Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 11 of 190
Found at i:3317837 original size:14 final size:14
Alignment explanation
Indices: 3317818--3317845 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3317808 AAATCAAACA
3317818 GAAATACCTTCAGC
1 GAAATACCTTCAGC
3317832 GAAATACCTTCAGC
1 GAAATACCTTCAGC
3317846 CATTGTCTGA
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:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (14 bp):
GAAATACCTTCAGC
Found at i:3319125 original size:19 final size:19
Alignment explanation
Indices: 3319103--3319139 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3319093 TTTAAAATAC
*
3319103 TTTTAAAATATTTTTTTAT
1 TTTTAAAATAATTTTTTAT
3319122 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
3319140 GTGTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:3319146 original size:20 final size:19
Alignment explanation
Indices: 3319104--3319146 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3319094 TTAAAATACT
* *
3319104 TTTAAAATATTTTTTTATT
1 TTTAAAATAATTTTTTATG
3319123 TTTAAAATAATTTTTTAGTG
1 TTTAAAATAATTTTTTA-TG
3319143 TTTA
1 TTTA
3319147 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTAAAATAATTTTTTATG
Found at i:3319314 original size:13 final size:13
Alignment explanation
Indices: 3319296--3319321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3319286 TAACCAGTTT
3319296 GATGAGCATATTC
1 GATGAGCATATTC
3319309 GATGAGCATATTC
1 GATGAGCATATTC
3319322 ACTTCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GATGAGCATATTC
Found at i:3330597 original size:22 final size:22
Alignment explanation
Indices: 3330571--3330612 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3330561 TTTGTTTTGA
3330571 TTTTTAAGTTCTCTTTATTTAC
1 TTTTTAAGTTCTCTTTATTTAC
* *
3330593 TTTTTAAGTTTTTTTTATTT
1 TTTTTAAGTTCTCTTTATTT
3330613 GTCCTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTTAAGTTCTCTTTATTTAC
Found at i:3330730 original size:20 final size:20
Alignment explanation
Indices: 3330707--3330767 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
3330697 AATTATATTT
3330707 TTTTAAAATTATTTTTTTAA
1 TTTTAAAATTATTTTTTTAA
**
3330727 TTTTAAATATTATTTTTAAAA
1 TTTTAAA-ATTATTTTTTTAA
3330748 TTTT-AAA-TATGTTTTTTAA
1 TTTTAAAATTAT-TTTTTTAA
3330767 T
1 T
3330768 AATATAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.09
19 8 0.23
20 9 0.26
21 15 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAAATTATTTTTTTAA
Found at i:3330730 original size:21 final size:21
Alignment explanation
Indices: 3330706--3330767 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
3330696 TAATTATATT
3330706 TTTTTAAAATTATTTTTTTAA
1 TTTTTAAAATTATTTTTTTAA
*
3330727 -TTTTAAATATTA-TTTTTAAA
1 TTTTTAAA-ATTATTTTTTTAA
*
3330747 ATTTT-AAA-TATGTTTTTTAA
1 TTTTTAAAATTAT-TTTTTTAA
3330767 T
1 T
3330768 AATATAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 23 0.68
21 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTAAAATTATTTTTTTAA
Found at i:3330743 original size:34 final size:33
Alignment explanation
Indices: 3330686--3330749 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
3330676 AAATGTTTTA
*
3330686 TTTTTAATTATAATTATATTTTTTTAAAATTATT
1 TTTTTAATTATAAATATA-TTTTTTAAAATTATT
*
3330720 TTTTTAATTTTAAATAT-TATTTTTAAAATT
1 TTTTTAATTATAAATATAT-TTTTTAAAATT
3330750 TTAAATATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 1 0.04
33 11 0.41
34 15 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (33 bp):
TTTTTAATTATAAATATATTTTTTAAAATTATT
Found at i:3330775 original size:21 final size:21
Alignment explanation
Indices: 3330710--3330775 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3330700 TATATTTTTT
** *
3330710 TAAA-ATTATTTTTTTAATTT
1 TAAATATTATTTTTAAAATTA
*
3330730 TAAATATTATTTTTAAAATTT
1 TAAATATTATTTTTAAAATTA
3330751 TAAATATGT-TTTTTAATAA-TA
1 TAAATAT-TATTTTTAA-AATTA
3330772 TAAA
1 TAAA
3330776 ACATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 4 0.10
21 33 0.82
22 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAAATATTATTTTTAAAATTA
Found at i:3330886 original size:30 final size:32
Alignment explanation
Indices: 3330828--3330889 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
3330818 TTATTATTTG
3330828 TTTTATAATATTTTTAATGTATATTTTAAATT
1 TTTTATAATATTTTTAATGTATATTTTAAATT
* *
3330860 TTTTA-AATATTTTTTATTTA-ATTTTAAATT
1 TTTTATAATATTTTTAATGTATATTTTAAATT
3330890 ATTGATTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 10 0.36
31 13 0.46
32 5 0.18
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (32 bp):
TTTTATAATATTTTTAATGTATATTTTAAATT
Found at i:3330991 original size:22 final size:20
Alignment explanation
Indices: 3330965--3331019 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
3330955 GACTTTTTTT
3330965 AAAATATATATTAAAAAAGGTA
1 AAAATATATATTAAAAAA--TA
* * *
3330987 AAAATTTATATTAGAAAATT
1 AAAATATATATTAAAAAATA
3331007 AAAATATATATTA
1 AAAATATATATTA
3331020 TAACTAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
AAAATATATATTAAAAAATA
Found at i:3334430 original size:8 final size:7
Alignment explanation
Indices: 3334402--3334429 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
3334392 CACCGAAATA
3334402 AAATTTT
1 AAATTTT
3334409 AAATTTT
1 AAATTTT
3334416 AAATTTT
1 AAATTTT
3334423 AAATTTT
1 AAATTTT
3334430 TATATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:3334685 original size:24 final size:24
Alignment explanation
Indices: 3334658--3334704 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3334648 TATATTTTAA
*
3334658 ATATTTTATAATATT-AAAATAATT
1 ATATTTAAT-ATATTAAAAATAATT
*
3334682 ATATTTAATATTTTAAAAATAAT
1 ATATTTAATATATTAAAAATAAT
3334705 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTTAATATATTAAAAATAATT
Found at i:3334690 original size:21 final size:22
Alignment explanation
Indices: 3334649--3334749 Score: 94
Period size: 21 Copynumber: 5.0 Consensus size: 22
3334639 TAAAAATAAT
*
3334649 ATATTTTAAAT-ATT-T-TATA
1 ATATTTTAAATAATTATATTTA
*
3334668 ATA-TTAAAATAATTATATTTA
1 ATATTTTAAATAATTATATTTA
*
3334689 ATATTTTAAA-AATAATATTTA
1 ATATTTTAAATAATTATATTTA
3334710 A-ATTTTAAAT-ATATATATTTA
1 ATATTTTAAATAAT-TATATTTA
*
3334731 AAATTTTAAAT-A-TATATTT
1 ATATTTTAAATAATTATATTT
3334750 TAAATTTAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
18 6 0.09
19 6 0.09
20 18 0.26
21 25 0.36
22 15 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTAAATAATTATATTTA
Found at i:3334692 original size:42 final size:41
Alignment explanation
Indices: 3334645--3334769 Score: 109
Period size: 42 Copynumber: 3.0 Consensus size: 41
3334635 TCTTTAAAAA
3334645 TAATATATTTTAAATAT-TTTATAATATTAAAATA-ATTATATT
1 TAATATATTTTAAATATATTTA-AAT-TTAAAATATA-TATATT
* *
3334687 TAATAT-TTTAAAAATAATATTTAAATTTTAAATATATATATT
1 TAATATATTT-TAAAT-ATATTTAAATTTAAAATATATATATT
*
3334729 TAA-A-ATTTTAAATATATATTTTAAATTTAAAAAATA-ATATT
1 TAATATATTTT-AA-ATATA-TTTAAATTTAAAATATATATATT
3334770 ATAAACCATT
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
41 17 0.24
42 43 0.61
43 6 0.09
44 4 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (41 bp):
TAATATATTTTAAATATATTTAAATTTAAAATATATATATT
Found at i:3334751 original size:21 final size:22
Alignment explanation
Indices: 3334681--3334774 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 22
3334671 TTAAAATAAT
* *
3334681 TATATTTAATATTTTAAAAATA
1 TATATTTAAAATTTTAAATATA
3334703 -ATATTT-AAATTTTAAATATA
1 TATATTTAAAATTTTAAATATA
3334723 TATATTTAAAATTTTAAATATA
1 TATATTTAAAATTTTAAATATA
* *
3334745 TAT-TTT-AAATTTAAAAAATA
1 TATATTTAAAATTTTAAATATA
3334765 -ATATTATAAA
1 TATATT-TAAA
3334775 CCATTCAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.03
20 26 0.41
21 16 0.25
22 19 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTTAAAATTTTAAATATA
Found at i:3336578 original size:2 final size:2
Alignment explanation
Indices: 3336571--3336605 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3336561 NNNNNTAATA
3336571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3336606 CTCCAAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3337115 original size:27 final size:28
Alignment explanation
Indices: 3337057--3337137 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 28
3337047 AAAAAATCAT
*
3337057 TTAAAAACTAATCTGTAAACATATAAAA
1 TTAAAAACTAATCTATAAACATATAAAA
* * *
3337085 -TAAAACCTAATC-ATAAACTTTTAAAA
1 TTAAAAACTAATCTATAAACATATAAAA
* *
3337111 TT-AAAAGTAAT-TATTAAAAATATAAAA
1 TTAAAAACTAATCTA-TAAACATATAAAA
3337138 ATTATTCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
26 19 0.46
27 22 0.54
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (28 bp):
TTAAAAACTAATCTATAAACATATAAAA
Found at i:3340373 original size:29 final size:29
Alignment explanation
Indices: 3340341--3340421 Score: 153
Period size: 29 Copynumber: 2.8 Consensus size: 29
3340331 TTTCTCTTAG
*
3340341 GTTACATTTTAGTCATTTATGTTTGCAAT
1 GTTACATTTTAGTCATTTATGTTTGAAAT
3340370 GTTACATTTTAGTCATTTATGTTTGAAAT
