Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 176 of 208
Found at i:53777490 original size:17 final size:18
Alignment explanation
Indices: 53777468--53777503 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
53777458 ACTTTATGTC
53777468 TTAAAA-AATATAATATA
1 TTAAAATAATATAATATA
53777485 TTAAAATTAATATAATATA
1 TTAAAA-TAATATAATATA
53777504 AGCCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAATATAATATA
Found at i:53803675 original size:59 final size:59
Alignment explanation
Indices: 53803583--53803700 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
53803573 AAATACAGAC
*
53803583 TTGATTTTAATTGAAAACATGATCGATTGAGGCAAAAACATTATAAACATGAATCAAAT
1 TTGATTTTAATTAAAAACATGATCGATTGAGGCAAAAACATTATAAACATGAATCAAAT
* *
53803642 TTGATTTTAATTAAAAACATGATCGATTGAGGCACAAACATTATAAGCATGAATCAAAT
1 TTGATTTTAATTAAAAACATGATCGATTGAGGCAAAAACATTATAAACATGAATCAAAT
53803701 AAATATGATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (59 bp):
TTGATTTTAATTAAAAACATGATCGATTGAGGCAAAAACATTATAAACATGAATCAAAT
Found at i:53807021 original size:19 final size:19
Alignment explanation
Indices: 53806996--53807041 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
53806986 AATGGTTAAA
53806996 AATAAAAA-TAAATAAAAGT
1 AATAAAAATTAAATAAAA-T
* *
53807015 TATAAAAATTTAATAAAAT
1 AATAAAAATTAAATAAAAT
53807034 AATAAAAA
1 AATAAAAA
53807042 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAAAATTAAATAAAAT
Found at i:53807022 original size:20 final size:19
Alignment explanation
Indices: 53806999--53807044 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
53806989 GGTTAAAAAT
*
53806999 AAAAATAAATAAAAGTTATA
1 AAAAATAAATAAAA-TAATA
* *
53807019 AAAATTTAATAAAATAATA
1 AAAAATAAATAAAATAATA
53807038 AAAAATA
1 AAAAATA
53807045 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAAATAAAATAATA
Found at i:53807055 original size:29 final size:29
Alignment explanation
Indices: 53807000--53807079 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
53806990 GTTAAAAATA
* * *
53807000 AAAATAA-ATAAAAGTTATAAAAATTTAAT
1 AAAATAAGAAAAAAATTAT-AAATTTTAAT
* *
53807029 AAAATAATAAAAAATATT-TAAATTTTATT
1 AAAATAAGAAAAAA-ATTATAAATTTTAAT
*
53807058 AAAATTAGAAAAAAATTATAAA
1 AAAATAAGAAAAAAATTATAAA
53807080 AATTGGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.07
29 31 0.74
30 6 0.14
31 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATAAGAAAAAAATTATAAATTTTAAT
Found at i:53807076 original size:20 final size:19
Alignment explanation
Indices: 53807057--53807123 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
53807047 TAAATTTTAT
53807057 TAAAATTAGAAAAAAATTA
1 TAAAATTAGAAAAAAATTA
*
53807076 TAAAAATTGGAAAAATAA-TA
1 T-AAAATTAGAAAAA-AATTA
53807096 TAGAAATATAGAAAAAAATTA
1 TA-AAAT-TAGAAAAAAATTA
53807117 TAAAATT
1 TAAAATT
53807124 TTATTAAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 3 0.07
20 25 0.61
21 13 0.32
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
TAAAATTAGAAAAAAATTA
Found at i:53809421 original size:20 final size:20
Alignment explanation
Indices: 53809396--53809437 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
53809386 AGGAAGATGA
53809396 TACTTAATTCA-TCTTTTATT
1 TACTTAATT-ATTCTTTTATT
*
53809416 TACTTAGTTATTCTTTTATT
1 TACTTAATTATTCTTTTATT
53809436 TA
1 TA
53809438 ATAAATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.62
Consensus pattern (20 bp):
TACTTAATTATTCTTTTATT
Found at i:53810030 original size:19 final size:19
Alignment explanation
Indices: 53810008--53810089 Score: 76
Period size: 19 Copynumber: 4.2 Consensus size: 19
53809998 TTTTGATACA
**
53810008 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTACAAT
**
53810027 TTTTATAAAATTTTACAATT
1 TTTTATAATTTTTTACAA-T
*
53810047 TTTTATATATTTTTTTACGAT
1 TTTTATA-A-TTTTTTACAAT
*
53810068 TTTTATAA-TTTTTATAAT
1 TTTTATAATTTTTTACAAT
53810086 TTTT
1 TTTT
53810090 TTTCTGTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
18 12 0.24
19 14 0.27
20 9 0.18
21 9 0.18
22 7 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:53810109 original size:10 final size:9
Alignment explanation
Indices: 53810008--53810166 Score: 79
Period size: 10 Copynumber: 16.4 Consensus size: 9
53809998 TTTTGATACA
53810008 TTTTATAATT
1 TTTTATAA-T
*
53810018 TTTTATGAT
1 TTTTATAAT
*
53810027 TTTTATAAAA
1 TTTTAT-AAT
*
53810037 TTTTACAATT
1 TTTTATAA-T
53810047 TTTTATATAT
1 TTTTATA-AT
*
53810057 TTTTTTACGAT
1 TTTTATA--AT
53810068 TTTTATAAT
1 TTTTATAAT
53810077 TTTTATAATT
1 TTTTATAA-T
* **
53810087 TTTTTTCTGT
1 TTTTAT-AAT
53810097 TTTTATATAT
1 TTTTATA-AT
*
53810107 TTTTAATTAAAA
1 TTTT-A-T-AAT
*
53810119 TTTAATAAT
1 TTTTATAAT
*
53810128 TTTTATAAC
1 TTTTATAAT
* *
53810137 TTTTATTTAG
1 TTTTA-TAAT
53810147 TTTTAT--T
1 TTTTATAAT
53810154 TTTTATAAT
1 TTTTATAAT
53810163 TTTT
1 TTTT
53810167 TTGCCACATG
Statistics
Matches: 113, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
7 6 0.05
9 39 0.35
10 51 0.45
11 11 0.10
12 5 0.04
13 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53810374 original size:86 final size:85
Alignment explanation
Indices: 53810273--53810450 Score: 250
Period size: 86 Copynumber: 2.1 Consensus size: 85
53810263 CCTAATGGTC
* * *
53810273 TTTTTTATGTATTTTGACAGTTCAAGTACCCAATTAAGTGC-AAAAAAAGGGGGGTTTAACTGCT
1 TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGG-CTAACTGCT
* *
53810337 TTTTTTGAAAAAGTTTGAGAA
65 TTTTTAGAAAAAATTTGAGAA
* * *
53810358 TTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGCAAAAAAAAGGGGGGCTAATTGCT
1 TTTTTT-ATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCT
*
53810423 TTTTTAGAAAAAATTTGAGAG
65 TTTTTAGAAAAAATTTGAGAA
53810444 TTTTTTA
1 TTTTTTA
53810451 CACCCTTAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
85 7 0.09
86 62 0.76
87 13 0.16
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.38
Consensus pattern (85 bp):
TTTTTTATGCATTTTGAAAGTTCAAGTACCCAATTAAGTGCAAAAAAAAGGGGGGCTAACTGCTT
TTTTAGAAAAAATTTGAGAA
Found at i:53812441 original size:3 final size:3
Alignment explanation
Indices: 53812427--53812463 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
53812417 NNNNNNNNNN
*
53812427 ATA ATA ATTA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53812464 TGAAATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53814407 original size:87 final size:85
Alignment explanation
Indices: 53814191--53814794 Score: 541
Period size: 87 Copynumber: 7.0 Consensus size: 85
53814181 GAGGTAAAAT
* * ** *
53814191 CTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TCATTTTAATCCGCTCCACT
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGAT-CTGAAATTTTAATCCACTCCACT
* * *
53814255 ATAATCTCAGGGAGATAGGATTAC
65 GTAACCTCAGGGAGATA--A-GAC
* * * * * * * * ** *
53814279 CAGCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCAC
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGAAATT-TT-AATCCACTCCAC
*
53814344 TGTAACCTCAGGGAGATAAAAC
64 TGTAACCTCAGGGAGATAAGAC
*** *
53814366 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGAAATTTTAATCCACTCCACTG
* *
53814431 TAACTTCAGGGAGATAGGAC
66 TAACCTCAGGGAGATAAGAC
* * * * * * ** *
53814451 AATGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTC
1 -CTG-ATGCGATCTACTCTGCTGTAACT-TCAGAGAGATAAGATCTGAAATT-TT-AATCCACTC
53814515 CACTGTAACCTCAGGGAGATAAGAC
61 CACTGTAACCTCAGGGAGATAAGAC
** *
53814540 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACT
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGAT-CTGAAATTTTAATCCACTCCACT
* *
53814604 GTAACTTCAGGGAGATAGGAC
65 GTAACCTCAGGGAGATAAGAC
* * * * * * ** *
53814625 AGTGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTC
1 -CTG-ATGCGATCTACTCTGCTGTAACT-TCAGAGAGATAAGATCTGAAATT-TT-AATCCACTC
53814689 CACTGTAACCTCAGGGAGATAAGAC
61 CACTGTAACCTCAGGGAGATAAGAC
*** *
53814714 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGAAATTTTAATCCACTCCACTG
*
53814779 TAATCTCAGGGAGATA
66 TAACCTCAGGGAGATA
53814795 GGATTACTAG
Statistics
Matches: 406, Mismatches: 93, Indels: 37
0.76 0.17 0.07
Matches are distributed among these distances:
85 80 0.20
86 14 0.03
87 182 0.45
88 48 0.12
89 58 0.14
90 24 0.06
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (85 bp):
CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTGAAATTTTAATCCACTCCACTG
TAACCTCAGGGAGATAAGAC
Found at i:53814434 original size:44 final size:44
Alignment explanation
Indices: 53814197--53815016 Score: 337
Period size: 44 Copynumber: 18.8 Consensus size: 44
53814187 AAATCTGATA
* * * * *
53814197 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
** * * * *** *
53814241 TAATCCGCTCCACTATAA-TCTCAGGGAGATAGGAT-TACCAGCTT
1 CGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTA-TTT
* * * ***
53814285 CAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTA-T-TT
* * * * * * *
53814331 CGGTCTACTCCACTGTAACCTCAGGGAGATAA-AAC-CTGA-TG
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
* ** *
53814372 CGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
** * * * * *
53814416 TAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-CAATGT-CTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATC-TTTTATTT
* ***
53814459 CGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTT
1 CGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTA-T-TT
* * * * * *
53814505 CGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTGA-TG
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
* ** * *
53814546 CGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
** * * * * *
53814590 TAATCCGCTCCACTGTAACTTCAGGGAGATAGGA-CAGTGT-CTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATC-TTTTATTT
* ***
53814633 CGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTT
