Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 5 of 21
Found at i:621613 original size:18 final size:18
Alignment explanation
Indices: 621545--621617 Score: 76
Period size: 18 Copynumber: 3.9 Consensus size: 18
621535 GAACGTATTT
621545 TAAATATAATTATAATTAA
1 TAAATATAATTATAA-TAA
*
621564 TTATAATAAATATTATAA-AA
1 -TA-AATATA-ATTATAATAA
*
621584 TAATTATAATTATAATAA
1 TAAATATAATTATAATAA
*
621602 TAAATATGATTATAAT
1 TAAATATAATTATAAT
621618 TAATTTTGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
17 7 0.16
18 20 0.44
19 2 0.04
20 4 0.09
21 5 0.11
22 7 0.16
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATATAATTATAATAA
Found at i:623040 original size:16 final size:16
Alignment explanation
Indices: 623021--623070 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
623011 AATTTTTTAT
623021 TAATTAAATAATAATA
1 TAATTAAATAATAATA
623037 TAATTAAATTAA-AAT-
1 TAATTAAA-TAATAATA
*
623052 T-ATTAAATATTAAATA
1 TAATTAAATAAT-AATA
623068 TAA
1 TAA
623071 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
13 2 0.07
14 6 0.21
15 4 0.14
16 12 0.43
17 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATTAAATAATAATA
Found at i:630148 original size:26 final size:26
Alignment explanation
Indices: 630119--630170 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
630109 ATATGCAAAG
630119 TGTACAAAAGAAATCACTTAATTCTA
1 TGTACAAAAGAAATCACTTAATTCTA
630145 TGTACAAAAGAAATCACTTAATTCTA
1 TGTACAAAAGAAATCACTTAATTCTA
630171 CTTGGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (26 bp):
TGTACAAAAGAAATCACTTAATTCTA
Found at i:633370 original size:12 final size:12
Alignment explanation
Indices: 633355--633412 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
633345 TGATCTCAAA
*
633355 ATTTATTTTATT
1 ATTTATTATATT
633367 ATTTATTATATT
1 ATTTATTATATT
**
633379 A-TTAAAATATT
1 ATTTATTATATT
633390 ATTT-TTATATT
1 ATTTATTATATT
633401 AATTT-TTATATT
1 -ATTTATTATATT
633413 TTATAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
11 14 0.36
12 25 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:637685 original size:17 final size:16
Alignment explanation
Indices: 637647--637696 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
637637 AAATATTTTA
637647 AAATTTA-TATAATAT
1 AAATTTATTATAATAT
*
637662 AAA-TTATTATCATATT
1 AAATTTATTATAATA-T
637678 AAATTTA-TATAAATAT
1 AAATTTATTAT-AATAT
637694 AAA
1 AAA
637697 ATATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 11 0.38
17 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATTTATTATAATAT
Found at i:637698 original size:17 final size:16
Alignment explanation
Indices: 637645--637710 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
637635 ACAAATATTT
637645 TAAAATT-TATATAATA
1 TAAAATTATATA-AATA
*
637661 T-AAATTAT-TATCATA
1 TAAAATTATATA-AATA
*
637676 TTAAATTTATATAAATA
1 -TAAAATTATATAAATA
*
637693 TAAAA-TATTTAAATA
1 TAAAATTATATAAATA
637708 TAA
1 TAA
637711 TTATGACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 23 0.56
16 7 0.17
17 9 0.22
18 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTATATAAATA
Found at i:638324 original size:18 final size:19
Alignment explanation
Indices: 638293--638330 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
638283 ATATACTAAT
638293 TTTTTAAAAATTAAATAAA
1 TTTTTAAAAATTAAATAAA
*
638312 TTTTT-AAATTTAAATAAA
1 TTTTTAAAAATTAAATAAA
638330 T
1 T
638331 AACTCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTTTAAAAATTAAATAAA
Found at i:639718 original size:10 final size:10
Alignment explanation
Indices: 639690--639723 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
639680 AATAAAGAGT
*
639690 ATTCAATTCA
1 ATTCAATTTA
639700 ATTCAATTTA
1 ATTCAATTTA
639710 ATTCAATTTTA
1 ATTCAA-TTTA
639721 ATT
1 ATT
639724 TAAACATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTCAATTTA
Found at i:639806 original size:28 final size:29
Alignment explanation
Indices: 639775--639835 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
639765 TTTAATTTTT
639775 AATAAAT-TTTAAATTTTAA-TAATATTAA
1 AATAAATATTTAAATTTTAACTAATA-TAA
* *
639803 AATAAATATTTTATTTTTAACTTAATATAA
1 AATAAATATTTAAATTTTAAC-TAATATAA
639833 AAT
1 AAT
639836 CTTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.25
29 10 0.36
30 6 0.21
31 5 0.18
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (29 bp):
AATAAATATTTAAATTTTAACTAATATAA
Found at i:639819 original size:46 final size:46
Alignment explanation
Indices: 639763--639860 Score: 119
Period size: 46 Copynumber: 2.1 Consensus size: 46
639753 AATTTATTTT
* * *
639763 TATTTAATTTTTAA-TAAATTTTAAAT-TTTAATAATATTAAAATAAA
1 TATTTTATTTTTAACTAAATATAAAATCTTTAA-AATATTAAAA-AAA
* *
639809 TATTTTATTTTTAACTTAATATAAAATCTTTAAAATATTATAAAAA
1 TATTTTATTTTTAACTAAATATAAAATCTTTAAAATATTAAAAAAA
639855 TATTTT
1 TATTTT
639861 TAAAAAACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
46 22 0.49
47 18 0.40
48 5 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (46 bp):
TATTTTATTTTTAACTAAATATAAAATCTTTAAAATATTAAAAAAA
Found at i:641728 original size:37 final size:38
Alignment explanation
Indices: 641683--641755 Score: 130
Period size: 37 Copynumber: 1.9 Consensus size: 38
641673 ATATCAAATC
641683 ATAATTTAAAATTTTTTATA-TTTTTATTTAAATTTTA
1 ATAATTTAAAATTTTTTATATTTTTTATTTAAATTTTA
*
641720 ATAATTTAAATTTTTTTATATTTTTTATTTAAATTT
1 ATAATTTAAAATTTTTTATATTTTTTATTTAAATTT
641756 AAATTAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (38 bp):
ATAATTTAAAATTTTTTATATTTTTTATTTAAATTTTA
Found at i:641757 original size:37 final size:36
Alignment explanation
Indices: 641683--641772 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 36
641673 ATATCAAATC
*
641683 ATAATTTAAAATTTTTTATATTTTTATTTAAATTTT
1 ATAATTTAAATTTTTTTATATTTTTATTTAAATTTT
641719 AATAATTTAAATTTTTTTATATTTTTTATTTAAA-TTT
1 -ATAATTTAAATTTTTTTATA-TTTTTATTTAAATTTT
*
641756 A-AA-TTAAATTTATTTAT
1 ATAATTTAAATTTTTTTAT
641773 CTTGATTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
34 13 0.26
35 2 0.04
36 1 0.02
37 22 0.44
38 12 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (36 bp):
ATAATTTAAATTTTTTTATATTTTTATTTAAATTTT
Found at i:641838 original size:22 final size:22
Alignment explanation
Indices: 641813--641855 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
641803 AAATAATAAA
641813 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
641835 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
641856 AATAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:642793 original size:12 final size:12
Alignment explanation
Indices: 642785--642809 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
642775 AAATTGGCGA
642785 CACAGTTGGCAG
1 CACAGTTGGCAG
642797 CACAGTTGGCAG
1 CACAGTTGGCAG
642809 C
1 C
642810 CTTTGTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (12 bp):
CACAGTTGGCAG
Found at i:647921 original size:2 final size:2
Alignment explanation
Indices: 647914--647949 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
647904 GTTTAAAACA
