Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_pilon, whole genome shotgun sequence
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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 56
Found at i:3855718 original size:80 final size:80
Alignment explanation
Indices: 3855582--3855794 Score: 300
Period size: 80 Copynumber: 2.7 Consensus size: 80
3855572 GTCCTTCGGG
* *
3855582 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
*
3855647 AGTAGTGAAATAAAC
66 AGTAGTGAAACAAAC
* * *
3855662 CCTTCAGTAAGTCTTTCGAGCATAATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCGCCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
* *
3855727 AGTAGTGAAGCAAAT
66 AGTAGTGAAACAAAC
* * * * * *
3855742 TCATCAATAAGTCTTTTGAACATGATGATGAAATCCTTCGGGTCATTTGTAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
3855795 TCTTTCGAGC
Statistics
Matches: 117, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 117 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
AGTAGTGAAACAAAC
Found at i:3856325 original size:53 final size:53
Alignment explanation
Indices: 3856208--3856402 Score: 218
Period size: 53 Copynumber: 3.7 Consensus size: 53
3856198 ATCACACCAT
* * * *
3856208 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGA-TG-A-CTGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
*
3856258 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
* * * * ****
3856311 AAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGCAAACCCATTTTTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
*
3856364 AAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAG
1 AAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAG
3856403 TAGACCCGTC
Statistics
Matches: 123, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 35 0.28
51 1 0.01
52 1 0.01
53 66 0.54
54 10 0.08
55 10 0.08
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAG
Found at i:3869520 original size:29 final size:28
Alignment explanation
Indices: 3869479--3869535 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
3869469 CATGGCAAAG
3869479 GGACTTATTGATTCTTTTAAAAATTTGA
1 GGACTTATTGATTCTTTTAAAAATTTGA
* *
3869507 GGACTTAATTGATTCTTTTGAAAGTTTGA
1 GGACTT-ATTGATTCTTTTAAAAATTTGA
3869536 ACGTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (28 bp):
GGACTTATTGATTCTTTTAAAAATTTGA
Found at i:3871297 original size:22 final size:22
Alignment explanation
Indices: 3871272--3871942 Score: 668
Period size: 22 Copynumber: 30.6 Consensus size: 22
3871262 CTAATTTAAA
*
3871272 ATTTATTTTAAAATATATATTG
1 ATTTATTTTAAAATATAGATTG
*
3871294 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
*
3871316 ATTTATTTTAAAATAT-GA--A
1 ATTTATTTTAAAATATAGATTG
*** ** *
3871335 AAAAAAATTAAAAAATAGATTG
1 ATTTATTTTAAAATATAGATTG
***
3871357 ATTTATTTTTAAAATAT-GAAAAA
1 ATTTA-TTTTAAAATATAG-ATTG
* *
3871380 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
3871402 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
*
3871424 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
3871446 ATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
***
3871468 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATAGATTG
*
3871489 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATAGATTG
*
3871512 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
3871534 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATAGATTG
* ***
3871556 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATAGATTG
* *
3871578 ATTTGTTTTAAAATAT-GTATTT
1 ATTTATTTTAAAATATAG-ATTG
* **
3871600 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATAGATTG
*
3871621 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATAGATTG
***
3871644 ATTTATTTTAAAATAT-GAAAAA
1 ATTTATTTTAAAATATAG-ATTG
*
3871666 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
* **
3871688 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATAGATTG
*
3871709 ATTTTATTTTAAAATATAAATTG
1 A-TTTATTTTAAAATATAGATTG
*
3871732 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
*
3871754 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
3871776 ATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
* ***
3871798 ATTTACTTTAAAATAT-GAAAAA
1 ATTTATTTTAAAATATAG-ATTG
*
3871820 AATTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
* ***
3871842 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATAGATTG
*
3871864 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
* *
3871886 ACTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTG
3871908 ATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAAATATAG-ATTG
3871930 ATTTATTTTAAAA
1 ATTTATTTTAAAA
3871943 AAATTTATTA
Statistics
Matches: 551, Mismatches: 78, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
19 10 0.02
20 2 0.00
21 11 0.02
22 506 0.92
23 22 0.04
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATAGATTG
Found at i:3871321 original size:44 final size:44
Alignment explanation
Indices: 3871272--3871942 Score: 768
Period size: 44 Copynumber: 15.3 Consensus size: 44
3871262 CTAATTTAAA
*
3871272 ATTTATTTTAAAATATATATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
* *** ** * *
3871316 ATTTATTTTAAAATAT-GA--AAAAAAAATTAAAAAATAGATTG
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
*** *
3871357 ATTTATTTTTAAAATAT-GAAAAAAATTATTTTAAAATATGGATTG
1 ATTTA-TTTTAAAATATAG-ATTGATTTATTTTAAAATATGGATTG
3871402 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
***
3871446 ATTTATTTTAAAATAT-GAATTGATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATAG-ATTGATTTATTTTAAAATATGGATTG
*
3871489 ATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
***
3871534 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
* * **
3871578 ATTTGTTTTAAAATAT-GTATTTATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATAG-ATTGATTTATTTTAAAATATGGATTG
* * ***
3871621 ATTTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAAAAA
1 A-TTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
* **
3871666 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
*
3871709 ATTTTATTTTAAAATATAAATTGATTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
* *
3871754 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
* *** * *
3871798 ATTTACTTTAAAATAT-GAAAAAAATTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATAG-ATTGATTTATTTTAAAATATGGATTG
* ***
3871842 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
* * *
3871886 ACTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
3871930 ATTTATTTTAAAA
1 ATTTATTTTAAAA
3871943 AAATTTATTA
Statistics
Matches: 554, Mismatches: 56, Indels: 34
0.86 0.09 0.05
Matches are distributed among these distances:
41 20 0.04
42 12 0.02
43 14 0.03
44 475 0.86
45 33 0.06
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (44 bp):
ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
Found at i:3872024 original size:31 final size:31
Alignment explanation
Indices: 3871967--3872025 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3871957 ACTTGTATGG
* *
3871967 ATTATTTAAATTTTAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
3871998 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
3872026 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:3872528 original size:30 final size:34
Alignment explanation
Indices: 3872453--3872530 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
3872443 TATAATTCAG
*
3872453 ATTATTTATA-ATTTATATTTTTAAAATTAAAAT
1 ATTATTAATATATTTATATTTTTAAAATTAAAAT
3872486 ATTATTTATAATATATTTATA-TTTT-AAA-T-AAAT
1 ATTA--T-TAATATATTTATATTTTTAAAATTAAAAT
3872519 ATTATTAATATA
1 ATTATTAATATA
3872531 CAAAAATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
30 7 0.17
31 1 0.03
33 12 0.30
34 1 0.03
35 4 0.10
36 8 0.20
37 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATTATTAATATATTTATATTTTTAAAATTAAAAT
Found at i:3872558 original size:10 final size:10
Alignment explanation
Indices: 3872545--3872569 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3872535 AATATTATTT
3872545 ATATATTAAC
1 ATATATTAAC
3872555 ATATATTAAC
1 ATATATTAAC
3872565 ATATA
1 ATATA
3872570 ATATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATTAAC
Found at i:3872581 original size:53 final size:52
Alignment explanation
Indices: 3872481--3872583 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 52
3872471 TTTTAAAATT
** * * *
3872481 AAAATATTATTTATAATATATTTATATTTTAAATAAATATTATTAATATACA
1 AAAATATTATTTATAATATATACATATATTAAATAAATATAAATAATATACA
3872533 AAAATATTATTTAT-ATAT-TAACATATATTAACATATAATATAAATAATATA
1 AAAATATTATTTATAATATAT-ACATATATTAA-ATA-AATATAAATAATATA
3872584 AATATATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 1 0.02
51 12 0.28
52 17 0.40
53 13 0.30
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (52 bp):
AAAATATTATTTATAATATATACATATATTAAATAAATATAAATAATATACA
Found at i:3873665 original size:2 final size:2
Alignment explanation
Indices: 3873658--3873700 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3873648 GTAATTTAAC
3873658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3873700 A
1 A
3873701 ATGTTGTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3873877 original size:15 final size:15
Alignment explanation
Indices: 3873839--3873923 Score: 104
Period size: 15 Copynumber: 5.9 Consensus size: 15
3873829 TGGTTTTCCA
*
3873839 GAAAATGAATTACTT
1 GAAAATGAATTACTG
3873854 G--AATGAATTACTG
1 GAAAATGAATTACTG
**
3873867 GAATTTGAATTACTG
1 GAAAATGAATTACTG
3873882 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
3873897 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
3873911 GAAAATGAATTAC
1 GAAAATGAATTAC
3873924 ATTTCTGTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
13 12 0.21
14 12 0.21
15 34 0.59
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:3873921 original size:29 final size:30
Alignment explanation
Indices: 3873855--3873923 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
3873845 GAATTACTTG
3873855 AATGAATTACTGGAATTTGAATTACTGGAA
1 AATGAATTACTGGAATTTGAATTACTGGAA
3873885 AATGAATTACTGGAATTTGAATT-CTGGAA
1 AATGAATTACTGGAATTTGAATTACTGGAA
3873914 AATGAATTAC
1 AATGAATTAC
3873924 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (30 bp):
AATGAATTACTGGAATTTGAATTACTGGAA
Found at i:3873929 original size:20 final size:20
Alignment explanation
Indices: 3873906--3873975 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
3873896 GGAATTTGAA
3873906 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
3873926 TTCTGTAAAATGAATTATAT
1 TTCTGGAAAATGAATTACAT
3873946 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
3873966 TTCTGGAAAA
1 TTCTGGAAAA
3873976 CATCTGGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:3874389 original size:36 final size:36
Alignment explanation