1 CGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTA-T-TT
* * * * * *
53814679 CGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTGA-TG
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
* ** *
53814720 CGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
** * * ** *
53814764 TAATCCGCTCCACTGTAA-TCTCAGGGAGATAGGAT-TACTAGCTT
1 CGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTA-TTT
* * * * **
53814808 CAATCTGTTCCGCTGTAA-TCTCAGGGAGATAAGATC--TGA-CA
1 CGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTATTT
* * * *
53814849 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTT
1 CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
* * **
53814893 -GAATCCGCTCCACTGTAA-TCTCAGGGAGATAGGAT-TACTATATT
1 CG-ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTAT-TT
* ***
53814937 CAATCTGCTCCACTGTAATCTT-AGGGAGATAAGATCTGAAATTCTT
1 CGATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATCTTTTA-T-TT
* *
53814983 CGGTCTGTTCCACTGTAA-TCTCAGGGAGATAAGA
1 CGATCTGCTCCACTGTAACT-TCAGGGAGATAAGA
53815017 CTTGACACGA
Statistics
Matches: 569, Mismatches: 162, Indels: 88
0.69 0.20 0.11
Matches are distributed among these distances:
41 116 0.20
42 7 0.01
43 81 0.14
44 232 0.41
45 10 0.02
46 123 0.22
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
CGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
Found at i:53814502 original size:174 final size:173
Alignment explanation
Indices: 53814180--53814846 Score: 1070
Period size: 174 Copynumber: 3.8 Consensus size: 173
53814170 TACTGCTTAA
* * * * *
53814180 GGAGGTAAAATCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTCATTTTAAT
1 GGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
* * *
53814245 CCGCTCCACTATAATCTCAGGGAGATAGGATTACCA-GCTTCAATCTGCTCCGCTGTAACCTCAG
66 CCGCTCCACTGTAATCTCAGGGAGATAGG---ACAATGCTTCAATCTGCTCCGCTGTAATCTCAG
53814309 GGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
128 GGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
*
53814355 GGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTTTAAT
1 GGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
*
53814420 CCGCTCCACTGTAA-CTTCAGGGAGATAGGACAATGTCTTCGATCTGCTCCGCTGTAATCTCAGG
66 CCGCTCCACTGTAATC-TCAGGGAGATAGGACAATG-CTTCAATCTGCTCCGCTGTAATCTCAGG
53814484 GAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
129 GAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
*
53814529 GGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
1 GGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
* *
53814594 CCGCTCCACTGTAA-CTTCAGGGAGATAGGACAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGG
66 CCGCTCCACTGTAATC-TCAGGGAGATAGGACAATG-CTTCAATCTGCTCCGCTGTAATCTCAGG
53814658 GAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
129 GAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
* *
53814703 GGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCTTTTATTTTAAT
1 GGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
* * *
53814768 CCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGTTCCGCTGTAATCTCAGG
66 CCGCTCCACTGTAATCTCAGGGAGATAGGA-CAAT-GCTTCAATCTGCTCCGCTGTAATCTCAGG
53814833 GAGATAAGATCTGA
129 GAGATAAGATCTGA
53814847 CACGATCTAC
Statistics
Matches: 468, Mismatches: 18, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
172 3 0.01
173 1 0.00
174 335 0.72
175 128 0.27
176 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (173 bp):
GGAGATAAAACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAAT
CCGCTCCACTGTAATCTCAGGGAGATAGGACAATGCTTCAATCTGCTCCGCTGTAATCTCAGGGA
GATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAG
Found at i:53815236 original size:88 final size:87
Alignment explanation
Indices: 53815063--53815322 Score: 308
Period size: 88 Copynumber: 3.0 Consensus size: 87
53815053 TAAGATCCTT
* * * * * *
53815063 TCTTCAATCTGCTTCACTACAATCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTCGTTGTTAA
1 TCTTCAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCGATCTGCTTCGCTGTTAA
*
53815128 CGCAGGAA-GACAAGATCTGCTA
66 CGCAGGAAGGTC-AGATCTGCTA
**
53815150 TCTTCAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTTTAATCTGCTTCGCTGTTA
1 TCTTCAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTA-TTTTCGATCTGCTTCGCTGTTA
*
53815215 ACGCAGGAAGGTCAGATCTGCTG
65 ACGCAGGAAGGTCAGATCTGCTA
* * * * * *
53815238 TCTTCAACCAGTTCCACCT-CAACCGATGGAGACAAAGCTTGTATCTTCGATCTGCTTCACTGTC
1 TCTTCAATCAGCTCCA-CTACAACCGATGGAGACAAGGCTT-TATTTTCGATCTGCTTCGCTGTT
* *
53815302 AAGGCAGGAAGGTAAGATCTG
64 AACGCAGGAAGGTCAGATCTG
53815323 TTGTCTTTGA
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
87 37 0.25
88 106 0.71
89 6 0.04
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (87 bp):
TCTTCAATCAGCTCCACTACAACCGATGGAGACAAGGCTTTATTTTCGATCTGCTTCGCTGTTAA
CGCAGGAAGGTCAGATCTGCTA
Found at i:53816132 original size:16 final size:16
Alignment explanation
Indices: 53816108--53816138 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53816098 AAGTATCATC
53816108 ATTCCAATGCAACATT
1 ATTCCAATGCAACATT
*
53816124 ATTCTAATGCAACAT
1 ATTCCAATGCAACAT
53816139 GCTTGCAAAG
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:0.39, C:0.23, G:0.06, T:0.32
Consensus pattern (16 bp):
ATTCCAATGCAACATT
Found at i:53816481 original size:21 final size:21
Alignment explanation
Indices: 53816455--53816501 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
53816445 GGTATAGCAA
53816455 GATCACCGT-ATGCCCCAATCT
1 GATCA-CGTCATGCCCCAATCT
* *
53816476 GATCACTTCATGCCCCATTCT
1 GATCACGTCATGCCCCAATCT
53816497 GATCA
1 GATCA
53816502 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28
Consensus pattern (21 bp):
GATCACGTCATGCCCCAATCT
Found at i:53816604 original size:8 final size:8
Alignment explanation
Indices: 53816593--53816632 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
53816583 CCATTTTTAC
53816593 TTTTTCAT
1 TTTTTCAT
53816601 TTTTTCA-
1 TTTTTCAT
53816608 TTTTTCA-
1 TTTTTCAT
53816615 TTTTT-AT
1 TTTTTCAT
53816622 TTTTCTCAT
1 TTTT-TCAT
53816631 TT
1 TT
53816633 CTTTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.03
7 16 0.55
8 8 0.28
9 4 0.14
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCAT
Found at i:53816609 original size:22 final size:21
Alignment explanation
Indices: 53816584--53816647 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
53816574 TTAGCCTCTC
53816584 CATTTTTACTTTTTCATTTTTT
1 CATTTTT-CTTTTTCATTTTTT
53816606 CATTTTTCATTTTT-ATTTTTCT
1 CATTTTTC-TTTTTCATTTTT-T
*
53816628 CA--TTTCTTTTTCTTTTTTT
1 CATTTTTCTTTTTCATTTTTT
53816647 C
1 C
53816648 TTCTTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 7 0.18
20 9 0.24
21 7 0.18
22 15 0.39
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (21 bp):
CATTTTTCTTTTTCATTTTTT
Found at i:53816611 original size:15 final size:14
Alignment explanation
Indices: 53816584--53816649 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
53816574 TTAGCCTCTC
*
53816584 CATTTTTACTTTTT
1 CATTTTTTCTTTTT
53816598 CATTTTTTCATTTTT
1 CATTTTTTC-TTTTT
*
53816613 CA-TTTTTATTTTT
1 CATTTTTTCTTTTT
**
53816626 C-TCATTTCTTTTT
1 CATTTTTTCTTTTT
*
53816639 CTTTTTTTCTT
1 CATTTTTTCTT
53816650 CTTTTTTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
13 15 0.36
14 20 0.48
15 7 0.17
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (14 bp):
CATTTTTTCTTTTT
Found at i:53816645 original size:7 final size:7
Alignment explanation
Indices: 53816584--53816626 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
53816574 TTAGCCTCTC
53816584 CATTTTT
1 CATTTTT
53816591 -ACTTTTT
1 CA-TTTTT
53816598 CATTTTTT
1 CA-TTTTT
53816606 CATTTTT
1 CATTTTT
53816613 CATTTTT
1 CATTTTT
53816620 -ATTTTT
1 CATTTTT
53816626 C
1 C
53816627 TCATTTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 7 0.22
7 17 0.53
8 8 0.25
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:53817584 original size:7 final size:7
Alignment explanation
Indices: 53817572--53817610 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
53817562 TTGACCTCTC
53817572 CTTTTTT
1 CTTTTTT
53817579 C-TTTTT
1 CTTTTTT
53817585 C-TTTTT
1 CTTTTTT
53817591 CTTTTTT
1 CTTTTTT
53817598 CTTTTTT
1 CTTTTTT
53817605 CTTTTT
1 CTTTTT
53817611 CTCCTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.39
7 19 0.61
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:53817585 original size:6 final size:6
Alignment explanation
Indices: 53817574--53817612 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
53817564 GACCTCTCCT
53817574 TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC T
53817613 CCTATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:53817590 original size:13 final size:13
Alignment explanation
Indices: 53817572--53817612 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
53817562 TTGACCTCTC
53817572 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
53817585 C-TTTTTCTTTTTT
1 CTTTTTTC-TTTTT
53817598 CTTTTTTCTTTTT
1 CTTTTTTCTTTTT
53817611 CT
1 CT
53817613 CCTATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.23
13 14 0.54
14 6 0.23
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
CTTTTTTCTTTTT
Found at i:53817621 original size:26 final size:26
Alignment explanation
Indices: 53817572--53817621 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
53817562 TTGACCTCTC
* *
53817572 CTTTTTTCTTTTTCTTTTTCTTTTTT
1 CTTTTTTCTTTTTCTCTATCTTTTTT
53817598 CTTTTTTCTTTTTCTCCTAT-TTTT
1 CTTTTTTCTTTTTCT-CTATCTTTT
53817622 GACTTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (26 bp):
CTTTTTTCTTTTTCTCTATCTTTTTT
Found at i:53817627 original size:26 final size:26
Alignment explanation
Indices: 53817572--53817627 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
53817562 TTGACCTCTC
