Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 3 of 32
Found at i:537610 original size:24 final size:24
Alignment explanation
Indices: 537565--537611 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
537555 ATTCATATTT
* **
537565 TATCATATTATAATTATATTATAA
1 TATCATATTAAAAAGATATTATAA
*
537589 TATCATATTAAAAAGATTTTATA
1 TATCATATTAAAAAGATATTATA
537612 TTTATATAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TATCATATTAAAAAGATATTATAA
Found at i:537676 original size:33 final size:32
Alignment explanation
Indices: 537604--537678 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
537594 TATTAAAAAG
* * *
537604 ATTTTATATTTATATAAATTTTTATATGTTAAT
1 ATTTTATA-TGATATAAATTTTAAAATGTTAAT
* * *
537637 AATTTATATGATATGAATTTTAAAATTTTATAT
1 ATTTTATATGATATAAATTTTAAAATGTTA-AT
537670 ATTTTATAT
1 ATTTTATAT
537679 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (32 bp):
ATTTTATATGATATAAATTTTAAAATGTTAAT
Found at i:537683 original size:19 final size:20
Alignment explanation
Indices: 537661--537750 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 20
537651 GAATTTTAAA
537661 ATTTTATATAT-TTTATATT
1 ATTTTATATATATTTATATT
** *
537680 ATTTT-T-TATACCATATCTT
1 ATTTTATATATA-TTTATATT
537699 ATTTTATATAATAATTTA-ATT
1 ATTTTATAT-AT-ATTTATATT
537720 ATTTTTATATTATATTTATATT
1 A-TTTTATA-TATATTTATATT
537742 -TTTTA-ATAT
1 ATTTTATATAT
537751 CGTTACATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 19
0.69 0.07 0.23
Matches are distributed among these distances:
17 3 0.05
18 4 0.07
19 16 0.29
20 6 0.11
21 9 0.16
22 16 0.29
23 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTATATATATTTATATT
Found at i:537723 original size:21 final size:23
Alignment explanation
Indices: 537697--537746 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
537687 ATACCATATC
537697 TTATTTTATATAATA-ATTTA-A
1 TTATTTTATATAATATATTTATA
*
537718 TTATTTT-TATATTATATTTATA
1 TTATTTTATATAATATATTTATA
537740 TT-TTTTA
1 TTATTTTA
537747 ATATCGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTTTATATAATATATTTATA
Found at i:537853 original size:8 final size:8
Alignment explanation
Indices: 537842--537978 Score: 66
Period size: 8 Copynumber: 15.8 Consensus size: 8
537832 AAATTTAATA
537842 ATTTATAT
1 ATTTATAT
537850 ATTTATAT
1 ATTTATAT
537858 CAAATTTATAT
1 ---ATTTATAT
537869 ATTTTATTAT
1 A-TTTA-TAT
537879 ATTATAATTAT
1 ATT-T-A-TAT
*
537890 ATTTAAAAT
1 ATTT-ATAT
537899 ATTTA-AT
1 ATTTATAT
537906 ATTTATAT
1 ATTTATAT
537914 AAATTT-TATT
1 --ATTTATA-T
*
537924 ACGTTA-AT
1 A-TTTATAT
537932 AATTTATAT
1 -ATTTATAT
537941 -TTTATAT
1 ATTTATAT
*
537948 ATTTAAAT
1 ATTTATAT
* *
537956 ATATATTT
1 ATTTATAT
537964 ATTTATACT
1 ATTTATA-T
537973 ATTTAT
1 ATTTAT
537979 TTAATATTTT
Statistics
Matches: 103, Mismatches: 9, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
7 14 0.14
8 33 0.32
9 27 0.26
10 13 0.13
11 16 0.16
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (8 bp):
ATTTATAT
Found at i:537875 original size:28 final size:26
Alignment explanation
Indices: 537825--537919 Score: 86
Period size: 28 Copynumber: 3.5 Consensus size: 26
537815 TAGCTTGATT
* *
537825 TTTACATAAATTTAATAATTTATATA
1 TTTATATAAATTTAATATTTTATATA
537851 TTTATATCAAATTTATATATTTTAT-TA
1 TTTATAT-AAATTTA-ATATTTTATATA
* *
537878 TATTATAATTATATTTAAAATATTTA-ATA
1 T-TTAT-A-TAAATTTAATAT-TTTATATA
537907 TTTATATAAATTT
1 TTTATATAAATTT
537920 TATTACGTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
26 12 0.21
27 11 0.19
28 19 0.33
29 14 0.25
30 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATATAAATTTAATATTTTATATA
Found at i:537917 original size:19 final size:19
Alignment explanation
Indices: 537842--537922 Score: 57
Period size: 19 Copynumber: 4.3 Consensus size: 19
537832 AAATTTAATA
*
537842 ATTTATATATTTATATCAA-
1 ATTTATATATTT-TATAAAT
*
537861 ATTTATATATTTTAT-TAT
1 ATTTATATATTTTATAAAT
537879 A-TTATAATTATATTTA-AAAT
1 ATTTAT-A-TAT-TTTATAAAT
537899 ATTTA-ATATTTATATAAAT
1 ATTTATATATTT-TATAAAT
537918 -TTTAT
1 ATTTAT
537923 TACGTTAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
17 7 0.14
18 14 0.27
19 20 0.39
20 7 0.14
21 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATATATTTTATAAAT
Found at i:537989 original size:12 final size:12
Alignment explanation
Indices: 537941--537987 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
537931 TAATTTATAT
537941 TTTATATATTTA
1 TTTATATATTTA
**
537953 AATATATATTTA
1 TTTATATATTTA
537965 TTTATACTATTTA
1 TTTATA-TATTTA
537978 TTTA-ATATTT
1 TTTATATATTT
537988 TATAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 5 0.17
12 15 0.50
13 10 0.33
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATATATTTA
Found at i:538249 original size:15 final size:15
Alignment explanation
Indices: 538229--538258 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
538219 ATATTTAATT
538229 TTTAATTTAATTAAA
1 TTTAATTTAATTAAA
538244 TTTAATTTAATTAAA
1 TTTAATTTAATTAAA
538259 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTTAATTAAA
Found at i:538518 original size:11 final size:11
Alignment explanation
Indices: 538491--538550 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
538481 ATTATTATTT
538491 AATAATA-A-A
1 AATAATATATA
538500 AATAATATATA
1 AATAATATATA
*
538511 ATTAATATA-A
1 AATAATATATA
* *
538521 AATAATATTTT
1 AATAATATATA
*
538532 ATTAATATAATA
1 AATAATAT-ATA
538544 AATAATA
1 AATAATA
538551 AAAAGTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 7 0.18
10 9 0.23
11 16 0.41
12 7 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAATATATA
Found at i:538524 original size:21 final size:21
Alignment explanation
Indices: 538493--538550 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
538483 TATTATTTAA
538493 TAATA-AAAATAATATATAAT
1 TAATATAAAATAATATATAAT
* *
538513 TAATATAAAATAATATTTTAT
1 TAATATAAAATAATATATAAT
538534 TAATATAATAAATAATA
1 TAATAT-A-AAATAATA
538551 AAAAGTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 5 0.15
21 19 0.58
22 1 0.03
23 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATATAAAATAATATATAAT
Found at i:538808 original size:14 final size:14
Alignment explanation
Indices: 538776--538812 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
538766 TATTATATTT
538776 TAATTAT-TTT-TA
1 TAATTATATTTATA
538788 T-ATTATATTTATA
1 TAATTATATTTATA
538801 TAATTATATTTA
1 TAATTATATTTA
538813 ATTTTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 4 0.18
13 3 0.14
14 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:538982 original size:93 final size:93
Alignment explanation
Indices: 538879--539051 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
538869 TCTATGGTGG
* *
538879 GTCACAAAAATGTACAATCAATAATTAGTTGAGAAAATTAAATGTTTTTATAGTGACTTTTTAAG
1 GTCACAAAAATGTACAATCAATAATTAGTTGAGAAAATTAAATGTGTTTATAGAGACTTTTTAAG
538944 ATGGGGAAAACTGAGTTGTGGTGGTGTT
66 ATGGGGAAAACTGAGTTGTGGTGGTGTT
** *
538972 GTCACAAAAATGTACGGTCAATTATTAGTTGAGAAAATTAAATGTGTTTATAGAGACTTTTTAAG
1 GTCACAAAAATGTACAATCAATAATTAGTTGAGAAAATTAAATGTGTTTATAGAGACTTTTTAAG
539037 ATGGGGAAAACTGAG
66 ATGGGGAAAACTGAG
539052 AACTATGGTT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.34
Consensus pattern (93 bp):
GTCACAAAAATGTACAATCAATAATTAGTTGAGAAAATTAAATGTGTTTATAGAGACTTTTTAAG
ATGGGGAAAACTGAGTTGTGGTGGTGTT
Found at i:541785 original size:41 final size:40
Alignment explanation
Indices: 541739--541850 Score: 101
Period size: 41 Copynumber: 2.8 Consensus size: 40
541729 GGGGTTTAAA