Indices: 3874202--3874523 Score: 248
Period size: 36 Copynumber: 9.2 Consensus size: 36
3874192 TGAAAACATT
* * *
3874202 TATATAT-TATATAGTTTTTTAAAACGTTTGTGAAAA
1 TATATATATATATAG-TTTTTAAAACATTTTTAAAAA
*
3874238 TAAATATAATATATAGTTTTTAAAACATTTTTGAAAACA
1 TATATAT-ATATATAGTTTTTAAAACATTTTT-AAAA-A
* * *
3874277 TGTATAT-TATATAG-TTTAAAAACA-TTTTGAAAA
1 TATATATATATATAGTTTTTAAAACATTTTTAAAAA
*
3874310 TATATA-ATATATAGTTTTTAAAACATTTTGAAAACA
1 TATATATATATATAGTTTTTAAAACATTTTTAAAA-A
* * *
3874346 TTTATATATATA-ATTTTTTAAAACGTTTTTAAAAA
1 TATATATATATATAGTTTTTAAAACATTTTTAAAAA
* * *
3874381 TAAAATATAATATATAGTTTTTAAAATA-TTTTGAAAA
1 T-ATATAT-ATATATAGTTTTTAAAACATTTTTAAAAA
*
3874418 TATATATATTATATAGTTTTTAAAACA-TTTT-AGAA
1 TATATATA-TATATAGTTTTTAAAACATTTTTAAAAA
* * *
3874453 -A-A-CTATATA-A-TTTTGAAAATATTTTTTAAAAA
1 TATATATATATATAGTTTTTAAAACA-TTTTTAAAAA
* **
3874485 TATATA-ATATA-A--TATTAAAATGTTTTTAAAAA
1 TATATATATATATAGTTTTTAAAACATTTTTAAAAA
3874517 TATATAT
1 TATATAT
3874524 TAGATTTTTA
Statistics
Matches: 233, Mismatches: 33, Indels: 43
0.75 0.11 0.14
Matches are distributed among these distances:
29 9 0.04
30 1 0.00
31 8 0.03
32 21 0.09
33 22 0.09
34 20 0.09
35 16 0.07
36 70 0.30
37 40 0.17
38 20 0.09
39 6 0.03
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATATATATATAGTTTTTAAAACATTTTTAAAAA
Found at i:3874460 original size:38 final size:36
Alignment explanation
Indices: 3874202--3874461 Score: 294
Period size: 37 Copynumber: 7.1 Consensus size: 36
3874192 TGAAAACATT
*
3874202 TATATATTATATAGTTTTTTAAAACGTTTGTGAAAATA
1 TATATATTATATAG-TTTTTAAAACATTT-TGAAAATA
* * *
3874240 AATATAATATATAGTTTTTAAAACATTTTTGAAAACA
1 TATATATTATATAGTTTTTAAAACA-TTTTGAAAATA
* *
3874277 TGTATATTATATAG-TTTAAAAACATTTTGAAAATA
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATA
*
3874312 TATA-A-TATATAGTTTTTAAAACATTTTGAAAACA
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATA
* * * *
3874346 TTTATA-TATATAATTTTTTAAAACGTTTTTAAAAATAA
1 TATATATTATAT-AGTTTTTAAAAC-ATTTTGAAAAT-A
* * *
3874384 AATATAATATATAGTTTTTAAAATATTTTGAAAATA
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATA
3874420 TATATATTATATAGTTTTTAAAACATTTTAGAAAACTA
1 TATATATTATATAGTTTTTAAAACATTTT-GAAAA-TA
3874458 TATA
1 TATA
3874462 ATTTTGAAAA
Statistics
Matches: 187, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
33 7 0.04
34 23 0.12
35 19 0.10
36 47 0.25
37 50 0.27
38 36 0.19
39 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATATTATATAGTTTTTAAAACATTTTGAAAATA
Found at i:3874483 original size:29 final size:29
Alignment explanation
Indices: 3874427--3874492 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
3874417 ATATATATAT
* * *
3874427 TATATAGTTTTTAAAACATTTTAGAAAAC
1 TATATAATTTTGAAAACATTTTAGAAAAA
* **
3874456 TATATAATTTTGAAAATATTTTTTAAAAA
1 TATATAATTTTGAAAACATTTTAGAAAAA
3874485 TATATAAT
1 TATATAAT
3874493 ATAATATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAATTTTGAAAACATTTTAGAAAAA
Found at i:3874516 original size:32 final size:34
Alignment explanation
Indices: 3874457--3874522 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
3874447 TTAGAAAACT
* *
3874457 ATATAATTTTGAAAATATTTTTTAAAAATATATA
1 ATATAATATTGAAAATAGTTTTTAAAAATATATA
3874491 ATATAATATT-AAAAT-GTTTTTAAAAATATATA
1 ATATAATATTGAAAATAGTTTTTAAAAATATATA
3874523 TTAGATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 16 0.53
33 5 0.17
34 9 0.30
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATAATATTGAAAATAGTTTTTAAAAATATATA
Found at i:3874523 original size:34 final size:34
Alignment explanation
Indices: 3874457--3874523 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3874447 TTAGAAAACT
* *
3874457 ATATAATTTTGAAAATATTTTTTAAAAATATATA
1 ATATAATATTGAAAATATTTTTAAAAAATATATA
*
3874491 ATATAATATT-AAAATGTTTTTAAAAATATATAT
1 ATATAATATTGAAAATATTTTTAAAAA-ATATAT
3874524 TAGATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (34 bp):
ATATAATATTGAAAATATTTTTAAAAAATATATA
Found at i:3874607 original size:15 final size:16
Alignment explanation
Indices: 3874580--3874612 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3874570 TTTCTTTTTA
3874580 TTTATTATTACTTATT
1 TTTATTATTACTTATT
*
3874596 TTTATT-TTACTTCTT
1 TTTATTATTACTTATT
3874611 TT
1 TT
3874613 GTTTCAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTATTACTTATT
Found at i:3875192 original size:16 final size:17
Alignment explanation
Indices: 3875171--3875203 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3875161 GCAAATACAG
3875171 AAACAAA-ACCAAAAAA
1 AAACAAATACCAAAAAA
3875187 AAACAAATACCAAAAAA
1 AAACAAATACCAAAAAA
3875204 CACCGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (17 bp):
AAACAAATACCAAAAAA
Found at i:3877091 original size:17 final size:18
Alignment explanation
Indices: 3877059--3877092 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3877049 CTCACTAACC
*
3877059 CTTTTATTTTTTTGTTCT
1 CTTTTATTTTTGTGTTCT
3877077 CTTTTA-TTTTGTGTTC
1 CTTTTATTTTTGTGTTC
3877093 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.74
Consensus pattern (18 bp):
CTTTTATTTTTGTGTTCT
Found at i:3881382 original size:84 final size:83
Alignment explanation
Indices: 3881140--3882006 Score: 941
Period size: 84 Copynumber: 10.4 Consensus size: 83
3881130 GCTCAAGGCC
* ** * *
3881140 AGAAGGGCTATCTGCCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGTTATCTGCTAACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
* * * *
3881205 GCAGAATAGCTTGAGTCG
66 GCAGCATAACTTAAGTCT
* * * * **
3881223 AGAAGGGCTATCTGC---CAAAGACCCTCGAGTTCGACTACGTTCAGCTTTGAAGGCACATCATT
1 AGAAGGGTTATCTGCTAACAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
* *
3881285 TGCAGTATAACTTAAGTCA
65 TGCAGCATAACTTAAGTCT
3881304 AGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCTAAC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
3881369 TGCAGCATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCT
* * * * * * *
3881388 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
1 AGAAGGGTTATCTGCTAAC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * *
3881453 TTACAGCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCT
*
3881473 AGAAGGGTTATCTG-TCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCT-AACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
3881537 TGCAGAATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCT
* * * * * *
3881556 AGAGGGGCTATCTGC---CAAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATT
1 AGAAGGGTTATCTGCTAACAAAGACCTTTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
* *
3881618 TGCAGTATAACTTAAGTCA
65 TGCAGCATAACTTAAGTCT
* * * * * * *
3881637 AGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
1 AGAAGGGTTATCTGCTAAC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * *
3881702 TTACAGCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCT
* * *
3881722 AGAAGGGTTATCTG-TCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCT-AACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
3881786 TGCAGCACAACTTAAGTCT
65 TGCAGCATAACTTAAGTCT
* * *
3881805 ACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCTGCTAAC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * *
3881869 TTACAGCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCT
* * *
3881889 AGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCAT
1 AGAAGGGTTATCTGCT-AAC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* *
3881953 TTGCAGCATAGCTTAAGTCC
64 TTGCAGCATAACTTAAGTCT
3881973 AGAAGGGTTATCTGCT---AAAGACCTTTGAGTTCGA
1 AGAAGGGTTATCTGCTAACAAAGACCTTTGAGTTCGA
3882007 TTATATTCAA
Statistics
Matches: 662, Mismatches: 101, Indels: 45
0.82 0.12 0.06
Matches are distributed among these distances:
80 71 0.11
81 87 0.13
83 93 0.14
84 276 0.42
85 135 0.20
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (83 bp):
AGAAGGGTTATCTGCTAACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCT
Found at i:3881630 original size:249 final size:249
Alignment explanation
Indices: 3881237--3882006 Score: 1023
Period size: 249 Copynumber: 3.1 Consensus size: 249
3881227 GGGCTATCTG
* * ** *
3881237 CCAAAGACCCTCGAGTTCGACTACGTTCAGCTTTGAAGGCACATCATTTGCAGTATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGAATAACTTAAGT
3881302 CAAGAAGGGTTATCTGCTAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
65 CAAGAAGGGTTATCTGC--ACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCA
*
3881367 TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACAC
127 TTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACAC
3881432 TCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
192 TCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
* *
3881490 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAACTTAAGTC
* * * * * *
3881555 GAGAGGGGCTATCTGC-C-AAAGACCCTCGAGTTCGACTACGTTCAGCTTCGAAGGCACATCATT
66 AAGAAGGGTTATCTGCACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TC-AAGGCACATCATT
*
3881618 TGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTC
129 TGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTC
3881683 AGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
194 AGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
* * *
3881739 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAACTTAAGTC
* * *
3881804 TACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCAT
66 AAGAAGGGTTATCTG-C-ACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCAT
* * * * ** * * * * * *
3881869 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA-CCTTCGAGTTCGACTCCGC
128 TTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACAC
* * * * * * *
3881933 TCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCCAGAAGGGTTATCTG---
192 TCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
* *
3881987 CTAAAGACCTTTGAGTTCGA
1 CCAAAGACCTTCGAGTTCGA
3882007 TTATATTCAA
Statistics
Matches: 459, Mismatches: 50, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
248 45 0.10
249 204 0.44
250 1 0.00
251 44 0.10
252 111 0.24
253 54 0.12
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (249 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAACTTAAGTC
AAGAAGGGTTATCTGCACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTG
CAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAAAGACCCTTAAGTTCGATTACACTCAG
CTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
Found at i:3881747 original size:333 final size:331
Alignment explanation
Indices: 3881131--3882071 Score: 1200
Period size: 333 Copynumber: 2.8 Consensus size: 331
3881121 TGTAGCTTAG
* * *
3881131 CTCAAGGCCAGAAGGGCTATCTGCCCACC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTG-CCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
*
3881195 CACATCATTTGCAGAATAGCTTGAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