* * **
53817572 CTTTTTTCTTTTTCTTTTTCTTTTTT
1 CTTTTTTCTTTTTCTCTATCTTTTGA
53817598 CTTTTTTCTTTTTCTCCTAT-TTTTGA
1 CTTTTTTCTTTTTCT-CTATCTTTTGA
53817624 CTTT
1 CTTT
53817628 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (26 bp):
CTTTTTTCTTTTTCTCTATCTTTTGA
Found at i:53817645 original size:8 final size:8
Alignment explanation
Indices: 53817632--53817671 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
53817622 GACTTTGATT
53817632 TTTTTTTA
1 TTTTTTTA
53817640 TTTTTTTGA
1 TTTTTTT-A
*
53817649 TTTTTTGA
1 TTTTTTTA
*
53817657 TTTTTTGA
1 TTTTTTTA
53817665 TTTTTTT
1 TTTTTTT
53817672 TTTGAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.76
9 7 0.24
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:53817652 original size:16 final size:16
Alignment explanation
Indices: 53817633--53817674 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
53817623 ACTTTGATTT
53817633 TTTTTTATTTTTTTGA
1 TTTTTTATTTTTTTGA
53817649 TTTTTTGA-TTTTTTGA
1 TTTTTT-ATTTTTTTGA
53817665 TTTTTT-TTTT
1 TTTTTTATTTT
53817675 GAGTCTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 20 0.83
17 1 0.04
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (16 bp):
TTTTTTATTTTTTTGA
Found at i:53822927 original size:17 final size:16
Alignment explanation
Indices: 53822905--53822938 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53822895 ATATATATAG
*
53822905 AATAAATAAAAAATAAA
1 AATAAA-AAAAAACAAA
53822922 AATAAAAAAAAACAAA
1 AATAAAAAAAAACAAA
53822938 A
1 A
53822939 CTAACGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (16 bp):
AATAAAAAAAAACAAA
Found at i:53822983 original size:3 final size:3
Alignment explanation
Indices: 53822969--53823013 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
53822959 CAAATAAAAC
* *
53822969 TAA TAA TGA TAA TAA TTAA TAA TAA TAA TAA TAA CAA TAA TAA TA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
53823014 TGAAATTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:53824245 original size:15 final size:14
Alignment explanation
Indices: 53824225--53824269 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
53824215 ATTGAGAAGC
*
53824225 AAAATAATCCAATAA
1 AAAATAATACAA-AA
*
53824240 AAAATAAAACAAAA
1 AAAATAATACAAAA
53824254 AAAATAATA-AAAA
1 AAAATAATACAAAA
53824267 AAA
1 AAA
53824270 TTATCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 7 0.26
14 10 0.37
15 10 0.37
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAATAATACAAAA
Found at i:53824699 original size:31 final size:30
Alignment explanation
Indices: 53824660--53824722 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
53824650 ACTGATTAAT
53824660 TGAATAAAA-TTCATACATAATAATACATGG
1 TGAATAAAACTT-ATACATAATAATACATGG
* *
53824690 TGAAGTAAAACTTATACGTAATAATATATGG
1 TGAA-TAAAACTTATACATAATAATACATGG
53824721 TG
1 TG
53824723 GAACTCAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 23 0.79
32 2 0.07
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (30 bp):
TGAATAAAACTTATACATAATAATACATGG
Found at i:53828036 original size:44 final size:43
Alignment explanation
Indices: 53827987--53828118 Score: 174
Period size: 44 Copynumber: 3.0 Consensus size: 43
53827977 ACTAATGTAA
* *
53827987 TATTTGATAGTACAAAATTAGTTGAAAATTTTAAAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAACTCTAAAAGAGCTAAT
* *
53828031 TATTTGCTAGTTCAAAATTAGTTGAAAACTCTAGAAGAGCTAAT
1 TATTTG-TAGTACAAAATTAGTTGAAAACTCTAAAAGAGCTAAT
* * *
53828075 TATTTTGTAGTATAAAATTAGTTGAAAGCTCTAGAAGAGCTAAT
1 TA-TTTGTAGTACAAAATTAGTTGAAAACTCTAAAAGAGCTAAT
53828119 ATATCAATAT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 75 0.95
45 4 0.05
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.36
Consensus pattern (43 bp):
TATTTGTAGTACAAAATTAGTTGAAAACTCTAAAAGAGCTAAT
Found at i:53831061 original size:27 final size:27
Alignment explanation
Indices: 53831030--53831275 Score: 275
Period size: 27 Copynumber: 9.1 Consensus size: 27
53831020 ACATAAATCC
53831030 ATTTCGGTCATTTTACCCTATAGGGGT
1 ATTTCGGTCATTTTACCCTATAGGGGT
*
53831057 ATTTCGGTCATTTTACCCCATAGGGGT
1 ATTTCGGTCATTTTACCCTATAGGGGT
* *
53831084 ATTTCGATCATTTTACCTTATA-GGGT
1 ATTTCGGTCATTTTACCCTATAGGGGT
* *
53831110 GTTTCGGTCATTCTACCCTATAGGGGT
1 ATTTCGGTCATTTTACCCTATAGGGGT
* * * * *
53831137 ATTTCAGTCATTCTATCTTATAAGGGT
1 ATTTCGGTCATTTTACCCTATAGGGGT
* *
53831164 ATTTCGGTCATTCTACCTTAT-GCGGGT
1 ATTTCGGTCATTTTACCCTATAG-GGGT
*
53831191 ATTTCGGTCATTTTACCTTAT-GGAGGT
1 ATTTCGGTCATTTTACCCTATAGG-GGT
* *
53831218 ATTTCAGTCATTCTACCCTATAGGGGT
1 ATTTCGGTCATTTTACCCTATAGGGGT
* * *
53831245 ATTTCGATTATTTTATCCTAT-GGAGGT
1 ATTTCGGTCATTTTACCCTATAGG-GGT
53831272 ATTT
1 ATTT
53831276 TGGTTATAAC
Statistics
Matches: 189, Mismatches: 25, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
26 25 0.13
27 162 0.86
28 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTCGGTCATTTTACCCTATAGGGGT
Found at i:53831089 original size:54 final size:54
Alignment explanation
Indices: 53831030--53831275 Score: 304
Period size: 54 Copynumber: 4.6 Consensus size: 54
53831020 ACATAAATCC
* * *
53831030 ATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCCATAGGGGT
1 ATTTCGGTCATTTTACCTTATAGGGGTATTTCGGTCATTCTACCCTATAGGGGT
* *
53831084 ATTTCGATCATTTTACCTTATA-GGGTGTTTCGGTCATTCTACCCTATAGGGGT
1 ATTTCGGTCATTTTACCTTATAGGGGTATTTCGGTCATTCTACCCTATAGGGGT
* * * * *
53831137 ATTTCAGTCATTCTATCTTATAAGGGTATTTCGGTCATTCTACCTTAT-GCGGGT
1 ATTTCGGTCATTTTACCTTATAGGGGTATTTCGGTCATTCTACCCTATAG-GGGT
*
53831191 ATTTCGGTCATTTTACCTTAT-GGAGGTATTTCAGTCATTCTACCCTATAGGGGT
1 ATTTCGGTCATTTTACCTTATAGG-GGTATTTCGGTCATTCTACCCTATAGGGGT
* *
53831245 ATTTCGATTATTTTATCC-TAT-GGAGGTATTT
1 ATTTCGGTCATTTTA-CCTTATAGG-GGTATTT
53831276 TGGTTATAAC
Statistics
Matches: 168, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
53 48 0.29
54 117 0.70
55 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (54 bp):
ATTTCGGTCATTTTACCTTATAGGGGTATTTCGGTCATTCTACCCTATAGGGGT
Found at i:53831273 original size:81 final size:80
Alignment explanation
Indices: 53831030--53831275 Score: 325
Period size: 81 Copynumber: 3.0 Consensus size: 80
53831020 ACATAAATCC
* * *
53831030 ATTTCGGTCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCCCATAGGGGTATTTCGATCAT
1 ATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATAGGGGTATTTCGATCAT
*
53831095 TTTACCTTATAGGGT
66 TTTACCTTATGGGGT
* * * * * *
53831110 GTTTCGGTCATTCTACCCTATAGGGGTATTTCAGTCATTCTATCTTATAAGGGTATTTCGGTCAT
1 ATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATAGGGGTATTTCGATCAT
*
53831175 TCTACCTTATGCGGGT
66 TTTACCTTATG-GGGT
* *
53831191 ATTTCGGTCATTTTACCTTAT-GGAGGTATTTCAGTCATTCTACCCTATAGGGGTATTTCGATTA
1 ATTTCGGTCATTTTACCCTATAGG-GGTATTTCAGTCATTCTACCCTATAGGGGTATTTCGATCA
53831255 TTTTATCC-TATGGAGGT
65 TTTTA-CCTTATGG-GGT
53831272 ATTT
1 ATTT
53831276 TGGTTATAAC
Statistics
Matches: 142, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
80 68 0.48
81 72 0.51
82 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (80 bp):
ATTTCGGTCATTTTACCCTATAGGGGTATTTCAGTCATTCTACCCTATAGGGGTATTTCGATCAT
TTTACCTTATGGGGT
Found at i:53833117 original size:2 final size:2
Alignment explanation
Indices: 53833080--53833109 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53833070 TTAAGTAGTA
53833080 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
53833110 GAATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53840318 original size:8 final size:8
Alignment explanation
Indices: 53840305--53840334 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
53840295 GTTACATTAT
53840305 ATGATGAA
1 ATGATGAA
53840313 ATGATGAA
1 ATGATGAA
53840321 ATGATGAA
1 ATGATGAA
53840329 ATGATG
1 ATGATG
53840335 TTAAATTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (8 bp):
ATGATGAA
Found at i:53840475 original size:42 final size:42
Alignment explanation
Indices: 53840428--53840526 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
53840418 TTCAGTATAG
* * * *
53840428 CTGATGATGCACTTATGTGCCAGTATATTTGCTTCGATTTC-T
1 CTGATGATGCACTTATGTGCCAATATAATTACTTCGA-TACAT
53840470 CTGATGATGCACTTATGTGCCAATATAATTACTTCGATACAT
1 CTGATGATGCACTTATGTGCCAATATAATTACTTCGATACAT
53840512 CTGATGATGCACTTA
1 CTGATGATGCACTTA
53840527 CGTGGAAGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.04
42 50 0.96
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (42 bp):
CTGATGATGCACTTATGTGCCAATATAATTACTTCGATACAT
Found at i:53845900 original size:24 final size:23
Alignment explanation
Indices: 53845866--53845912 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
53845856 TTTACGTTCT
53845866 GGAAAGCTAAAAGAAAAAGAAAAA
1 GGAAAGCTAAAAG-AAAAGAAAAA
*
53845890 GGAAAGTTAAAAGAAAAGAAAAA
1 GGAAAGCTAAAAGAAAAGAAAAA
53845913 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.06
Consensus pattern (23 bp):
GGAAAGCTAAAAGAAAAGAAAAA
Found at i:53845907 original size:17 final size:18
Alignment explanation
Indices: 53845880--53845918 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
53845870 AGCTAAAAGA
* *
53845880 AAAAGAAAAAGGAAAGTT
1 AAAAGAAAAAGAAAAATT
53845898 AAAAG-AAAAGAAAAATT
1 AAAAGAAAAAGAAAAATT
53845915 AAAA
1 AAAA
53845919 TTATAGGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAATT
Found at i:53849200 original size:5 final size:5
Alignment explanation
Indices: 53849190--53849265 Score: 152
Period size: 5 Copynumber: 15.2 Consensus size: 5
53849180 GATTGTCTAT
53849190 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
53849240 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
53849266 GCACGAGTTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 71 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:53849424 original size:17 final size:16
Alignment explanation