1 GTTACATTTTAGTCATTTATGTTTGAAAT
3340399 GTTACATTTTAGTCATTTATGTT
1 GTTACATTTTAGTCATTTATGTT
3340422 AATGTGTTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.53
Consensus pattern (29 bp):
GTTACATTTTAGTCATTTATGTTTGAAAT
Found at i:3341607 original size:13 final size:13
Alignment explanation
Indices: 3341591--3341630 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3341581 TTTAAACCAA
3341591 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
3341604 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
3341617 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
3341630 A
1 A
3341631 TTGCAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 5 0.22
13 13 0.57
14 5 0.22
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3341922 original size:16 final size:16
Alignment explanation
Indices: 3341901--3341952 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
3341891 TTTGGTTCGC
3341901 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3341917 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
3341933 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
3341949 TGTA
1 TGTA
3341953 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3342408 original size:16 final size:17
Alignment explanation
Indices: 3342387--3342424 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3342377 NNNNNNNNAT
*
3342387 AATATAATTATTATT-A
1 AATATAATTATAATTAA
3342403 AATAT-ATTATAATTAA
1 AATATAATTATAATTAA
3342419 AATATA
1 AATATA
3342425 TAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAATTATAATTAA
Found at i:3342432 original size:14 final size:15
Alignment explanation
Indices: 3342387--3342434 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3342377 NNNNNNNNAT
*
3342387 AATATAATTATTATTA
1 AATAT-ATTATAATTA
3342403 AATATATTATAATTA
1 AATATATTATAATTA
*
3342418 AA-ATA-TATAATTT
1 AATATATTATAATTA
3342431 AATA
1 AATA
3342435 AAATTCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 9 0.31
14 4 0.14
15 11 0.38
16 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATTATAATTA
Found at i:3345685 original size:20 final size:20
Alignment explanation
Indices: 3345660--3345697 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3345650 AAGAAACAGA
*
3345660 TGGAGCAAATTGGCAGAAAC
1 TGGAGCAAATCGGCAGAAAC
3345680 TGGAGCAAATCGGCAGAA
1 TGGAGCAAATCGGCAGAA
3345698 GCAAAAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.32, T:0.13
Consensus pattern (20 bp):
TGGAGCAAATCGGCAGAAAC
Found at i:3363540 original size:18 final size:16
Alignment explanation
Indices: 3363517--3363551 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
3363507 GTTTAAAATT
3363517 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
3363535 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
3363551 T
1 T
3363552 CCTCATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:3378828 original size:34 final size:34
Alignment explanation
Indices: 3378785--3378857 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
3378775 CCATGATTGA
3378785 AATTATGTCTAGAAGCATTATTCCGATAATTCAC
1 AATTATGTCTAGAAGCATTATTCCGATAATTCAC
3378819 AATTATGTCTAGAAGCATTATTCCGATAATTCAC
1 AATTATGTCTAGAAGCATTATTCCGATAATTCAC
3378853 AATTA
1 AATTA
3378858 CTTAATCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (34 bp):
AATTATGTCTAGAAGCATTATTCCGATAATTCAC
Found at i:3382699 original size:3 final size:3
Alignment explanation
Indices: 3382691--3382729 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3382681 AGAATATATT
3382691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3382730 GAATTTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3386377 original size:124 final size:126
Alignment explanation
Indices: 3386155--3386431 Score: 470
Period size: 124 Copynumber: 2.2 Consensus size: 126
3386145 CCACGAGGGC
* *
3386155 GCGATTTTATACTATTTGCTTAGAAACGTCAAAAAAAATTTTATTTCTTACATGACCAACTATAG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATGTTATTTCTTACATGACCAACTATAG
* *
3386220 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGTTAGAA
66 CGAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* *
3386281 GCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAA-GTTATTTCTTACATGACTAACTGTAG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATGTTATTTCTTACATGACCAACTATAG
3386344 CGAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
66 CGAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
3386405 GCGATTTTATACTATTTGAC-CAGAAAC
1 GCGATTTTATACTATTTG-CTCAGAAAC
3386432 ACCAACTCGA
Statistics
Matches: 144, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
124 107 0.74
125 8 0.06
126 29 0.20
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (126 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATGTTATTTCTTACATGACCAACTATAG
CGAAATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:3392571 original size:24 final size:24
Alignment explanation
Indices: 3392543--3392594 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3392533 TTTCTAGACG
* *
3392543 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
3392567 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
3392591 ATTT
1 ATTT
3392595 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:3397199 original size:33 final size:34
Alignment explanation
Indices: 3397162--3397234 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
3397152 ATGTATACTT
* *
3397162 AAATAACATTAAGATAGCT-AC-AAATTAACAATC
1 AAATAACATTAAAATAG-TAACAAAATTAACAATA
* *
3397195 AAATACCTTTAAAATAGTAACAAAATTAACAATA
1 AAATAACATTAAAATAGTAACAAAATTAACAATA
3397229 AAATAA
1 AAATAA
3397235 GATTTATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 1 0.03
33 16 0.48
34 16 0.48
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (34 bp):
AAATAACATTAAAATAGTAACAAAATTAACAATA
Found at i:3400788 original size:22 final size:22
Alignment explanation
Indices: 3400726--3400811 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
3400716 ATTGTTCAAA
* **
3400726 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
3400748 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
3400770 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
3400792 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
3400812 CACAAGGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:3404931 original size:13 final size:13
Alignment explanation
Indices: 3404910--3404940 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3404900 TGACACCTAA
3404910 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
*
3404923 TTTTTTTTTTCTT
1 TTTTCTTTTTCTT
3404936 TTTTC
1 TTTTC
3404941 CCTTAAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:3418472 original size:21 final size:21
Alignment explanation
Indices: 3418430--3418472 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3418420 TGTAATCTTT
*
3418430 ACAGAGAACAAAGGAATACAA
1 ACAGAGAACAAAGCAATACAA
*
3418451 ACAGAGAACGAAATCAAT-CAA
1 ACAGAGAAC-AAAGCAATACAA
3418472 A
1 A
3418473 GTATCAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.16, G:0.16, T:0.07
Consensus pattern (21 bp):
ACAGAGAACAAAGCAATACAA
Found at i:3429361 original size:17 final size:18
Alignment explanation
Indices: 3429328--3429373 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
3429318 TATACATTCT
3429328 TTTTAATTATATAT-AAA
1 TTTTAATTATATATAAAA
*
3429345 TTTTAATTCA-ATGTAAAA
1 TTTTAATT-ATATATAAAA
3429363 TTTTACATTAT
1 TTTTA-ATTAT
3429374 CGAGGAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 11 0.46
18 10 0.42
19 3 0.12
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTAATTATATATAAAA
Found at i:3431149 original size:75 final size:75
Alignment explanation
Indices: 3431023--3431178 Score: 258
Period size: 75 Copynumber: 2.1 Consensus size: 75
3431013 CCTTTAAGGG
* * *
3431023 CATGAATCCGAATCCCGCTAAGGCAAAAATGATAAAACATTTCCCTGGAGGACCTTAGGTGCTCC
1 CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
* *
3431088 CGATAAACTC
66 CAAGAAACTC
*
3431098 CATGAATCTGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
1 CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
3431163 CAAGAAACTC
66 CAAGAAACTC
3431173 CATGAA
1 CATGAA
3431179 CCCCTTTGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (75 bp):
CATGAATCCGAATCCCACTAAGGCAAAAATGATAAAACATTTCCCTAGAGGACCTTAGGCGCTCC
CAAGAAACTC
Found at i:3431486 original size:16 final size:16
Alignment explanation
Indices: 3431465--3431530 Score: 123
Period size: 16 Copynumber: 4.1 Consensus size: 16
3431455 TGGTTCGCTA
3431465 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
*
3431481 TATTGGATTAAAGGTG
1 TATTGGATTAGAGGTG
3431497 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
3431513 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
3431529 TA
1 TA
3431531 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TATTGGATTAGAGGTG
Found at i:3431783 original size:16 final size:16
Alignment explanation
Indices: 3431746--3431787 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3431736 TTAATCATAT
