Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001524.1 Hibiscus syriacus cultivar Beakdansim tig00002990_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 185638
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:962 original size:2 final size:2
Alignment explanation
Indices: 955--1008 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
945 GGCGCCCCTC
955 AT AT AT 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 AT AT AT
997 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1009 TAAATTATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9469 original size:92 final size:90
Alignment explanation
Indices: 9312--9490 Score: 225
Period size: 92 Copynumber: 2.0 Consensus size: 90
9302 AACTCTAACC
** * * * *
9312 TTTTTATTAATTTTTGAATTATTATACGACCTTGTGGTAACCCAATATGGGGTATGATCTACATT
1 TTTTTATTAATTTTTGAATTATTATACGACCTTGCAGTAACCCAATACGGGGTACGACCCACATT
*
9377 ATTA-TGGTTTGGACTCTATTAATCT
66 ATTACT-GTATGGACTCTATTAATCT
* * * *
9402 TTTTTATTAATTTTTTTGAATTATTATACGACCTTGCAGTGACCCGATCCGGGGTACGACCCGCA
1 TTTTTATTAA--TTTTTGAATTATTATACGACCTTGCAGTAACCCAATACGGGGTACGACCCACA
9467 TTATTACTGTATGGACTCTATTAA
64 TTATTACTGTATGGACTCTATTAA
9491 CACTAACTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
90 10 0.13
92 64 0.85
93 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (90 bp):
TTTTTATTAATTTTTGAATTATTATACGACCTTGCAGTAACCCAATACGGGGTACGACCCACATT
ATTACTGTATGGACTCTATTAATCT
Found at i:9519 original size:14 final size:14
Alignment explanation
Indices: 9500--9542 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
9490 ACACTAACTT
9500 TGCTAACCGCTAAC
1 TGCTAACCGCTAAC
*
9514 TGCTAACTGCTAAC
1 TGCTAACCGCTAAC
** *
9528 CACTAACCGTTAAC
1 TGCTAACCGCTAAC
9542 T
1 T
9543 TGTTATTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.26
Consensus pattern (14 bp):
TGCTAACCGCTAAC
Found at i:9541 original size:21 final size:21
Alignment explanation
Indices: 9500--9542 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9490 ACACTAACTT
* *
9500 TGCTAACCGCTAACTGCTAAC
1 TGCTAACCACTAACCGCTAAC
*
9521 TGCTAACCACTAACCGTTAAC
1 TGCTAACCACTAACCGCTAAC
9542 T
1 T
9543 TGTTATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.26
Consensus pattern (21 bp):
TGCTAACCACTAACCGCTAAC
Found at i:12887 original size:64 final size:63
Alignment explanation
Indices: 12811--12969 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 63
12801 AATTAAATTG
* *
12811 AACATCGAATGCATTTCATGCATCGATGCACATACCAT-CACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATACACCGATGCACTCAGGATATTT-TG-
12874 A
63 A
* * * *
12875 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATACATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATACACCGATGCACTCAGGATATTTTGA
**
12939 AACATCGAATGCACATGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
12970 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.74
65 18 0.21
66 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATACACCGATGCACTCAGGATATTTTGA
Found at i:21511 original size:65 final size:63
Alignment explanation
Indices: 21442--21601 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 63
21432 AATTAAATTG
* *
21442 AACATTGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTGAGGATATTT-TG-
21506 A
63 A
* * ** *
21507 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTGAGGATATTTTGA
* *
21571 AACATCGAATGTACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
21602 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.35
65 49 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTGAGGATATTTTGA
Found at i:21617 original size:64 final size:63
Alignment explanation
Indices: 21442--21621 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