65 CACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTA
* *
3881260 CGTTCAGCTTTGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCTAACAA
130 CGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGC-AACTA
* * * * * * * *
3881325 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGA
194 AAGACCTTTGAGTTCGATTACACTCAGCTTCAAGGGCAAATCATTTACAGCATAACTCAAGGCAA
* * * *
3881389 GAAGGGTTATCTGCCAACTAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATATCAT
259 GAAGGGTTATCTGTC-ACCAAAGA-CCTTCAAGTTCGACTACACTCAGCTCCAA-GGCATATCAT
*
3881453 TTACAGCATAA
321 TTACAGCACAA
*
3881464 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
*
3881529 ACATCATTTGCAGAATAGCTTAAGTCGAGAGGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
66 ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
3881594 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACTAA
131 GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTG-CAACTAA
* * * *
3881659 AGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATATCATTTACAGCATAACTCAAGGCTAG
195 AGACCTTTGAGTTCGATTACACTCAGCTTCAAGGGCAAATCATTTACAGCATAACTCAAGGCAAG
* * *
3881724 AAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGC
260 AAGGGTTATCTGTCACCAAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCATATCATTTAC
3881789 AGCACAA
325 AGCACAA
* * * * *
3881796 CTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACG
1 CTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-G
* * * * * * * *
3881860 GCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTC
64 GCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTCGAGTTC
* * * * * *
3881925 GACTCCGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCCAGAAGGGTTATCTG--
125 GACTACGTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCA
* * * * * *
3881987 -CTAAAGACCTTTGAGTTCGATTATATTCAACTT--AGAGGCAAATCAAGCTTACAGAATAGCTC
190 ACTAAAGACCTTTGAGTTCGATTACACTCAGCTTCAAG-GGCAAATC-A-TTTACAGCATAACTC
3882049 AAGGCAAGAAGGGTTATCTGTCA
252 AAGGCAAGAAGGGTTATCTGTCA
3882072 ATAAAATTGT
Statistics
Matches: 538, Mismatches: 57, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
330 2 0.00
331 7 0.01
332 79 0.15
333 334 0.62
334 41 0.08
335 2 0.00
336 47 0.09
337 26 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (331 bp):
CTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
ACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTAC
GTTCAGCTTCGAAGGCACATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCAACTAAA
GACCTTTGAGTTCGATTACACTCAGCTTCAAGGGCAAATCATTTACAGCATAACTCAAGGCAAGA
AGGGTTATCTGTCACCAAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACA
GCACAA
Found at i:3882716 original size:37 final size:36
Alignment explanation
Indices: 3882659--3882945 Score: 278
Period size: 37 Copynumber: 7.8 Consensus size: 36
3882649 TGCAAATGGA
* * *
3882659 TTTTATAAAATATATTTGAAAACATTTATATATATAG
1 TTTT-TAAAACATTTTTGAAAACATATATATATATAG
* * * *
3882696 TTTTTTAAAACGTTTGTGAAAATAAATATAATATATAG
1 -TTTTTAAAACATTTTTGAAAACATATAT-ATATATAG
*
3882734 TTTTTAAAACATTTTTGAAAACATGTATATTATATAG
1 TTTTTAAAACATTTTTGAAAACATATATA-TATATAG
* *
3882771 -TTTAAAAACA-TTTTGAAAATATATA-ATATATAG
1 TTTTTAAAACATTTTTGAAAACATATATATATATAG
*
3882804 TTTTTAAAACA-TTTTGAAAACATTTATATATTATATAAT
1 TTTTTAAAACATTTTTGAAAACA--TATATA-TATAT-AG
* * * *
3882843 TTTTTAAAACGTTTTTAAAAATAAAATATAATATATAG
1 TTTTTAAAACATTTTTGAAAA-CATATAT-ATATATAG
* *
3882881 TTTTTAAAATATTTTTGAAAATATATATATTATATAG
1 TTTTTAAAACATTTTTGAAAACATATATA-TATATAG
*
3882918 TTTTTAAAACATTTTAGAAAAC-TATATA
1 TTTTTAAAACATTTTTGAAAACATATATA
3882946 ATTTTGAAAA
Statistics
Matches: 206, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
33 7 0.03
34 20 0.10
35 13 0.06
36 21 0.10
37 79 0.38
38 36 0.17
39 20 0.10
40 9 0.04
41 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTTAAAACATTTTTGAAAACATATATATATATAG
Found at i:3882895 original size:147 final size:148
Alignment explanation
Indices: 3882659--3882947 Score: 435
Period size: 147 Copynumber: 2.0 Consensus size: 148
3882649 TGCAAATGGA
* * *
3882659 TTTTATAAAATATATTTGAAAACATTTATATATATAGTTTTTTAAAACGTTTGTGAAAATAAATA
1 TTTTATAAAACATATTTGAAAACATTTATATATATAATTTTTTAAAACGTTTGTAAAAATAAATA
*
3882724 TAATATATAGTTTTTAAAACATTTTTGAAAACATGTATATTATATAG-TTTAAAAACATTTT-GA
66 TAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGTTTTAAAAACATTTTAGA
3882787 AAA-TATATAATATATAG
131 AAACTATATAATATATAG
*
3882804 TTTT-TAAAACAT-TTTGAAAACATTTATATATTATATAATTTTTTAAAACGTTTTTAAAAATAA
1 TTTTATAAAACATATTTGAAAACA-TT-TATA-TATATAATTTTTTAAAACGTTTGTAAAAAT-A
* * *
3882867 AATATAATATATAGTTTTTAAAATATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTT
62 AATATAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGTTTTAAAAACATTT
3882932 TAGAAAACTATATAAT
127 TAGAAAACTATATAAT
3882948 TTTGAAAATA
Statistics
Matches: 129, Mismatches: 8, Indels: 9
0.88 0.05 0.06
Matches are distributed among these distances:
143 10 0.08
144 9 0.07
145 8 0.06
146 27 0.21
147 49 0.38
148 13 0.10
149 5 0.04
150 8 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (148 bp):
TTTTATAAAACATATTTGAAAACATTTATATATATAATTTTTTAAAACGTTTGTAAAAATAAATA
TAATATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATAGTTTTAAAAACATTTTAGA
AAACTATATAATATATAG
Found at i:3882955 original size:29 final size:29
Alignment explanation
Indices: 3882911--3882976 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
3882901 ATATATATAT
* * *
3882911 TATATAGTTTTTAAAACATTTTAGAAAAC
1 TATATAATTTTGAAAACATTTTAGAAAAA
* **
3882940 TATATAATTTTGAAAATATTTTTTAAAAA
1 TATATAATTTTGAAAACATTTTAGAAAAA
3882969 TATATAAT
1 TATATAAT
3882977 ATATAATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAATTTTGAAAACATTTTAGAAAAA
Found at i:3882985 original size:114 final size:111
Alignment explanation
Indices: 3882659--3882975 Score: 263
Period size: 109 Copynumber: 2.8 Consensus size: 111
3882649 TGCAAATGGA
* * * * *
3882659 TTTTATAAAATATATTTGAAAACATTTATATATATAGTTTTTTAAAACGTTTGTG-AAA-ATAAA
1 TTTT-TAAAACAT-TTTGAAAATATATA-ATATATAG-TTTTTAAAACATTT-TGAAAACATATA
* * * * * * * ** *
3882722 TATAATATAT-AGTTTTTAAAACATTTTTGAAAA-CATGTATATTATATAG
61 TATATTAAATAATTTTTTAAAACATATATAAAAATAAAATATAATATATAG
* *
3882771 -TTTAAAAACATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTGAAAACATTTATATAT
1 TTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTGAAAACATATATATAT
* * * *
3882835 TATATAATTTTTTAAAACGTTTTTAAAAATAAAATATAATATATAG
66 TAAATAATTTTTTAAAACATATATAAAAATAAAATATAATATATAG
*
3882881 TTTTTAAAATATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTTAGAAAAC-TATAT
1 TTTTTAAAACA-TTTTGAAAATATATA-A-TATATAGTTTTTAAAACATTTT-GAAAACATATAT
*
3882945 AATTTTGAAA-ATATTTTTTAAAA-ATATATAA
62 -ATATT-AAATA-ATTTTTTAAAACATATATAA
3882976 TATATAATAT
Statistics
Matches: 170, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
106 2 0.01
107 16 0.09
108 20 0.12
109 32 0.19
110 18 0.11
111 11 0.06
112 15 0.09
113 1 0.01
114 26 0.15
115 16 0.09
116 13 0.08
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (111 bp):
TTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTGAAAACATATATATAT
TAAATAATTTTTTAAAACATATATAAAAATAAAATATAATATATAG
Found at i:3882997 original size:34 final size:36
Alignment explanation
Indices: 3882940--3883015 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 36
3882930 TTTAGAAAAC
* *
3882940 TATATAATTTTGAAAATATTTTTTAAAAATATATAA
1 TATATAATATTGAAAATAGTTTTTAAAAATATATAA
*
3882976 TATATAATATT-AAAAT-GTTTTTAAAAATATATAT
1 TATATAATATTGAAAATAGTTTTTAAAAATATATAA
3883010 TATATA
1 TATATA
3883016 GATTTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 22 0.59
35 5 0.14
36 10 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATAATATTGAAAATAGTTTTTAAAAATATATAA
Found at i:3882998 original size:65 final size:64
Alignment explanation
Indices: 3882872--3883008 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 64
3882862 AATAAAATAT
* * * * *
3882872 AATATATAGTTTTTAAAATATTTTTGAAAATATATATATTATATAGTTTTTAAAACATTTTAGAA
1 AATATATAATTTTGAAAATATTTTTGAAAATATATATAATATATAGATATTAAAACATTTTA-AA
* **
3882937 AACTATATAATTTTGAAAATATTTTTTAAAA-ATATATAATATATA-ATATTAAAATGTTTTTAA
1 AA-TATATAATTTTGAAAATATTTTTGAAAATATATATAATATATAGATATTAAAA-CATTTTAA
3883000 A
64 A
3883001 AATATATA
1 AATATATA
3883009 TTATATAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
63 6 0.10
64 11 0.18
65 20 0.32
66 25 0.40
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (64 bp):
AATATATAATTTTGAAAATATTTTTGAAAATATATATAATATATAGATATTAAAACATTTTAAA
Found at i:3883684 original size:17 final size:18
Alignment explanation
Indices: 3883664--3883697 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3883654 GCAAATACAG
3883664 AAACAAA-ACCAAAAAAA
1 AAACAAATACCAAAAAAA
3883681 AAACAAATACCAAAAAA
1 AAACAAATACCAAAAAA
3883698 CACCGAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.79, C:0.18, G:0.00, T:0.03
Consensus pattern (18 bp):
AAACAAATACCAAAAAAA
Found at i:3884980 original size:29 final size:29
Alignment explanation
Indices: 3884889--3884993 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
3884879 CTTTACTAAA
* * *
3884889 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATTAAAATATAAAAAAAATATTAT
3884918 -TCATTATTAAATATATAAAAAAAATATTAT
1 AT-ATTATTAAA-ATATAAAAAAAATATTAT
*
3884948 ATATTATTAAAATA-AAAATATAATATCT-T
1 ATATTATTAAAATATAAAA-AAAATAT-TAT
*
3884977 ATATTATTATAATATAA
1 ATATTATTAAAATATAA
3884994 TTGATTATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
28 5 0.08
29 31 0.48
30 28 0.43
31 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (29 bp):
ATATTATTAAAATATAAAAAAAATATTAT
Found at i:3885031 original size:22 final size:23
Alignment explanation
Indices: 3885006--3885049 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3884996 GATTATTTTA
3885006 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
3885028 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
3885050 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:3885054 original size:22 final size:22
Alignment explanation
Indices: 3885010--3885066 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3885000 ATTTTATATA
* *
3885010 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
3885031 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
3885053 ATATTTTAAATATT
1 ATATTATAAATATT
3885067 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:3885065 original size:52 final size:51
Alignment explanation
Indices: 3884946--3885066 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
3884936 AAAAAATATT
**
3884946 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
3884997 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
3885051 ATATATTTTAAATATT
1 ATATATTTTAAATATT
3885067 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:3885314 original size:42 final size:42
