Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold20
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: 3599867
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51021 characters in sequence are not A, C, G, or T
File 21 of 25
Found at i:3005447 original size:32 final size:33
Alignment explanation
Indices: 3005398--3005470 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
3005388 AACCGTTAAC
3005398 TGTATCGATTACATAAGTGTTGTATCGATACAA
1 TGTATCGATTACATAAGTGTTGTATCGATACAA
*
3005431 TGTATCGA-TACATAAGTTTTGTATCGATACAA
1 TGTATCGATTACATAAGTGTTGTATCGATACAA
3005463 TGTTATCG
1 TG-TATCG
3005471 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 25 0.66
33 13 0.34
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (33 bp):
TGTATCGATTACATAAGTGTTGTATCGATACAA
Found at i:3005455 original size:19 final size:18
Alignment explanation
Indices: 3005398--3005461 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
3005388 AACCGTTAAC
3005398 TGTATCGATTACATAAGTGT
1 TGTATCGA-TACATAAGT-T
3005418 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
3005431 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
3005450 TGTATCGATACA
1 TGTATCGATACA
3005462 ATGTTATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 15 0.39
20 8 0.21
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:3005532 original size:13 final size:13
Alignment explanation
Indices: 3005514--3005540 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3005504 CATTACTAAA
3005514 TGTATCGATACAT
1 TGTATCGATACAT
3005527 TGTATCGATACAT
1 TGTATCGATACAT
3005540 T
1 T
3005541 TGATCTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3008795 original size:3 final size:3
Alignment explanation
Indices: 3008787--3008837 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3008777 AAATTAATCA
3008787 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3008835 TAT
1 TAT
3008838 ATGTAACAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3009029 original size:3 final size:3
Alignment explanation
Indices: 3009021--3009052 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3009011 ACCATTTCGT
3009021 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3009053 CATCATCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3009057 original size:3 final size:3
Alignment explanation
Indices: 3009051--3009121 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
3009041 AATAATAATA
3009051 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3009099 ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC AT
3009122 ATAAATCACT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:3011484 original size:20 final size:20
Alignment explanation
Indices: 3011459--3011536 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
3011449 TTTTTACCCA
*
3011459 GATGTATCGATACATTTTTT
1 GATGTATCGATACATTCTTT
* * *
3011479 GATGTATCAATACA-TGTAT
1 GATGTATCGATACATTCTTT
* *
3011498 GAATGTATCGACACATTCTTC
1 G-ATGTATCGATACATTCTTT
*
3011519 AATGTATCGATACATTCT
1 GATGTATCGATACATTCT
3011537 GTCTTTTTAC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.09
20 40 0.87
21 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (20 bp):
GATGTATCGATACATTCTTT
Found at i:3014930 original size:20 final size:20
Alignment explanation
Indices: 3014883--3014957 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
3014873 AAAAAGACAT
* ** *
3014883 AATGTATTGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
3014903 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
3014923 TATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
3014943 AATGTATCGATACAT
1 AATGTATCGATACAT
3014958 CAAGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:3014951 original size:40 final size:39
Alignment explanation
Indices: 3014880--3014957 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3014870 GGTAAAAAGA
* * *
3014880 CATAATGTATTGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3014919 CATATATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3014958 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3015668 original size:28 final size:28
Alignment explanation
Indices: 3015587--3017487 Score: 1176
Period size: 28 Copynumber: 65.4 Consensus size: 28
3015577 AAAGAGTGTT
* * *
3015587 ACTGACTTGCGTGAGCTTTAAAAGGGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
* *
3015617 ACTGATTTGCGTGGGCTTTAAAAGGATGCC
1 ACTGACTT--GTGGGCTTTGAAAGGATGCC
*
3015647 ACTGACTCGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
3015675 ACTAACTTGTGGGCTTTGAAAGG-TGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
3015702 ACTGACTCGTGGGCTTTGAAAAGG-TACC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
** * *
3015730 ACTGACTCATGGGC-CTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
3015757 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
3015785 ACTGACTCGTGGGCTTTGAAAAGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
3015813 ACTGACTTGCGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGA-TGCC
*
3015844 ACTGACTTGTGTGGGCTTTGAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
* *
3015874 ACTAACTCGTGGGCTTTGAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
3015902 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
3015930 ACTGACTCGTGGGATTTGAAAAGG-TACC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
3015958 ACTGACTTGCGTGAGCTTTAAAAGGAGTGCC
1 ACTGACTT--GTGGGCTTTGAAAGGA-TGCC
* *
3015989 ACTGACTTGTGTGGGCTTTAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
3016019 ACTGACTTGTGGGCTTTGAAA-GAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
3016047 ACTGAATTGTGGGCTTCGCAATGG-TGCC
1 ACTGACTTGTGGGCTTTG-AAAGGATGCC
* *
3016075 ACTGACTTGTGGGCTTCGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
3016103 ACTGACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * *
3016131 ACTAACTTGTAGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
3016159 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
3016188 ACTGATTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
3016217 ACTGACTTGTGGGCTTTTAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
*
3016246 ACGGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * *
3016275 ACTAACTTGTGTGGGTTTTAAAAGGGTGCC
1 ACTGAC-T-TGTGGGCTTTGAAAGGATGCC
* * * *
3016305 ACTGACTTATGGGCTCTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
3016333 ACTAACTTGTGGGCTTTGAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
*
3016361 ACTGACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
3016390 ACTAACTTGTGGGCTTTGAAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
3016419 ACTGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
3016448 ACTGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
3016477 ACTGACTTGTGGGCTTTGAAAGGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* *
3016506 ACTGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* * *
3016538 ACCGACTTGTGTGGGTTTTGAAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTTGAAA--GGATGCC
* *
3016570 ACCGACTTATGTGGGCTTTGAAATAGGTTGCC
1 ACTGAC-T-TGTGGGCTTTG-AA-AGGATGCC
* *
3016602 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTTGAAA--GGATGCC
* *
3016634 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTTGAAA--GGATGCC
* *
3016666 ACTGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* * *
3016698 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* *
3016730 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTTGAAA--GGATGCC
* * *
3016762 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* * *
3016794 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* * *
3016826 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* * *
3016858 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* * *
3016890 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTT-GAA-AGGATGCC
* *
3016922 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCC
1 ACTGAC-T-TGTGGGCTTTGAAA--GGATGCC
* *
3016954 ACCGACTTGTGTGAGCTTTGAAATGGGTGCC
1 ACTGACTTGTG-G-GCTTTGAAA-GGATGCC
* * * * *
3016985 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
3017012 ACAGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
3017039 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
3017066 ACGGAGTTGTGGTC-TTAAAAGGGATGCC
1 ACTGACTTGTGGGCTTTGAAA-GGATGCC
* * * * *
3017094 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
3017121 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
3017148 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * **
3017175 ACGGAGTTGTGGAG-TTAAAAAGG-TGCC
1 ACTGACTTGTGG-GCTTTGAAAGGATGCC
* * * ** *
3017202 ACGGAGTTGTGGACTTAAAAAGG-TGCT
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * *
3017229 ACGGAGTTGTGGACTTTGAAAGG-TGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
3017256 ACAGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
3017283 ACGGAGTTGTGGACTTT-AAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * *
3017311 ACGGAGTTGTGGACTTTG-AAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * * *
3017338 ACGGAGTTGTGGAC-TTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
3017365 ACGGAGTTGTGGACTTT-AAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * *
3017393 ACGGAGTTGTGGACTTT-AAAAGAGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * * * *
3017421 ACGGAGTTGT-GGATTTAAAAGGGTGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* * * *
3017448 ACAGAGTTGTGGACTTTAAAAGGATGCC
1 ACTGACTTGTGGGCTTTGAAAGGATGCC
* *
3017476 ACGGAGTTGTGG
1 ACTGACTTGTGG
3017488 ACTTCAAAAA
Statistics
Matches: 1680, Mismatches: 127, Indels: 130
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.01
27 345 0.21
28 490 0.29
29 236 0.14
30 89 0.05
31 100 0.06
32 393 0.23
33 12 0.01
34 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (28 bp):
ACTGACTTGTGGGCTTTGAAAGGATGCC
Found at i:3016545 original size:32 final size:32
Alignment explanation
Indices: 3016340--3016995 Score: 859
Period size: 32 Copynumber: 21.1 Consensus size: 32
3016330 GCCACTAACT
* *
3016340 TGTGGGCTTT-GAAAGGG-TGCCACTGAC-T-
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* * * **
3016368 TGTGGGCTTTGAAAAGAG-TGCCACTAAC-T-
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* * * *
3016397 TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* *
3016426 TGTGGGCTTT-GAAAGGAG-TGCCACTGAC-T-
1 TGTGGGCTTTGGAATGG-GTTGCCACCGACTTG
* *
3016455 TGTGGGCTTT-GAAAGGAG-TGCCACTGAC-T-
1 TGTGGGCTTTGGAATGG-GTTGCCACCGACTTG
* *
3016484 TGTGGGCTTT-GAAAGGAG-TGCCACTGACTTG
1 TGTGGGCTTTGGAATGG-GTTGCCACCGACTTG
3016515 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* * *
3016547 TGTGGGTTTTGAAATGGGTTGCCACCGACTTA
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* *
3016579 TGTGGGCTTTGAAATAGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
*
3016611 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* *
3016643 TGTGGGCTTTGAAATGGGTTGCCACTGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016675 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016707 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
*
3016739 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016771 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016803 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016835 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016867 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016899 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
*
3016931 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
