Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009352.1 Hibiscus syriacus cultivar Beakdansim tig00113156_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: 624088
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:466106 original size:17 final size:17
Alignment explanation
Indices: 466076--466109 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
466066 ATCGAAACTT
*
466076 TAACTGATTAATTAAAA
1 TAACTAATTAATTAAAA
*
466093 TAACTAATTTATTAAAA
1 TAACTAATTAATTAAAA
466110 ACTTGACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TAACTAATTAATTAAAA
Found at i:466677 original size:3 final size:3
Alignment explanation
Indices: 466671--466759 Score: 169
Period size: 3 Copynumber: 29.7 Consensus size: 3
466661 GCAGCTTTTC
466671 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
466719 CTT CTT CTT CTT CTT CTT ATT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
466760 CCTCCTCCTC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:468546 original size:15 final size:15
Alignment explanation
Indices: 468526--468558 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
468516 ACCGTCACCC
468526 AAAAT-CCATAAATCT
1 AAAATCCCA-AAATCT
468541 AAAATCCCAAAATCT
1 AAAATCCCAAAATCT
468556 AAA
1 AAA
468559 TTTTTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATCCCAAAATCT
Found at i:473585 original size:2 final size:2
Alignment explanation
Indices: 473578--473602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
473568 TTTGCTTCAC
473578 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
473603 TCATTGTTTA
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:491055 original size:3 final size:3
Alignment explanation
Indices: 491049--491078 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
491039 ATGAGAGTCT
491049 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
491079 TAGAGAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:491769 original size:260 final size:258
Alignment explanation
Indices: 491313--491828 Score: 932
Period size: 260 Copynumber: 2.0 Consensus size: 258
491303 GTCAGAAGAG
491313 ACAAAGAATTCGCACGTGAATTATATGTCAATATATGATTGGTAGATATGATAGTAATATTTAGG
1 ACAAAGAATTCGCACGTGAATTATATGTCAATATATGATTGGTAGATATGATAGTAATATTTAGG
491378 GTAACTATAAAAATGGTCAATTTTTTCACAAGTTTTTTTATTCATTAAATGTTTAAAAATAATAT
66 GTAACTATAAAAATGGTCAATTTTTTCACAAGTTTTTTTATTCATTAAATGTTTAAAAATAATAT
491443 TTGGTGAACTATATTATGATTTATAATGTTTTGGTCATTGATATATAAGTTTTATTTTTATAATG
131 TTGGTGAACTATATTATGATTTATAATGTTTTGGTCATTGATATATAAGTTTTATTTTTATAATG
491508 TTATGATTGATATACAAGGTTATTG-ATAT-A-ACTTAAATGATGTTAGTTTGTTGAAGTATA
196 TTATGATTGATATACAAGGTTATTGAATATAAGACTTAAATGATGTTAGTTTGTTGAAGTATA
491568 ACAAAGAATTCGCACGTGAATTATATGTC-ATATATGATTGGTAGATATGATAGTAATATTTAGG
1 ACAAAGAATTCGCACGTGAATTATATGTCAATATATGATTGGTAGATATGATAGTAATATTTAGG
*
491632 GTAAACTATAAAAATGGTCAATTTTTTTCACAAGTTTTATTTTTATCATTAAATGTTTAAAAAAT
66 GT-AACTATAAAAATGGTCAA-TTTTTTCACAAGTTTT-TTTAT-TCATTAAATGTTT-AAAAAT
491697 AATATTTTGGTGAACTATATTATGATTTATAATGTTTTGGTCATTGATATATAAGTTTTATTTTT
126 AATA-TTTGGTGAACTATATTATGATTTATAATGTTTTGGTCATTGATATATAAGTTTTATTTTT
491762 ATAATGTTATGATTGATATACAAGGTTATTGATATATAAGACTTAAATGATGTTAGTTTGTTGAA
190 ATAATGTTATGATTGATATACAAGGTTATTGA-ATATAAGACTTAAATGATGTTAGTTTGTTGAA
491827 GT
254 GT
491829 TATATGTTAG
Statistics
Matches: 250, Mismatches: 1, Indels: 11
0.95 0.00 0.04
Matches are distributed among these distances:
254 37 0.15
255 47 0.19
256 16 0.06
257 4 0.02
258 13 0.05
259 10 0.04
260 91 0.36
262 4 0.02
263 1 0.00
264 27 0.11
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (258 bp):
ACAAAGAATTCGCACGTGAATTATATGTCAATATATGATTGGTAGATATGATAGTAATATTTAGG
GTAACTATAAAAATGGTCAATTTTTTCACAAGTTTTTTTATTCATTAAATGTTTAAAAATAATAT
TTGGTGAACTATATTATGATTTATAATGTTTTGGTCATTGATATATAAGTTTTATTTTTATAATG
TTATGATTGATATACAAGGTTATTGAATATAAGACTTAAATGATGTTAGTTTGTTGAAGTATA
Found at i:497302 original size:17 final size:17
Alignment explanation
Indices: 497280--497312 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
497270 TGAGATCACA
497280 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
497297 ATATTATATTTTATAT
1 ATATTATATTTTATAT
497313 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:498296 original size:37 final size:37
Alignment explanation
Indices: 498223--498296 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
498213 ACCAAAAACC
* *
498223 CAACCCAAAAATCTACATCCTCCACCTGAACTTGACT
1 CAACCCAAAAATCTACATCCTCCACCTCAACCTGACT
* * *
498260 CAACCCAAAAATTTTATATCTTCCACC-CAACCTGACT
1 CAACCCAAAAA-TCTACATCCTCCACCTCAACCTGACT
498297 TGAAAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 19 0.61
38 12 0.39
ACGTcount: A:0.35, C:0.36, G:0.04, T:0.24
Consensus pattern (37 bp):
CAACCCAAAAATCTACATCCTCCACCTCAACCTGACT
Found at i:499140 original size:31 final size:31
Alignment explanation
Indices: 499082--499142 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
499072 AAGGGAACGG
* *
499082 TCCCTAACATTATTGACCGATTTGATTTTAA
1 TCCCTAACATTATCGACCGATTCGATTTTAA
*
499113 TCCCTAACATTATCGATGCG-TTCGATTTTA
1 TCCCTAACATTATCGA-CCGATTCGATTTTA
499143 GTTTCTCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (31 bp):
TCCCTAACATTATCGACCGATTCGATTTTAA
Found at i:503434 original size:24 final size:24