Alignment explanation
Indices: 3885255--3885369 Score: 203
Period size: 42 Copynumber: 2.7 Consensus size: 42
3885245 ATGAATTACA
*
3885255 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
3885297 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
3885339 TTCCGAAAAATGAATTACGTGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
3885370 AGAAATTCAG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:3887396 original size:14 final size:14
Alignment explanation
Indices: 3887379--3887406 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3887369 TTTGAATTAA
3887379 AAAATATTTTTTAT
1 AAAATATTTTTTAT
3887393 AAAATATTTTTTAT
1 AAAATATTTTTTAT
3887407 TCACATTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AAAATATTTTTTAT
Found at i:3889080 original size:22 final size:21
Alignment explanation
Indices: 3889054--3889103 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
3889044 TTGCATTTCG
3889054 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATA-TCTACAGTTGT
*
3889076 TGTTGCG--ATCTACAGTTGT
1 CGTTGCGATATCTACAGTTGT
3889095 CGTTGCGAT
1 CGTTGCGAT
3889104 TTTCCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 17 0.71
20 1 0.04
22 6 0.25
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (21 bp):
CGTTGCGATATCTACAGTTGT
Found at i:3889087 original size:19 final size:19
Alignment explanation
Indices: 3889065--3889103 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3889055 GTTGCGATAG
*
3889065 TCTACAGTTGTTGTTGCGA
1 TCTACAGTTGTCGTTGCGA
3889084 TCTACAGTTGTCGTTGCGA
1 TCTACAGTTGTCGTTGCGA
3889103 T
1 T
3889104 TTTCCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (19 bp):
TCTACAGTTGTCGTTGCGA
Found at i:3889744 original size:5 final size:5
Alignment explanation
Indices: 3889725--3889786 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
3889715 GCCATCCTTC
* * * * *
3889725 TCGTC TCGTT TCGTG TCGTG CCGTG CCGTG CCGTG TCGTG TCGTGG TCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGT-G TCGTG
3889776 TCGTGG TCGTG
1 TCGT-G TCGTG
3889787 GTAATACGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
5 41 0.80
6 10 0.20
ACGTcount: A:0.00, C:0.26, G:0.39, T:0.35
Consensus pattern (5 bp):
TCGTG
Found at i:3889898 original size:22 final size:22
Alignment explanation
Indices: 3889871--3889914 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3889861 CAAGAATTTT
3889871 AACAACTGTAGACTATCGCAAC
1 AACAACTGTAGACTATCGCAAC
3889893 AACAACTGTAGACTATCGCAAC
1 AACAACTGTAGACTATCGCAAC
3889915 GAATTTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.14, T:0.18
Consensus pattern (22 bp):
AACAACTGTAGACTATCGCAAC
Found at i:3889929 original size:19 final size:19
Alignment explanation
Indices: 3889907--3889953 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
3889897 ACTGTAGACT
3889907 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
3889926 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
3889945 ATCGCAACG
1 ATCGCAACG
3889954 CGAAATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:3889967 original size:20 final size:20
Alignment explanation
Indices: 3889942--3889980 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3889932 ACGAATTTGG
3889942 AAAATCGCAACGCGAAATGA
1 AAAATCGCAACGCGAAATGA
3889962 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
3889981 CAACGCGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGCGAAATGA
Found at i:3890493 original size:20 final size:20
Alignment explanation
Indices: 3890388--3890661 Score: 196
Period size: 20 Copynumber: 13.6 Consensus size: 20
3890378 GATTTTCCAT
****
3890388 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAATCCGTA
**
3890408 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
3890428 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
3890447 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
3890469 AATCGCAACGCGTATCCATA
1 AATCGCAACGCGAATCCGTA
*
3890489 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* *
3890510 AATCGCAACGCGATTACGTA
1 AATCGCAACGCGAATCCGTA
* *
3890530 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
3890550 AATCGCAATGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
** *
3890570 AATCGCAACTAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
3890590 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
3890610 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
* *
3890631 AATCGTAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
3890651 AATCGCAACGC
1 AATCGCAACGC
3890662 AATTTTTAAA
Statistics
Matches: 204, Mismatches: 39, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.00
20 151 0.74
21 51 0.25
22 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:3890571 original size:40 final size:41
Alignment explanation
Indices: 3890449--3890664 Score: 271
Period size: 41 Copynumber: 5.3 Consensus size: 41
3890439 GATTCTGACT
** * *
3890449 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
3890490 ATCGCAACGACAATACGTAAAATCGCAACGCG-ATTACGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTA-TCCGTAA
* * *
3890531 ATCGCAATG-CGAATACGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTAA
* * *
3890571 ATCGCAACTAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
3890611 ATCGCAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
3890652 ATCGCAACG-CAAT
1 ATCGCAACGACAAT
3890665 TTTTAAAGCG
Statistics
Matches: 153, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
40 74 0.48
41 79 0.52
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:3891249 original size:20 final size:20
Alignment explanation
Indices: 3891224--3891295 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
3891214 TTCTAAACTT
*
3891224 AAAATCGCAATATGAAAATG
1 AAAATCGCAACATGAAAATG
*
3891244 AAAATCGCAACACGAAAATG
1 AAAATCGCAACATGAAAATG
**
3891264 ACTATCGCAACGAGTG-AAATG
1 AAAATCGCAAC-A-TGAAAATG
3891285 AAAATCGCAAC
1 AAAATCGCAAC
3891296 GAGAGAATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 27 0.63
21 15 0.35
22 1 0.02
ACGTcount: A:0.50, C:0.18, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACATGAAAATG
Found at i:3891285 original size:21 final size:21
Alignment explanation
Indices: 3891239--3891298 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
3891229 CGCAATATGA
*
3891239 AAATGAAAATCGCAAC-ACG-A
1 AAATGAAAATCGCAACGA-GTG
**
3891259 AAATGACTATCGCAACGAGTG
1 AAATGAAAATCGCAACGAGTG
3891280 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
3891299 AGAATCACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.13
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGTG
Found at i:3891317 original size:33 final size:33
Alignment explanation
Indices: 3891280--3891344 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
3891270 GCAACGAGTG
3891280 AAATGAAAATCGCAACGAGAGAATCACAACGCT
1 AAATGAAAATCGCAACGAGAGAATCACAACGCT
* * *
3891313 AAATGAAAATCGCAAGGAGATAATCGCAACGC
1 AAATGAAAATCGCAACGAGAGAATCACAACGC
3891345 GAAACCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCACAACGCT
Found at i:3891355 original size:33 final size:33
Alignment explanation
Indices: 3891285--3891356 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
3891275 GAGTGAAATG
* **
3891285 AAAATCGCAACGAGAGAATCACAACGCTAAATG
1 AAAATCGCAACGAGAGAATCACAACGCGAAACC
* * *
3891318 AAAATCGCAAGGAGATAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCACAACGCGAAACC
3891351 AAAATC
1 AAAATC
3891357 ACATTGCGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCACAACGCGAAACC
Found at i:3891444 original size:20 final size:19
Alignment explanation
Indices: 3891360--3891467 Score: 109
Period size: 20 Copynumber: 5.8 Consensus size: 19
3891350 CAAAATCACA
3891360 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
3891379 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
3891398 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
3891412 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
3891432 TTGCGATTTTCATTCTCTCA
1 TTGCGATTTTCATT-TCGCG
*
3891452 TTTCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3891468 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 3 0.04
19 28 0.38
20 30 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:3893515 original size:21 final size:21
Alignment explanation
Indices: 3893491--3893557 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3893481 TCATTCATCG
3893491 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3893512 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3893533 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3893554 AGAG
1 AGAG
3893558 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3893515 original size:42 final size:42
Alignment explanation
Indices: 3893448--3893557 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
3893438 GTCATCCCTC
* * * * *
3893448 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCATCG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-TCATCG
* * *
3893491 -AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCATCG
*
3893532 AAGAGGT-CCCTCCCACCATTCAAGAG
1 AAGA-GTCCCCTCCCACCGTTCAAGAG
3893558 CCCGATTCAC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.07
42 50 0.89
43 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.22
Consensus pattern (42 bp):
AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCATCG
Found at i:3895104 original size:19 final size:19
Alignment explanation
Indices: 3895082--3895202 Score: 93
Period size: 19 Copynumber: 6.8 Consensus size: 19
3895072 CGAAACTAAA
*
3895082 TTCGCGTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
3895101 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
3895116 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
3895134 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
3895153 TTCCGCGTTGCGATTTTCA-
1 TT-CGCGTTGCGATTTTCAT
3895172 ----CGTTGCGATTTT-AGT
1 TTCGCGTTGCGATTTTCA-T
3895187 TTCGCGTTGCGATTTT
1 TTCGCGTTGCGATTTT
3895203 GTCGTTGCGA
Statistics
Matches: 79, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
13 1 0.01
14 21 0.27
16 3 0.04
17 3 0.04
19 38 0.48
20 13 0.16
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:3895178 original size:53 final size:52
Alignment explanation
Indices: 3895097--3895199 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 52
3895087 GTTACGATTT
* *
3895097 TCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCA-TTTCGCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCACGTTGCGATTTT-AGTTTCGCATTGCGATAG
* *
3895149 TCATTTCCGCGTTGCGATTTTCACGTTGCGATTTTAGTTTCGCGTTGCGAT
1 TCATTT-CGCGTTGCGATTCTCACGTTGCGATTTTAGTTTCGCATTGCGAT
3895200 TTTGTCGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 7 0.16
53 38 0.84
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (52 bp):