Indices: 53849402--53849433 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
53849392 AATAGTTGTG
53849402 ATAATTATACATTTAAC
1 ATAATTATA-ATTTAAC
53849419 ATAATTATAATTTAA
1 ATAATTATAATTTAA
53849434 TAGAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATTTAAC
Found at i:53849455 original size:43 final size:44
Alignment explanation
Indices: 53849384--53849487 Score: 111
Period size: 44 Copynumber: 2.3 Consensus size: 44
53849374 TTTAAAAAGT
* * * * *
53849384 TGAAATAAAATAGTTGTGATAATTATACATTTA-ACATAATTATAA
1 TGAAAT-AAA-AGTTATGGTAATAATACATTTACAAATAATTAGAA
** *
53849429 TTTAATAGAAGTTATGGTAATAATACATTTACAAATAATTAGAA
1 TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
53849473 TGAAATAAAAGTTAT
1 TGAAATAAAAGTTAT
53849488 TCTAATTTTA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
43 19 0.40
44 24 0.51
45 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.37
Consensus pattern (44 bp):
TGAAATAAAAGTTATGGTAATAATACATTTACAAATAATTAGAA
Found at i:53849670 original size:22 final size:23
Alignment explanation
Indices: 53849645--53849695 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
53849635 ATGTTATATG
53849645 TTGAATATGTTT-TAAT-TATTAT
1 TTGAATAT-TTTCTAATATATTAT
* *
53849667 TTGAAAATTTTCTATTATATTAT
1 TTGAATATTTTCTAATATATTAT
53849690 TTGAAT
1 TTGAAT
53849696 TGATAAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 10 0.42
23 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (23 bp):
TTGAATATTTTCTAATATATTAT
Found at i:53851158 original size:16 final size:16
Alignment explanation
Indices: 53851137--53851178 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
53851127 TTTAAAAAAA
*
53851137 TATAAAATTTGGATTT
1 TATAAAATTTGAATTT
53851153 TATAAATATTTTGAATTT
1 TATAAA-A-TTTGAATTT
53851171 TA-AAAATT
1 TATAAAATT
53851179 ATTTTGAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 2 0.09
16 7 0.30
17 4 0.17
18 10 0.43
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TATAAAATTTGAATTT
Found at i:53851211 original size:20 final size:19
Alignment explanation
Indices: 53851144--53851210 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
53851134 AAATATAAAA
* *
53851144 TTTGGATTTTATAAA-TAT
1 TTTGAATTTTAAAAATTAT
53851162 TTTGAATTTTAAAAATTAT
1 TTTGAATTTTAAAAATTAT
*
53851181 TTTGAACTTTTGAAAATTAT
1 TTTGAA-TTTTAAAAATTAT
*
53851201 TTTGTATTTT
1 TTTGAATTTT
53851211 TTGTTGAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.30
19 13 0.30
20 17 0.40
ACGTcount: A:0.33, C:0.01, G:0.09, T:0.57
Consensus pattern (19 bp):
TTTGAATTTTAAAAATTAT
Found at i:53855478 original size:15 final size:14
Alignment explanation
Indices: 53855458--53855488 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
53855448 TGTTATCATC
53855458 TTTTAATTTAATTTA
1 TTTTAATTT-ATTTA
53855473 TTTTAATTTATTTA
1 TTTTAATTTATTTA
53855487 TT
1 TT
53855489 AAATTACGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAATTTATTTA
Found at i:53859318 original size:29 final size:29
Alignment explanation
Indices: 53859272--53859331 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
53859262 CCTTAGTACC
*
53859272 TTAAGATCATGTTACAAGATCTGGACAGG
1 TTAACATCATGTTACAAGATCTGGACAGG
* *
53859301 TTAACATCATGTTCCAAGATTTGGACAGG
1 TTAACATCATGTTACAAGATCTGGACAGG
53859330 TT
1 TT
53859332 CCTCTTCGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (29 bp):
TTAACATCATGTTACAAGATCTGGACAGG
Found at i:53873068 original size:27 final size:27
Alignment explanation
Indices: 53873028--53873080 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
53873018 CATAATCCTT
*
53873028 GTGTTTACTATCCTGTTAGAATATTCC
1 GTGTTTAATATCCTGTTAGAATATTCC
* * *
53873055 GTGTTTAATGTCCTGTTGGACTATTC
1 GTGTTTAATATCCTGTTAGAATATTC
53873081 TACGATGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (27 bp):
GTGTTTAATATCCTGTTAGAATATTCC
Found at i:53883624 original size:6 final size:6
Alignment explanation
Indices: 53883613--53883653 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
53883603 AGGATTTCTA
*
53883613 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATT ATTAT
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTAT
53883654 ATTTACACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTATC
Found at i:53890012 original size:36 final size:36
Alignment explanation
Indices: 53889972--53890049 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
53889962 ACAAAGACTA
* * *
53889972 TCACATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAACAACACACCCACATATTCACTG
* *
53890008 TCACATGGCATGAACAACACACCCTCATATTCACTT
1 TCACATGGCATGAACAACACACCCACATATTCACTG
53890044 TCACAT
1 TCACAT
53890050 CATTCATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (36 bp):
TCACATGGCATGAACAACACACCCACATATTCACTG
Found at i:53890789 original size:20 final size:21
Alignment explanation
Indices: 53890752--53890791 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
53890742 TTTTGGGTTT
53890752 TAACTAAAACATTCAATTTTCA
1 TAACTAAAACA-TCAATTTTCA
53890774 TAACTAAAAC-TCAATTTT
1 TAACTAAAACATCAATTTT
53890792 AAAGTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (21 bp):
TAACTAAAACATCAATTTTCA
Found at i:53892513 original size:24 final size:24
Alignment explanation
Indices: 53892463--53892515 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53892453 TTTCTAGAAG
* * *
53892463 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGAATTTATTAGCACAATAT
*
53892487 ATTTAGAATTTATTAGCACAATTT
1 ATTTAGAATTTATTAGCACAATAT
53892511 ATTTA
1 ATTTA
53892516 ACCTACAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
ATTTAGAATTTATTAGCACAATAT
Found at i:53894524 original size:26 final size:26
Alignment explanation
Indices: 53894494--53894546 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
53894484 TTTTTTGACC
53894494 TACGAATTTAGCTTATAAATAGTCTT
1 TACGAATTTAGCTTATAAATAGTCTT
53894520 TACGAATTTAGCTTATAAATAGTCTT
1 TACGAATTTAGCTTATAAATAGTCTT
53894546 T
1 T
53894547 TTTTTATAAC
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:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (26 bp):
TACGAATTTAGCTTATAAATAGTCTT
Found at i:53896896 original size:16 final size:16
Alignment explanation
Indices: 53896877--53896917 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
53896867 ATAAGTTTAT
53896877 TTAATTATAATTAAAA
1 TTAATTATAATTAAAA
53896893 TTAATTATAATTAAAA
1 TTAATTATAATTAAAA
53896909 TTAATTATA
1 TTAATTATA
53896918 TTTTTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATTATAATTAAAA
Found at i:53908842 original size:21 final size:22
Alignment explanation
Indices: 53908800--53908842 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
53908790 TTATTCTCAA
* **
53908800 ATTTCTTATTTTACTATTTTTG
1 ATTTCTTATATTACTAAATTTG
53908822 ATTTCTT-TATTACTAAATTTG
1 ATTTCTTATATTACTAAATTTG
53908843 TTCATTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.63
Consensus pattern (22 bp):
ATTTCTTATATTACTAAATTTG
Found at i:53909189 original size:19 final size:19
Alignment explanation
Indices: 53909165--53909268 Score: 163
Period size: 19 Copynumber: 5.5 Consensus size: 19
53909155 AATCTTCAGG
53909165 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53909184 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
53909203 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53909222 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
53909241 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53909260 GATATGCAA
1 GATATGCAA
53909269 GAAGATATGA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 75 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:53909215 original size:38 final size:38
Alignment explanation
Indices: 53909172--53909268 Score: 185
Period size: 38 Copynumber: 2.6 Consensus size: 38
53909162 AGGGATATGC
53909172 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
53909210 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
53909248 AATCTTAGATATGATATGCAA
1 AATCTTAGATATGATATGCAA
53909269 GAAGATATGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:53913150 original size:8 final size:8
Alignment explanation
Indices: 53913137--53913174 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
53913127 GGGGATGACA
53913137 AAAAAAAC
1 AAAAAAAC
53913145 AAAAAAAC
1 AAAAAAAC
*
53913153 AAAAAAAA
1 AAAAAAAC
53913161 AACAAAAAC
1 AA-AAAAAC
53913170 AAAAA
1 AAAAA
53913175 CAAAATCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:53913154 original size:17 final size:17
Alignment explanation
Indices: 53913134--53913179 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
53913124 AAAGGGGATG
53913134 ACAAAAAAAACAA-AAAA
1 ACAAAAAAAA-AACAAAA
53913151 ACAAAAAAAAAACAAAA
1 ACAAAAAAAAAACAAAA
53913168 ACAAAAACAAAA
1 ACAAAAA-AAAA
53913180 TCTACCAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.07
17 21 0.78
18 4 0.15
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (17 bp):
ACAAAAAAAAAACAAAA
Found at i:53913156 original size:6 final size:6
Alignment explanation
Indices: 53913134--53913179 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
53913124 AAAGGGGATG
53913134 ACAAAA A-AAACA A-AAAA ACAAAA A-AAAA ACAAAA ACAAAA ACAAAA
1 ACAAAA ACAAA-A ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA
53913180 TCTACCAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:53913159 original size:11 final size:11
Alignment explanation
Indices: 53913136--53913179 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
53913126 AGGGGATGAC
*
53913136 AAAAAA-AACA
1 AAAAAACAAAA
53913146 AAAAAACAAAA
1 AAAAAACAAAA
53913157 AAAAAACAAAA
1 AAAAAACAAAA
53913168 ACAAAAACAAAA
1 A-AAAAACAAAA
53913180 TCTACCAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 6 0.19
11 15 0.48
12 10 0.32