647914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
647950 TTCGTGAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:652860 original size:13 final size:13
Alignment explanation
Indices: 652842--652939 Score: 51
Period size: 13 Copynumber: 8.3 Consensus size: 13
652832 TCACTTAACA
*
652842 CACCTAACATTTT
1 CACCTAACATTCT
652855 CACCTAACATTCT
1 CACCTAACATTCT
652868 CA-CTAAACA--CAT
1 CACCT-AACATTC-T
652880 CACCTAACA----
1 CACCTAACATTCT
*
652889 CACTTAACATTCT
1 CACCTAACATTCT
*
652902 CACC-AA-ATACAT
1 CACCTAACATTC-T
652914 CACCTAACA----
1 CACCTAACATTCT
652923 CACCTAACATTCT
1 CACCTAACATTCT
652936 CACC
1 CACC
652940 AAATACACTT
Statistics
Matches: 67, Mismatches: 4, Indels: 28
0.68 0.04 0.28
Matches are distributed among these distances:
9 17 0.25
11 4 0.06
12 16 0.24
13 29 0.43
14 1 0.01
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.24
Consensus pattern (13 bp):
CACCTAACATTCT
Found at i:652868 original size:47 final size:47
Alignment explanation
Indices: 652812--652905 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
652802 TTAACACACT
* * *
652812 TAACATTCTCACCAAATACATCACTTAACACACCTAACATTTTCACC
1 TAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
* *
652859 TAACATTCTCACTAAACACATCACCTAACACACTTAACATTCTCACC
1 TAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
652906 AAATACATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (47 bp):
TAACATTCTCACCAAACACATCACCTAACACACCTAACATTCTCACC
Found at i:652943 original size:34 final size:34
Alignment explanation
Indices: 652855--652946 Score: 157
Period size: 34 Copynumber: 2.7 Consensus size: 34
652845 CTAACATTTT
* *
652855 CACCTAACATTCTCACTAAACACATCACCTAACA
1 CACCTAACATTCTCACCAAATACATCACCTAACA
*
652889 CACTTAACATTCTCACCAAATACATCACCTAACA
1 CACCTAACATTCTCACCAAATACATCACCTAACA
652923 CACCTAACATTCTCACCAAATACA
1 CACCTAACATTCTCACCAAATACA
652947 CTTAACAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (34 bp):
CACCTAACATTCTCACCAAATACATCACCTAACA
Found at i:653784 original size:22 final size:24
Alignment explanation
Indices: 653752--653796 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
653742 TATAAATATT
653752 TTATAACT-AAAATTTTT-CTTTC
1 TTATAACTAAAAATTTTTACTTTC
*
653774 TTATAATTAAAAATTTTTACTTT
1 TTATAACTAAAAATTTTTACTTT
653797 TATTAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 9 0.45
24 4 0.20
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATAACTAAAAATTTTTACTTTC
Found at i:654543 original size:30 final size:31
Alignment explanation
Indices: 654478--654545 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
654468 GTTAAGAGTT
* *
654478 AATTTTTATAAATTGATAATACATATTTTTTA
1 AATTTTTATAAATTGAT-ATACAAATTTATTA
654510 AATTTTTATAAATATGAT-TA-AAATTTATTA
1 AATTTTTATAAAT-TGATATACAAATTTATTA
654540 AATTTT
1 AATTTT
654546 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 14 0.42
31 2 0.06
32 13 0.39
33 4 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (31 bp):
AATTTTTATAAATTGATATACAAATTTATTA
Found at i:654594 original size:18 final size:20
Alignment explanation
Indices: 654571--654610 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
654561 ATTTTTTAAT
654571 ATTTATATT-AAA-TTAAAA
1 ATTTATATTAAAATTTAAAA
*
654589 ATTTATTTTAAAATTTAAAA
1 ATTTATATTAAAATTTAAAA
654609 AT
1 AT
654611 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 3 0.16
20 8 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTATATTAAAATTTAAAA
Found at i:657911 original size:28 final size:28
Alignment explanation
Indices: 657858--657911 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
657848 ATGAAATTAA
* *
657858 TATGAAAAATAATTAAAGTACGATATGG
1 TATGAAAAATAAATAAAGTACAATATGG
*
657886 TATGAAAAATAACATAAA-TATAATAT
1 TATGAAAAATAA-ATAAAGTACAATAT
657912 AAAAATATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.30
Consensus pattern (28 bp):
TATGAAAAATAAATAAAGTACAATATGG
Found at i:657986 original size:16 final size:17
Alignment explanation
Indices: 657952--657987 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
657942 AATGAATTAT
*
657952 TAATACTTTAAAATTTA
1 TAATACTTTAAAATATA
657969 TAATACTTT-AAATATA
1 TAATACTTTAAAATATA
657985 TAA
1 TAA
657988 AAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATACTTTAAAATATA
Found at i:658181 original size:14 final size:14
Alignment explanation
Indices: 658163--658192 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
658153 ACTCAACACG
658163 AAAAATAATATAAAT
1 AAAAAT-ATATAAAT
658178 AAAAATATATAAAT
1 AAAAATATATAAAT
658192 A
1 A
658193 TATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAATATATAAAT
Found at i:658750 original size:26 final size:26
Alignment explanation
Indices: 658719--658776 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
658709 TTTACATAAA
*
658719 ATAAA-TTATTAATATGTAAAATTTAT
1 ATAAATTTA-TAATATGTAAAATATAT
*
658745 ATAAATTTATAATATTTAAAATATAT
1 ATAAATTTATAATATGTAAAATATAT
*
658771 AAAAAT
1 ATAAAT
658777 AATATAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.89
27 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATAAATTTATAATATGTAAAATATAT
Found at i:658778 original size:56 final size:56
Alignment explanation
Indices: 658631--658774 Score: 168
Period size: 56 Copynumber: 2.6 Consensus size: 56
658621 GAAACATAAC
* **
658631 ATAAATATATAAATATTTTAAAATTTAATAAAATAAATTATTAACATGTAAGCTTTAT
1 ATAAATTTAT-AATA-TTTAAAATTTAATAAAATAAATTATTAACATGTAAAATTTAT
* * *
658689 A-ATATTTA-AATGTATTAAAATTTACATAAAATAAATTATTAATATGTAAAATTTAT
1 ATAAATTTATAATAT-TTAAAATTTA-ATAAAATAAATTATTAACATGTAAAATTTAT
*
658745 ATAAATTTATAATATTTAAAATAT-ATAAAA
1 ATAAATTTATAATATTTAAAATTTAATAAAA
658775 ATAATATAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
54 1 0.01
55 19 0.26
56 29 0.40
57 19 0.26
58 5 0.07
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (56 bp):
ATAAATTTATAATATTTAAAATTTAATAAAATAAATTATTAACATGTAAAATTTAT
Found at i:658998 original size:2 final size:2
Alignment explanation
Indices: 658991--659015 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
658981 ACTGTGAGGA
658991 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 A
659016 ATAAAGTCAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:659409 original size:17 final size:17
Alignment explanation
Indices: 659389--659428 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
659379 AATATACATA
*
659389 AAATATATATCTGTAAT
1 AAATATATAACTGTAAT
*
659406 AAATAAATAACTGTAAT
1 AAATATATAACTGTAAT
659423 -AATATA
1 AAATATA
659429 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (17 bp):
AAATATATAACTGTAAT
Found at i:660662 original size:53 final size:54
Alignment explanation
Indices: 660570--660679 Score: 204
Period size: 53 Copynumber: 2.0 Consensus size: 54
660560 ACAAAATTTT
660570 TTGTAATTATTATATATATATATATATGTAATCTTTCCCTTAATTCACTCGAAAA
1 TTGTAATTATTATATATATATATATA-GTAATCTTTCCCTTAATTCACTCGAAAA
660625 TTGTAATTATTATATATATATATATA-TAATCTTTCCCTTAATTCACTCGAAAA
1 TTGTAATTATTATATATATATATATAGTAATCTTTCCCTTAATTCACTCGAAAA
660678 TT
1 TT
660680 ATTATATTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