21432 AATTAAATTG
* * * * *
21442 AACATTGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTGAGGATTTTATGAA
* * ** *
21507 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTT-TG-
1 AACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTGAGGAT-TTTATGA
21570 A
63 A
*
21571 AACATCGAATGTACTTGATGCATCGATGCACTCTTAG-TGCACCGATGCACT
1 AACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
21622 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 44 0.44
65 50 0.51
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTGAGGATTTTATGAA
Found at i:22789 original size:85 final size:81
Alignment explanation
Indices: 22693--22891 Score: 199
Period size: 80 Copynumber: 2.4 Consensus size: 81
22683 CATAGATTAT
* * **
22693 TATATTTATATATATTTTAATACTATATTATATTTATTTATTTTCACAAA-TATACTA-TATATT
1 TATATATATATATATTATAATACTATATTATA--TA--TA-TTTCA-AAACTATA-TATTATACA
22756 TATTTTTCAAACCACATATATA-
59 TATTTTTCAAACCACATATATAG
* *
22778 TATATATATATATATTCA-AACACTATATTCTATATATTTCAAAACTATATATTATACATATTTT
1 TATATATATATATATT-ATAATACTATATTATATATATTTCAAAACTATATATTATACATATTTT
* *
22842 TCAAACTATATATATAG
65 TCAAACCACATATATAG
* *
22859 TATATATATATATAACTATAATATTATATTATA
1 TATATATATATAT-ATTATAATACTATATTATA
22892 AAATAAACCA
Statistics
Matches: 96, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
79 5 0.05
80 33 0.34
81 16 0.17
82 13 0.14
83 2 0.02
85 27 0.28
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (81 bp):
TATATATATATATATTATAATACTATATTATATATATTTCAAAACTATATATTATACATATTTTT
CAAACCACATATATAG
Found at i:22812 original size:24 final size:22
Alignment explanation
Indices: 22784--22827 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 22
22774 TATATATATA
22784 TATATATATTCAAACACTATATTC
1 TATATAT-TTCAAA-ACTATATTC
22808 TATATATTTCAAAACTATAT
1 TATATATTTCAAAACTATAT
22828 ATTATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 7 0.35
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATATTTCAAAACTATATTC
Found at i:22828 original size:24 final size:23
Alignment explanation
Indices: 22774--22887 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 23
22764 AAACCACATA
22774 TATATATATATATATATATTCAAAC
1 TATATAT-TATATATAT-TTCAAAC
*
22799 -ACTATATTCTATATATTTCAAAAC
1 TA-TATATTATATATATTTC-AAAC
*
22823 TATATATTATACATATTTTTCAAAC
1 TATATATTAT--ATATATTTCAAAC
22848 TATATATATAGTATATATATAT-ATAAC
1 TATATAT-TA-TATATAT-T-TCA-AAC
22875 TATAATATTATAT
1 TAT-ATATTATAT
22888 TATAAAATAA
Statistics
Matches: 74, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
23 3 0.04
24 20 0.27
25 22 0.30
26 15 0.20
27 10 0.14
28 4 0.05
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.46
Consensus pattern (23 bp):
TATATATTATATATATTTCAAAC
Found at i:22833 original size:22 final size:25
Alignment explanation
Indices: 22776--22867 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 25
22766 ACCACATATA
22776 TATATATATATATATATTCAAACAC
1 TATATATATATATATATTCAAACAC
*
22801 TATAT-TCTATATAT-TTCAAA-AC
1 TATATATATATATATATTCAAACAC
* *
22823 TATATATTATACATATTTTTCAAACTA-
1 TATATA-TATATATA-TATTCAAAC-AC
22850 TATATATAGTATATATAT
1 TATATATA-TATATATAT
22868 ATATAACTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
22 7 0.13
23 6 0.11
24 14 0.25
25 6 0.11
26 10 0.18
27 11 0.20
28 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (25 bp):
TATATATATATATATATTCAAACAC
Found at i:22882 original size:15 final size:17
Alignment explanation
Indices: 22848--22887 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
22838 TTTTTCAAAC
*
22848 TATATATATAGTATATA
1 TATATATATACTATATA
22865 TATATATA-ACTATA-A
1 TATATATATACTATATA
22880 TAT-TATAT
1 TATATATAT
22888 TATAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 4 0.19