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:53915067 original size:44 final size:45
Alignment explanation
Indices: 53915019--53915200 Score: 97
Period size: 44 Copynumber: 4.1 Consensus size: 45
53915009 CCTGAAAAAC
53915019 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGACAGT
** * ** * * * ** **
53915063 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA-T
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCT-AAGACAGT
* * * ** * * ** **
53915108 AGTGGAGTACATTGAAG---CCAGAAATTCTACTTCCTTGGACAAC
1 AGTGGAATAGATTGAAGATTTCAGATCTTAT-CTCCCTAAGACAGT
53915151 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAG-CAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGACAGT
53915195 AGTGGA
1 AGTGGA
53915201 GCAGATCGAA
Statistics
Matches: 96, Mismatches: 35, Indels: 14
0.66 0.24 0.10
Matches are distributed among these distances:
42 9 0.09
43 20 0.21
44 37 0.39
45 22 0.23
46 8 0.08
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGACAGT
Found at i:53915581 original size:132 final size:132
Alignment explanation
Indices: 53914799--53915566 Score: 1243
Period size: 132 Copynumber: 5.8 Consensus size: 132
53914789 CTGCATTGAC
* * * * * *
53914799 AGTGAAGCAGATCGAAGATGACGAATTTTACCTCCTTGTGGTTACAATGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
53914864 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
66 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
53914929 GT
131 GT
* *
53914931 AGTGGAGCAGATCGAAGATGGTGGATTTTACTTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
* *
53914996 GTAATTCTACTTCCCTGAAAAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
66 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
53915061 GT
131 GT
53915063 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
* *
53915128 GAAATTCTACTTCCTTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
66 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
53915193 GT
131 GT
* *
53915195 AGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTATGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
* * *
53915260 GTAATTCTACTTCCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCTAATCACCCTAAGCA
66 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
53915325 GT
131 GT
* *
53915327 AGTGGAGCAAATCAAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
* *
53915392 ATAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTATCTCCCTAAGCA
66 GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
53915457 GT
131 GT
* * * *
53915459 AGTGGAGCAGATCGAAGAAGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGACA
1 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
* * * *
53915524 GTAA-TCATA-TCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATT
66 GTAATTC-TACT-TCCCTGGACAACAGTGGAATAGATTGAAGATT
53915567 GTAAGTCCAA
Statistics
Matches: 591, Mismatches: 43, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
131 3 0.01
132 588 0.99
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCA
GTAATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA
GT
Found at i:53915917 original size:19 final size:19
Alignment explanation
Indices: 53915893--53916003 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
53915883 AATCTTCAGG
53915893 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53915912 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
53915931 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53915950 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
53915969 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
53915988 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
53916004 AGATATAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:53915943 original size:38 final size:38
Alignment explanation
Indices: 53915900--53916003 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
53915890 AGGGATATGC
53915900 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
53915938 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
53915976 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
53916004 AGATATAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:53917840 original size:21 final size:20
Alignment explanation
Indices: 53917793--53917849 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
53917783 ATATTTTCCA
*
53917793 TGAAAAAATAATAAAAAAGG
1 TGAAAAAATAAAAAAAAAGG
*
53917813 TGCAAAAATAAAAAAAATATGG
1 TGAAAAAATAAAAAAAA-A-GG
*
53917835 -GAAAAAAGAAAAAAA
1 TGAAAAAATAAAAAAA
53917850 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 15 0.48
21 14 0.45
22 2 0.06
ACGTcount: A:0.72, C:0.02, G:0.14, T:0.12
Consensus pattern (20 bp):
TGAAAAAATAAAAAAAAAGG
Found at i:53930436 original size:31 final size:31
Alignment explanation
Indices: 53930396--53930472 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
53930386 CATATGAGTC
*
53930396 CCTTTATGGCCAAGAACCCCCACATCACTTA
1 CCTTAATGGCCAAGAACCCCCACATCACTTA
53930427 CCTTAATGGCCAAGAACCCCCACATCACTTA
1 CCTTAATGGCCAAGAACCCCCACATCACTTA
53930458 CCTTAATGGCCAAGA
1 CCTTAATGGCCAAGA
53930473 GCATCATTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.36, G:0.12, T:0.21
Consensus pattern (31 bp):
CCTTAATGGCCAAGAACCCCCACATCACTTA
Found at i:53934967 original size:263 final size:263
Alignment explanation
Indices: 53934500--53935031 Score: 965
Period size: 263 Copynumber: 2.0 Consensus size: 263
53934490 CTTCCCACCC
53934500 CTGTCTTGAAGGGCAACTTTCCATACATGGCTCTTTATGGTGAAGATCCTTCTTATAATCATCTA
1 CTGTCTTGAAGGGCAACTTTCCATACATGGCTCTTTATGGTGAAGATCCTTCTTATAATCATCTA
* *
53934565 CGCGTGTTTGGATGCTACTGTTTTCCTTATCATCGACCCTTTCACAATCATAAATTGGAATTTCG
66 CGCGTGTTTGGATGCTACTGCTTTCCTTATCATCGACCATTTCACAATCATAAATTGGAATTTCG
*
53934630 ATCTCAACCAAGCACATTTTTAGGGTATAGTTCTCAGCACAAAGGGTATCAGTGTCTTATACCAG
131 ATCTCAACCAAGCACATTTTTAGGGTATAATTCTCAGCACAAAGGGTATCAGTGTCTTATACCAG
* * *
53934695 GCGGTAAAATTGTCATTTCTCGCCATGTTATTTTTTATGAACACCACTTTTTACATCTTAATCAT
196 ACGGTAAAATTCTCATTTCTCGCCATGTTATTTTTTACGAACACCACTTTTTACATCTTAATCAT
53934760 CCT
261 CCT
* *
53934763 CTGTCTTGAAGGGCGACTTTCCATACATGGCTTTTTATGGTGAAGATCCTTCTTATAATCATCTA
1 CTGTCTTGAAGGGCAACTTTCCATACATGGCTCTTTATGGTGAAGATCCTTCTTATAATCATCTA
*
53934828 CGCGTGTTTGGATGCTACTGCTTTCCTTATCTTCGACCATTTCACAATCATAAATTGGAATTTCG
66 CGCGTGTTTGGATGCTACTGCTTTCCTTATCATCGACCATTTCACAATCATAAATTGGAATTTCG
*
53934893 ATCTCAACCATGCACATTTTTAGGGTATAATTCTCAGCACAAAGGGTATCAGTGTCTTATACCAG
131 ATCTCAACCAAGCACATTTTTAGGGTATAATTCTCAGCACAAAGGGTATCAGTGTCTTATACCAG
*
53934958 ACGGTAAAATTCTCATTTCTCGCCATGTTATTTTTTACGAACACCGCTTTTTACATCTTAATCAT
196 ACGGTAAAATTCTCATTTCTCGCCATGTTATTTTTTACGAACACCACTTTTTACATCTTAATCAT
53935023 CCT
261 CCT
53935026 CTGTCT
1 CTGTCT
53935032 ACTAACCTAA
Statistics
Matches: 258, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
263 258 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (263 bp):
CTGTCTTGAAGGGCAACTTTCCATACATGGCTCTTTATGGTGAAGATCCTTCTTATAATCATCTA
CGCGTGTTTGGATGCTACTGCTTTCCTTATCATCGACCATTTCACAATCATAAATTGGAATTTCG
ATCTCAACCAAGCACATTTTTAGGGTATAATTCTCAGCACAAAGGGTATCAGTGTCTTATACCAG
ACGGTAAAATTCTCATTTCTCGCCATGTTATTTTTTACGAACACCACTTTTTACATCTTAATCAT
CCT
Found at i:53941441 original size:12 final size:12
Alignment explanation
Indices: 53941424--53941448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53941414 CACGGCCGTC
53941424 TCCCAGCCTATG
1 TCCCAGCCTATG
53941436 TCCCAGCCTATG
1 TCCCAGCCTATG
53941448 T
1 T
53941449 ACTCATTCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.28
Consensus pattern (12 bp):
TCCCAGCCTATG
Found at i:53949053 original size:30 final size:30
Alignment explanation
Indices: 53949019--53949083 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
53949009 CACAAGAGCG
* * *
53949019 TGTGTCTAGCCCATGT-GACACACATGGGCT
1 TGTGTCCAGCCCATGTGGA-ACACATAGGCA
*
53949049 TGTGTCCAGCTCATGTGGAACACATAGGCA
1 TGTGTCCAGCCCATGTGGAACACATAGGCA
53949079 TGTGT
1 TGTGT
53949084 ACAAGCCGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (30 bp):
TGTGTCCAGCCCATGTGGAACACATAGGCA
Found at i:53952266 original size:17 final size:17
Alignment explanation
Indices: 53952225--53952258 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53952215 ATGATAATAA
*
53952225 AATAAAACT-AAGGAAT
1 AATAAAAATAAAGGAAT
53952241 AATAAAAATAAAGGAAT
1 AATAAAAATAAAGGAAT
53952258 A
1 A
53952259 TAATAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (17 bp):
AATAAAAATAAAGGAAT
Found at i:53952385 original size:23 final size:23
Alignment explanation
Indices: 53952357--53952400 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
53952347 CATGAACAAA
*
53952357 ATAATAA-TAAACAAATGGAAAGC
1 ATAATAAGAAAACAAA-GGAAAGC
53952380 ATAATAAGAAAACAAAGGAAA
1 ATAATAAGAAAACAAAGGAAA
53952401 ATACATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (23 bp):
ATAATAAGAAAACAAAGGAAAGC
Found at i:53952427 original size:15 final size:13
Alignment explanation
Indices: 53952398--53952446 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 13
53952388 AAAACAAAGG
53952398 AAAATACATATAAT
1 AAAATA-ATATAAT
53952412 AGAAATAATATAAAT
1 A-AAATAATAT-AAT
53952427 AAGAATAATA-AAT
1 AA-AATAATATAAT
53952440 AAAATAA
1 AAAATAA
53952447 AATACTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 6 0.19
15 16 0.50
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATAATATAAT
Found at i:53953464 original size:20 final size:21
Alignment explanation
Indices: 53953435--53953492 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
53953425 TTATTTTTTA
*
53953435 TAATTAAAAATTAAT-TGAAT
1 TAATTAAAAAATAATATGAAT
*
53953455 TAATTCAAAAATAATATGAAAT
1 TAATTAAAAAATAATATG-AAT
*
53953477 AAAGTTAAAAGAATAA
1 TAA-TTAAAA-AATAA
53953493 GTAGAATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
21 2 0.07
22 5 0.17