Alignment explanation
Indices: 503407--503454 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
503397 TAGACATGAT
503407 TTTATGTCTTTAAAGGTCTTCAAA
1 TTTATGTCTTTAAAGGTCTTCAAA
503431 TTTATGTCTTTAAAGGTCTTCAAA
1 TTTATGTCTTTAAAGGTCTTCAAA
503455 CCTCTTCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (24 bp):
TTTATGTCTTTAAAGGTCTTCAAA
Found at i:503545 original size:15 final size:15
Alignment explanation
Indices: 503522--503645 Score: 89
Period size: 14 Copynumber: 8.2 Consensus size: 15
503512 ATAAGGTTAA
*
503522 TATTTTAAAATAATT
1 TATTATAAAATAATT
503537 TATTATAAAATAATTT
1 TATTATAAAATAA-TT
*
503553 TATTTTAAAA-AATT
1 TATTATAAAATAATT
*
503567 TATTATAAAA-ATTT
1 TATTATAAAATAATT
*
503581 TATT-TAAAATAAAT
1 TATTATAAAATAATT
503595 TA-TA-AAATATGGATTGATT
1 TATTATAAA-AT--A---ATT
*
503614 TATTTTAAAATAATT
1 TATTATAAAATAATT
*
503629 TATT-TTAAATAATT
1 TATTATAAAATAATT
503643 TAT
1 TAT
503646 AGTATGAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
13 9 0.10
14 36 0.40
15 21 0.24
16 12 0.13
18 1 0.01
19 4 0.04
20 3 0.03
21 3 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TATTATAAAATAATT
Found at i:503569 original size:30 final size:28
Alignment explanation
Indices: 503522--503595 Score: 103
Period size: 28 Copynumber: 2.5 Consensus size: 28
503512 ATAAGGTTAA
503522 TATTTTAAAATAATTTATTATAAAATAATTT
1 TATTTTAAAA-AATTTATTAT-AAA-AATTT
503553 TATTTTAAAAAATTTATTATAAAAATTT
1 TATTTTAAAAAATTTATTATAAAAATTT
*
503581 TATTTAAAATAAATT
1 TATTTTAAA-AAATT
503596 ATAAAATATG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 13 0.32
29 8 0.20
30 10 0.24
31 10 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTTAAAAAATTTATTATAAAAATTT
Found at i:503664 original size:21 final size:21
Alignment explanation
Indices: 503648--503686 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
503638 TAATTTATAG
503648 TATGAATTGATTTATTTAAAA
1 TATGAATTGATTTATTTAAAA
503669 TATGAATTGATTT-TTTAA
1 TATGAATTGATTTATTTAA
503687 TAATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (21 bp):
TATGAATTGATTTATTTAAAA
Found at i:503710 original size:51 final size:49
Alignment explanation
Indices: 503602--503732 Score: 162
Period size: 51 Copynumber: 2.7 Consensus size: 49
503592 AATTATAAAA
* * *
503602 TATGGATTGATTTATTTTAAA-AT-AATTTA-TTTTAAATAATTTATAG
1 TATGGAATGATTTATTTAAAATATGAATTGATTTTTAAATAATTTATAG
*
503648 TAT-GAATTGATTTATTTAAAATATGAATTGATTTTTTAATAATTTATTTAG
1 TATGGAA-TGATTTATTTAAAATATGAATTGATTTTTAAATAATTTA--TAG
*
503699 TATGGAATGATTTATTTAAAATATGGATTGATTT
1 TATGGAATGATTTATTTAAAATATGAATTGATTT
503733 ATTATTGTGT
Statistics
Matches: 73, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
45 2 0.03
46 16 0.22
47 2 0.03
48 5 0.07
49 13 0.18
51 32 0.44
52 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (49 bp):
TATGGAATGATTTATTTAAAATATGAATTGATTTTTAAATAATTTATAG
Found at i:503713 original size:19 final size:20
Alignment explanation
Indices: 503689--503735 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
503679 TTTTTTAATA
*
503689 ATTTATTT-AGTATGGAATG
1 ATTTATTTAAATATGGAATG
*
503708 ATTTATTTAAAATATGGATTG
1 ATTTATTT-AAATATGGAATG
503729 ATTTATT
1 ATTTATT
503736 ATTGTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
21 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (20 bp):
ATTTATTTAAATATGGAATG
Found at i:503804 original size:38 final size:39
Alignment explanation
Indices: 503757--503830 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
503747 TGAATTGATA
*
503757 TATTTTAAATAATTT-TAGTATGGATTGATTTATTTATT
1 TATTTTAAATAATTTATAGTATGAATTGATTTATTTATT
503795 TATTTTAAATAATTTATAGTATGAATTGATTTATTT
1 TATTTTAAATAATTTATAGTATGAATTGATTTATTT
503831 TAAAATATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 15 0.44
39 19 0.56
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (39 bp):
TATTTTAAATAATTTATAGTATGAATTGATTTATTTATT
Found at i:503832 original size:22 final size:22
Alignment explanation
Indices: 503814--503856 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
503804 TAATTTATAG
503814 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
503836 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
503857 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:503940 original size:78 final size:79
Alignment explanation
Indices: 503836--503982 Score: 253
Period size: 78 Copynumber: 1.9 Consensus size: 79
503826 TATTTTAAAA
*
503836 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGAATGATTTA-TTTAAAATATGGATTGAT
1 TATGAATTGATATATTTTAAATAATTTA-TAGTATGGAATGATTTATTTTAAAATATGGATTGAT
503900 TTATTATTGCAGTTG
65 TTATTATTGCAGTTG
*
503915 TATGAATTGATATA-TTTAAATAATTTATAGTATGGATTGATTTATTTTAAAATATGGATTGATT
1 TATGAATTGATATATTTTAAATAATTTATAGTATGGAATGATTTATTTTAAAATATGGATTGATT
503979 TATT
66 TATT
503983 TTAAATAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
77 16 0.25
78 36 0.55
79 13 0.20
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.50
Consensus pattern (79 bp):
TATGAATTGATATATTTTAAATAATTTATAGTATGGAATGATTTATTTTAAAATATGGATTGATT
TATTATTGCAGTTG
Found at i:503970 original size:22 final size:22
Alignment explanation
Indices: 503945--503987 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
503935 TAATTTATAG
