AGGCACTTATGTGT
1 AGGCACTTATGTGT
45677487 TGTATATTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 7 0.24
21 21 0.72
22 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.27, T:0.36
Consensus pattern (20 bp):
AGGCACTTATGTGTCGTTAC
Found at i:45679563 original size:14 final size:13
Alignment explanation
Indices: 45679530--45679560 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
45679520 TGAAATTTTT
*
45679530 ATAATTTTAAAAA
1 ATAAATTTAAAAA
45679543 ATAAATTTAAAAA
1 ATAAATTTAAAAA
45679556 ATAAA
1 ATAAA
45679561 ATTAGAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAATTTAAAAA
Found at i:45681173 original size:24 final size:24
Alignment explanation
Indices: 45681145--45681196 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
45681135 TTTCTAGAAG
*
45681145 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGTATTTATTAGCATAATAT
*
45681169 ATTTAGTATTTATTAGCATAATTT
1 ATTTAGTATTTATTAGCATAATAT
45681193 ATTT
1 ATTT
45681197 GACCTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGTATTTATTAGCATAATAT
Found at i:45685310 original size:6 final size:6
Alignment explanation
Indices: 45685299--45685324 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45685289 CATGGCCTGT
45685299 CAACAG CAACAG CAACAG CAACAG CA
1 CAACAG CAACAG CAACAG CAACAG CA
45685325 GTAGCAGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:45690723 original size:12 final size:12
Alignment explanation
Indices: 45690697--45690737 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
45690687 GTATTTTACT
*
45690697 AAAATAATACC-
1 AAAAAAATACCA
45690708 AAAAAAATACCA
1 AAAAAAATACCA
45690720 AAAAAATATA-CA
1 AAAAAA-ATACCA
45690732 AAAAAA
1 AAAAAA
45690738 TTTATTTACC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.37
12 14 0.52
13 3 0.11
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAATACCA
Found at i:45690724 original size:10 final size:11
Alignment explanation
Indices: 45690697--45690738 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
45690687 GTATTTTACT
*
45690697 AAAATAATACC
1 AAAAAAATACC
45690708 AAAAAAATACC
1 AAAAAAATACC
*
45690719 AAAAAAATATAC
1 AAAAAAATA-CC
45690731 AAAAAAAT
1 AAAAAAAT
45690739 TTATTTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.74, C:0.12, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATACC
Found at i:45691112 original size:25 final size:25
Alignment explanation
Indices: 45691084--45691134 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
45691074 GTTGTTTTAG
45691084 TACATTATATTTGAAATGTATTAAT
1 TACATTATATTTGAAATGTATTAAT
45691109 TACATTATATTTGAAATGTATTAAT
1 TACATTATATTTGAAATGTATTAAT
45691134 T
1 T
45691135 TACTGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (25 bp):
TACATTATATTTGAAATGTATTAAT
Found at i:45691151 original size:26 final size:25
Alignment explanation
Indices: 45691084--45691151 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
45691074 GTTGTTTTAG
*
45691084 TACATTATATTTGAAATGTATTAAT
1 TACATTATATTTAAAATGTATTAAT
*
45691109 TACATTATATTTGAAATGTATTAATT
1 TACATTATATTTAAAATGTATTAA-T
*
45691135 TAC-TGTATTTTTAAAAT
1 TACAT-TATATTTAAAAT
45691152 AAATTTAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
25 25 0.64
26 14 0.36
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.50
Consensus pattern (25 bp):
TACATTATATTTAAAATGTATTAAT
Found at i:45691264 original size:177 final size:177
Alignment explanation
Indices: 45690933--45691282 Score: 465
Period size: 177 Copynumber: 2.0 Consensus size: 177
45690923 ATTTTAGTAT
* * * * *
45690933 ATTATATTTGAAATATATTCATTTAGTATGTTTTTTAAATAAATTTAAAAAAATCCTTATTTCAG
1 ATTATATTTGAAATATATTAATTTACTATATTTTTAAAATAAATTTAAAAAAACCCTTATTTCAG
* * * *
45690998 CCCTTTGTTTGTATCTTTTTTCCAAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTT
66 CCCTCTGTTCGTATCTTTTTTCCAAATTTTATTACTTT--ATAAAAAAATACTATTTTCGTATTT
* *
45691063 TATTATTTTACGTTGTTTTAGTACATTATATTTGAAATGTATTAATTAC
129 TATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTAC
* *
45691112 ATTATATTTGAAATGTATTAATTTACTGTATTTTTAAAATAAATTTAGTAAAAAACCCTTATTTC
1 ATTATATTTGAAATATATTAATTTACTATATTTTTAAAATAAATTTA--AAAAAACCCTTATTTC
* **