* * * *
3016963 TGTGAGCTTTGAAATGGG-TGCCACGGAGTTG
1 TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
3016994 TG
1 TG
3016996 GACTTAAAAG
Statistics
Matches: 598, Mismatches: 24, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
28 14 0.02
29 122 0.20
30 1 0.00
31 24 0.04
32 437 0.73
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (32 bp):
TGTGGGCTTTGGAATGGGTTGCCACCGACTTG
Found at i:3016583 original size:64 final size:64
Alignment explanation
Indices: 3015793--3016995 Score: 965
Period size: 64 Copynumber: 20.0 Consensus size: 64
3015783 CCACTGACTC
* * * * *
3015793 GTGGGCTTTGAAA-AGG-TGCCACTGACTTGCGTGGGCTTT-GAAAGGAG-TGCCACTGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGG-GTTGCCACCGACTTGT
** * * * *
3015854 GTGGGCTTTGAAA-GGG-TGCCACTAAC-T-CGTGGGCTTT-GAA-AGGATGCCACTGAC-T-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * * ** * * *
3015910 GTGGGCTTTGAAA-GAG-TGCCACTGAC-T-CGTGGGATTT-GAAAAGG-TACCACTGACTTGC
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * * * *
3015968 GTGAGCTTT-AAAAGGAG-TGCCACTGACTTGTGTGGGCTTT-AAAAGGG-TGCCACTGAC-T-T
1 GTGGGCTTTGAAATGG-GTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * * * *
3016027 GTGGGCTTTGAAA-GAG-TGCCACTGA-AT-TGTGGGCTTCGCAAT-GG-TGCCACTGAC-T-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * **
3016083 GTGGGCTTCGAAA-GGG-TGCCACTGAC-T-TGTGGGCTTT-GAAAGGG-TGCCACTAAC-T-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * * * *
3016139 GTAGGCTTTGAAA-GGG-TGCCACTGA-TT-TGTGGGCTTTGAAAAGAG-TGCCACTGA-TT-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * * * *
3016196 GTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTT-TAAAGGAG-TGCCACGGAC-T-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGG-GTTGCCACCGACTTGT
** ** * *
3016254 GTGGGCTTTGAAA-GGAG-TGCCACTAACTTGTGTGGG-TTTTAAAAGGG-TGCCACTGAC-T-T
1 GTGGGCTTTGAAATGG-GTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * ** * *
3016313 ATGGGCTCT-AAAAGGG-TGCCACTAAC-T-TGTGGGCTTT-GAAAGGG-TGCCACTGAC-T-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * ** * * * *
3016369 GTGGGCTTTGAAAAGAG-TGCCACTAAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-T
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * *
3016427 GTGGGCTTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGCTTT-GAAAGGAG-TGCCACTGAC-T-
1 GTGGGCTTTGAAATGG-GTTGCCACCGACTTGTGTGGGCTTTGGAATGG-GTTGCCACCGACTTG
3016484 T
64 T
*
3016485 GTGGGCTTTGAAA-GGAG-TGCCACTGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAATGG-GTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * *
3016548 GTGGGTTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATAGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* *
3016612 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
*
3016676 GTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
3016740 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
*
3016804 GTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
*
3016868 GTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
* * * *
3016932 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGAGCTTTGAAATGGG-TGCCACGGAGTTGT
1 GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
3016995 G
1 G
3016996 GACTTAAAAG
Statistics
Matches: 1030, Mismatches: 75, Indels: 72
0.88 0.06 0.06
Matches are distributed among these distances:
55 2 0.00
56 181 0.18
57 80 0.08
58 191 0.19
59 59 0.06
60 28 0.03
61 60 0.06
62 1 0.00
63 27 0.03
64 401 0.39
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (64 bp):
GTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGT
Found at i:3016612 original size:96 final size:90
Alignment explanation
Indices: 3015587--3017076 Score: 1369
Period size: 96 Copynumber: 16.8 Consensus size: 90
3015577 AAAGAGTGTT
* * * *
3015587 ACTGACTTGCGTGAGCTTTAAAAGGGTGCCACTGA-TTTGCGTGGGCTTT-AAAAGGATGCCACT
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTT--GTGGGCTTTGAAAAGGGTGCCACT
* *
3015650 GAC-T-CGTGGGCTTTGAAAGAGTGCC
64 GACTTGTGTGGGCTTTGAAAGGGTGCC
* * *
3015675 ACTAAC-T-TGTGGGCTTTGAAA-GGTGCCACTGAC-TCGTGGGCTTTGAAAA-GGTACCACTGA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
** *
3015735 C-T-CATGGGC-CTGAAAGGGTGCC
66 CTTGTGTGGGCTTTGAAAGGGTGCC
* *
3015757 ACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGAC-TCGTGGGCTTTGAAAA-GGTGCCACTGA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
*
3015818 CTTGCGTGGGCTTTGAAAGGAGTGCC
66 CTTGTGTGGGCTTTGAAAGG-GTGCC
* * *
3015844 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAAC-TCGTGGGCTTTG-AAAGGATGCCACTGA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
*
3015907 C-T-TGTGGGCTTTGAAAGAGTGCC
66 CTTGTGTGGGCTTTGAAAGGGTGCC
* * * * * *
3015930 ACTGAC-T-CGTGGGATTTGAAAAGGTACCACTGACTTGCGTGAGCTTT-AAAAGGAGTGCCACT
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT-TGTGGGCTTTGAAAAGG-GTGCCACT
*
3015992 GACTTGTGTGGGCTTTAAAAGGGTGCC
64 GACTTGTGTGGGCTTTGAAAGGGTGCC
* * * * *
3016019 ACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGA-ATTGTGGGCTTCG-CAATGGTGCCACTGA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
*
3016080 C-T-TGTGGGCTTCGAAAGGGTGCC
66 CTTGTGTGGGCTTTGAAAGGGTGCC
* *
3016103 ACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACTAAC-TTGTAGGCTTTG-AAAGGGTGCCACTGA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
*
3016164 -TT-TGTGGGCTTTGAAAAGAGTGCC
66 CTTGTGTGGGCTTTG-AAAGGGTGCC
* * *
3016188 ACTGA-TT-TGTGGGCTTTGAAAAGAGTGCCACTGAC-TTGTGGGCTTT-TAAAGGAGTGCCACG
1 ACTGACTTGTGTGGGCTTTG-AAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGG-GTGCCACT
3016249 GAC-T-TGTGGGCTTTGAAAGGAGTGCC
64 GACTTGTGTGGGCTTTGAAAGG-GTGCC
* * * * * *
3016275 ACTAACTTGTGTGGGTTTTAAAAGGGTGCCACTGAC-TTATGGGCTCT-AAAAGGGTGCCACTAA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
3016338 C-T-TGTGGGCTTTGAAAGGGTGCC
66 CTTGTGTGGGCTTTGAAAGGGTGCC
* * *
3016361 ACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTAAC-TTGTGGGCTTTGAAAAGAGTGCCACTG
1 ACTGACTTGTGTGGGCTTTG-AAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTG
3016423 AC-T-TGTGGGCTTTGAAAGGAGTGCC
65 ACTTGTGTGGGCTTTGAAAGG-GTGCC
3016448 ACTGAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGAC-TTGTGGGCTTTG-AAAGGAGTGCCACT
1 ACTGACTTGTGTGGGCTTTGAAAGG-GTGCCACTGACTTTGTGGGCTTTGAAAAGG-GTGCCACT
*
3016509 GACTTGTGTGGGCTTTGGAATGGGTTGCC
64 GACTTGTGTGGGCTTT-GAAAGGG-TGCC
* * * *
3016538 ACCGACTTGTGTGGGTTTTGAAATGGGTTGCCACCGACTTATGTGGGCTTTGAAATAGGTTGCCA
1 ACTGACTTGTGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAA-AGGGTGCCA
*
3016603 CCGACTTGTGTGGGCTTTGAAATGGGTTGCC
62 CTGACTTGTGTGGGCTTTGAAA-GGG-TGCC
* * *
3016634 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTGTGTGGGCTTTGGAATGGGTTGCCA
1 ACTGACTTGTGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-TGCCA
* *
3016699 CCGACTTGTGTGGGCTTTGGAATGGGTTGCC
62 CTGACTTGTGTGGGCTTT-GAAAGGG-TGCC
* * * *
3016730 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCA
1 ACTGACTTGTGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-TGCCA
* *
3016795 CCGACTTGTGTGGGCTTTGGAATGGGTTGCC
62 CTGACTTGTGTGGGCTTT-GAAAGGG-TGCC
* * * * *
3016826 ACCGACTTGTGTGGGCTTTGGAATGGGTTGCCACCGACTTGTGTGGGCTTTGGAATGGGTTGCCA
1 ACTGACTTGTGTGGGCTTT-GAAAGGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGG-TGCCA
* *
3016891 CCGACTTGTGTGGGCTTTGGAATGGGTTGCC
62 CTGACTTGTGTGGGCTTT-GAAAGGG-TGCC
* * * *
3016922 ACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGAGCTTTGAAATGGGTGCCAC
1 ACTGACTTGTGTGGGCTTTGAAA-GGG-TGCCACTGACTT-TGTGGGCTTTGAAAAGGGTGCCAC
* * * *
3016987 GGA-GT-TGTGGAC-TTAAAAGGGTGCC
63 TGACTTGTGTGGGCTTTGAAAGGGTGCC
* * * * * * * *
3017012 ACAGA-GT-TGTGGAC-TTAAAAGGGTGCCACGGA-GTTGTGGAC-TT-AAAAGGGTGCCACGGA
1 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
*
3017071 GTTGTG
66 CTTGTG
3017077 GTCTTAAAAG
Statistics
Matches: 1240, Mismatches: 110, Indels: 109
0.85 0.08 0.07
Matches are distributed among these distances:
81 15 0.01
82 34 0.03
83 71 0.06
84 121 0.10
85 79 0.06
86 140 0.11
87 163 0.13
88 50 0.04
89 116 0.09
90 22 0.02
91 6 0.00
92 16 0.01
93 17 0.01
94 2 0.00
95 27 0.02
96 352 0.28
97 9 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (90 bp):
ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTTGTGGGCTTTGAAAAGGGTGCCACTGA
CTTGTGTGGGCTTTGAAAGGGTGCC
Found at i:3017008 original size:27 final size:27
Alignment explanation
Indices: 3016978--3017496 Score: 824
Period size: 27 Copynumber: 19.0 Consensus size: 27
3016968 GCTTTGAAAT
3016978 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3017005 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3017032 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3017059 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3017086 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
3017114 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3017141 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3017168 GGGTGCCACGGAGTTGTGGAGTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3017195 AGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
3017222 AGGTGCTACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
3017250 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3017276 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* **
3017304 GAGTGCCACGGAGTTGTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3017331 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3017358 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
3017386 GAGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
3017414 GAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3017441 GGGTGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
3017469 GGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
3017497 AGAAATGCCA
Statistics
Matches: 459, Mismatches: 26, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
26 5 0.01
27 315 0.69
28 139 0.30
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:3017119 original size:82 final size:82
Alignment explanation
Indices: 3016950--3017496 Score: 832
Period size: 82 Copynumber: 6.6 Consensus size: 82
3016940 TGAAATGGGT
* * * *
3016950 TGCCACCGACTTGTGTGAGCTTTGAAATGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACA
1 TGCCACGGAGTTGTG-GA-CTTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
3017015 GAGTTGTGGACTTAAAAGGG
63 GAGTTGTGGACTTAAAAGGG
*
3017035 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGA
3017099 GTTGTGGACTTAAAAGGG
65 GTTGTGGACTTAAAAGGG
3017117 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
* *
3017181 TTGTGGAGTTAAAAAGG
66 TTGTGGACTTAAAAGGG
* * * *
3017198 TGCCACGGAGTTGTGGAC-TTAAAAAGGTGCTACGGAGTTGTGGACTTTGAAA-GGTGCCACAGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGA
3017261 GTTGTGGACTTAAAAGGG
65 GTTGTGGACTTAAAAGGG
* **
3017279 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTGAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
3017344 TTGTGGACTTAAAAGGG
66 TTGTGGACTTAAAAGGG
* *
3017361 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGA
*
3017426 GTTGTGGATTTAAAAGGG
65 GTTGTGGACTTAAAAGGG
* *
3017444 TGCCACAGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTTCAAAA
1 TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAA
3017497 AGAAATGCCA
Statistics
Matches: 429, Mismatches: 27, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
81 148 0.34
82 186 0.43
83 80 0.19
84 2 0.00
85 13 0.03
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (82 bp):
TGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
TTGTGGACTTAAAAGGG
Found at i:3025983 original size:20 final size:20
Alignment explanation
Indices: 3025936--3026010 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
3025926 AAAAAGACAT
* ** *
3025936 AATGTATTGATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
3025956 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
3025976 TATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
3025996 AATGTATCGATACAT
1 AATGTATCGATACAT
3026011 CAAGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:3026004 original size:40 final size:39
Alignment explanation
Indices: 3025933--3026010 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3025923 GGTAAAAAGA
* * *
3025933 CATAATGTATTGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3025972 CATATATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3026011 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3028684 original size:13 final size:13
Alignment explanation
Indices: 3028666--3028695 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3028656 GTTTCGGCCT
*
3028666 TATTCATTACTAA
1 TATTCATAACTAA
3028679 TATTCATAACTAA
1 TATTCATAACTAA
3028692 TATT
1 TATT
3028696 TACTATAATT
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:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTCATAACTAA
Found at i:3032864 original size:18 final size:18
Alignment explanation
Indices: 3032841--3032877 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3032831 GCAACATTAA
3032841 TAAAGATATTGGGACAAC
1 TAAAGATATTGGGACAAC
*
3032859 TAAAGATATTGGGAGAAC
1 TAAAGATATTGGGACAAC
3032877 T
1 T
3032878 GAACTTACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (18 bp):
TAAAGATATTGGGACAAC
Found at i:3034822 original size:2 final size:2
Alignment explanation
Indices: 3034815--3034855 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3034805 GTAAAGCTAC
3034815 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
3034856 CCCTTAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3036911 original size:49 final size:48
Alignment explanation
Indices: 3036845--3036965 Score: 125
Period size: 53 Copynumber: 2.4 Consensus size: 48
3036835 TTTTCTATGT
* ** *
3036845 AAAGTATGGATACTTTGTAATATAAATATACTGCTACTTTTTCTTACAC
1 AAAGTATGGATATTTTGTAATATAAATATAAAG-TACTTTTTATTACAC
**
3036894 AAAGTATGGATATTTTGTTTTGTAATATAAATATAAAGTTTTTTTTATTACAC
1 AAAGTATGGATA-----TTTTGTAATATAAATATAAAGTACTTTTTATTACAC
*
3036947 AAAGTATGAATATTTTGTA
1 AAAGTATGGATATTTTGTA
3036966 TAAAAAAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
48 7 0.12
49 12 0.20
53 23 0.38
54 18 0.30
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (48 bp):
AAAGTATGGATATTTTGTAATATAAATATAAAGTACTTTTTATTACAC
Found at i:3036952 original size:53 final size:54
Alignment explanation
Indices: 3036858--3036964 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 54
3036848 GTATGGATAC
** * *
3036858 TTTGTAATATAAATATACTGCTACTTTTTCTTACACAAAGTATGGATATTTTGT
1 TTTGTAATATAAATATAAAGCTACTTTTTATTACACAAAGTATGAATATTTTGT
**
3036912 TTTGTAATATAAATATAAAG-TTTTTTTTATTACACAAAGTATGAATATTTTGT
1 TTTGTAATATAAATATAAAGCTACTTTTTATTACACAAAGTATGAATATTTTGT
3036965 ATAAAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 29 0.62
54 18 0.38
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (54 bp):
TTTGTAATATAAATATAAAGCTACTTTTTATTACACAAAGTATGAATATTTTGT
Found at i:3039015 original size:32 final size:32
Alignment explanation
Indices: 3038948--3039016 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
3038938 AAAAATTGTA
* * ** *
3038948 AAATAATATTTTAGTAATAATTATATTATTAT
1 AAATAATATTTTAATAACAACCATAATATTAT
*
3038980 AAATAATATTTTAATAACAACCATAATATTTT
1 AAATAATATTTTAATAACAACCATAATATTAT
3039012 AAATA
1 AAATA
3039017 TTTATATGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (32 bp):
AAATAATATTTTAATAACAACCATAATATTAT
Found at i:3039049 original size:14 final size:15
Alignment explanation
Indices: 3039010--3039071 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
3039000 CCATAATATT
*
3039010 TTAAATATTTATATGA
1 TTAAATATTTA-ATAA
*
3039026 TT-AATGTTTAATAA
1 TTAAATATTTAATAA
*
3039040 TTAAA-ATTT-ATATT
1 TTAAATATTTAATA-A
3039054 TTAAATATTTAAT-A
1 TTAAATATTTAATAA
3039068 TTAA
1 TTAA
3039072 TATAATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
13 3 0.08
14 17 0.46
15 13 0.35
16 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TTAAATATTTAATAA
Found at i:3039064 original size:29 final size:29
Alignment explanation
Indices: 3039010--3039071 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
3039000 CCATAATATT
*
3039010 TTAAATATTTATATGATTAATGTTTAATAA
1 TTAAATATTTATATGATTAATATTTAAT-A
*
3039040 TTAAA-ATTTATAT-TTTAAATATTTAATA
1 TTAAATATTTATATGATT-AATATTTAATA
3039068 TTAA
1 TTAA
3039072 TATAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 7 0.24
29 17 0.59
30 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TTAAATATTTATATGATTAATATTTAATA
Found at i:3039065 original size:22 final size:22
Alignment explanation
Indices: 3039005--3039074 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
3038995 AACAACCATA
3039005 ATATTTTAAATATTT-ATATGATT
1 ATATTTTAAATATTTAATAT--TT
* *
3039028 A-ATGTTT-AATAATTAAAATTT
1 ATAT-TTTAAATATTTAATATTT
*
3039049 ATATTTTAAATATTTAATATTA
1 ATATTTTAAATATTTAATATTT
3039071 ATAT
1 ATAT
3039075 AATATTTTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
21 6 0.16
22 25 0.66
23 7 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (22 bp):
ATATTTTAAATATTTAATATTT
Found at i:3043207 original size:21 final size:22
Alignment explanation
Indices: 3043173--3043220 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
3043163 CAATAAAAGT
3043173 TGCA-TATTTCCATCCAATAAA
1 TGCATTATTTCCATCCAATAAA
*
3043194 TGCATTATTT-CATCCAATCAA
1 TGCATTATTTCCATCCAATAAA
3043215 TGCATT
1 TGCATT
3043221 TTTTTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (22 bp):
TGCATTATTTCCATCCAATAAA
Found at i:3043651 original size:18 final size:19
Alignment explanation
Indices: 3043620--3043655 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3043610 AATATTTAAA
3043620 TAAATATATATTAAAATTT
1 TAAATATATATTAAAATTT
3043639 TAAATAT-TATTAAAATT
1 TAAATATATATTAAAATT
3043656 AATTTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATATATATTAAAATTT
Found at i:3044712 original size:31 final size:31
Alignment explanation
Indices: 3044677--3044754 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
3044667 ATTAATTAAA
*
3044677 ATAAAATATAAATATATATCTTAAAATTTAT
1 ATAAAATATAAATATATATATTAAAATTTAT
*
3044708 ATAAAATA-AATTATTATTATATTAAAATTTAT
1 ATAAAATATAAATA-TA-TATATTAAAATTTAT
*
3044740 -TTAAATAT-AATATAT
1 ATAAAATATAAATATAT
3044755 TTTAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
29 1 0.03
30 6 0.15
31 19 0.47
32 14 0.35
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
ATAAAATATAAATATATATATTAAAATTTAT
Found at i:3044713 original size:36 final size:34
Alignment explanation
Indices: 3044673--3044754 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 34
3044663 ATTAATTAAT
*
3044673 TAAAATAAAATATAAATATATATCTTAAAATTTATA
1 TAAAATAAAATAT-AATAT-TATATTAAAATTTATA
* *
3044709 TAAAAT-AAAT-TATTATTATATTAAAATTTATT
1 TAAAATAAAATATAATATTATATTAAAATTTATA
*
3044741 TAAATATAATATAT
1 TAAA-ATAAAATAT
3044755 TTTAAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
32 18 0.46
33 6 0.15
34 4 0.10
35 5 0.13
36 6 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAAATAAAATATAATATTATATTAAAATTTATA
Found at i:3044792 original size:29 final size:29
Alignment explanation
Indices: 3044757--3044812 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
3044747 TAATATATTT
3044757 TAAATATAATTAT-AACATAA-TAAAATATA
1 TAAATATAA-TATGAA-ATAATTAAAATATA
3044786 TAAATATAATATGAAATAATTAAAATA
1 TAAATATAATATGAAATAATTAAAATA
3044813 AAATAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAATATAATATGAAATAATTAAAATATA
Found at i:3045144 original size:13 final size:13
Alignment explanation
Indices: 3045128--3045171 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3045118 ATATTTTAAT
3045128 AAATATTAAATAA
1 AAATATTAAATAA
* * *
3045141 AAATTTTGAATAT
1 AAATATTAAATAA
3045154 AAATATTTAAATAA
1 AAATA-TTAAATAA
3045168 AAAT
1 AAAT
3045172 TTTGAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAATATTAAATAA
Found at i:3045156 original size:26 final size:28
Alignment explanation
Indices: 3045124--3045184 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 28
3045114 ATTTATATTT
3045124 TAATAAATA-TTAAATAAAAATTTTGAA
1 TAATAAATATTTAAATAAAAATTTTGAA
3045151 T-ATAAATATTTAAATAAAAATTTTGAA
1 TAATAAATATTTAAATAAAAATTTTGAA
3045178 TAATAAA
1 TAATAAA
3045185 AGAGTTATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 7 0.22
27 20 0.62
28 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (28 bp):
TAATAAATATTTAAATAAAAATTTTGAA
Found at i:3045426 original size:18 final size:18
Alignment explanation
Indices: 3045405--3045442 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3045395 ATTAATTTTT
*
3045405 TTAATTACATA-AAAATAA
1 TTAATTA-ATATAAAAAAA
3045423 TTAATTAATATAAAAAAA
1 TTAATTAATATAAAAAAA
3045441 TT
1 TT
3045443 TACGTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAATTAATATAAAAAAA
Found at i:3045502 original size:2 final size:2
Alignment explanation
Indices: 3045497--3045534 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3045487 AATTAGATGA
3045497 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3045535 TCACATCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3045849 original size:22 final size:22
Alignment explanation
Indices: 3045824--3045962 Score: 103
Period size: 22 Copynumber: 6.3 Consensus size: 22
3045814 TTAATAATAA
3045824 AAAAATATTTAAATTTAATTAT
1 AAAAATATTTAAATTTAATTAT
* *
3045846 AAAAATATTTAAATATGAA-TAC
1 AAAAATATTTAAAT-TTAATTAT
*
3045868 AAAAATAATTATATTAATTTTATT-T
1 AAAAAT-ATT-TA--AATTTAATTAT
* *
3045893 -AAATTA-TT--ATTTAATAAT
1 AAAAATATTTAAATTTAATTAT
3045911 AAAAATTATTTAAATTTAATTAT
1 AAAAA-TATTTAAATTTAATTAT
* *
3045934 AAAAATATATAAATATGAA-TAT
1 AAAAATATTTAAAT-TTAATTAT
3045956 AAAAATA
1 AAAAATA
3045963 ATTTTTTATT
Statistics
Matches: 92, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.07
18 1 0.01
19 3 0.03
20 2 0.02
21 3 0.03
22 41 0.45
23 24 0.26
24 6 0.07
25 2 0.02
26 4 0.04
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
AAAAATATTTAAATTTAATTAT
Found at i:3045916 original size:20 final size:22
Alignment explanation
Indices: 3045804--3045939 Score: 81
Period size: 23 Copynumber: 6.2 Consensus size: 22
3045794 GATTCTATTT
3045804 AAATTA-TT-ATTTAATAATAAA
1 AAATTATTTAATTTAATAAT-AA
* *
3045825 AAAATATTTAAATTTAATTATAA
1 AAATTATTT-AATTTAATAATAA
* *
3045848 AAA-TATTTAAATATGAATACAAAA
1 AAATTATTT-AAT-TTAATA-ATAA
**
3045872 ATAATTATATTAATTT--T-ATTT
1 A-AATTAT-TTAATTTAATAATAA
3045893 AAATTA-TT-ATTTAATAATAA
1 AAATTATTTAATTTAATAATAA
*
3045913 AAATTATTTAAATTTAATTATAA
1 AAATTATTT-AATTTAATAATAA
3045936 AAAT
1 AAAT
3045940 ATATAAATAT
Statistics
Matches: 89, Mismatches: 12, Indels: 26
0.70 0.09 0.20
Matches are distributed among these distances:
17 4 0.04
18 2 0.02
19 1 0.01
20 13 0.15
21 9 0.10
22 11 0.12
23 25 0.28
24 13 0.15
25 3 0.03
26 6 0.07
27 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
AAATTATTTAATTTAATAATAA
Found at i:3045949 original size:88 final size:89
Alignment explanation
Indices: 3045799--3045965 Score: 300
Period size: 88 Copynumber: 1.9 Consensus size: 89
3045789 TGTTGGATTC
*
