Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007894.1 Hibiscus syriacus cultivar Beakdansim tig00110279_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: 1425917
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:418497 original size:62 final size:62
Alignment explanation
Indices: 418424--418608 Score: 327
Period size: 61 Copynumber: 3.0 Consensus size: 62
418414 TAAACGGTCA
* *
418424 CTTAATTATAAGATATAATTATATTAAATCTTCGACTATTAAAAATTATAAAATGATCCTCT
1 CTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGATCATCT
418486 CTTAATTATAAGATATAATTATATTAAATCATCGACTATT-AAAATTATAAAATGATCATCT
1 CTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGATCATCT
* *
418547 CTTAATTATAAGATATAATTATATTAAATCCTCGACTATTAAAAATTATAAAATGGTCATCT
1 CTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGATCATCT
418609 AACTATAATA
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
61 59 0.50
62 59 0.50
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.39
Consensus pattern (62 bp):
CTTAATTATAAGATATAATTATATTAAATCATCGACTATTAAAAATTATAAAATGATCATCT
Found at i:420712 original size:31 final size:31
Alignment explanation
Indices: 420669--420737 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
420659 AAATACCATT
* * *
420669 AATTTATTAAATTGTTATAAAATAAT-TATTA
1 AATTTATCAAATTATTATAAAACAATCT-TTA
420700 AATTTATCAAATTATTATAAAACAATCTTTA
1 AATTTATCAAATTATTATAAAACAATCTTTA
420731 AATTTAT
1 AATTTAT
420738 TAAAAGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (31 bp):
AATTTATCAAATTATTATAAAACAATCTTTA
Found at i:421927 original size:32 final size:32
Alignment explanation
Indices: 421891--421957 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
421881 TTTCGAGTGA
421891 GATCAGATCAGTTGAAGGATACATATTTTTCG
1 GATCAGATCAGTTGAAGGATACATATTTTTCG
*
421923 GATCAGATTAGTTGAAGGATACATATTTTTCG
1 GATCAGATCAGTTGAAGGATACATATTTTTCG
421955 GAT
1 GAT
421958 TAGGTATGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.36
Consensus pattern (32 bp):
GATCAGATCAGTTGAAGGATACATATTTTTCG
Found at i:423757 original size:24 final size:24
Alignment explanation
Indices: 423730--423801 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
423720 GTAAACGGAG
*
423730 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
423754 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
423778 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
423801 A
1 A
423802 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:423761 original size:12 final size:12
Alignment explanation
Indices: 423734--423802 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
423724 ACGGAGATAT
* *
423734 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
423746 CAGAATTCATAT
1 CAGAATTCAGAA
423758 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
423770 CAGAATCCAGAT
1 CAGAATTCAGAA
423782 CAGAA-TCAGAA
1 CAGAATTCAGAA
423793 CAGAATTCAG
1 CAGAATTCAG
423803 GTAACGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 32 0.71
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:424938 original size:18 final size:18
Alignment explanation
Indices: 424917--424951 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
424907 TTTTACTTCC
* *
424917 ATCCGATCTTATTATTTA
1 ATCCAATCTTATCATTTA
424935 ATCCAATCTTATCATTT
1 ATCCAATCTTATCATTT
424952 CCTTCAGTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.03, T:0.49
Consensus pattern (18 bp):
ATCCAATCTTATCATTTA
Found at i:426284 original size:13 final size:13
Alignment explanation
Indices: 426266--426326 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
426256 GGTCAACGCC
*
426266 GGTCAACGGTTCG
1 GGTCAACGGGTCG
426279 GGTCAACAGGTCGGGTCG
1 GGTCAAC--G--GG-TCG
426297 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
426310 GGTAAACGGGTCG
1 GGTCAACGGGTCG
426323 GGTC
1 GGTC
426327 GGGTTATGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 25 0.62
14 2 0.05
15 1 0.03
16 1 0.03
17 1 0.03
18 10 0.25
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:426299 original size:18 final size:18
Alignment explanation
Indices: 426276--426312 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
426266 GGTCAACGGT
426276 TCGGGTCAACAGGTCGGG
1 TCGGGTCAACAGGTCGGG
*
426294 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACAGGTCGGG
426312 T
1 T
426313 AAACGGGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.46, T:0.19
Consensus pattern (18 bp):
TCGGGTCAACAGGTCGGG
Found at i:426304 original size:31 final size:31
Alignment explanation
Indices: 426266--426330 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
426256 GGTCAACGCC
* *
426266 GGTCAACGGTTCGGGTCAACAGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACAGGTCGGGTCG
*
426297 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACAGGTCGGGTCG
426328 GGT
1 GGT
426331 TATGACCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.15, C:0.20, G:0.46, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACAGGTCGGGTCG
Found at i:426763 original size:17 final size:16
Alignment explanation
Indices: 426741--426774 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
426731 TAAAGACAGT
426741 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
426758 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
426774 A
1 A
426775 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:427294 original size:24 final size:24
Alignment explanation
Indices: 427250--427299 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
427240 ATAAAGAACC
*
427250 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
427274 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
427298 AA
1 AA
427300 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:437025 original size:17 final size:16
Alignment explanation
Indices: 437003--437036 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
436993 TAAAGACAGT
437003 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
437020 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
437036 A
1 A
437037 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:437555 original size:24 final size:24
Alignment explanation
Indices: 437511--437560 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
437501 ATAAAGAACC
*
437511 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
437535 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
437559 AA
1 AA
437561 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:439819 original size:7 final size:7
Alignment explanation
Indices: 439807--439850 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
439797 ATTATTCTCG
439807 CCCATTC
1 CCCATTC
439814 CCCATTC
1 CCCATTC
439821 CCCATTC
1 CCCATTC
439828 CCCATTC
1 CCCATTC
439835 CCCATTC
1 CCCATTC
439842 CCCATTC
1 CCCATTC
439849 CC
1 CC
439851 GATCACTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.14, C:0.59, G:0.00, T:0.27
Consensus pattern (7 bp):
CCCATTC
Found at i:444520 original size:3 final size:3
Alignment explanation
Indices: 444512--444549 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
444502 CATAGCCATT
*
444512 TTC TTC TTC TTC TTC TTC TTG TTC TTC TT- TTAC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TT
444550 ATTCGTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:448784 original size:20 final size:20
Alignment explanation
Indices: 448740--448784 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
448730 GGTTGTGGTC
* *
448740 ATTTCTAGCCGTTGGGGATG
1 ATTTTTAGCCGTTGAGGATG
448760 ATTTTTAGCCGTTTGAGGATG
1 ATTTTTAGCCG-TTGAGGATG
448781 -TTTT
1 ATTTT
448785 CTTTGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.16, C:0.11, G:0.29, T:0.44
Consensus pattern (20 bp):
ATTTTTAGCCGTTGAGGATG
Found at i:449333 original size:18 final size:18
Alignment explanation
Indices: 449300--449334 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
449290 TTCTCTGTTA
* *
449300 ATTATTATTGTTATTTTT
1 ATTATTATTATAATTTTT
449318 ATTATTATTATAATTTT
1 ATTATTATTATAATTTT
449335 AATTTTCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTATTATTATAATTTTT
Found at i:456883 original size:7 final size:7
Alignment explanation
Indices: 456871--456937 Score: 134
Period size: 7 Copynumber: 9.6 Consensus size: 7
456861 CAAGACAGAC
456871 GAGAAGA
1 GAGAAGA
456878 GAGAAGA
1 GAGAAGA
456885 GAGAAGA
1 GAGAAGA
456892 GAGAAGA
1 GAGAAGA
456899 GAGAAGA
1 GAGAAGA
456906 GAGAAGA
1 GAGAAGA
456913 GAGAAGA
1 GAGAAGA
456920 GAGAAGA
1 GAGAAGA
456927 GAGAAGA
1 GAGAAGA
456934 GAGA
1 GAGA
456938 GTGTTCGGGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAGAAGA
Found at i:457512 original size:31 final size:31
Alignment explanation
Indices: 457444--457513 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
457434 AAAATTTATT
* * * *
457444 TTTTAGTTTAATTACTTAACTTTCAAATTAC
1 TTTTAATTTAATCACTCAACATTCAAATTAC
* **
457475 TCTTAATTTAATCACTCAACATTCAAATTTG
1 TTTTAATTTAATCACTCAACATTCAAATTAC
457506 TTTTAATT
1 TTTTAATT
457514 ATATTTTAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTTAATTTAATCACTCAACATTCAAATTAC
Found at i:464499 original size:14 final size:14
Alignment explanation
Indices: 464482--464511 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
464472 ATTTTAATAC
464482 CTCACCATTAACTA
1 CTCACCATTAACTA
464496 CTCACCATTAACTA
1 CTCACCATTAACTA
464510 CT
1 CT