541739 ATTATTCAAATTAAATTAAATTAAATTTAAATAATTATTTT
1 ATTATT-AAATTAAATTAAATTAAATTTAAATAATTATTTT
* * *
541780 ATTATTTAAA-TAATATTAAAAT-ATTTTTAA-AATTATTTT
1 ATTA-TTAAATTAA-ATTAAATTAAATTTAAATAATTATTTT
*
541819 A-TATTAATATT--TTTATAATTAAATTTAAATAA
1 ATTATTAA-ATTAAATTA-AATTAAATTTAAATAA
541851 AAAATTTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
36 3 0.05
37 7 0.12
38 9 0.16
39 13 0.23
40 9 0.16
41 14 0.25
42 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (40 bp):
ATTATTAAATTAAATTAAATTAAATTTAAATAATTATTTT
Found at i:542007 original size:14 final size:14
Alignment explanation
Indices: 541985--542018 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
541975 ACGTATTATG
*
541985 AATAAATTAAAATT
1 AATATATTAAAATT
541999 AATATATTAAAATT
1 AATATATTAAAATT
*
542013 TATATA
1 AATATA
542019 AATAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATTAAAATT
Found at i:542036 original size:16 final size:17
Alignment explanation
Indices: 542012--542046 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
542002 ATATTAAAAT
542012 TTATATAAAT-AAATAA
1 TTATATAAATAAAATAA
*
542028 TTATTTAAATAAAATAA
1 TTATATAAATAAAATAA
542045 TT
1 TT
542047 TATCACCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATATAAATAAAATAA
Found at i:543371 original size:15 final size:17
Alignment explanation
Indices: 543346--543381 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
543336 AGATGATATT
543346 AAAATTATTAAA-AATA
1 AAAATTATTAAATAATA
543362 AAAATT-TTAAATAATA
1 AAAATTATTAAATAATA
543378 AAAA
1 AAAA
543382 AATATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTATTAAATAATA
Found at i:544384 original size:15 final size:15
Alignment explanation
Indices: 544360--544399 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
544350 TTATTTTATA
544360 ATTATATTTAAAAAT
1 ATTATATTTAAAAAT
* * *
544375 ATTTTATTTATATAT
1 ATTATATTTAAAAAT
544390 ATTATATTTA
1 ATTATATTTA
544400 TATTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATATTTAAAAAT
Found at i:545134 original size:2 final size:2
Alignment explanation
Indices: 545124--545161 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
545114 TCTCTCTCTC
*
545124 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
545162 AAGCTTATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:548079 original size:37 final size:34
Alignment explanation
Indices: 548012--548101 Score: 96
Period size: 37 Copynumber: 2.6 Consensus size: 34
548002 TAATCAAATT
548012 TAATTAGATT-AATT-ATTAATTTTAAAAAATTAA
1 TAATTA-ATTAAATTAATTAATTTTAAAAAATTAA
548045 TAATTAATTAAATTAATTAATTTTTATAATAAATTAA
1 TAATTAATTAAATTAATTAA-TTTTA-AA-AAATTAA
* *
548082 T-TTTAAATTAAATAAATTAA
1 TAATT-AATTAAATTAATTAA
548102 ATCTATTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
32 3 0.06
33 10 0.20
34 5 0.10
35 5 0.10
36 4 0.08
37 22 0.45
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (34 bp):
TAATTAATTAAATTAATTAATTTTAAAAAATTAA
Found at i:548093 original size:16 final size:16
Alignment explanation
Indices: 548052--548099 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
548042 TAATAATTAA
548052 TTAAATT-AATTAATTT
1 TTAAATTAAATTAA-TT
548068 TTATAA-TAAATTAATT
1 TTA-AATTAAATTAATT
*
548084 TTAAATTAAATAAATT
1 TTAAATTAAATTAATT
548100 AAATCTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 2 0.07
16 18 0.64
17 8 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATTAAATTAATT
Found at i:558196 original size:3 final size:3
Alignment explanation
Indices: 558188--558229 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
558178 TCTCCGAGCG
* *
558188 CTT CTT CTT CTT CTC CTT CTC CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
558230 TTTCCTTCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:558517 original size:21 final size:21
Alignment explanation
Indices: 558493--558565 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
558483 GTATATAATA
*
558493 AATATATATTAAAATTTATAT
1 AATATATAATAAAATTTATAT
*
558514 AATATATAAAAAAATTTAAATAT
1 AATATATAATAAAATTT--ATAT
**
558537 AAT-TATAAT-AAATAAATAT
1 AATATATAATAAAATTTATAT
558556 AATATA-AATA
1 AATATATAATA
558566 TGTAAATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.23
20 2 0.05
21 19 0.44
22 5 0.12
23 7 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATATAATAAAATTTATAT
Found at i:558525 original size:19 final size:19
Alignment explanation
Indices: 558496--558561 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
558486 TATAATAAAT
*
558496 ATATATTAAAATTTATATA
1 ATATATAAAAATTTATATA
558515 ATATATAAAAAAATTTAAATATA
1 ATATAT--AAAAATTT--ATATA
**
558538 AT-TATAATAAATAAATATA
1 ATATATAA-AAATTTATATA
558557 ATATA
1 ATATA
558562 AATATGTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
19 13 0.34
20 4 0.11
21 11 0.29
22 3 0.08
23 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATATAAAAATTTATATA
Found at i:558559 original size:24 final size:23
Alignment explanation
Indices: 558510--558566 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
558500 ATTAAAATTT
*
558510 ATATAATATATAAAAAAATTTAA
1 ATATAATATATAAAAAAATATAA
*
558533 ATATAATTATAATAAATAAATAT-A
1 ATATAA-TAT-ATAAAAAAATATAA
558557 ATATAA-ATAT
1 ATATAATATAT
558567 GTAAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 6 0.20
24 10 0.33
25 10 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAATATATAAAAAAATATAA
Found at i:558753 original size:16 final size:15
Alignment explanation
Indices: 558726--558771 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
558716 TTAGATTCAA
*
558726 ATTAATATTTATATT
1 ATTAAAATTTATATT
558741 ATTAAAAATTTATATTT
1 ATT-AAAATTTATA-TT
*
558758 ATTAATATTTATAT
1 ATTAAAATTTATAT
558772 ATTTTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAAAATTTATATT
Found at i:561371 original size:24 final size:24
Alignment explanation
Indices: 561339--561387 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
561329 GAAAGTACAC
561339 TAGCATAACATCACATTAAATTAT
1 TAGCATAACATCACATTAAATTAT
561363 TAGCATAACATCACATTAAATTAT
1 TAGCATAACATCACATTAAATTAT
561387 T
1 T
561388 TTAAGTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (24 bp):
TAGCATAACATCACATTAAATTAT
Found at i:568510 original size:2 final size:2
Alignment explanation
Indices: 568503--568539 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
568493 TTTAAAACAA
568503 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
568540 AACCGGAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:568968 original size:28 final size:27
Alignment explanation
Indices: 568937--569005 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
568927 TATATAAATT
**
568937 AAATTAATTTTTACTTTTTATTTAATAA
1 AAATTAATTTTTA-TTTTTAAATAATAA
*
568965 AAATAAATATTTTATTTTTAAATAATAA
1 AAATTAAT-TTTTATTTTTAAATAATAA
*
568993 AAAATATATTTTT
1 AAATTA-ATTTTT
569006 TAAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 27 0.79
29 7 0.21
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
AAATTAATTTTTATTTTTAAATAATAA
Found at i:568977 original size:22 final size:22
Alignment explanation
Indices: 568952--569014 Score: 60
Period size: 25 Copynumber: 2.8 Consensus size: 22
568942 AATTTTTACT
568952 TTTTATTTAATAAAAATAAATA
1 TTTTATTTAATAAAAATAAATA
568974 TTTTATTTTTAAATAATAAA-AAATA
1 TTTTA--TTT-AATAA-AAATAAATA
568999 TATTT-TTTAA-AAAAAT
1 T-TTTATTTAATAAAAAT
569015 TAAAATAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
20 3 0.09
21 2 0.06
22 7 0.20
23 3 0.09
24 3 0.09
25 11 0.31