*
3431746 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3431762 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3431777 TTAAAATATAT
1 TTAAAATATAT
3431788 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3431794 original size:14 final size:15
Alignment explanation
Indices: 3431755--3431801 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3431745 TTTAAACATA
*
3431755 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3431770 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
* *
3431784 A-TATAATTTAATAA
1 ATTATAATTAAATAT
3431798 ATTA
1 ATTA
3431802 CTTATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 9 0.33
14 5 0.19
15 13 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3439734 original size:30 final size:32
Alignment explanation
Indices: 3439676--3439752 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 32
3439666 AAAAATTTAG
3439676 AAAATATATATAAAAACATAAATATTTATAAA
1 AAAATATATATAAAAACATAAATATTTATAAA
** **
3439708 AAAATATA-ATAAAAATTTAAAT-TTTATATT
1 AAAATATATATAAAAACATAAATATTTATAAA
*
3439738 AATAT-TATATAAAAA
1 AAAATATATATAAAAA
3439753 AATCCCCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 2 0.05
30 17 0.44
31 12 0.31
32 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
AAAATATATATAAAAACATAAATATTTATAAA
Found at i:3441098 original size:9 final size:9
Alignment explanation
Indices: 3441071--3441107 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3441061 TGAGTTTTCG
3441071 AATTCGAAT
1 AATTCGAAT
* *
3441080 AACTCAAAT
1 AATTCGAAT
3441089 AATTCGAAT
1 AATTCGAAT
3441098 AATTCGAAT
1 AATTCGAAT
3441107 A
1 A
3441108 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3441377 original size:30 final size:31
Alignment explanation
Indices: 3441329--3441388 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3441319 AAACCTTTTA
*
3441329 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* * *
3441359 TTTTCTCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
3441389 TCCCACCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:3447852 original size:12 final size:12
Alignment explanation
Indices: 3447818--3447852 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3447808 CGGACAGTAT
3447818 TAATTTTTTATA
1 TAATTTTTTATA
*
3447830 TTATTTGTTTATA
1 TAATTT-TTTATA
3447843 TAATTTTTTA
1 TAATTTTTTA
3447853 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:3447894 original size:8 final size:9
Alignment explanation
Indices: 3447868--3447892 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3447858 TATATAATAC
3447868 ATTAAAAAT
1 ATTAAAAAT
3447877 ATTAAAAAT
1 ATTAAAAAT
3447886 ATTAAAA
1 ATTAAAA
3447893 TAAATATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:3448015 original size:19 final size:17
Alignment explanation
Indices: 3447981--3448016 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
3447971 CTAAAATAGT
3447981 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
3447998 AACAAGAATTATACAATAA
1 AACAA-AATTA-ACAATAA
3448017 CAATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:3451725 original size:24 final size:24
Alignment explanation
Indices: 3451656--3451726 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
3451646 ATTTGGGAAT
* *
3451656 GGTGGAGGATATGGCGACGGTGAC
1 GGTGGTGGATATGGCGACGGTGGC
* *
3451680 GGAGGTGGATATGGCGGCGGTGGC
1 GGTGGTGGATATGGCGACGGTGGC
* *
3451704 GGTGGTGGATATGGTGATGGTGG
1 GGTGGTGGATATGGCGACGGTGG
3451727 GTCTCGTTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.15, C:0.08, G:0.55, T:0.21
Consensus pattern (24 bp):
GGTGGTGGATATGGCGACGGTGGC
Found at i:3454222 original size:72 final size:75
Alignment explanation
Indices: 3454146--3454293 Score: 212
Period size: 76 Copynumber: 2.0 Consensus size: 75
3454136 TATTTTCTAA
* * *
3454146 TTTTTTATAGTTTTGCA-CT-TGT-TTAGAATGAAATGGACAAATGTATATCCAGATTCAAATAT
1 TTTTTTATAGTTTTACACCTATGTATTAGAATGAAATGAACAAATGTATATCCAGATCCAAATAT
3454208 TATTTAATAT
66 TATTTAATAT
* * *
3454218 TTTTTTATAGTTTTACACCTATTTAATTAGAATGAAATGAAGAAATGTGTATCCAGATCCAAATA
1 TTTTTTATAGTTTTACACCTATGT-ATTAGAATGAAATGAACAAATGTATATCCAGATCCAAATA
3454283 TTATTTAATAT
65 TTATTTAATAT
3454294 ATTTGTATCT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
72 16 0.24
73 2 0.03
74 2 0.03
76 46 0.70
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (75 bp):
TTTTTTATAGTTTTACACCTATGTATTAGAATGAAATGAACAAATGTATATCCAGATCCAAATAT
TATTTAATAT
Found at i:3456851 original size:19 final size:17
Alignment explanation
Indices: 3456817--3456856 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
3456807 AATAAACAAA
*
3456817 AAAATAAATAAATAAAT
1 AAAATAAAGAAATAAAT
3456834 AAAATAGAAGAAAGTAAAT
1 AAAATA-AAGAAA-TAAAT
3456853 AAAA
1 AAAA
3456857 AACGCAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
AAAATAAAGAAATAAAT
Found at i:3457701 original size:44 final size:44
Alignment explanation
Indices: 3457653--3458417 Score: 374
Period size: 44 Copynumber: 17.8 Consensus size: 44
3457643 ATGTGGTTTT
* * * *
3457653 AATCTGCTCCGCTGCAA-CTTTAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * *
3457697 AATCTACTCTGCTATAATCTCAGGGAGATAAGATTACTATCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * *
3457741 AATCTGTTCTGCTGTAATCTCAGGGAGATAAGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * * *
3457785 GATCTGCTCCGCTGTAATCTCAGGGAGATAAAATCTGCAATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACTA-TCTTC
** * * *
3457831 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TAC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* ** ** *
3457872 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C-AT-TT-
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * * * * *
3457911 AATCCGTTCCACTATAATCTCAAGGAGATAGGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * * *
3457955 GATCTGTTCCGCTGTAATCTCTGGGAGATAAGATCT-GTAATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACT-A-TCTTC
** * * * *
3458001 GGTCTGCTCCACTGTAATCTCAAGGAGATAAGA--CCTGA--TAC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* * ** * *
3458042 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * * *
3458081 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTT
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * *
3458125 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACTA-TCTTC
** * * *
3458171 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TAC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* ** ** * *
3458212 GATCCACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCGCTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * * * *
3458251 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATATTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
* **
3458295 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * * *
3458339 AATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGA-TATTTTTC
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** * *
3458385 GGTCTACTCCACTGTAATCTCAGGGAGATAAGA
1 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
3458418 CCTGTATAAT
Statistics
Matches: 562, Mismatches: 117, Indels: 82
0.74 0.15 0.11
Matches are distributed among these distances:
39 75 0.13
40 10 0.02
41 90 0.16
42 2 0.00
43 4 0.01
44 238 0.42
45 11 0.02
46 132 0.23
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
Found at i:3457745 original size:88 final size:88
Alignment explanation
Indices: 3457653--3458417 Score: 242
Period size: 90 Copynumber: 8.9 Consensus size: 88
3457643 ATGTGGTTTT
* * *
3457653 AATCTGCTCCGCTGCAA-CTTTAGGGAGATAGGATTACTAGCTTCAATCTACTCTGCTATAATCT
1 AATCTGCTCCGCTGCAATC-TCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCT
3457717 CAGGGAGATAAGATTACTATCTTC
65 CAGGGAGATAAGATTACTATCTTC
* * * * ** * *
3457741 AATCTGTTCTGCTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTCCGCTGTAATCTC
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTC
* * *
3457806 AGGGAGATAAAATCTGCAATTCTTC
66 AGGGAGATAAGAT-TACTA-TCTTC
** * * * * * * * ** *
3457831 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATACGATCCACTCTACTGTAA-CTT
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATC-T
*
3457892 CAGAGAGATAAGA-T-C-AT-TT-
65 CAGGGAGATAAGATTACTATCTTC
* * * ** * * * ** ** *
3457911 AATCCGTTCCACTATAATCTCAAGGAGATAGGATTACTATCTTTGATCTGTTCCGCTGTAATCTC
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTC
* *
3457976 TGGGAGATAAGATCT-GTAATTCTTC
66 AGGGAGATAAGAT-TACT-A-TCTTC
** * * * * * * * ** *
3458001 GGTCTGCTCCACTGTAATCTCAAGGAGATAAGA--CCT-GATACGATCTACTCTACTGTAA-CTT
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATC-T
* *
3458062 CAGAGAGATAAGA-T-C---CTTT
65 CAGGGAGATAAGATTACTATCTTC
* * * * * * ** * *
3458081 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTC
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTC
* *
3458146 AGGGAGATAAGATCTGCAATTCTTC
66 AGGGAGATAAGAT-TACTA-TCTTC
** * * * * * * * ** *
3458171 GGTCTGCTCCACTGTAATCTCAGGGAGATAAGA--CCT-GATACGATCCACTCTACTGTAA-CTT