464512 TTTTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (14 bp):
CTCACCATTAACTA
Found at i:464524 original size:79 final size:79
Alignment explanation
Indices: 464429--464592 Score: 328
Period size: 79 Copynumber: 2.1 Consensus size: 79
464419 AATTATACCT
464429 TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
1 TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
464494 TACTCACCATTAAC
66 TACTCACCATTAAC
464508 TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
1 TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
464573 TACTCACCATTAAC
66 TACTCACCATTAAC
464587 TACTTT
1 TACTTT
464593 CTGCTTCATC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (79 bp):
TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
TACTCACCATTAAC
Found at i:464578 original size:14 final size:14
Alignment explanation
Indices: 464561--464590 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
464551 ATTTTAATAC
464561 CTCACCATTAACTA
1 CTCACCATTAACTA
464575 CTCACCATTAACTA
1 CTCACCATTAACTA
464589 CT
1 CT
464591 TTCTGCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (14 bp):
CTCACCATTAACTA
Found at i:464616 original size:79 final size:79
Alignment explanation
Indices: 464429--464614 Score: 282
Period size: 79 Copynumber: 2.3 Consensus size: 79
464419 AATTATACCT
* * * *
464429 TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
1 TACTTTCTACTTCATCTCATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
464494 TACTCACCATTAAC
66 TACTCACCATTAAC
* * * *
464508 TACTTTTTATTTCATTTTATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
1 TACTTTCTACTTCATCTCATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
464573 TACTCACCATTAAC
66 TACTCACCATTAAC
*
464587 TACTTTCTGCTTCATCTCACTATCTAAA
1 TACTTTCTACTTCATCTCA-TATCTAAA
464615 TTTTTAACAA
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 93 0.92
80 8 0.08
ACGTcount: A:0.32, C:0.20, G:0.01, T:0.47
Consensus pattern (79 bp):
TACTTTCTACTTCATCTCATATCTAAAATTAAATTTTTATTTCATTTTAATACCTCACCATTAAC
TACTCACCATTAAC
Found at i:473519 original size:18 final size:18
Alignment explanation
Indices: 473496--473583 Score: 140
Period size: 18 Copynumber: 4.9 Consensus size: 18
473486 GCGTAGAATT
*
473496 TGTCCCGTAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
473514 TGTCCCGAAAGACCACTG
1 TGTCCCGAAGGACCACTG
473532 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
* *
473550 TGTTCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTG
473568 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
473584 GTAGACCCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:474174 original size:20 final size:22
Alignment explanation
Indices: 474149--474206 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
474139 ATTCCCTTGA
474149 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
474169 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
474192 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
474207 CTACCTATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:480439 original size:81 final size:81
Alignment explanation
Indices: 480304--480495 Score: 237
Period size: 81 Copynumber: 2.4 Consensus size: 81
480294 GACATATGCA
* * *
480304 GTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTTTTCATGTCCTTTAAGACCAACATC
1 GTTACGCTTGGCCTTGGTTCAAAATCACTAGTGAATGGTTCTTCATCTCCTTTAAGACCAACATC
* *
480369 ATCGCCTCCAT-AGCTC
66 ATCGCCACCATAAG-AC
* * * *
480385 GTTACGCTTGGCCTTAGTTCAAAATGACT-GATGAATGGCTTCTTC-TCTCGTTTAAGACCAGCA
1 GTTACGCTTGGCCTTGGTTCAAAATCACTAG-TGAATGG-TTCTTCATCTCCTTTAAGACCAACA
*
480448 TCATTGCCACCATAAGAC
64 TCATCGCCACCATAAGAC
*
480466 GTTACGCTTGGCCTCGGTTCAAAATCACTA
1 GTTACGCTTGGCCTTGGTTCAAAATCACTA
480496 TCGACATAAG
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
80 1 0.01
81 86 0.91
82 7 0.07
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (81 bp):
GTTACGCTTGGCCTTGGTTCAAAATCACTAGTGAATGGTTCTTCATCTCCTTTAAGACCAACATC
ATCGCCACCATAAGAC
Found at i:480491 original size:204 final size:202
Alignment explanation
Indices: 479951--480644 Score: 950
Period size: 204 Copynumber: 3.4 Consensus size: 202
479941 CTTCACTGCC
* * * *
479951 TTAAGATCAACATCGTCGCCTCCGTAGGCCGTTACGCTTGGCCTCGGTTCAAAAT-ACCAGTGAA
1 TTAAGACCAACATCATCGCCTCCATAGGCCGTTACGCTTGGCCTCGGTTCAAAATGACGA-TGAA
* * * *
480015 TGGCTTCTTCTCTTGTTTAAGGCCAACATCATTGCTACCATAAGACGTTACGCTTGGCCTCGGTT
65 TGGCTTCTTCTCTCGTTTAAGACCAGCATCATTGCCACCATAAGACGTTACGCTTGGCCTCGGTT
* * * * *
480080 CAAAATCACTACTAACATAGGCTGTTACGCTTGGCCTTGGCTCAAAATCACTGGTGAATTGTTTC
130 CAAAATCACT-CTGACATAAGCAGTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTTC
480145 TTATG-CGCT
194 TTATGTC-CT
* * *
480154 TTAAGACCAGCATCATTGCCTCCATAGGCCGTTACGCTTGGCCTCGGTTC-AAA-GTCGATGAAT
1 TTAAGACCAACATCATCGCCTCCATAGGCCGTTACGCTTGGCCTCGGTTCAAAATGACGATGAAT
* * *
480217 GGCTTCTTCTCCCTTTTAAGACCAGCATCATTGCCACCATAAGATGTTACGCTTGGCCTCGGTTC
66 GGCTTCTTCTCTCGTTTAAGACCAGCATCATTGCCACCATAAGACGTTACGCTTGGCCTCGGTTC
*
480282 AAAATCACTGCTGACATATGCAGTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTT-T
131 AAAATCACT-CTGACATAAGCAGTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTTCT
480346 TCATGTCCT
195 T-ATGTCCT
**
480355 TTAAGACCAACATCATCGCCTCCATA-GCTCGTTACGCTTGGCCTTAGTTCAAAATGACTGATGA
1 TTAAGACCAACATCATCGCCTCCATAGGC-CGTTACGCTTGGCCTCGGTTCAAAATGAC-GATGA
480419 ATGGCTTCTTCTCTCGTTTAAGACCAGCATCATTGCCACCATAAGACGTTACGCTTGGCCTCGGT
64 ATGGCTTCTTCTCTCGTTTAAGACCAGCATCATTGCCACCATAAGACGTTACGCTTGGCCTCGGT
*
480484 TCAAAATCACTATCGACATAAGCAGTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTT
129 TCAAAATCACTCT-GACATAAGCAGTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTT
*
480549 CTTTTGTCCT
193 CTTATGTCCT
* *** * * * ** * *
480559 TTTAGACCGGTATCATCACCTCCATAGGCAGTTACGCTTGGCCTCGGTTTAAAAACAATGGTGAA
1 TTAAGACCAACATCATCGCCTCCATAGGCCGTTACGCTTGGCCTCGG-TTCAAAATGACGATGAA
480624 TGGCTTCTTCTCTCGTTTAAG
65 TGGCTTCTTCTCTCGTTTAAG
480645 GTATCGGTTC
Statistics
Matches: 436, Mismatches: 44, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
200 4 0.01
201 168 0.39
202 9 0.02
203 48 0.11
204 196 0.45
205 11 0.03
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.31
Consensus pattern (202 bp):
TTAAGACCAACATCATCGCCTCCATAGGCCGTTACGCTTGGCCTCGGTTCAAAATGACGATGAAT
GGCTTCTTCTCTCGTTTAAGACCAGCATCATTGCCACCATAAGACGTTACGCTTGGCCTCGGTTC
AAAATCACTCTGACATAAGCAGTTACGCTTGGCCTTGGCTCAAAATCACTAGTGAATGGTTTCTT
ATGTCCT
Found at i:480517 original size:42 final size:42
Alignment explanation
Indices: 480458--480537 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
480448 TCATTGCCAC
*
480458 CATAAGACGTTACGCTTGGCCTCGGTTCAAAATCACTATCGA
1 CATAAGACGTTACGCTTGGCCTCGGCTCAAAATCACTATCGA
*
480500 CATAAG-CAGTTACGCTTGGCCTTGGCTCAAAATCACTA
1 CATAAGAC-GTTACGCTTGGCCTCGGCTCAAAATCACTA
480538 GTGAATGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (42 bp):
CATAAGACGTTACGCTTGGCCTCGGCTCAAAATCACTATCGA
Found at i:480604 original size:123 final size:123
Alignment explanation
Indices: 480385--480612 Score: 289
Period size: 123 Copynumber: 1.9 Consensus size: 123
480375 TCCATAGCTC
* * *
480385 GTTACGCTTGGCCTTAGTTCAAAATGACTGATGAATGGCTTCTTCTCTCGTTTAAGACCAGCATC
1 GTTACGCTTGGCCTTAGCTCAAAATCACTGATGAATGGCTTCTTCTCTCCTTTAAGACCAGCATC
**
480450 ATTGCCACCATAAGACGTTACGCTTGGCCTCGGTTCAAAATCACTATCGACATAAGCA
66 ATCACCACCATAAGACGTTACGCTTGGCCTCGGTTCAAAATCACTATCGACATAAGCA
* * * * * * *
480508 GTTACGCTTGGCCTTGGCTCAAAATCACT-AGTGAATGGTTTCTTTTGTCCTTTTAGACCGGTAT
1 GTTACGCTTGGCCTTAGCTCAAAATCACTGA-TGAATGGCTTCTTCTCTCCTTTAAGACCAGCAT
* * *
480572 CATCACCTCCAT-AGGCAGTTACGCTTGGCCTCGGTTTAAAA
65 CATCACCACCATAAGAC-GTTACGCTTGGCCTCGGTTCAAAA
480613 ACAATGGTGA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
122 4 0.05
123 84 0.95
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.32
Consensus pattern (123 bp):
GTTACGCTTGGCCTTAGCTCAAAATCACTGATGAATGGCTTCTTCTCTCCTTTAAGACCAGCATC
ATCACCACCATAAGACGTTACGCTTGGCCTCGGTTCAAAATCACTATCGACATAAGCA
Found at i:480813 original size:42 final size:42
Alignment explanation
Indices: 480750--480912 Score: 177
Period size: 42 Copynumber: 3.9 Consensus size: 42
480740 TCATCACCGC
* *
480750 CATAGGCTGTTACACTAGGCCTCGGTCCAAAGTCACTGCTGA
1 CATAGGCTGTTACACTTGGCCTCGGTCCAAAATCACTGCTGA
* * * *
480792 CATAGGTTGTTACGCTTGGCCTCGGTTCAAAATCACTACTGA
1 CATAGGCTGTTACACTTGGCCTCGGTCCAAAATCACTGCTGA
* * * *
480834 CATAGGTTGTTACGCTTGACCTCGG-CTCAAAATCACTGGTGA
1 CATAGGCTGTTACACTTGGCCTCGGTC-CAAAATCACTGCTGA
* * *
480876 CATAAGCAGTTACACTTGGCCTTGG-CTCAAAATCACT
1 CATAGGCTGTTACACTTGGCCTCGGTC-CAAAATCACT
480913 AGTGTATGGT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 104 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (42 bp):
CATAGGCTGTTACACTTGGCCTCGGTCCAAAATCACTGCTGA
Found at i:480894 original size:84 final size:84
Alignment explanation
Indices: 480750--480913 Score: 204
Period size: 84 Copynumber: 2.0 Consensus size: 84
480740 TCATCACCGC
* * * ** *
480750 CATAGGCTGTTACACTAGGCCTCGGTCCAAAGTCACTGCTGACATAGGTTGTTACGCTTGGCCTC
1 CATAGGCTGTTACACTAGACCTCGGTCCAAAATCACTGCTGACATAAGCAGTTACACTTGGCCTC
*
480815 GGTTCAAAATCACTACTGA
66 GGCTCAAAATCACTACTGA
* * * *
480834 CATAGGTTGTTACGCTTGACCTCGG-CTCAAAATCACTGGTGACATAAGCAGTTACACTTGGCCT
1 CATAGGCTGTTACACTAGACCTCGGTC-CAAAATCACTGCTGACATAAGCAGTTACACTTGGCCT
*
480898 TGGCTCAAAATCACTA
65 CGGCTCAAAATCACTA