26 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTATTTAATAAAAATAAATA
Found at i:570053 original size:19 final size:19
Alignment explanation
Indices: 570006--570063 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
569996 AATCCTTCTA
*
570006 TAAT-TTTAAATT-TTTTA
1 TAATATTTAAATTATTTTT
*
570023 TAA-A-TTATATTATTTTT
1 TAATATTTAAATTATTTTT
*
570040 TAATATTTAAATTATTATT
1 TAATATTTAAATTATTTTT
570059 TAATA
1 TAATA
570064 ATAAAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 6 0.18
17 10 0.30
18 1 0.03
19 16 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATATTTAAATTATTTTT
Found at i:570070 original size:19 final size:18
Alignment explanation
Indices: 570031--570089 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
570021 TATAAATTAT
* *
570031 ATTATTTTTTAATATTTAA
1 ATTA-TTTTTAATAATAAA
570050 ATTATTATTTAATAATAAA
1 ATTATT-TTTAATAATAAA
*
570069 ATAATATTTTAAATAATAAA
1 AT--TATTTTTAATAATAAA
570089 A
1 A
570090 AATCTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 16 0.47
20 12 0.35
21 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTTTTAATAATAAA
Found at i:570300 original size:15 final size:15
Alignment explanation
Indices: 570280--570309 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
570270 TAAATGAAAG
570280 ATTTAAATTTAAAAA
1 ATTTAAATTTAAAAA
570295 ATTTAAATTTAAAAA
1 ATTTAAATTTAAAAA
570310 TTTTTTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAATTTAAAAA
Found at i:570428 original size:18 final size:17
Alignment explanation
Indices: 570407--570464 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
570397 TTTAAAATTT
570407 ATATAATATAAATTATTA
1 ATATAATA-AAATTATTA
570425 ATAT-ATAAAATTATATAA
1 ATATAATAAAATTAT-T-A
*
570443 ATATAA-AAAATT-TAA
1 ATATAATAAAATTATTA
570458 ATATAAT
1 ATATAAT
570465 TATGATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
15 7 0.20
16 7 0.20
17 5 0.14
18 15 0.43
19 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATAAAATTATTA
Found at i:570435 original size:16 final size:16
Alignment explanation
Indices: 570380--570480 Score: 72
Period size: 15 Copynumber: 6.3 Consensus size: 16
570370 GAATAATTAA
570380 AAAATATATATAAATATTTT
1 AAAAT-TATATAAATA---T
570400 AAAATT-TATATAATAT
1 AAAATTATATA-AATAT
570416 -AAATTAT-TAATATAT
1 AAAATTATATAA-ATAT
570431 AAAATTATATAAATAT
1 AAAATTATATAAATAT
* *
570447 AAAA-AATTTAAATAT
1 AAAATTATATAAATAT
570462 --AATTATGAT-AATAT
1 AAAATTAT-ATAAATAT
570476 AAAAT
1 AAAAT
570481 ACTCAAATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
13 2 0.03
14 8 0.12
15 21 0.31
16 20 0.29
17 3 0.04
18 4 0.06
19 5 0.07
20 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
AAAATTATATAAATAT
Found at i:570462 original size:31 final size:31
Alignment explanation
Indices: 570399--570479 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
570389 ATAAATATTT
**
570399 TAAAATT-TATATAATATAAATTATTAATATA
1 TAAAATTATATA-AATATAAAAAATTAATATA
570430 TAAAATTATATAAATATAAAAAATTTAA-ATA
1 TAAAATTATATAAATATAAAAAA-TTAATATA
570461 T--AATTATGAT-AATATAAAA
1 TAAAATTAT-ATAAATATAAAA
570480 TACTCAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
29 15 0.33
30 2 0.04
31 20 0.44
32 8 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAAATTATATAAATATAAAAAATTAATATA
Found at i:570488 original size:29 final size:29
Alignment explanation
Indices: 570433--570490 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
570423 TAATATATAA
* *
570433 AATTATATAAATATAAAAAATTTAAATAT
1 AATTATATAAATATAAAAAACTCAAATAT
*
570462 AATTATGAT-AATATAAAATACTCAAATAT
1 AATTAT-ATAAATATAAAAAACTCAAATAT
570491 GATATGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (29 bp):
AATTATATAAATATAAAAAACTCAAATAT
Found at i:572057 original size:8 final size:8
Alignment explanation
Indices: 572044--572117 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
572034 TGTATTAAAA
572044 ATTTATAT
1 ATTTATAT
572052 ATTTATAT
1 ATTTATAT
*
572060 AATTTTTTAT
1 -A-TTTATAT
*
572070 ATTAATA-
1 ATTTATAT
572077 ATTTATAT
1 ATTTATAT
* *
572085 -TATATAA
1 ATTTATAT
572092 ATTTTAATAT
1 A-TTT-ATAT
572102 ATTTATAT
1 ATTTATAT
572110 ATTTATAT
1 ATTTATAT
572118 CATGTTAATA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
7 11 0.21
8 24 0.46
9 7 0.13
10 10 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:572072 original size:18 final size:17
Alignment explanation
Indices: 572049--572101 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 17
572039 TAAAAATTTA
572049 TATATTTATATAATTTTT
1 TATA-TTATATAATTTTT
572067 TATATTA-ATAA---TT
1 TATATTATATAATTTTT
*
572080 TATATTATATAAATTTT
1 TATATTATATAATTTTT
*
572097 AATAT
1 TATAT
572102 ATTTATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 9 0.30
14 4 0.13
16 4 0.13
17 9 0.30
18 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTATATAATTTTT
Found at i:572080 original size:33 final size:33
Alignment explanation
Indices: 572036--572150 Score: 103
Period size: 33 Copynumber: 3.4 Consensus size: 33
572026 TATATATTTG
*
572036 TATTAAAAATTTATATATTTATATAATTTTTTA
1 TATTAATAATTTATATATTTATATAATTTTTTA
* *
572069 TATTAATAATTTATAT-TATATA-AATTTTAATA
1 TATTAATAATTTATATATTTATATAATTTT-TTA
*
572101 TATTTATATATTTATATCATGTTAATATTAA-TTTTTA
1 TATTAATA-ATTTATAT-AT-TT-ATA-TAATTTTTTA
*
572138 TA-TAATATTTTAT
1 TATTAATAATTTAT
572151 TTAAATTACG
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
31 6 0.09
32 14 0.21
33 23 0.35
35 6 0.09
36 5 0.08
37 7 0.11
38 3 0.05
39 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
TATTAATAATTTATATATTTATATAATTTTTTA
Found at i:572108 original size:18 final size:17
Alignment explanation
Indices: 572045--572117 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 17
572035 GTATTAAAAA
572045 TTTATATATTTATATAAT
1 TTTATATATTTATA-AAT
* *
572063 TTTTTATATTAAT-AA-
1 TTTATATATTTATAAAT
*
572078 TTTATAT-TATATAAAT
1 TTTATATATTTATAAAT
*
572094 TTTAATATATTTATATA-
1 TTT-ATATATTTATAAAT
572111 TTTATAT
1 TTTATAT
572118 CATGTTAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
14 3 0.07
15 8 0.18
16 9 0.20
17 7 0.16
18 17 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATATATTTATAAAT
Found at i:572267 original size:3 final size:3
Alignment explanation
Indices: 572259--572288 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
572249 GTTATTTCAA
572259 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
572289 TTTATTTTTA
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):
AAT
Found at i:573001 original size:26 final size:25
Alignment explanation
Indices: 572958--573006 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
572948 TAATACTTTA
*
572958 ATTATTATATTTATAAAATAAAATTT
1 ATTATTATATTTACAAAA-AAAATTT
572984 ATTATTA-ATTTAACAAAAAAAAT
1 ATTATTATATTT-ACAAAAAAAAT
573007 ATAATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTATTATATTTACAAAAAAAATTT
Found at i:573005 original size:25 final size:26
Alignment explanation
Indices: 572958--573006 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
572948 TAATACTTTA
*
572958 ATTATTATATTTATAAAATAAAATTT
1 ATTATTATATTTATAAAAAAAAATTT
572984 ATTATTA-ATTTA-ACAAAAAAAAT
1 ATTATTATATTTATA-AAAAAAAAT
573007 ATAATGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 13 0.62
26 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTATTATATTTATAAAAAAAAATTT
Found at i:573066 original size:16 final size:16
Alignment explanation
Indices: 573047--573108 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
573037 AAATATAATT
573047 AATATAATATATTTAA