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATC-T
* *
3458232 CAGAGAGATAAGA-T-C---CTTT
65 CAGGGAGATAAGATTACTATCTTC
* * * * * ** * * *
3458251 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTATATTCGATCTGCTCCGCTGTAATCTC
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTC
**
3458316 AGGGAGATAAGATCT-CTGGCTTC
66 AGGGAGATAAGAT-TACTATCTTC
* * * * ** ** * *
3458339 AATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGA-TATTTTTCGGTCTACTCCACTGTAAT
1 AATCTGCTCCGCTGCAATCTCAGGGAGATAAGAT-T-ACTA-GCTTCAATCTACTCCGCTATAAT
3458403 CTCAGGGAGATAAGA
63 CTCAGGGAGATAAGA
3458418 CCTGTATAAT
Statistics
Matches: 517, Mismatches: 120, Indels: 78
0.72 0.17 0.11
Matches are distributed among these distances:
80 89 0.17
81 2 0.00
82 7 0.01
83 83 0.16
84 5 0.01
85 7 0.01
86 4 0.01
87 80 0.15
88 105 0.20
89 9 0.02
90 126 0.24
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (88 bp):
AATCTGCTCCGCTGCAATCTCAGGGAGATAAGATTACTAGCTTCAATCTACTCCGCTATAATCTC
AGGGAGATAAGATTACTATCTTC
Found at i:3457948 original size:170 final size:170
Alignment explanation
Indices: 3457752--3458378 Score: 1053
Period size: 170 Copynumber: 3.7 Consensus size: 170
3457742 ATCTGTTCTG
* * *
3457752 CTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAA
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
*
3457817 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
66 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCT
* *
3457882 ACTGTAACTTCAGAGAGATAAGATCATTTAATCCGTTCCA
131 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
* * *
3457922 CTATAATCTCAAGGAGATAGGATTACTATCTTTGATCTGTTCCGCTGTAATCTCTGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* *
3457987 ATCTGTAATTCTTCGGTCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCTACTCT
66 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCT
3458052 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
131 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
3458092 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
*
3458157 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGATAAGACCTGATACGATCCACTCT
66 ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCT
3458222 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
131 ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
* *
3458262 CTGTAATCTCAAGGAGATAGGATTACTATATTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
1 CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
* ** * *
3458327 ATCT-C--TGGCTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGATCTGATA
66 ATCTGCAAT-TCTTCGGTCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATA
3458379 TTTTTCGGTC
Statistics
Matches: 431, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
167 1 0.00
168 39 0.09
169 1 0.00
170 390 0.90
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (170 bp):
CTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAG
ATCTGCAATTCTTCGGTCTGCTCCACTGTAATCTCAAGGAGATAAGACCTGATACGATCCACTCT
ACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCA
Found at i:3466486 original size:17 final size:18
Alignment explanation
Indices: 3466454--3466490 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
3466444 TCTGCACAGT
3466454 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
3466472 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
3466489 AT
1 AT
3466491 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:3470973 original size:25 final size:20
Alignment explanation
Indices: 3470925--3470962 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3470915 AAAAAGTTAT
3470925 AGAAAATAAACAAAAAAGGA
1 AGAAAATAAACAAAAAAGGA
3470945 AGAAAATAAACAAAAAAG
1 AGAAAATAAACAAAAAAG
3470963 AAACGCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (20 bp):
AGAAAATAAACAAAAAAGGA
Found at i:3472434 original size:21 final size:20
Alignment explanation
Indices: 3472386--3472446 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
3472376 GAACCCCAAA
* *
3472386 CCTAAACCCTAAATGTTGAAT
1 CCTAAACCCTAAATCTTG-AG
*
3472407 CCCAAACCCTAAATCTTGAG
1 CCTAAACCCTAAATCTTGAG
*
3472427 CCTTAAACCTTAAATCTTGA
1 CC-TAAACCCTAAATCTTGA
3472447 ACTTAAATCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (20 bp):
CCTAAACCCTAAATCTTGAG
Found at i:3475470 original size:19 final size:21
Alignment explanation
Indices: 3475442--3475490 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
3475432 GGATTTTTAC
*
3475442 TAAAATAATA-CAAAAGAA-A
1 TAAAAAAATACCAAAAGAATA
*
3475461 TAAAAAAATACCAAAATAATA
1 TAAAAAAATACCAAAAGAATA
3475482 TATAAAAAA
1 TA-AAAAAA
3475491 ATTATTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 7 0.28
21 3 0.12
22 6 0.24
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAAATACCAAAAGAATA
Found at i:3481649 original size:16 final size:16
Alignment explanation
Indices: 3481625--3481663 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3481615 TAGATGTATT
3481625 CATTAGAAAAATGATA
1 CATTAGAAAAATGATA
*
3481641 CATTGGAAAAATGATA
1 CATTAGAAAAATGATA
*
3481657 AATTAGA
1 CATTAGA
3481664 CTGGACCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (16 bp):
CATTAGAAAAATGATA
Found at i:3481803 original size:51 final size:51
Alignment explanation
Indices: 3481748--3481850 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
3481738 TAAATCCTGA
3481748 GTTAGTCATTAACCATGCATATGTAACTCATGTGCTTTTATATAAGTGGAG
1 GTTAGTCATTAACCATGCATATGTAACTCATGTGCTTTTATATAAGTGGAG
*
3481799 GTTAGTCATTAACTATGCATATGTAACTCATGTGCTTTTATATAAGTGGAG
1 GTTAGTCATTAACCATGCATATGTAACTCATGTGCTTTTATATAAGTGGAG
3481850 G
1 G
3481851 CTTATGCTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (51 bp):
GTTAGTCATTAACCATGCATATGTAACTCATGTGCTTTTATATAAGTGGAG
Found at i:3483058 original size:25 final size:25
Alignment explanation
Indices: 3482984--3483070 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 25
3482974 ACAATATTAT
*
3482984 TTTTA-TAGATTTAATATTAAATTTA
1 TTTTATTA-ATTTAATATTAAAGTTA
* * * *
3483009 ATTTAAT-ACTT-ATCTTAATAG-TA
1 TTTTATTAATTTAATATTAA-AGTTA
3483032 TTTTATTAATTTAATATTAAAGTTA
1 TTTTATTAATTTAATATTAAAGTTA
* *
3483057 TTATATTAAATTAA
1 TTTTATTAATTTAA
3483071 ATTTAATATG
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
23 13 0.28
24 9 0.19
25 24 0.51
26 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
TTTTATTAATTTAATATTAAAGTTA
Found at i:3483074 original size:62 final size:63
Alignment explanation
Indices: 3482997--3483115 Score: 179
Period size: 62 Copynumber: 1.9 Consensus size: 63
3482987 TATAGATTTA
* * * *
3482997 ATATTAAATTTAATTTAATACT-TATCTTAAT-AGTATTTTATTAATTTAATATTAAAGTTATT
1 ATATTAAATTAAATTTAATA-TGGATCTTAATAAGTATTATATTAATTGAATATTAAAGTTATT
3483059 ATATTAAATTAAATTTAATATGGATCTTAATAAGTATTATATTAATTGAATATTAAA
1 ATATTAAATTAAATTTAATATGGATCTTAATAAGTATTATATTAATTGAATATTAAA
3483116 ATGATTAAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.53
63 23 0.45
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (63 bp):
ATATTAAATTAAATTTAATATGGATCTTAATAAGTATTATATTAATTGAATATTAAAGTTATT
Found at i:3484224 original size:43 final size:43
Alignment explanation
Indices: 3484134--3484395 Score: 219
Period size: 43 Copynumber: 6.1 Consensus size: 43
3484124 TTATGTGGAA
* * * *
3484134 AAACGCCAG-TATAGAACATGATC-TTTAGTGACG-TTTCTCACAA
1 AAACGCC-GCTATAGAACATGA-CATTTAGCGGCGCTTT-TCCCAC
* *
3484177 AAACGCCTCTATAGAACATGGCATTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACATTTAGCGGCGCTTTTCCCAC
* * * *
3484220 AAACGCTGTTATAGAACATGACCTCTAGCGGCGC-TTTCCCTAC
1 AAACGCCGCTATAGAACATGACATTTAGCGGCGCTTTTCCC-AC
* **
3484263 AAACGCCGCTATAGGACATGACATTTAGCGATG-TTTTCCCTAC
1 AAACGCCGCTATAGAACATGACATTTAGCGGCGCTTTTCCC-AC
** * * * * *
3484306 AAACGTAGCTAAAGAACATGACTTTTAGCAGCTCTTTTACCAC
1 AAACGCCGCTATAGAACATGACATTTAGCGGCGCTTTTCCCAC
* * ** *
3484349 AAATGCCGCTATAGAACATGACCTTTAATGGCGCTTTTCCCAA
1 AAACGCCGCTATAGAACATGACATTTAGCGGCGCTTTTCCCAC
3484392 AAAC
1 AAAC
3484396 ACCGTTAAAA
Statistics
Matches: 172, Mismatches: 41, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
42 7 0.04
43 156 0.91
44 9 0.05
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACATTTAGCGGCGCTTTTCCCAC
Found at i:3493068 original size:22 final size:22
Alignment explanation
Indices: 3493043--3493085 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
3493033 TAGCTTTTTC
3493043 TAAAA-TATATACTTTATTAATG
1 TAAAATTATATA-TTTATTAATG
3493065 TAAAATTTATATATTTATTAA
1 TAAAA-TTATATATTTATTAA
3493086 ATTTTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAATTATATATTTATTAATG
Found at i:3493870 original size:19 final size:18
Alignment explanation
Indices: 3493837--3493879 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3493827 AAGGATTATA
*
3493837 TAAAAGTTTTCAAAAAAT
1 TAAAATTTTTCAAAAAAT
* *
3493855 TATAAATTTTTTAAAATAT
1 TA-AAATTTTTCAAAAAAT
3493874 TAAAAT
1 TAAAAT
3493880 ATCTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAAATTTTTCAAAAAAT
Found at i:3493908 original size:21 final size:22
Alignment explanation
Indices: 3493870--3493910 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3493860 ATTTTTTAAA
* *
3493870 ATATTAAAATATCTTAAAATTT
1 ATATAAAAATAACTTAAAATTT
3493892 ATATAAAAATAAC-TAAAAT
1 ATATAAAAATAACTTAAAAT
3493911 GAAAAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATAAAAATAACTTAAAATTT
Found at i:3494381 original size:20 final size:17
Alignment explanation
Indices: 3494344--3494383 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
3494334 TTATTAAAAT
3494344 ATTATAAAAATTTGAAA
1 ATTATAAAAATTTGAAA
3494361 ATTATAGAAAATCTATGAAA
1 ATTATA-AAAAT-T-TGAAA
3494381 ATT
1 ATT
3494384 GTTAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 1 0.05
20 8 0.40
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (17 bp):
ATTATAAAAATTTGAAA
Found at i:3494470 original size:19 final size:20
Alignment explanation
Indices: 3494423--3494470 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3494413 AAAAAATAGT
*
3494423 AAATGTTATAAAATATTATTA
1 AAATGTTATAAAATA-TATGA
* *
3494444 ATATGTTATGAAATA-ATGA
1 AAATGTTATAAAATATATGA
3494463 AAATGTTA
1 AAATGTTA
3494471 AATAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.43
21 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATGTTATAAAATATATGA
Found at i:3494534 original size:20 final size:20
Alignment explanation
Indices: 3494501--3494538 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3494491 GAAATTATAG
* *
3494501 AAAATTATATAAAAATAATT
1 AAAATGATAAAAAAATAATT
3494521 AAAATGATAAAAAAATAA
1 AAAATGATAAAAAAATAA
3494539 AAAAAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAATGATAAAAAAATAATT
Found at i:3494544 original size:20 final size:20
Alignment explanation
Indices: 3494501--3494544 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3494491 GAAATTATAG
* * **
3494501 AAAATTATATAAAAATAATT
1 AAAATGATAAAAAAATAAAA
3494521 AAAATGATAAAAAAATAAAA
1 AAAATGATAAAAAAATAAAA
3494541 AAAA
1 AAAA
3494545 AAGTTATAAA
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:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATGATAAAAAAATAAAA
Found at i:3510245 original size:24 final size:23
Alignment explanation
Indices: 3510217--3510268 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
3510207 AGTATAACAT
3510217 TTTTTTTATAAATAAAAATATTAA
1 TTTTTTTATAAATAAAAATATT-A
*
3510241 TTTTTTTATAAATAACAATATTA
1 TTTTTTTATAAATAAAAATATTA
3510264 TTTTT
1 TTTTT
3510269 ATAATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTTTATAAATAAAAATATTA
Found at i:3510279 original size:24 final size:25
Alignment explanation
Indices: 3510219--3510281 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
3510209 TATAACATTT
3510219 TTTTTATAA-ATA-AA-AATATTAA
1 TTTTTATAATATATAACAATATTAA
* *
3510241 TTTTT-TTATAAATAACAATATT-A
1 TTTTTATAATATATAACAATATTAA
3510264 TTTTTATAATATATAACA
1 TTTTTATAATATATAACA
3510282 TTGATACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.06
22 7 0.21
23 8 0.24
24 16 0.48
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTTATAATATATAACAATATTAA
Found at i:3510962 original size:18 final size:20
Alignment explanation
Indices: 3510940--3510981 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3510930 CAATTCTTAA
3510940 AAATTTA-AAT-AAATATTT
1 AAATTTAGAATGAAATATTT
*
3510958 TAA-TTAGAATGAAATATTT
1 AAATTTAGAATGAAATATTT
3510977 AAATT
1 AAATT
3510982 AACTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.16
18 5 0.26
19 10 0.53
20 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
AAATTTAGAATGAAATATTT
Found at i:3512571 original size:15 final size:15
Alignment explanation
Indices: 3512531--3512578 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
3512521 CACTACTTAA
3512531 TATTTATAAAAGAAT
1 TATTTATAAAAGAAT
* * *
3512546 T-TCTACCAAAAAAAT
1 TATTTA-TAAAAGAAT
3512561 TATTTATAAAAGAAT
1 TATTTATAAAAGAAT
3512576 TAT
1 TAT
3512579 AATTACTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 3 0.12
15 19 0.76
16 3 0.12
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (15 bp):
TATTTATAAAAGAAT
Found at i:3514055 original size:19 final size:19
Alignment explanation
Indices: 3514027--3514063 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3514017 CGCATATTTG
3514027 ATTATCTAATTTAATTTTA
1 ATTATCTAATTTAATTTTA
* *
3514046 ATTATTTAATTTTATTTT
1 ATTATCTAATTTAATTTT
3514064 TGCATTTATA
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTATCTAATTTAATTTTA
Found at i:3516672 original size:2 final size:2
Alignment explanation
Indices: 3516661--3516707 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
3516651 CATTCCACTC
3516661 AT AT -T 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
3516702 AT AT AT
1 AT AT AT
3516708 CATCTCATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3535079 original size:26 final size:26
Alignment explanation
Indices: 3535043--3535093 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
3535033 GAGCCCATTC
3535043 CTATTTTTATTTTGTGGGAAAGGTCA
1 CTATTTTTATTTTGTGGGAAAGGTCA
3535069 CTATTTTTATTTTGTGGGAAAGGTC
1 CTATTTTTATTTTGTGGGAAAGGTC
3535094 TTTTTAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.47
Consensus pattern (26 bp):
CTATTTTTATTTTGTGGGAAAGGTCA
Found at i:3535638 original size:106 final size:106
Alignment explanation
Indices: 3535453--3535662 Score: 420
Period size: 106 Copynumber: 2.0 Consensus size: 106
3535443 TTTAAGTAAT
3535453 AAATCGATGACTAGAGTATAAGGCATCTTTCTCAAGGAGAGAAAGTGGTGTTCATAAAGGCTATT
1 AAATCGATGACTAGAGTATAAGGCATCTTTCTCAAGGAGAGAAAGTGGTGTTCATAAAGGCTATT
3535518 CTTCAATCCATCCCAACCTACATTATGGCTTGTTTCTTATA
66 CTTCAATCCATCCCAACCTACATTATGGCTTGTTTCTTATA
3535559 AAATCGATGACTAGAGTATAAGGCATCTTTCTCAAGGAGAGAAAGTGGTGTTCATAAAGGCTATT
1 AAATCGATGACTAGAGTATAAGGCATCTTTCTCAAGGAGAGAAAGTGGTGTTCATAAAGGCTATT
3535624 CTTCAATCCATCCCAACCTACATTATGGCTTGTTTCTTA
66 CTTCAATCCATCCCAACCTACATTATGGCTTGTTTCTTA
3535663 CTCTTTAAAT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (106 bp):
AAATCGATGACTAGAGTATAAGGCATCTTTCTCAAGGAGAGAAAGTGGTGTTCATAAAGGCTATT
CTTCAATCCATCCCAACCTACATTATGGCTTGTTTCTTATA
Found at i:3537111 original size:16 final size:16
Alignment explanation
Indices: 3537090--3537121 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3537080 GACAGATCGA
3537090 TTATTGGGGCACTCAT
1 TTATTGGGGCACTCAT
3537106 TTATTGGGGCACTCAT
1 TTATTGGGGCACTCAT
3537122 CAGAGATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
TTATTGGGGCACTCAT
Found at i:3544453 original size:13 final size:13
Alignment explanation
Indices: 3544435--3544460 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3544425 CATATTTGAT
3544435 TAAGTAAATATGG
1 TAAGTAAATATGG
3544448 TAAGTAAATATGG
1 TAAGTAAATATGG
3544461 AATGTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
TAAGTAAATATGG
Found at i:3544935 original size:50 final size:50
Alignment explanation
Indices: 3544725--3545157 Score: 489
Period size: 50 Copynumber: 8.7 Consensus size: 50
3544715 TATGTGATTT
* *
3544725 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAAAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * * **
3544775 CC-CGTAAGATCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * * * * * * **
3544824 CCATATAAGACCATATCTGGGATATGACATTGGCA--GTACAAGAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGGTC
3544873 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
3544923 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* *
3544973 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* **
3545023 CCATGTAAGACTATGTCTGGGACATGGTGTTGGCACC-AGGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GATGAGAGGTC
* * * * * * * **
3545073 CTC-CGTAAGACCATGTCTAGGACATGGCATGGGCATCAATATGGGAACTC
1 C-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
* * *
3545123 CCATGTAAGACCATATCTGGGATATGACATTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
3545158 GTACAGGAAA
Statistics
Matches: 322, Mismatches: 53, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.00
49 80 0.25
50 238 0.74
51 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTC
Found at i:3545087 original size:150 final size:148
Alignment explanation
Indices: 3544725--3545205 Score: 628
Period size: 150 Copynumber: 3.2 Consensus size: 148
3544715 TATGTGATTT
* *
3544725 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAAAGGTCCCCGTAAGATCATGT
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCGTAAGACCATGT
* * *
3544790 TTGGGACATGGCATGGGCACCGATATGAGAACTCCCATATAAGACCATATCTGGGATATGACATT
66 CTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGACATGACATT
3544855 GGCAGTACAAGAAACATC
131 GGCAGTACAAGAAACATC
* *
3544873 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATG
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC-CGTAAGACCATG
* * ** * * *
3544938 TCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGT
65 TCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGACATGACAT
* * *
3545003 TGGCACCG-AGATGAGAA-GTC
130 TGGCA--GTACAAGA-AACATC