480914 GTGTATGGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
83 1 0.01
84 66 0.99
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (84 bp):
CATAGGCTGTTACACTAGACCTCGGTCCAAAATCACTGCTGACATAAGCAGTTACACTTGGCCTC
GGCTCAAAATCACTACTGA
Found at i:481132 original size:204 final size:203
Alignment explanation
Indices: 480842--481396 Score: 678
Period size: 204 Copynumber: 2.7 Consensus size: 203
480832 GACATAGGTT
* * **
480842 GTTACGCTTGACCTCGGCTCAAAATCACTGGTGACATAAGCAGTTACACTTGGCCTTGGCTCAAA
1 GTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAGCAGTTACACTTGGCCTTGGCTCAAA
* * * * *
480907 ATCACTAGTGTATGGTTTCTTATGTCCATTAAGACCAACATCATCGCTTCCATAGGTCGTTATAC
66 ATCACTA-TGAATGATTTCTTATGTCCATTAAGACCAACATCATCGCCTCCATAGGCCGTTACAC
* * * *
480972 TTGGCCTCGGTTCAAAATAACCGATGAATGGCTTCTTCTCTCGTTTAAGATCAACATCATTGCCA
130 TTGGCCTCGGTTCAAAAGAACCGACGAATGACTTCTTCTCTCGTTTAAGACCAACATCATTGCCA
481037 CCATAAGAC
195 CCATAAGAC
* * * *
481046 GTTACTCTTGGCCTCGGTTCAAAATCACTACTGATATAAGCTGTAACACTTGGCCTTGGCTCAAA
1 GTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAGCAGTTACACTTGGCCTTGGCTCAAA
* * * *
481111 GTCACTACTGAATGATTTCTTATGTCCTTTAAGACCAGCATCATCGCCTCCATAGGCCGTTACGC
66 ATCACTA-TGAATGATTTCTTATGTCCATTAAGACCAACATCATCGCCTCCATAGGCCGTTACAC
* * * * *
481176 TTGGTCTCGGTTCAAAAGCACTGGCGAATGACTTCTTCTCTCGTTTAAGGCCAACATCATTGCCA
130 TTGGCCTCGGTTCAAAAGAACCGACGAATGACTTCTTCTCTCGTTTAAGACCAACATCATTGCCA
*
481241 CCATAAGCC
195 CCATAAGAC
* * * * *
481250 GTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAGGCCGTTACGCTTGGTCTTGGTTCAAA
1 GTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAGCAGTTACACTTGGCCTTGGCTCAAA
* *** * * * * * * *
481315 ATCACCGATGAATGATTTCTTCCCTCCTTTGAGACCAACACCATCTCCGCCATAGGCTGTTACGC
66 ATCA-CTATGAATGATTTCTTATGTCCATTAAGACCAACATCATCGCCTCCATAGGCCGTTACAC
* *
481380 TAGGCTTCGGTTCAAAA
130 TTGGCCTCGGTTCAAAA
481397 TCATTGCTGG
Statistics
Matches: 300, Mismatches: 50, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
204 298 0.99
205 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (203 bp):
GTTACGCTTGGCCTCGGTTCAAAATCACTACTGACATAAGCAGTTACACTTGGCCTTGGCTCAAA
ATCACTATGAATGATTTCTTATGTCCATTAAGACCAACATCATCGCCTCCATAGGCCGTTACACT
TGGCCTCGGTTCAAAAGAACCGACGAATGACTTCTTCTCTCGTTTAAGACCAACATCATTGCCAC
CATAAGAC
Found at i:481234 original size:81 final size:81
Alignment explanation
Indices: 481120--481278 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 81
481110 AGTCACTACT
* * * * * *
481120 GAATGATTTCTTATGTCCTTTAAGACCAGCATCATCGCCTCCATAGGCCGTTACGCTTGGTCTCG
1 GAATGACTTCTTATCTCCTTTAAGACCAACATCATCGCCACCATAAGCCGTTACGCTTGGCCTCG
481185 GTTCAAAAGCACTGGC
66 GTTCAAAAGCACTGGC
* * * *
481201 GAATGACTTCTTCTCTCGTTTAAGGCCAACATCATTGCCACCATAAGCCGTTACGCTTGGCCTCG
1 GAATGACTTCTTATCTCCTTTAAGACCAACATCATCGCCACCATAAGCCGTTACGCTTGGCCTCG
*
481266 GTTCAAAATCACT
66 GTTCAAAAGCACT
481279 ACTGACATAG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (81 bp):
GAATGACTTCTTATCTCCTTTAAGACCAACATCATCGCCACCATAAGCCGTTACGCTTGGCCTCG
GTTCAAAAGCACTGGC
Found at i:481380 original size:123 final size:123
Alignment explanation
Indices: 481161--481519 Score: 407
Period size: 123 Copynumber: 2.9 Consensus size: 123
481151 TCATCGCCTC
* * * ** * * *
481161 CATAGGCCGTTACGCTTGGTCTCGGTTCAAAAGCACTGGCGAATGACTTCTTCTCTCGTTTAAGG
1 CATAGGCCGTTACGCTTGGTCTTGGTTCAAAATCACCGATGAATGATTTCTTCTCTCCTTTAAGA
*
481226 CCAACATCAT-TGCCACCATAAGCCGTTACGCTTGGCCTCGGTTCAAAATCACTACTGA
66 CCAACACCATCT-CCACCATAAGCCGTTACGCTTGGCCTCGGTTCAAAATCACTACTGA
* *
481284 CATAGGCCGTTACGCTTGGTCTTGGTTCAAAATCACCGATGAATGATTTCTTCCCTCCTTTGAGA
1 CATAGGCCGTTACGCTTGGTCTTGGTTCAAAATCACCGATGAATGATTTCTTCTCTCCTTTAAGA
* * * * * * * *
481349 CCAACACCATCTCCGCCATAGGCTGTTACGCTAGGCTTCGGTTCAAAATCATTGCTGG
66 CCAACACCATCTCCACCATAAGCCGTTACGCTTGGCCTCGGTTCAAAATCACTACTGA
* * * * * *
481407 CATAAGCTGTTACGCTTGGCCTTGGCTCAAAATCACC-AGTGAATGGTTTCTTTTCTCCTTTAAG
1 CATAGGCCGTTACGCTTGGTCTTGGTTCAAAATCACCGA-TGAATGATTTCTTCTCTCCTTTAAG
* * * * * *
481471 ACCAGCACCATCACCTCCATAAGCCGTCACACTTGGTCTCGGTTCAAAA
65 ACCAACACCATCTCCACCATAAGCCGTTACGCTTGGCCTCGGTTCAAAA
481520 ACACCAGCGA
Statistics
Matches: 197, Mismatches: 37, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
122 1 0.01
123 195 0.99
124 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (123 bp):
CATAGGCCGTTACGCTTGGTCTTGGTTCAAAATCACCGATGAATGATTTCTTCTCTCCTTTAAGA
CCAACACCATCTCCACCATAAGCCGTTACGCTTGGCCTCGGTTCAAAATCACTACTGA
Found at i:481582 original size:327 final size:327
Alignment explanation
Indices: 480957--481604 Score: 814
Period size: 327 Copynumber: 2.0 Consensus size: 327
480947 TCATCGCTTC
* * * * *
480957 CATAGGTCGTTATACTTGGCCTCGGTTCAAAATAACCGATGAATGGCTTCTTCTCTCGTTTAAGA
1 CATAGGCCGTTACACTTGGCCTCGGTTCAAAATAACCGATGAATGACTTCTTCCCTCCTTTAAGA
* * * * *
481022 TCAACATCATTGCCACCATAAGACGTTACTCTTGGCCTCGGTTCAAAATCACTACTGATATAAGC
66 CCAACACCATTGCCACCATAAGACGTTACGCTAGGCCTCGGTTCAAAATCACTACTGACATAAGC
* * * *
481087 TGTAACACTTGGCCTTGGCTCAAAGTCACTACTGAATGATTTCTTATGTCCTTTAAGACCAGCAT
131 TGTAACACTTGGCCTTGGCTCAAAATCACCACTGAATGATTTCTTATCTCCTTTAAGACCAGCAC
* * * * * ** * *
481152 CATCGCCTCCATAGGCCGTTACGCTTGGTCTCGGTTCAAAAGCACTGGCGAATGACTTCTTCTCT
196 CATCACCTCCATAAGCCGTCACACTTGGTCTCGGTTCAAAAACACCAGCGAACGACTTCTTCACT
* * * * *
481217 CGTTTAAGGCCAACATCATTGCCACCATAAGCCGTTACGCTTGGCCTCGGTTCAAAATCACTACT
261 CGGTGAAGACCAACATCATTGCCACCATAAGACGTTACGCTTGGCATCGGTTCAAAATCACTACT
481282 GA
326 GA
* * * * * *
481284 CATAGGCCGTTACGCTTGGTCTTGGTTCAAAATCACCGATGAATGATTTCTTCCCTCCTTTGAGA
1 CATAGGCCGTTACACTTGGCCTCGGTTCAAAATAACCGATGAATGACTTCTTCCCTCCTTTAAGA
* * * * * *
481349 CCAACACCATCT-CCGCCAT-AGGCTGTTACGCTAGGCTTCGGTTCAAAATCATTGCTGGCATAA
66 CCAACACCAT-TGCCACCATAAGAC-GTTACGCTAGGCCTCGGTTCAAAATCACTACTGACATAA
* * * * *
481412 GCTGTTACGCTTGGCCTTGGCTCAAAATCACCAGTGAATGGTTTCTTTTCTCCTTTAAGACCAGC
129 GCTGTAACACTTGGCCTTGGCTCAAAATCACCACTGAATGATTTCTTATCTCCTTTAAGACCAGC
**
481477 ACCATCACCTCCATAAGCCGTCACACTTGGTCTCGGTTCAAAAACACCAGCGAACGGTTTCTTCA
194 ACCATCACCTCCATAAGCCGTCACACTTGGTCTCGGTTCAAAAACACCAGCGAACGACTTCTTCA
* * *
481542 CTCGGTGAAGACCAACATCGTTGCCACCGTAGGACGTTACGCTTGGCATCGGTTCAAAATCAC
259 CTCGGTGAAGACCAACATCATTGCCACCATAAGACGTTACGCTTGGCATCGGTTCAAAATCAC
481605 CAGCGCCGGC
Statistics
Matches: 269, Mismatches: 50, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
326 3 0.01
327 265 0.99
328 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (327 bp):
CATAGGCCGTTACACTTGGCCTCGGTTCAAAATAACCGATGAATGACTTCTTCCCTCCTTTAAGA
CCAACACCATTGCCACCATAAGACGTTACGCTAGGCCTCGGTTCAAAATCACTACTGACATAAGC
TGTAACACTTGGCCTTGGCTCAAAATCACCACTGAATGATTTCTTATCTCCTTTAAGACCAGCAC
CATCACCTCCATAAGCCGTCACACTTGGTCTCGGTTCAAAAACACCAGCGAACGACTTCTTCACT
CGGTGAAGACCAACATCATTGCCACCATAAGACGTTACGCTTGGCATCGGTTCAAAATCACTACT
GA
Found at i:484746 original size:23 final size:21
Alignment explanation
Indices: 484705--484751 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
484695 AATCTTTTAA
*
484705 AATCCTAGAAATACTAAAGAT
1 AATCCTAGAAATACAAAAGAT
484726 AATCCTAAGAAAATACAAAAGAT
1 AATCCT-AG-AAATACAAAAGAT
484749 AAT
1 AAT
484752 TCTGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
23 15 0.65
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCCTAGAAATACAAAAGAT
Found at i:484777 original size:24 final size:26
Alignment explanation
Indices: 484748--484796 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
484738 ATACAAAAGA
484748 TAATTCTGAAAA-AT-AATT-TAAATT
1 TAATTCT-AAAAGATAAATTCTAAATT
484772 TAATTCTAAAAGATAAATTCTAAAT
1 TAATTCTAAAAGATAAATTCTAAAT
484797 CTTGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 9 0.41
25 4 0.18
26 5 0.23
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (26 bp):
TAATTCTAAAAGATAAATTCTAAATT
Found at i:485031 original size:69 final size:69
Alignment explanation
Indices: 484908--485071 Score: 197
Period size: 69 Copynumber: 2.4 Consensus size: 69
484898 GTTTCATGCC
* * * ** * *
484908 CAATTACCTATCTCAGGAGGACATGAAGAATGCTTTTCTCAAGGACTTCGACCCCAACCGTCCTC
1 CAATTACCTATCTCATGAGGCCATGAAAAACACTTTTCTCAAAGACTTCAACCCCAACCGTCCTC
484973 -AGTA
66 GA-TA
* *
484977 CAATTACCTATCTCATGAGGCCATGAAAAACACTTTTCTCAAATATTTCAACCCCAACCGTCCTC
1 CAATTACCTATCTCATGAGGCCATGAAAAACACTTTTCTCAAAGACTTCAACCCCAACCGTCCTC
485042 GATA
66 GATA
* *
485046 CAATTATCTATC-CCTAGAGGCCATGA
1 CAATTACCTATCTCAT-GAGGCCATGA
485072 TCTCTTTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
68 2 0.02
69 79 0.96
70 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.26
Consensus pattern (69 bp):
CAATTACCTATCTCATGAGGCCATGAAAAACACTTTTCTCAAAGACTTCAACCCCAACCGTCCTC
GATA
Found at i:485553 original size:13 final size:14
Alignment explanation
Indices: 485535--485563 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
485525 TAGCTTAATA
485535 AAAAATAA-ATTTT
1 AAAAATAACATTTT
485548 AAAAATAACATTTT
1 AAAAATAACATTTT
485562 AA
1 AA
485564 TTATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAAATAACATTTT
Found at i:492610 original size:2 final size:2
Alignment explanation
Indices: 492603--492633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
492593 AAAACTAGTT
492603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
492634 TAGACTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:494510 original size:127 final size:128
Alignment explanation
Indices: 494348--494584 Score: 404
Period size: 127 Copynumber: 1.9 Consensus size: 128