503945 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
503967 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
503988 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:504005 original size:32 final size:32
Alignment explanation
Indices: 503967--504159 Score: 221
Period size: 32 Copynumber: 6.7 Consensus size: 32
503957 TATTTTAAAA
503967 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
503999 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
504021 TATGGATTGATTTATTTTAAAT-ATTTGATTAG
1 TATGGATTGATTTATTTTAAATAATTT-ATTAG
504053 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
504075 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
504107 TATGGATTTATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
504139 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
504160 ATATTGATTT
Statistics
Matches: 137, Mismatches: 2, Indels: 44
0.75 0.01 0.24
Matches are distributed among these distances:
22 28 0.20
23 8 0.06
25 3 0.02
26 4 0.03
28 4 0.03
29 3 0.02
31 8 0.06
32 79 0.58
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:504013 original size:54 final size:54
Alignment explanation
Indices: 503915--504257 Score: 407
Period size: 54 Copynumber: 6.3 Consensus size: 54
503905 ATTGCAGTTG
* *
503915 TATGAATTGATATA-TTTAAATAATTTA-TAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
503967 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
504021 TATGGATTGATTTATTTTAAAT-ATTTGATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTT-ATTAGTATGGATTGATTTATTTTAAAA
*
504075 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT---TAA---A--A
* * ** * **
504138 GTATGGATTGATTTATTTTAAA-ATATTGATT--TAT---TTTAAATAATTTATTA
1 -TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATTTATTTTAAAA
* *
504188 TATGAATTGATTTATTTTAAATACTTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
504242 TATGGATTGATTTATT
1 TATGGATTGATTTATT
504258 ATTGTTGTAT
Statistics
Matches: 251, Mismatches: 19, Indels: 40
0.81 0.06 0.13
Matches are distributed among these distances:
49 25 0.10
50 2 0.01
51 3 0.01
52 12 0.05
53 17 0.07
54 139 0.55
55 9 0.04
58 5 0.02
59 6 0.02
61 1 0.00
62 3 0.01
63 2 0.01
64 27 0.11
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:504050 original size:22 final size:22
Alignment explanation
Indices: 503999--504041 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
503989 AATTTATTAG
503999 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
504021 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
504042 TATTTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:504063 original size:86 final size:82
Alignment explanation
Indices: 503967--504365 Score: 387
Period size: 86 Copynumber: 4.9 Consensus size: 82
503957 TATTTTAAAA
* * ** * *
503967 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAAAT-ATTGATT-GTAT--ATTTAAATAATTTATAATATGGATTGA
504031 TTTATTTTAAATATTTGATTAG
62 TTTATTTTAAATATTT-ATTAG
* * * *
504053 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTAT
1 TATGGATTGATTTATTTTAAAATATTGATTG-TATA-TTTAAATAATTTA-TAATATGGATTGAT
504118 TTATTTTAAATAATTTATTAG
63 TTATTTTAAAT-ATTTATTAG
* *
504139 TATGGATTGATTTATTTTAAAATATTGATT-TAT-TTTAAATAATTTATTATATGAATTGATTTA
1 TATGGATTGATTTATTTTAAAATATTGATTGTATATTTAAATAATTTATAATATGGATTGATTTA
504202 TTTTAAATACTTTATTAG
66 TTTTAAATA-TTTATTAG
* * * *
504220 TATGGATTGATTTATTTTAAAATATGGATTG---ATTT--ATTATTGT-T-GTAT-AATTGA-TT
1 TATGGATTGATTTATTTTAAAATATTGATTGTATATTTAAATAATT-TATAATATGGATTGATTT
504276 -TTTTAAATAATTTATTAG
65 ATTTTAAAT-ATTTATTAG
* * * *
504294 TATGTATTGATTTATTTTAAAATATATAATT-TAT-TTTTAATAATTTATTAGTATGGATTGATT
1 TATGGATTGATTTATTTTAAAATAT-TGATTGTATATTTAAATAATTTA-TAATATGGATTGATT
504357 TATTTTAAA
64 TATTTTAAA
504366 ATATGGATTG
Statistics
Matches: 267, Mismatches: 24, Indels: 47
0.79 0.07 0.14
Matches are distributed among these distances:
74 40 0.15
75 6 0.02
76 9 0.03
77 4 0.01
78 11 0.04
79 2 0.01
80 8 0.03
81 63 0.24
82 15 0.06
83 7 0.03
84 3 0.01
85 10 0.04
86 81 0.30
87 8 0.03
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (82 bp):
TATGGATTGATTTATTTTAAAATATTGATTGTATATTTAAATAATTTATAATATGGATTGATTTA
TTTTAAATATTTATTAG
Found at i:504079 original size:22 final size:22
Alignment explanation
Indices: 504053--504095 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
504043 ATTTGATTAG
504053 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
504075 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
504096 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:504103 original size:14 final size:15
Alignment explanation
Indices: 504084--504217 Score: 51
Period size: 14 Copynumber: 8.5 Consensus size: 15
504074 ATATGGATTG
504084 ATTTATTTT-AAATA
1 ATTTATTTTGAAATA
* * *
504098 ATTTATTAGTATGGATTT
1 ATTTATT--T-TGAAATA
504116 ATTTATTTT-AAATA
1 ATTTATTTTGAAATA
* * *
504130 ATTTATTAGTATGGATTG
1 ATTTATT--T-TGAAATA
*
504148 ATTTATTTTAAAATA
1 ATTTATTTTGAAATA
504163 TTGATTTATTTT-AAATA
1 ---ATTTATTTTGAAATA
* *
504180 ATTTATTATATGAATTG
1 ATTTATT-T-TGAAATA
504197 ATTTATTTT-AAATA
1 ATTTATTTTGAAATA
*
504211 CTTTATT
1 ATTTATT
504218 AGTATGGATT
Statistics
Matches: 88, Mismatches: 18, Indels: 28
0.66 0.13 0.21
Matches are distributed among these distances:
14 32 0.36