3045799 TATTTAAATTATTATTTAATAATAAAAAAATATTTAAATTTAATTATAAAAATATTTAAATATGA
1 TATTTAAATTATTATTTAATAATAAAAAAATATTTAAATTTAATTATAAAAATATATAAATATGA
3045864 ATACAAAAATAATTATATTAATTT
66 ATACAAAAATAATTATATTAATTT
*
3045888 TATTTAAATTATTATTTAATAAT-AAAAATTATTTAAATTTAATTATAAAAATATATAAATATGA
1 TATTTAAATTATTATTTAATAATAAAAAAATATTTAAATTTAATTATAAAAATATATAAATATGA
*
3045952 ATATAAAAATAATT
66 ATACAAAAATAATT
3045966 TTTTATTATA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 52 0.69
89 23 0.31
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (89 bp):
TATTTAAATTATTATTTAATAATAAAAAAATATTTAAATTTAATTATAAAAATATATAAATATGA
ATACAAAAATAATTATATTAATTT
Found at i:3046710 original size:57 final size:57
Alignment explanation
Indices: 3046622--3046735 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
3046612 ATGATAATAA
* * *
3046622 GCAATTGATGTTTTCACCATCATAATTAAATATTATTCATAGATAGAAGATAAGTTT
1 GCAATGGATGTTTTCACCATCATAATTAAATATGATTCACAGATAGAAGATAAGTTT
*
3046679 GCAATGGATGTTTTCACCATCATAATTAAATATGATTCACAGATAGAAGATAGGTTT
1 GCAATGGATGTTTTCACCATCATAATTAAATATGATTCACAGATAGAAGATAAGTTT
3046736 AAGAGACCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (57 bp):
GCAATGGATGTTTTCACCATCATAATTAAATATGATTCACAGATAGAAGATAAGTTT
Found at i:3046851 original size:6 final size:7
Alignment explanation
Indices: 3046831--3046857 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3046821 ATAAAATTTT
3046831 AATAAAA
1 AATAAAA
3046838 AATAAAA
1 AATAAAA
3046845 AATAAAA
1 AATAAAA
3046852 AATAAA
1 AATAAA
3046858 GTAAAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:3047083 original size:22 final size:22
Alignment explanation
Indices: 3047058--3047102 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3047048 ATAGTTTATT
*
3047058 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAAAATA
3047080 TAAATATTAATATAAAAAAATA
1 TAAATATTAATATAAAAAAATA
3047102 T
1 T
3047103 TTTTTATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAAAATA
Found at i:3047089 original size:29 final size:32
Alignment explanation
Indices: 3047029--3047087 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
3047019 TTGAATTATT
**
3047029 ATTTAATAATAAAAAATATATAGTTTATTTAA
1 ATTTAATAATAAAAAATATATAGAATATTTAA
*
3047061 ATTTAATTAT-AAAAATATATA-AATATT
1 ATTTAATAATAAAAAATATATAGAATATT
3047088 AATATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 4 0.17
31 11 0.46
32 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (32 bp):
ATTTAATAATAAAAAATATATAGAATATTTAA
Found at i:3048087 original size:11 final size:10
Alignment explanation
Indices: 3048056--3048086 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
3048046 AATATAATAT
3048056 TTTTATTAAAA
1 TTTT-TTAAAA
3048067 TTTTTTAAAA
1 TTTTTTAAAA
3048077 TTTTTTAAAA
1 TTTTTTAAAA
3048087 AATTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:3050413 original size:11 final size:11
Alignment explanation
Indices: 3050397--3050432 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3050387 ACAATCAATG
3050397 TATTTATATTA
1 TATTTATATTA
3050408 TATTTATATTA
1 TATTTATATTA
*
3050419 TTTTTTATATTA
1 -TATTTATATTA
3050431 TA
1 TA
3050433 ATCATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTTATATTA
Found at i:3050984 original size:16 final size:15
Alignment explanation
Indices: 3050963--3050999 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
3050953 ATTTAAATTT
3050963 TTTTAATAATATATAA
1 TTTTAA-AATATATAA
3050979 TTTT-AAATATATAA
1 TTTTAAAATATATAA
3050993 TTTTAAA
1 TTTTAAA
3051000 TTACAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 13 0.65
15 3 0.15
16 4 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAAAATATATAA
Found at i:3050989 original size:14 final size:14
Alignment explanation
Indices: 3050970--3051000 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3050960 TTTTTTTAAT
3050970 AATATATAATTTTA
1 AATATATAATTTTA
3050984 AATATATAATTTTA
1 AATATATAATTTTA
3050998 AAT
1 AAT
3051001 TACAGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATATAATTTTA
Found at i:3051115 original size:5 final size:5
Alignment explanation
Indices: 3051105--3051144 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
3051095 AAAAATTAAG
3051105 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
3051145 CAAATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:3051271 original size:2 final size:2
Alignment explanation
Indices: 3051264--3051316 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
3051254 ACAACCACGC
*
3051264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3051306 AT AA AT AT AT A
1 AT AT AT AT AT A
3051317 GATGGTTGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3052548 original size:173 final size:171
Alignment explanation
Indices: 3052033--3052633 Score: 737
Period size: 170 Copynumber: 3.6 Consensus size: 171
3052023 ATCTATCTAC
* * * *
3052033 ATAAATATTTATTATTTAATGATCAC-----GTATATAATAAATAATTT-TTTTTTTGATATATT
1 ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAAATAATTTATTTTTTTAATATATA
* *
3052092 ATTGGA-GTTGAGATAAGGATATTAGGATTTGAATTCAAACTTTCATACCAATATAAACTTCTTG
66 ATTTGAGGTTGAGATAAGGATATTAAGATTTGAATTCAAACTTTCATACCAATAT-AACTTCTTG
* * *
3052156 TCACTCGATAAAAAGATTTCTATCATTAATTAATCTTTTGAA
130 TCACTCGATAAAAAGATTGCTAACAATAATTAATCTTTTGAA
* * * * *
3052198 ATAAATATTTATTATTTGATAAT--CATATGATATGTAATAAATAATTGATTTTTTTAATTTATA
1 ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAAATAATTTATTTTTTTAATATATA
* ** * * *
3052261 ATTTGAAGTTGAGACGAGGATATT-AGAATTTGAATTCAAACTTTTATACCAATATAATTTTTTG
66 ATTTGAGGTTGAGATAAGGATATTAAG-ATTTGAATTCAAACTTTCATACCAATATAACTTCTTG
* * *
3052325 TCACTCAAT-AAAAGATTGCT-ACAATTAATTAATCTCTTAAA
130 TCACTCGATAAAAAGATTGCTAACAA-TAATTAATCTTTTGAA
* *
3052366 ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAGATAATTGGTTTTTTTTTAATATA
1 ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAAATAATT--TATTTTTTTAATATA
* * * *
3052431 TAATTT-AGGTTGGGATAAGGATATTAAGTTTTGAATTCAAACTTTCATACCGATATAGACCTCT
64 TAATTTGAGGTTGAGATAAGGATATTAAGATTTGAATTCAAACTTTCATACCAATATA-ACTTCT
* *
3052495 TGTCACTCGGTAAAAAGATTGCTAACAATAATTAATTTTTTGAA
128 TGTCACTCGATAAAAAGATTGCTAACAATAATTAATCTTTTGAA
*
3052539 ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAAATAATTAATTTTTTT-ATATATA
1 ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAAATAATTTATTTTTTTAATATATA
*
3052603 ATTTGAGGTTGAGATGAA-GATATTAGGATTT
66 ATTTGAGGTTGAGAT-AAGGATATTAAGATTT
3052634 AATAAGATAG
Statistics
Matches: 368, Mismatches: 49, Indels: 32
0.82 0.11 0.07
Matches are distributed among these distances:
163 1 0.00
165 21 0.06
167 2 0.01
168 61 0.17
169 33 0.09
170 73 0.20
171 68 0.18
172 34 0.09
173 71 0.19
174 4 0.01
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (171 bp):
ATAAATATTTATTATTTAATAATCACATAAGGTATGTAATAAATAATTTATTTTTTTAATATATA
ATTTGAGGTTGAGATAAGGATATTAAGATTTGAATTCAAACTTTCATACCAATATAACTTCTTGT
CACTCGATAAAAAGATTGCTAACAATAATTAATCTTTTGAA
Found at i:3061511 original size:19 final size:19
Alignment explanation
Indices: 3061487--3061554 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3061477 AATTCAACAA
3061487 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3061506 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3061521 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3061538 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3061555 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3061526 original size:13 final size:13
Alignment explanation
Indices: 3061508--3061532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3061498 ACATAAGTTT
3061508 TGTATCGATACAA
1 TGTATCGATACAA
3061521 TGTATCGATACA
1 TGTATCGATACA
3061533 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3061530 original size:32 final size:32
Alignment explanation
Indices: 3061489--3061551 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3061479 TTCAACAATT
*
3061489 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3061521 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3061552 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3061612 original size:13 final size:13
Alignment explanation
Indices: 3061594--3061619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3061584 CATTTTTCTG
3061594 TGTATCGATACAT
1 TGTATCGATACAT
3061607 TGTATCGATACAT
1 TGTATCGATACAT
3061620 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3061616 original size:33 final size:33
Alignment explanation
Indices: 3061574--3061640 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3061564 GCCAAGGAAA
***
3061574 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3061607 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3061640 T
1 T
3061641 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3064187 original size:31 final size:28
Alignment explanation
Indices: 3064104--3064173 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
3064094 CTTCACAATC
* * ***
3064104 GGGGACACTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
3064131 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
3064159 GGGGATACTCCAACC
1 GGGGATACTCCAACC
3064174 TCGACTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.20
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:3064218 original size:51 final size:51
Alignment explanation
Indices: 3064159--3064331 Score: 204
Period size: 52 Copynumber: 3.4 Consensus size: 51
3064149 TTATTTCCGA
* ***
3064159 GGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * * * *
3064210 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTC-ATAATC
*
3064262 GGGGATACTCCAACAC-CGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CTCGATTTTATTTCC-AAAATACCAATTTTTCATAATC
*
3064314 GAGGATACTCCAACCTCG
1 GGGGATACTCCAACCTCG
3064332 TTATTTCATC
Statistics
Matches: 101, Mismatches: 17, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
51 37 0.37
52 49 0.49
53 15 0.15
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:3064275 original size:52 final size:52
Alignment explanation
Indices: 3063984--3064328 Score: 193
Period size: 51 Copynumber: 6.6 Consensus size: 52
3063974 TTGAGTTGCT
* * * * * *
3063984 CAATTCTCCACAATCGAGGATATTCCAACTCCGATTTTACTTT-C-AAAACAT
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTA-TTTCCAAAAACAC
* * *
3064035 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAAACAC
* * * * * *** * *
3064088 CAATTTCTTCACAATCGGGGACACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAATTT-TCCATAATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACAC
** * * * * * *
3064141 CAA--CCCCGTTATTTCCGAGGGGATACTCCAACCTCGACTTTATTTCC-AAAATAT
1 CAATTTTCC-ATA-AT-C--GGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
** * * *
3064195 TGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
3064246 CAATTTTCCTTTAATCGGGGATACTCCAACACCGATTTTATTTCCAAAAATAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
* * *
3064299 CAATTTTTCACAATCGAGGATACTCCAACC
1 CAATTTTCCATAATCGGGGATACTCCAACC
3064329 TCGTTATTTC
Statistics
Matches: 215, Mismatches: 62, Indels: 33
0.69 0.20 0.11
Matches are distributed among these distances:
50 4 0.02
51 71 0.33
52 53 0.25
53 36 0.17
54 26 0.12
55 18 0.08
56 3 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (52 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACAC
Found at i:3064402 original size:211 final size:211
Alignment explanation
Indices: 3063995--3064402 Score: 579
Period size: 211 Copynumber: 1.9 Consensus size: 211
3063985 AATTCTCCAC
* * **
3063995 AATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTTTCTATAATCGGGGATACTC
1 AATCGAGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* *
3064060 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
* * * * * *
3064125 ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCTCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCAA
3064190 AATATTGATTTTTCAT
196 AATATTGATTTTTCAT
* * * *
3064206 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGAGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* * *
3064271 CCAACACCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGTT
65 CCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
* *
3064334 ATTTCATCGGGGATACTCCAACCCCATTACTTCCGAGGGAACACTCCAACCCCG-TTATTATCTC
130 A-ATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGAACACTCCAACCCCGACT-TTATCTC
3064398 CAAAA
193 CAAAA
3064403 CATTAAATTT
Statistics
Matches: 173, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
210 28 0.16
211 110 0.64
212 35 0.20
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (211 bp):
AATCGAGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTTA
ATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCAA
AATATTGATTTTTCAT
Found at i:3069740 original size:25 final size:24
Alignment explanation
Indices: 3069711--3069794 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
3069701 AAAAATGATG
*
3069711 AAAAAGTCAAAAGTAAACACACAA
1 AAAAAGTCAAAAGAAAACACACAA
*
3069735 ACAAAAGTCAAAAGCAAACACA-AA
1 A-AAAAGTCAAAAGAAAACACACAA
* *
3069759 AAACAGAACAAAA-AAAACACACAA
1 AAAAAG-TCAAAAGAAAACACACAA
3069783 AAAAAGTGCAAA
1 AAAAAGT-CAAA
3069795 TGCAAAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
23 11 0.22
24 20 0.40
25 19 0.38
ACGTcount: A:0.69, C:0.18, G:0.08, T:0.05
Consensus pattern (24 bp):
AAAAAGTCAAAAGAAAACACACAA
Found at i:3071140 original size:31 final size:31
Alignment explanation
Indices: 3071065--3071217 Score: 150
Period size: 31 Copynumber: 4.9 Consensus size: 31
3071055 ATACCTTCTT
* * *
3071065 AAAGTTCACGACTCAGTGGCATTTTGTC-CT
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
*
3071095 AAAGTCTACGACTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* *
3071126 AAAGTCCACAACTCAGTGGCAATCTCTTT-T-C
1 AAAGTCCACGACTCAGTGGC-AT-TTTTTCTCC
* *
3071157 AAAGTCCACGACTCAGTGGCATCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* * * *
3071188 AAAGCCCACAACTCCGTGGCACCTTTTTCT
1 AAAGTCCACGACTCAGTGGCA-TTTTTTCT
3071218 TTTCAAAGCC
Statistics
Matches: 102, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
29 3 0.03
30 28 0.27
31 58 0.57
32 9 0.09
33 4 0.04
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTTTCTCC
Found at i:3071228 original size:34 final size:34
Alignment explanation
Indices: 3071150--3071365 Score: 168
Period size: 35 Copynumber: 6.5 Consensus size: 34
3071140 AGTGGCAATC
* * * *
3071150 TCTTTTCAAAGTCCACGACTCAGTGGCATC-TTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
3071183 TC--TTCAAAGCCCACAACTCCGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* *
3071215 TCTTTTCAAAGCCCACAATTCCGTGGTACCCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCA-CCTTTT
* *
3071250 TCTTTTTAAAGCCCACAACTCCATGGCACTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
* * *
3071285 TCCCTTTT--AAGTCCACAATTTCGTGGCACC----
1 T--CTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* *
3071315 -CTTTT--AAGTCCACAACTCCGTGGCATCTTTCT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTT-T
*
3071347 CCTTTTCAAAAGCCCACAA
1 TCTTTTC-AAAGCCCACAA
3071366 GTTGGTACAA
Statistics
Matches: 149, Mismatches: 18, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
27 24 0.16
31 22 0.15
32 5 0.03
33 7 0.05
34 24 0.16
35 53 0.36
36 9 0.06
37 5 0.03
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (34 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:3071316 original size:27 final size:27
Alignment explanation
Indices: 3071286--3071339 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3071276 CACTCTTTTT
* *
3071286 CCCTTTTAAGTCCACAATTTCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
3071313 CCCTTTTAAGTCCACAACTCCGTGGCA
1 CCCTTTTAAGTCCACAACTCCGTGGCA
3071340 TCTTTCTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (27 bp):
CCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:3071316 original size:70 final size:68
Alignment explanation
Indices: 3071188--3071319 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 68
3071178 TCTTTTCTTC
* *
3071188 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAATTCCGTGGTACCCTTTTTCT
1 AAAGCCCACAACTCCATGGCACCTTTTTCTTTT-AAAGCCCACAATTCCGTGGCACCCTTTTTCT
3071253 TTTT
65 TTTT
* *
3071257 AAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTT-AAGTCCACAATTTCGTGGCACCCTTTT
1 AAAGCCCACAACTCCATGGCAC-CTTTTT--CTTTTAAAGCCCACAATTCCGTGGCACCCTTTT
3071320 AAGTCCACAA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
69 21 0.38
70 30 0.54
72 5 0.09
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (68 bp):
AAAGCCCACAACTCCATGGCACCTTTTTCTTTTAAAGCCCACAATTCCGTGGCACCCTTTTTCTT
TTT
Found at i:3071483 original size:49 final size:49
Alignment explanation
Indices: 3071413--3072035 Score: 654
Period size: 49 Copynumber: 12.8 Consensus size: 49
3071403 GGCGTTTTCT
* *
3071413 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * *
3071462 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
*
3071511 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATC
* * * *
3071563 TTTAAGACCAATGTCGCTGGCCTTGAATAAGCACATTGGCA-C-----C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
3071606 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * * * *
3071655 TTTAAGACCAATGTTGCTGGCCTTGAATCAGCACA-TCG-A-C---ACC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
*
3071698 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * *
3071747 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
*
3071790 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATC
* * *
3071842 TTTAAGTCCAATATCACTGGCCTTGAATTAGCATATTGGCACCTACGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT---TTATC
* * * *
3071894 TTTAAGTCCAATGTCGCTGGCCTTAAATCA-CACATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* *
3071942 TTTAAGTCCAAAATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATC
** * * *
3071994 TTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCA
1 TTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
3072036 TTCTTCTCAT
Statistics
Matches: 478, Mismatches: 64, Indels: 60
0.79 0.11 0.10
Matches are distributed among these distances:
43 107 0.22
44 4 0.01
45 1 0.00
46 2 0.00
47 1 0.00
48 35 0.07
49 167 0.35
51 13 0.03
52 116 0.24
53 31 0.06
55 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
Found at i:3071627 original size:43 final size:43
Alignment explanation
Indices: 3071562--3071834 Score: 303
Period size: 43 Copynumber: 6.1 Consensus size: 43
3071552 CCTTCGTCAT
* *
3071562 CTTTAAGACCAATGTCGCTGGCCTTGAATAAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
3071605 CTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C
* * * *
3071649 TTTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATCGACAC
1 -----CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
3071697 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C
*
3071741 TTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 -----CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
3071789 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
3071832 CTT
1 CTT
3071835 CGTCATCTTT
Statistics
Matches: 193, Mismatches: 25, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
43 115 0.60
44 2 0.01
48 2 0.01
49 74 0.38
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:3071698 original size:92 final size:92
Alignment explanation
Indices: 3071413--3071974 Score: 676
Period size: 92 Copynumber: 5.9 Consensus size: 92
3071403 GGCGTTTTCT
* *
3071413 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCG
* *
3071478 CTGGCCTTGAATCAGCACATTGGCACCTTCATC
66 CTGGCCTTGAATCAGCACA-TCG-A----CACC
*
3071511 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGACCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTTAAGACCAATG
* * *
3071576 TCGCTGGCCTTGAATAAGCACATTGGCACC
63 TCGCTGGCCTTGAATCAGCACATCGACACC
* * *
3071606 TTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTTG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCG
3071671 CTGGCCTTGAATCAGCACATCGACACC
66 CTGGCCTTGAATCAGCACATCGACACC
*
3071698 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCG
* *
3071763 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATCGACACC
* * *
3071790 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTCGTCATCTTTAAGTCCAATA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTTAAGACCAATG
* * * *
3071855 TCACTGGCCTTGAATTAGCATATTGGCACCTACGTCATC
63 TCGCTGGCCTTGAA-T--C--A---GCACAT-CGACACC
* * * * * **
3071894 TTTAAGTCCAATGTCGCTGGCCTTAAATCA-CACATTGGCACCTTCATCTTTAAGTCCAAAATCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCG
3071958 CTGGCCTTGAATCAGCA
66 CTGGCCTTGAATCAGCA
3071975 TATTGGCGCC
Statistics
Matches: 415, Mismatches: 34, Indels: 36
0.86 0.07 0.07
Matches are distributed among these distances:
92 176 0.42
93 1 0.00
94 1 0.00
95 73 0.18
96 1 0.00
97 1 0.00
98 44 0.11
99 1 0.00
100 32 0.08
101 36 0.09
103 17 0.04
104 32 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATCGACACC
Found at i:3071847 original size:236 final size:230
Alignment explanation
Indices: 3071461--3072035 Score: 618
Period size: 236 Copynumber: 2.4 Consensus size: 230
3071451 GCACCTTTGT
* * * * * *
3071461 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
* * *
3071526 GCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAAT
66 GCTGGCCTTGAATCAGCACATT---G-----G-CACCTTTAAGACCAATATCGCTGGCCTTGAAT
** **
3071591 AAGCACATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCT-TTGTC
122 AAGCACATTGGCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTATCATC
* *
3071655 TTTAAGACCAATGTTGCTGGCCTTGAATCAGCACA-TCG-A-CAC
187 TTTAAGACCAATGTCGCTGGCCTTAAATCA-CACATTCGCACCAC
*
3071697 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
* * *
3071762 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
66 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATATCGCTGGCCTTGAATAAGCACATT
* *
3071827 GGCTCCTTCGTCATCTTTAAGTCCAATATCACTGGCCTTGAATTAGCATATTGGCACCTACGTCA
131 -G-------G-CACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTA--TCA
* * *
3071892 TCTTTAAGTCCAATGTCGCTGGCCTTAAATCACACATTGGCACCTTCAT
185 TCTTTAAGACCAATGTCGCTGGCCTTAAATCACACATTCGCA-C--CAC
* * *
3071941 CTTTAAGTCCAAAATCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAACCCAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTTAAGA-CCAA
*
3072006 TGTCGTTGGCCTTGAATCAGCACATTGGCA
62 TGTCGCTGGCCTTGAATCAGCACATTGGCA
3072036 TTCTTCTCAT
Statistics
Matches: 288, Mismatches: 29, Indels: 32
0.83 0.08 0.09
Matches are distributed among these distances:
227 36 0.12
228 2 0.01
233 1 0.00
235 1 0.00
236 123 0.43
238 4 0.01
239 32 0.11
240 1 0.00
244 46 0.16
246 1 0.00
247 8 0.03
248 33 0.11
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (230 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGACCAATATCGCTGGCCTTGAATAAGCACATT
GGCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTATCATCTTTAAGACC
AATGTCGCTGGCCTTAAATCACACATTCGCACCAC
Found at i:3071975 original size:100 final size:103
Alignment explanation
Indices: 3071789--3072054 Score: 358
Period size: 100 Copynumber: 2.6 Consensus size: 103
3071779 ACATTGGCAC