494338 AGGCAGGGGC
*
494348 CATTTTTTGGTTAGAAATGAGTGCCACTCTAGTGGTTTCCTAATTTTCTTGCTTGTTAAACTTCT
1 CATTTTTTGGTTAGAAATGAGTGCCACTCGAGTGGTTTCCTAATTTTCTTGCTTGTTAAACTTCT
*
494413 GACCCATCAATGCTGTTCTCACAC-TCATTTTTCTTGTAGTATTCGTGTTCTATACTTTCCGA
66 GACCCATCAATGCTGTTCTCACACTTCATTTTTCTTGAAGTATTCGTGTTCTATACTTTCCGA
* * * *
494475 CATTTTTTTGTTAGAAATGGGTGCCATTGGAGTGGTTTCCTAATTTTCTTGCTTGTTAAACTTCT
1 CATTTTTTGGTTAGAAATGAGTGCCACTCGAGTGGTTTCCTAATTTTCTTGCTTGTTAAACTTCT
*
494540 GACCCATCAATGCTGTTCTTACACTTCATTTTTCTTGAAGTATTC
66 GACCCATCAATGCTGTTCTCACACTTCATTTTTCTTGAAGTATTC
494585 TATGCTCGTG
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
127 83 0.81
128 19 0.19
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (128 bp):
CATTTTTTGGTTAGAAATGAGTGCCACTCGAGTGGTTTCCTAATTTTCTTGCTTGTTAAACTTCT
GACCCATCAATGCTGTTCTCACACTTCATTTTTCTTGAAGTATTCGTGTTCTATACTTTCCGA
Found at i:502786 original size:16 final size:16
Alignment explanation
Indices: 502765--502795 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
502755 ATTTTAGAAA
502765 AAATAAAAATCAAATC
1 AAATAAAAATCAAATC
502781 AAATAAAAATCAAAT
1 AAATAAAAATCAAAT
502796 AAGACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAAATCAAATC
Found at i:502804 original size:16 final size:16
Alignment explanation
Indices: 502769--502806 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
502759 TAGAAAAAAT
*
502769 AAAAATCAAATCAAAT
1 AAAAATCAAATCAAAC
502785 AAAAATCAAAT-AAGAC
1 AAAAATCAAATCAA-AC
502801 AAAAAT
1 AAAAAT
502807 TTCATTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAATCAAATCAAAC
Found at i:504867 original size:40 final size:40
Alignment explanation
Indices: 504823--504904 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
504813 AGCAGGTTTA
504823 TAATACACTTCGGTGTATATGATGGGCACAACATTATGTG
1 TAATACACTTCGGTGTATATGATGGGCACAACATTATGTG
* * *
504863 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGATGGGCACAACATTATGTG
504903 TA
1 TA
504905 GCACTACAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGATGGGCACAACATTATGTG
Found at i:505107 original size:45 final size:45
Alignment explanation
Indices: 505009--505132 Score: 169
Period size: 45 Copynumber: 2.8 Consensus size: 45
504999 GTAAGCATAC
** * * *
505009 AAATAAGCTTACGAGCTTATGAAAT-AATGACAAATATATTAGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGATAAGTATATTAGAA
* *
505053 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGGATAAATGATAAGTATATTAGAA
*
505098 AAATAAGCTTACGAGCTTATAGGATAAATGATAAG
1 AAATAAGCTTACGAGCTTATGGGATAAATGATAAG
505133 AAATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 23 0.33
45 47 0.67
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.28
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGATAAGTATATTAGAA
Found at i:505126 original size:25 final size:25
Alignment explanation
Indices: 505053--505126 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
505043 TATATTAGTA
*
505053 AAATAAGCTTACGAGCTTATGGGAT
1 AAATAAGCTTACGAGCTTATAGGAT
* * *
505078 AAAT--G-GTA--AG-TATATTGGAA
1 AAATAAGCTTACGAGCT-TATAGGAT
505098 AAATAAGCTTACGAGCTTATAGGAT
1 AAATAAGCTTACGAGCTTATAGGAT
505123 AAAT
1 AAAT
505127 GATAAGAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 1 0.03
20 12 0.33
22 3 0.08
23 3 0.08
25 16 0.44
26 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (25 bp):
AAATAAGCTTACGAGCTTATAGGAT
Found at i:512823 original size:28 final size:28
Alignment explanation
Indices: 512742--512812 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
512732 AAATTACATG
*
512742 TTTAGTACCTAAACTATCCTTTTTTTGT
1 TTTAGTACCTAAACTATCATTTTTTTGT
512770 TTTAGTACCTAAACTATCATTTTTTTGT
1 TTTAGTACCTAAACTATCATTTTTTTGT
512798 TTTAGTACCTAAACT
1 TTTAGTACCTAAACT
512813 TTTAATTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTAGTACCTAAACTATCATTTTTTTGT
Found at i:514878 original size:17 final size:18
Alignment explanation
Indices: 514837--514879 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
514827 ATAATGTTTT
*
514837 TTTATAAATATAATAATA
1 TTTAAAAATATAATAATA
514855 TTTAAAAATA-AATAA-A
1 TTTAAAAATATAATAATA
*
514871 TTTCAAAAT
1 TTTAAAAAT
514880 CACCAGATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTAAAAATATAATAATA
Found at i:516597 original size:21 final size:21
Alignment explanation
Indices: 516573--516784 Score: 122
Period size: 21 Copynumber: 9.5 Consensus size: 21
516563 TGTCGCCTCC
*
516573 CCACCACCACCCGTCTTCTCT
1 CCACCACCACCCGTCTTCTCA
* * *
516594 CCACC-TCATCCGGTCCTCTCA
1 CCACCACCA-CCCGTCTTCTCA
* * * * *
516615 CCGCCTCCTCCAGTCTACTCA
1 CCACCACCACCCGTCTTCTCA
516636 CCACCACCACCCGTCTACTCTCCA
1 CCACCACCACCCGTCT--TCT-CA
*
516660 CCCCCACCACCTCCAGTTCTT-TCA
1 CCACCACCA-C-CC-G-TCTTCTCA
*
516684 CCACCACCACCAGTCTACTCTCCA
1 CCACCACCACCCGTCT--TCT-CA
*
516708 CCACCACCACCTCCAGTCCTCTCA
1 CCACCACCA-C-CC-GTCTTCTCA
* * * *
516732 CCCCCACCACCAGTCTACTCT
1 CCACCACCACCCGTCTTCTCA
*
516753 CCACCACCACCCGTCTACTCA
1 CCACCACCACCCGTCTTCTCA
*
516774 CCACCTCCACC
1 CCACCACCACC
516785 TAAACCGGAC
Statistics
Matches: 146, Mismatches: 29, Indels: 32
0.71 0.14 0.15
Matches are distributed among these distances:
20 5 0.03
21 74 0.51
22 4 0.03
23 5 0.03
24 41 0.28
25 6 0.04
26 4 0.03
27 4 0.03
28 3 0.02
ACGTcount: A:0.19, C:0.57, G:0.05, T:0.19
Consensus pattern (21 bp):
CCACCACCACCCGTCTTCTCA
Found at i:516673 original size:48 final size:46
Alignment explanation
Indices: 516621--516763 Score: 205
Period size: 48 Copynumber: 3.0 Consensus size: 46
516611 CTCACCGCCT
*
516621 CCTCCAGTCTACTCACCACCACCACCCGTCTACTCTCCACCCCCACCA
1 CCTCCAGTCT-CTCACCACCACCACCAGTCTACTCTCCA-CCCCACCA
*
516669 CCTCCAGTTCTTTCACCACCACCACCAGTCTACTCTCCACCACCACCA
1 CCTCCAG-TCTCTCACCACCACCACCAGTCTACTCTCCACC-CCACCA
*
516717 CCTCCAGTCCTCTCACCCCCACCACCAGTCTACTCTCCACCACCACC
1 CCTCCAGT-CTCTCACCACCACCACCAGTCTACTCTCCACC-CCACC
516764 CGTCTACTCA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
47 3 0.03
48 82 0.93
49 3 0.03
ACGTcount: A:0.21, C:0.57, G:0.04, T:0.18
Consensus pattern (46 bp):
CCTCCAGTCTCTCACCACCACCACCAGTCTACTCTCCACCCCACCA
Found at i:516701 original size:69 final size:69
Alignment explanation
Indices: 516624--516784 Score: 186
Period size: 69 Copynumber: 2.3 Consensus size: 69
516614 ACCGCCTCCT
* * *
516624 CCAGTCTACTCACCACCACCACC-CGTCTACT-CTC-CACCCCCACCACCTCCAGTTCT-TTCAC
1 CCAGTCTACTCACCACCACCACCACCTCCACTCCTCTCACCCCCACCA---CCAG-TCTACTCAC
516685 CACCACCA
62 CACCACCA
* * *
516693 CCAGTCTACTCTCCACCACCACCACCTCCAGTCCTCTCACCCCCACCACCAGTCTACTCTCCACC
1 CCAGTCTACTCACCACCACCACCACCTCCACTCCTCTCACCCCCACCACCAGTCTACTCACCACC
516758 ACCA
66 ACCA
* *
516762 CCCGTCTACTCACCACCTCCACC
1 CCAGTCTACTCACCACCACCACC
516785 TAAACCGGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
68 3 0.04
69 57 0.72
70 5 0.06
71 3 0.04
72 11 0.14
ACGTcount: A:0.21, C:0.57, G:0.04, T:0.18
Consensus pattern (69 bp):
CCAGTCTACTCACCACCACCACCACCTCCACTCCTCTCACCCCCACCACCAGTCTACTCACCACC
ACCA
Found at i:518513 original size:34 final size:34
Alignment explanation
Indices: 518474--518558 Score: 170
Period size: 34 Copynumber: 2.5 Consensus size: 34
518464 CGATTATATA
518474 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
518508 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
518542 TATATATATAATATTTT
1 TATATATATAATATTTT
518559 CGGGTTCGGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:518555 original size:9 final size:9
Alignment explanation
Indices: 518466--518555 Score: 69
Period size: 9 Copynumber: 9.8 Consensus size: 9
518456 CCCCGCCCCG
518466 ATTATATAT
1 ATTATATAT
518475 ATATATATAAT
1 AT-TATAT-AT
*
518486 ATTTTATAT
1 ATTATATAT
*
518495 ATTTTATATT
1 ATTATATA-T
518505 AATTATATAT
1 -ATTATATAT
518515 A-TA-ATAT
1 ATTATATAT
*
518522 TTTATATAT
1 ATTATATAT
*
518531 TTTATAT-T
1 ATTATATAT
518539 AATTATATAT
1 -ATTATATAT
*
518549 ATAATAT
1 ATTATAT
518556 TTTCGGGTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
7 4 0.06
8 5 0.07
9 36 0.53
10 12 0.18
11 11 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATATAT
Found at i:518599 original size:25 final size:27
Alignment explanation
Indices: 518548--518599 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
518538 TAATTATATA
**
518548 TATAATATTTTCGGGTTCGGGTTCGGG
1 TATAATATTTTCGGGTTCGGGGACGGG
518575 TATAATA-TTTCGGG-TCGGGGACGGG
1 TATAATATTTTCGGGTTCGGGGACGGG
518600 GCAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
26 7 0.30
27 7 0.30
ACGTcount: A:0.17, C:0.12, G:0.37, T:0.35
Consensus pattern (27 bp):
TATAATATTTTCGGGTTCGGGGACGGG
Found at i:523796 original size:48 final size:48
Alignment explanation
Indices: 523741--523838 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
523731 TAATCAATAG
523741 TACGTTGAACTCGTTTTTAGGTTTAAAATATTTTCTAAGATAAAAAGA
1 TACGTTGAACTCGTTTTTAGGTTTAAAATATTTTCTAAGATAAAAAGA
523789 TACGTTGAACTCGTTTTTAGGTTTAAAATATTTTCTAAGATAAAAAGA
1 TACGTTGAACTCGTTTTTAGGTTTAAAATATTTTCTAAGATAAAAAGA
523837 TA
1 TA
523839 TTAAAGGTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (48 bp):
TACGTTGAACTCGTTTTTAGGTTTAAAATATTTTCTAAGATAAAAAGA
Found at i:532677 original size:29 final size:31
Alignment explanation
Indices: 532609--532678 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
532599 TTTAAAAACT
*
532609 AGTGGTATAATTGTATCAAAAATCAAAGTTT
1 AGTGGTATAATTGTATCAAAAATCAAAGTTC
* * * *