45691177 GGCCCTCTGTTCGTAT-TTTTTTCCCGGATTTTATTA-TTT-TAAAAAAATACTATTTTC-TAAT
64 AGCCCTCTGTTCGTATCTTTTTT-CCAAATTTTATTACTTTATAAAAAAATACTATTTTCGT-AT
*
45691238 TTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATT
127 TTTATTATTTTACATTATTTTAGTACATTATATTTGAAATGTATT
45691283 CATTTAGTGT
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
176 1 0.01
177 60 0.40
179 41 0.27
180 9 0.06
181 39 0.26
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.51
Consensus pattern (177 bp):
ATTATATTTGAAATATATTAATTTACTATATTTTTAAAATAAATTTAAAAAAACCCTTATTTCAG
CCCTCTGTTCGTATCTTTTTTCCAAATTTTATTACTTTATAAAAAAATACTATTTTCGTATTTTA
TTATTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTAC
Found at i:45703393 original size:41 final size:40
Alignment explanation
Indices: 45703348--45703495 Score: 154
Period size: 40 Copynumber: 3.7 Consensus size: 40
45703338 AGCGGCATTT
* *
45703348 TTAGCGGCGTTTGAATAAAAAACATCGCTATAGATCGAGCA
1 TTAGCGGCGCTT-AATAAAAAACACCGCTATAGATCGAGCA
* **
45703389 TTAGCGGCGCTTATTAAAAAAGGCCGCTATAGATCGAGCA
1 TTAGCGGCGCTTAATAAAAAACACCGCTATAGATCGAGCA
** * * * *
45703429 TTAGCGGCGCTTTTTCAAAAACGCCGCTATAGGTCGACCA
1 TTAGCGGCGCTTAATAAAAAACACCGCTATAGATCGAGCA
* *
45703469 CTAGCGGCGCCTT-TTAAAAAACACCGC
1 TTAGCGGCG-CTTAATAAAAAACACCGC
45703496 AAAAAAAATT
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 79 0.85
41 14 0.15
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGCTTAATAAAAAACACCGCTATAGATCGAGCA
Found at i:45703418 original size:40 final size:39
Alignment explanation
Indices: 45703363--45703495 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 39
45703353 GGCGTTTGAA
**
45703363 TAAAAAACATCGCTATAGATCGAGCATTAGCGGCGCTTAT
1 TAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTT-T
*
45703403 TAAAAAAGGCCGCTATAGATCGAGCATTAGCGGCGCTTTT
1 TAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGC-TTT
* * * *
45703443 TCAAAAACGCCGCTATAGGTCGACCACTAGCGGCGCCTTT
1 TAAAAAACGCCGCTATAGATCGAGCATTAGCGGCG-CTTT
*
45703483 TAAAAAACACCGC
1 TAAAAAACGCCGC
45703496 AAAAAAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
40 78 0.96
41 3 0.04
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (39 bp):
TAAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTT
Found at i:45703570 original size:40 final size:40
Alignment explanation
Indices: 45703524--45703605 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
45703514 CGCTTTAGTG
*
45703524 GCATTAGCGGCGCTTTTTAAAAAATGCCACTATAGATCGA
1 GCATTAGCGGCGCTTTTTAAAAAACGCCACTATAGATCGA
* * *
45703564 GCATTAGCGGTGCTTTTTGAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTAAAAAACGCCACTATAGATCGA
45703604 GC
1 GC
45703606 TTTATGGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTAAAAAACGCCACTATAGATCGA
Found at i:45703674 original size:21 final size:22
Alignment explanation
Indices: 45703645--45703687 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
45703635 TTTAAGTATT
*
45703645 GAGATTTAAGATTTAGGGGTTA
1 GAGATTTAAGAGTTAGGGGTTA
*
45703667 GAGA-TTAAGGGTTAGGGGTTA
1 GAGATTTAAGAGTTAGGGGTTA
45703688 AGGGTTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (22 bp):
GAGATTTAAGAGTTAGGGGTTA
Found at i:45703864 original size:14 final size:14
Alignment explanation
Indices: 45703840--45703893 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
45703830 TTAATTATCA
45703840 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
* *
45703854 TTGTGGTTTAGGGT
1 TTATAGTTTAGGGT
*
45703868 ATATAGTTTAGGGT
1 TTATAGTTTAGGGT
45703882 TTA-AGATTTAGG
1 TTATAG-TTTAGG
45703894 AGTTACTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 2 0.06
14 31 0.94
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:45703928 original size:15 final size:14
Alignment explanation
Indices: 45703908--45703956 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
45703898 ACTGTTTTAA
45703908 GGTTTATGGATTAT
1 GGTTTATGGATTAT
*
45703922 GGGTTTAGGGATTAT
1 -GGTTTATGGATTAT
* *
45703937 GATTTATGGTTTAT
1 GGTTTATGGATTAT
45703951 GGTTTA
1 GGTTTA
45703957 AGGGTTGGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:45703953 original size:7 final size:7
Alignment explanation