1 AATATAATATATTTAA
*
573063 AATATATTATATTT-A
1 AATATAATATATTTAA
** *
573078 TGTTTAATA-ATTTAA
1 AATATAATATATTTAA
*
573093 AATATTAAAATATTTA
1 AATA-TAATATATTTA
573109 TATTATTTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
14 4 0.12
15 8 0.24
16 17 0.50
17 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATATAATATATTTAA
Found at i:573106 original size:31 final size:31
Alignment explanation
Indices: 573051--573109 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
573041 ATAATTAATA
**
573051 TAATATATTTAAAATATATTATATTTATGTT
1 TAATATATTTAAAATATAAAATATTTATGTT
573082 TAATA-ATTTAAAATATTAAAATATTTAT
1 TAATATATTTAAAATA-TAAAATATTTAT
573110 ATTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (31 bp):
TAATATATTTAAAATATAAAATATTTATGTT
Found at i:573237 original size:33 final size:31
Alignment explanation
Indices: 573197--573268 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
573187 ATAATTATTT
**
573197 ATATTATATGTATATTAATTTTAATAAATTAATA
1 ATATTATATGTA-AAAAATTTT-A-AAATTAATA
*
573231 AT-TTATATTTAAAAAATTTTAAAATTAATA
1 ATATTATATGTAAAAAATTTTAAAATTAATA
573261 ATATTATA
1 ATATTATA
573269 ATTATTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 11 0.32
31 6 0.18
32 7 0.21
33 8 0.24
34 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATATTATATGTAAAAAATTTTAAAATTAATA
Found at i:573285 original size:11 final size:10
Alignment explanation
Indices: 573270--573307 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
573260 AATATTATAA
573270 TTATTATATT
1 TTATTATATT
573280 TATATTATATT
1 T-TATTATATT
573291 TTA-TATATT
1 TTATTATATT
573300 ATTATTAT
1 -TTATTAT
573308 TACACGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.24
10 6 0.24
11 13 0.52
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATTATATT
Found at i:573286 original size:20 final size:19
Alignment explanation
Indices: 573261--573307 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
573251 AAAATTAATA
573261 ATATTATAATTATTATAT-TT
1 ATATTAT-ATT-TTATATATT
573281 ATATTATATTTTATATATT
1 ATATTATATTTTATATATT
573300 ATTATTAT
1 A-TATTAT
573308 TACACGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.24
19 6 0.24
20 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATATTTTATATATT
Found at i:573674 original size:23 final size:24
Alignment explanation
Indices: 573627--573745 Score: 79
Period size: 23 Copynumber: 5.0 Consensus size: 24
573617 ATCTTTATTA
573627 TAAAT-TAA-AATATTAAAAATAT
1 TAAATATAATAATATTAAAAATAT
* *
573649 TAAATATAATAAT-TTAATAATTT
1 TAAATATAATAATATTAAAAATAT
*
573672 TAATTATAATTAATAATATAAAAATAAT
1 TAAATATAA-TAAT-AT-TAAAAAT-AT
* * * *
573700 ATAAACATAATATTTATAAAAAATTT
1 -TAAATATAATA-ATATTAAAAATAT
573726 TAAA-AT-ATAATA-TAAAAATA
1 TAAATATAATAATATTAAAAATA
573746 ATATATATGA
Statistics
Matches: 75, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
21 6 0.08
22 7 0.09
23 22 0.29
24 9 0.12
25 4 0.05
26 2 0.03
27 12 0.16
28 5 0.07
29 8 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATAATAATATTAAAAATAT
Found at i:573699 original size:11 final size:11
Alignment explanation
Indices: 573683--573750 Score: 66
Period size: 11 Copynumber: 5.8 Consensus size: 11
573673 AATTATAATT
573683 AATAATATAAA
1 AATAATATAAA
573694 AATAATATAAA
1 AATAATATAAA
*
573705 CATAATATTTATAA
1 AATAATA--TA-AA
*
573719 AA-AATTTTAAA
1 AATAA-TATAAA
573730 ATATAATATAAA
1 A-ATAATATAAA
573742 AATAATATA
1 AATAATATA
573751 TATGATACGA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 28 0.60
12 9 0.19
13 6 0.13
14 4 0.09
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATATAAA
Found at i:573792 original size:22 final size:22
Alignment explanation
Indices: 573767--573846 Score: 72
Period size: 22 Copynumber: 3.4 Consensus size: 22
573757 ACGAATATAT
*
573767 ATATAAATAAAATAAAATATTA
1 ATATAAATAAAATAAAATAATA
* *
573789 ATATAAA-AAAATTTATATAATA
1 ATATAAATAAAA-TAAAATAATA
573811 ATATAATATTTTAAATATAAAATAATA
1 ATATAA-A---TAAA-ATAAAATAATA
573838 ATATAAATA
1 ATATAAATA
573847 TCAACATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
21 4 0.09
22 20 0.43
23 3 0.07
26 1 0.02
27 17 0.37
28 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAAATAAAATAAAATAATA
Found at i:573830 original size:19 final size:19
Alignment explanation
Indices: 573760--573847 Score: 67
Period size: 18 Copynumber: 4.7 Consensus size: 19
573750 ATATGATACG
573760 AATATATATATAA-ATAAAAT
1 AATA-ATATA-AATATAAAAT
* *
573780 AA-AATATTAATATAAAAA
1 AATAATATAAATATAAAAT
* * *
573798 AAT-TTATATA-ATAATAT
1 AATAATATAAATATAAAAT
* *
573815 AATATTTTAAATATAAAAT
1 AATAATATAAATATAAAAT
573834 AATAATATAAATAT
1 AATAATATAAATAT
573848 CAACATATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 9
0.71 0.16 0.12
Matches are distributed among these distances:
17 10 0.19
18 21 0.40
19 19 0.37
20 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATAATATAAATATAAAAT
Found at i:573855 original size:27 final size:27
Alignment explanation
Indices: 573805--573858 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
573795 AAAAATTTAT
* *
573805 ATAATAATATAATATTTTAAATATAAA
1 ATAATAATATAATATATCAAATATAAA
573832 ATAATAATATAA-ATATCAACATATAAA
1 ATAATAATATAATATATCAA-ATATAAA
573859 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAATAATATAATATATCAAATATAAA
Found at i:574126 original size:24 final size:24
Alignment explanation
Indices: 574099--574174 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
574089 GTAATTTGAT
*
574099 TAAATTTTTATTAATATTTAATAA
1 TAAATATTTATTAATATTTAATAA
574123 TAAATATTTATTTAA-ATTTAATTATA
1 TAAATATTTA-TTAATATTTAA-TA-A
* *
574149 TAAATATATATAAATA-TTAAT-A
1 TAAATATTTATTAATATTTAATAA
574171 TAAA
1 TAAA
574175 ATAATTTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 5 0.11
24 16 0.36
25 13 0.29
26 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAAATATTTATTAATATTTAATAA
Found at i:574186 original size:24 final size:25
Alignment explanation
Indices: 574101--574195 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 25
574091 AATTTGATTA
574101 AATTTTTATTAATATTTAATA-ATAAAT
1 AATTTTTA--AATA-TTAATATATAAAT
*
574128 ATTTATTTAAAT-TTAATTATATAAAT
1 AATT-TTTAAATATTAA-TATATAAAT
* *
574154 -ATATATAAATATTAATATA-AAAT
1 AATTTTTAAATATTAATATATAAAT
*
574177 AATTTTTAAAATTTTAATA
1 AATTTTT-AAATATTAATA
574196 GTATTTAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
23 4 0.07
24 18 0.33
25 17 0.31
26 9 0.16
27 3 0.05
28 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTTTTAAATATTAATATATAAAT
Found at i:576985 original size:29 final size:28
Alignment explanation
Indices: 576947--577002 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
576937 ACTTTGTAAG
*
576947 AAAAATCAATGAAATTAAAAGTATAATAAT
1 AAAAATCAATAAAATT--AAGTATAATAAT
576977 AAAAA-CAATAAAATTAAGTATAATAA
1 AAAAATCAATAAAATTAAGTATAATAA
577003 CATTGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 11 0.44
29 9 0.36
30 5 0.20
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAAATCAATAAAATTAAGTATAATAAT
Found at i:581130 original size:25 final size:25
Alignment explanation
Indices: 581081--581128 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
581071 TAAAAATTTA
*
581081 TTTTTATTTAATTTAATTATTAAAT
1 TTTTTATTTAATTCAATTATTAAAT
*
581106 TTTTTATTTTATTCAATT-TTAAA
1 TTTTTATTTAATTCAATTATTAAA
581129 ATAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATTTAATTCAATTATTAAAT
Found at i:581830 original size:28 final size:29
Alignment explanation