532640 AGTGTTATAATTG-A-CAACATTGAAAGTTC
1 AGTGGTATAATTGTATCAAAAATCAAAGTTC
532669 AGTGGTATAA
1 AGTGGTATAA
532679 GCGATACATC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 20 0.61
30 1 0.03
31 12 0.36
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (31 bp):
AGTGGTATAATTGTATCAAAAATCAAAGTTC
Found at i:533271 original size:60 final size:59
Alignment explanation
Indices: 533216--533355 Score: 165
Period size: 60 Copynumber: 2.4 Consensus size: 59
533206 GTAAAAAATA
* *
533216 TACAAATGGTCCCTCGACTATAG-GTATTGTTTTATTAAGTCTCCCGATTGTTAAAAGT
1 TACAAATGGTCCCTCGACTATAGAGTATTGTTTTATTAAGTCCCCCGACTGTTAAAAGT
* * * * * * *
533274 TACATAATAGTCCTTTGACTCTAGAGTGTTGTTTTATTGAGTCCCCCGGCTGTTAAAAGT
1 TACA-AATGGTCCCTCGACTATAGAGTATTGTTTTATTAAGTCCCCCGACTGTTAAAAGT
*
533334 TACAAAATGGTCACTCGACTAT
1 TAC-AAATGGTCCCTCGACTAT
533356 TCATTATGTT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
58 4 0.06
59 15 0.23
60 45 0.69
61 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (59 bp):
TACAAATGGTCCCTCGACTATAGAGTATTGTTTTATTAAGTCCCCCGACTGTTAAAAGT
Found at i:534846 original size:108 final size:112
Alignment explanation
Indices: 534728--534961 Score: 359
Period size: 116 Copynumber: 2.1 Consensus size: 112
534718 AATTTATATA
* * *
534728 TATATATATAATTACACAAATA-G-AA-CAAT-TTTTAGTTGACAAGTTGAGAGCATCATCTTCA
1 TATATATATAATTACACAAATAGGAAATCAATGATTTAGTTAACAAGTTGAGAGCACCATCTTCA
*
534789 TTGAGTATTTAAATTTAACCTTTGAAAATTCCACCTAAGTTTCACAT
66 TTGAGTATTTAAATTTAACCTTTGAAAATTCCACCTAAGTTCCACAT
534836 TATATATATAATTACACAAATAGGACAATTTTCAATGATTTAGTTAACAAGTTGAGAGCACCATC
1 TATATATATAATTACACAAATAGGA-AA---TCAATGATTTAGTTAACAAGTTGAGAGCACCATC
*
534901 TTCGTTGAGTATTTAAATTTAACCTTTGAAAATTCCACCTAAGTTCCACAT
62 TTCATTGAGTATTTAAATTTAACCTTTGAAAATTCCACCTAAGTTCCACAT
534952 TATATATATA
1 TATATATATA
534962 TAGGTGTAAG
Statistics
Matches: 113, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
108 22 0.19
109 1 0.01
111 2 0.02
115 4 0.04
116 84 0.74
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (112 bp):
TATATATATAATTACACAAATAGGAAATCAATGATTTAGTTAACAAGTTGAGAGCACCATCTTCA
TTGAGTATTTAAATTTAACCTTTGAAAATTCCACCTAAGTTCCACAT
Found at i:538351 original size:60 final size:59
Alignment explanation
Indices: 538262--538401 Score: 151
Period size: 60 Copynumber: 2.3 Consensus size: 59
538252 TTAAATGTTC
* *
538262 CAATTTCATCCTCAAACTATGATTATCATTATAAATTAAT-CATCAAAC-TTTTGAACATTT
1 CAATTTCATCC-CAAACTATGACTATCATTATAAATTAATAC-CCAAACTTTTTGAACA-TT
* **
538322 CAATTTCATCTCCAAACTATGACCT-TCATTTTAAATTTGTACCCAAACTTTTTGAACATT
1 CAATTTCATC-CCAAACTATGA-CTATCATTATAAATTAATACCCAAACTTTTTGAACATT
*
538382 CTAATTTCAACCCAAACTAT
1 C-AATTTCATCCCAAACTAT
538402 ACATATATAC
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
60 49 0.71
61 20 0.29
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.39
Consensus pattern (59 bp):
CAATTTCATCCCAAACTATGACTATCATTATAAATTAATACCCAAACTTTTTGAACATT
Found at i:538638 original size:58 final size:58
Alignment explanation
Indices: 538542--538724 Score: 178
Period size: 57 Copynumber: 3.1 Consensus size: 58
538532 ACATAATGAA
* **
538542 TTTAGGGATGAAA-TTGCAATATTCAAAAGTTTGGGGACTAATTTAGAA-AGGTTCATAG
1 TTTAGGGA-GAAACTAG-AATATTCAAAAGTTTAAGGACTAATTTAGAAGAGGTTCATAG
* **
538600 TTTAGGGAAGAAACTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAATCATAG
1 TTTAGGG-AGAAACTAGAATATTCAAAAGTTTAAGGACTAATTTAGAA-GAGGTTCATAG
* * ** *
538660 TTT-GGG-GATAGTAGAATATTCAAATTTTTAAGGACTAATTTAAAATGAGAGTT-ATAG
1 TTTAGGGAGAAACTAGAATATTCAAAAGTTTAAGGACTAATTTAGAA-GAG-GTTCATAG
538717 TTTAGGGA
1 TTTAGGGA
538725 CATATGATGC
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
57 44 0.42
58 43 0.41
59 6 0.06
60 11 0.11
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (58 bp):
TTTAGGGAGAAACTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAGAGGTTCATAG
Found at i:538646 original size:29 final size:29
Alignment explanation
Indices: 538563--538649 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
538553 AATTGCAATA
* *
538563 TTCAAAAGTTTGGGGACTAATTTAGAAAGG
1 TTCAAAAGTTTAGGGACTAATTTAG-AATG
* ** **
538593 TTC-ATAGTTTAGGGAAGAAACTAGAATG
1 TTCAAAAGTTTAGGGACTAATTTAGAATG
*
538621 TTCAAAAGTTTAAGGACTAATTTAGAATG
1 TTCAAAAGTTTAGGGACTAATTTAGAATG
538650 AGAATCATAG
Statistics
Matches: 43, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
28 6 0.14
29 34 0.79
30 3 0.07
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (29 bp):
TTCAAAAGTTTAGGGACTAATTTAGAATG
Found at i:539207 original size:17 final size:16
Alignment explanation
Indices: 539159--539208 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
539149 TGATTATTTT
539159 AATTACTAAAAT-TTA
1 AATTACTAAAATATTA
539174 AATTTA-TAAATAATATTA
1 AA-TTACT-AA-AATATTA
539192 AATTCACTAAAATATTA
1 AATT-ACTAAAATATTA
539209 TAAAATTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 12 0.41
18 8 0.28
19 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTACTAAAATATTA
Found at i:548517 original size:13 final size:13
Alignment explanation
Indices: 548488--548522 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
548478 ATAACTAATA
*
548488 ATATTAAAT-ATT
1 ATATTAAATAAAT
548500 ATATTAAATAAAT
1 ATATTAAATAAAT
548513 ATATTAAATA
1 ATATTAAATA
548523 TTTATGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:549900 original size:125 final size:126
Alignment explanation
Indices: 549677--549913 Score: 458
Period size: 125 Copynumber: 1.9 Consensus size: 126
549667 TCTATACATT
549677 GTACCCATTATTTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC
1 GTACCCATTATTTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC
549742 AGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
66 AGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
*
549803 GTACCTATTATTTCACTATTCACGTGAAGGCGCGTT-CCGGGGGCGCGCCTTCCATTATTTCGTC
1 GTACCCATTATTTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC
549867 AGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 AGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
549914 ATAACTTAAA
Statistics
Matches: 110, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
125 75 0.68
126 35 0.32
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (126 bp):
GTACCCATTATTTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTC
AGAGAATATTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
Found at i:550362 original size:33 final size:34
Alignment explanation
Indices: 550301--550400 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
550291 AAATTTAATG
*
550301 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
550335 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
550368 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
550401 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:551008 original size:21 final size:21
Alignment explanation
Indices: 550920--551013 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
550910 TATGGTATAA
*
550920 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
550941 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
550962 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
550983 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
551004 AACCCTGCGG
1 AACCCTGCGG
551014 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:551043 original size:21 final size:21
Alignment explanation
Indices: 551017--551064 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
551007 CCTGCGGAGA
*
551017 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
551038 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
551059 GGGCAT
1 TGGCAT
551065 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:555580 original size:29 final size:29
Alignment explanation
Indices: 555547--555641 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
555537 AAATCTACTG
555547 ACTATTAAAAGTTACAAAATGGTCTTTTA
1 ACTATTAAAAGTTACAAAATGGTCTTTTA
** * ** * *
555576 ACTATGGAGAGTTACTTTATTGAGT-TATTTG
1 ACTATTAAAAGTTAC-AAAATG-GTCT-TTTA
* *
555607 ACTATTAAAAGTTACAAAATGGTCATTCA
1 ACTATTAAAAGTTACAAAATGGTCTTTTA
555636 ACTATT
1 ACTATT
555642 CACTATGTTT
Statistics
Matches: 46, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
29 22 0.48
30 7 0.15
31 17 0.37
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (29 bp):
ACTATTAAAAGTTACAAAATGGTCTTTTA
Found at i:555596 original size:60 final size:60
Alignment explanation
Indices: 555527--555640 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
555517 CTATATGATA
* *
555527 TTACTTTATTAAATCTA-CTGACTATTAAAAGTTACAAAATGGTCTTTTAACTATGGAGAG
1 TTACTTTATTAAAT-TATCTGACTATTAAAAGTTACAAAATGGTCATTCAACTATGGAGAG
* * *
555587 TTACTTTATTGAGTTATTTGACTATTAAAAGTTACAAAATGGTCATTCAACTAT
1 TTACTTTATTAAATTATCTGACTATTAAAAGTTACAAAATGGTCATTCAACTAT
555641 TCACTATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (60 bp):
TTACTTTATTAAATTATCTGACTATTAAAAGTTACAAAATGGTCATTCAACTATGGAGAG
Found at i:561028 original size:103 final size:102
Alignment explanation
Indices: 560849--561062 Score: 331
Period size: 103 Copynumber: 2.1 Consensus size: 102
560839 GCATCAAATT
* * *
560849 TATCTTGATGTGTCAATGTTAAAGATCATAAACTTTATTCTCTAAAGTCAAATGATTATCATATA
1 TATCTCGATGAGTCAATGTTAAAGATCAGAAACTTTATTCTCTAAAGTCAAATGATTATCATATA
560914 TTGATGCAAGATTTATCGT-CAGTTGCTTTACGTGGTTG
66 TTGATGCAAGATTTA-C-TACAGTTGCTTTACGTGGTTG