53 29 0.53
55 26 0.47
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (54 bp):
TTGTAATTATTATATATATATATATAGTAATCTTTCCCTTAATTCACTCGAAAA
Found at i:662989 original size:22 final size:22
Alignment explanation
Indices: 662951--662994 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
662941 TTAAATTGTT
*
662951 AAAATTAATAAATTATATTAAA
1 AAAATTAATAAATTATAATAAA
662973 AAAATTAATATAA-TATAATAAA
1 AAAATTAATA-AATTATAATAAA
662995 TACTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATTAATAAATTATAATAAA
Found at i:663840 original size:15 final size:16
Alignment explanation
Indices: 663812--663841 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
663802 CGTATGTTGT
663812 TTTGTTTAATTAATTA
1 TTTGTTTAATTAATTA
663828 TTTGTTT-ATTAATT
1 TTTGTTTAATTAATT
663842 TTTTATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (16 bp):
TTTGTTTAATTAATTA
Found at i:663929 original size:13 final size:13
Alignment explanation
Indices: 663911--663935 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
663901 TTACTAATTC
663911 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
663924 AAAAAAAAAAAA
1 AAAAAAAAAAAA
663936 ACTCTTTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.00, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:664995 original size:16 final size:16
Alignment explanation
Indices: 664976--665016 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
664966 ACTTGATATA
664976 ATATAAAAAAATAAAT
1 ATATAAAAAAATAAAT
*
664992 ATATAAATAAATAAAT
1 ATATAAAAAAATAAAT
665008 ATATCAAAA
1 ATAT-AAAA
665017 TCTAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATATAAAAAAATAAAT
Found at i:665001 original size:12 final size:12
Alignment explanation
Indices: 664984--665104 Score: 50
Period size: 12 Copynumber: 9.4 Consensus size: 12
664974 TAATATAAAA
664984 AAATAAATATAT
1 AAATAAATATAT
*
664996 AAATAAATAAAT
1 AAATAAATATAT
* *
665008 ATATCAAA-ATCT
1 AAAT-AAATATAT
665020 AAATAAA-ATAAT
1 AAATAAATAT-AT
** *
665032 TTATTAATATATT
1 AAATAAATATA-T
*
665045 AAAAAATATATAT
1 AAATAA-ATATAT
*
665058 AATATATAATATTTT
1 AA-ATA-AATA-TAT
665073 AAATATAAT-TAT
1 AAATA-AATATAT
665085 AATATAAAATAATAT
1 AA-AT-AAAT-ATAT
665100 AAATA
1 AAATA
665105 CGATAATAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
11 5 0.06
12 29 0.36
13 17 0.21
14 20 0.25
15 10 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:665051 original size:28 final size:28
Alignment explanation
Indices: 665020--665100 Score: 69
Period size: 28 Copynumber: 2.8 Consensus size: 28
665010 ATCAAAATCT
*
665020 AAATA-AAATAATTTATTAATATATTAAA
1 AAATATAAATAATATA-TAATATATTAAA
* *
665048 AAATATATATAATATATAATATTTTAAA
1 AAATATAAATAATATATAATATATTAAA
665076 TATAATTATAATATAA-A-ATAATATA
1 -A-AA-TATAA-ATAATATATAATATA
665101 AATACGATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
28 16 0.37
29 9 0.21
30 9 0.21
31 5 0.12
32 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATATAAATAATATATAATATATTAAA
Found at i:665068 original size:16 final size:16
Alignment explanation
Indices: 664971--665119 Score: 56
Period size: 14 Copynumber: 9.8 Consensus size: 16
664961 TTTAAACTTG
* *
664971 ATATAATATA-AAAAA
1 ATATAATATATATAAT
664986 ATA-AATATATA-AAT
1 ATATAATATATATAAT
* *
665000 AAATAA-ATATATCAAA
1 ATATAATATATAT-AAT
* *
665016 ATCTAA-ATAAAATAAT
1 ATATAATAT-ATATAAT
*
665032 TTATTAATATAT-TAA-
1 ATA-TAATATATATAAT
665047 A-A-AATATATATAAT
1 ATATAATATATATAAT
*
665061 ATATAATAT-TTTAA-
1 ATATAATATATATAAT
665075 ATATAATTATAATATAA-
1 ATATAA-TAT-ATATAAT
*
665092 A-ATAATATAAATACGAT
1 ATATAATATATATA--AT
665109 A-ATAATATATA
1 ATATAATATATA
665120 CATAATTAAA
Statistics
Matches: 102, Mismatches: 15, Indels: 32
0.68 0.10 0.21
Matches are distributed among these distances:
12 7 0.07
13 3 0.03
14 27 0.26
15 17 0.17
16 24 0.24
17 22 0.22
18 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (16 bp):
ATATAATATATATAAT
Found at i:665095 original size:27 final size:25
Alignment explanation
Indices: 664973--665130 Score: 75
Period size: 27 Copynumber: 6.4 Consensus size: 25
664963 TAAACTTGAT
* *
664973 ATAATATAAAAAAATA-AATATATAA
1 ATAATATAAATATATATAATATA-AA
* *
664998 ATAA-ATAAATATATCAAAATCT-AA
1 ATAATATAAATATAT-ATAATATAAA
* *
665022 ATAAAAT-AATTTAT-TAATAT--A
1 ATAATATAAATATATATAATATAAA
* *
665043 TTAA-A-AAATATATATAATATATA
1 ATAATATAAATATATATAATATAAA
* *
665066 ATATTTTAAATATAATTATAATATAAA
1 ATAATATAAATAT-A-TATAATATAAA
* *
665093 ATAATATAAATACGATAATAATATATAC
1 ATAATATAAATA-TAT-ATAATATA-AA
665121 ATAAT-TAAAT
1 ATAATATAAAT
665131 TAATTACAAT
Statistics
Matches: 103, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
20 7 0.07
21 10 0.10
22 4 0.04
23 3 0.03
24 20 0.19
25 13 0.13
26 6 0.06
27 34 0.33
28 6 0.06
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (25 bp):
ATAATATAAATATATATAATATAAA
Found at i:665744 original size:16 final size:15
Alignment explanation
Indices: 665718--665775 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
665708 GAGCTTCACA
665718 TAATTAAAATTTAAT
1 TAATTAAAATTTAAT
665733 TAATTAAAAATTT-A-
1 TAATT-AAAATTTAAT
*
665747 -AATTTAAATTTAA-
1 TAATTAAAATTTAAT
* *
665760 TATTTATAATTTAAT
1 TAATTAAAATTTAAT
665775 T
1 T
665776 TTTAACTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 6 0.17
13 5 0.14
14 10 0.29
15 7 0.20
16 7 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTAAAATTTAAT
Found at i:665770 original size:14 final size:13
Alignment explanation
Indices: 665740--665780 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
665730 AATTAATTAA
665740 AAATTTAA-ATTT
1 AAATTTAATATTT
665752 AAATTTAATATTT
1 AAATTTAATATTT
*
665765 ATAATTTAATTTTT
1 A-AATTTAATATTT
665779 AA
1 AA
665781 CTATACGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.31
13 6 0.23
14 12 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAATTTAATATTT
Found at i:665775 original size:19 final size:18
Alignment explanation
Indices: 665721--665776 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
665711 CTTCACATAA
665721 TTAAAATTT-AA-TTAAT
1 TTAAAATTTAAATTTAAT
*
665737 TAAAAATTTAAATTTAAAT
1 TTAAAATTTAAATTT-AAT
*
665756 TTAATATTTATAATTTAAT
1 TTAAAATTTA-AATTTAAT
665775 TT
1 TT
665777 TTAACTATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 2 0.06
19 16 0.48
20 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAAATTTAAATTTAAT
Found at i:665776 original size:5 final size:6
Alignment explanation
Indices: 665740--665773 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
665730 AATTAATTAA
665740 AAATTT AAATTT AAATTT AATATTT ATAATTT AA
1 AAATTT AAATTT AAATTT AA-ATTT A-AATTT AA
665774 TTTTTAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 15 0.58
7 10 0.38
8 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:667846 original size:23 final size:23
Alignment explanation
Indices: 667816--667864 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
667806 ACTCTGCATG
667816 ATCAGATTCATTCATATCATATT
1 ATCAGATTCATTCATATCATATT
667839 ATCAGATTCATTCATATCATATT