TCATTTCGCGTTGCGATTCTCACGTTGCGATTTTAGTTTCGCATTGCGATAG
Found at i:3895195 original size:33 final size:34
Alignment explanation
Indices: 3895151--3895233 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 34
3895141 TGCGATAGTC
3895151 ATTTCCGCGTTGCGATTTTCACGTTGCGA-TTTT
1 ATTTCCGCGTTGCGATTTTCACGTTGCGATTTTT
**
3895184 AGTTT-CGCGTTGCGATTTTGTCGTTGCGATTTTT
1 A-TTTCCGCGTTGCGATTTTCACGTTGCGATTTTT
3895218 ATTTCCGCGTTGCGAT
1 ATTTCCGCGTTGCGAT
3895234 AGACATTAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
33 26 0.58
34 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (34 bp):
ATTTCCGCGTTGCGATTTTCACGTTGCGATTTTT
Found at i:3895210 original size:14 final size:14
Alignment explanation
Indices: 3895158--3895216 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
3895148 GTCATTTCCG
**
3895158 CGTTGCGATTTTCA
1 CGTTGCGATTTTGT
3895172 CGTTGCGATTTTAGTTT
1 CGTTGCGATTTT-G--T
3895189 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3895205 CGTTGCGATTTT
1 CGTTGCGATTTT
3895217 TATTTCCGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 24 0.63
16 1 0.03
18 1 0.03
19 12 0.32
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3895621 original size:41 final size:40
Alignment explanation
Indices: 3895575--3895687 Score: 115
Period size: 41 Copynumber: 2.8 Consensus size: 40
3895565 GAAATTCAGT
* *
3895575 ATTGCGATAGTCAGAATCTCGTTGCGATTTAGCGTATTA-TC
1 ATTGCGATAGTCAGAATCGCGTTGCGATTTA-CGGA-TACTC
* * *
3895616 GTTGCGAT--TTACGGATACGCGTTGCGATTTTACGGATACTC
1 ATTGCGATAGTCA-GAAT-CGCGTTGCGA-TTTACGGATACTC
3895657 ATTGCGATAGTCAGAATCGCGTTGCGATTTA
1 ATTGCGATAGTCAGAATCGCGTTGCGATTTA
3895688 TATGTTCGCG
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
39 2 0.03
40 9 0.16
41 38 0.66
42 7 0.12
43 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCGCGTTGCGATTTACGGATACTC
Found at i:3895649 original size:21 final size:21
Alignment explanation
Indices: 3895615--3895664 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3895605 AGCGTATTAT
3895615 CGTTGCGA-TTTACGGATACG
1 CGTTGCGATTTTACGGATACG
*
3895635 CGTTGCGATTTTACGGATACT
1 CGTTGCGATTTTACGGATACG
*
3895656 CATTGCGAT
1 CGTTGCGAT
3895665 AGTCAGAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
CGTTGCGATTTTACGGATACG
Found at i:3895696 original size:20 final size:20
Alignment explanation
Indices: 3895673--3895725 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
3895663 ATAGTCAGAA
*
3895673 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
3895693 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
3895713 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3895726 ATGGAAACTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:3897791 original size:20 final size:20
Alignment explanation
Indices: 3897748--3897791 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3897738 CACATTTTAC
* * * *
3897748 AAATATATAAAAATAATAAT
1 AAATAAATAAAAACAACAAA
3897768 AAATAAATAAAAACAACAAA
1 AAATAAATAAAAACAACAAA
3897788 AAAT
1 AAAT
3897792 CCTATTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATAAATAAAAACAACAAA
Found at i:3899622 original size:37 final size:37
Alignment explanation
Indices: 3899549--3899623 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
3899539 ACTATAAGAT
* *
3899549 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
3899586 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
3899623 A
1 A
3899624 AAGTTTAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:3905642 original size:12 final size:12
Alignment explanation
Indices: 3905625--3905661 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
3905615 AACACATAAG
*
3905625 ATACAACCGACA
1 ATACAACTGACA
3905637 ATACAACTGACA
1 ATACAACTGACA
3905649 ATACAACTGACA
1 ATACAACTGACA
3905661 A
1 A
3905662 AACCACCCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.51, C:0.27, G:0.08, T:0.14
Consensus pattern (12 bp):
ATACAACTGACA
Found at i:3913838 original size:191 final size:190
Alignment explanation
Indices: 3913482--3913851 Score: 643
Period size: 191 Copynumber: 1.9 Consensus size: 190
3913472 TAGCAATCTA
*
3913482 GGATTTAGGGTGGCTAACACAGATATTTGAAATTGAAAACTAATATTAATTATAAAATTTTGAAT
1 GGATTTAGGGTGGCTAACACAGATATTTGAAATTGAAAACTAACATTAATTATAAAATTTTGAAT
*
3913547 TTAAACAAAATTCAATTTTTCTGGTAGAAAAATTCTTAACATATTTTTGGGATATTTTTAAATAA
66 TTAAACAAAATTCAATTTTACTGGTAGAAAAATTCTTAACATATTTTTGGGATATTTTTAAATAA
*
3913612 AGTACCCCATATATGTTATATGTATCTGCATATAAGAATGTCCTATTTCTGATTAGGGTT
131 ACTACCCCATATATGTTATATGTATCTGCATATAAGAATGTCCTATTTCTGATTAGGGTT
* **
3913672 GGATTTATGGTGGCTAACACAGATATTTGGCATTGAAAACTAACATTAATTATAAAATTTTGAAT
1 GGATTTAGGGTGGCTAACACAGATATTTGAAATTGAAAACTAACATTAATTATAAAATTTTGAAT
*
3913737 TTAAACAAAAATTGAATTTTACTGGTAGAAAAATTCTTAACAT-TATTTTGGGATATTTTTAAAT
66 TTAAAC-AAAATTCAATTTTACTGGTAGAAAAATTCTTAACATAT-TTTTGGGATATTTTTAAAT
*
3913801 AAACTACCCCATATATGTTATATGTATCTGTATATAAGAATGTCCTATTTC
129 AAACTACCCCATATATGTTATATGTATCTGCATATAAGAATGTCCTATTTC
3913852 CGGTTACATT
Statistics
Matches: 170, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
190 68 0.40
191 102 0.60
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (190 bp):
GGATTTAGGGTGGCTAACACAGATATTTGAAATTGAAAACTAACATTAATTATAAAATTTTGAAT
TTAAACAAAATTCAATTTTACTGGTAGAAAAATTCTTAACATATTTTTGGGATATTTTTAAATAA
ACTACCCCATATATGTTATATGTATCTGCATATAAGAATGTCCTATTTCTGATTAGGGTT
Found at i:3925233 original size:37 final size:41
Alignment explanation
Indices: 3925151--3925235 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 41
3925141 TAAATCATTG
* *
3925151 ATTTTGACTTTTGAAAACTCTAAATCATTTTTCAAAATTTC
1 ATTTTGACTTTTCAAAACTCTAAATCATTTTTCAAAATTTA
*
3925192 ATTTTGA-TTTTCAAAA-TC-AAATCA-TTTTC-AACTTTAA
1 ATTTTGACTTTTCAAAACTCTAAATCATTTTTCAAAATTT-A
3925229 ATTTTGA
1 ATTTTGA
3925236 AATTAATTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 5 0.12
37 12 0.30
38 6 0.15
39 2 0.05
40 8 0.20
41 7 0.17
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (41 bp):
ATTTTGACTTTTCAAAACTCTAAATCATTTTTCAAAATTTA
Found at i:3932058 original size:38 final size:38
Alignment explanation
Indices: 3932008--3932238 Score: 266
Period size: 38 Copynumber: 6.0 Consensus size: 38
3931998 AATCTTTCAA
*
3932008 TGTTATTCTTGACTTCATCGTGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
3932046 TGTTATTATTGACTTCATCGTGAAGAGATGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
3932084 TGTTATTCTTGACTTCCTCGTGAAGAGAATTCAATATT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
3932122 TTTTATTCTTGACTCCCTCGTGAGGATG-AGTCAATCTTTCAT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATC--T--T
* * * *
3932164 TGTTATTTTTAACTTCCTTGTGAAAAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
3932202 TGTTATTCTTGACTCCCTCGTTAAGAGGAGTCAATCT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
3932239 AACATAAGTA
Statistics
Matches: 161, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
38 129 0.80
39 1 0.01
40 2 0.01
41 1 0.01
42 28 0.17
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (38 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
Found at i:3932094 original size:76 final size:77
Alignment explanation
Indices: 3932008--3932239 Score: 288
Period size: 80 Copynumber: 3.0 Consensus size: 77
3931998 AATCTTTCAA
* * * *
3932008 TGTTATTCTTGACTTCATCGTGAAGAGAAGTCAATCTTTGTTATTATTGACTTCATCGTGAAGA-
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAG
3932072 GATGTCAATCT-T
66 GA-GTCAATCTAT
* * * * *
3932084 TGTTATTCTTGACTTCCTCGTGAAGAGAATTCAATATTTTTTATTCTTGACTCCCTCGTGAGGAT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAG
3932149 GAGTCAATCTTTCAT
66 GAGTCAATC--T-AT
* * * * *
3932164 TGTTATTTTTAACTTCCTTGTGAAAAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTTAAGAG
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAG
3932229 GAGTCAATCTA
66 GAGTCAATCTA
3932240 ACATAAGTAA
Statistics
Matches: 133, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
76 63 0.47
77 3 0.02
78 2 0.02
80 65 0.49
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (77 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAG
GAGTCAATCTAT
Found at i:3934397 original size:38 final size:38
Alignment explanation
Indices: 3934338--3934524 Score: 252
Period size: 38 Copynumber: 4.9 Consensus size: 38
3934328 AATCTTTCAA
* *
3934338 TGTTTTTCTTGACTTCCTCGTGAAGAGAAGTCATTATT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATATT
* *
3934376 TGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATATT
* * * *
3934414 T-TTCATTCCTGACTTCCTCGTAAAGAGAAGTCGATCTT
1 TGTT-ATTCTTGACTTCCTCGTGAAGAGAAGTCAATATT
*
3934452 TGTTATTCTTGACTTTCTCGTGAAGAGAAGTCAATATT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATATT
*
3934490 TGTTATTCTTGACTCCCTCGTGAAGATG-AGTCAAT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAAT
3934525 CTTTCAGTGT
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
37 2 0.02
38 126 0.96
39 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (38 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATATT
Found at i:3934527 original size:76 final size:76
Alignment explanation
Indices: 3934338--3934566 Score: 264
Period size: 76 Copynumber: 3.0 Consensus size: 76
3934328 AATCTTTCAA
* * * * *
3934338 TGTTTTTCTTGACTTCCTCGTGAAGAGAAGTCATTATTTGTTATTATTGACTTCCTCGTGAAGAG
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCGTGAAGAG
*
3934403 AAGTCAATCTT
66 AAGTCAATATT
* * *
3934414 T-TTCATTCCTGACTTCCTCGTAAAGAGAAGTCGATCTTTGTTATTCTTGACTTTCTCGTGAAGA
1 TGTT-ATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCGTGAAGA
3934478 GAAGTCAATATT
65 GAAGTCAATATT
* * * *
3934490 TGTTATTCTTGACTCCCTCGTGAAGATG-AGTCAATCTTTCAGTGTCCTTCTTGACTTTCTTGCG
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTTT--GT-T-ATTCTTGACTTTCTCGTG
*
3934554 AAGAGGAGTCAAT
61 AAGAGAAGTCAAT
3934567 CTTTTGGTGT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
75 2 0.02
76 94 0.73
77 3 0.02
78 2 0.02
79 1 0.01
80 27 0.21
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (76 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTTCTCGTGAAGAG
AAGTCAATATT
Found at i:3934602 original size:45 final size:45
Alignment explanation
Indices: 3934489--3934845 Score: 262
Period size: 45 Copynumber: 8.0 Consensus size: 45
3934479 AAGTCAATAT
* ** * * *
3934489 TTGTTATTCTTGACTCCCTCGTGAAGATGAGTCAATCTTTCAG--
1 TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATATTTCAGTA
* *** * ** *
3934532 -TGTCCTTCTTGACTTTCTTGCGAAGAGGAGTCAATCTTTTGGTG
1 TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATATTTCAGTA
* * *
3934576 TTGTC-TTCCTTGACTTTCTTATGAAGAGGAGTCAATATTTTAGTG
1 TTGTCATT-CTTGACTTTCTCATGAAGAGGAGTCAATATTTCAGTA
* *
3934621 TTGTCATTCTTGACTTTCTCATGAAGAGAAGTCAA-ACTCTCAGTA
1 TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATA-TTTCAGTA