23 5 0.17
24 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (21 bp):
TAATTAAAAAATAATATGAAT
Found at i:53956240 original size:25 final size:25
Alignment explanation
Indices: 53956212--53956291 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
53956202 CTTCCAAGCA
*
53956212 AAATATCAGGAAGCTCGTGAGAGCT
1 AAATATCAGGAAGCTCGTGAGAGCC
* *
53956237 AAATAACAGGAAGCTTGTGAGAGCC
1 AAATATCAGGAAGCTCGTGAGAGCC
* * **
53956262 AAGTATCGGGAAGCTCACGAGAGCC
1 AAATATCAGGAAGCTCGTGAGAGCC
53956287 AAATA
1 AAATA
53956292 CTGGGATGCT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.39, C:0.17, G:0.28, T:0.16
Consensus pattern (25 bp):
AAATATCAGGAAGCTCGTGAGAGCC
Found at i:53958458 original size:16 final size:16
Alignment explanation
Indices: 53958410--53958460 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
53958400 AACGAAATTT
53958410 TCATACGATATTTCTA
1 TCATACGATATTTCTA
*
53958426 TCATA-AAT-TTTCT-
1 TCATACGATATTTCTA
53958439 TCATACGATATTTCTA
1 TCATACGATATTTCTA
53958455 TCATAC
1 TCATAC
53958461 AACTCTCCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 7 0.23
16 11 0.37
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (16 bp):
TCATACGATATTTCTA
Found at i:53961381 original size:379 final size:379
Alignment explanation
Indices: 53960682--53961443 Score: 1359
Period size: 379 Copynumber: 2.0 Consensus size: 379
53960672 AAAATTCACA
53960682 TTTGCTAAATTTAGCATACAGTTGTTTTTCTCACAAATTTTGCAGAACAATTCTCAGATGTTCGG
1 TTTGCTAAATTTAGCATACAGTTGTTTTTCTCACAAATTTTGCAGAACAATTCTCAGATGTTCGG
* *
53960747 CATGTTCAGTCTCATCTCGGGAATATACCAGAATATCATCAATAAATACCATAACAAATCTACCA
66 CATGTTCAGTCCCATCTCGGGAATATACCAGAATATCATCAATAAATACCACAACAAATCTACCA
* *
53960812 AATACAATTTGAAAATTCTATTCATCAAATCTATAAATACTGCATGTGCATTAATTAAAAAAACA
131 AATACAATTTGAAAATTCTATTCATCAAATCCATAAATACCGCATGTGCATTAATTAAAAAAACA
* *
53960877 GCATCACAAGGAATTCATAATATCCGTACTTGGTTCTGAATGTTGTTTCCGGTATATTAGAATCT
196 GCATCAAAAGGAATTCATAATATCCGTACTTGGTTCTGAATGTTGTTTCCGGCATATTAGAATCT
* * *
53960942 TTCACTCGTAACTGATAATAACCAGAATGGATATCAATATTTGAAAACATTGTGGCACCCTTCAA
261 TTCACTCGTAACTGATAATAACCAGAACGGAGATCAATATTTGAAAACATTATGGCACCCTTCAA
53961007 TTGATCAAACAAATCATCAATACGAGGTAGTAGATATTTATTCTTGATTGTAAC
326 TTGATCAAACAAATCATCAATACGAGGTAGTAGATATTTATTCTTGATTGTAAC
53961061 TTTGCTAAATTTAGCATACAGTTGTTTTTCTCACAAATTTTGCAGAACAATTCTCAGATGTTCGG
1 TTTGCTAAATTTAGCATACAGTTGTTTTTCTCACAAATTTTGCAGAACAATTCTCAGATGTTCGG
53961126 CATGTTCAGTCCCATCTCGGGAATATACCAGAATATCATCAATAAATACCACAACAAATCTATCC
66 CATGTTCAGTCCCATCTCGGGAATATACCAGAATATCATCAATAAATACCACAACAAATCTA-CC
*
53961191 AAATA-AGATTTGAAAATTTTATTCATCAAATCCATAAATACCGCATGTGCATTAATT-AAAAAA
130 AAATACA-ATTTGAAAATTCTATTCATCAAATCCATAAATACCGCATGTGCATTAATTAAAAAAA
*
53961254 C-GACATCAAAAGGAATTCATAATATCTGTACTTGGTTCTGAATGTTGTTTCCGGCATATTAGAA
194 CAG-CATCAAAAGGAATTCATAATATCCGTACTTGGTTCTGAATGTTGTTTCCGGCATATTAGAA
53961318 TCTTTCACTCGTAACTGATAATAACCAGAACGGAGATCAATATTTGAAAACATTATGGCACCCTT
258 TCTTTCACTCGTAACTGATAATAACCAGAACGGAGATCAATATTTGAAAACATTATGGCACCCTT
* *
53961383 CAATTGATCAAACAAATCATCAATATGAGGTAGTGGATATTTATTCTTGATTGTAAC
323 CAATTGATCAAACAAATCATCAATACGAGGTAGTAGATATTTATTCTTGATTGTAAC
53961440 TTTG
1 TTTG
53961444 TTGAGCTATC
Statistics
Matches: 367, Mismatches: 13, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
378 1 0.00
379 312 0.85
380 54 0.15
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (379 bp):
TTTGCTAAATTTAGCATACAGTTGTTTTTCTCACAAATTTTGCAGAACAATTCTCAGATGTTCGG
CATGTTCAGTCCCATCTCGGGAATATACCAGAATATCATCAATAAATACCACAACAAATCTACCA
AATACAATTTGAAAATTCTATTCATCAAATCCATAAATACCGCATGTGCATTAATTAAAAAAACA
GCATCAAAAGGAATTCATAATATCCGTACTTGGTTCTGAATGTTGTTTCCGGCATATTAGAATCT
TTCACTCGTAACTGATAATAACCAGAACGGAGATCAATATTTGAAAACATTATGGCACCCTTCAA
TTGATCAAACAAATCATCAATACGAGGTAGTAGATATTTATTCTTGATTGTAAC
Found at i:53965455 original size:29 final size:27
Alignment explanation
Indices: 53965415--53965481 Score: 116
Period size: 29 Copynumber: 2.4 Consensus size: 27
53965405 CCACAAAATA
53965415 GGTAAAATGACCAAAATACCCTTAAAG
1 GGTAAAATGACCAAAATACCCTTAAAG
53965442 GGTAGTAAATGACCAAAATACCCTTAAAG
1 GGTA--AAATGACCAAAATACCCTTAAAG
53965471 GGTAAAATGAC
1 GGTAAAATGAC
53965482 TAGTTTACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 11 0.29
29 27 0.71
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.19
Consensus pattern (27 bp):
GGTAAAATGACCAAAATACCCTTAAAG
Found at i:53965691 original size:26 final size:28
Alignment explanation
Indices: 53965652--53965729 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 28
53965642 AAGTAAACTT
* *
53965652 TTACTGGCAGCTTTGTTGCGATA-A-TG
1 TTACTGGCAACTTTGTTGCGATACATTA
*
53965678 TTACTGGCAACTTTGCTGCGATACTATTA
1 TTACTGGCAACTTTGTTGCGATAC-ATTA
* *
53965707 TTACTGGTAACTTTGTTGTGATA
1 TTACTGGCAACTTTGTTGCGATA
53965730 TTGGTGAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
26 21 0.49
28 1 0.02
29 21 0.49
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (28 bp):
TTACTGGCAACTTTGTTGCGATACATTA
Found at i:53965901 original size:28 final size:28
Alignment explanation
Indices: 53965842--53965895 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
53965832 ACTGAAATTG
* *
53965842 TATTGGGCTAAGGCCCACACTGTTACTA
1 TATTAGGCTAAGGCCCACACTGTCACTA
53965870 TATTAGGCTAAGGCCCACACTG-CACT
1 TATTAGGCTAAGGCCCACACTGTCACT
53965896 GTTATTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (28 bp):
TATTAGGCTAAGGCCCACACTGTCACTA
Found at i:53968199 original size:16 final size:16
Alignment explanation
Indices: 53968178--53968215 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
53968168 TTTGGTATTG
53968178 AGCTCCTGCCTGGAGC
1 AGCTCCTGCCTGGAGC
53968194 AGCTCCTGCCTGGAGC
1 AGCTCCTGCCTGGAGC
53968210 AGCTCC
1 AGCTCC
53968216 AGTGGCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.13, C:0.39, G:0.29, T:0.18
Consensus pattern (16 bp):
AGCTCCTGCCTGGAGC
Found at i:53972955 original size:25 final size:26
Alignment explanation
Indices: 53972927--53973009 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
53972917 ATGGGGTTGG
**
53972927 GATACTGTTACTGGCATTTTTG-AGC
1 GATACTGTTACTGGCAGCTTTGCAGC
* *
53972952 GATACTGTCACTGGCAGCTTTGCTGC
1 GATACTGTTACTGGCAGCTTTGCAGC
* * * *
53972978 GATACTGTTACTAGTAGCTTTCCTGC
1 GATACTGTTACTGGCAGCTTTGCAGC
53973004 GATACT
1 GATACT
53973010 ATTATTATTG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 19 0.39
26 30 0.61
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (26 bp):
GATACTGTTACTGGCAGCTTTGCAGC
Found at i:53987760 original size:129 final size:128
Alignment explanation
Indices: 53987530--53987815 Score: 416
Period size: 129 Copynumber: 2.2 Consensus size: 128
53987520 ACATTTGTAC
* * * *
53987530 TTTTCCTCTAAAACTTTTACTCCCCTCTCATCCCACCCCTATCTACCCCAAACCCATTTACCCCC
1 TTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCACCCCCATCTACCCCAAACCCATTTACCCCC
* * * *
53987595 ATTTTAGTCCCCCATTTATTTTCCTCTAAAATTTTACTTTCGCAAAAACCCTCAAAACTTTTTA
66 ATTTTACTCCCCCATTTAATTTCCTCTAAAATTTTAC-TCCCCAAAAACCCTCAAAACTTTTTA
* *
53987659 TTTTCCCCCAAAACTTTTACTCCCCTCCCCTCCCACCCCCATCTACCCTAAACCCATTT-CCCCC
1 TTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCACCCCCATCTACCCCAAACCCATTTACCCCC
*
53987723 ATTTTACTCCCTCTATTTAATTTCCT-TCAAAATTTTACTCCCCAAAAACCCTCAAAACTTTTTA
66 ATTTTACTCCC-CCATTTAATTTCCTCT-AAAATTTTACTCCCCAAAAACCCTCAAAACTTTTTA
*
53987787 ATTTCCCCCAAAACTTTTACT-CCCTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCCTCCCA
53987816 CTTTCCCCCC
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
127 7 0.05
128 60 0.42
129 75 0.53
ACGTcount: A:0.25, C:0.40, G:0.01, T:0.35
Consensus pattern (128 bp):
TTTTCCCCCAAAACTTTTACTCCCCTCCCATCCCACCCCCATCTACCCCAAACCCATTTACCCCC
ATTTTACTCCCCCATTTAATTTCCTCTAAAATTTTACTCCCCAAAAACCCTCAAAACTTTTTA
Found at i:53991549 original size:2 final size:2
Alignment explanation
Indices: 53991542--53991571 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53991532 ATTTAAGCTC
53991542 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
53991572 GAAGGGATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53994238 original size:2 final size:2
Alignment explanation
Indices: 53994233--53994282 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
53994223 CTCTCACTTC
53994233 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
53994275 CT CA CT CT
1 CT CT CT CT
53994283 TTTCCCCCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:53994860 original size:4 final size:4
Alignment explanation
Indices: 53994851--53994881 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
53994841 TGTAAATCTT
53994851 GATG GATG GATG GATG GATG GATG GATG GAT
1 GATG GATG GATG GATG GATG GATG GATG GAT
53994882 CACCTGGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
GATG
Found at i:53999716 original size:29 final size:30
Alignment explanation
Indices: 53999683--53999749 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
53999673 AAATCAAAAT
*
53999683 TTTATATATAAAATTACACA-AAACTAAAG
1 TTTATATACAAAATTACACATAAACTAAAG
* * *
53999712 TTTATGTACATAATTACACATTAAACTATAG
1 TTTATATACAAAATTACACA-TAAACTAAAG
53999743 TTTATAT
1 TTTATAT
53999750 TGGTATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 17 0.55
31 14 0.45
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTATATACAAAATTACACATAAACTAAAG
Found at i:54000382 original size:19 final size:19
Alignment explanation
Indices: 54000358--54000408 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
54000348 AGTTTATAAC
54000358 ATAAAACTTAAAT-TTATTA
1 ATAAAACTTAAATATTA-TA
*
54000377 ATAAAA-TAAAATATTATA
1 ATAAAACTTAAATATTATA
54000395 ATATAAACATTAAA
1 ATA-AAAC-TTAAA
54000409 AATATATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
21 4 0.15