* * *
560952 TATCTCGATGAGTCAGTGTTAAAGATCAGAGACTTTATTCTCTAAAGTCATATGATTATCATATA
1 TATCTCGATGAGTCAATGTTAAAGATCAGAAACTTTATTCTCTAAAGTCAAATGATTATCATATA
*
561017 TTGATTCAAGATTTACTACCAGTTGCTTTACGTGGTTG
66 TTGATGCAAGATTTACTA-CAGTTGCTTTACGTGGTTG
561055 TATCTCGA
1 TATCTCGA
561063 ATAAGGTGAA
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
101 1 0.01
102 1 0.01
103 100 0.98
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (102 bp):
TATCTCGATGAGTCAATGTTAAAGATCAGAAACTTTATTCTCTAAAGTCAAATGATTATCATATA
TTGATGCAAGATTTACTACAGTTGCTTTACGTGGTTG
Found at i:564670 original size:2 final size:2
Alignment explanation
Indices: 564663--564690 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
564653 ACTCTGTATG
564663 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
564691 GCTTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:568661 original size:2 final size:2
Alignment explanation
Indices: 568654--568681 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
568644 AGTGATGCAC
568654 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
568682 GATGTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569075 original size:59 final size:60
Alignment explanation
Indices: 569006--569148 Score: 243
Period size: 59 Copynumber: 2.4 Consensus size: 60
568996 ATAGACAAGT
*
569006 GACCATTTTGTAACTTTTAATAGTAAAGGGATTCAACAAAGTAACACACTATTATT-GGG
1 GACCATTTTGTAACTTTTAATAGTAAAGGGATTCAACAAAGTAACACACTATTATTAGAG
* *
569065 GACCATTTTGTAACTTTTAATAGTAAAGTGATTCAACAAAGTAACACATTATTATTAGAG
1 GACCATTTTGTAACTTTTAATAGTAAAGGGATTCAACAAAGTAACACACTATTATTAGAG
*
569125 GATCATTTTGTAACTTTTAATAGT
1 GACCATTTTGTAACTTTTAATAGT
569149 TGGGGGGTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 54 0.68
60 25 0.32
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTAAAGGGATTCAACAAAGTAACACACTATTATTAGAG
Found at i:569354 original size:28 final size:28
Alignment explanation
Indices: 569314--569371 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
569304 CCATATGTAA
569314 TGAGGTGAGGGGAGGTAAGGTAGTAGGC
1 TGAGGTGAGGGGAGGTAAGGTAGTAGGC
569342 TGAGGTGAGGGGAGGTAAGGTAGTAGGC
1 TGAGGTGAGGGGAGGTAAGGTAGTAGGC
569370 TG
1 TG
569372 CCACCAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.53, T:0.19
Consensus pattern (28 bp):
TGAGGTGAGGGGAGGTAAGGTAGTAGGC
Found at i:570211 original size:31 final size:30
Alignment explanation
Indices: 570157--570216 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
570147 TAAAATTATG
* *
570157 AGGGTAACTTGAGCTTATCAAATTCTAAGA
1 AGGGTAACATGAGCTTATAAAATTCTAAGA
*
570187 AGGGTGAACATGAGTTTATAAAATTCTAAG
1 AGGGT-AACATGAGCTTATAAAATTCTAAG
570217 GGGACGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (30 bp):
AGGGTAACATGAGCTTATAAAATTCTAAGA
Found at i:570896 original size:43 final size:43
Alignment explanation
Indices: 570849--570939 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
570839 TGAGATTAAA
*
570849 CGACACAAAGGGTGTTTATGTTAACTCGGGTTCAATTCTCATT
1 CGACACAAAGGGTGTTTATGTTAACTCGGGTTCAATTCTCAAT
*
570892 CGACACAAAGGGTGTTTATGTTAATTCGGGTTCAATTCTCAAT
1 CGACACAAAGGGTGTTTATGTTAACTCGGGTTCAATTCTCAAT
570935 CGACA
1 CGACA
570940 TTCAGTCAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (43 bp):
CGACACAAAGGGTGTTTATGTTAACTCGGGTTCAATTCTCAAT
Found at i:575174 original size:2 final size:2
Alignment explanation
Indices: 575167--575191 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
575157 GTGATTAATT
575167 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
575192 TTAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:575237 original size:22 final size:22
Alignment explanation
Indices: 575212--575257 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
575202 AAGAATTTTT
575212 TATT-TGTATATTAATAAAAATA
1 TATTATGTA-ATTAATAAAAATA
* *
575234 TATTATTTAATTATTAAAAATA
1 TATTATGTAATTAATAAAAATA
575256 TA
1 TA
575258 ATAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATGTAATTAATAAAAATA
Found at i:575248 original size:33 final size:34
Alignment explanation
Indices: 575223--575295 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
575213 ATTTGTATAT
575223 TAATAAAAATATATT-ATTTAATTA-TTAAAAATA
1 TAAT-AAAATATATTAATTTAATTATTTAAAAATA
*
575256 TAATAAAATATATTAATTTAATCATTT-AAAATA
1 TAATAAAATATATTAATTTAATTATTTAAAAATA
575289 TAATAAA
1 TAATAAA
575296 TAATTATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
32 10 0.27
33 25 0.68
34 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (34 bp):
TAATAAAATATATTAATTTAATTATTTAAAAATA
Found at i:577303 original size:60 final size:60
Alignment explanation
Indices: 577209--577354 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
577199 ATTTTAGGGT
* * ** *
577209 AAAG-TACATAAATGGTC-CCCGACTATAGCTTACTGCTTTATTAAGTTCAC-T-GATTATTA
1 AAAGTTACA-AAATGATCACCCAACTATAGAGTACTGCTTTATTAAG-TC-CTTCGACTATTA
* * * *
577268 AAAGTTACAAAATGATCATCTAACTATAGAGTACTGCTTTGTTGAGTCCTTCGACTATTA
1 AAAGTTACAAAATGATCACCCAACTATAGAGTACTGCTTTATTAAGTCCTTCGACTATTA
577328 AAAGTTACAAAATGATCACCCAACTAT
1 AAAGTTACAAAATGATCACCCAACTAT
577355 TCATTATGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 14 0.19
60 57 0.79
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (60 bp):
AAAGTTACAAAATGATCACCCAACTATAGAGTACTGCTTTATTAAGTCCTTCGACTATTA
Found at i:579657 original size:5 final size:5
Alignment explanation
Indices: 579647--579690 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
579637 GGAAATGTCT
* * *
579647 TTTTC TTTTC TTTTC TTTTC GTTTC CTTTC TTTTC TGTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
579691 TCTTATCCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:580569 original size:13 final size:13
Alignment explanation
Indices: 580549--580592 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
580539 TGGTTTTATC
580549 AACTGATTTGATT
1 AACTGATTTGATT
* *
580562 AGCTGATTTGATA
1 AACTGATTTGATT
*
580575 AATTGATTTGATT
1 AACTGATTTGATT
580588 AACTG
1 AACTG
580593 TTTATATAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (13 bp):
AACTGATTTGATT
Found at i:580684 original size:2 final size:2
Alignment explanation
Indices: 580679--580709 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
580669 AGTTGTTAAG
580679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
580710 TTTATAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:580819 original size:19 final size:18
Alignment explanation
Indices: 580795--580840 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
580785 TAAAAATTAG
580795 TGAATATTTCTTAAAATTT
1 TGAATATTT-TTAAAATTT
*
580814 TGAATATATTTTTAAATTT
1 TGAATAT-TTTTAAAATTT
580833 T-AATATTT
1 TGAATATTT
580841 ACAAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 2 0.08
18 5 0.20
19 16 0.64
20 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
TGAATATTTTTAAAATTT
Found at i:581660 original size:3 final size:3
Alignment explanation
Indices: 581652--581690 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
581642 GCTTTTACAT
* * *
581652 TAA TAA TAA TAA TAA TAA TAA TAA CAG TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
581691 ATCTGTGGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:590688 original size:21 final size:21
Alignment explanation
Indices: 590664--590704 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
590654 GATAAAAAAT
*
590664 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
590685 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
590705 TTTAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:590836 original size:24 final size:25
Alignment explanation
Indices: 590792--590840 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
590782 ATATGTTAAC
590792 AAAACCGATAAAACATCTAATAATAA
1 AAAACCGATAAAACA-CTAATAATAA
590818 AAAACTCGATAAAA-A-TAATAATA
1 AAAAC-CGATAAAACACTAATAATA
590841 TTTTTGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.36
26 6 0.27
27 8 0.36
ACGTcount: A:0.63, C:0.12, G:0.04, T:0.20
Consensus pattern (25 bp):
AAAACCGATAAAACACTAATAATAA
Found at i:591491 original size:16 final size:16
Alignment explanation
Indices: 591470--591525 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
591460 TTAATCGCTA
591470 AATGATTCAAATGTTG
1 AATGATTCAAATGTTG
***
591486 AATGATT-AAGCATTG
1 AATGATTCAAATGTTG
591501 AATGATTCAAATGTTG
1 AATGATTCAAATGTTG
591517 AATGATTCA
1 AATGATTCA
591526 GAGGCTCTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (16 bp):
AATGATTCAAATGTTG
Found at i:591492 original size:31 final size:31
Alignment explanation
Indices: 591454--591523 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
591444 GTTTACTTCA
* *
591454 GAATGATTAATCGCTAAATGATTCAAATGTT
1 GAATGATTAAGCACTAAATGATTCAAATGTT
* *
591485 GAATGATTAAGCATTGAATGATTCAAATGTT
1 GAATGATTAAGCACTAAATGATTCAAATGTT
591516 GAATGATT
1 GAATGATT
591524 CAGAGGCTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (31 bp):
GAATGATTAAGCACTAAATGATTCAAATGTT
Found at i:592935 original size:20 final size:20
Alignment explanation
Indices: 592910--592957 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
592900 GAAATTTAAA
*
592910 TTAGGATTTGTCTCTTATTT
1 TTAGGATTTATCTCTTATTT
* *
592930 TTAGGAATTATCTTTTATTT
1 TTAGGATTTATCTCTTATTT
*
592950 ATAGGATT
1 TTAGGATT
592958 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (20 bp):
TTAGGATTTATCTCTTATTT
Found at i:593150 original size:17 final size:18