Indices: 45703840--45703956 Score: 56
Period size: 7 Copynumber: 16.4 Consensus size: 7
45703830 TTAATTATCA
*
45703840 TTATAGT
1 TTATGGT
*
45703847 TTAGGGT
1 TTATGGT
*
45703854 TTGTGGT
1 TTATGGT
*
45703861 TTAGGGT
1 TTATGGT
* *
45703868 ATATAGT
1 TTATGGT
*
45703875 TTAGGGT
1 TTATGGT
* *
45703882 TTAAGAT
1 TTATGGT
*
45703889 TTA-GGAG
1 TTATGG-T
*
45703896 TTACTGTT
1 TTA-TGGT
*
45703904 TTAAGGT
1 TTATGGT
*
45703911 TTATGGA
1 TTATGGT
45703918 TTATGGGT
1 TTAT-GGT
* *
45703926 TTAGGGA
1 TTATGGT
*
45703933 TTATGAT
1 TTATGGT
45703940 TTATGGT
1 TTATGGT
45703947 TTATGGT
1 TTATGGT
45703954 TTA
1 TTA
45703957 AGGGTTGGGG
Statistics
Matches: 77, Mismatches: 29, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
6 1 0.01
7 67 0.87
8 8 0.10
9 1 0.01
ACGTcount: A:0.22, C:0.01, G:0.29, T:0.48
Consensus pattern (7 bp):
TTATGGT
Found at i:45703968 original size:14 final size:15
Alignment explanation
Indices: 45703951--45703987 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
45703941 TATGGTTTAT
*
45703951 GGTTTAAGGG-TTGG
1 GGTTTAAGGGCTAGG
45703965 GGTTTAAGGGCTAGG
1 GGTTTAAGGGCTAGG
45703980 GGTTTAAG
1 GGTTTAAG
45703988 ATTTATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.19, C:0.03, G:0.46, T:0.32
Consensus pattern (15 bp):
GGTTTAAGGGCTAGG
Found at i:45704008 original size:29 final size:28
Alignment explanation
Indices: 45703910--45704010 Score: 69
Period size: 29 Copynumber: 3.5 Consensus size: 28
45703900 TGTTTTAAGG
* * *
45703910 TTTATGGATTATGGGTTTAGGGATTATGA
1 TTTATGGTTTAGGGGTTTA-AGATTATGA
* * ** *
45703939 TTTATGGTTTA-TGGTTTAAGGGTTGGGG
1 TTTATGGTTTAGGGGTTTAA-GATTATGA
* **
45703967 TTTAAGGGCTAGGGGTTTAAGATTTATGA
1 TTTATGGTTTAGGGGTTTAAGA-TTATGA
45703996 TTTATGGTTTAGGGG
1 TTTATGGTTTAGGGG
45704011 ATAAAGGATA
Statistics
Matches: 51, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
28 19 0.37
29 32 0.63
ACGTcount: A:0.21, C:0.01, G:0.35, T:0.44
Consensus pattern (28 bp):
TTTATGGTTTAGGGGTTTAAGATTATGA
Found at i:45705238 original size:22 final size:22
Alignment explanation
Indices: 45705193--45705257 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 22
45705183 AACTAATCCT
45705193 CTCTCAAATTTC-CTCTAAATTTC
1 CTCTCAAATTTCTCTC-AAA-TTC
45705216 CTCTC-AATTTGCTCTCAAATTC
1 CTCTCAAATTT-CTCTCAAATTC
45705238 CT-TCCAAATTTCTCTCAAAT
1 CTCT-CAAATTTCTCTCAAAT
45705258 CCATATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.03
22 20 0.53
23 14 0.37
24 3 0.08
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.42
Consensus pattern (22 bp):
CTCTCAAATTTCTCTCAAATTC
Found at i:45705256 original size:11 final size:11
Alignment explanation
Indices: 45705192--45705257 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
45705182 AAACTAATCC
45705192 TCTCTCAAATT
1 TCTCTCAAATT
45705203 TC-CTCTAAATT
1 TCTCTC-AAATT
45705214 TCCTCTC-AATT
1 T-CTCTCAAATT
45705225 TGCTCTCAAATT
1 T-CTCTCAAATT
*
45705237 CCT-TCCAAATT
1 TCTCT-CAAATT
45705248 TCTCTCAAAT
1 TCTCTCAAAT
45705258 CCATATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.09
11 33 0.72
12 6 0.13
13 3 0.07
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.42
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:45707132 original size:18 final size:18
Alignment explanation
Indices: 45707105--45707144 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
45707095 CAGGTGAGTT
*
45707105 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
45707123 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
45707141 TCCT
1 TCCT
45707145 TTTCCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:45711169 original size:125 final size:125
Alignment explanation
Indices: 45710792--45711156 Score: 597
Period size: 125 Copynumber: 2.9 Consensus size: 125
45710782 CCCAAATATG
* *
45710792 CTACTGTAGCAAAAGCGCGTCCACGAGGGCACGCTTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGCGCTTTCACAAATTCTTCTCAAATAGCATCCTGC
45710857 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * *
45710917 CTACTGTAGCAAAAGCGCGTCCAC-TAGCGCGTGCTTTCACAAATTCTTCTCAAATAGCACCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAAG-GCGCGCTTTCACAAATTCTTCTCAAATAGCATCCTG