Indices: 581799--581861 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
581789 TTTTTTCAGT
581799 TCATGTCGTGTTAAT-ATTATTTTT-TATG
1 TCATGTCGTGTT-ATGATTATTTTTCTATG
* * *
581827 TCATATTGTGTTTTGATTATTTTTCTATG
1 TCATGTCGTGTTATGATTATTTTTCTATG
*
581856 TTATGT
1 TCATGT
581862 TTGTGATGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.04
28 19 0.68
29 8 0.29
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.60
Consensus pattern (29 bp):
TCATGTCGTGTTATGATTATTTTTCTATG
Found at i:590853 original size:17 final size:17
Alignment explanation
Indices: 590798--590878 Score: 60
Period size: 17 Copynumber: 4.8 Consensus size: 17
590788 ATTTAATATA
590798 TTTTATATTCATATAAATT
1 TTTTATATT-ATAT-AATT
* *
590817 TTTTATA-CAT-TAATA
1 TTTTATATTATATAATT
*
590832 ATTTATATTATATAATT
1 TTTTATATTATATAATT
* *
590849 TTTTAAATTAT-TTATAT
1 TTTTATATTATATAAT-T
*
590866 ATTTATATTATAT
1 TTTTATATTATAT
590879 TTTAATTATT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
15 9 0.19
16 6 0.12
17 25 0.52
18 1 0.02
19 7 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTATATTATATAATT
Found at i:590870 original size:34 final size:34
Alignment explanation
Indices: 590787--590878 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 34
590777 ATTATAATAG
*
590787 TATTTAATATATTTTATATTCATATAAATTTTTTATA
1 TATTT-ATATA-TTTATATT-ATATAAATTTTTTAAA
* *
590824 CATTAATA-ATTTATATTATAT-AATTTTTTAAA
1 TATTTATATATTTATATTATATAAATTTTTTAAA
590856 TTATTTATATATTTATATTATAT
1 -TATTTATATATTTATATTATAT
590879 TTTAATTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
32 10 0.21
33 10 0.21
34 21 0.44
35 1 0.02
36 3 0.06
37 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (34 bp):
TATTTATATATTTATATTATATAAATTTTTTAAA
Found at i:592722 original size:17 final size:17
Alignment explanation
Indices: 592689--592734 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
592679 TTAAATATAA
592689 TATATTAATATTTTATT
1 TATATTAATATTTTATT
592706 TATA-TAAT-TTTTATAT
1 TATATTAATATTTTAT-T
592722 TATAATT-ATATTT
1 TAT-ATTAATATTT
592735 AAAATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 7 0.28
18 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATTAATATTTTATT
Found at i:592740 original size:26 final size:28
Alignment explanation
Indices: 592688--592748 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
592678 ATTAAATATA
*
592688 ATATATTAATATTTTATTTATATAATTT
1 ATATATTAATATTATATTTATATAATTT
*
592716 TTATATT-ATAATTATATTTA-A-AATTT
1 ATATATTAAT-ATTATATTTATATAATTT
592742 ATATATT
1 ATATATT
592749 TAGATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 11 0.38
27 3 0.10
28 15 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATATTAATATTATATTTATATAATTT
Found at i:592743 original size:19 final size:18
Alignment explanation
Indices: 592721--592776 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
592711 AATTTTTATA
592721 TTATAATTATATTTAAAAT
1 TTATAATTATA-TTAAAAT
*
592740 TTATATATT-TAGATAAAAT
1 TTATA-ATTATA-TTAAAAT
592759 TT-TAA-TATATTAAAAT
1 TTATAATTATATTAAAAT
592775 TT
1 TT
592777 TTTATTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 9 0.28
17 3 0.09
18 2 0.06
19 15 0.47
20 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATAATTATATTAAAAT
Found at i:592843 original size:18 final size:19
Alignment explanation
Indices: 592801--592850 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
592791 AATATCGATA
592801 TAATATTAT-TTTATATAT
1 TAATATTATATTTATATAT
592819 TAATATTATATTTATAT-T
1 TAATATTATATTTATATAT
**
592837 TTTTATTATATTTA
1 TAATATTATATTTA
592851 GATAAGATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATATTATATTTATATAT
Found at i:594233 original size:2 final size:2
Alignment explanation
Indices: 594226--594253 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
594216 GGGATTTAAT
594226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
594254 AAAGATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:594667 original size:22 final size:23
Alignment explanation
Indices: 594642--594695 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
594632 AAAATTATGA
*
594642 ATATTGAAATTTAA-TTTTAAAT-
1 ATATT-AAATATAACTTTTAAATC
*
594664 ATATTAAATATAACTTTTCAATC
1 ATATTAAATATAACTTTTAAATC
*
594687 ATATAAAAT
1 ATATTAAAT
594696 TTTAAATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.26
22 12 0.44
23 8 0.30
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATTAAATATAACTTTTAAATC
Found at i:596015 original size:21 final size:21
Alignment explanation
Indices: 595958--596015 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
595948 TAATATTTAA
*
595958 TAAATCTAAATTTAAAAATTT
1 TAAATCTAAATTTATAAATTT
* *
595979 TTAATCTTAATATTATAAA-TT
1 TAAATCTAAAT-TTATAAATTT
596000 TAAATCTCAAATTTAT
1 TAAATCT-AAATTTAT
596016 TAGATATGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAATCTAAATTTATAAATTT
Found at i:596760 original size:18 final size:17
Alignment explanation
Indices: 596729--596772 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
596719 ATTTATATTT
*
596729 AAAATATTATATATTTATA
1 AAAAT-TTAAATATTT-TA
596748 AAAATTTAAATATTTTA
1 AAAATTTAAATATTTTA
*
596765 ATAATTTA
1 AAAATTTA
596773 TTTATATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 9 0.39
18 9 0.39
19 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATTTAAATATTTTA
Found at i:596782 original size:25 final size:25
Alignment explanation
Indices: 596756--596837 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
596746 TAAAAATTTA
*
596756 AATATTTTAATAATTTATT-TATAT
1 AATATTTTAATAATTTTTTATATAT
* *
596780 AA-ATTTAAATAAATTCATGTTTTTATAT
1 AATATTTTAAT-AATT--T-TTTATATAT
*
596808 AATATTTTAATTATTTTTTATATAT
1 AATATTTTAATAATTTTTTATATAT
596833 AATAT
1 AATAT
596838 AATTATATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 7 0.15
24 6 0.13
25 13 0.28
26 2 0.04
27 2 0.04
28 10 0.21
29 7 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (25 bp):
AATATTTTAATAATTTTTTATATAT
Found at i:596829 original size:23 final size:23
Alignment explanation
Indices: 596756--596831 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
596746 TAAAAATTTA
*
596756 AATATTTTAATAATTTATTTATAT
1 AATATTTTAATTATTT-TTTATAT
596780 AA-ATTTAAATAAATTCATGTTTTTATAT
1 AATATTT---T-AATT-AT-TTTTTATAT
596808 AATATTTTAATTATTTTTTATAT
1 AATATTTTAATTATTTTTTATAT
596831 A
1 A
596832 TAATATAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
23 14 0.32
24 4 0.09
25 4 0.09
26 2 0.05
27 3 0.07
28 11 0.25
29 6 0.14
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (23 bp):
AATATTTTAATTATTTTTTATAT
Found at i:596840 original size:22 final size:23
Alignment explanation
Indices: 596799--596843 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
596789 TAAATTCATG
* *
596799 TTTTTATATAATATTTTAATTAT
1 TTTTTATATAATAATATAATTAT
596822 TTTTTATAT-ATAATATAATTAT
1 TTTTTATATAATAATATAATTAT
596844 ATTATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTTATATAATAATATAATTAT
Found at i:596851 original size:25 final size:25
Alignment explanation
Indices: 596694--596852 Score: 68
Period size: 25 Copynumber: 6.6 Consensus size: 25
596684 AAATTTTATC
*
596694 AATTATATTATTTT-TATATATTAT
1 AATTATATTATTTTATATATAATAT
* * *
596718 AATT-TA-TATTTAAAATATTATAT
1 AATTATATTATTTTATATATAATAT
* ** * * *
596741 ATTTATAAAAATTTA-A-ATATTTT
1 AATTATATTATTTTATATATAATAT
* *
596764 AATAAT-TTA-TTTATATA-AATTT
1 AATTATATTATTTTATATATAATAT
* * *
596786 AAATAAATTCATGTTTTTATATAATAT
1 AATTATATT-AT-TTTATATATAATAT
*