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAACTTAAATATTATA
Found at i:54005859 original size:131 final size:131
Alignment explanation
Indices: 54005687--54006077 Score: 392
Period size: 131 Copynumber: 3.0 Consensus size: 131
54005677 AATAAATTGT
* * * ** * *
54005687 TGTTAAATATTATAATATTAGCAATGACTTTAAAATGTTGTTACATAATTTAATTTTTTACCTAT
1 TGTTAAACATTAAAATATTAACAACAACATTAAAATGTTGTTACATAATTTAATTTTTTACTTAT
* * * * * *
54005752 TAACCGTAACAACACAATTTGTCGTTGTGAATTATTAATAAAATGTGTAACAACCAAATAAGTT-
66 TAATCGCAACAACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACAAAATAAGTTA
*
54005816 G
131 C
* * * * * * *
54005817 TTTCTAAACGTTAAAATATTAACAGCAACATTAAAATGTTGTTGCATAAATTAATTTTATGCTTA
1 TGT-TAAACATTAAAATATTAACAACAACATTAAAATGTTGTTACATAATTTAATTTTTTACTTA
* * * * * * *
54005882 TTCATCGCAACGACATGATTTGTCATTGTGAATTCTTAATAAAATTTGTAACAA-GACACAAGTT
65 TTAATCGCAACAACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACAAAATAAGTT
54005946 AC
130 AC
* * * * ** *
54005948 TGTTAAACATTAAAATATTAGCAATAACCTTAAAATGTCGTTATGTAATTTAATCTTTTACTTAT
1 TGTTAAACATTAAAATATTAACAACAACATTAAAATGTTGTTACATAATTTAATTTTTTACTTAT
* * * *
54006013 TAATAGCAATGAA-ACGATTTGTCATTGTTAATTATTAATAAAATTTTTAACAACAAAATAAGTT
66 TAATCGCAA-CAACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACAAAATAAGTT
54006077 A
130 A
54006078 GTATTAACAA
Statistics
Matches: 205, Mismatches: 52, Indels: 7
0.78 0.20 0.03
Matches are distributed among these distances:
130 101 0.49
131 104 0.51
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (131 bp):
TGTTAAACATTAAAATATTAACAACAACATTAAAATGTTGTTACATAATTTAATTTTTTACTTAT
TAATCGCAACAACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACAAAATAAGTTA
C
Found at i:54006012 original size:130 final size:129
Alignment explanation
Indices: 54005687--54006076 Score: 395
Period size: 130 Copynumber: 3.0 Consensus size: 129
54005677 AATAAATTGT
* * * * *
54005687 TGTTAAATATTATAATATTAGCAATGACTTTAAAATGTTGTTACATAATTTAATTTTTTACCTAT
1 TGTTAAACATTAAAATATTAGCAATAACATTAAAATGTTGTTACATAATTTAA-TTTTTACTTAT
* * * * * * * *
54005752 TAACCGTAACAACACAATTTGTCGTTGTGAATTATTAATAAAATGTGTAACAACCAAATAAGTTG
65 TAATCGCAACGACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACCAAACAAGTTC
* * * ** * * *
54005817 TTTCTAAACGTTAAAATATTAACAGCAACATTAAAATGTTGTTGCATAAATTAATTTTATGCTTA
1 TGT-TAAACATTAAAATATTAGCAATAACATTAAAATGTTGTTACATAATTTAATTTT-TACTTA
* * * * *
54005882 TTCATCGCAACGACATGATTTGTCATTGTGAATTCTTAATAAAATTTGTAACAA-GACACAAGTT
64 TTAATCGCAACGACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACCAAACAAGTT
54005946 AC
129 -C
* * **
54005948 TGTTAAACATTAAAATATTAGCAATAACCTTAAAATGTCGTTATGTAATTTAATCTTTTACTTAT
1 TGTTAAACATTAAAATATTAGCAATAACATTAAAATGTTGTTACATAATTTAAT-TTTTACTTAT
* * * * * * *
54006013 TAATAGCAATGAAACGATTTGTCATTGTTAATTATTAATAAAATTTTTAACAACAAAATAAGTT
65 TAATCGCAACGACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACCAAACAAGTT
54006077 AGTATTAACA
Statistics
Matches: 206, Mismatches: 49, Indels: 9
0.78 0.19 0.03
Matches are distributed among these distances:
130 105 0.51
131 101 0.49
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (129 bp):
TGTTAAACATTAAAATATTAGCAATAACATTAAAATGTTGTTACATAATTTAATTTTTACTTATT
AATCGCAACGACACGATTTGTCATTGTGAATTATTAATAAAATTTGTAACAACCAAACAAGTTC
Found at i:54007596 original size:20 final size:19
Alignment explanation
Indices: 54007546--54007596 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
54007536 GATAAATTAT
54007546 AATAAAAAAGAAAAGAAATA
1 AATAAAAAA-AAAAGAAATA
*
54007566 AACGAAAAAAAAAAGAAATCA
1 AA-TAAAAAAAAAAGAAAT-A
54007587 AATAAGAAAA
1 AATAA-AAAA
54007597 TATATATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.78, C:0.04, G:0.10, T:0.08
Consensus pattern (19 bp):
AATAAAAAAAAAAGAAATA
Found at i:54011467 original size:24 final size:24
Alignment explanation
Indices: 54011440--54011520 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 24
54011430 AAGCATAAGT
54011440 TGAGATGGTTAATCCTTAAAAATA
1 TGAGATGGTTAATCCTTAAAAATA
**
54011464 TGAGATTTTTAAGT--TTAATAAATATA
1 TGAGATGGTTAA-TCCTT-A-AAA-ATA
54011490 TTGAGATGGTTAATCCTTAAAAATA
1 -TGAGATGGTTAATCCTTAAAAATA
54011515 TGAGAT
1 TGAGAT
54011521 TTTTAAGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
23 2 0.04
24 17 0.37
25 7 0.15
26 7 0.15
27 11 0.24
28 2 0.04
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (24 bp):
TGAGATGGTTAATCCTTAAAAATA
Found at i:54011498 original size:51 final size:51
Alignment explanation
Indices: 54011439--54011542 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
54011429 AAAGCATAAG
54011439 TTGAGATGGTTAATCCTTAAAAATATGAGATTTTTAAGTTTAATAAATATA
1 TTGAGATGGTTAATCCTTAAAAATATGAGATTTTTAAGTTTAATAAATATA
54011490 TTGAGATGGTTAATCCTTAAAAATATGAGATTTTTAAGTTTAATAAATATA
1 TTGAGATGGTTAATCCTTAAAAATATGAGATTTTTAAGTTTAATAAATATA
54011541 TT
1 TT
54011543 ATATTATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (51 bp):
TTGAGATGGTTAATCCTTAAAAATATGAGATTTTTAAGTTTAATAAATATA
Found at i:54011537 original size:24 final size:23
Alignment explanation
Indices: 54011455--54011539 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 23
54011445 TGGTTAATCC
54011455 TTAAAAATATGAGATTTTTAAGT
1 TTAAAAATATGAGATTTTTAAGT
**
54011478 TTAATAAATATATTGAGATGGTTAA-T
1 TT-A-AAA-ATA-TGAGATTTTTAAGT
54011504 CCTTAAAAATATGAGATTTTTAAGT
1 --TTAAAAATATGAGATTTTTAAGT
54011529 TTAATAAATAT
1 TTAA-AAATAT
54011540 ATTATATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
23 6 0.12
24 17 0.34
25 7 0.14
26 7 0.14
27 11 0.22
28 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (23 bp):
TTAAAAATATGAGATTTTTAAGT
Found at i:54011572 original size:3 final size:3
Alignment explanation
Indices: 54011566--54011609 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
54011556 ATAAAGATAT
54011566 TTA TTA -TA TT- TTA TTA TTA TATA TTA -TA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
54011608 TT
1 TT
54011610 TATAAAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.22
3 25 0.69
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:54011590 original size:15 final size:16
Alignment explanation
Indices: 54011566--54011612 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 16
54011556 ATAAAGATAT
*
54011566 TTATTATATTTTATTA
1 TTATTATATTATATTA
54011582 TTA-TATATTATATTA
1 TTATTATATTATATTA
54011597 TTATTATATTAT-TTA
1 TTATTATATTATATTA
54011612 T
1 T
54011613 AAAGTAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTATATTATATTA
Found at i:54012487 original size:36 final size:37
Alignment explanation
Indices: 54012415--54012487 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
54012405 TAATATTGAC
* *
54012415 TTGAAAATGAAAAAGTGAATTTTGAATTGAATTGTGA
1 TTGAAAATGAAAAAGTGAATATTGAATTGAAATGTGA
*
54012452 TTGAAAGTGAAAAAGTGAA-ATTGAATTGAAATGTGA
1 TTGAAAATGAAAAAGTGAATATTGAATTGAAATGTGA
54012488 AATTGGAGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 15 0.45
37 18 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (37 bp):
TTGAAAATGAAAAAGTGAATATTGAATTGAAATGTGA
Found at i:54020854 original size:41 final size:41
Alignment explanation
Indices: 54020809--54020900 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
54020799 ACTGGCACTT
* * * *
54020809 AGCCTGCTAGACATATAGTTTGAAATGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAATCTGAAATGTTTCACCGGCAATA
* *
54020850 AGCCTGCTAGACATAAAATCTGAATTGTTTCACTGGCAATA
1 AGCCTGCTAGACATAAAATCTGAAATGTTTCACCGGCAATA
54020891 AGCCTGCTAG
1 AGCCTGCTAG
54020901 GTGCTAAGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAATCTGAAATGTTTCACCGGCAATA
Found at i:54024421 original size:13 final size:13
Alignment explanation
Indices: 54024386--54024429 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
54024376 AAATAGGACG
*
54024386 AATAAAATAATAA
1 AATAAAACAATAA
*
54024399 TAAT-AGACAATAA
1 -AATAAAACAATAA
54024412 AATAAAACAATAA
1 AATAAAACAATAA
54024425 AATAA
1 AATAA
54024430 TAAACTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 3 0.12
13 20 0.77
14 3 0.12
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (13 bp):
AATAAAACAATAA
Found at i:54024424 original size:23 final size:23
Alignment explanation
Indices: 54024372--54024416 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
54024362 AGAAGAAACG
*
54024372 ACAAAAATAGGACGAATAAAATA
1 ACAATAATAGGACGAATAAAATA
*
54024395 ATAATAATA-GAC-AATAAAATA
1 ACAATAATAGGACGAATAAAATA
54024416 A
1 A
54024417 AACAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 3 0.15
23 7 0.35
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.18
Consensus pattern (23 bp):
ACAATAATAGGACGAATAAAATA
Found at i:54024487 original size:13 final size:14
Alignment explanation
Indices: 54024458--54024489 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54024448 CAAACTAGGG
54024458 AATAA-GAATGAAT
1 AATAATGAATGAAT
54024471 AATAATGAATGAA-
1 AATAATGAATGAAT
54024484 AATAAT
1 AATAAT
54024490 AAAATACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (14 bp):
AATAATGAATGAAT
Found at i:54024887 original size:5 final size:5
Alignment explanation
Indices: 54024864--54024911 Score: 73
Period size: 5 Copynumber: 9.8 Consensus size: 5
54024854 AAAAATAAAT
54024864 AATA- AATA- AATATG AATAG AATAG AATAG AATAG AATAG AATAG AATA
1 AATAG AATAG AATA-G AATAG AATAG AATAG AATAG AATAG AATAG AATA
54024912 AAAATAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.19
5 30 0.71
6 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (5 bp):
AATAG
Found at i:54027408 original size:18 final size:18
Alignment explanation
Indices: 54027382--54027432 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
54027372 TAAAAGAAAG
54027382 AATATAAAATAAAAATTA-
1 AATA-AAAATAAAAATTAT
*
54027400 AACTAAAAACAAAAATTAT
1 AA-TAAAAATAAAAATTAT
*