*
45710981 CTAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
* * * * *
45711042 CTATTGTAGCAAAAGCGCGTCCACGAAGGCGCGATTTCACAAATTCTTATCAAACAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGCGCTTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
45711107 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCAACTCAAAATTATTT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT
45711157 ATTTTAAGAC
Statistics
Matches: 221, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
124 1 0.00
125 218 0.99
126 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAAGGCGCGCTTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
Found at i:45711932 original size:58 final size:59
Alignment explanation
Indices: 45711829--45711947 Score: 154
Period size: 58 Copynumber: 2.0 Consensus size: 59
45711819 TATCAGAATC
* * *
45711829 AAGTGTATTTTAAGCAGTATCTGATTTTCTACTGTAAACTCGAAGGTTCTT-TGTAGTTT
1 AAGTGTATATTAAGCAATATCTGATTTTCTACTGTAAACTCGAAGGTT-TTATGGAGTTT
* *
45711888 AAGTGTATATTAAGCAAT-TTTGATATTTC-GCTGTAAACTCGAAGGTTTTATGGAGTTT
1 AAGTGTATATTAAGCAATATCTGAT-TTTCTACTGTAAACTCGAAGGTTTTATGGAGTTT
45711946 AA
1 AA
45711948 CTAATTTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
57 2 0.04
58 31 0.58
59 20 0.38
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (59 bp):
AAGTGTATATTAAGCAATATCTGATTTTCTACTGTAAACTCGAAGGTTTTATGGAGTTT
Found at i:45714186 original size:9 final size:9
Alignment explanation
Indices: 45714168--45714223 Score: 76
Period size: 9 Copynumber: 6.2 Consensus size: 9
45714158 TTATTTTTGG
*
45714168 TTAACTGAA
1 TTAACCGAA
*
45714177 TTAATCGAA
1 TTAACCGAA
*
45714186 TTACCCGAA
1 TTAACCGAA
*
45714195 TTACCCGAA
1 TTAACCGAA
45714204 TTAACCGAA
1 TTAACCGAA
45714213 TTAACCGAA
1 TTAACCGAA
45714222 TT
1 TT
45714224 GAATCACTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (9 bp):
TTAACCGAA
Found at i:45714969 original size:23 final size:23
Alignment explanation
Indices: 45714935--45715001 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
45714925 ACCCATATGA
45714935 CTGCAAATTGAAGCGTTTAAA-TG
1 CTGCAAATTGAAGCG-TTAAAGTG
* *
45714958 CTGTAAATTGAAGTGTTAAAGTG
1 CTGCAAATTGAAGCGTTAAAGTG
*
45714981 CTGCAAATTGAAGTGTTAAAG
1 CTGCAAATTGAAGCGTTAAAG
45715002 GGCAAACATC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 5 0.12
23 35 0.88
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (23 bp):
CTGCAAATTGAAGCGTTAAAGTG
Found at i:45715801 original size:43 final size:43
Alignment explanation
Indices: 45715745--45715857 Score: 165
Period size: 43 Copynumber: 2.6 Consensus size: 43
45715735 TTTTCATGAC
*
45715745 CTTTAGC-AGCGTTTGTAGGAAAAGCGCCGTTAAAGGTCATGTT
1 CTTTAGCGA-CGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTT
*
45715788 CTTTAGCGACGTTTGTAGAAAAAGCGCCGCTAAAGGTCATGTT
1 CTTTAGCGACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTT
* * *
45715831 CTTTAGCGGCATTTTTAGGAAAAGCGC
1 CTTTAGCGACGTTTGTAGGAAAAGCGC
45715858 AACTCAATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 62 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
CTTTAGCGACGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTT
Found at i:45718074 original size:18 final size:17
Alignment explanation
Indices: 45718045--45718078 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
45718035 ATATTTTCAA
45718045 TTTAAATTATAATTATT
1 TTTAAATTATAATTATT
45718062 TTTAAATTTATAATTAT
1 TTTAAA-TTATAATTAT
45718079 CATAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTAAATTATAATTATT
Found at i:45718737 original size:36 final size:34
Alignment explanation
Indices: 45718679--45718746 Score: 91
Period size: 36 Copynumber: 1.9 Consensus size: 34
45718669 CAGTAAAATA
* *
45718679 TTTTCCGTAAAATGATTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTCTGGAAAATATTTTAC
*
45718713 TTTTCTGTCAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGT-AAAATAATTT-CTGGAAAATATTTT
45718747 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.24
35 9 0.31
36 13 0.45
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (34 bp):
TTTTCCGTAAAATAATTTCTGGAAAATATTTTAC
Found at i:45718811 original size:32 final size:32