15 6 0.07
16 6 0.07
17 17 0.19
18 27 0.31
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (15 bp):
ATTTATTTTGAAATA
Found at i:504200 original size:31 final size:32
Alignment explanation
Indices: 504162--504240 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
504152 ATTTTAAAAT
504162 ATTGATTTATTTTAAATAATTTATTA-TATGA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
* *
504193 ATTGATTTATTTTAAATACTTTATTAGTATGG
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
504225 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
504241 ATATGGATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 25 0.56
32 20 0.44
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:504227 original size:81 final size:81
Alignment explanation
Indices: 504020--504365 Score: 456
Period size: 81 Copynumber: 4.3 Consensus size: 81
504010 TTATTTTAAA
504020 ATATGGATTGATTTATTTTAAAT-ATTTGATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATATGGATTGATTTATTTTAAATAATTT-ATTAGTATGGATTGATTTATTTT-AAA-AT--ATTG
504084 ATTTATTTTAAATAATTTATT
61 ATTTATTTTAAATAATTTATT
*
504105 AGTATGGATTTATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTT
1 A-TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTT
504170 ATTTTAAATAATTTATT
65 ATTTTAAATAATTTATT
* * * *
504187 ATATGAATTGATTTATTTTAAATACTTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 ATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTTA
* *
504252 -TTT--ATTA-TTGTT
66 TTTTAAATAATTTATT
* * * *
504264 GTAT-AATTGA-TT-TTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATATAATTT
1 ATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-TGATTT
*
504326 ATTTTTAATAATTTATT
65 ATTTTAAATAATTTATT
504343 AGTATGGATTGATTTATTTTAAA
1 A-TATGGATTGATTTATTTTAAA
504366 ATATGGATTG
Statistics
Matches: 232, Mismatches: 18, Indels: 24
0.85 0.07 0.09
Matches are distributed among these distances:
74 41 0.18
75 6 0.03
76 9 0.04
77 7 0.03
78 6 0.03
79 4 0.02
80 6 0.03
81 64 0.28
82 28 0.12
83 7 0.03
84 2 0.01
85 4 0.02
86 44 0.19
87 4 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (81 bp):
ATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATTGATTTA
TTTTAAATAATTTATT
Found at i:504361 original size:32 final size:32
Alignment explanation
Indices: 504322--504416 Score: 102
Period size: 32 Copynumber: 3.3 Consensus size: 32
504312 AAAATATATA
504322 ATTTATTTTTAATAATTTATTAGTATGGATTG
1 ATTTATTTTTAATAATTTATTAGTATGGATTG
504354 ATTTA--TTT--TAA---A--A-TATGGATTG
1 ATTTATTTTTAATAATTTATTAGTATGGATTG
* *
504376 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTTAATAATTTATTAGTATGGATTG
504408 ATTTATTTT
1 ATTTATTTT
504417 AAAATATGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
22 14 0.27
23 1 0.02
24 2 0.04
25 1 0.02
26 3 0.06
28 3 0.06
29 1 0.02
30 3 0.06
31 1 0.02
32 22 0.43
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.56
Consensus pattern (32 bp):
ATTTATTTTTAATAATTTATTAGTATGGATTG
Found at i:504370 original size:22 final size:22
Alignment explanation
Indices: 504345--504387 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
504335 AATTTATTAG
504345 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
504367 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
504388 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:504399 original size:54 final size:54
Alignment explanation
Indices: 503792--504451 Score: 372
Period size: 54 Copynumber: 12.4 Consensus size: 54
503782 TGATTTATTT
* *
503792 ATTTATTTTAAATAATTTA-TAGTATGAATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
503845 ATTTATTTTAAATAATTTATTAGTATGGAATGATTTA-TTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * *
503898 ATTTATTATTGCAGT--TGTA-T-GAATTGATAT-ATTTAAATAATTTATAGTATGGATTG
1 ATTTATT-TT-AAATAATTTATTAGTATGGAT-TGATTT--AT--TTTAAAATATGGATTG
** ** * ** * * *
503954 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
** ** * ** * * *
504008 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATATTTGATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
** ** * ** * * * *
504062 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTT
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
504116 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA-AT--ATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* **
504166 ATTTATTTTAAATAATTTATTA-TATGAATTGATTTATTTT-AAATACTTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA-TGGATT-G
** * ** * * * **** *
504220 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTTGTAT-AATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTAAAATATGGATTG
* *
504273 A-TT-TTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATAT--A-TA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
504322 ATTTATTTTTAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
504376 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
504430 ATCTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
504452 TTGTAGTTGT
Statistics
Matches: 505, Mismatches: 67, Indels: 69
0.79 0.10 0.11
Matches are distributed among these distances:
49 22 0.04
50 29 0.06
51 65 0.13
52 21 0.04
53 56 0.11
54 252 0.50
55 21 0.04
56 34 0.07
57 5 0.01
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:504453 original size:125 final size:124