** * * *
3934666 TTGTCATTCTTGACTTTCTCGCGAGGAGGAGTCAATAGTTCGGTA
1 TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATATTTCAGTA
* * *
3934711 TTAT-TTTCCTTGACTTTCTCATGAAGAGGAGTCAATATTTTAGTA
1 TTGTCATT-CTTGACTTTCTCATGAAGAGGAGTCAATATTTCAGTA
* ** ** ** *
3934756 TTGTCGTTCTTGACTTTCTCGCGAAGATAAGTCGTTAGTTT-AGTG
1 TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATA-TTTCAGTA
* * * *
3934801 TTGTCCTTCTTGACTTTCTCACGGAGAGGGGTCAACT-TTTCAGTA
1 TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAA-TATTTCAGTA
3934846 GTATCCTTAA
Statistics
Matches: 251, Mismatches: 51, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
42 33 0.13
44 8 0.03
45 201 0.80
46 9 0.04
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (45 bp):
TTGTCATTCTTGACTTTCTCATGAAGAGGAGTCAATATTTCAGTA
Found at i:3934805 original size:135 final size:135
Alignment explanation
Indices: 3934532--3934835 Score: 385
Period size: 135 Copynumber: 2.3 Consensus size: 135
3934522 AATCTTTCAG
* ** * * * *
3934532 TGTCCTTCTTGACTTTCTTGCGAAGAGGAGTCAATCTTTTGGTGTTGTCTTCCTTGACTTTCTTA
1 TGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATAGTTCGGTATTATCTTCCTTGACTTTCTCA
* *
3934597 TGAAGAGGAGTCAATATTTTAGTGTTGTCATTCTTGACTTTCTCATGAAGAGAAGTCAAACTCTC
66 TGAAGAGGAGTCAATATTTTAGTATTGTCATTCTTGACTTTCTCACGAAGAGAAGTCAAACTCTC
3934662 AGTAT
131 AGTAT
* * *
3934667 TGTCATTCTTGACTTTCTCGCGAGGAGGAGTCAATAGTTCGGTATTATTTTCCTTGACTTTCTCA
1 TGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATAGTTCGGTATTATCTTCCTTGACTTTCTCA
* * * ** *
3934732 TGAAGAGGAGTCAATATTTTAGTATTGTCGTTCTTGACTTTCTCGCGAAGATAAGTCGTTAGT-T
66 TGAAGAGGAGTCAATATTTTAGTATTGTCATTCTTGACTTTCTCACGAAGAGAAGTC-AAACTCT
* *
3934796 TAGTGT
130 CAGTAT
* * *
3934802 TGTCCTTCTTGACTTTCTCACGGAGAGGGGTCAA
1 TGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAA
3934836 CTTTTCAGTA
Statistics
Matches: 143, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
135 141 0.99
136 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (135 bp):
TGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATAGTTCGGTATTATCTTCCTTGACTTTCTCA
TGAAGAGGAGTCAATATTTTAGTATTGTCATTCTTGACTTTCTCACGAAGAGAAGTCAAACTCTC
AGTAT
Found at i:3934829 original size:90 final size:89
Alignment explanation
Indices: 3934532--3934835 Score: 306
Period size: 90 Copynumber: 3.4 Consensus size: 89
3934522 AATCTTTCAG
** * * * **
3934532 TGTCCTTCTTGACTTTCTTGCGAAGAGGAGTCAATCTTTTGGTGTTGTCTTCCTTGACTTTCTTA
1 TGTCCTTCTTGACTTTCTCACGAAGAGGAGTCAATATTTTAGTATTGTCTT-CTTGACTTTCTCG
* *
3934597 TGAAGAGGAGTCAATATTTTAGTGT
65 CGAAGAGGAGTCAATAGTTTAGTGT
* * * * *
3934622 TGTCATTCTTGACTTTCTCATGAAGAGAAGTCAA-ACTCTCAGTATTGTCATTCTTGACTTTCTC
1 TGTCCTTCTTGACTTTCTCACGAAGAGGAGTCAATA-TTTTAGTATTGTC-TTCTTGACTTTCTC
* ** *
3934686 GCGAGGAGGAGTCAATAGTTCGGTAT
64 GCGAAGAGGAGTCAATAGTTTAGTGT
* * *
3934712 TAT-TTTCCTTGACTTTCTCATGAAGAGGAGTCAATATTTTAGTATTGTCGTTCTTGACTTTCTC
1 TGTCCTT-CTTGACTTTCTCACGAAGAGGAGTCAATATTTTAGTATTGTC-TTCTTGACTTTCTC
** **
3934776 GCGAAGATAAGTCGTTAGTTTAGTGT
64 GCGAAGAGGAGTCAATAGTTTAGTGT
* *
3934802 TGTCCTTCTTGACTTTCTCACGGAGAGGGGTCAA
1 TGTCCTTCTTGACTTTCTCACGAAGAGGAGTCAA
3934836 CTTTTCAGTA
Statistics
Matches: 172, Mismatches: 37, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
89 2 0.01
90 165 0.96
91 5 0.03
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (89 bp):
TGTCCTTCTTGACTTTCTCACGAAGAGGAGTCAATATTTTAGTATTGTCTTCTTGACTTTCTCGC
GAAGAGGAGTCAATAGTTTAGTGT
Found at i:3935637 original size:134 final size:132
Alignment explanation
Indices: 3935392--3936118 Score: 800
Period size: 134 Copynumber: 5.5 Consensus size: 132
3935382 TAATGTTTGC
* *
3935392 TTTTCAGATTTGGTCTTCCTGAAGAGCAAG-GAAGCAAAACAAATTCGATTTAATCTTCCCTGAA
1 TTTTCAGATTTGGTCTTCCTGAAGAGC-AGCGAAGCAAATC-AATTCGATTCAATCTTCCCTGAA
* * *
3935456 GAGCAGCGAAGTGAATCAAAATTTCCTCGAGTTTGACCTCCCCTAAAGAGTAGTGGAGAAGATTC
64 GAGCAACTAAGTGAATCAAAATTTCCTCGAGTCTGA-CTCCCCTAAAGAGTAGTGGAGAAGATTC
3935521 TTCTT
128 TTCTT
* * *
3935526 TTTTCAGATTTGGTCTTCCTGAAGAGCAGCAAATCAAATCAAATTCGATTTAATCTTCCCTGAAG
1 TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATC-AATTCGATTCAATCTTCCCTGAAG
* ** *
3935591 AGCAACTAAGTGAATCAAAATTTCCTCGAGTCTGACATCCCTTAAAGAGTAGAAGA-ACATATTC
65 AGCAACTAAGTGAATCAAAATTTCCTCGAGTCTGAC-TCCCCTAAAGAGTAGTGGAGA-AGATTC
*
3935655 TTCAT
128 TTCTT
* *
3935660 TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCGAATCAAATTCGACTCAATCTTCCCTGAAG
1 TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATC-AATTCGATTCAATCTTCCCTGAAG
* * * * * *
3935725 AGCAGCGATGTGAATCAAAATTTCCTCAAGTCTAACCTCCCCTAAAGAGTAGTGGAGTAGATTCT
65 AGCAACTAAGTGAATCAAAATTTCCTCGAGTCTGA-CTCCCCTAAAGAGTAGTGGAGAAGATTCT
3935790 TCTT
129 TCTT
* *
3935794 CTTTT-AGATTTGGTCTTCCTGAA-AGCA---AATC--A-C-ATTCGATTCAATCTTCGCTGAAG
1 -TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAATTCGATTCAATCTTCCCTGAAG
* * * * *
3935850 AGC-AGTGAAGTGGATCAAAGTTTCCTCGAGTATGATCTCCCCTAAAGAGTAGTGGA-ACATATT
65 AGCAACT-AAGTGAATCAAAATTTCCTCGAGTCTGA-CTCCCCTAAAGAGTAGTGGAGA-AGATT
*
3935913 TTTCTT
127 CTTCTT
* * * *
3935919 CTTTCAGATTTGGT-TTGCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTCAA
1 TTTTCAGATTTGGTCTT-CCTGAAGAGCAGCGAAGCAAATCAATTC-GATTCAATCTTCCCTGAA
* * * * * *
3935983 GAGC-AGTGAAGTGGATCAAAGTTTTCTCGAATCTGATCTCCCCTAAAGAGTAGTGGAGCAGATT
64 GAGCAACT-AAGTGAATCAAAATTTCCTCGAGTCTGA-CTCCCCTAAAGAGTAGTGGAGAAGATT
*
3936047 ATTCTT
127 CTTCTT
* * * *
3936053 CTTTCAAATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAG
1 TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAATTC-GATTCAATCTTCCCTGAAG
3936118 A
65 A
3936119 ACAGTGGAAT
Statistics
Matches: 517, Mismatches: 55, Indels: 42
0.84 0.09 0.07
Matches are distributed among these distances:
124 5 0.01
125 90 0.17
126 4 0.01
127 1 0.00
128 1 0.00
129 3 0.01
130 3 0.01
131 1 0.00
132 1 0.00
133 12 0.02
134 389 0.75
135 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (132 bp):
TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCAAATCAATTCGATTCAATCTTCCCTGAAGA
GCAACTAAGTGAATCAAAATTTCCTCGAGTCTGACTCCCCTAAAGAGTAGTGGAGAAGATTCTTC
TT
Found at i:3935975 original size:259 final size:262
Alignment explanation
Indices: 3935392--3936118 Score: 909
Period size: 259 Copynumber: 2.7 Consensus size: 262
3935382 TAATGTTTGC
* *
3935392 TTTTCAGATTTGGTCTTCCTGAAGAGCAAGGAAGCAAAACAAATTCGATTTAATCTTCCCTGAAG
1 TTTTCAGATTTGGTCTTCCTGAAGAGC-AGGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAG
* *
3935457 AGCAGCGAAGTGAATCAAAATTTCCTCGAGTTTGACCTCCCCTAAAGAGTAGTGGAGAAGATTCT
65 AGCAGCGAAGTGAATCAAAATTTCCTCAAGTCTGACCTCCCCTAAAGAGTAGTGGAGAAGATTCT
*
3935522 TCTT-TTTTCAGATTTGGTCTTCCTGAAGAGCAGCAAATCAAATCAAATTCGATTTAATCTTCCC
130 TCTTCTTTT-AGATTTGGTCTTCCTG-A-AG-AGCAAATC-AATC-AATTCGATTCAATCTTCCC
* *
3935586 TGAAGAGCAACTAAGTGAATCAAAATTTCCTCGAGTCTGACATCCCTTAAAGAGTAGAAGAACAT
189 TGAAGAGCAACTAAGTGAATCAAAATTTCCTCGAGTATGACATCCCCTAAAGAGTAGAAGAACAT
3935651 ATTCTTCAT
254 ATTCTTCAT
* *
3935660 TTTTCAGATTTGGTCTTCCTGAAGAGCAGCGAAGCGAATCAAATTCGACTCAATCTTCCCTGAAG
1 TTTTCAGATTTGGTCTTCCTGAAGAGCAG-GAAGCAAATCAAATTCGATTCAATCTTCCCTGAAG
* * *
3935725 AGCAGCGATGTGAATCAAAATTTCCTCAAGTCTAACCTCCCCTAAAGAGTAGTGGAGTAGATTCT
65 AGCAGCGAAGTGAATCAAAATTTCCTCAAGTCTGACCTCCCCTAAAGAGTAGTGGAGAAGATTCT
*
3935790 TCTTCTTTTAGATTTGGTCTTCCTGAA-AGCAAATC-A-C-ATTCGATTCAATCTTCGCTGAAGA
130 TCTTCTTTTAGATTTGGTCTTCCTGAAGAGCAAATCAATCAATTCGATTCAATCTTCCCTGAAGA
* * * ** *
3935851 GC-AGTGAAGTGGATCAAAGTTTCCTCGAGTATGATC-TCCCCTAAAGAGTAGTGGAACATATTT
195 GCAACT-AAGTGAATCAAAATTTCCTCGAGTATGA-CATCCCCTAAAGAGTAGAAGAACATATTC
3935914 TTC-T
258 TTCAT
* *
3935918 TCTTTCAGATTTGGT-TTGCCTGAAGAGCAGTGAAGCAAATC-GATTCTGATTCAATCTTCCCTC
1 T-TTTCAGATTTGGTCTT-CCTGAAGAGCAG-GAAGCAAATCAAATTC-GATTCAATCTTCCCTG
* * * * * *
3935981 AAGAGCAGTGAAGTGGATCAAAGTTTTCTCGAA-TCTGATCTCCCCTAAAGAGTAGTGGAGCAGA
62 AAGAGCAGCGAAGTGAATCAAAATTTCCTC-AAGTCTGACCTCCCCTAAAGAGTAGTGGAGAAGA
* * * * *
3936045 TTATTCTTCTTTCAAATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTT
126 TTCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAGCA---AATC-AATCAATTC-GATTCAATCTT
3936110 CCCTGAAGA
186 CCCTGAAGA
3936119 ACAGTGGAAT
Statistics
Matches: 405, Mismatches: 37, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
258 10 0.02
259 204 0.50
260 7 0.02
261 1 0.00
262 1 0.00
263 3 0.01
264 8 0.02
265 1 0.00
266 2 0.00
267 7 0.02
268 157 0.39
269 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (262 bp):
TTTTCAGATTTGGTCTTCCTGAAGAGCAGGAAGCAAATCAAATTCGATTCAATCTTCCCTGAAGA
GCAGCGAAGTGAATCAAAATTTCCTCAAGTCTGACCTCCCCTAAAGAGTAGTGGAGAAGATTCTT
CTTCTTTTAGATTTGGTCTTCCTGAAGAGCAAATCAATCAATTCGATTCAATCTTCCCTGAAGAG
CAACTAAGTGAATCAAAATTTCCTCGAGTATGACATCCCCTAAAGAGTAGAAGAACATATTCTTC
AT
Found at i:3938347 original size:14 final size:14
Alignment explanation
Indices: 3938323--3938359 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3938313 GATTAGAAGA
3938323 TATTTTA-TTAATT
1 TATTTTATTTAATT
3938336 GTA-TTTATTTAATT
1 -TATTTTATTTAATT
3938350 TATTTTATTT
1 TATTTTATTT
3938360 TGTATCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TATTTTATTTAATT
Found at i:3939982 original size:36 final size:35
Alignment explanation
Indices: 3939931--3940038 Score: 132
Period size: 38 Copynumber: 3.0 Consensus size: 35
3939921 TTTTAAATGG
* *
3939931 TTTTTGAAGATATATAATATAGTTTTTAAAATCATA
1 TTTTTGAAAACATATAATATAGTTTTTAAAA-CATA
3939967 TTTTTGAAAACATATAATATATAGTTTTTAAAACATA
1 TTTTTGAAAACATAT-A-ATATAGTTTTTAAAACATA
3940004 TTTTTTGAAAACATAT-ATA-A-TTTTTAAAAACATA
1 -TTTTTGAAAACATATAATATAGTTTTT-AAAACATA
3940038 T
1 T
3940039 AATATATAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
33 6 0.09
34 9 0.14
35 3 0.05
36 13 0.20
37 5 0.08
38 30 0.45
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (35 bp):
TTTTTGAAAACATATAATATAGTTTTTAAAACATA
Found at i:3939991 original size:38 final size:38
Alignment explanation
Indices: 3939897--3940020 Score: 143
Period size: 38 Copynumber: 3.4 Consensus size: 38
3939887 ATATATTTTA
* * **
3939897 TTTTAAAAATATATAATATATAGTTTTT-AAAT--GGT
1 TTTTGAAAACATATAATATATAGTTTTTAAAATCATAT
* *
3939932 TTTTGAAGATATAT-A-ATATAGTTTTTAAAATCATAT
1 TTTTGAAAACATATAATATATAGTTTTTAAAATCATAT
3939968 TTTTGAAAACATATAATATATAGTTTTTAAAA-CATATT
1 TTTTGAAAACATATAATATATAGTTTTTAAAATCATA-T
3940006 TTTTGAAAACATATA
1 TTTTGAAAACATATA
3940021 TAATTTTTAA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
33 11 0.14
34 5 0.06
35 12 0.16
36 13 0.17
37 5 0.06
38 31 0.40
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAATCATAT
Found at i:3940028 original size:71 final size:71
Alignment explanation
Indices: 3939897--3940038 Score: 173
Period size: 71 Copynumber: 2.0 Consensus size: 71
3939887 ATATATTTTA
* * * *
3939897 TTTTAAAAATATATAATATATAGTTTTTAAATGGTTTTTGAAGATATATAATATAGTTTTTAAAA
1 TTTTAAAAACATATAATATATAGTTTTTAAATAGTTTTTGAAGATACATAATATAATTTTTAAAA