1 ATCAGATTCATTCATATCATATT
667862 ATC
1 ATC
667865 TCTTTGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.43
Consensus pattern (23 bp):
ATCAGATTCATTCATATCATATT
Found at i:668244 original size:9 final size:10
Alignment explanation
Indices: 668224--668260 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
668214 AAATTCATTC
668224 AAAATTTAAA
1 AAAATTTAAA
668234 AAAATTTAAA
1 AAAATTTAAA
668244 AAAATTTTTAAA
1 AAAA--TTTAAA
668256 AAAAT
1 AAAAT
668261 ATTACAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:669448 original size:2 final size:2
Alignment explanation
Indices: 669441--669465 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
669431 ATGTGACAAT
669441 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
669466 TTTGCTACAT
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:671907 original size:13 final size:14
Alignment explanation
Indices: 671889--671936 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
671879 AAAAATTAAA
671889 AATATTTTAT-ATT
1 AATATTTTATAATT
671902 AATA-TTTATAATT
1 AATATTTTATAATT
* *
671915 AA-ATTTTAAAAAT
1 AATATTTTATAATT
671928 AAT-TTTTAT
1 AATATTTTAT
671937 TATTTAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 6 0.21
13 23 0.79
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATTTTATAATT
Found at i:671951 original size:21 final size:20
Alignment explanation
Indices: 671919--671958 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
671909 ATAATTAAAT
*
671919 TTTAAAAATAATTTTTATTA
1 TTTAAAAATAATTTATATTA
*
671939 TTTAAATAGTAATTTATATT
1 TTTAAA-AATAATTTATATT
671959 GATCCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAAAAATAATTTATATTA
Found at i:672530 original size:17 final size:17
Alignment explanation
Indices: 672495--672532 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
672485 ATTTGATGTA
*
672495 TTTTTATTTGTGTTAAT
1 TTTTTATTTATGTTAAT
672512 TTTTGTATTTATGTT-AT
1 TTTT-TATTTATGTTAAT
672529 TTTT
1 TTTT
672533 ATGTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (17 bp):
TTTTTATTTATGTTAAT
Found at i:672541 original size:18 final size:18
Alignment explanation
Indices: 672495--672539 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
672485 ATTTGATGTA
*
672495 TTTT-TATTTGTGTTAAT
1 TTTTGTATTTATGTTAAT
*
672512 TTTTGTATTTATGTTATT
1 TTTTGTATTTATGTTAAT
672530 TTTATGTATT
1 TTT-TGTATT
672540 ATTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 14 0.58
19 6 0.25
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTTGTATTTATGTTAAT
Found at i:672606 original size:31 final size:34
Alignment explanation
Indices: 672556--672643 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 34
672546 ATTATTATAT
* * *
672556 TTAAAATATTATAAATTTATAT-AATTTTAAAATA
1 TTAATATATT-TATATTTATATAAAATTTAAAATA
*
672590 TTAATA-ATTTAT-TTTATATAAAAATTTAATATA
1 TTAATATATTTATATTTATAT-AAAATTTAAAATA
*
672623 TTTATATATTTATATTTATAT
1 TTAATATATTTATATTTATAT
672644 TATAATATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 7 0.16
32 2 0.04
33 18 0.40
34 11 0.24
35 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
TTAATATATTTATATTTATATAAAATTTAAAATA
Found at i:672613 original size:26 final size:26
Alignment explanation
Indices: 672544--672627 Score: 82
Period size: 26 Copynumber: 3.2 Consensus size: 26
672534 TGTATTATTA
672544 TTATTATTATATTTAAAATATT-ATAAAT
1 TTATT-TTATA-TTAAAATATTAAT-AAT
* * *
672572 TTATATAATTTTAAAATATTAATAAT
1 TTATTTTATATTAAAATATTAATAAT
*
672598 TTATTTTATATAAAAAT-TTAATATAT
1 TTATTTTATATTAAAATATTAATA-AT
672624 TTAT
1 TTAT
672628 ATATTTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 6 0.13
26 32 0.68
27 5 0.11
28 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTATTTTATATTAAAATATTAATAAT
Found at i:672636 original size:6 final size:6
Alignment explanation
Indices: 672627--672682 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
672617 AATATATTTA
672627 TATATT TATATT TATATT ATAATATT T-TATT TATATT T-TATGT TAATTATT
1 TATATT TATATT TATATT -T-ATATT TATATT TATATT TATAT-T T-A-TATT
672678 TATAT
1 TATAT
672683 CAATTTAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
5 8 0.19
6 22 0.51
7 3 0.07
8 7 0.16
9 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:672638 original size:14 final size:14
Alignment explanation
Indices: 672613--672682 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
672603 TTATATAAAA
672613 ATTTAATATATTTAT
1 ATTT-ATATATTTAT
672628 ATATT-TATATTTAT
1 AT-TTATATATTTAT
672642 A-TTATAATATTT-T
1 ATTTAT-ATATTTAT
672655 ATTTATAT-TTTAT
1 ATTTATATATTTAT
* *
672668 GTTAAT-TATTTAT
1 ATTTATATATTTAT
672681 AT
1 AT
672683 CAATTTAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
12 6 0.13
13 16 0.35
14 20 0.43
15 2 0.04
16 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (14 bp):
ATTTATATATTTAT
Found at i:672644 original size:20 final size:20
Alignment explanation
Indices: 672619--672682 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
672609 AAAAATTTAA
672619 TATATTTATATATTTATATT
1 TATATTTATATATTTATATT
672639 TATA-TTATAATATTT-TATT
1 TATATTTAT-ATATTTATATT
* *
672658 TATATTT-TATGTTAATTATT
1 TATATTTATATATTTA-TATT
672678 TATAT
1 TATAT
672683 CAATTTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 13 0.34
20 21 0.55
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATATTTATATATTTATATT
Found at i:673337 original size:63 final size:63
Alignment explanation
Indices: 673238--673361 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
673228 CATGCAGCTT
673238 CATTGGCCTGACCAATATATAAGTATATAAAAGAGGCTATTAGAACTCGCAGCAGAAAAGGTG
1 CATTGGCCTGACCAATATATAAGTATATAAAAGAGGCTATTAGAACTCGCAGCAGAAAAGGTG
* *
673301 CATTGGCCTGACCAATATATATGTATATAAAAGAGGCTATTAGCACTCGCAGCAGAAAAGG
1 CATTGGCCTGACCAATATATAAGTATATAAAAGAGGCTATTAGAACTCGCAGCAGAAAAGG
673362 AGGAAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (63 bp):
CATTGGCCTGACCAATATATAAGTATATAAAAGAGGCTATTAGAACTCGCAGCAGAAAAGGTG
Found at i:674882 original size:20 final size:20
Alignment explanation
Indices: 674857--674901 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
674847 ATTTTAAAAA
*
674857 TAATTATATAAAATATAAAT
1 TAATTAAATAAAATATAAAT
* * *
674877 TAATTAAATTAAATTTCAAT
1 TAATTAAATAAAATATAAAT
674897 TAATT
1 TAATT
674902 TACTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTAAATAAAATATAAAT
Found at i:675180 original size:28 final size:28
Alignment explanation
Indices: 675121--675190 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
675111 TCACCCATTT
*
675121 ATTTGTCAAAAATAGTGATTATTTTGTG
1 ATTTGTCAAAAATGGTGATTATTTTGTG
* *
675149 -TTTGTCAAAAATGGTGGTTTTCTTTG-G
1 ATTTGTCAAAAATGGTGATTAT-TTTGTG
* *
675176 ATTTGTTAAATATGG
1 ATTTGTCAAAAATGG
675191 AGGCTTGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 19 0.54
28 16 0.46
ACGTcount: A:0.27, C:0.04, G:0.21, T:0.47
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGATTATTTTGTG
Found at i:680394 original size:2 final size:2
Alignment explanation
Indices: 680387--680421 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