Alignment explanation
Indices: 504197--504441 Score: 298
Period size: 125 Copynumber: 1.9 Consensus size: 124
504187 ATATGAATTG
*
504197 ATTTATTTTAAATACTTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA-TTATTATTG
** * * * * *
504262 TTGTATAATTGATTTTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATATA
65 TTAAATAATTGATTGTATAAATAATTTATTAATATGGATTGATCTATTTTAAAATATATA
*
504322 ATTTATTTTTAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA-T-TTATT-T
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTATTATTGT
* * *
504384 TAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATCTATTTTAAA
66 TAAATAATTGATT-GTATA-AATAATTTA--TT--AATATGGATTGATCTATTTTAAA
504442 TAATTTATTA
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
121 11 0.11
122 8 0.08
123 8 0.08
125 55 0.54
127 20 0.20
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (124 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTATTATTGT
TAAATAATTGATTGTATAAATAATTTATTAATATGGATTGATCTATTTTAAAATATATA
Found at i:504500 original size:31 final size:31
Alignment explanation
Indices: 504465--504524 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
504455 TAGTTGTATG
* * *
504465 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
504496 AATTATTTAAATCTCAATATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
504525 CTTTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:506904 original size:118 final size:118
Alignment explanation
Indices: 506702--506995 Score: 333
Period size: 119 Copynumber: 2.5 Consensus size: 118
506692 AAACTATGCA
* * * **
506702 TTTAGTACCTAAACTATCAGTTTTCATCCGTTTA-TACCTAAACTTTCAAAATTTTCAAAATCAT
1 TTTAGTACCTAAACTATCAGTTTTAATCCTTTTAGTATCTAAACTTTC---ATTTTTTAAATCAT
* *
506766 AACTAATTTTTAGTTATTGTTTCATTTTAGTATAATGCCGTT-AAAACTTAACATG
63 AACTAATGTTTAGTTATTGTTTCATTTTAGTACAATGCCGTTAAAAACTTAACATG
* * * *
506821 TTTAGTACCTGAACTATCAGTTTTAATCCATTTTAGTATCTAAATTTTCATTTTTTAAATTATAC
1 TTTAGTACCTAAACTATCAGTTTTAATCC-TTTTAGTATCTAAACTTTCATTTTTTAAATCATAA
* *** **
506886 CTAATGTTTAGTTATTGTTTCATTTTAGTACCATTTTGTTAAAAACTTAATGTG
65 CTAATGTTTAGTTATTGTTTCATTTTAGTACAATGCCGTTAAAAACTTAACATG
* * *
506940 CTTAGTACCTAAACTATCAATTTTAGTCCGTTTTAGTAAT-TAAACTTTCATTTTTT
1 TTTAGTACCTAAACTATCAGTTTTAATCC-TTTTAGT-ATCTAAACTTTCATTTTTT
506996 TTCAAAACTT
Statistics
Matches: 148, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
118 46 0.31
119 85 0.57
120 6 0.04
121 11 0.07
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (118 bp):
TTTAGTACCTAAACTATCAGTTTTAATCCTTTTAGTATCTAAACTTTCATTTTTTAAATCATAAC
TAATGTTTAGTTATTGTTTCATTTTAGTACAATGCCGTTAAAAACTTAACATG
Found at i:512752 original size:29 final size:29
Alignment explanation
Indices: 512650--512752 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 29
512640 GAACATAATG
* *
512650 AATAGTTAAGTGATCATTTTGTAACTTTT
1 AATAGTTAAGGGACCATTTTGTAACTTTT
** ****
512679 AATAGTCGAGGGACTCAACAAAGTAACATTTT
1 AATAGTTAAGGGAC-C-ATTTTGTAAC-TTTT
512711 -ATAGTTGAA-GGACCATTTTGTAACTTTT
1 AATAGTT-AAGGGACCATTTTGTAACTTTT
512739 AATAGTTAAGGGAC
1 AATAGTTAAGGGAC
512753 TTAATAAAGC
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 6 0.11
29 26 0.48
30 2 0.04
31 15 0.28
32 5 0.09
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (29 bp):
AATAGTTAAGGGACCATTTTGTAACTTTT
Found at i:515163 original size:9 final size:9
Alignment explanation
Indices: 515151--515183 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
515141 AATTATTCTT
515151 ATTAAAAAA
1 ATTAAAAAA
515160 ATTAAAAAA
1 ATTAAAAAA
*
515169 AATAAAAAA
1 ATTAAAAAA
515178 A-TAAAA
1 ATTAAAA
515184 TTGACGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:515340 original size:2 final size:2
Alignment explanation
Indices: 515333--515362 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
515323 CTCAACTTTC
515333 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
515363 TATTTTTACT
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:520908 original size:21 final size:21
Alignment explanation
Indices: 520884--520927 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
520874 GTTTCAACTA
*
520884 AGTTGTTAAAAGTTGGTTAAG
1 AGTTGTTAAAAGTTAGTTAAG
**
520905 AGTTGTTACTAGTTAGTTAAG
1 AGTTGTTAAAAGTTAGTTAAG
520926 AG
1 AG
520928 AAGTTTGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (21 bp):
AGTTGTTAAAAGTTAGTTAAG
Found at i:524205 original size:33 final size:33
Alignment explanation
Indices: 524068--524207 Score: 253
Period size: 33 Copynumber: 4.2 Consensus size: 33
524058 CCTGTTCGTC
*
524068 CCCGTGCTCCTCGCCTTGCAATGCACTAAATCA
1 CCCGTTCTCCTCGCCTTGCAATGCACTAAATCA
*
524101 CCCGTGCTCCTCGCCTTGCAATGCACTAAATCA
1 CCCGTTCTCCTCGCCTTGCAATGCACTAAATCA
524134 CCCGTTCTCCTCGCCTTGCAATGCACTAAATCA
1 CCCGTTCTCCTCGCCTTGCAATGCACTAAATCA
*
524167 CCCGTTCTCCTCGCCTTGCAATGCACTAGATCA
1 CCCGTTCTCCTCGCCTTGCAATGCACTAAATCA
524200 CCCGTTCT
1 CCCGTTCT
524208 TTCTTTCTTC
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 105 1.00
ACGTcount: A:0.19, C:0.40, G:0.14, T:0.26
Consensus pattern (33 bp):
CCCGTTCTCCTCGCCTTGCAATGCACTAAATCA
Found at i:536048 original size:12 final size:13
Alignment explanation
Indices: 536020--536045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536010 AAATTCCTAA