596813 -TTTA-ATTATTTTTTATATATAATAT
1 AATTATATTA--TTTTATATATAATAT
596838 AATTATATTATTTTA
1 AATTATATTATTTTA
596853 AAAATTATTA
Statistics
Matches: 96, Mismatches: 25, Indels: 27
0.65 0.17 0.18
Matches are distributed among these distances:
21 4 0.04
22 14 0.15
23 23 0.24
24 9 0.09
25 25 0.26
26 13 0.14
27 8 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (25 bp):
AATTATATTATTTTATATATAATAT
Found at i:597236 original size:27 final size:29
Alignment explanation
Indices: 597206--597272 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
597196 ATTTCAAACT
597206 TATTATATTTAATACT-AA-TT-TTTATAA
1 TATTATATTTAATA-TAAATTTATTTATAA
*
597233 TATTATATTAAATATAAATTTATTTATAA
1 TATTATATTTAATATAAATTTATTTATAA
597262 -ATTATAATTTA
1 TATTAT-ATTTA
597273 TAATATATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 1 0.03
27 15 0.44
28 7 0.21
29 11 0.32
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTATATTTAATATAAATTTATTTATAA
Found at i:597270 original size:18 final size:17
Alignment explanation
Indices: 597227--597274 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
597217 ATACTAATTT
597227 TTATAATATTATATTAAA
1 TTATAAT-TTATATTAAA
*
597245 -TATAAATTTATTTATAAA
1 TTAT-AATTTATAT-TAAA
597263 TTATAATTTATA
1 TTATAATTTATA
597275 ATATATCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 8 0.32
18 14 0.56
19 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTATAATTTATATTAAA
Found at i:598319 original size:20 final size:19
Alignment explanation
Indices: 598282--598320 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
598272 TGATTTCATA
* *
598282 TTTATATTATTTTTTATTT
1 TTTATATTATATTATATTT
598301 TTTATAATTATATTATATTT
1 TTTAT-ATTATATTATATTT
598321 AAATTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATATTATATTATATTT
Found at i:598898 original size:13 final size:13
Alignment explanation
Indices: 598880--598920 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
598870 TATTATATTA
598880 TTATTTTAAATAT
1 TTATTTTAAATAT
*
598893 TTATTTT-AATAA
1 TTATTTTAAATAT
598905 TT-TTTTAAATTAT
1 TTATTTTAAA-TAT
598918 TTA
1 TTA
598921 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 8 0.35
13 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTTTAAATAT
Found at i:599495 original size:24 final size:24
Alignment explanation
Indices: 599465--599511 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
599455 TTGATTGGAA
599465 ATATTATATGTTA-ATTATATTTAT
1 ATATTATAT-TTATATTATATTTAT
599489 ATATTATATTTATATTATATTTA
1 ATATTATATTTATATTATATTTA
599512 AAATTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATATTATATTTATATTATATTTAT
Found at i:599496 original size:13 final size:12
Alignment explanation
Indices: 599465--599510 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
599455 TTGATTGGAA
*
599465 ATATTATATGTT
1 ATATTATATTTT
599477 A-ATTATATTTAT
1 ATATTATATTT-T
599489 ATATTATA-TTT
1 ATATTATATTTT
599500 ATATTATATTT
1 ATATTATATTT
599511 AAAATTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 17 0.57
12 7 0.23
13 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:600404 original size:5 final size:5
Alignment explanation
Indices: 600396--600428 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
600386 TGGGTTTTTT
600396 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
600429 TTTTTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:600835 original size:15 final size:14
Alignment explanation
Indices: 600799--600843 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
600789 GATAAAAAAT
600799 AATTTAAATTTAAA
1 AATTTAAATTTAAA
*
600813 AGAATTAAATTTAATA
1 A-ATTTAAATTTAA-A
600829 AATTTAAATATTAAA
1 AATTTAAAT-TTAAA
600844 TTTAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 19 0.73
16 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AATTTAAATTTAAA
Found at i:600844 original size:22 final size:22
Alignment explanation
Indices: 600816--600866 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
600806 ATTTAAAAGA
600816 ATTAAATTTAATAAATTTAAAT
1 ATTAAATTTAATAAATTTAAAT
*
600838 ATTAAATTTAATTAATTTAAAT
1 ATTAAATTTAATAAATTTAAAT
*
600860 TTTAAAT
1 ATTAAAT
600867 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAAATTTAATAAATTTAAAT
Found at i:600869 original size:16 final size:16
Alignment explanation
Indices: 600795--600873 Score: 63
Period size: 16 Copynumber: 4.7 Consensus size: 16
600785 AATCGATAAA
*
600795 AAATAATTTAAATTTA
1 AAATAATTTAAATTTT
*
600811 AAAGAA-TTAAATTTAAT
1 AAATAATTTAAATTT--T
600828 AAATTTAAATATTAAA-TTT
1 AAA--T-AAT-TTAAATTTT
*
600847 AATTAATTTAAATTTT
1 AAATAATTTAAATTTT
600863 AAATAATTTAA
1 AAATAATTTAA
600874 TAACTAAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
15 13 0.26
16 21 0.42
17 4 0.08
19 3 0.06
20 2 0.04
21 2 0.04
22 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (16 bp):
AAATAATTTAAATTTT
Found at i:602018 original size:19 final size:19
Alignment explanation
Indices: 601991--602044 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 19
601981 TAATAATTAT
* * *
601991 TTTATTTATATTATTTAAA
1 TTTAATTATAATATATAAA
602010 TTTAATTATAATATATAAA
1 TTTAATTATAATATATAAA
* *
602029 ATTAA-TATAAAATATA
1 TTTAATTATAATATATA
602045 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATTATAATATATAAA
Found at i:602030 original size:20 final size:18
Alignment explanation
Indices: 602006--602044 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
601996 TTATATTATT
* *
602006 TAAATTTAATTATAATATA
1 TAAAATTAA-TATAAAATA
602025 TAAAATTAATATAAAATA
1 TAAAATTAATATAAAATA
602043 TA
1 TA
602045 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATTAATATAAAATA
Found at i:602281 original size:24 final size:24
Alignment explanation
Indices: 602244--602291 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
602234 TTTATATATT
602244 TATATTATTAAATTT-AAATAAAA
1 TATATTATTAAATTTGAAATAAAA
* *
602267 TATATTTATTTAATTTGAATTAAAA
1 TATA-TTATTAAATTTGAAATAAAA
602292 AAAATTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TATATTATTAAATTTGAAATAAAA
Found at i:602951 original size:12 final size:12
Alignment explanation
Indices: 602934--602964 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
602924 CTCCGAGCGC
602934 GCGAGAGAGAGA
1 GCGAGAGAGAGA
602946 GCGAGAGAGAGA
1 GCGAGAGAGAGA
*
602958 GAGAGAG
1 GCGAGAG
602965 TTGGTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.52, T:0.00
Consensus pattern (12 bp):
GCGAGAGAGAGA
Found at i:608363 original size:20 final size:20
Alignment explanation
Indices: 608338--608375 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
608328 AAAATTGTGG
*
608338 AAGTTAGTGAAAACTATTGT
1 AAGTTAGTGAAAAATATTGT
608358 AAGTTAGTGAAAAATATT
1 AAGTTAGTGAAAAATATT
608376 ATTTCGGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (20 bp):
AAGTTAGTGAAAAATATTGT
Found at i:608485 original size:2 final size:2
Alignment explanation
Indices: 608478--608507 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
608468 TCCATCGGAA
608478 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
608508 GTGCTTATTC
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:608965 original size:16 final size:17
Alignment explanation
Indices: 608936--608968 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
608926 CAACGGTATT
*
608936 TTAAAAAATTTTATATA
1 TTAAAAAATATTATATA
608953 TTAAAAAA-ATTATATA
1 TTAAAAAATATTATATA
608969 AATATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAAAAATATTATATA
Found at i:608990 original size:20 final size:19