* * * *
3071789 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTCGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTC-TCATCTTTAAGTCCAAA
*
3071854 ATCACTGGCCTTGAATTAGCATATTGGCACCTACGTCAT
65 ATCACTGGCCTTGAATCAGCATATTGGCACCTACGTCAT
*
3071893 CTTTAAGTCCAATGTCGCTGGCCTTAAATCA-CACATTGGCACC-T-TCATCTTTAAGTCCAAAA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCTCATCTTTAAGTCCAAAA
* * *
3071955 TCGCTGGCCTTGAATCAGCATATTGGCGCCTTCGTCAT
66 TCACTGGCCTTGAATCAGCATATTGGCACCTACGTCAT
** * * *
3071993 CTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGTC
1 CTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCTCATCTTTAAGTC
3072055 TAATGTCGTT
Statistics
Matches: 142, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
100 55 0.39
101 23 0.16
102 11 0.08
103 11 0.08
104 30 0.21
105 12 0.08
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (103 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCTCATCTTTAAGTCCAAAA
TCACTGGCCTTGAATCAGCATATTGGCACCTACGTCAT
Found at i:3071987 original size:152 final size:145
Alignment explanation
Indices: 3071413--3072093 Score: 635
Period size: 144 Copynumber: 4.7 Consensus size: 145
3071403 GGCGTTTTCT
* ** *
3071413 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TTGTCTTTAAGACCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTTAAGTCCAATGTC
* *
3071477 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAG
66 GCTGGCCTTAAATCAGCACATTGGCA----C--CTTTAAGTCCAAAATCGCTGGCCTTGAATCAG
3071542 CATATTGGCGCCTTCGTCATC
125 CATATTGGCGCCTTCGTCATC
* * * * *
3071563 TTTAAGACCAATGTCGCTGGCCTTGAATAAGCACATTGGCA-----C--CTTTAAGTCCAATATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTTAAGTCCAATGTC
* * * * ** *
3071621 GTTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAG
66 GCTGGCCTTAAATCAGCACATTGGCA-C-----CTTTAAGTCCAAAATCGCTGGCCTTGAATCAG
* * *
3071686 C--A-------CATCGACACC
125 CATATTGGCGCCTTCGTCATC
** *
3071698 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TTGTCTTTAAGACCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTTAAGTCCAATGTC
* *
3071762 GCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
66 GCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAAAATCGCTGGCCTTGAATCAGCATATT
*
3071827 GGCTCCTTCGTCATC
131 GGCGCCTTCGTCATC
* *
3071842 TTTAAGTCCAATATCACTGGCCTTGAATTAGCATATTGGCACCTACGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-C-TCATCTTTAAGTCCAATG
3071907 TCGCTGGCCTTAAATCA-CACATTGGCACCTTCATCTTTAAGTCCAAAATCGCTGGCCTTGAATC
64 TCGCTGGCCTTAAATCAGCACATTGGCA----C--CTTTAAGTCCAAAATCGCTGGCCTTGAATC
3071971 AGCATATTGGCGCCTTCGTCATC
123 AGCATATTGGCGCCTTCGTCATC
** * * * * * *
3071994 TTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCTAAT
1 TTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--CCTCTCATCTTTAAGTCCAAT
* * * * *
3072059 GTCGTTGACCGTGAATCAGCACATTGACATCCTTT
63 GTCGCTGGCCTTAAATCAGCACATTGGCA-CCTTT
3072094 TTCTCATCTT
Statistics
Matches: 445, Mismatches: 55, Indels: 63
0.79 0.10 0.11
Matches are distributed among these distances:
135 74 0.17
137 1 0.00
140 1 0.00
141 39 0.09
142 1 0.00
144 118 0.27
146 10 0.02
147 31 0.07
149 4 0.01
150 38 0.09
151 2 0.00
152 54 0.12
153 60 0.13
154 10 0.02
155 2 0.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (145 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCTCATCTTTAAGTCCAATGTC
GCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAAAATCGCTGGCCTTGAATCAGCATATT
GGCGCCTTCGTCATC
Found at i:3072119 original size:55 final size:52
Alignment explanation
Indices: 3071984--3072131 Score: 170
Period size: 55 Copynumber: 2.8 Consensus size: 52
3071974 ATATTGGCGC
* * *
3071984 CTTCGTCATCTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATT
1 CTTC-TCATCTTT-AAACCTAATGTCGTTGGCCGTGAATCAGCACATTGACATT
* ** *
3072038 CTTCTCATCTTCAAGTCTAATGTCGTTGACCGTGAATCAGCACATTGACATCCTT
1 CTTCTCATCTTTAAACCTAATGTCGTTGGCCGTGAATCAGCACATTGACA---TT
* *
3072093 TTTCTCATCTTTAAACCTAATATCGTTGGCCGTGAATCA
1 CTTCTCATCTTTAAACCTAATGTCGTTGGCCGTGAATCA
3072132 ACGTATTGGT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 32 0.41
53 7 0.09
54 4 0.05
55 35 0.45
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (52 bp):
CTTCTCATCTTTAAACCTAATGTCGTTGGCCGTGAATCAGCACATTGACATT
Found at i:3072805 original size:19 final size:18
Alignment explanation
Indices: 3072781--3072843 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
3072771 AAACCGTAAC
3072781 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
3072800 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
3072813 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
3072832 TGTATCGATACA
1 TGTATCGATACA
3072844 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:3072818 original size:13 final size:13
Alignment explanation
Indices: 3072800--3072824 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3072790 ACATAAGTGT
3072800 TGTATCGATACAA
1 TGTATCGATACAA
3072813 TGTATCGATACA
1 TGTATCGATACA
3072825 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3072822 original size:32 final size:32
Alignment explanation
Indices: 3072781--3072851 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
3072771 AAACCGTAAC
3072781 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3072813 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3072845 TGTATCG
1 TGTATCG
3072852 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3072913 original size:13 final size:13
Alignment explanation
Indices: 3072895--3072921 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3072885 CATTACTAAA
3072895 TGTATCGATACAT
1 TGTATCGATACAT
3072908 TGTATCGATACAT
1 TGTATCGATACAT
3072921 T
1 T
3072922 TGATCTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3078635 original size:20 final size:20
Alignment explanation
Indices: 3078610--3078683 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
3078600 TTTTACTCAG
3078610 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3078630 ATGTATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
*
3078650 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
3078670 ATGTATCGATACAT
1 ATGTATCGATACAT
3078684 GTATTAAAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3078670 original size:40 final size:40
Alignment explanation
Indices: 3078610--3078687 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
3078600 TTTTACTCAG
* *
3078610 ATGTATCGATACATTTTTCAATGTATCGATATATGTATGA
1 ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
3078650 ATGTATCGATACATTCTTCAATGTATCGATACATGTAT
1 ATGTATCGATACATTCTTCAATGTATCGATACATGTAT
3078688 TAAAACTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATGTATGA
Found at i:3079619 original size:22 final size:23
Alignment explanation
Indices: 3079594--3079640 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
3079584 TTTTAACATG
3079594 TCCAGCA-TCTCATTGAATG-TTA
1 TCCAGCAGT-TCATTGAATGATTA
*
3079616 TCCATCAGTTCATTGAATGATTA
1 TCCAGCAGTTCATTGAATGATTA
3079639 TC
1 TC
3079641 ACATTTTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (23 bp):
TCCAGCAGTTCATTGAATGATTA
Found at i:3092291 original size:6 final size:6
Alignment explanation
Indices: 3092282--3092330 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
3092272 CAAAATGCAA
* * *
3092282 AAAAAA AAAAAC AACAAC AAAAAC AAAAACC AAAAAA AAAATAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAA-C AAAAAC AAAA-AC AAAAA
3092331 AGGAGGGGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 25 0.69
7 11 0.31
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:3092303 original size:13 final size:13
Alignment explanation
Indices: 3092281--3092331 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
3092271 TCAAAATGCA
*
3092281 AAAAAAAAAAAAC
1 AAAAACAAAAAAC
*
3092294 AACAAC-AAAAAC
1 AAAAACAAAAAAC
3092306 AAAAACCAAAAAA-
1 AAAAA-CAAAAAAC
3092319 AAAATACAAAAAA
1 AAAA-ACAAAAAA
3092332 GGAGGGGTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 10 0.31
13 16 0.50
14 6 0.19
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (13 bp):
AAAAACAAAAAAC
Found at i:3093563 original size:28 final size:28
Alignment explanation
Indices: 3093518--3093901 Score: 364
Period size: 28 Copynumber: 13.5 Consensus size: 28
3093508 TATGACACTT
* * *
3093518 TTTCAAAGCCCCCTAGTCCGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3093546 TTTCAGAGCCCACAAGTCAGTGGTAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
3093574 TTTTTCAAAGTCCACAAGCCAGTGGCA-CC
1 --TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
3093603 TTTCAGAG-CCATAAGTCAGTGGTAACCC
1 TTTCAAAGCCCACAAGTCAGTGG-CATCC
*
3093631 TTTTCAAAGCCCACAAGCCAGTGGCA-CC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
3093659 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * ** *
3093686 TTTTCAAAGTCTACAAGTCAACGGCATCT
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3093715 TTTCAAAGCCCACAAGTTAGTGGCATCCC
1 TTTCAAAGCCCACAAGTCAGTGGCAT-CC
*
3093744 TTTTTAAAGCCCA-AAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3093772 TTTCAAAGCCTACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
3093800 TTTCAGAGCCCACAAGTCAGTAGCAACCC
1 TTTCAAAGCCCACAAGTCAGTGGC-ATCC
*
3093829 TTTTCAAAGCCCACAAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
3093858 TTTCAGAGCCCATAAGTTAGTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
3093886 TGTTTTAAAGCCCACA
1 --TTTCAAAGCCCACA
3093902 CAGGTCGATG
Statistics
Matches: 293, Mismatches: 48, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
26 12 0.04
27 44 0.15
28 131 0.45
29 30 0.10
30 76 0.26
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:3093776 original size:85 final size:85
Alignment explanation
Indices: 3093539--3093867 Score: 355
Period size: 85 Copynumber: 3.9 Consensus size: 85
3093529 CCTAGTCCGT
* * * * * *
3093539 GGCATCCTTTCAGAGCCCACAAGTCAGTGGTAACCTTTTTCAAAGTCCACAAGCCAGTGGCA-CC
1 GGCATCTTTTCAAAGCCCACAAGTCAGTGG-CACCCTTTTCAAAGCCCACAAGTCAGTGGCATCC
* * **
3093603 TTTCAGAGCC-ATAAGTCAGT
65 TTTCAAAGCCTACAAGTCAAC
* * *
3093623 GGTAACCCTTTTCAAAGCCCACAAGCCAGTGGCA-CC-TTTCAAAGCCCACAAGTCAGTGGCA-C
1 GG-CA-TCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATC
*
3093685 CTTTTCAAAGTCTACAAGTCAAC
64 C-TTTCAAAGCCTACAAGTCAAC
* *
3093708 GGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCCTTTTTAAAGCCCA-AAGTCAGTGGCATCC
1 GGCATCTTTTCAAAGCCCACAAGTCAGTGGCA-CCCTTTTCAAAGCCCACAAGTCAGTGGCATCC
**
3093772 TTTCAAAGCCTACAAGTCAGT
65 TTTCAAAGCCTACAAGTCAAC
* * * *
3093793 GGCATCCTTTCAGAGCCCACAAGTCAGTAGCAACCCTTTTCAAAGCCCACAAGTTAGTGGCATCC
1 GGCATCTTTTCAAAGCCCACAAGTCAGTGGC-ACCCTTTTCAAAGCCCACAAGTCAGTGGCATCC
*
3093858 TTTCAGAGCC
65 TTTCAAAGCC
3093868 CATAAGTTAG
Statistics
Matches: 206, Mismatches: 29, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
83 50 0.24
84 12 0.06
85 85 0.41
86 59 0.29
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (85 bp):
GGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCCT
TTCAAAGCCTACAAGTCAAC
Found at i:3093868 original size:113 final size:113
Alignment explanation
Indices: 3093517--3093901 Score: 413
Period size: 113 Copynumber: 3.4 Consensus size: 113
3093507 ATATGACACT
* * * * *
3093517 TTTTCAAAGCCCCCTAGTCCGTGGCATCCTTTCAGAGCCCACAAGTCAGTGGTAACCTTTTTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGG-CACC-TTTTCAA
* * * * * *
3093582 AGTCCACAAGCCAGTGGCACC-TTTCAGAG-CCATAAGTCAGTGGTAACCC
64 AGTCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGG-CATCC
*
3093631 TTTTCAAAGCCCACAAGCCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
* ** *
3093695 TCTACAAGTCAACGGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCC
66 TCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCAT-CC
* * *
3093744 TTTTTAAAGCCCA-AAGTCAGTGGCATCCTTTCAAAGCCTACAAGTCAGTGGCATCC-TTTCAGA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAA
* *
3093807 GCCCACAAGTCAGTAGCAACCCTTTTCAAAGCCCACAAGTTAGTGGCATCC
65 GTCCACAAGTCAGTGGC-A-CCTTTTCAAAGCCCACAAGTTAGTGGCATCC
* * * * *
3093858 -TTTCAGAGCCCATAAGTTAGTGGCAACCTGTTTTAAAGCCCACA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCC--TTTCAAAGCCCACA
3093902 CAGGTCGATG
Statistics
Matches: 229, Mismatches: 32, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
111 23 0.10
112 22 0.10
113 104 0.45
114 40 0.17
115 28 0.12
116 12 0.05
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (113 bp):
TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAG
TCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTTAGTGGCATCC
Found at i:3094918 original size:51 final size:51
Alignment explanation
Indices: 3094839--3094979 Score: 201
Period size: 51 Copynumber: 2.8 Consensus size: 51
3094829 ACATATTTTT
* * * * *
3094839 CCCAGATATATCAATACATGTATGAATGTATCGATACATTCTATCTCTTTA
1 CCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTCTTTA
*
3094890 CCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTA
1 CCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTCTTTA
* * *
3094941 CCCAGATGTCTCGGTACATTTTTCAATATATCGATACAT
1 CCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
3094980 CTAGTTAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (51 bp):
CCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTCTTTA
Found at i:3098304 original size:21 final size:23
Alignment explanation
Indices: 3098278--3098319 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3098268 TAGCCATTAT
*
3098278 AATGGA-ATTC-CACTTTCATCA
1 AATGGACATTCACACATTCATCA
3098299 AATGGACATTCACACATTCAT
1 AATGGACATTCACACATTCAT
3098320 AATTGAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (23 bp):
AATGGACATTCACACATTCATCA
Found at i:3098491 original size:15 final size:15
Alignment explanation
Indices: 3098471--3098536 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
3098461 TTTAACATTT
3098471 ATAAAAAATAAATAA
1 ATAAAAAATAAATAA
* *
3098486 ATAAAAAA-AGTATAT
1 ATAAAAAATA-AATAA
3098501 ATAAAAAAT-AAT-A
1 ATAAAAAATAAATAA
3098514 ATAATAATAATAAAGTAA
1 ATAA-AA-AATAAA-TAA
3098532 ATAAA
1 ATAAA
3098537 GAAAAAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
13 4 0.10
14 5 0.12
15 22 0.55
16 2 0.05
17 2 0.05
18 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
ATAAAAAATAAATAA
Found at i:3098640 original size:14 final size:14
Alignment explanation
Indices: 3098592--3098650 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
3098582 TATTTTCAAG
*
3098592 CATTTCATGCA-TG
1 CATTTCATGCATTT
* *
3098605 CATTTCACGTAATTT
1 CATTTCATG-CATTT
3098620 GCATTTCATGCATTT
1 -CATTTCATGCATTT
3098635 CATTTCATGCATTT
1 CATTTCATGCATTT
3098649 CA
1 CA
3098651 CCAAGTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
13 8 0.21
14 17 0.45
15 5 0.13
16 8 0.21
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (14 bp):
CATTTCATGCATTT
Found at i:3098873 original size:39 final size:40
Alignment explanation
Indices: 3098765--3098880 Score: 123
Period size: 39 Copynumber: 2.9 Consensus size: 40
3098755 CTGCTACTAC
* *
3098765 AATAA-AGCTATTGCAAATGGCAGCAATGAAG-ATCAAATT
1 AATAATAGCTACTGCAAATGGCAGCAATGAAGAATGAAA-T
* *
3098804 AA-AACTGGAGCTACTGCAAACGGCAACAATGAAGAATGAAA-
1 AATAA-T--AGCTACTGCAAATGGCAGCAATGAAGAATGAAAT
*
3098845 AATAATAGCTACTGTAAATGGCAGCAATGAAGAATG
1 AATAATAGCTACTGCAAATGGCAGCAATGAAGAATG
3098881 CAATTAAGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
38 2 0.03
39 29 0.45
41 3 0.05
42 25 0.39
43 5 0.08
ACGTcount: A:0.47, C:0.14, G:0.21, T:0.19
Consensus pattern (40 bp):
AATAATAGCTACTGCAAATGGCAGCAATGAAGAATGAAAT
Found at i:3099442 original size:19 final size:19
Alignment explanation
Indices: 3099409--3099458 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
3099399 GTAGCAACAT
3099409 CAACAGCAACAATCAA-CAAC
1 CAACAGCAAC-ATCAAGC-AC
*
3099429 CAACAGCAACATCAAGCGC
1 CAACAGCAACATCAAGCAC
3099448 CAACAGCAACA
1 CAACAGCAACA
3099459 ACACAGTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.50, C:0.36, G:0.10, T:0.04
Consensus pattern (19 bp):
CAACAGCAACATCAAGCAC
Found at i:3112102 original size:13 final size:12
Alignment explanation
Indices: 3112075--3112118 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
3112065 TATTATGCAT
*
3112075 AAAAAAAAAGGA
1 AAAAAAAAATGA
*
3112087 AAAAATAAAATTA
1 AAAAA-AAAATGA
3112100 AAAAGAAAAATGA
1 AAAA-AAAAATGA
3112113 AAAAAA
1 AAAAAA
3112119 TGAAAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 7 0.26
13 19 0.70
14 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:3113510 original size:42 final size:42
Alignment explanation
Indices: 3113442--3113704 Score: 203
Period size: 42 Copynumber: 6.3 Consensus size: 42
3113432 ATTGATCTAG
* * * *
3113442 CCCTAGGAAACTTTCCTACCCTCAGTCTGCTTGTCGGCTGTGA
1 CCCT-GGAGACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGA
* *
3113485 CCCTGGAGACTTTTCTACCCTCAGTCTACCTATCGGCTTTGA
1 CCCTGGAGACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGA
* * * *
3113527 CCCTGGAGACTAT-CT-CATCTAAAGTCTGCCTATCAGCTTTGA
1 CCCTGGAGACTTTCCTAC-CCT-CAGTCTGCCTATCGGCTTTGA
* * * * *
3113569 CCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTTGA
1 CCCTGGAGACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGA
* * * * * * *
3113611 CCTTGGAGAC-TACCT-CATCTAAAGTTTGCCTGTCAGCTTTGA
1 CCCTGGAGACTTTCCTAC-CCT-CAGTCTGCCTATCGGCTTTGA
* * **
3113653 -CTTGGAGACTTTCCTACCCTCAGTCTGCCTGTCAACTTTGA
1 CCCTGGAGACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGA
*
3113694 CCCTGTAGACT
1 CCCTGGAGACT
3113705 GCCTTACCTC
Statistics
Matches: 176, Mismatches: 35, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
40 2 0.01
41 36 0.20
42 129 0.73
43 8 0.05
44 1 0.01
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.33
Consensus pattern (42 bp):
CCCTGGAGACTTTCCTACCCTCAGTCTGCCTATCGGCTTTGA
Found at i:3113721 original size:42 final size:42
Alignment explanation
Indices: 3113521--3113726 Score: 170
Period size: 42 Copynumber: 4.9 Consensus size: 42
3113511 TACCTATCGG
* * * * * * *
3113521 CTTTGACCCTGGAGACTATCTCATCTAAAGTCTGCCTATCAG
1 CTTTGACCTTGGAGACTACCTTACCTCAAGTCTGCCTGTCAA
* * *
3113563 CTTTGACCTTAGAGACTTTCC-TACCTTC-AGTCTGCCTGTCGA
1 CTTTGACCTTGGAGAC-TACCTTACC-TCAAGTCTGCCTGTCAA
* * * * *
3113605 CTTTGACCTTGGAGACTACCTCATCTAAAGTTTGCCTGTCAG
1 CTTTGACCTTGGAGACTACCTTACCTCAAGTCTGCCTGTCAA
*
3113647 CTTTGA-CTTGGAGACTTTCC-TACCCTC-AGTCTGCCTGTCAA
1 CTTTGACCTTGGAGAC-TACCTTA-CCTCAAGTCTGCCTGTCAA
* * *
3113688 CTTTGACCCTGTAGACTGCCTTACCTCAAGTCTGCCTGT
1 CTTTGACCTTGGAGACTACCTTACCTCAAGTCTGCCTGT
3113727 TGGTTTTGAC
Statistics
Matches: 128, Mismatches: 27, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
41 39 0.30
42 86 0.67
43 3 0.02
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.33
Consensus pattern (42 bp):
CTTTGACCTTGGAGACTACCTTACCTCAAGTCTGCCTGTCAA
Found at i:3113725 original size:83 final size:84
Alignment explanation
Indices: 3113465--3113726 Score: 328
Period size: 84 Copynumber: 3.1 Consensus size: 84
3113455 TCCTACCCTC
* * * * * * * *
3113465 AGTCTGCTTGTCGGCTGTGACCCTGGAGACTTTTCTACCCTCAGTCTACCTATCGGCTTTGACCC
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCC
* *
3113530 TGGAGACTATCTCATCTAA
66 TGGAGACTACCTCACCTAA
* * * *
3113549 AGTCTGCCTATCAGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTTGACCT
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCC
*
3113614 TGGAGACTACCTCATCTAA
66 TGGAGACTACCTCACCTAA
* *
3113633 AGTTTGCCTGTCAGCTTTGA-CTTGGAGACTTTCCTACCCTCAGTCTGCCTGTCAACTTTGACCC
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCC
* * * *
3113697 TGTAGACTGCCTTACCTCA
66 TGGAGACTACCTCACCTAA
3113716 AGTCTGCCTGT
1 AGTCTGCCTGT
3113727 TGGTTTTGAC
Statistics
Matches: 153, Mismatches: 25, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
83 64 0.42
84 89 0.58
ACGTcount: A:0.18, C:0.30, G:0.19, T:0.33
Consensus pattern (84 bp):
AGTCTGCCTGTCAGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTGTCGACTTTGACCC
TGGAGACTACCTCACCTAA
Found at i:3114246 original size:15 final size:14
Alignment explanation
Indices: 3114226--3114289 Score: 60
Period size: 15 Copynumber: 4.4 Consensus size: 14
3114216 TTTAACATTT
3114226 ATAAAAAAGTAATAA
1 ATAAAAAA-TAATAA
3114241 ATAAAAAATATATATA
1 ATAAAAAATA-ATA-A
3114257 TATAAAATAATAAT-A
1 -ATAAAA-AATAATAA
*
3114272 ATAAAAAA-AGTAA
1 ATAAAAAATAATAA
3114285 ATAAA
1 ATAAA
3114290 GAAAAAAAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
12 2 0.05
13 8 0.19
14 8 0.19
15 12 0.28
16 1 0.02
17 8 0.19
18 4 0.09
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (14 bp):
ATAAAAAATAATAA
Found at i:3114365 original size:14 final size:14
Alignment explanation
Indices: 3114344--3114449 Score: 101
Period size: 13 Copynumber: 7.5 Consensus size: 14
3114334 CATATTTTCA
3114344 TGCATTTCATGCAT
1 TGCATTTCATGCAT
*
3114358 TACATTTCATGCA-
1 TGCATTTCATGCAT
* *
3114371 TGCATTTCACGTAAT
1 TGCATTTCATG-CAT
3114386 TCGCATTTCATGCAT
1 T-GCATTTCATGCAT
*
3114401 TCCATTTCATGCA-
1 TGCATTTCATGCAT
* *
3114414 TGCATTTCGTGTAATT
1 TGCATTTCATG-CA-T
3114430 TGCATTTCATGCA-
1 TGCATTTCATGCAT
3114443 TGCATTT
1 TGCATTT
3114450 TACGTAATGT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
13 25 0.34
14 25 0.34
15 5 0.07
16 19 0.26
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (14 bp):
TGCATTTCATGCAT
Found at i:3114392 original size:43 final size:43
Alignment explanation
Indices: 3114345--3114443 Score: 162
Period size: 43 Copynumber: 2.3 Consensus size: 43
3114335 ATATTTTCAT
3114345 GCATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTC
1 GCATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTC
* ** *
3114388 GCATTTCATGCATTCCATTTCATGCATGCATTTCGTGTAATTT
1 GCATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTC
3114431 GCATTTCATGCAT
1 GCATTTCATGCAT
3114444 GCATTTTACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (43 bp):
GCATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTC
Found at i:3114438 original size:29 final size:29
Alignment explanation
Indices: 3114403--3114472 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
3114393 TCATGCATTC
**
3114403 CATTTCATGCATGCATTTCGTGTAAT-TT
1 CATTTCATGCATGCATTTCACGTAATGTT
*
3114431 GCATTTCATGCATGCATTTTACGTAATGTT
1 -CATTTCATGCATGCATTTCACGTAATGTT
3114461 CATTTCATGCAT
1 CATTTCATGCAT
3114473 TTCACCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 35 0.95
30 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (29 bp):
CATTTCATGCATGCATTTCACGTAATGTT
Found at i:3114696 original size:39 final size:39
Alignment explanation
Indices: 3114591--3114709 Score: 127
Period size: 39 Copynumber: 3.0 Consensus size: 39
3114581 CTGCTGCTAC
*
3114591 AATAA-AGCTGTTGCAAATGGCAGCAATGAAG-AT-CAA
1 AATAACAGCTGCTGCAAATGGCAGCAATGAAGAATGCAA
* * * *
3114627 ATTAAAGCTGGAGCTGCTGCAAACGACAGCAATGAAGAATGGAA
1 AAT-AA-C---AGCTGCTGCAAATGGCAGCAATGAAGAATGCAA
3114671 AATAACAGCTGCTGCAAATGGCAGCAATGAAGAATGCAA
1 AATAACAGCTGCTGCAAATGGCAGCAATGAAGAATGCAA
3114710 TTAAGCTGCT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
36 2 0.03
37 2 0.03
39 30 0.45
42 24 0.36
43 4 0.06
44 4 0.06
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.17
Consensus pattern (39 bp):