536020 TAAATAACGATTT
1 TAAATAACGATTT
536033 TAAATAACGATTT
1 TAAATAACGATTT
536046 AAAAAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAAATAACGATTT
Found at i:536523 original size:2 final size:2
Alignment explanation
Indices: 536516--536541 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
536506 TTTTACTTCC
536516 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
536542 GATGCTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:541836 original size:19 final size:19
Alignment explanation
Indices: 541809--541890 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
541799 ATAGTACCTA
*
541809 TATAGTATATACTTATAAG
1 TATAATATATACTTATAAG
541828 TATAATATATACTTAT-A-
1 TATAATATATACTTATAAG
541845 T-T-ATA-A-ACTTATAAG
1 TATAATATATACTTATAAG
*
541860 TATAATATATACTTATAAT
1 TATAATATATACTTATAAG
541879 TATATATATATA
1 TATA-ATATATA
541891 TATATATATA
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
13 6 0.11
14 2 0.04
15 4 0.07
16 2 0.04
17 4 0.07
18 2 0.04
19 27 0.50
20 7 0.13
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (19 bp):
TATAATATATACTTATAAG
Found at i:541855 original size:32 final size:32
Alignment explanation
Indices: 541809--541882 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
541799 ATAGTACCTA
* *
541809 TATAGTATATACTTATAAGTATAATATATACT
1 TATATTATAAACTTATAAGTATAATATATACT
541841 TATATTATAAACTTATAAGTATAATATATACT
1 TATATTATAAACTTATAAGTATAATATATACT
541873 TATAATTATA
1 TAT-ATTATA
541883 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 33 0.85
33 6 0.15
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATTATAAACTTATAAGTATAATATATACT
Found at i:541884 original size:2 final size:2
Alignment explanation
Indices: 541860--541905 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
541850 AACTTATAAG
541860 TA TA -A TA TA TA CT- TA TA -A T- 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
541899 TA TA TA T
1 TA TA TA T
541906 TAAAATTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 34 0.87
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:546735 original size:33 final size:33
Alignment explanation
Indices: 546688--546756 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
546678 CAGTAGTTGC
*
546688 ATATTAACTGAGATATAGTATTTATTTGTAATT
1 ATATTAACTAAGATATAGTATTTATTTGTAATT
546721 ATATTAACTAAGATATAGTATTTATTTGTAATT
1 ATATTAACTAAGATATAGTATTTATTTGTAATT
546754 ATA
1 ATA
546757 GATCAGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (33 bp):
ATATTAACTAAGATATAGTATTTATTTGTAATT
Found at i:554457 original size:3 final size:3
Alignment explanation
Indices: 554449--554516 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
554439 AACCATGCCC
554449 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
554497 CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CT
554517 CTCCATCCGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:557390 original size:16 final size:17
Alignment explanation
Indices: 557369--557420 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
557359 TCATATTCAT
557369 AAATTAAATAATAAC-A
1 AAATTAAATAATAACTA
* *
557385 AAATTAATTAATGACTA
1 AAATTAAATAATAACTA
*
557402 AAATAAAATAA-AA-TA
1 AAATTAAATAATAACTA
557417 AAAT
1 AAAT
557421 AAAAATTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 6 0.20
16 14 0.47
17 10 0.33
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATTAAATAATAACTA
Found at i:557410 original size:5 final size:5
Alignment explanation
Indices: 557400--557424 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
557390 AATTAATGAC
557400 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
557425 ATTAACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:559893 original size:20 final size:20
Alignment explanation
Indices: 559868--559908 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
559858 GATGATCTTG
559868 ACATGGAAATGGGGAAAGGT
1 ACATGGAAATGGGGAAAGGT
559888 ACATGGAAATGGGGAAAGGT
1 ACATGGAAATGGGGAAAGGT
559908 A
1 A
559909 AGATGAGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.05, G:0.39, T:0.15
Consensus pattern (20 bp):
ACATGGAAATGGGGAAAGGT
Found at i:563323 original size:31 final size:30
Alignment explanation
Indices: 563280--563339 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
563270 ACTTAATGTG
*
563280 TTTAGTACCTAAACTATCAGTTTTATTCCGT
1 TTTAGTACCTAAACTATCAATTTT-TTCCGT
* *
563311 TTTAGTATCTAAACTTTCAATTTTTTCCG
1 TTTAGTACCTAAACTATCAATTTTTTCCG
563340 AAACATAACG
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:0.25, C:0.18, G:0.08, T:0.48
Consensus pattern (30 bp):
TTTAGTACCTAAACTATCAATTTTTTCCGT
Found at i:563419 original size:27 final size:27
Alignment explanation
Indices: 563381--563478 Score: 169
Period size: 27 Copynumber: 3.6 Consensus size: 27
563371 AAAATGAAAC
563381 AAAAATTAAATTTTAGGTATAGTTTTT
1 AAAAATTAAATTTTAGGTATAGTTTTT
563408 AAAAATTAAATTTTAGGTATAGTTTTT
1 AAAAATTAAATTTTAGGTATAGTTTTT
*
563435 AAAAATTAAATTTTAGGTATAGTTTTA
1 AAAAATTAAATTTTAGGTATAGTTTTT
*
563462 AAAAATTGAAAGTTTAG
1 AAAAATT-AAATTTTAG
563479 ATACTAAAAC
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 60 0.88
28 8 0.12
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (27 bp):
AAAAATTAAATTTTAGGTATAGTTTTT