*
3939962 TCATAT
66 ACATAT
* *
3939968 TTTTGAAAACATATAATATATAGTTTTTAAAACATATTTTTTGAA-A-ACAT-ATATAATTTTTA
1 TTTTAAAAACATATAATATATAGTTTTT--AA-ATAGTTTTTGAAGATACATAATATAATTTTTA
3940030 AAAACATAT
63 AAAACATAT
3940039 AATATATAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
71 45 0.74
72 3 0.05
73 3 0.05
74 10 0.16
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (71 bp):
TTTTAAAAACATATAATATATAGTTTTTAAATAGTTTTTGAAGATACATAATATAATTTTTAAAA
ACATAT
Found at i:3940038 original size:17 final size:17
Alignment explanation
Indices: 3939985--3940041 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
3939975 AACATATAAT
*
3939985 ATATAGTTTTT-AAAAC
1 ATATAATTTTTAAAAAC
*
3940001 ATAT--TTTTTGAAAACAT
1 ATATAATTTTT-AAAA-AC
3940018 ATATAATTTTTAAAAAC
1 ATATAATTTTTAAAAAC
3940035 ATATAAT
1 ATATAAT
3940042 ATATAGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 5 0.15
16 7 0.21
17 13 0.38
18 4 0.12
19 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATAATTTTTAAAAAC
Found at i:3940043 original size:24 final size:25
Alignment explanation
Indices: 3940016--3940071 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
3940006 TTTTGAAAAC
3940016 ATATATAATTTTTAAAAACATA-TA
1 ATATATAATTTTTAAAAACATATTA
* *
3940040 ATATATAGTTTTTGAAAACATATTA
1 ATATATAATTTTTAAAAACATATTA
*
3940065 TTATATA
1 ATATATA
3940072 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATATAATTTTTAAAAACATATTA
Found at i:3940089 original size:59 final size:57
Alignment explanation
Indices: 3939966--3940092 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
3939956 TTAAAATCAT
* *
3939966 ATTTTTGAAAACATATAATATATAGTTTTTAAAACATATTTTTTGAAAACATATATA
1 ATTTTTAAAAACATATAATATATAGTTTTTAAAACATATTTTATGAAAACATATATA
* *
3940023 ATTTTTAAAAACATATAATATATAGTTTTTGAAAACATATTATTAT-ATATATATATATA
1 ATTTTTAAAAACATATAATATATAGTTTTT-AAAACATATT-TTATGA-AAACATATATA
*
3940082 GTTTTTAAAAA
1 ATTTTTAAAAA
3940093 ATGATTTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
57 29 0.47
58 11 0.18
59 22 0.35
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (57 bp):
ATTTTTAAAAACATATAATATATAGTTTTTAAAACATATTTTATGAAAACATATATA
Found at i:3940204 original size:19 final size:19
Alignment explanation
Indices: 3940182--3940238 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
3940172 TATTTTTTTA
3940182 ATATATACATATAATTATT
1 ATATATACATATAATTATT
3940201 ATATAT---T-T--TT-TT
1 ATATATACATATAATTATT
3940213 AATATATACATATAATTATT
1 -ATATATACATATAATTATT
3940233 ATATAT
1 ATATAT
3940239 TATTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
12 2 0.07
13 8 0.27
15 1 0.03
16 2 0.07
17 1 0.03
19 14 0.47
20 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATACATATAATTATT
Found at i:3940204 original size:30 final size:30
Alignment explanation
Indices: 3940137--3940236 Score: 125
Period size: 32 Copynumber: 3.3 Consensus size: 30
3940127 TTTGAGAACA
*
3940137 TATTATATTGTTTTTGAA-ATATA-ATGTACAT
1 TATTATATT-TTTTT-AATATATACATATA-AT
3940168 TA-TATATTTTTTTAATATATACATATAAT
1 TATTATATTTTTTTAATATATACATATAAT
3940197 TATTATATATTTTTTTAATATATACATATAAT
1 TA-T-TATATTTTTTTAATATATACATATAAT
3940229 TATTATAT
1 TATTATAT
3940237 ATTATTATTA
Statistics
Matches: 63, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
28 2 0.03
29 14 0.22
30 15 0.24
31 3 0.05
32 29 0.46
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (30 bp):
TATTATATTTTTTTAATATATACATATAAT
Found at i:3940207 original size:32 final size:32
Alignment explanation
Indices: 3940166--3940239 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
3940156 TATAATGTAC
3940166 ATTATATATTTTTTTAATATATACATATAATT
1 ATTATATATTTTTTTAATATATACATATAATT
3940198 ATTATATATTTTTTTAATATATACATATAATT
1 ATTATATATTTTTTTAATATATACATATAATT
3940230 ATTATATATT
1 ATTATATATT
3940240 ATTATTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (32 bp):
ATTATATATTTTTTTAATATATACATATAATT
Found at i:3940885 original size:78 final size:78
Alignment explanation
Indices: 3940736--3940885 Score: 212
Period size: 78 Copynumber: 1.9 Consensus size: 78
3940726 GTTTGAAACG
** * * *
3940736 CAAAGATCAGAGCAACTTGGACTGAGCGATCCGAGATCTCTAGTCAAACACGAACCATGAACAAC
1 CAAAGATCAGAGCAACTCAGACTGAACCATCCGAGATCTCTAGTCAAACACGAACCACGAACAAC
**
3940801 TGAGAAACAACCC
66 CAAGAAACAACCC
*
3940814 CAAAGATCAGAGCAACTCAGACTGAACCATCCGAGATCTCT-GATCAAACATGAACCACGAACAA
1 CAAAGATCAGAGCAACTCAGACTGAACCATCCGAGATCTCTAG-TCAAACACGAACCACGAACAA
3940878 CCAAGAAA
65 CCAAGAAA
3940886 TAACTCTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 1 0.02
78 62 0.98
ACGTcount: A:0.42, C:0.27, G:0.17, T:0.13
Consensus pattern (78 bp):
CAAAGATCAGAGCAACTCAGACTGAACCATCCGAGATCTCTAGTCAAACACGAACCACGAACAAC
CAAGAAACAACCC
Found at i:3941602 original size:17 final size:17
Alignment explanation
Indices: 3941582--3941619 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3941572 TTAATCCTTT
3941582 TTTAATATTTCTTTTAA
1 TTTAATATTTCTTTTAA
* *
3941599 TTTAATATTTTTTTTCA
1 TTTAATATTTCTTTTAA
3941616 TTTA
1 TTTA
3941620 TTTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATATTTCTTTTAA
Found at i:3941619 original size:22 final size:22
Alignment explanation
Indices: 3941589--3941640 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3941579 TTTTTTAATA
*
3941589 TTTCTTTTAATTTAATATTT-TT
1 TTTCATTT-ATTTAATATTTATT
**
3941611 TTTCATTTATTTTTTATTTATT
1 TTTCATTTATTTAATATTTATT
3941633 TTTCATTT
1 TTTCATTT
3941641 TCGTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTCATTTATTTAATATTTATT
Found at i:3941629 original size:11 final size:11
Alignment explanation
Indices: 3941605--3941640 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3941595 TTAATTTAAT
3941605 ATTT-TTTTTC
1 ATTTATTTTTC
*
3941615 ATTTATTTTTT
1 ATTTATTTTTC
3941626 ATTTATTTTTC
1 ATTTATTTTTC
3941637 ATTT
1 ATTT
3941641 TCGTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTATTTTTC
Found at i:3941647 original size:22 final size:21
Alignment explanation
Indices: 3941604--3941652 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3941594 TTTAATTTAA
*
3941604 TATTTTTTTTCATTTATTTTT
1 TATTTTTTTTCATTTATGTTT
3941625 TATTTATTTTTCATTT-TCGTTT
1 TATTT-TTTTTCATTTAT-GTTT
3941647 TATTTT
1 TATTTT
3941653 ATCATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (21 bp):
TATTTTTTTTCATTTATGTTT
Found at i:3947311 original size:19 final size:19
Alignment explanation
Indices: 3947275--3947311 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3947265 TGAAAATGAT
*
3947275 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
3947294 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
3947312 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:3956056 original size:14 final size:15
Alignment explanation
Indices: 3956037--3956068 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
3956027 TGAGGATTAG
3956037 AGAATCCAAAA-TCA
1 AGAATCCAAAATTCA
3956051 AGAATCCAAAATTCA
1 AGAATCCAAAATTCA
3956066 AGA
1 AGA
3956069 TTGGAAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.56, C:0.19, G:0.09, T:0.16
Consensus pattern (15 bp):
AGAATCCAAAATTCA
Found at i:3957148 original size:35 final size:35
Alignment explanation
Indices: 3957109--3957360 Score: 234
Period size: 36 Copynumber: 7.1 Consensus size: 35
3957099 TTTCGAAATT
* *
3957109 ATATAATATATAGTTTTTAAATA-GTTTTTGAAGAT
1 ATATAATATATAGTTTTTAAA-ACGTTTTTGAAAAC
*
3957144 ATAT-A-ATATAGTTTTTGAAAACATATTTTTGAAAAC
1 ATATAATATATAGTTTTT-AAAAC--GTTTTTGAAAAC
* **
3957180 ATATAATATGTAG-TTAAAAAACGATTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAACG-TTTTTGAAAAC
*
3957215 ATATAATATATAGTTTTTAAAATGATTTTT--AAA-
1 ATATAATATATAGTTTTTAAAACG-TTTTTGAAAAC
* * *
3957248 A-A-CATATATAGTTTTGAAAACATGTTTTTGGAAAC
1 ATATAATATATAGTTTTTAAAAC--GTTTTTGAAAAC
*
3957283 ATATAATATATAATTTTTAAAACGGTTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAC-GTTTTTGAAAAC
*
3957319 ATATATTATATAGTTTTTAAAAACGATTTTTGAAAAC
1 ATATAATATATAGTTTTT-AAAACG-TTTTTGAAAAC
3957356 ATATA
1 ATATA
3957361 TAACATATAT
Statistics
Matches: 179, Mismatches: 21, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
31 16 0.09
32 6 0.03
33 14 0.08
34 10 0.06
35 28 0.16
36 60 0.34
37 40 0.22
38 5 0.03
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (35 bp):
ATATAATATATAGTTTTTAAAACGTTTTTGAAAAC
Found at i:3957174 original size:14 final size:14
Alignment explanation
Indices: 3957155--3957183 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3957145 TATAATATAG
3957155 TTTTTGAAAACATA
1 TTTTTGAAAACATA
3957169 TTTTTGAAAACATA
1 TTTTTGAAAACATA
3957183 T
1 T
3957184 AATATGTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:3957283 original size:32 final size:31
Alignment explanation
Indices: 3957220--3957287 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
3957210 AAAACATATA
*
3957220 ATATATAGTTTTTAAAATGATTTTTAAAAAC
1 ATATATAGTTTTAAAAATGATTTTTAAAAAC
**
3957251 ATATATAGTTTTGAAAACATG-TTTTTGGAAAC
1 ATATATAGTTTT-AAAA-ATGATTTTTAAAAAC
3957283 ATATA
1 ATATA
3957288 ATATATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.38
32 17 0.53
33 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATGATTTTTAAAAAC
Found at i:3957445 original size:29 final size:28
Alignment explanation
Indices: 3957384--3957459 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
3957374 CTTTGAGAAC
* * *
3957384 ATATTATATTGTTTTTGAAATATAATAT
1 ATATTATATAGTTTTTTAAATACAATAT
3957412 ATATTATATAGTTTTTTAATATACACATAT
1 ATATTATATAGTTTTTTAA-ATACA-ATAT
*
3957442 -TATTATATATTATTTTTA
1 ATATTATATAGT-TTTTTA
3957460 GTTTTTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 17 0.41
29 14 0.34
30 10 0.24
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (28 bp):
ATATTATATAGTTTTTTAAATACAATAT
Found at i:3957489 original size:20 final size:19
Alignment explanation
Indices: 3957461--3957500 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3957451 TTATTTTTAG
3957461 TTTTTTTTACTTCCATTTT
1 TTTTTTTTACTTCCATTTT
* *
3957480 TTTTTATTTATTTTCATTTT
1 TTTTT-TTTACTTCCATTTT
3957500 T
1 T
3957501 ATATGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTTACTTCCATTTT
Found at i:3958997 original size:16 final size:17
Alignment explanation
Indices: 3958962--3958998 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3958952 TTAATCATTC
3958962 TTTAATATTTCTTTTAA
1 TTTAATATTTCTTTTAA
*
3958979 TTTAATATTT-TTTTCA
1 TTTAATATTTCTTTTAA
3958995 TTTA
1 TTTA
3958999 TTTTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATATTTCTTTTAA
Found at i:3959057 original size:5 final size:6
Alignment explanation
Indices: 3959000--3959054 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
3958990 TTTCATTTAT
*
3959000 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCG TTTT-A TTTT-A
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA
3959046 TTTT-A TTTT
1 TTTTCA TTTT
3959055 ATTATTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 14 0.30
6 33 0.70
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTCA
Found at i:3959956 original size:2 final size:2
Alignment explanation
Indices: 3959949--3959974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3959939 CGAGGAAATG
3959949 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3959975 GCTTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3960003 original size:2 final size:2
Alignment explanation
Indices: 3959996--3960027 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3959986 GATTTTTGAA
3959996 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3960028 GTTTTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3961225 original size:16 final size:17
Alignment explanation
Indices: 3961204--3961241 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3961194 TGGTCTTTTA
3961204 ATTTTAA-AATAATTTC
1 ATTTTAACAATAATTTC
*
3961220 ATTTTAATCAATAATTTT
1 ATTTTAA-CAATAATTTC
3961238 ATTT
1 ATTT
3961242 GTTTGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
18 12 0.63
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAACAATAATTTC
Found at i:3962059 original size:16 final size:17
Alignment explanation
Indices: 3962033--3962066 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3962023 TCACTCTTTA
3962033 TTTATTTTATAAGATTT
1 TTTATTTTATAAGATTT
*
3962050 TTTA-TTTATAATATTT
1 TTTATTTTATAAGATTT
3962066 T
1 T
3962067 GTATGTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTATTTTATAAGATTT
Found at i:3963668 original size:60 final size:60
Alignment explanation
Indices: 3963537--3963648 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
3963527 TGTAAATGTG
* *
3963537 TCAA-TTCATCCCTAAACTATGACTATCATTCTAAATTAGTCATTAAACTTTTGAACATT
1 TCAATTTCATCCCCAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAACATT
*
3963596 TCAATTTCATCCCCAAACTATGACCT-TCATTCTAAATT-GATCCTCAAACTTTT
1 TCAATTTCATCCCCAAACTATGA-CTATCATTCTAAATTAG-TCATCAAACTTTT
3963649 TATGCTTCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
59 5 0.11
60 40 0.85
61 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.38
Consensus pattern (60 bp):
TCAATTTCATCCCCAAACTATGACTATCATTCTAAATTAGTCATCAAACTTTTGAACATT
Found at i:3963914 original size:60 final size:60
Alignment explanation
Indices: 3963845--3963979 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
3963835 TAGAAAGAAT
* * * *
3963845 GTCAGAGTTTAAGGATGAAATTAGAATGTTTAAAAGTTTAAAGACTAATTTACAATAAGA
1 GTCATAGTTTAAGGATGAAATTAGAATATTTAAAAGTTTAAAGACCAATTTAAAATAAGA
** * * * *
3963905 GTCATAGTTTGGGGATGAAATTGGAATATTTAAAAGTTTAAATACCAATTTAAAATGAGG
1 GTCATAGTTTAAGGATGAAATTAGAATATTTAAAAGTTTAAAGACCAATTTAAAATAAGA
*
3963965 GTTATAGTTTAAGGA
1 GTCATAGTTTAAGGA
3963980 CATATGATGC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.33
Consensus pattern (60 bp):
GTCATAGTTTAAGGATGAAATTAGAATATTTAAAAGTTTAAAGACCAATTTAAAATAAGA
Found at i:3965920 original size:3 final size:3
Alignment explanation
Indices: 3965912--3965937 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3965902 TGTAAAGTAA
3965912 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
3965938 TAAAACTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3967131 original size:11 final size:12
Alignment explanation
Indices: 3967109--3967139 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
3967099 CAGTCGCATT
3967109 TTTTATATTATA
1 TTTTATATTATA
3967121 TTTTA-ATTATA
1 TTTTATATTATA
3967132 TTTTATAT
1 TTTTATAT
3967140 CACATGTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATATTATA
Found at i:3977333 original size:10 final size:10
Alignment explanation
Indices: 3977318--3977344 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3977308 CGACAGCAAG
3977318 GAGAAATGGA
1 GAGAAATGGA
3977328 GAGAAATGGA
1 GAGAAATGGA
3977338 GAGAAAT
1 GAGAAAT
3977345 CATGAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.37, T:0.11
Consensus pattern (10 bp):
GAGAAATGGA
Found at i:3979974 original size:2 final size:2
Alignment explanation
Indices: 3979969--3979995 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3979959 GTGTGTGTGT
3979969 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 G
3979996 GACTTGGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3984349 original size:3 final size:3
Alignment explanation
Indices: 3984341--3984365 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3984331 AGAAATAAGA
3984341 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3984366 GCTAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3986009 original size:20 final size:20
Alignment explanation
Indices: 3985972--3986010 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3985962 ATGTTGCATC
*
3985972 AAATTAATATTTTTTAATTT
1 AAATTAATATTTTATAATTT
3985992 AAATTAAT-TTTATATAATT
1 AAATTAATATTT-TATAATT
3986011 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTAATATTTTATAATTT
Found at i:4001649 original size:18 final size:18
Alignment explanation
Indices: 4001626--4001662 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4001616 TAAGGGGGAG
4001626 TAATTTCAAAACTTGATT
1 TAATTTCAAAACTTGATT
4001644 TAATTTCAAAACTTGATT
1 TAATTTCAAAACTTGATT
4001662 T
1 T
4001663 CAAAATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TAATTTCAAAACTTGATT
Found at i:4008549 original size:44 final size:44
Alignment explanation
Indices: 4008285--4008547 Score: 337
Period size: 44 Copynumber: 6.0 Consensus size: 44
4008275 CCCCTTGAAA
***
4008285 AACATTTCGCTTGATTTTGTCACATAAGGAGTTGGATCAACATC
1 AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACATC
* * *
4008329 AACATTTCACTTGATTCCATCACATAAGCAGTTGGATCAGCATC
1 AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACATC
** *
4008373 AACATTTCGCTTGATTCCATTTCATAAGGAGTTGGATTAACATC
1 AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACATC
* * * *
4008417 AATATTTTGGTTGATTCCATCACATAAGGAGTTGTATCAACATC
1 AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACATC
* * * * *
4008461 AACATTTTGGTTAATTCCATCACATAAGTAGTTGGATCAACATT
1 AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACATC
* * *
4008505 AACATTTCGCTTGATTCTATCACGTAAGGAGTTGGGTCAACAT
1 AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACAT
4008548 TATCTCACTT
Statistics
Matches: 188, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 188 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (44 bp):
AACATTTCGCTTGATTCCATCACATAAGGAGTTGGATCAACATC
Found at i:4008769 original size:36 final size:36
Alignment explanation
Indices: 4008656--4008769 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
4008646 TTAAAATAGT
* *
4008656 TTTTATCTCACTTGAGATTGTTTTCCTTAAAACAGA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
*
4008692 TTTTATCTCACTTGAGATTGTTTTT-TTAAAGACATA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAA-ACAAA
* *
4008728 CTTTATCTCAGTTGAGATTGTTTTTCTTAAAACAAA
1 TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
4008764 TTTTAT
1 TTTTAT
4008770 TTAACTTAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
35 5 0.07
36 60 0.86
37 5 0.07
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (36 bp):
TTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA
Found at i:4009020 original size:3 final size:3
Alignment explanation
Indices: 4009014--4009051 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
4009004 TGTTTTTTTC
* *
4009014 ATT ATT ATT ACT ATT ATT ATT TTT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4009052 TATAAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:4009054 original size:12 final size:12
Alignment explanation
Indices: 4009008--4009048 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
4008998 CATAATTGTT
4009008 TTTTTCATTATTA
1 TTTTT-ATTATTA
**
4009021 TTACTATTATTA
1 TTTTTATTATTA
4009033 TTTTTATTATTA
1 TTTTTATTATTA
4009045 TTTT
1 TTTT
4009049 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:4012389 original size:21 final size:21
Alignment explanation
Indices: 4012285--4012382 Score: 151
Period size: 21 Copynumber: 4.7 Consensus size: 21
4012275 TTCTGGGTAG
4012285 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
*
4012306 TGTGCATCAATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
4012327 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
* **
4012348 TGTGCATCCATATATCTTCAA
1 TGTGCATCGATGCATCTTCAA
*
4012369 TGTGTATCGATGCA
1 TGTGCATCGATGCA
4012383 CTCTCAAATA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:4012514 original size:20 final size:20
Alignment explanation
Indices: 4012489--4012526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4012479 CACATGTTAA
*
4012489 AGAATGCATCGATGCACTGT
1 AGAATGCACCGATGCACTGT
*
4012509 AGAATGTACCGATGCACT
1 AGAATGCACCGATGCACT
4012527 TCAATGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCACCGATGCACTGT
Found at i:4015067 original size:24 final size:24
Alignment explanation
Indices: 4015035--4015090 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
4015025 CTATTCTTTC
4015035 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
4015059 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
4015083 GCTTCAAT
1 GCTTCAAT
4015091 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:4020266 original size:27 final size:27
Alignment explanation
Indices: 4020223--4020293 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
4020213 ATTTGTGACG
4020223 ATGGCGGTGGC-AGCATCGGGTAAGGGA
1 ATGGCGGTGGCGA-CATCGGGTAAGGGA
* * *
4020250 ATGGCGGCGGCGACATCTGGTAATGGA
1 ATGGCGGTGGCGACATCGGGTAAGGGA
*
4020277 AAGGCGGTGGCGACATC
1 ATGGCGGTGGCGACATC
4020294 ATATATGGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.44, T:0.15
Consensus pattern (27 bp):
ATGGCGGTGGCGACATCGGGTAAGGGA
Found at i:4022021 original size:9 final size:9
Alignment explanation
Indices: 4021991--4022044 Score: 60
Period size: 8 Copynumber: 6.3 Consensus size: 9
4021981 CTGCAAAAAA
4021991 AAATTAAAT
1 AAATTAAAT
*
4022000 -AAGTAAA-
1 AAATTAAAT
*
4022007 ATATTAAAT
1 AAATTAAAT
4022016 AAATTAAAT
1 AAATTAAAT
*
4022025 -ACTTAAAT
1 AAATTAAAT
4022033 AAATTAAAT
1 AAATTAAAT
4022042 AAA
1 AAA
4022045 AAATATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 18 0.50
9 18 0.50
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAATTAAAT
Found at i:4022041 original size:17 final size:16
Alignment explanation
Indices: 4021993--4022042 Score: 73
Period size: 17 Copynumber: 3.1 Consensus size: 16
4021983 GCAAAAAAAA
* *
4021993 ATTAAATAAGTAAAAT
1 ATTAAATAAATTAAAT
4022009 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
4022025 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
4022042 A
1 A
4022043 AAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Done.