Alignment explanation
Indices: 608938--608990 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
608928 ACGGTATTTT
*
608938 AAAAAAT-TTTATATATTA
1 AAAAAATATTTAAATATTA
*
608956 AAAAAATTATATAAATATTA
1 AAAAAA-TATTTAAATATTA
*
608976 ATATAAATATTTAAA
1 A-AAAAATATTTAAA
608991 AAATAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 1 0.04
20 17 0.61
21 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAAATATTTAAATATTA
Found at i:613305 original size:2 final size:2
Alignment explanation
Indices: 613298--613328 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
613288 TAGCTTTGAA
613298 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
613329 AGAAGAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:614144 original size:22 final size:22
Alignment explanation
Indices: 614114--614162 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
614104 TCAAAATATA
*
614114 TTAAAATATTTT-TATATTAATT
1 TTAAAATATTTTATA-ATTAAAT
*
614136 TTAATATATTTTATAATTAAAT
1 TTAAAATATTTTATAATTAAAT
614158 TTAAA
1 TTAAA
614163 TAAAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAAATATTTTATAATTAAAT
Found at i:615648 original size:32 final size:29
Alignment explanation
Indices: 615603--615666 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
615593 ATCATAAATA
* *
615603 TAAAAATAAAAATAATTTTTTAATATTATTT
1 TAAAAATAAAAATAA-ATTTTAA-ATTAGTT
*
615634 TAAATAATACAAATAAATTTTAAATTAGTT
1 TAAA-AATAAAAATAAATTTTAAATTAGTT
615664 TAA
1 TAA
615667 CCCATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.31
31 10 0.34
32 10 0.34
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TAAAAATAAAAATAAATTTTAAATTAGTT
Found at i:616321 original size:16 final size:17
Alignment explanation
Indices: 616297--616330 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
616287 ATTTAATATA
616297 ATAAAAAAT-ATTTATT
1 ATAAAAAATGATTTATT
*
616313 ATAATAAATGATTTATT
1 ATAAAAAATGATTTATT
616330 A
1 A
616331 ATTCATTTTA
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:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATAAAAAATGATTTATT
Found at i:616491 original size:32 final size:33
Alignment explanation
Indices: 616430--616500 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
616420 AATTACTAAA
*
616430 ATATAATATTAATATATAAATATATTAAAATTT
1 ATATAATATAAATATATAAATATATTAAAATTT
*
616463 ATATAATATAAATA-ATTAATATGA-TAAAATTT
1 ATATAATATAAATATATAAATAT-ATTAAAATTT
616495 ATATAA
1 ATATAA
616501 AAATATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 21 0.60
33 14 0.40
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAATTT
Found at i:616709 original size:23 final size:24
Alignment explanation
Indices: 616675--616724 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
616665 TCAGCCTCAC
*
616675 TATTTTTTTATA-TAAAAATTTTA
1 TATTTTTATATATTAAAAATTTTA
*
616698 TATTTTTATATATTATAAATTTTA
1 TATTTTTATATATTAAAAATTTTA
616722 TAT
1 TAT
616725 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTTTTATATATTAAAAATTTTA
Found at i:617412 original size:21 final size:22
Alignment explanation
Indices: 617373--617425 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
617363 AATATTTTTG
* *
617373 AATTAAAATAATATTTAAATA-T
1 AATTATAA-AATATATAAATATT
617395 AATTATAAAATATATAAATATT
1 AATTATAAAATATATAAATATT
617417 AA-TATAAAA
1 AATTATAAAA
617426 ATAATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTATAAAATATATAAATATT
Found at i:618120 original size:2 final size:2
Alignment explanation
Indices: 618113--618200 Score: 117
Period size: 2 Copynumber: 45.0 Consensus size: 2
618103 TCTATAATTT
* * * * *
618113 TA TA TA TA TA TA TT TA TA TA TA TG TT TC TA GA -A T- 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
618153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
618195 TA TA TA
1 TA TA TA
618201 GAAGGAGACA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
1 2 0.03
2 75 0.97
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:618473 original size:10 final size:9
Alignment explanation
Indices: 618458--618581 Score: 59
Period size: 8 Copynumber: 13.8 Consensus size: 9
618448 TGTTCATTTA
618458 ATTAAATAAT
1 ATTAAAT-AT
618468 ATTAAATAT
1 ATTAAATAT
618477 ATTATAATTAT
1 ATTA-AA-TAT
*
618488 AATATAAAAAT
1 -AT-TAAATAT
618499 A-TAAATAT
1 ATTAAATAT
*
618507 -TTTAA-AT
1 ATTAAATAT
*
618514 -TTATATA-
1 ATTAAATAT
618521 ATTAAA-AT
1 ATTAAATAT
618529 ATT-AATAT
1 ATTAAATAT
*
618537 ATTAAAATTT
1 ATT-AAATAT
618547 ATATAAATAT
1 AT-TAAATAT
*
618557 AAAATAAAT-T
1 --ATTAAATAT
618567 ATTAAAT-T
1 ATTAAATAT
618575 ATTAAAT
1 ATTAAAT
618582 TTAATTTTAT
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
7 8 0.09
8 36 0.40
9 6 0.07
10 22 0.24
11 11 0.12
12 5 0.06
13 2 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTAAATAT
Found at i:618493 original size:11 final size:11
Alignment explanation
Indices: 618463--618565 Score: 51
Period size: 11 Copynumber: 10.0 Consensus size: 11
618453 ATTTAATTAA
618463 ATAATATTAAAT
1 ATAATA-TAAAT
* *
618475 ATATTATAATT
1 ATAATATAAAT
618486 ATAATAT-AA-
1 ATAATATAAAT
618495 A-AATATAAAT
1 ATAATATAAAT
*
618505 AT--TTTAAAT
1 ATAATATAAAT
* *
618514 -TTATATAATT
1 ATAATATAAAT
* *
618524 AAAATATTAAT
1 ATAATATAAAT
*
618535 ATATTA-AAAT
1 ATAATATAAAT
*
618545 -TTATATAAAT
1 ATAATATAAAT
*
618555 ATAAAATAAAT
1 ATAATATAAAT
618566 TATTAAATTA
Statistics
Matches: 65, Mismatches: 18, Indels: 17
0.65 0.18 0.17
Matches are distributed among these distances:
8 6 0.09
9 12 0.18
10 14 0.22
11 28 0.43
12 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:618504 original size:30 final size:29
Alignment explanation
Indices: 618453--618568 Score: 105
Period size: 30 Copynumber: 4.0 Consensus size: 29
618443 CTTAATGTTC
618453 ATTTAAT-TAAATAATATTAAATATATTATA
1 ATTTAATATAAA-AATA-TAAATATATTATA
*
618483 ATTATAATATAAAAATATAAATATTTTA-A
1 ATT-TAATATAAAAATATAAATATATTATA
* * *
618512 ATTTATATAATTAAAATATTAATATATTAAA
1 ATTTA-AT-ATAAAAATATAAATATATTATA
* *
618543 ATTT-ATATAAATATA-AAATAAATTAT
1 ATTTAATATAAAAATATAAATATATTAT
618569 TAAATTATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
27 8 0.11
28 9 0.12
29 8 0.11
30 30 0.42
31 13 0.18
32 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTTAATATAAAAATATAAATATATTATA
Found at i:618781 original size:23 final size:21
Alignment explanation
Indices: 618755--618809 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 21
618745 TTTTAAATTT
*
618755 TTATTAATAAATATTTTATAAAA
1 TTATTAATAAATAATTTAT--AA
618778 TTATTATATTAAATAATTTATAA
1 TTATTA-A-TAAATAATTTATAA
618801 TTATTAATA
1 TTATTAATA
618810 TATTTAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 2 0.07
22 1 0.03
23 14 0.48
24 1 0.03
25 11 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTAATAAATAATTTATAA
Found at i:618790 original size:25 final size:25
Alignment explanation
Indices: 618740--618819 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 25
618730 ATATTATTCT
* * *
618740 ATATTTT-TTAAATTTTTATTAATAA
1 ATATTTTATAAAATTATTA-TATTAA
618765 ATATTTTATAAAATTATTATATTAA
1 ATATTTTATAAAATTATTATATTAA
* * * *
618790 ATAATTTATAATTATTAATATATTTA
1 ATATTTTATAA-AATTATTATATTAA
618816 ATAT
1 ATAT
618820 AACATATTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
25 22 0.49
26 23 0.51
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTTTATAAAATTATTATATTAA
Found at i:618840 original size:12 final size:12
Alignment explanation
Indices: 618796--618842 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