AATAACAGCTGCTGCAAATGGCAGCAATGAAGAATGCAA
Found at i:3115248 original size:119 final size:119
Alignment explanation
Indices: 3115116--3115343 Score: 393
Period size: 119 Copynumber: 1.9 Consensus size: 119
3115106 CACGAAACGG
* * * * *
3115116 CAGCCACAACAACCAACCAAAACAGTAGCAATCGAAGCAAAGCAGCAAGCAATACCAGCTGCAGA
1 CAGCCACAACAACCAACCAAAACAGCAGCAATCAAAGCAAAACAGCAACCAATACCAGCCGCAGA
*
3115181 TGAAGCAACGCAAAAACAGTAGCGACAACAGCATTTGAAGCAAGTGCGAAACAA
66 TGAAGCAACGCAAAAACAGCAGCGACAACAGCATTTGAAGCAAGTGCGAAACAA
*
3115235 CAGCCACAACAACCAACCAAAACAGCAGCAATCAAAGCAAAATAGCAACCAATACCAGCCGCAGA
1 CAGCCACAACAACCAACCAAAACAGCAGCAATCAAAGCAAAACAGCAACCAATACCAGCCGCAGA
3115300 TGAAGCAACGCAAAAACAGCAGCGACAACAGCATTTGAAGCAAG
66 TGAAGCAACGCAAAAACAGCAGCGACAACAGCATTTGAAGCAAG
3115344 CAACCAGCAA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (119 bp):
CAGCCACAACAACCAACCAAAACAGCAGCAATCAAAGCAAAACAGCAACCAATACCAGCCGCAGA
TGAAGCAACGCAAAAACAGCAGCGACAACAGCATTTGAAGCAAGTGCGAAACAA
Found at i:3122478 original size:19 final size:19
Alignment explanation
Indices: 3122450--3122494 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3122440 ATATTATATA
3122450 ATAT-AATATAATAAAAAT
1 ATATAAATATAATAAAAAT
*
3122468 ATATAAATATAATACAAAT
1 ATATAAATATAATAAAAAT
3122487 ATATAAAT
1 ATATAAAT
3122495 TACTTTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAAATATAATAAAAAT
Found at i:3122748 original size:2 final size:2
Alignment explanation
Indices: 3122741--3122766 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3122731 CACATCATCC
3122741 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
3122767 TCTCCTTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3123041 original size:19 final size:20
Alignment explanation
Indices: 3122984--3123036 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
3122974 AGTATGATAG
3122984 ATATATTTAAATATAATTTTA
1 ATATATTT-AATATAATTTTA
*
3123005 ATATATATT--TATGATTTTA
1 ATATAT-TTAATATAATTTTA
3123024 ATATATTTAATAT
1 ATATATTTAATAT
3123037 TTTTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.07
19 15 0.54
20 3 0.11
21 6 0.21
22 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATATTTAATATAATTTTA
Found at i:3123713 original size:2 final size:2
Alignment explanation
Indices: 3123706--3123735 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3123696 AAATAAAGAA
3123706 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
3123736 CAACGTAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3124576 original size:18 final size:18
Alignment explanation
Indices: 3124523--3124579 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
3124513 ACGAGATAAA
**
3124523 TATTAAATATAAAATATT
1 TATTAAATATATTATATT
* *
3124541 TATTATAT-TATTTTTATT
1 TATTAAATATA-TTATATT
3124559 TATTAAATATATTATATT
1 TATTAAATATATTATATT
3124577 TAT
1 TAT
3124580 ATTATATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 2 0.06
18 27 0.87
19 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTAAATATATTATATT
Found at i:3124582 original size:11 final size:11
Alignment explanation
Indices: 3124543--3124589 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
3124533 AAAATATTTA
*
3124543 TTATATTATTT
1 TTATATTATAT
*
3124554 TTAT-TTATTAA
1 TTATATTA-TAT
*
3124565 ATATATTATAT
1 TTATATTATAT
3124576 TTATATTATAT
1 TTATATTATAT
3124587 TTA
1 TTA
3124590 AAATTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTATAT
Found at i:3124907 original size:27 final size:25
Alignment explanation
Indices: 3124835--3124904 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 25
3124825 ATGATAAAAA
*
3124835 TTTAAAATTAATTAAAATAATATTTT
1 TTTAAAATTAATTAAAATAATA-ATT
* ** *
3124861 ATTTTATTTTAATTATAATAATAATT
1 -TTTAAAATTAATTAAAATAATAATT
3124887 TTTAAAATTAAATTAAAA
1 TTTAAAATT-AATTAAAA
3124905 ATATTTTATT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
25 6 0.18
26 9 0.27
27 18 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTAAAATTAATTAAAATAATAATT
Found at i:3129655 original size:2 final size:2
Alignment explanation
Indices: 3129650--3129680 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3129640 ATGTTTGAGT
3129650 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3129681 GGAGGGGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3129689 original size:6 final size:6
Alignment explanation
Indices: 3129680--3129718 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
3129670 GAGAGAGAGA
*
3129680 GGGAGG GGGA-G GGG-GG GAGAGG GGGAGG GGGAGG GGGAG
1 GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG GGGAG
3129719 AGAGAGAGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 7 0.24
6 22 0.76
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (6 bp):
GGGAGG
Found at i:3129699 original size:22 final size:22
Alignment explanation
Indices: 3129672--3129724 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
3129662 GAGAGAGAGA
3129672 GAGAGAGAGGGAGGGGGAGGGG
1 GAGAGAGAGGGAGGGGGAGGGG
* *
3129694 GGGAGAGGGGGAGGGGGAGGGG
1 GAGAGAGAGGGAGGGGGAGGGG
3129716 GAGAGAGAG
1 GAGAGAGAG
3129725 AGAGAGGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (22 bp):
GAGAGAGAGGGAGGGGGAGGGG
Found at i:3134489 original size:50 final size:50
Alignment explanation
Indices: 3134434--3134531 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
3134424 TTTTTTCTCA
*
3134434 TGGCTATTACGAAATAATTAGTAAATTAAGAGTTATCATTTATCTTTTCG
1 TGGCTATTACGAAATAATTAGTAAATTAAGAGTTACCATTTATCTTTTCG
3134484 TGGCTATTACGAAATAATTAGTAAATTAAGAGTTACCATTTATCTTTT
1 TGGCTATTACGAAATAATTAGTAAATTAAGAGTTACCATTTATCTTTT
3134532 TAGACTATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (50 bp):
TGGCTATTACGAAATAATTAGTAAATTAAGAGTTACCATTTATCTTTTCG
Found at i:3139158 original size:29 final size:27
Alignment explanation
Indices: 3139126--3139193 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
3139116 GGATGTGTGT
* *
3139126 AAATTTAATTATTTTAAATATGATATAAA
1 AAATATAA-TATTTTAAATA-AATATAAA
*
3139155 AAATATAATATTTTTAATAAATATAAA
1 AAATATAATATTTTAAATAAATATAAA
3139182 TTAAATATAATA
1 --AAATATAATA
3139194 AATATGATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.21
28 10 0.29
29 17 0.50
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
AAATATAATATTTTAAATAAATATAAA
Found at i:3139614 original size:21 final size:22
Alignment explanation
Indices: 3139573--3139629 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
3139563 TATAACCCTT
3139573 TATTAATTTTAATTTTATTATTA
1 TATT-ATTTTAATTTTATTATTA
3139596 TATTATTTT-ATCTTT-TTATTA
1 TATTATTTTAAT-TTTATTATTA
*
3139617 TAATA-TTTAATTT
1 TATTATTTTAATTT
3139630 CGTTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.16
21 14 0.45
22 8 0.26
23 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTATTTTAATTTTATTATTA
Found at i:3139986 original size:2 final size:2
Alignment explanation
Indices: 3139979--3140009 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3139969 TAAAAAGCAA
3139979 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
3140010 CACAAATAGT
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:3142890 original size:2 final size:2
Alignment explanation
Indices: 3142883--3142908 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3142873 TAGAAAACAA
3142883 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
3142909 TCAAAGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3144518 original size:21 final size:20
Alignment explanation
Indices: 3144502--3144570 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 20
3144492 AAATTAATTT
* *
3144502 TTAATTTAATTTAATTATTA
1 TTAAATTAAATTAATTATTA
*
3144522 TTAAATTAAATTAA--A-AA
1 TTAAATTAAATTAATTATTA
*
3144539 TTAAA-TAATTTAA--ATTA
1 TTAAATTAAATTAATTATTA
3144556 TTAAA-TAAATTAATT
1 TTAAATTAAATTAATT
3144571 TTTAATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 8 0.20
17 19 0.47
18 1 0.03
20 12 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATTAAATTAATTATTA
Found at i:3144528 original size:16 final size:17
Alignment explanation
Indices: 3144489--3144577 Score: 56
Period size: 16 Copynumber: 5.1 Consensus size: 17
3144479 AAAAATTAGT
* *
3144489 TTAAAATTAATTTTTAA
1 TTAAATTTAATTATTAA
*
3144506 TTTAATTTAATTATT-A
1 TTAAATTTAATTATTAA
* **
3144522 TTAAATTAAATTAAAAA
1 TTAAATTTAATTATTAA
3144539 TTAAATAATTTAAATTATTAA
1 TT--A-AATTT-AATTATTAA
* *
3144560 ATAAA-TTAATTTTTAA
1 TTAAATTTAATTATTAA
3144576 TT
1 TT
3144578 TTTAACTTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
16 21 0.39
17 17 0.31
18 2 0.04
19 2 0.04
20 4 0.07
21 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATTTAATTATTAA
Found at i:3144533 original size:37 final size:34
Alignment explanation
Indices: 3144492--3144605 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 34
3144482 AATTAGTTTA
3144492 AAATTAATTTTTAATTTAATTTAATTATTATTAAATT
1 AAATTAATTTTTAATTTAATTTAA--ATTATTAAA-T
*** *
3144529 AAATTAAAAATTAA-ATAATTTAAATTATTAAAT
1 AAATTAATTTTTAATTTAATTTAAATTATTAAAT
*
3144562 AAATTAATTTTTAATTTTTAACTTT-AATAATTAAAT
1 AAATTAATTTTTAA--TTTAA-TTTAAATTATTAAAT
*
3144598 AATTTAAT
1 AAATTAAT
3144606 ATATTTTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
33 12 0.19
34 9 0.14
36 28 0.44
37 14 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (34 bp):
AAATTAATTTTTAATTTAATTTAAATTATTAAAT
Found at i:3144543 original size:17 final size:17
Alignment explanation
Indices: 3144521--3144568 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3144511 TTTAATTATT
3144521 ATTAAATTAAATTAAA-A
1 ATTAAA-TAAATTAAATA
* *
3144538 ATTAAATAATTTAAATT
1 ATTAAATAAATTAAATA
3144555 ATTAAATAAATTAA
1 ATTAAATAAATTAA
3144569 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAATAAATTAAATA
Found at i:3144592 original size:16 final size:15
Alignment explanation
Indices: 3144573--3144623 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
3144563 AATTAATTTT
3144573 TAATTTTTAACTTTAA
1 TAATTTTTAA-TTTAA
**
3144589 TAATTAAATAATTTAA
1 TAATT-TTTAATTTAA
3144605 TATATTTTTAA-TTAA
1 TA-ATTTTTAATTTAA
3144620 TAAT
1 TAAT
3144624 AAAAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 6 0.21
16 15 0.52
17 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTTTTAATTTAA
Found at i:3144601 original size:31 final size:28
Alignment explanation
Indices: 3144559--3144657 Score: 87
Period size: 31 Copynumber: 3.4 Consensus size: 28
3144549 TAAATTATTA
3144559 AATAAATTAATTTTTAATTTTTAACTTTAAT
1 AATAAA-TAATTTTTAATTTTTAA--TTAAT
*
3144590 AATTAAATAATTTAATATATTTTTAATTAAT
1 AA-TAAATAATTT-TTA-ATTTTTAATTAAT
*
3144621 AATAAA-AAATTTTAA-TTTTAAGTTAA-
1 AATAAATAATTTTTAATTTTTAA-TTAAT
3144647 ACATAAATAAT
1 A-ATAAATAAT
3144658 CAAATATTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
26 7 0.12
27 10 0.17
28 4 0.07
29 4 0.07
30 4 0.07
31 15 0.26
32 6 0.10
33 8 0.14
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (28 bp):
AATAAATAATTTTTAATTTTTAATTAAT
Found at i:3144956 original size:18 final size:18
Alignment explanation
Indices: 3144933--3145025 Score: 75
Period size: 19 Copynumber: 5.2 Consensus size: 18
3144923 ATTTATATAT
*
3144933 TATTATTGAATTAAATAA
1 TATTATTTAATTAAATAA
*
3144951 TATTATTTTATT-AATAA
1 TATTATTTAATTAAATAA
* *
3144968 T-TT-TTAAAAATAAATAA
1 TATTATT-TAATTAAATAA
* *
3144985 TAATTTTTTAATAAAATAA
1 T-ATTATTTAATTAAATAA
*
3145004 TATTATTTAATTTATATAA
1 TATTATTTAA-TTAAATAA
3145023 TAT
1 TAT
3145026 AAATTTATCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
15 2 0.03
16 4 0.07
17 12 0.21
18 18 0.31
19 20 0.34
20 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (18 bp):
TATTATTTAATTAAATAA
Done.