15 4 0.19
16 5 0.24
17 8 0.38
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATATATACTATATA
Found at i:22907 original size:15 final size:15
Alignment explanation
Indices: 22889--22934 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
22879 ATATTATATT
22889 ATAAAATAAACCAAA
1 ATAAAATAAACCAAA
*
22904 ATAAAATAAAACAAAA
1 ATAAAAT-AAACCAAA
*
22920 ATAAACTAAA-CAAA
1 ATAAAATAAACCAAA
22934 A
1 A
22935 GGAAACTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 10 0.37
16 13 0.48
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (15 bp):
ATAAAATAAACCAAA
Found at i:25201 original size:18 final size:19
Alignment explanation
Indices: 25178--25220 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
25168 TTGACCGTTG
25178 AATTTTAC-CAAAAAGTCA
1 AATTTTACTCAAAAAGTCA
*
25196 AATTTT-CTGAAAAAGTCA
1 AATTTTACTCAAAAAGTCA
*
25214 TATTTTA
1 AATTTTA
25221 TGTTTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (19 bp):
AATTTTACTCAAAAAGTCA
Found at i:29334 original size:16 final size:17
Alignment explanation
Indices: 29301--29339 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
29291 GGTCTTCATT
29301 TTAATTTGAAATAATTTA
1 TTAATTTG-AATAATTTA
*
29319 TTAATTTG-ATAGTTTA
1 TTAATTTGAATAATTTA
29335 TTAAT
1 TTAAT
29340 AATTTTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (17 bp):
TTAATTTGAATAATTTA
Found at i:29751 original size:37 final size:37
Alignment explanation
Indices: 29700--29953 Score: 325
Period size: 37 Copynumber: 7.1 Consensus size: 37
29690 TATATATAAA
*
29700 ATTTTGAAAACATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
* *
29737 GTTTTGAAAACATATATATAATATATAGTTTTTAAAAAAT
1 ATTTTG-AAA-ATATATATAATATATAGTTTTT-GAAAAT
**
29777 ATTTTGAAAATATATATAATATATAGTTTTAAAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
29814 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
*
29851 A---T-----TATATAT-ATATATAGTTTTTGAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
*
29879 ATTTTGAAAAAATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
*
29916 ATTTTGAAAATGTATAT-AT-TATAGTTTTT-AAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
29950 ATTT
1 ATTT
29954 ATATATTATA
Statistics
Matches: 193, Mismatches: 12, Indels: 27
0.83 0.05 0.12
Matches are distributed among these distances:
28 19 0.10
29 7 0.04
31 1 0.01
34 10 0.05
35 10 0.05
36 8 0.04
37 80 0.41
38 24 0.12
39 24 0.12
40 10 0.05
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (37 bp):
ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
Found at i:29786 original size:13 final size:12
Alignment explanation
Indices: 29766--29828 Score: 56
Period size: 13 Copynumber: 5.1 Consensus size: 12
29756 AATATATAGT
*
29766 TTTTAAAAAATA
1 TTTTAAAATATA
29778 TTTTGAAAATATA
1 TTTT-AAAATATA
* *
29791 -TATAATATATA
1 TTTTAAAATATA
*
29802 GTTTTAAAAAATA
1 -TTTTAAAATATA
29815 TTTTGAAAATATA
1 TTTT-AAAATATA
29828 T
1 T
29829 ATAATATATA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
11 7 0.17
12 10 0.25
13 23 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (12 bp):
TTTTAAAATATA
Found at i:29844 original size:26 final size:28
Alignment explanation
Indices: 29815--29877 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
29805 TTAAAAAATA
29815 TTTTGAAAATA-TATATA-ATATATAGT
1 TTTTGAAAATATTATATATATATATAGT
29841 TTTTGAAAATATTATATATATATATAGT
1 TTTTGAAAATATTATATATATATATAGT
29869 TTTTGAAAA
1 TTTTGAAAA
29878 CATTTTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 18 0.51
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTTGAAAATATTATATATATATATAGT
Found at i:29885 original size:65 final size:64
Alignment explanation
Indices: 29778--29918 Score: 230