Alignment explanation
Indices: 593121--593161 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
593111 TATAAAATTA
593121 CTTTTCTTTTTTA-CTTT
1 CTTTTCTTTTTTATCTTT
*
593138 CTTTT-TTTCTTTATTTTT
1 CTTTTCTTT-TTTATCTTT
593156 CTTTTC
1 CTTTTC
593162 AAGTTTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 9 0.45
18 8 0.40
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTCTTTTTTATCTTT
Found at i:595141 original size:60 final size:59
Alignment explanation
Indices: 595037--595194 Score: 226
Period size: 60 Copynumber: 2.6 Consensus size: 59
595027 CATTTATTTC
* * * *
595037 AAATTAGTGCTTAAACTTTAAAAATTCCAATTACATCCTCAAACTATGACTCTCATTCT
1 AAATTAGTCCTTAAACTTTTAAAATTCCAATTTCATCCCCAAACTATGACTCTCATTCT
*
595096 AAATTAGTCCTTAAACTTTTTAAAATTCCAATTTCATCCCCAAACTATGAGTCTCATTCT
1 AAATTAGTCCTTAAAC-TTTTAAAATTCCAATTTCATCCCCAAACTATGACTCTCATTCT
* **
595156 AAATTAGTCCCTAAACTTTTAGATCTTCCAATTTCATCC
1 AAATTAGTCCTTAAACTTTTA-AAATTCCAATTTCATCC
595195 AAATATGTAG
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
59 20 0.22
60 69 0.78
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (59 bp):
AAATTAGTCCTTAAACTTTTAAAATTCCAATTTCATCCCCAAACTATGACTCTCATTCT
Found at i:595411 original size:59 final size:59
Alignment explanation
Indices: 595312--595469 Score: 194
Period size: 59 Copynumber: 2.6 Consensus size: 59
595302 GTATAATTTA
* * ** *
595312 GGATAAAATTGAAATATTTATAAAGTTTGGGGACCAATTTAGAATGAGACTCATAGTTTGG
1 GGATGAAATTGGAAT-TTTA-AAAGTTTAAGGACTAATTTAGAATGAGACTCATAGTTTGG
*
595373 GG-TGAAATTGGAATTTTAAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTTTGG
1 GGATGAAATTGGAATTTT-AAAAGTTTAAGGACTAATTTAGAATGAGACTCATAGTTTGG
* *
595432 GGATGTAATTGGAAATTTT-AAAGTTTAAGAACTAATTT
1 GGATGAAATTGG-AATTTTAAAAGTTTAAGGACTAATTT
595470 GAAATAAAGG
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
59 59 0.69
60 19 0.22
61 8 0.09
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (59 bp):
GGATGAAATTGGAATTTTAAAAGTTTAAGGACTAATTTAGAATGAGACTCATAGTTTGG
Found at i:595486 original size:59 final size:59
Alignment explanation
Indices: 595347--595494 Score: 169
Period size: 59 Copynumber: 2.5 Consensus size: 59
595337 TTTGGGGACC
* * * *
595347 AATTTAGAATGAGACTCATAGTTTGGGG-TGAAATTGGAATTTTAAAAAGTTTAAGGACT
1 AATTTAGAATAAGAGTAATAGTTTGGGGATGAAATTGGAATTTT-AAAAGTTTAAGAACT
* * *
595406 AATTTAGAATGAGAGTCATAGTTTGGGGATGTAATTGGAAATTTT-AAAGTTTAAGAACT
1 AATTTAGAATAAGAGTAATAGTTTGGGGATGAAATTGG-AATTTTAAAAGTTTAAGAACT
595465 AATTT-GAAATAA-AGGTAATAGTTTGGGGAT
1 AATTTAG-AATAAGA-GTAATAGTTTGGGGAT
595495 ATATGATGCA
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
58 2 0.03
59 64 0.80
60 8 0.10
61 6 0.08
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (59 bp):
AATTTAGAATAAGAGTAATAGTTTGGGGATGAAATTGGAATTTTAAAAGTTTAAGAACT
Found at i:595548 original size:16 final size:16
Alignment explanation
Indices: 595527--595559 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
595517 TTTAAATCAC
595527 GTTTTTTTATTAACCT
1 GTTTTTTTATTAACCT
595543 GTTTTTTTATTAACCT
1 GTTTTTTTATTAACCT
595559 G
1 G
595560 AAGTAAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (16 bp):
GTTTTTTTATTAACCT
Found at i:606067 original size:2 final size:2
Alignment explanation
Indices: 606062--606086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
606052 ACACACACAC
606062 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
606087 ATAAATGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:606954 original size:12 final size:13
Alignment explanation
Indices: 606923--606954 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
606913 CCCTCATCAG
606923 ATTCATCATCTTC
1 ATTCATCATCTTC
606936 ATT-ATCATCTTC
1 ATTCATCATCTTC
606948 -TTCATCA
1 ATTCATCA
606955 ACACCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 13 0.72
13 3 0.17
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTCATCATCTTC
Found at i:613838 original size:21 final size:22
Alignment explanation
Indices: 613809--613855 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
613799 AAAGCCAAAA
613809 CTATACTGCACATATATCTTAT
1 CTATACTGCACATATATCTTAT
613831 CTAT-CTGCACATATATCTTAT
1 CTATACTGCACATATATCTTAT
613852 CTAT
1 CTAT
613856 GAATCCTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (22 bp):
CTATACTGCACATATATCTTAT
Found at i:618623 original size:28 final size:28
Alignment explanation
Indices: 618548--618615 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
618538 TCTAGGGGCC
618548 TAACGTTACAAACGTTACCATTTAAGTG
1 TAACGTTACAAACGTTACCATTTAAGTG
618576 TAACGTTACAAACGTTACCATTTAAGTG
1 TAACGTTACAAACGTTACCATTTAAGTG
618604 TAACGTTACAAA
1 TAACGTTACAAA
618616 TATTACCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (28 bp):
TAACGTTACAAACGTTACCATTTAAGTG
Found at i:619509 original size:2 final size:2
Alignment explanation
Indices: 619502--619528 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
619492 GCACTTAGCA
619502 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 A
619529 AACAACTTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:622491 original size:19 final size:19
Alignment explanation
Indices: 622469--622552 Score: 55
Period size: 19 Copynumber: 4.3 Consensus size: 19
622459 AATGAATGTC
622469 ATAATTTAAAGATAAAATT
1 ATAATTTAAAGATAAAATT
**
622488 ATAATATTTAAAAGTATAAAGGT
1 AT-A-ATTT-AAAG-ATAAAATT
622511 -TAATTTAAA-ATAAGAATT
1 ATAATTTAAAGATAA-AATT
* * * *
622529 AGAGTTTAGAGATGAAATT
1 ATAATTTAAAGATAAAATT
622548 ATAAT
1 ATAAT
622553 ATTCGTAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
17 4 0.08
18 2 0.04
19 18 0.38
20 8 0.17
21 5 0.10
22 5 0.10
23 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (19 bp):
ATAATTTAAAGATAAAATT
Found at i:622518 original size:60 final size:58
Alignment explanation
Indices: 622454--622582 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 58
622444 TAGGGACCAT
* *
622454 TTTAAAAT-GAATGTCATAATTTAAAGATAAAATTATAATATT-TAAAAGTATAAAGGTTAA
1 TTTAAAATAGAAT-T-AGAATTTAAAGATAAAATTATAATATTCTAAAA-T-TAAAGATTAA
* * *
622514 TTTAAAATAAGAATTAGAGTTTAGAGATGAAATTATAATATTCGTAAAATTAAAGATTAA
1 TTTAAAAT-AGAATTAGAATTTAAAGATAAAATTATAATATTC-TAAAATTAAAGATTAA
622574 TTTAAAATA
1 TTTAAAATA
622583 AAAATTAAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
59 1 0.02
60 48 0.80
61 2 0.03
62 9 0.15
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.36
Consensus pattern (58 bp):
TTTAAAATAGAATTAGAATTTAAAGATAAAATTATAATATTCTAAAATTAAAGATTAA
Found at i:622583 original size:60 final size:60
Alignment explanation
Indices: 622473--622589 Score: 166
Period size: 60 Copynumber: 1.9 Consensus size: 60
622463 AATGTCATAA
* *
622473 TTTAAAGATAAAATTATAATATTTAAAAGTATAAAGGTTAATTTAAAATAAGAATTAGAG
1 TTTAAAGATAAAATTATAATATTTAAAAGTATAAAGATTAATTTAAAATAAAAATTAGAG
* *
622533 TTTAGAGATGAAATTATAATATTCGTAAAA-T-TAAAGATTAATTTAAAATAAAAATTA
1 TTTAAAGATAAAATTATAATATT--TAAAAGTATAAAGATTAATTTAAAATAAAAATTA
622590 AATTTTCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 45 0.88
61 1 0.02
62 5 0.10
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.36
Consensus pattern (60 bp):
TTTAAAGATAAAATTATAATATTTAAAAGTATAAAGATTAATTTAAAATAAAAATTAGAG
Found at i:623251 original size:20 final size:20
Alignment explanation
Indices: 623226--623264 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
623216 AACATGGAAA
623226 TTTTCGCAACACGAATTTCG
1 TTTTCGCAACACGAATTTCG
*
623246 TTTTCGCAACGCGAATTTC
1 TTTTCGCAACACGAATTTC
623265 TCAAATCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (20 bp):
TTTTCGCAACACGAATTTCG
Found at i:623674 original size:20 final size:21
Alignment explanation
Indices: 623649--623689 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
623639 ACGAATTTGC
623649 CAAATTCGC-AACTCAGATTT
1 CAAATTCGCAAACTCAGATTT
* *
623669 CAAATTGGCAAACTCGGATTT
1 CAAATTCGCAAACTCAGATTT
623690 TTTCTATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (21 bp):
CAAATTCGCAAACTCAGATTT
Found at i:623895 original size:19 final size:19
Alignment explanation
Indices: 623833--623903 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
623823 CCATGTTCGA
623833 GTTGCGAATTTAGAAA-CTGT
1 GTTGCGAATTT-GAAATC-GT
* **
623853 GTTGCGAAATTGGAGTTCGT
1 GTTGCG-AATTTGAAATCGT
*
623873 GTTGCGAATTTGAAATCGC
1 GTTGCGAATTTGAAATCGT
*
623892 GTTGCGATTTTG
1 GTTGCGAATTTG
623904 TTGGTTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 20 0.49
20 16 0.39
21 5 0.12
ACGTcount: A:0.23, C:0.11, G:0.30, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATCGT
Found at i:625377 original size:511 final size:511
Alignment explanation
Indices: 624399--625364 Score: 1430
Period size: 511 Copynumber: 1.9 Consensus size: 511
624389 AAGTCTAAGG
624399 GCATAATTAGTGGGTCATAACTCATTAGTTCTTAATCGATGGTTTCCTCGAATAAGCTTTTACTT
1 GCATAATTAGTGGGTCATAACTCATTAGTTCTTAATCGATGGTTTCCTCGAATAAGCTTTTACTT
*
624464 GGTCATTTCATAAAGCTATACCACTAAATGTGACATTTCAAATCTGATTTAAGAGTTTCAGTTGA
66 GGTCATTTCATAAAGCTATACCACTAAATGTGACATTTCAAATCTGATTTAAGAGTTTCAATTGA
* * * **
624529 ATTTTGAGTAACCCAATAATTACAGGGTAAGTTGTGTATTTAATATTTAAATTATTGCTTTTAAT
131 ATTTTGAGTAACCCAATAATTACAGGGTAAGTTGTGCATTTAATATCTAAACTATCACTTTTAAT
* * * * *
624594 TTATTTTAATATTTAAATTTTTATTTAAAAAAAAAAATTATATATAACGTTTAGTTTTCATTTGA
196 CTATTTTAATACTTAAATTTTTATTTAAAAAAAAAAATCATATATAACGTTTAATTTTCATTTCA
* ** *