Alignment explanation
Indices: 45718736--45718811 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
45718726 TAATTTACTG
* *
45718736 GAAAATATTTTCTGGTGTTTGGATGAATCTGT
1 GAAAATATTTTCTGCTGTTTGGATGAATCTCT
*
45718768 GTAAAATATTTTCTGCTGTTTGGCA-G-ATTTCCT
1 G-AAAATATTTTCTGCTGTTTGG-ATGAATCT-CT
45718801 GAAAATATTTT
1 GAAAATATTTT
45718812 TCAGAAAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 14 0.37
33 23 0.61
34 1 0.03
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (32 bp):
GAAAATATTTTCTGCTGTTTGGATGAATCTCT
Found at i:45721670 original size:33 final size:33
Alignment explanation
Indices: 45721633--45721698 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
45721623 TACATAAGTA
45721633 AGAAAAAAAAAGAGATTAAATCACTATTTGGGG
1 AGAAAAAAAAAGAGATTAAATCACTATTTGGGG
45721666 AGAAAAAAAAAGAGATTAAATCACTATTTGGGG
1 AGAAAAAAAAAGAGATTAAATCACTATTTGGGG
45721699 CCTAAAGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.06, G:0.21, T:0.21
Consensus pattern (33 bp):
AGAAAAAAAAAGAGATTAAATCACTATTTGGGG
Found at i:45721976 original size:31 final size:30
Alignment explanation
Indices: 45721941--45722028 Score: 76
Period size: 31 Copynumber: 3.0 Consensus size: 30
45721931 CTAATGTGAG
45721941 AAAAATTGTCAAGTTCAGGGCCTAACTTGGA
1 AAAAATTG-CAAGTTCAGGGCCTAACTTGGA
* * * * *
45721972 AAAAA----AAGTTAAGGTCCCAATTTGGG
1 AAAAATTGCAAGTTCAGGGCCTAACTTGGA
*
45721998 AACAATTGCCAAGTTCAGGGCCTAACTTGGA
1 AAAAATTG-CAAGTTCAGGGCCTAACTTGGA
45722029 CAAACAAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
26 20 0.49
31 21 0.51
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (30 bp):
AAAAATTGCAAGTTCAGGGCCTAACTTGGA
Found at i:45721981 original size:26 final size:26
Alignment explanation
Indices: 45721951--45722045 Score: 64
Period size: 31 Copynumber: 3.3 Consensus size: 26
45721941 AAAAATTGTC
45721951 AAGTTCAGGGCCTAACTTGGAAAAAA
1 AAGTTCAGGGCCTAACTTGGAAAAAA
* * * * **
45721977 AAGTTAAGGTCCCAATTTGGGAACAATTGCC
1 AAGTTCAGGGCCTAACTT-GGAA-AA---AA
45722008 AAGTTCAGGGCCTAACTTGGACAAACAAA
1 AAGTTCAGGGCCTAACTTGG--AAA-AAA
45722037 AAGTTCAGG
1 AAGTTCAGG
45722046 CTCCAATATG
Statistics
Matches: 49, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
26 14 0.29
27 4 0.08
28 2 0.04
29 9 0.18
30 2 0.04
31 15 0.31
32 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (26 bp):
AAGTTCAGGGCCTAACTTGGAAAAAA
Found at i:45722073 original size:60 final size:57
Alignment explanation
Indices: 45721902--45722074 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 57
45721892 TTTTCAAAGA
* * *
45721902 CTAACTTGGACAAAAAAAAATTGCAAGTCCTAATGTGAGAAAAATTG-TCAAGTTCAGGGC
1 CTAACTTGGACAAAAAAAAGTT-CAGGTCC-AATATGA-AAAAATTGCT-AAGTTCAGGGC
* * * * *
45721962 CTAACTTGG--AAAAAAAAGTTAAGGTCCCAATTTGGGAACAATTGCCAAGTTCAGGGC
1 CTAACTTGGACAAAAAAAAGTTCAGGT-CCAATAT-GAAAAAATTGCTAAGTTCAGGGC
45722019 CTAACTTGGACAAACAAAAAGTTCAGGCTCCAATATGAAAAAAGTTGCTAAGTTCA
1 CTAACTTGGACAAA-AAAAAGTTCAGG-TCCAATATGAAAAAA-TTGCTAAGTTCA
45722075 AGCCCCAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
57 34 0.37
58 13 0.14
59 8 0.09
60 37 0.40
61 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (57 bp):
CTAACTTGGACAAAAAAAAGTTCAGGTCCAATATGAAAAAATTGCTAAGTTCAGGGC
Found at i:45722971 original size:39 final size:40
Alignment explanation
Indices: 45722918--45723004 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
45722908 ATGTGTCAGA
* * *
45722918 AAATCGGGTCCATGTCAGCGCGA-TTACTTACGTGGCAA-C
1 AAATCGCGTCCATGTAAGCGCGATTTACTGACGTGG-AAGC
*
45722957 AAATCGCGTCCATGTAAGCGCGATTTGCTGACGTGGAAGC
1 AAATCGCGTCCATGTAAGCGCGATTTACTGACGTGGAAGC
45722997 AAATCGCG
1 AAATCGCG
45723005 CTTACGTGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 23 0.55
40 19 0.45
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
AAATCGCGTCCATGTAAGCGCGATTTACTGACGTGGAAGC
Found at i:45733051 original size:25 final size:29
Alignment explanation
Indices: 45732999--45733057 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 29
45732989 GAACTCAAAG
*
45732999 GGAAAGAGACAAAGAAAGAAAGAAGAAAA
1 GGAAAGAGACAAAGAAAAAAAGAAGAAAA
*
45733028 GGAAAG-GA-AAA-AAAAAAAG-AGAAAT
1 GGAAAGAGACAAAGAAAAAAAGAAGAAAA