Period size: 65 Copynumber: 2.2 Consensus size: 64
29768 TTAAAAAATA
* *
29778 TTTTGAAAATA-TATATAATATATAGTTTTAAAAAATATTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATTATATAATATATAGTTTTAAAAAACATTTTGAAAAAATATATAATATATAGT
**
29841 TTTTGAAAATATTATATATATATATAGTTTTTGAAAACATTTTGAAAAAATATATAATATATAGT
1 TTTTGAAAATATTATATA-ATATATAGTTTTAAAAAACATTTTGAAAAAATATATAATATATAGT
29906 TTTTGAAAATATT
1 TTTTGAAAATATT
29919 TTGAAAATGT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 11 0.15
64 6 0.08
65 55 0.76
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (64 bp):
TTTTGAAAATATTATATAATATATAGTTTTAAAAAACATTTTGAAAAAATATATAATATATAGT
Found at i:29894 original size:30 final size:28
Alignment explanation
Indices: 29815--29896 Score: 78
Period size: 28 Copynumber: 2.9 Consensus size: 28
29805 TTAAAAAATA
* *
29815 TTTTGAAAATA-TAT-ATAATATATAGT
1 TTTTGAAAACATTATAAAAATATATAGT
* * *
29841 TTTTGAAAATATTATATATATATATAGT
1 TTTTGAAAACATTATAAAAATATATAGT
*
29869 TTTTGAAAACATTTTGAAAAAATATATA
1 TTTTGAAAACATTAT--AAAAATATATA
29897 ATATATAGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 11 0.24
27 3 0.07
28 22 0.49
30 9 0.20
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (28 bp):
TTTTGAAAACATTATAAAAATATATAGT
Found at i:29897 original size:102 final size:101
Alignment explanation
Indices: 29738--29965 Score: 331
Period size: 102 Copynumber: 2.3 Consensus size: 101
29728 TTTGAAAATG
* * *
29738 TTTTGAAAACA-TATATATAATATATAGTTTTTAAAAAATATTTTGAAAATATATATAATATATA
1 TTTTGAAAATATTATATAT-ATATATAGTTTTTAAAAAACATTTTGAAAAAATATATAATATATA
29802 GTTTTAAAAAATATTTTGAAAATATATATAATATATAGT
65 GTTTTAAAAAATATTTTGAAAATATATAT-AT-TATAGT
*
29841 TTTTGAAAATATTATATATATATATAGTTTTT-GAAAACATTTTGAAAAAATATATAATATATAG
1 TTTTGAAAATATTATATATATATATAGTTTTTAAAAAACATTTTGAAAAAATATATAATATATAG
** *
29905 TTTTTGAAAATATTTTGAAAATGTATATATTATAGT
66 TTTTAAAAAATATTTTGAAAATATATATATTATAGT
29941 TTTT-AAAATATT-TATATAT-TATAGT
1 TTTTGAAAATATTATATATATATATAGT
29966 ATATTATTTG
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
97 6 0.05
98 7 0.06
99 8 0.07
100 10 0.09
101 2 0.02
102 54 0.46
103 23 0.20
104 7 0.06
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (101 bp):
TTTTGAAAATATTATATATATATATAGTTTTTAAAAAACATTTTGAAAAAATATATAATATATAG
TTTTAAAAAATATTTTGAAAATATATATATTATAGT
Found at i:29948 original size:23 final size:25
Alignment explanation
Indices: 29917--29965 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29907 TTTGAAAATA
29917 TTTTG-AAA-ATGTATATATTATAG
1 TTTTGAAAATATGTATATATTATAG
* *
29940 TTTTTAAAATATTTATATATTATAG
1 TTTTGAAAATATGTATATATTATAG
29965 T
1 T
29966 ATATTATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 3 0.14
25 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
TTTTGAAAATATGTATATATTATAG
Found at i:29968 original size:37 final size:37
Alignment explanation
Indices: 29849--29972 Score: 127
Period size: 35 Copynumber: 3.5 Consensus size: 37
29839 GTTTTTGAAA
* *
29849 ATATTATATATATA-TATAGTTTTTGAAAACATTTTG
1 ATATAATATATATATTATAGTTTTTGAAAATATTTTG
* *
29885 AAAAAATATATA-ATATATAGTTTTTGAAAATATTTTG
1 ATATAATATATATAT-TATAGTTTTTGAAAATATTTTG
*
29922 A-A-AATGTATATATTATAGTTTTT-AAAATA-TTT-
1 ATATAATATATATATTATAGTTTTTGAAAATATTTTG
*
29954 ATATATTATAGTATATTAT
1 ATATAATATA-TATATTAT
29973 TTGTTATATT
Statistics
Matches: 75, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.01
33 4 0.05
34 10 0.13
35 26 0.35
36 12 0.16
37 22 0.29
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (37 bp):
ATATAATATATATATTATAGTTTTTGAAAATATTTTG
Found at i:29983 original size:22 final size:22
Alignment explanation
Indices: 29944--30001 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
29934 TTATAGTTTT
*