Found at i:564790 original size:27 final size:28
Alignment explanation
Indices: 564760--564820 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
564750 TTAACCGTTA
564760 ATTAATC-AAACTAATTCAATTCGATCG
1 ATTAATCTAAACTAATTCAATTCGATCG
*
564787 ATTAA-CTAAACTAATTCGATTCGATCG
1 ATTAATCTAAACTAATTCAATTCGATCG
564814 ATTAATC
1 ATTAATC
564821 GGATTAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (28 bp):
ATTAATCTAAACTAATTCAATTCGATCG
Found at i:578890 original size:20 final size:21
Alignment explanation
Indices: 578849--578898 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
578839 AAAGCAGTCC
578849 AAAACAAAATAGGACATCT-A
1 AAAACAAAATAGGACATCTAA
578869 AAAACAAAATAGAGA-A-CTTAA
1 AAAACAAAATAG-GACATC-TAA
578890 AAAACAAAA
1 AAAACAAAA
578899 ACCTAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.04
20 14 0.52
21 12 0.44
ACGTcount: A:0.68, C:0.12, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAACAAAATAGGACATCTAA
Found at i:589444 original size:2 final size:2
Alignment explanation
Indices: 589433--589464 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
589423 ATGTATTATG
589433 TA TA -A 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 TA T
589465 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:590079 original size:2 final size:2
Alignment explanation
Indices: 590070--590099 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
590060 TTTTTTTAAA
590070 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
590100 GAAAACTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:590370 original size:39 final size:39
Alignment explanation
Indices: 590284--590370 Score: 88
Period size: 39 Copynumber: 2.2 Consensus size: 39
590274 TATTAAGTTG
* * *
590284 AAATAA-TTTAATAAATTAAAAATTTAGAAGAGTATAAT
1 AAATAATTTTAATAAATGAAAAATTTAGAACAGTAAAAT
* **
590322 AATAAAATTTTAA-AAATGAAAAATTTAGAACTTTAAAATT
1 AA-ATAATTTTAATAAATGAAAAATTTAGAACAGTAAAA-T
590362 AAATAATTT
1 AAATAATTT
590371 GAGGATTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
38 2 0.05
39 29 0.74
40 8 0.21
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (39 bp):
AAATAATTTTAATAAATGAAAAATTTAGAACAGTAAAAT
Found at i:596633 original size:11 final size:13
Alignment explanation
Indices: 596617--596648 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
596607 TATTCTTATT
596617 AAAAACAAA-A-A
1 AAAAACAAAGAGA
596628 AAAAACAAAGAGA
1 AAAAACAAAGAGA
596641 AAAAACAA
1 AAAAACAA
596649 CCGACGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAACAAAGAGA
Found at i:597323 original size:30 final size:30
Alignment explanation
Indices: 597288--597347 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
597278 TCTTAACTAG
* *
597288 ATTTTTAATCTTTTCTTATATGGTCGTTAC
1 ATTTTTAATCTTTTATTATATGATCGTTAC
597318 ATTTTTAATCTTTTATTATATGATCGTTAC
1 ATTTTTAATCTTTTATTATATGATCGTTAC
597348 GTGATCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (30 bp):
ATTTTTAATCTTTTATTATATGATCGTTAC
Found at i:599398 original size:22 final size:23
Alignment explanation
Indices: 599355--599400 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
599345 TTACCCTAGT
599355 TTAAATATAGTGATTTTTAAATAA
1 TTAAATATAGTGA-TTTTAAATAA
*
599379 TTAATTATAGTGA-TTTAAATAA
1 TTAAATATAGTGATTTTAAATAA
599401 ATAGTTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (23 bp):
TTAAATATAGTGATTTTAAATAA
Found at i:599408 original size:22 final size:23
Alignment explanation
Indices: 599360--599408 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
599350 CTAGTTTAAA
*
599360 TATAGTGATTTTTAAATAATTAAT
1 TATAGTGA-TTTTAAATAAATAAT
*
599384 TATAGTGA-TTTAAATAAATAGT
1 TATAGTGATTTTAAATAAATAAT
599406 TAT
1 TAT
599409 GTAGTTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 15 0.65
24 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (23 bp):
TATAGTGATTTTAAATAAATAAT
Found at i:602923 original size:21 final size:21
Alignment explanation
Indices: 602899--602955 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
602889 ATTCAACTTT
602899 AATTTAATTTAGATTGTATT-C-
1 AATTTAATTTA-ATT-TATTCCA
*
602920 AATTTAAATTAATTTATTCCA
1 AATTTAATTTAATTTATTCCA
602941 AATTTAAATTTAATT
1 AATTT-AATTTAATT
602956 CAGATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 15 0.48
22 8 0.26
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (21 bp):
AATTTAATTTAATTTATTCCA
Found at i:610156 original size:66 final size:67
Alignment explanation
Indices: 610063--610211 Score: 246
Period size: 67 Copynumber: 2.2 Consensus size: 67
610053 ACCCATTCAA
* *
610063 GGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
1 GGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
610127 GG
66 GG
* *
610129 GGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
1 GGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
610194 GG
66 GG
*
610196 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
610212 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 25 0.32
67 52 0.68
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (67 bp):
GGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAG
GG
Found at i:610200 original size:20 final size:20
Alignment explanation
Indices: 610175--610212 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
610165 GAATGCTAGA
*