45733053 GGAAA
1 GGAAA
45733058 AGCAGGGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 10 0.36
26 7 0.25
27 3 0.11
28 2 0.07
29 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (29 bp):
GGAAAGAGACAAAGAAAAAAAGAAGAAAA
Found at i:45741784 original size:19 final size:20
Alignment explanation
Indices: 45741743--45741784 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
45741733 TTTAACATTT
**
45741743 ATAATATATTTATAATTGTA
1 ATAATATATTTATAATTAAA
*
45741763 ATAA-ATATTTATTATTAAA
1 ATAATATATTTATAATTAAA
45741782 ATA
1 ATA
45741785 TTAATATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATAATATATTTATAATTAAA
Found at i:45742333 original size:73 final size:73
Alignment explanation
Indices: 45742249--45742425 Score: 248
Period size: 73 Copynumber: 2.4 Consensus size: 73
45742239 CCTCTCCTAA
* *
45742249 TCATTTTTGTCTTTGCTATGCAAGGG-ATCTCACTATTCATTCTTGGTTGCTTTTGCCAGTGAAT
1 TCATTTTTGTCTTTGCTATGC-AGGGAATCTCACTATTCATTCTTGGTTGCATTTGCCAGGGAAT
*
45742313 CACTCTTGT
65 CACTCCTGT
* * * *
45742322 TCATTTCTGTCTTTGCTCTGCAGGGAATCTCACTATTCATTTTTGGTTGCATTTGGCAGGGAATC
1 TCATTTTTGTCTTTGCTATGCAGGGAATCTCACTATTCATTCTTGGTTGCATTTGCCAGGGAATC
45742387 ACTCCTGT
66 ACTCCTGT
* * *
45742395 TCATTTTTGTCTTTGCTCTGTAGAGAATCTC
1 TCATTTTTGTCTTTGCTATGCAGGGAATCTC
45742426 CCTTGTTCAT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
72 4 0.04
73 89 0.96
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (73 bp):
TCATTTTTGTCTTTGCTATGCAGGGAATCTCACTATTCATTCTTGGTTGCATTTGCCAGGGAATC
ACTCCTGT
Found at i:45742350 original size:37 final size:36
Alignment explanation
Indices: 45742309--45742435 Score: 105
Period size: 37 Copynumber: 3.5 Consensus size: 36
45742299 TTTTGCCAGT
45742309 GAATCACTCTTGTTCATTTCTGTCTTTGCTCTGCAGG
1 GAATCACTCTTGTTCATTT-TGTCTTTGCTCTGCAGG
* * * ** *
45742346 GAATCTCAC-TATTCATTTT-TGGTTGCATTTGGCAGG
1 GAATCACTCTTGTTCATTTTGTCTTTGC-TCT-GCAGG
* * *
45742382 GAATCACTCCTGTTCATTTTTGTCTTTGCTCTGTAGA
1 GAATCACTCTTGTTCA-TTTTGTCTTTGCTCTGCAGG
* *
45742419 GAATCTCCCTTGTTCAT
1 GAATCACTCTTGTTCAT
45742436 CTTTTGTTTT
Statistics
Matches: 68, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
34 5 0.07
35 3 0.04
36 21 0.31
37 28 0.41
38 6 0.09
39 5 0.07
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (36 bp):
GAATCACTCTTGTTCATTTTGTCTTTGCTCTGCAGG
Found at i:45742381 original size:36 final size:35
Alignment explanation
Indices: 45742271--45742403 Score: 92
Period size: 37 Copynumber: 3.7 Consensus size: 35
45742261 TTGCTATGCA
* *
45742271 AGGG-ATCTCACTATTCATTCTTGGTTGCTTTTGCC
1 AGGGAATCTCACTATTCATTTTTGGTTGC-TTTGGC
* * * * ** *
45742306 AGTGAATCACTCTTGTTCATTTCTGTCTTTGCTCT-GC
1 AGGGAATCTCAC-TATTCATTT-T-TGGTTGCTTTGGC
45742343 AGGGAATCTCACTATTCATTTTTGGTTGCATTTGGC
1 AGGGAATCTCACTATTCATTTTTGGTTGC-TTTGGC
*
45742379 AGGGAATCACTC-CTGTTCATTTTTG
1 AGGGAAT--CTCACTATTCATTTTTG
45742404 TCTTTGCTCT
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
34 5 0.07
35 6 0.08
36 22 0.30
37 29 0.40
38 6 0.08
39 5 0.07
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.43
Consensus pattern (35 bp):
AGGGAATCTCACTATTCATTTTTGGTTGCTTTGGC
Found at i:45743340 original size:22 final size:22
Alignment explanation
Indices: 45743315--45743359 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
45743305 ATGTTTAATA
45743315 ATATTGAAAAATATAAT-ATTTT
1 ATATT-AAAAATATAATAATTTT
* *
45743337 ATATTAATAATTTAATAATTTT
1 ATATTAAAAATATAATAATTTT
45743359 A
1 A
45743360 AATATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTAAAAATATAATAATTTT
Found at i:45754770 original size:21 final size:24
Alignment explanation
Indices: 45754730--45754772 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
45754720 GAGAGGTCCA
45754730 TTCTACTTAAAGTAGAATATTATT
1 TTCTACTTAAAGTAGAATATTATT
45754754 TTCTA-TTAAA-TA-AATATTA
1 TTCTACTTAAAGTAGAATATTA
45754773 CTTGCGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 5 0.26
24 5 0.26
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (24 bp):
TTCTACTTAAAGTAGAATATTATT
Found at i:45756295 original size:21 final size:20
Alignment explanation