54027419 AATAAAATTAAAAA
1 AATAAAAATAAAAA
54027433 AGGCAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAAAATAAAAATTAT
Found at i:54036848 original size:42 final size:44
Alignment explanation
Indices: 54036801--54036887 Score: 124
Period size: 42 Copynumber: 2.0 Consensus size: 44
54036791 AGGGTAAATC
* *
54036801 CAACAACCCATGTTTATCTTCTCCTCTTTTTAAA-T-TATTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTATTTTT
* *
54036843 CAACAACCTAAGATTATCTTCTCCTTTTTTTAAATTCTATTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTATTTTT
54036887 C
1 C
54036888 TAGGATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 30 0.77
43 1 0.03
44 8 0.21
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.49
Consensus pattern (44 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTATTTTT
Found at i:54049634 original size:20 final size:20
Alignment explanation
Indices: 54049609--54049646 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54049599 CTCAATCGAG
*
54049609 GATAATTAATTATTTAATTA
1 GATAATTAAGTATTTAATTA
*
54049629 GATAATTAGGTATTTAAT
1 GATAATTAAGTATTTAAT
54049647 CGATCATAGG
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:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (20 bp):
GATAATTAAGTATTTAATTA
Found at i:54050145 original size:33 final size:34
Alignment explanation
Indices: 54050096--54050160 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
54050086 TTTTTGTACA
*
54050096 TAATTAAAATATTTTTATTTTTGAAT-TTTTTAGT
1 TAATTAAAATAATTTTATTTTT-AATATTTTTAGT
54050130 TAATT-AAATAATTTTATTTTTAATATTTTTA
1 TAATTAAAATAATTTTATTTTTAATATTTTTA
54050161 CTTACATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 3 0.10
33 21 0.72
34 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (34 bp):
TAATTAAAATAATTTTATTTTTAATATTTTTAGT
Found at i:54056849 original size:26 final size:27
Alignment explanation
Indices: 54056820--54056877 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
54056810 TCGTGATATC
*
54056820 CAAGTCAAGTCACGCGATACCC-GATT
1 CAAGTCAAGTCACGCAATACCCGGATT
* *
54056846 CAAGTCATGTCACGCAATACCCGGTTT
1 CAAGTCAAGTCACGCAATACCCGGATT
54056873 CAAGT
1 CAAGT
54056878 ATCGCGACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (27 bp):
CAAGTCAAGTCACGCAATACCCGGATT
Found at i:54063406 original size:50 final size:50
Alignment explanation
Indices: 54063296--54063643 Score: 353
Period size: 50 Copynumber: 6.9 Consensus size: 50
54063286 ACATTAAGAG
*
54063296 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
*
54063347 GATTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * *
54063400 GATGAGA-GTCTCATGTAAGACCATGTCAGGGACATGGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * * *
54063449 GATGAGAGGTCTCATGTAAGACCATGTCAGGGACATTGCGTTGGCACCGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * **
54063499 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* *** * * *
54063549 TATGAGAACCCCCATGTAAGACCATATCTGGGATATGGCATTGGCAGC-A
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * * ** * * *
54063598 CAAGAAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
54063644 TGTTATATTC
Statistics
Matches: 255, Mismatches: 36, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
49 83 0.33
50 125 0.49
51 1 0.00
53 3 0.01
54 6 0.02
55 1 0.00
56 36 0.14
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:54063593 original size:100 final size:99
Alignment explanation
Indices: 54063296--54063643 Score: 360
Period size: 99 Copynumber: 3.5 Consensus size: 99
54063286 ACATTAAGAG
*
54063296 GATGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGT
1 GATGAGAGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-C-TT---A-TATGAGAGGT
54063360 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
60 CCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* * * * ** * *
54063400 GATGAGAGTCTCATGTAAGACCATGTCAGGGACATGGCGTTGGCACCGAGATGAGAGGTCTCATG
1 GATGAGAGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTTATATGAGAGGTCCCATG
* *
54063465 TAAGACCATGTCAGGGACATTGCGTTGGCACCGA
66 TAAGACCATGTCTGGGACATGGCGTTGGCACCGA
* * ***
54063499 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTTATATGAGAACCCCCAT
1 GATGAGA-GTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTTATATGAGAGGTCCCAT
* * * *
54063564 GTAAGACCATATCTGGGATATGGCATTGGCAGCACAA
65 GTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGA
* * * * * *
54063601 GA-AACA-TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 GATGAGAGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
54063644 TGTTATATTC
Statistics
Matches: 204, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
99 84 0.41
100 71 0.35
101 3 0.01
102 4 0.02
104 8 0.04
105 34 0.17
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (99 bp):
GATGAGAGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACTTATATGAGAGGTCCCATG
TAAGACCATGTCTGGGACATGGCGTTGGCACCGA
Found at i:54071038 original size:23 final size:24
Alignment explanation
Indices: 54071008--54071062 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
54070998 TAAATTATAA
54071008 AAACTAAAAATG-AAAGAAAAACT
1 AAACTAAAAATGCAAAGAAAAACT
* *
54071031 AAACTAAATATGCTAAAGAAAATCT
1 AAACTAAAAATGC-AAAGAAAAACT
*
54071056 AAGCTAA
1 AAACTAA
54071063 GTGAATCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 11 0.41
25 16 0.59
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.18
Consensus pattern (24 bp):
AAACTAAAAATGCAAAGAAAAACT
Found at i:54079683 original size:28 final size:28
Alignment explanation
Indices: 54079637--54079690 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
54079627 ACAAATTGAA
54079637 TCTTGGAAAGAAAAAATTCCTCAAGTAG
1 TCTTGGAAAGAAAAAATTCCTCAAGTAG
54079665 TCTTGGAAAGAAAAAATTCCTCAAGT
1 TCTTGGAAAGAAAAAATTCCTCAAGT
54079691 CGTCGAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (28 bp):
TCTTGGAAAGAAAAAATTCCTCAAGTAG
Found at i:54088357 original size:28 final size:27
Alignment explanation
Indices: 54088326--54088386 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
54088316 AAACAACATG
54088326 AATT-ACAAATTGAATCTTGGAAAGAAAA
1 AATTCACAAATTG--TCTTGGAAAGAAAA
* *
54088354 AATTCCTCAAGTTGTCTTGGAAAGAAAA
1 AATT-CACAAATTGTCTTGGAAAGAAAA
54088382 AATTC
1 AATTC
54088387 CTCAAGTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 1 0.03
28 22 0.76
30 6 0.21
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (27 bp):
AATTCACAAATTGTCTTGGAAAGAAAA
Found at i:54088387 original size:28 final size:28
Alignment explanation
Indices: 54088340--54088393 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
54088330 ACAAATTGAA
54088340 TCTTGGAAAGAAAAAATTCCTCAAGTTG
1 TCTTGGAAAGAAAAAATTCCTCAAGTTG
54088368 TCTTGGAAAGAAAAAATTCCTCAAGT
1 TCTTGGAAAGAAAAAATTCCTCAAGT
54088394 CGTCGAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (28 bp):
TCTTGGAAAGAAAAAATTCCTCAAGTTG
Found at i:54106051 original size:50 final size:50
Alignment explanation
Indices: 54105991--54106086 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
54105981 TTTGTTCCTC
* * *
54105991 TGCTGCTTCTTTGATCCTCTACTGGTGTTGGTTCTTTGTTCTTCTGGTTG
1 TGCTGCTTCTTTGATCCTCTACTGATGCTGGTTCTTTGTTCCTCTGGTTG
* * *
54106041 TGCTGGTTCTTTGTTCCTCTGCTGATGCTGGTTCTTTGTTCCTCTG
1 TGCTGCTTCTTTGATCCTCTACTGATGCTGGTTCTTTGTTCCTCTG
54106087 CTGGTGTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.03, C:0.22, G:0.24, T:0.51
Consensus pattern (50 bp):
TGCTGCTTCTTTGATCCTCTACTGATGCTGGTTCTTTGTTCCTCTGGTTG
Found at i:54106087 original size:25 final size:24
Alignment explanation
Indices: 54105973--54106089 Score: 118
Period size: 25 Copynumber: 5.0 Consensus size: 24
54105963 TTCTCTCATC
*
54105973 GCTGGTTATTTGTTCCTCTGC--T
1 GCTGGTTCTTTGTTCCTCTGCTGT
* *
54105995 GC---TTCTTTGATCCTCTACTGGT
1 GCTGGTTCTTTGTTCCTCTGCT-GT
* * *
54106017 GTTGGTTCTTTGTTCTTCTGGTTGT
1 GCTGGTTCTTTGTTCCTCT-GCTGT
54106042 GCTGGTTCTTTGTTCCTCTGCTGAT
1 GCTGGTTCTTTGTTCCTCTGCTG-T
54106067 GCTGGTTCTTTGTTCCTCTGCTG
1 GCTGGTTCTTTGTTCCTCTGCTG
54106090 GTGTTTTGTT
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
19 13 0.17
22 4 0.05
24 3 0.04
25 55 0.72
26 1 0.01
ACGTcount: A:0.03, C:0.22, G:0.24, T:0.50
Consensus pattern (24 bp):
GCTGGTTCTTTGTTCCTCTGCTGT
Found at i:54106090 original size:19 final size:19
Alignment explanation
Indices: 54106066--54106104 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
54106056 CCTCTGCTGA
54106066 TGCTGGT-TCTTTGTTCCTC
1 TGCTGGTGT-TTTGTTCCTC
54106085 TGCTGGTGTTTTGTTCCTC
1 TGCTGGTGTTTTGTTCCTC
54106104 T
1 T
54106105 TCTCCACCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.54
Consensus pattern (19 bp):
TGCTGGTGTTTTGTTCCTC
Found at i:54106962 original size:24 final size:24
Alignment explanation
Indices: 54106935--54107006 Score: 144
Period size: 24 Copynumber: 3.0 Consensus size: 24
54106925 TATTTCTTTT
54106935 AATGCTTGCATGCTCTTGATTACC
1 AATGCTTGCATGCTCTTGATTACC
54106959 AATGCTTGCATGCTCTTGATTACC
1 AATGCTTGCATGCTCTTGATTACC
54106983 AATGCTTGCATGCTCTTGATTACC
1 AATGCTTGCATGCTCTTGATTACC
54107007 GTATTCTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (24 bp):
AATGCTTGCATGCTCTTGATTACC
Found at i:54107526 original size:28 final size:28
Alignment explanation
Indices: 54107461--54107548 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
54107451 TCAGAGTTAG
* **
54107461 GTTTATGTTAAATAAATGTGTATCTAATAT
1 GTTTATGTTAAACAAATG-GTAAATAA-AT
* *
54107491 GTGTATGTTAAACAAGTGGTAAATAAAT
1 GTTTATGTTAAACAAATGGTAAATAAAT
*
54107519 GTTTATGTTAAACAAATTGTAAATAAAT
1 GTTTATGTTAAACAAATGGTAAATAAAT
54107547 GT
1 GT
54107549 GTATAAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
28 29 0.58
29 6 0.12
30 15 0.30
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (28 bp):
GTTTATGTTAAACAAATGGTAAATAAAT
Done.