680377 TTGAATGACA
680387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
680422 GAAGGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:680640 original size:28 final size:30
Alignment explanation
Indices: 680609--680668 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 30
680599 AAGTAACGTC
* *
680609 AATTTAATTATTAA-ATT-TATAAAAAAAT
1 AATTAAATTATTAATATTAAATAAAAAAAT
* *
680637 AATTAAATTTTTAATATTAAATAATAAAAT
1 AATTAAATTATTAATATTAAATAAAAAAAT
680667 AA
1 AA
680669 AAGTATGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
29 3 0.12
30 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (30 bp):
AATTAAATTATTAATATTAAATAAAAAAAT
Found at i:682981 original size:20 final size:22
Alignment explanation
Indices: 682942--682982 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
682932 ATTTTTTGGG
682942 TTATAAATTAAAAATTATATTA
1 TTATAAATTAAAAATTATATTA
*
682964 TTAT-AATT-AAATTTATATT
1 TTATAAATTAAAAATTATATT
682983 TTAATTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATAAATTAAAAATTATATTA
Found at i:683724 original size:18 final size:19
Alignment explanation
Indices: 683687--683727 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
683677 ATTAAATTCA
**
683687 AGTTTTTGATAAATTTTTG
1 AGTTTTTGATAAATAATTG
683706 AGTTTTTGATAAA-AATTG
1 AGTTTTTGATAAATAATTG
683724 AGTT
1 AGTT
683728 GATATAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
AGTTTTTGATAAATAATTG
Found at i:684679 original size:23 final size:21
Alignment explanation
Indices: 684646--684691 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 21
684636 AAAATTTTTT
684646 AATATTAATTAAAAATAAAAA
1 AATATTAATTAAAAATAAAAA
684667 AATATATACATTAAAAATAAAAA
1 AATAT-TA-ATTAAAAATAAAAA
684690 AA
1 AA
684692 GCTCAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 5 0.22
22 2 0.09
23 16 0.70
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
AATATTAATTAAAAATAAAAA
Found at i:685487 original size:11 final size:11
Alignment explanation
Indices: 685471--685514 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
685461 TATAAATTTA
685471 TATATTTATAT
1 TATATTTATAT
685482 TATATTTATAT
1 TATATTTATAT
*
685493 TAT-TTTTTAT
1 TATATTTATAT
*
685503 TATAATTATAT
1 TATATTTATAT
685514 T
1 T
685515 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATATTTATAT
Found at i:685488 original size:27 final size:27
Alignment explanation
Indices: 685458--685535 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
685448 ATTCTAATAG
685458 ATTTATAAATTTATATATTTATATTAT
1 ATTTATAAATTTATATATTTATATTAT
* *
685485 ATTTATATTATTT-TTTA-TTATAATTAT
1 ATTTATA-AATTTATATATTTAT-ATTAT
*
685512 ATTT-TAAAAATTATATATTTATAT
1 ATTTAT-AAATTTATATATTTATAT
685536 AAATTTTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 8 0.20
27 25 0.61
28 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTATAAATTTATATATTTATATTAT
Found at i:685503 original size:21 final size:20
Alignment explanation
Indices: 685466--685514 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
685456 AGATTTATAA
685466 ATTTATA-TATTTATATTAT
1 ATTTATATTATTTATATTAT
*
685485 ATTTATATTATTTTTTATTAT
1 ATTTATATTA-TTTATATTAT
*
685506 AATTATATT
1 ATTTATATT
685515 TTAAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 7 0.27
20 2 0.08
21 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTATATTATTTATATTAT
Found at i:685549 original size:20 final size:20
Alignment explanation
Indices: 685522--685568 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
685512 ATTTTAAAAA
*
685522 TTATATATTTAT-ATAAATT
1 TTATATATTAATAATAAATT
*
685541 TTAATATATTAATAATTAATT
1 TT-ATATATTAATAATAAATT
685562 TTATATA
1 TTATATA
685569 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 14 0.58
21 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATATATTAATAATAAATT
Found at i:685587 original size:34 final size:34
Alignment explanation
Indices: 685510--685590 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
685500 TATTATAATT
*
685510 ATATTTTAAAAATTATATATTTATATAAATTTTA
1 ATATTTTAATAATTATATATTTATATAAATTTTA
*
685544 ATATATTAATAATTA-AT-TTTATATAAAATTTTA
1 ATATTTTAATAATTATATATTTATAT-AAATTTTA
685577 ATATTTT--TAATTAT
1 ATATTTTAATAATTAT
685591 TCAAATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.14
32 7 0.17
33 16 0.38
34 13 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATATTTTAATAATTATATATTTATATAAATTTTA
Found at i:686804 original size:6 final size:6
Alignment explanation
Indices: 686754--686833 Score: 79
Period size: 6 Copynumber: 13.3 Consensus size: 6
686744 CGCAGTTGAA
* * * * * * * *
686754 GGAGCT GGAGAT GGGGTT GGGGTT GGGGTT GAAGTT GGGGTT GGAGAT
1 GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT
*
686802 GGAGAT GGAGTT GGAGTT GGAGTT GGAGTT GG
1 GGAGTT GGAGTT GGAGTT GGAGTT GGAGTT GG
686834 TGACGGTGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.16, C:0.01, G:0.55, T:0.28
Consensus pattern (6 bp):
GGAGTT
Found at i:686844 original size:12 final size:12
Alignment explanation
Indices: 686829--686859 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
686819 TGGAGTTGGA
686829 GTTGGTGACGGT
1 GTTGGTGACGGT
686841 GTTGGTGACGGT
1 GTTGGTGACGGT
*
686853 GTGGGTG
1 GTTGGTG
686860 TGGGTGTGGG
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:0.06, C:0.06, G:0.55, T:0.32
Consensus pattern (12 bp):
GTTGGTGACGGT
Found at i:686884 original size:18 final size:18
Alignment explanation
Indices: 686838--686884 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
686828 AGTTGGTGAC
*
686838 GGTGTTGGTGACGGTGTG
1 GGTGTTGGTGTCGGTGTG
* *
686856 GGTGTGGGTGTGGGTG-G
1 GGTGTTGGTGTCGGTGTG
686873 GGTTGTTGGTGT
1 GG-TGTTGGTGT
686885 AGCAGCTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.02, C:0.02, G:0.60, T:0.36
Consensus pattern (18 bp):
GGTGTTGGTGTCGGTGTG
Found at i:686934 original size:15 final size:15
Alignment explanation
Indices: 686894--686934 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
686884 TAGCAGCTGG
* *
686894 TGGTGGTGAAGATGT
1 TGGTGGAGATGATGT
*
686909 TGGTGGGGATGATGT
1 TGGTGGAGATGATGT
686924 TGGTGGAGATG
1 TGGTGGAGATG
686935 TCGGTGCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.51, T:0.32
Consensus pattern (15 bp):
TGGTGGAGATGATGT
Found at i:688028 original size:19 final size:19
Alignment explanation
Indices: 688010--688076 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
688000 TTAAAATTAT
688010 AATAAAATAATTATTTTATATA
1 AATAAAATAATTA-TTT-TA-A
688032 AATAAAATAA--A-TTTAA
1 AATAAAATAATTATTTTAA
**
688048 AATAAAATAATTATAATAA
1 AATAAAATAATTATTTTAA
688067 AATAAAATAA
1 AATAAAATAA
688077 AATATTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.28
17 2 0.05
18 3 0.08
19 13 0.32
20 1 0.03
22 10 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAAAATAATTATTTTAA
Found at i:688028 original size:38 final size:38
Alignment explanation
Indices: 687993--688079 Score: 117
Period size: 38 Copynumber: 2.4 Consensus size: 38
687983 ACATTTATTA
* *
687993 AAATAAATTAAAATTATAATAAAATAATTATTTTATAT