* *
3545023 CCATGTAAGACTATGTCTGGGACATGGTGTTGGCACC-AGGATGAGAGGTCCTCCGTAAGACCAT
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATGAGAGGTCC-CCGTAAGACCAT
* * * * *
3545087 GTCTAGGACATGGCATGGGCATCAATATGGGAACTCCCATGTAAGACCATATCTGGGATATGACA
64 GTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGACATGACA
*
3545152 TTGGCAGTACAGGAAACATC
129 TTGGCAGTACAAGAAACATC
* * *
3545172 TCAT-TAAGACCATGTGTGGGACATGGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
3545206 TGTTATTATC
Statistics
Matches: 284, Mismatches: 41, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
148 79 0.28
149 80 0.28
150 121 0.43
151 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (148 bp):
CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCGTAAGACCATGT
CTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGTAAGACCATATCTGGGACATGACATT
GGCAGTACAAGAAACATC
Found at i:3546722 original size:23 final size:23
Alignment explanation
Indices: 3546684--3546734 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3546674 GGGAGAGAAA
* *
3546684 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
3546707 TGTAATACCCCAAAAATTACTAC
1 TGTAATACCCCAAAAATTACTAC
*
3546730 AGTAA
1 TGTAA
3546735 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCAAAAATTACTAC
Found at i:3548551 original size:102 final size:102
Alignment explanation
Indices: 3548322--3548687 Score: 538
Period size: 103 Copynumber: 3.6 Consensus size: 102
3548312 TTGCATATAA
** * * *
3548322 AGGGGTTGCTGTGTGTTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
3548387 TAAATGTGGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGT-GAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
3548425 AGGGGTTGCTAAGTGCTGATTCCCCTAC-CTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCCGACTC-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
3548489 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
* * * *
3548527 ATGGGTTGCTAAGTGCTGATTCCCCGACCCATTTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGACTCA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
* *
3548592 TGAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCA
65 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
** * * *
3548630 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGG-TGCTAAGTGCGGAATCCACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACC
3548688 AACAACGGTT
Statistics
Matches: 243, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
101 18 0.07
102 65 0.27
103 160 0.66
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3551870 original size:2 final size:2
Alignment explanation
Indices: 3551865--3551932 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
3551855 ACACACACGC
3551865 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
3551907 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
3551933 TCAAATAGCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3554420 original size:9 final size:9
Alignment explanation
Indices: 3554398--3554433 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
3554388 CTTCCTTTAT
3554398 AATGCCTAGC
1 AATG-CTAGC
*
3554408 AATGCTGGC
1 AATGCTAGC
3554417 AATGCTAGC
1 AATGCTAGC
3554426 AATGCTAG
1 AATGCTAG
3554434 AAATTCACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (9 bp):
AATGCTAGC
Found at i:3555543 original size:29 final size:30
Alignment explanation
Indices: 3555503--3555568 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
3555493 ACATATTGTA
**
3555503 TTTAGGGATTGCTCACATATGGGTCAAA-T
1 TTTAGGGATTGCTCACATAAAGGTCAAATT
*
3555532 TTTAGGGATTGCTCCCATAAAGGTCAAATT
1 TTTAGGGATTGCTCACATAAAGGTCAAATT
3555562 TTTAGGG
1 TTTAGGG
3555569 CCCAACCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (30 bp):
TTTAGGGATTGCTCACATAAAGGTCAAATT
Found at i:3556235 original size:6 final size:7
Alignment explanation
Indices: 3556205--3556233 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3556195 TTATTCATTT
3556205 AATAAAA
1 AATAAAA
3556212 AATAAAA
1 AATAAAA
3556219 AATAAAA
1 AATAAAA
3556226 AATAAAA
1 AATAAAA
3556233 A
1 A
3556234 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AATAAAA
Found at i:3568397 original size:18 final size:18
Alignment explanation
Indices: 3568374--3568409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3568364 AGTAAGTAAT
* *
3568374 GTGTTTTTGATGTATTTA
1 GTGTTTTTCATGCATTTA
3568392 GTGTTTTTCATGCATTTA
1 GTGTTTTTCATGCATTTA
3568410 ATTTCAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.19, T:0.58
Consensus pattern (18 bp):
GTGTTTTTCATGCATTTA
Found at i:3570382 original size:17 final size:17
Alignment explanation
Indices: 3570342--3570374 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3570332 TGAGTTGAGA
3570342 AAATT-ATTTAATTAAT
1 AAATTAATTTAATTAAT
*
3570358 AAATTAATTTAGTTAAT
1 AAATTAATTTAATTAAT
3570375 TATTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
AAATTAATTTAATTAAT
Found at i:3570387 original size:21 final size:21
Alignment explanation
Indices: 3570349--3570396 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
3570339 AGAAAATTAT
* *
3570349 TTAATTAATAAATTAATTTAG
1 TTAATTAATAAATCAATTAAG
* * *
3570370 TTAATTATTTAATCAATTAAT
1 TTAATTAATAAATCAATTAAG
3570391 TTAATT
1 TTAATT
3570397 GATTAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATTAATAAATCAATTAAG
Found at i:3570401 original size:13 final size:13
Alignment explanation
Indices: 3570343--3570402 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
3570333 GAGTTGAGAA
*
3570343 AATTATTTAA-TT
1 AATTAATTAATTT
*
3570355 AATAAATTAATTT
1 AATTAATTAATTT
*
3570368 AGTTAATT-ATTT
1 AATTAATTAATTT
*
3570380 AATCAATTAATTT
1 AATTAATTAATTT
*
3570393 AATTGATTAA
1 AATTAATTAA
3570403 ATAAACAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
12 18 0.47
13 20 0.53
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:3570401 original size:25 final size:25
Alignment explanation
Indices: 3570343--3570401 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
3570333 GAGTTGAGAA
* *
3570343 AATTATTTAATTAATAAATTAATTT
1 AATTAATTATTTAATAAATTAATTT
* *
3570368 AGTTAATTATTTAATCAATTAATTT
1 AATTAATTATTTAATAAATTAATTT
*
3570393 AATTGATTA
1 AATTAATTA
3570402 AATAAACAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (25 bp):
AATTAATTATTTAATAAATTAATTT
Found at i:3575942 original size:23 final size:25
Alignment explanation
Indices: 3575912--3575959 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3575902 ACTTTAGTGC
3575912 TTAAAGTG-AACA-ACACTTCGATG
1 TTAAAGTGTAACATACACTTCGATG
*
3575935 TTAAAGTGTAACATGCACTTCGATG
1 TTAAAGTGTAACATACACTTCGATG
3575960 CTTTAGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.36
24 4 0.18
25 10 0.45
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (25 bp):
TTAAAGTGTAACATACACTTCGATG
Found at i:3576031 original size:16 final size:16
Alignment explanation
Indices: 3576010--3576082 Score: 74
Period size: 16 Copynumber: 4.6 Consensus size: 16
3576000 TACTAAGGGC
**
3576010 TAAGTGAAGCAAGTGG
1 TAAGTGAAATAAGTGG
**
3576026 TAAGTGAAATAAGTTC
1 TAAGTGAAATAAGTGG
* *
3576042 TAAGTTAAATAAATGG
1 TAAGTGAAATAAGTGG
**
3576058 TAAGTGATGTAAGTGG
1 TAAGTGAAATAAGTGG
3576074 TAAGTGAAA
1 TAAGTGAAA
3576083 ATTTTATGTT
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.42, C:0.03, G:0.27, T:0.27
Consensus pattern (16 bp):
TAAGTGAAATAAGTGG
Found at i:3577449 original size:26 final size:26
Alignment explanation
Indices: 3577433--3577485 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3577423 AGATAAATAT
3577433 TAGTTAGTACAAATTTAAATAAAGAA
1 TAGTTAGTACAAATTTAAATAAAGAA
3577459 TAGTTAGTACAAATTTAAATAAAGAA
1 TAGTTAGTACAAATTTAAATAAAGAA
3577485 T
1 T
3577486 CATGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (26 bp):
TAGTTAGTACAAATTTAAATAAAGAA
Found at i:3577451 original size:22 final size:22
Alignment explanation
Indices: 3577426--3577480 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 22
3577416 TGTTTTTAGA
*
3577426 TAAATATTAGTTAGTACAAATT
1 TAAATAATAGTTAGTACAAATT
3577448 TAAATAAAGAATAGTTAGTACAAATT
1 TAAAT----AATAGTTAGTACAAATT
3577474 TAAATAA
1 TAAATAA
3577481 AGAATCATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
22 7 0.25
26 21 0.75
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (22 bp):
TAAATAATAGTTAGTACAAATT
Found at i:3587598 original size:14 final size:14
Alignment explanation
Indices: 3587576--3587607 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3587566 ATCCGGTACG
*
3587576 CATAGTAGCCTGCA
1 CATAATAGCCTGCA
3587590 CATAATAGCCTGCA
1 CATAATAGCCTGCA
3587604 CATA
1 CATA
3587608 GTACTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (14 bp):
CATAATAGCCTGCA
Found at i:3587635 original size:65 final size:65
Alignment explanation
Indices: 3587523--3587658 Score: 166
Period size: 65 Copynumber: 2.1 Consensus size: 65
3587513 ATACCTAGTT
* * * * * *
3587523 CACATAGTAGCTTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCATAGTAGCCTG
1 CACATAATAGCCTGCACATAGTACTACACACGTGATCCAAACTATCCGATACACATACTAGCCTG
*** *
3587588 CACATAATAGCCTGCACATAGTACTACACACGTGA-CCATTTTCATCCGATACACGTACTAGCCT
1 CACATAATAGCCTGCACATAGTACTACACACGTGATCCAAACT-ATCCGATACACATACTAGCCT
3587652 G
65 G
3587653 CACATA
1 CACATA
3587659 GTACTACACA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 3 0.05
65 57 0.95
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (65 bp):
CACATAATAGCCTGCACATAGTACTACACACGTGATCCAAACTATCCGATACACATACTAGCCTG
Found at i:3587671 original size:51 final size:50
Alignment explanation
Indices: 3587595--3587776 Score: 197
Period size: 51 Copynumber: 3.6 Consensus size: 50
3587585 CTGCACATAA
* *
3587595 TAGCCTGCACATAGTACTACACACGTGACCATTTTCATCCGATACACGTAC
1 TAGCCTGCACATAGTACTACACACGTGACCA-TATCATCCGATACACGTAG
* * * * * *
3587646 TAGCCTGCACATAGTACTACACACGTGATCGA-AGCTATTCGGTACGCATAG
1 TAGCCTGCACATAGTACTACACACGTGA-CCATATC-ATCCGATACACGTAG
* * * *
3587697 TAGCCTGCACATTGTACTACACATGCGACC-TATCATTCCGTTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCATATCA-TCCGATACACGTAG
*
3587747 TAGCCTGCACATAGTACTACACATGTGACC
1 TAGCCTGCACATAGTACTACACACGTGACC
3587777 TAGCAACTTC
Statistics
Matches: 108, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.01
50 42 0.39
51 63 0.58
52 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGCCTGCACATAGTACTACACACGTGACCATATCATCCGATACACGTAG
Found at i:3589796 original size:4 final size:4
Alignment explanation
Indices: 3589787--3589821 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3589777 AAAATGTAAT
*
3589787 TTAA TTAA TTAA TTAA TTAG TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
3589822 TATCAACACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:3603706 original size:12 final size:13
Alignment explanation
Indices: 3603673--3603698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3603663 TTATAAATAT
3603673 ATATACAAGTAAA
1 ATATACAAGTAAA
3603686 ATATACAAGTAAA
1 ATATACAAGTAAA
3603699 TTTACAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
ATATACAAGTAAA
Found at i:3604339 original size:13 final size:13
Alignment explanation
Indices: 3604316--3604355 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
3604306 AGCCGAATCT
*
3604316 TAAAGAAATAACAA
1 TAAA-AAATAAAAA
3604330 TAAAAAATAAAAA
1 TAAAAAATAAAAA
3604343 T-AAAAATAAAAA
1 TAAAAAATAAAAA
3604355 T
1 T
3604356 CAAATCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 9 0.36
14 4 0.16
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:3604341 original size:6 final size:6
Alignment explanation
Indices: 3604321--3604355 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
3604311 AATCTTAAAG
*
3604321 AAATAA CAATAAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AAAT-AA AAATAA AAATAA AAATAA AAAT
3604356 CAAATCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:3605229 original size:44 final size:44
Alignment explanation
Indices: 3605177--3606079 Score: 611
Period size: 44 Copynumber: 20.3 Consensus size: 44
3605167 CTACCGATAT
* * *
3605177 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
* ** * *
3605221 ATGAAGACAAGATCCACT-T-TTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTT-GATCTACTTC-ACACCAGTAC
* * *
3605265 GGGAAGATAAGATCTG-T-TCCTTTGATCTACTTCACGCCAGTAC
1 AGGAAGACAAGATCTGCTAT-CTTTGATCTACTTCACACCAGTAC
* * * * *
3605308 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCACCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCA-CACCAGTAC
* *
3605353 GGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
* * *
3605397 ATGAAGACAAGATCTGCT-T-TTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTT-GATCTACTTC-ACACCAGTAC
* * * * *
3605441 GGGGAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
* * * * ** * * * *
3605485 ATGAAGACAAGATCTGTTTTATTCAATCTGCTTTACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
** * * * * * * *
3605529 ATAAAGATAGGATTTGCTCTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACACCAGTAC
* * * * * * *
3605574 GGGAAGACGAGATCTGCTTTCTTCGATATACTCCACCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCA-CACCAGTAC
* * * * * * * *
3605619 GGGGAGACAATATATGTTGTATTTGATCTACTTCACGCC-GATAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAG-TAC
* * * * * * *
3605663 ATGAAGACAAGATCAGTTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACACCAGTAC
* * *
3605708 GGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
* * *
3605752 ATGAAGACAAGATCTGCTTTCTTTGATCTACTTTGC-CACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTAC-TT-CACACCAGTAC
* * *
3605797 GGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
** * * * *
3605841 ATAAAGACAATATCTGCTTTCTTTGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACACCAGTAC
* * * * * *
3605886 GGGAAGACAAGATCTGC-ATATTCGATCCACTTCGCTACC-GATAT
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCAC-ACCAG-TAC
* * * * **
3605930 AGGAAGACAGGACCTGATGTCTTTGATCTACTTCATGCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
* * * * * *
3605974 ATGAAGACAAGATCTACTTTTCCTTTGATCTGCTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGC-TAT-CTTTGATCTACTTC-ACACCAGTAC
* * * * **
3606021 GGGAAGGCAAGATCTGTTACCTTTGATCTACTTCATGCCAGTAC
1 AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
*
3606065 ATGAAGACAAGATCT
1 AGGAAGACAAGATCT
3606080 ACTTTCTTCG
Statistics
Matches: 651, Mismatches: 181, Indels: 54
0.73 0.20 0.06
Matches are distributed among these distances:
42 6 0.01
43 48 0.07
44 328 0.50
45 233 0.36
46 18 0.03
47 18 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTTGATCTACTTCACACCAGTAC
Found at i:3605409 original size:89 final size:89
Alignment explanation
Indices: 3605153--3605902 Score: 924
Period size: 89 Copynumber: 8.5 Consensus size: 89
3605143 AATCTGTGTA
* * * * *
3605153 TTCGATCCACTTCGCTACC-GATATAGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCA
1 TTCGATCTACTTCGCCACCAG-TATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCA
**
3605217 GTACATGAAGACAAGATCCACTTT-
65 GTACATGAAGACAAGATCTGCTTTC
*
3605241 TTCGATCTACTTCGCCACCAGTATGGGAAGATAAGATCTG-T-TCCTTTGATCTACTTCACGCCA
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAT-CTTTGATCTACTTCACGCCA
3605304 GTACATGAAGACAAGATCTGCTTTC
65 GTACATGAAGACAAGATCTGCTTTC
* * *
3605329 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACTCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
3605394 TACATGAAGACAAGATCTGCTTT-
66 TACATGAAGACAAGATCTGCTTTC
* * *
3605417 TTCGATCTACTTCGCCACCAGTATGGGGAGACAAGATCTGGTATCTCTGATCTACTTCACGCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* *
3605482 TACATGAAGACAAGATCTGTTTTA
66 TACATGAAGACAAGATCTGCTTTC
* * **** * * * * * * *
3605506 TTCAATCTGCTTTACGCCA--A-TACATAAAGATAGGATTTGCTCTCTTCGATCTACTTCGCCAC
1 TTCGATCTAC-TT-CGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGC
*** *
3605568 CAGTATGGGAAGACGAGATCTGCTTTC
63 CAGTACATGAAGACAAGATCTGCTTTC
* * * * * * * * *
3605595 TTCGATATACTCCACCACCAGTATGGGGAGACAATATATGTTGTATTTGATCTACTTCACGCC-G
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* *
3605659 ATACATGAAGACAAGATCAGTTTTC
66 -TACATGAAGACAAGATCTGCTTTC
*
3605684 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
3605749 TACATGAAGACAAGATCTGCTTTC
66 TACATGAAGACAAGATCTGCTTTC
* * *
3605773 TTTGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGGTATCTTTGATCTACTTCACGCCAG
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
* *
3605838 TACATAAAGACAATATCTGCTTTC
66 TACATGAAGACAAGATCTGCTTTC
*
3605862 TTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
1 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC
3605903 ATATTCGATC
Statistics
Matches: 564, Mismatches: 84, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
86 1 0.00
87 47 0.08
88 177 0.31
89 306 0.54
90 28 0.05
91 5 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (89 bp):
TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAG
TACATGAAGACAAGATCTGCTTTC
Found at i:3606274 original size:44 final size:44
Alignment explanation
Indices: 3606205--3606299 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 44
3606195 TTATGGAGAT
* * * *
3606205 AAGATCTGTTTCTTTGATCTACTTCA-CGCCAGTACATGAAGAC
1 AAGATCTGTTTCATGGATCTACTTCACCACCAGTACAGGAAGAC
**
3606248 AAGATCTGTTTTCATGGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATCTG-TTTCATGGATCTACTTCACCACCAGTACAGGAAGAC
3606293 AAGATCT
1 AAGATCT
3606300 TTTGCATTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 8 0.18
44 16 0.36
45 20 0.45
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
AAGATCTGTTTCATGGATCTACTTCACCACCAGTACAGGAAGAC
Found at i:3607601 original size:49 final size:51
Alignment explanation
Indices: 3607535--3607656 Score: 142
Period size: 51 Copynumber: 2.4 Consensus size: 51
3607525 GGTCTAAGGT
* *
3607535 GCCCTTTGT-GAGTTTTCACCTTAGCCTCTC-CATTTTTTTT-ACTCAAGGC
1 GCCCTTTGTAG-GCTTTCACCTTAGCCTCTCTCATTTTTTTTGACTCAAAGC
* * * * * *
3607584 TCCCTTTGTAGGGTTTCACCCTGGTCTCTCTCTTTTTTTTTGACTCAAAGC
1 GCCCTTTGTAGGCTTTCACCTTAGCCTCTCTCATTTTTTTTGACTCAAAGC