624659 TTTTAGTATACCGTCGTTAAAAACTTAACGGGTTTAGGATTTAAACTATTGGTTTTGGTCTATTT
261 TTTTAGTATACCGTCATTAAAAACTTAACGGGTTTAGGACCTAAACTATTGGTTTTGGCCTATTT
* * *
624724 TAGTACCTAATCTTTCAATTTTTTCTTCAAAATTTAACGTTAAATTTTGAACATGATACTAAAAT
326 TAATACCTAAACTTTCAATTTTTTCTTCAAAAATTAACGTTAAATTTTGAACATGATACTAAAAT
** **
624789 AAAACAACAACTAAATTTTTAATGGCGGGGATAATGAAATAAAACAAAAACTAAACTTTAAGTAT
391 AAAACAACAAAAAAAAATTTAATGGCGGGGATAATGAAATAAAACAAAAACTAAACTTTAAGTAT
624854 GATTTTTTTGAAAAATTAAAAAATTAAGTCCAAAACTAATAGATTAGGTATTATAC
456 GATTTTTTTGAAAAATTAAAAAATTAAGTCCAAAACTAATAGATTAGGTATTATAC
*
624910 GCATAATT-GTGGGTCATACACTCATTTGTT-TTAATCGATGGTTTCCTCGAATAAGCTTTTACT
1 GCATAATTAGTGGGTCATA-ACTCATTAGTTCTTAATCGATGGTTTCCTCGAATAAGCTTTTACT
624973 TGGTCATTTCATAAAGCTATACCACTAAATGTGACATTTCAAATCTGATTTAAGAGTTTCAATTG
65 TGGTCATTTCATAAAGCTATACCACTAAATGTGACATTTCAAATCTGATTTAAGAGTTTCAATTG
*
625038 AATTTTGAGTAACCCAATAATTATAGGGGTAAGTTGTGCATTTAATATCTAAACTATCACTTTTA
130 AATTTTGAGTAACCCAATAATTACA-GGGTAAGTTGTGCATTTAATATCTAAACTATCACTTTTA
* ***** * * *
625103 ATCTATTTTAGTACTTAAATTTTTATTTCTTTTAAAAAGTCATCTCTAACGTTTAATTTTCATTT
194 ATCTATTTTAATACTTAAATTTTTATTTAAAAAAAAAAATCATATATAACGTTTAATTTTCATTT
** * *
625168 CATTTTAGTATATGGTCATTAAAAACTTAACGTGTTTAGTACCTAAACTATTGGTTTTGGCCTA-
259 CATTTTAGTATACCGTCATTAAAAACTTAACGGGTTTAGGACCTAAACTATTGGTTTTGGCCTAT
* * * *
625232 TTTAATACTTAAACTTTC-ATTTTTTTTTCAAAAATTAATGTT-AATTTTGAACGGTG-TACTAA
324 TTTAATACCTAAACTTTCAATTTTTTCTTCAAAAATTAACGTTAAATTTTGAAC-ATGATACTAA
* * *
625294 AATGAAACAA-AAAAAAAAATTTAATGGC-GGGATAATGAAAT-GAA-AAAAATTAAACTTTAAG
388 AATAAAACAACAAAAAAAAATTTAATGGCGGGGATAATGAAATAAAACAAAAACTAAACTTTAAG
*
625355 TATGGTTTTT
453 TATGATTTTT
625365 CAAAAATTTG
Statistics
Matches: 407, Mismatches: 45, Indels: 13
0.88 0.10 0.03
Matches are distributed among these distances:
504 25 0.06
505 2 0.00
506 13 0.03
507 14 0.03
508 25 0.06
509 23 0.06
510 146 0.36
511 159 0.39
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (511 bp):
GCATAATTAGTGGGTCATAACTCATTAGTTCTTAATCGATGGTTTCCTCGAATAAGCTTTTACTT
GGTCATTTCATAAAGCTATACCACTAAATGTGACATTTCAAATCTGATTTAAGAGTTTCAATTGA
ATTTTGAGTAACCCAATAATTACAGGGTAAGTTGTGCATTTAATATCTAAACTATCACTTTTAAT
CTATTTTAATACTTAAATTTTTATTTAAAAAAAAAAATCATATATAACGTTTAATTTTCATTTCA
TTTTAGTATACCGTCATTAAAAACTTAACGGGTTTAGGACCTAAACTATTGGTTTTGGCCTATTT
TAATACCTAAACTTTCAATTTTTTCTTCAAAAATTAACGTTAAATTTTGAACATGATACTAAAAT
AAAACAACAAAAAAAAATTTAATGGCGGGGATAATGAAATAAAACAAAAACTAAACTTTAAGTAT
GATTTTTTTGAAAAATTAAAAAATTAAGTCCAAAACTAATAGATTAGGTATTATAC
Found at i:625426 original size:32 final size:32
Alignment explanation
Indices: 625365--625428 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
625355 TATGGTTTTT
*
625365 CAAAAATTTGAAAGTTGATGTATTCAAACATA
1 CAAAAATTTGAAAGTTGATGTATTAAAACATA
*
625397 CAAAAA-TTGATAA-TTTATGTATTAAAAACATA
1 CAAAAATTTGA-AAGTTGATGTATT-AAAACATA
625429 ATTTACCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (32 bp):
CAAAAATTTGAAAGTTGATGTATTAAAACATA
Found at i:631317 original size:16 final size:16
Alignment explanation
Indices: 631287--631317 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
631277 TAATATTGAA
*
631287 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
631303 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
631318 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:640763 original size:83 final size:83
Alignment explanation
Indices: 640624--640782 Score: 221
Period size: 83 Copynumber: 1.9 Consensus size: 83
640614 AAAAAGTAGA
* * * *
640624 AACAAATGATGTAAAATAGTTGACAAGGAATATATACTTAGCATATTTGTTTAAGGCCTACATAA
1 AACAAAAGATGTAAAACAGTTGACAAGGAATATATACTTAACATATTTATTTAAGGCCTACATAA
*
640689 AATATCATAAAATACATC
66 AAGATCATAAAATACATC
* * * *
640707 AACAAAAGATGTCAAACAGTTGACATGGAAT-TAATATTTAACATATTTATTTAAGGCCTGCATA
1 AACAAAAGATGTAAAACAGTTGACAAGGAATAT-ATACTTAACATATTTATTTAAGGCCTACATA
640771 AAAGATCATAAA
65 AAAGATCATAAA
640783 CAGGGACTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
82 1 0.02
83 65 0.98
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (83 bp):
AACAAAAGATGTAAAACAGTTGACAAGGAATATATACTTAACATATTTATTTAAGGCCTACATAA
AAGATCATAAAATACATC
Found at i:643871 original size:23 final size:22
Alignment explanation
Indices: 643794--643871 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
643784 TCCTTAAGGA
**
643794 CATTTTATATGGCACTTCGGTG
1 CATTTTACGTGGCACTTCGGTG
* * * * *
643816 CAATTCTACGCGGTACTTCGATA
1 C-ATTTTACGTGGCACTTCGGTG
643839 CAATTTTACGTGGCACTTCGGTG
1 C-ATTTTACGTGGCACTTCGGTG
643862 CATTTATACG
1 CATTT-TACG
643872 AGCTATGGTG
Statistics
Matches: 42, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
22 5 0.12
23 37 0.88
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (22 bp):
CATTTTACGTGGCACTTCGGTG
Found at i:646962 original size:21 final size:21
Alignment explanation
Indices: 646936--646986 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
646926 AGTATAGAAT
646936 GTGGATCCTGAA-TGATGCGG-G
1 GTGGATCCTGAACT-ATG-GGAG
*
646957 GTGGATCTTGAACTATGGGAG
1 GTGGATCCTGAACTATGGGAG
646978 GTGGATCCT
1 GTGGATCCT
646987 AAACGATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.08
21 23 0.88
22 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.27
Consensus pattern (21 bp):
GTGGATCCTGAACTATGGGAG
Found at i:647248 original size:21 final size:21
Alignment explanation
Indices: 647220--647305 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
647210 ATTATAGGGG
647220 TCCACCTCCCATTC-TTCAAGA
1 TCCACCTCCCA-TCATTCAAGA
* *
647241 TTCACCTCTCATCATTCAAGA
1 TCCACCTCCCATCATTCAAGA
* *
647262 GGCC-CCTCCCATCATTCAGGA
1 -TCCACCTCCCATCATTCAAGA
* *
647283 TCCACCTCCCATCGTTCAGGA
1 TCCACCTCCCATCATTCAAGA
647304 TC
1 TC
647306 AATCCCTCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.07
21 49 0.91
22 1 0.02
ACGTcount: A:0.22, C:0.41, G:0.10, T:0.27
Consensus pattern (21 bp):
TCCACCTCCCATCATTCAAGA
Found at i:648963 original size:33 final size:33
Alignment explanation
Indices: 648915--649013 Score: 112
Period size: 33 Copynumber: 3.1 Consensus size: 33
648905 GTTTGGCAAG
* * *
648915 TTGGAAATTTTATCTTGGTTGATGGTCAACTTA
1 TTGGAAAATTCATCTTGGTTGATGGCCAACTTA
*
648948 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGATGGCCAACTTA
* * * *
648981 TTGGAAAAATC-T-TTGGTAGGTGGCCAATTTA
1 TTGGAAAATTCATCTTGGTTGATGGCCAACTTA
649012 TT
1 TT
649014 TTTCATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 19 0.32
32 1 0.02
33 39 0.66
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.40
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGATGGCCAACTTA
Found at i:653999 original size:39 final size:39
Alignment explanation
Indices: 653906--654004 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 39
653896 AAACAAAGAG
* *
653906 GAAAATGGGGAATCAGGGATTGAAGGGTGAGAGAGAAAT
1 GAAAATGGGGAATTAGGGATTGAAGGGCGAGAGAGAAAT
**
653945 GAAAAT-GAAATATTAGGGATTG-AGGTGCGAGAG-GAAAAT
1 GAAAATGGGGA-ATTAGGGATTGAAGG-GCGAGAGAG-AAAT
653984 GAAAATGGGGAATTAGGGATT
1 GAAAATGGGGAATTAGGGATT
654005 TTAGCAAGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
38 6 0.12
39 42 0.84
40 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.37, T:0.19
Consensus pattern (39 bp):
GAAAATGGGGAATTAGGGATTGAAGGGCGAGAGAGAAAT
Found at i:654856 original size:19 final size:18
Alignment explanation
Indices: 654814--654864 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
654804 AATGCATTTT
*
654814 ATGCACCGATGCACAACA
1 ATGCATCGATGCACAACA
* *
654832 ATGCATCGATGCATAGACC
1 ATGCATCGATGCACA-ACA
*
654851 ATGCATCGGTGCAC
1 ATGCATCGATGCAC
654865 TCTAGGCTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (18 bp):
ATGCATCGATGCACAACA
Found at i:661340 original size:6 final size:6
Alignment explanation
Indices: 661329--661355 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
661319 TCTTCCAGCA
661329 TTTTCC TTTTCC TTTTCC TTTTCC TTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTT
661356 CGGAGCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCC
Found at i:664208 original size:61 final size:61
Alignment explanation
Indices: 664135--664254 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 61
664125 ACAATTTGCT
664135 CGAAAAATTAAAGCAGAGTTGCTTGCAATTGACCAAACATCAATCATCTTTCTCTCAAAAG
1 CGAAAAATTAAAGCAGAGTTGCTTGCAATTGACCAAACATCAATCATCTTTCTCTCAAAAG
* *
664196 CGAAAAATTAAAGCAGAGTTGCTTGCAATTGACCAAACATTAATCATCTTTCTTTCAAA
1 CGAAAAATTAAAGCAGAGTTGCTTGCAATTGACCAAACATCAATCATCTTTCTCTCAAA
664255 CAATCACACA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (61 bp):
CGAAAAATTAAAGCAGAGTTGCTTGCAATTGACCAAACATCAATCATCTTTCTCTCAAAAG
Found at i:665532 original size:2 final size:2
Alignment explanation
Indices: 665525--665609 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
665515 AATTACAAAT
665525 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
665567 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
665609 T
1 T
665610 GCTCGAGCTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:667239 original size:16 final size:16
Alignment explanation
Indices: 667218--667261 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
667208 TAATAAATAA
667218 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
667234 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
667250 ACGAACATAAAC
1 ACGAACATAAAC
667262 ATTGGAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Done.