1 AAATAAAATAAAATTAAAATAAAATAATTATTTTATAT
* *
688031 AAATAAAATAAATTTAAAATAAAATAATTA--TAATA-
1 AAATAAAATAAAATTAAAATAAAATAATTATTTTATAT
688066 AAATAAAATAAAAT
1 AAATAAAATAAAAT
688080 ATTGTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
35 13 0.30
36 4 0.09
38 27 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (38 bp):
AAATAAAATAAAATTAAAATAAAATAATTATTTTATAT
Found at i:688039 original size:5 final size:5
Alignment explanation
Indices: 688031--688080 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
688021 TATTTTATAT
* * *
688031 AAATA AAATA AATTTA AAATA AAAT- AATTA TAATA AAATA AAATA AAATA
1 AAATA AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
688081 TTGTAAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 3 0.08
5 30 0.81
6 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (5 bp):
AAATA
Found at i:688879 original size:5 final size:5
Alignment explanation
Indices: 688857--688911 Score: 69
Period size: 5 Copynumber: 10.8 Consensus size: 5
688847 TAAATTTAAA
688857 ATATT A-ATT -TATTT ATATT ATATTT ATATT ATATT ATATTT ATATT
1 ATATT ATATT ATA-TT ATATT ATA-TT ATATT ATATT ATA-TT ATATT
688903 ATATT ATAT
1 ATATT ATAT
688912 CTTAATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.09
5 29 0.64
6 12 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATATT
Found at i:688882 original size:11 final size:11
Alignment explanation
Indices: 688866--688930 Score: 75
Period size: 11 Copynumber: 6.1 Consensus size: 11
688856 AATATTAATT
688866 TATTTATATTA
1 TATTTATATTA
688877 TATTTATATTA
1 TATTTATATTA
688888 TA-TTATATT-
1 TATTTATATTA
688897 TATATTATATTA
1 TAT-TTATATTA
688909 TATCTTA-ATTA
1 TAT-TTATATTA
*
688920 T-TTTTTATTA
1 TATTTATATTA
688930 T
1 T
688931 TTCAAATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
9 4 0.08
10 13 0.27
11 25 0.52
12 6 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATATTA
Found at i:688883 original size:36 final size:37
Alignment explanation
Indices: 688813--688884 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
688803 TTTTGAGTTT
* * *
688813 ATTTACAAACATTTATTTGTTTGTATAATATTTATAA
1 ATTTACAAACATTAATTTATTTATATAATATTTATAA
* *
688850 ATTTA-AAATATTAATTTATTTATATTATATTTATA
1 ATTTACAAACATTAATTTATTTATATAATATTTATA
688885 TTATATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (37 bp):
ATTTACAAACATTAATTTATTTATATAATATTTATAA
Found at i:688890 original size:16 final size:16
Alignment explanation
Indices: 688857--688920 Score: 98
Period size: 16 Copynumber: 4.1 Consensus size: 16
688847 TAAATTTAAA
688857 ATATTA-ATTTAT-TT
1 ATATTATATTTATATT
688871 ATATTATATTTATATT
1 ATATTATATTTATATT
688887 ATATTATATTTATATT
1 ATATTATATTTATATT
688903 ATATTATATCTTA-ATT
1 ATATTATAT-TTATATT
688919 AT
1 AT
688921 TTTTTATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
14 6 0.13
15 6 0.13
16 32 0.68
17 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATATTTATATT
Found at i:688920 original size:21 final size:20
Alignment explanation
Indices: 688857--688930 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
688847 TAAATTTAAA
688857 ATATTA-ATT-TATTTATATT
1 ATATTATATTATATTTA-ATT
*
688876 ATATTTATATTATATTATATTT
1 ATA-TTATATTATATT-TAATT
688898 ATATTATATTATATCTTAATT
1 ATATTATATTATAT-TTAATT
* *
688919 ATTTTTTATTAT
1 ATATTATATTAT
688931 TTCAAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 28 0.61
22 10 0.22
23 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATTATATTATATTTAATT
Found at i:689353 original size:15 final size:16
Alignment explanation
Indices: 689333--689364 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
689323 AATATAAAAT
689333 TTTATATATT-TAATA
1 TTTATATATTATAATA
689348 TTTATATATTATAATA
1 TTTATATATTATAATA
689364 T
1 T
689365 GACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATATATTATAATA
Found at i:689815 original size:3 final size:3
Alignment explanation
Indices: 689809--689839 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
689799 TAATTTTTAG
689809 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
689840 CTCTTACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:691554 original size:16 final size:16
Alignment explanation
Indices: 691530--691564 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
691520 ATTTTTATTA
691530 TTTAATATATA-TATC
1 TTTAATATATATTATC
691545 TTTAATTATATATTATC
1 TTTAA-TATATATTATC
691562 TTT
1 TTT
691565 TTTTTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 6 0.33
17 7 0.39
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATATATATTATC
Found at i:692244 original size:8 final size:8
Alignment explanation
Indices: 692231--692259 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
692221 CTATTTTAAA
692231 TTTAAATT
1 TTTAAATT
692239 TTTAAATT
1 TTTAAATT
692247 TTTAAATT
1 TTTAAATT
692255 TTTAA
1 TTTAA
692260 TCAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTAAATT
Found at i:693084 original size:12 final size:12
Alignment explanation
Indices: 693067--693091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
693057 TAAAATTTTA
693067 TTTAATTTTAAT
1 TTTAATTTTAAT
693079 TTTAATTTTAAT
1 TTTAATTTTAAT
693091 T
1 T
693092 ATAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATTTTAAT
Found at i:693802 original size:21 final size:21
Alignment explanation
Indices: 693778--693817 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
693768 GTTTAAAAAT
693778 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
693799 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
693818 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:697437 original size:18 final size:17
Alignment explanation
Indices: 697416--697482 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
697406 AAAAAACAAA
697416 AAATTATTTTAAAAATAT
1 AAATTATTTTAAAAAT-T
697434 AAA-TATTTT--AAATT
1 AAATTATTTTAAAAATT
* *
697448 ATATTATATTAAAAATT
1 AAATTATTTTAAAAATT
697465 AATATTAATTTTTAAAAA
1 AA-ATT-A-TTTTAAAAA
697483 AATACAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 3 0.08
15 9 0.23
17 12 0.31
18 6 0.15
19 1 0.03
20 8 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTATTTTAAAAATT
Found at i:697800 original size:21 final size:22
Alignment explanation
Indices: 697776--697825 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
697766 ACATATTTTA
697776 AATTATA-TTTTATAAATT-AAT
1 AATTATATTTTTA-AAATTAAAT
697797 AATT-TATTTTTAAAATTAAAT
1 AATTATATTTTTAAAATTAAAT
*
697818 TATTATAT
1 AATTATAT
697826 AATTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTATATTTTTAAAATTAAAT
Found at i:697802 original size:27 final size:27
Alignment explanation
Indices: 697750--697802 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
697740 TAAAATATTT
*
697750 ATTATTTTTAAAATATACATATTTTAA
1 ATTATTTTTAAAATATACATAATTTAA
697777 ATTATATTTTATAAAT-TA-ATAATTTA
1 ATTAT-TTTTA-AAATATACATAATTTA
697803 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 12 0.52
28 7 0.30
29 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATTTTTAAAATATACATAATTTAA
Found at i:697835 original size:30 final size:28
Alignment explanation
Indices: 697791--697860 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 28
697781 TATTTTATAA
697791 ATTAATAATTTATTTTTAAAATTAAATT
1 ATTAATAATTTATTTTTAAAATTAAATT
697819 ATTATATAATTTTATTTTTAAAATT-AATT
1 ATTA-ATAA-TTTATTTTTAAAATTAAATT
697848 AATT--TAATTTATT
1 -ATTAATAATTTATT
697861 AAAAAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.15
27 3 0.08
28 4 0.10
29 8 0.21
30 18 0.46
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTAATAATTTATTTTTAAAATTAAATT
Found at i:697845 original size:50 final size:50
Alignment explanation
Indices: 697751--697864 Score: 135
Period size: 49 Copynumber: 2.2 Consensus size: 50
697741 AAAATATTTA
* *
697751 TTATTTTTAAAATATACATATTTTAAATTATATTTTATAAATTAA-TAAT
1 TTATTTTTAAAATATAAATATTATAAATTATATTTTATAAATTAATTAAT
*
697800 TTATTTTTAAAAT-TAAATTATTATATAATTTTATTTT-TAAAATTAATTAAT
1 TTATTTTTAAAATATAAA-TATTATA-AATTATATTTTAT-AAATTAATTAAT
697851 TTAATTTATTAAAA
1 TT-ATTT-TTAAAA
697865 AAATATTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
48 3 0.05
49 20 0.36
50 17 0.30
51 6 0.11
52 4 0.07
53 6 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (50 bp):
TTATTTTTAAAATATAAATATTATAAATTATATTTTATAAATTAATTAAT
Found at i:698256 original size:3 final size:3
Alignment explanation
Indices: 698243--698283 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
698233 ATCGAGTGTG
* *
698243 AAT ATAT AAT AAT AAT AAT GAT GAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
698284 TATAGTATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:698573 original size:2 final size:2
Alignment explanation
Indices: 698566--698605 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
698556 GATTTTTACA
* *
698566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
698606 TGGGTTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:704332 original size:20 final size:20
Alignment explanation
Indices: 704307--704358 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
704297 AATTTAATTT
704307 AAATATTTATTATATTATTA
1 AAATATTTATTATATTATTA
704327 AAATA-TTATT-T-TTATTA
1 AAATATTTATTATATTATTA
704344 ATATATATTT-TTATA
1 A-A-ATATTTATTATA
704359 ATTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
17 7 0.26
18 2 0.07
19 10 0.37
20 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATATTTATTATATTATTA
Found at i:704354 original size:15 final size:17
Alignment explanation
Indices: 704307--704390 Score: 68
Period size: 17 Copynumber: 5.0 Consensus size: 17
704297 AATTTAATTT
704307 AAATATTTATTATATTATTA
1 AAATA-TTATT-T-TTATTA
704327 AAATATTATTTTTATTA
1 AAATATTATTTTTATTA
*
704344 ATATA-TATTTTTA-T-
1 AAATATTATTTTTATTA
* * * *
704358 AATTA-AATTTTAATAA
1 AAATATTATTTTTATTA
704374 AAATATTATTTTTATTA
1 AAATATTATTTTTATTA
704391 TTAAATAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 12 0.24
17 18 0.35
18 1 0.02
19 5 0.10
20 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATATTATTTTTATTA
Found at i:704399 original size:28 final size:30
Alignment explanation
Indices: 704343--704401 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
704333 TATTTTTATT
704343 AATATATATTTTTATAATTAAATTTTAATAAA
1 AATATATATTTTTATAATTAAA--TTAATAAA
*
704375 AATAT-TATTTTTATTATTAAA-TAATAA
1 AATATATATTTTTATAATTAAATTAATAA
704402 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 6 0.23
31 15 0.58
32 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATATATTTTTATAATTAAATTAATAAA
Found at i:704457 original size:26 final size:26
Alignment explanation
Indices: 704390--704457 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
704380 TATTTTTATT
704390 ATTAAATAATAATTTAAATTTATAAAA
1 ATTAAATAAT-ATTTAAATTTATAAAA
** *
704417 ATTTATTTAATATTT-AATTTATATAA
1 A-TTAAATAATATTTAAATTTATAAAA
*
704443 ATTAGATAATGATTT
1 ATTAAATAAT-ATTT
704458 TTGGAAGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
25 7 0.21
26 15 0.44
27 5 0.15
28 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
ATTAAATAATATTTAAATTTATAAAA
Found at i:707327 original size:3 final size:3
Alignment explanation
Indices: 707319--707357 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
707309 AGGTGCAAAT
707319 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
707358 TAGCACCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:709041 original size:2 final size:2
Alignment explanation
Indices: 709029--709065 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
709019 ATCATTTTAT
709029 TA TA T- 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
709066 AGTTTGGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:709875 original size:2 final size:2
Alignment explanation
Indices: 709863--709898 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
709853 ATGAGGAAAC
*
709863 GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
709899 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:709903 original size:2 final size:2
Alignment explanation
Indices: 709898--709926 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
709888 AGAGAGAGAG
709898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
709927 CACTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:712918 original size:2 final size:2
Alignment explanation
Indices: 712911--712938 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
712901 GTTATAGGTA
712911 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
712939 GTATTGTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:714068 original size:23 final size:23
Alignment explanation
Indices: 714042--714113 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
714032 TATTATTAAA
714042 TATTATTTAAATTTTAAATTATT
1 TATTATTTAAATTTTAAATTATT
* * **
714065 TATTATTT-TATATTCAAATTAAA
1 TATTATTTAAAT-TTTAAATTATT
*
714088 TATTTTTTAATATTTTAAATTTATT
1 TATTATTTAA-ATTTTAAA-TTATT
714113 T
1 T
714114 TAAGTCGAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
22 2 0.06
23 23 0.64
24 5 0.14
25 6 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTTAAATTTTAAATTATT
Found at i:718184 original size:2 final size:2
Alignment explanation
Indices: 718177--718203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
718167 GCAAGATACT
718177 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 T
718204 GCTAGCTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:720180 original size:11 final size:12
Alignment explanation
Indices: 720148--720184 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
720138 TAAATTTAAT
*
720148 TATAAATATTAA
1 TATAAATAATAA
720160 TATAAA-AATAA
1 TATAAATAATAA
720171 T-TAAATAATAA
1 TATAAATAATAA
720182 TAT
1 TAT
720185 GAGTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 4 0.18
11 11 0.50
12 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TATAAATAATAA
Found at i:720359 original size:1 final size:1
Alignment explanation
Indices: 720353--720382 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
720343 TTCCCTCCCT
*