Indices: 45756270--45756319 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
45756260 TTTAACAACA
45756270 ATATTACAAAAT-ATATAATT
1 ATATTACAAAATAATA-AATT
*
45756290 AGTATTAAAAAATAATAAATT
1 A-TATTACAAAATAATAAATT
45756311 AT-TTACAAA
1 ATATTACAAA
45756320 TAGAAAAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 15 0.58
22 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATTACAAAATAATAAATT
Found at i:45763900 original size:3 final size:3
Alignment explanation
Indices: 45763880--45764028 Score: 163
Period size: 3 Copynumber: 49.7 Consensus size: 3
45763870 AAATTTGATG
* *
45763880 TTA TTA TGA TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
45763928 TTA TTA TTA TTA TTA TTA TCA TCA TCA TCA TTA GTA TTA TCA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** * *
45763976 TTA TTA TTA TTA TTA TCA TTA GTA TTA TTA GCA TCA TTA GTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45764024 TTA TT
1 TTA TT
45764029 TTAAATTTTA
Statistics
Matches: 124, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 124 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:45764161 original size:18 final size:17
Alignment explanation
Indices: 45764135--45764191 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
45764125 ACATAGACTT
*
45764135 TTTTATTATTTTATTTA
1 TTTTCTTATTTTATTTA
45764152 TTTTCGTTATTGTTA-TTA
1 TTTTC-TTATT-TTATTTA
*
45764170 TTGTCTTATTTGATATTTA
1 TTTTCTTATTT--TATTTA
45764189 TTT
1 TTT
45764192 ATTTATGTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 9 0.28
18 14 0.44
19 8 0.25
ACGTcount: A:0.19, C:0.04, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTCTTATTTTATTTA
Found at i:45764633 original size:71 final size:70
Alignment explanation
Indices: 45764517--45764659 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 70
45764507 CTTTTCAAAC
* * *
45764517 TCAAGTTTTAAACGATCTCGAGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGATTCCA
1 TCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACT-GACATGATCCCA
45764582 TTTTTT
65 TTTTTT
* *
45764588 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGACATGATCCCTT
1 TCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGACATGATCCCAT
45764653 TTTTT
66 TTTTT
45764658 TC
1 TC
45764660 GAGATAGCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 17 0.25
71 50 0.75
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (70 bp):
TCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGACATGATCCCAT
TTTTT
Found at i:45767229 original size:9 final size:9
Alignment explanation
Indices: 45767211--45767285 Score: 53
Period size: 9 Copynumber: 7.8 Consensus size: 9
45767201 ATATATATAT
45767211 ATCAATTTA
1 ATCAATTTA
*
45767220 ATCCATTTA
1 ATCAATTTA
*
45767229 ATCAATATA
1 ATCAATTTA
*
45767238 TAT-ATATATA
1 -ATCA-ATTTA
45767248 TATCAATTTA
1 -ATCAATTTA
*
45767258 ATCCATTTA
1 ATCAATTTA
45767267 ATCAACTTTTA
1 ATCAA--TTTA
45767278 ATTCAATT
1 A-TCAATT
45767286 GAATGTCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
9 28 0.52
10 16 0.30
11 6 0.11
12 4 0.07
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.45
Consensus pattern (9 bp):
ATCAATTTA
Found at i:45767251 original size:38 final size:38
Alignment explanation
Indices: 45767195--45767271 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
45767185 TAATATATAT
*
45767195 ATATGTATATATATATATCAATTTAATCCATTTAATCA
1 ATATATATATATATATATCAATTTAATCCATTTAATCA
45767233 ATATATATATATATATATCAATTTAATCCATTTAATCA
1 ATATATATATATATATATCAATTTAATCCATTTAATCA
45767271 A
1 A
45767272 CTTTTAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.44
Consensus pattern (38 bp):
ATATATATATATATATATCAATTTAATCCATTTAATCA
Found at i:45768007 original size:25 final size:25
Alignment explanation
Indices: 45767956--45768007 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
45767946 CTTGCATTTC
* *
45767956 TTCTTTCTTTCTTTTCCTTTTTCTT
1 TTCTTTCTTTCCTTTCCTGTTTCTT
45767981 TTCTTTCTTTCCTTT-CTGTTTCGTT
1 TTCTTTCTTTCCTTTCCTGTTTC-TT
45768006 TT
1 TT
45768008 GGCTTGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.00, C:0.23, G:0.04, T:0.73
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCCTGTTTCTT
Found at i:45772054 original size:17 final size:17
Alignment explanation
Indices: 45772032--45772065 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
45772022 ACATGTTAGG
45772032 TTCGTCTACTAATATAA
1 TTCGTCTACTAATATAA
45772049 TTCGTCTACTAATATAA
1 TTCGTCTACTAATATAA
45772066 GTTGTCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (17 bp):
TTCGTCTACTAATATAA
Found at i:45775311 original size:4 final size:4
Alignment explanation
Indices: 45775293--45775333 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
45775283 CAAATGTTTC
45775293 ATTT A-TT ATTTT ATTT ATTT ATCTT ATTT ATTT ATTT ATTT
1 ATTT ATTT A-TTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT
45775334 GTTTTGTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 24 0.71
5 7 0.21
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:45778145 original size:33 final size:32
Alignment explanation
Indices: 45778090--45778162 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
45778080 TATATAGTAA
* * *
45778090 AAAAATTAAAATATTTATTTTAGACATGATA-TT
1 AAAAATTAAAAAAATTAATTTAG--ATGATATTT
45778123 AAAAATTAAAAAAATTAATTTAGATGATATTT
1 AAAAATTAAAAAAATTAATTTAGATGATATTT
45778155 AAATAATT
1 AAA-AATT
45778163 GAATATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.17
32 5 0.14
33 24 0.69
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.40
Consensus pattern (32 bp):
AAAAATTAAAAAAATTAATTTAGATGATATTT
Found at i:45778497 original size:10 final size:9
Alignment explanation
Indices: 45778473--45778503 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
45778463 GCATTTAATT
45778473 AATTTTTAA
1 AATTTTTAA
45778482 AATTTTTAA
1 AATTTTTAA
*
45778491 AAGTTTTAA
1 AATTTTTAA
45778500 AATT
1 AATT
45778504 ATAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (9 bp):
AATTTTTAA
Found at i:45778510 original size:18 final size:18
Alignment explanation
Indices: 45778476--45778510 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45778466 TTTAATTAAT
* *
45778476 TTTTAAAATTTTTAAAAG
1 TTTTAAAATTATAAAAAG
45778494 TTTTAAAATTATAAAAA
1 TTTTAAAATTATAAAAA
45778511 TTATTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTTAAAATTATAAAAAG
Found at i:45778566 original size:19 final size:19
Alignment explanation
Indices: 45778517--45778566 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
45778507 AAAATTATTT
45778517 TTAAAAAATA-AAAAATCA
1 TTAAAAAATATAAAAATCA
*
45778535 TTAAAAAAGTATAAAAATGA
1 TTAAAAAA-TATAAAAATCA
45778555 -TAAAAATATATA
1 TTAAAAA-ATATA
45778567 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.29
19 12 0.43
20 8 0.29
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
TTAAAAAATATAAAAATCA
Found at i:45779902 original size:3 final size:3
Alignment explanation
Indices: 45779894--45779925 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
45779884 GCATATCCTC
45779894 TCA TCA TCA TCA TCA TCA TCA TCA T-A TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
45779926 CCTTTAGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:45783470 original size:2 final size:2
Alignment explanation
Indices: 45783463--45783494 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
45783453 CAAAAACAAC
*
45783463 AT AT AT AT AC 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
45783495 TAAATCTTAC
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:45783779 original size:13 final size:13
Alignment explanation
Indices: 45783761--45783790 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
45783751 ATTTCACATT
45783761 CATTTCAATTTCC
1 CATTTCAATTTCC
45783774 CATTTCAATTTCC
1 CATTTCAATTTCC
45783787 CATT
1 CATT
45783791 CCATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
CATTTCAATTTCC
Found at i:45784211 original size:18 final size:18
Alignment explanation
Indices: 45784165--45784212 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
45784155 CCAAACACAC
45784165 CAGTAAACAGTAATCATAA
1 CAGT-AACAGTAATCATAA
* *
45784184 CGGTAGCAGTAA-CATGAA
1 CAGTAACAGTAATCAT-AA
45784202 CAGTAACAGTA
1 CAGTAACAGTA
45784213 TTCAACACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19
Consensus pattern (18 bp):
CAGTAACAGTAATCATAA
Done.