610175 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
610195 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
610213 TGAGAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:610547 original size:29 final size:29
Alignment explanation
Indices: 610513--610584 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
610503 CATATTATGA
* *
610513 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
610542 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
610571 TGCATGACATGAAT
1 TACATGACATGAAT
610585 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:610640 original size:30 final size:30
Alignment explanation
Indices: 610598--610674 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
610588 CAGAAAAGTT
* *
610598 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
610629 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
610659 ATATGACTACGTGATA
1 ATATGACTATGTGATA
610675 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:610907 original size:13 final size:13
Alignment explanation
Indices: 610889--610951 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
610879 TTATATGGCA
610889 CTACGGTGCAATT
1 CTACGGTGCAATT
610902 CTACGG-GC-A--
1 CTACGGTGCAATT
*
610911 CTTCGGTGCAATT
1 CTACGGTGCAATT
610924 CTACGG-GC-A--
1 CTACGGTGCAATT
*
610933 CTTCGGTGCAATT
1 CTACGGTGCAATT
610946 CTACGG
1 CTACGG
610952 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:610917 original size:22 final size:22
Alignment explanation
Indices: 610885--610965 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
610875 ATCATTATAT
*
610885 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
610907 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
610929 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
610952 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
610966 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:617026 original size:21 final size:21
Alignment explanation
Indices: 617000--617042 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
616990 TTTTCGGGCT
* *
617000 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
617021 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
617042 A
1 A
617043 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:617096 original size:65 final size:67
Alignment explanation
Indices: 617022--617170 Score: 239
Period size: 66 Copynumber: 2.3 Consensus size: 67
617012 ACCCATTCAA
* *
617022 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
617086 -G
66 GG
* *
617087 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
617152 GG
66 GG
*
617154 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
617171 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
65 26 0.34
66 34 0.44
67 17 0.22
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:617159 original size:20 final size:20
Alignment explanation
Indices: 617134--617171 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
617124 GAATGCTAGA
*
617134 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
617154 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
617172 TGAGAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:617506 original size:29 final size:29
Alignment explanation
Indices: 617472--617543 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
617462 CATATTATGA
* *
617472 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
617501 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
617530 TGCATGACATGAAT
1 TACATGACATGAAT
617544 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:617599 original size:30 final size:30
Alignment explanation
Indices: 617557--617633 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
617547 CAGAAAAGTT
* *
617557 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
617588 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
617618 ATATGACTACGTGATA
1 ATATGACTATGTGATA
617634 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:617866 original size:13 final size:13
Alignment explanation
Indices: 617848--617910 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
617838 TTATATGGCA
617848 CTACGGTGCAATT
1 CTACGGTGCAATT
617861 CTACGG-GC-A--
1 CTACGGTGCAATT
*
617870 CTTCGGTGCAATT
1 CTACGGTGCAATT
617883 CTACGG-GC-A--
1 CTACGGTGCAATT
*
617892 CTTCGGTGCAATT
1 CTACGGTGCAATT
617905 CTACGG
1 CTACGG
617911 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:617876 original size:22 final size:22
Alignment explanation
Indices: 617844--617924 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
617834 ATCATTATAT
*
617844 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
617866 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
617888 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
617911 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
617925 TTTATATGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:619567 original size:29 final size:29
Alignment explanation
Indices: 619525--619583 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
619515 ATTTTCACCT
619525 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
619554 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
619583 A
1 A
619584 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Done.