720353 CCCCCCCCCCCCCCCCCCCCCCCCCACCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
720383 AATTATCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:722215 original size:2 final size:2
Alignment explanation
Indices: 722208--722243 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
722198 CCCAAGCCTC
722208 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
722244 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:722248 original size:2 final size:2
Alignment explanation
Indices: 722243--722277 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
722233 TCTCTCTCTC
*
722243 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
722278 TACACTACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:723463 original size:27 final size:27
Alignment explanation
Indices: 723366--723466 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 27
723356 TATCGTATAT
* *
723366 TATTATATTATAATTATATTTAAAATA
1 TATTATATTTTAATTATTTTTAAAATA
* * * *
723393 TTTTATA-TTTATATAAATTTAAAAAT-
1 TATTATATTTTA-ATTATTTTTAAAATA
*
723419 TCA-TATATTTATAA-TATTTTTATAATA
1 T-ATTATATTT-TAATTATTTTTAAAATA
723446 TATTATATTTTAATTATTTTT
1 TATTATATTTTAATTATTTTT
723467 TATCTTATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
26 20 0.36
27 34 0.61
28 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTATATTTTAATTATTTTTAAAATA
Found at i:726965 original size:12 final size:12
Alignment explanation
Indices: 726948--726974 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
726938 TTTTTTCATT
726948 TTTATATTTGAA
1 TTTATATTTGAA
726960 TTTATATTTGAA
1 TTTATATTTGAA
726972 TTT
1 TTT
726975 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTATATTTGAA
Found at i:729419 original size:2 final size:2
Alignment explanation
Indices: 729412--729445 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
729402 ACTTTAAAAT
729412 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
729446 GCTATTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:730728 original size:79 final size:79
Alignment explanation
Indices: 730595--730754 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 79
730585 TTACGAACTT
*
730595 TTATAGGTTTAATGCTTTTGTGGATCAAGTTGTTGCATTTAATGATGTTGGTTACCTTAATATAA
1 TTATAGGTTTAATGCTTTTGTGGATCAAGTTGTTGCATTTAATGATGTTCGTTACCTTAATATAA
730660 TGATTTTCACTGCA
66 TGATTTTCACTGCA
730674 TTATAGGTTTAATGCTTTTGTGGATCAAGTTGTTGCATTTAATGATGTTCGTTACCTTAATATAA
1 TTATAGGTTTAATGCTTTTGTGGATCAAGTTGTTGCATTTAATGATGTTCGTTACCTTAATATAA
730739 TGATTTTCACTGCA
66 TGATTTTCACTGCA
730753 TT
1 TT
730755 TAGATGTAAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (79 bp):
TTATAGGTTTAATGCTTTTGTGGATCAAGTTGTTGCATTTAATGATGTTCGTTACCTTAATATAA
TGATTTTCACTGCA
Found at i:730924 original size:47 final size:47
Alignment explanation
Indices: 730855--730950 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
730845 CAAAGTAAAT
730855 CAATTTCAAGGTCCTCACATTGGATGATATATTTATTTTTCGGAGTA
1 CAATTTCAAGGTCCTCACATTGGATGATATATTTATTTTTCGGAGTA
* * *
730902 CAATTTCAAGGTCCTTATATTGGATGATTTATTTATTTTTCGGAGTA
1 CAATTTCAAGGTCCTCACATTGGATGATATATTTATTTTTCGGAGTA
730949 CA
1 CA
730951 CTTGATGAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.43
Consensus pattern (47 bp):
CAATTTCAAGGTCCTCACATTGGATGATATATTTATTTTTCGGAGTA
Found at i:733688 original size:17 final size:17
Alignment explanation
Indices: 733631--733700 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 17
733621 TATTTAAGAT
733631 ATTTTAAAAAT--ATTA
1 ATTTTAAAAATAAATTA
* *
733646 AATATACAAAATAAATTA
1 ATTTTA-AAAATAAATTA
* *
733664 A--ATAAAAATAAATTT
1 ATTTTAAAAATAAATTA
733679 ATTTTAAAAATAAATTA
1 ATTTTAAAAATAAATTA
733696 ATTTT
1 ATTTT
733701 TACCATAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
15 15 0.33
16 8 0.18
17 17 0.38
18 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTTAAAAATAAATTA
Found at i:733768 original size:14 final size:14
Alignment explanation
Indices: 733725--733768 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
733715 AAAATTAAAT
733725 TAATTTA-ATTATA
1 TAATTTATATTATA
*
733738 TAATATATATT-TCA
1 TAATTTATATTAT-A
733752 TAATTTATATTATA
1 TAATTTATATTATA
733766 TAA
1 TAA
733769 AAATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.27
14 18 0.69
15 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTTATATTATA
Found at i:734370 original size:3 final size:3
Alignment explanation
Indices: 734362--734387 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
734352 TTAAGTTTGA
734362 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
734388 CTTAGTCTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:734761 original size:5 final size:5
Alignment explanation
Indices: 734751--734802 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
734741 TGACCATTGC
* * * *
734751 AGAAA AGAAA AGAAA AGAAA AGAAA GGAAA GGAAA GGAAA GGAAA CAGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA -AGAAA
734802 A
1 A
734803 TGCACATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
5 40 0.91
6 4 0.09
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:734771 original size:15 final size:15
Alignment explanation
Indices: 734751--734802 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
734741 TGACCATTGC
*
734751 AGAAAAGAAAAGAAA
1 AGAAAAGAAAGGAAA
734766 AGAAAAGAAAGGAAA
1 AGAAAAGAAAGGAAA
* *
734781 GGAAAGGAAAGGAAA
1 AGAAAAGAAAGGAAA
734796 CAGAAAA
1 -AGAAAA
734803 TGCACATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
15 27 0.87
16 4 0.13
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAGGAAA
Found at i:735621 original size:48 final size:48
Alignment explanation
Indices: 735550--735645 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
735540 TAATTCTACC
735550 AACCCATTTTAAATCCTGTCATCAAGCACATGGACAGAATTGCTGGAT
1 AACCCATTTTAAATCCTGTCATCAAGCACATGGACAGAATTGCTGGAT
735598 AACCCATTTTAAATCCTGTCATCAAGCACATGGACAGAATTGCTGGAT
1 AACCCATTTTAAATCCTGTCATCAAGCACATGGACAGAATTGCTGGAT
735646 TACTATGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (48 bp):
AACCCATTTTAAATCCTGTCATCAAGCACATGGACAGAATTGCTGGAT
Found at i:735723 original size:2 final size:2
Alignment explanation
Indices: 735716--735746 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
735706 TAGTGACTTC
*
735716 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
735747 GCAAATACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:735760 original size:15 final size:15
Alignment explanation
Indices: 735740--735773 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
735730 ATATATATAT
*
735740 AAATATAGCAAATAC
1 AAATATAGCAAAAAC
735755 AAATATAGCAAAAAC
1 AAATATAGCAAAAAC
735770 AAAT
1 AAAT
735774 GAACGAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATATAGCAAAAAC
Found at i:736220 original size:3 final size:3
Alignment explanation
Indices: 736212--736246 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
736202 GCTGCCCCCC
*
736212 ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
736247 CAAGAACCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Done.