618786 TTAAATAATT
*
618796 TATAATTATTAA
1 TATAAATATTAA
618808 TAT--AT-TTAA
1 TATAAATATTAA
618817 TATAACATATTAA
1 TATAA-ATATTAA
618830 TATAAATATTAA
1 TATAAATATTAA
618842 T
1 T
618843 TTAATTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
9 7 0.23
10 1 0.03
12 13 0.43
13 9 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TATAAATATTAA
Found at i:637040 original size:20 final size:20
Alignment explanation
Indices: 636999--637041 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
636989 TAAGTATTTT
* * *
636999 TTAAAAAATTTGTTACATAC
1 TTAAAAAATTTATTAAAAAC
637019 TTAAAAAATTTATTAAAAAC
1 TTAAAAAATTTATTAAAAAC
637039 TTA
1 TTA
637042 TATTTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAAAAAATTTATTAAAAAC
Found at i:638436 original size:2 final size:2
Alignment explanation
Indices: 638431--638455 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
638421 ATATATAGAT
638431 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
638456 ATTTTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:638959 original size:14 final size:15
Alignment explanation
Indices: 638921--638960 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
638911 GTTAATACAT
*
638921 AATTAAAAATCATTAA
1 AATT-AAAATAATTAA
638937 AATTAAAATAATTAA
1 AATTAAAATAATTAA
638952 AA-TAAAATA
1 AATTAAAATA
638961 TATTTACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 12 0.52
16 4 0.17
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AATTAAAATAATTAA
Found at i:639061 original size:16 final size:18
Alignment explanation
Indices: 639040--639078 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
639030 GTTAACAAAT
*
639040 AAATATA-TCAAATA-TA
1 AAATATATTAAAATATTA
639056 AAATATATTAAAATATTA
1 AAATATATTAAAATATTA
639074 AAATA
1 AAATA
639079 AATACAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 6 0.30
18 7 0.35
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATATTAAAATATTA
Found at i:640164 original size:18 final size:18
Alignment explanation
Indices: 640111--640166 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
640101 TCATAATATG
*
640111 AATAAAATATATTTAAATA
1 AATAAAA-AAATTTAAATA
*
640130 AATAAAAAAATTCAAATA
1 AATAAAAAAATTTAAATA
* *
640148 ACA-AAACACATTTAAATA
1 A-ATAAAAAAATTTAAATA
640166 A
1 A
640167 GATATATATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 23 0.74
19 8 0.26
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (18 bp):
AATAAAAAAATTTAAATA
Found at i:642781 original size:20 final size:20
Alignment explanation
Indices: 642750--642815 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
642740 AATGGAAAAG
642750 AAAGAGTCTAAAGCTGATAAC
1 AAAGA-TCTAAAGCTGATAAC
642771 AAAGATCTAAA---G--AA-
1 AAAGATCTAAAGCTGATAAC
*
642785 AGAG-TCTAAAGCTGATAAC
1 AAAGATCTAAAGCTGATAAC
642804 AAAGATCTAAAG
1 AAAGATCTAAAG
642816 AAATCTCCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 15
0.68 0.04 0.28
Matches are distributed among these distances:
13 6 0.17
14 3 0.08
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 3 0.08
20 13 0.36
21 5 0.14
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAGATCTAAAGCTGATAAC
Found at i:642783 original size:33 final size:33
Alignment explanation
Indices: 642746--642818 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
642736 TGAAAATGGA
642746 AAAGAAAGAGTCTAAAGCTGATAACAAAGATCT
1 AAAGAAAGAGTCTAAAGCTGATAACAAAGATCT
642779 AAAGAAAGAGTCTAAAGCTGATAACAAAGATCT
1 AAAGAAAGAGTCTAAAGCTGATAACAAAGATCT
642812 AAAGAAA
1 AAAGAAA
642819 TCTCCTGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.55, C:0.11, G:0.18, T:0.16
Consensus pattern (33 bp):
AAAGAAAGAGTCTAAAGCTGATAACAAAGATCT
Found at i:645084 original size:25 final size:25
Alignment explanation
Indices: 645055--645107 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
645045 TTTTGATAAT
*
645055 TAATATTTGTTATA-ATTAATTAAAA
1 TAATATTTATTATATA-TAATTAAAA
*
645080 TAATATTTATTATATATAATTATAA
1 TAATATTTATTATATATAATTAAAA
645105 TAA
1 TAA
645108 ATAAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATATTTATTATATATAATTAAAA
Found at i:646866 original size:2 final size:2
Alignment explanation
Indices: 646861--646886 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
646851 CAGGCCCCCC
646861 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
646887 GAGAGCTAAA
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:649340 original size:25 final size:21
Alignment explanation
Indices: 649289--649335 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
649279 GATAAGTTTG
649289 ATTTAAAAAATTATTTTTTTA
1 ATTTAAAAAATTATTTTTTTA
* *
649310 ATTTAAATAA-TATATTTTT-
1 ATTTAAAAAATTATTTTTTTA
649329 ATTTAAA
1 ATTTAAA
649336 TTTAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 8 0.33
21 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAAAAATTATTTTTTTA
Found at i:655023 original size:15 final size:14
Alignment explanation
Indices: 655002--655040 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
654992 CTTTGGAGAG
655002 TCATACTGCTTTGA
1 TCATACTGCTTTGA
655016 TACATACTGCTTTGA
1 T-CATACTGCTTTGA
655031 T-ATACTGCTT
1 TCATACTGCTT
655041 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 14 0.58
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (14 bp):
TCATACTGCTTTGA
Found at i:661738 original size:18 final size:19
Alignment explanation
Indices: 661692--661743 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
661682 TGTAAGTTGG
*
661692 AATATATTATTTATTCTATT
1 AATAT-TTATTTATTATATT
* *
661712 AAAAATTATTT-TTATATT
1 AATATTTATTTATTATATT
*
661730 AATATTTATATATT
1 AATATTTATTTATT
661744 TTATAATTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
18 14 0.56
19 8 0.32
20 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
AATATTTATTTATTATATT
Found at i:661764 original size:22 final size:21
Alignment explanation
Indices: 661721--661760 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
661711 TAAAAATTAT
*
661721 TTTTATATTAATATTTATATA
1 TTTTATATTAATATTTAAATA
661742 TTTTATAATTAA-ATTTAAA
1 TTTTAT-ATTAATATTTAAA
661761 ATATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATATTAATATTTAAATA
Found at i:667091 original size:13 final size:13
Alignment explanation
Indices: 667075--667118 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
667065 ATATAATTAC
667075 ATAATATTAAAAA
1 ATAATATTAAAAA
*
667088 ATAA-ATTAAAAT
1 ATAATATTAAAAA
*
667100 ATAATATGAAAAA
1 ATAATATTAAAAA
667113 ATAATA
1 ATAATA
667119 AATACATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAATATTAAAAA
Found at i:667138 original size:8 final size:8
Alignment explanation
Indices: 667127--667258 Score: 55
Period size: 8 Copynumber: 16.0 Consensus size: 8
667117 TAAATACATA
667127 ATATAAAT
1 ATATAAAT
667135 ATATAAAT
1 ATATAAAT
*
667143 ATTTACAA-
1 ATATA-AAT
* *
667151 ATTTATAT
1 ATATAAAT
667159 ATTATAAAT
1 A-TATAAAT
667168 -TATTAAA-
1 ATA-TAAAT
667175 ATAATAAAATTT
1 AT-AT-AAA--T
667187 ATATAAAT
1 ATATAAAT
667195 ATA-AAAT
1 ATATAAAT
*
667202 ATTTTAAAT
1 A-TATAAAT
667211 ATAATTATAAT
1 AT-A-TA-AAT
667222 ATAATAAA-
1 AT-ATAAAT
*
667230 ATAT-ATT
1 ATATAAAT
667237 A-ATAAA-
1 ATATAAAT
667243 ATATAAAT
1 ATATAAAT
667251 ATATAAAT
1 ATATAAAT
667259 TATTATATCT
Statistics
Matches: 97, Mismatches: 8, Indels: 38
0.68 0.06 0.27
Matches are distributed among these distances:
6 4 0.04
7 17 0.18
8 40 0.41
9 18 0.19
10 7 0.07
11 9 0.09
12 2 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Done.