3607635 GCCCTTTGTAGGCTTTCACCTT
1 GCCCTTTGTAGGCTTTCACCTT
3607657 GGTCCCACCT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 23 0.38
50 10 0.17
51 27 0.45
ACGTcount: A:0.12, C:0.29, G:0.16, T:0.43
Consensus pattern (51 bp):
GCCCTTTGTAGGCTTTCACCTTAGCCTCTCTCATTTTTTTTGACTCAAAGC
Found at i:3610382 original size:19 final size:20
Alignment explanation
Indices: 3610358--3610397 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3610348 AAAGGTTTTT
* *
3610358 AATGCATATG-ATGCAATGA
1 AATGCAAATGCATGAAATGA
3610377 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
3610397 A
1 A
3610398 TGCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:3612185 original size:12 final size:13
Alignment explanation
Indices: 3612159--3612184 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3612149 TTACAAATAT
3612159 ATATACAAGTAAA
1 ATATACAAGTAAA
3612172 ATATACAAGTAAA
1 ATATACAAGTAAA
3612185 TTTACAAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
ATATACAAGTAAA
Found at i:3612190 original size:12 final size:12
Alignment explanation
Indices: 3612159--3612192 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3612149 TTACAAATAT
3612159 ATATACAAGTAAA
1 ATATACAAGT-AA
3612172 ATATACAAGTAA
1 ATATACAAGTAA
*
3612184 ATTTACAAG
1 ATATACAAG
3612193 CATGTGTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (12 bp):
ATATACAAGTAA
Found at i:3612663 original size:18 final size:19
Alignment explanation
Indices: 3612624--3612683 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
3612614 GTGTAAGTGT
* *
3612624 ATAAAAATAATG-ATGATG
1 ATAAAAATAATGAATAATA
3612642 ATAAAAATAATGAATAAT-
1 ATAAAAATAATGAATAATA
* *
3612660 ATAATAATAAT-AAAAATA
1 ATAAAAATAATGAATAATA
3612678 ATAAAA
1 ATAAAA
3612684 TAGTTAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 5 0.14
18 27 0.75
19 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
ATAAAAATAATGAATAATA
Found at i:3612677 original size:9 final size:9
Alignment explanation
Indices: 3612642--3612683 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3612632 AATGATGATG
3612642 ATAAAAATA
1 ATAAAAATA
*
3612651 ATGAATAAT-
1 AT-AAAAATA
*
3612660 ATAATAATA
1 ATAAAAATA
3612669 ATAAAAATA
1 ATAAAAATA
3612678 ATAAAA
1 ATAAAA
3612684 TAGTTAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 6 0.21
9 18 0.62
10 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
ATAAAAATA
Found at i:3613416 original size:13 final size:13
Alignment explanation
Indices: 3613393--3613430 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
3613383 AGCCGAATCT
*
3613393 TAAAGAAATAACAA
1 TAAA-AAATAAAAA
3613407 TAAAAAATAAAAA
1 TAAAAAATAAAAA
3613420 T-AAAAATAAAA
1 TAAAAAATAAAA
3613431 TCCCTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 9 0.39
14 4 0.17
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:3615944 original size:11 final size:11
Alignment explanation
Indices: 3615904--3616075 Score: 81
Period size: 11 Copynumber: 16.9 Consensus size: 11
3615894 GGCCCATTTT
3615904 TATTTT-AAAA
1 TATTTTAAAAA
3615914 -ATTTTAAAAA
1 TATTTTAAAAA
**
3615924 -ATTAAAAAAAA
1 TATT-TTAAAAA
3615935 TATTTTAAAAA
1 TATTTTAAAAA
3615946 TATTTTAAAAA
1 TATTTTAAAAA
3615957 TATTTT--AAA
1 TATTTTAAAAA
3615966 -A--TTAAAAA
1 TATTTTAAAAA
* **
3615974 AATTAAAAAAAA
1 TATT-TTAAAAA
3615986 TATTTT--AAA
1 TATTTTAAAAA
3615995 -A--TTAAAAA
1 TATTTTAAAAA
* **
3616003 AATTAAAAAAA
1 TATTTTAAAAA
3616014 GTATTTTAAAAA
1 -TATTTTAAAAA
3616026 TATTTT--AAA
1 TATTTTAAAAA
3616035 -A-TTTAAAAA
1 TATTTTAAAAA
* * *
3616044 AAATTAAAAAA
1 TATTTTAAAAA
* *
3616055 TATGTAAAAAA
1 TATTTTAAAAA
3616066 TATTTTAAAA
1 TATTTTAAAA
3616076 TTAAAAAATA
Statistics
Matches: 123, Mismatches: 20, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
6 4 0.03
7 3 0.02
8 9 0.07
9 19 0.15
10 8 0.07
11 61 0.50
12 19 0.15
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:3615981 original size:8 final size:9
Alignment explanation
Indices: 3615963--3616013 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
3615953 AAAATATTTT
3615963 AAAATTAAA
1 AAAATTAAA
3615972 AAAATTAAAA
1 AAAATT-AAA
***
3615982 AAAATATTTT
1 AAAAT-TAAA
3615992 AAAATTAAA
1 AAAATTAAA
3616001 AAAATTAAA
1 AAAATTAAA
3616010 AAAA
1 AAAA
3616014 GTATTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 20 0.59
10 13 0.38
11 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAATTAAA
Found at i:3615984 original size:29 final size:29
Alignment explanation
Indices: 3615952--3616024 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
3615942 AAAATATTTT
3615952 AAAAATATTTTAAAATTAAAAAAATTAAA
1 AAAAATATTTTAAAATTAAAAAAATTAAA
3615981 AAAAATATTTTAAAATTAAAAAAATTAAA
1 AAAAATATTTTAAAATTAAAAAAATTAAA
*
3616010 AAAAGTATTTTAAAA
1 AAAAATATTTTAAAA
3616025 ATATTTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAAATATTTTAAAATTAAAAAAATTAAA
Found at i:3615985 original size:40 final size:39
Alignment explanation
Indices: 3615963--3616083 Score: 165
Period size: 40 Copynumber: 3.1 Consensus size: 39
3615953 AAAATATTTT
**
3615963 AAAATTAAAAAAAT-TAAAAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAATATTTAAAAAATATTTTAAAATTAAA
*
3616001 AAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAA
1 AAAATTAAAAAAA-TATTTAAAAAATATTTTAAAA-TT-AAA
*
3616043 AAAATT-AAAAAATATGTAAAAAATATTTTAAAATTAAA
1 AAAATTAAAAAAATATTTAAAAAATATTTTAAAATTAAA
3616081 AAA
1 AAA
3616084 TATATATTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
38 19 0.26
39 3 0.04
40 35 0.47
41 8 0.11
42 9 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (39 bp):
AAAATTAAAAAAATATTTAAAAAATATTTTAAAATTAAA
Found at i:3616020 original size:80 final size:79
Alignment explanation
Indices: 3615904--3616083 Score: 240
Period size: 80 Copynumber: 2.2 Consensus size: 79
3615894 GGCCCATTTT
* **
3615904 TATTTTAAAAATTTTAAAAAATTAAAAAAAATATTTTAAAAATATTTTAAAAATATT-TTAAAAT
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAAATATTTTAAAAATATTTT-AAAAT-TTAAAAAAAT
3615968 TAAAAAA-AT-TAAAAAAAA
62 TAAAAAATATGT--AAAAAA
*
3615986 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAATTAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTT-AAAAAAATTAA
3616051 AAAATATGTAAAAAA
65 AAAATATGTAAAAAA
3616066 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
3616084 TATATATTTA
Statistics
Matches: 90, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
78 2 0.02
79 5 0.06
80 70 0.78
81 6 0.07
82 7 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (79 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTTAAAAAAATTAAA
AAATATGTAAAAAA
Found at i:3623765 original size:27 final size:27
Alignment explanation
Indices: 3623735--3623797 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
3623725 AATTTTTCAT
**
3623735 AAAGG-TATCCCTTTTAGAGTTTGCCAC
1 AAAGGCTAT-CCTTTTAGAGTTCACCAC
*
3623762 AAAGGCTATTCTTTTAGAGTTCACCAC
1 AAAGGCTATCCTTTTAGAGTTCACCAC
3623789 AAAGGCTAT
1 AAAGGCTAT
3623798 TCTTAGTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (27 bp):
AAAGGCTATCCTTTTAGAGTTCACCAC
Found at i:3623798 original size:27 final size:27
Alignment explanation
Indices: 3623745--3623801 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
3623735 AAAGGTATCC
**
3623745 CTTTTAGAGTTTGCCACAAAGGCTATT
1 CTTTTAGAGTTCACCACAAAGGCTATT
3623772 CTTTTAGAGTTCACCACAAAGGCTATT
1 CTTTTAGAGTTCACCACAAAGGCTATT
3623799 CTT
1 CTT
3623802 AGTTGTCGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (27 bp):
CTTTTAGAGTTCACCACAAAGGCTATT
Found at i:3629625 original size:64 final size:64
Alignment explanation
Indices: 3629517--3629641 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
3629507 TACCAAACTA
* * * *
3629517 ATATATAGTTTGTTAAGAAATTAAAAATTAGACTATAAATATATGTGTGAAAAATATTTAAATGT
1 ATATATAATTTATCAAGAAACTAAAAATTAGACTATAAATATATGTGT-AAAAATATTTAAATGT
*
3629582 ATATATAATTTATCAAGAAACT-AAAATTAGGCTATAAATATATGTGTAAAAATATTTAAA
1 ATATATAATTTATCAAGAAACTAAAAATTAGACTATAAATATATGTGTAAAAATATTTAAA
3629642 AATATCGACA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 13 0.24
64 24 0.44
65 18 0.33
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (64 bp):
ATATATAATTTATCAAGAAACTAAAAATTAGACTATAAATATATGTGTAAAAATATTTAAATGT
Found at i:3629905 original size:18 final size:16
Alignment explanation
Indices: 3629879--3629917 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
3629869 ATTTTAAGAA
*
3629879 ATATTTTTTTATAATTTT
1 ATATATTTTTAT--TTTT
3629897 ATATATTTTTATTTTT
1 ATATATTTTTATTTTT
3629913 ATATA
1 ATATA
3629918 ATTGTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATATATTTTTATTTTT
Found at i:3629909 original size:26 final size:27
Alignment explanation
Indices: 3629880--3629930 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
3629870 TTTTAAGAAA
*
3629880 TATTTTTTTATAATT-TTATATATTTT
1 TATTTTTATATAATTGTTATATATTTT
3629906 TATTTTTATATAATTGTTATATATT
1 TATTTTTATATAATTGTTATATATT
3629931 ACAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TATTTTTATATAATTGTTATATATTTT
Done.