29944 TAAAATATTTA-TATATTATAG
1 TAAATTATTTATTATATTATAG
* * *
29965 TATATTATTTGTTATATTATTG
1 TAAATTATTTATTATATTATAG
29987 TAAATTATTTATTAT
1 TAAATTATTTATTAT
30002 TTTCATTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 8 0.27
22 22 0.73
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TAAATTATTTATTATATTATAG
Found at i:30074 original size:13 final size:13
Alignment explanation
Indices: 30058--30095 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
30048 CCAAATAGGG
30058 AGTCCAAGATCCA
1 AGTCCAAGATCCA
* *
30071 AGTCCAAGGTTCA
1 AGTCCAAGATCCA
30084 AGTCCAA-ATCCA
1 AGTCCAAGATCCA
30096 GAGGGGATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (13 bp):
AGTCCAAGATCCA
Found at i:33184 original size:19 final size:19
Alignment explanation
Indices: 33151--33200 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
33141 GATCCTCATT
* *
33151 TTAATTTGA-AATAATTTA
1 TTAATTTAATAATAATATA
33169 TTAATTTAATAATAATATA
1 TTAATTTAATAATAATATA
*
33188 TTAATTTATTAAT
1 TTAATTTAATAAT
33201 TCCTTTTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAATTTAATAATAATATA
Found at i:35441 original size:64 final size:63
Alignment explanation
Indices: 35359--35515 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 63
35349 TTCAGTGTGT
* * *
35359 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCAAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCATT-AAAATGAAAACATCAAAGGCAATTAGTGC
* * ** * *
35423 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCAAAGGCAATTAGTGC
* *
35487 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
35516 ATGTTAAAGA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
63 3 0.04
64 69 0.86
65 8 0.10
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCAAAGGCAATTAGTGC
Found at i:35548 original size:20 final size:22
Alignment explanation
Indices: 35503--35560 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
35493 GCATGGGTAG
35503 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
35527 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
35547 TGTATCGATGCACT
1 TGCATCGATGCACT
35561 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:36776 original size:245 final size:245
Alignment explanation
Indices: 36346--36832 Score: 956
Period size: 245 Copynumber: 2.0 Consensus size: 245
36336 GGAACATATA
36346 AGATAAGCTAGATGGGAAAGATACATATGCTTAAATAAAATTATGATATATGGGTTGTATGATAG
1 AGATAAGCTAGATGGGAAAGATACATATGCTTAAATAAAATTATGATATATGGGTTGTATGATAG
*
36411 AAATCTAAGGAGTCATATTAGAAAGTTATAGGTATTATATGAACTGAATTAGGTAAATAGATTAG
66 AAATCTAAGGAGTCATATTAGAAAGTTATAGGTATTATATGAACTGAATTAAGTAAATAGATTAG
*
36476 ATTAGTATATAAATGAAATAATAGAAGTGATATATGTTTATAAGTATGACAGAGGTGATATGATC
131 ATTAGTATATAAATAAAATAATAGAAGTGATATATGTTTATAAGTATGACAGAGGTGATATGATC
36541 TAGGTGAATATCATAGAATAAGGTGTAAGCTATATGATATAATATAAATG
196 TAGGTGAATATCATAGAATAAGGTGTAAGCTATATGATATAATATAAATG
36591 AGATAAGCTAGATGGGAAAGATACATATGCTTAAATAAAATTATGATATATGGGTTGTATGATAG
1 AGATAAGCTAGATGGGAAAGATACATATGCTTAAATAAAATTATGATATATGGGTTGTATGATAG
36656 AAATCTAAGGAGTCATATTAGAAAGTTATAGGTATTATATGAACTGAATTAAGTAAATAGATTAG
66 AAATCTAAGGAGTCATATTAGAAAGTTATAGGTATTATATGAACTGAATTAAGTAAATAGATTAG
36721 ATTAGTATATAAATAAAATAATAGAAGTGATATATGTTTATAAGTATGACAGAGGTGATATGATC
131 ATTAGTATATAAATAAAATAATAGAAGTGATATATGTTTATAAGTATGACAGAGGTGATATGATC
36786 TAGGTGAATATCATAGAATAAGGTGTAAGCTATATGATATAATATAA
196 TAGGTGAATATCATAGAATAAGGTGTAAGCTATATGATATAATATAA
36833 GTTATTTTAT
Statistics
Matches: 240, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 240 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.32
Consensus pattern (245 bp):
AGATAAGCTAGATGGGAAAGATACATATGCTTAAATAAAATTATGATATATGGGTTGTATGATAG
AAATCTAAGGAGTCATATTAGAAAGTTATAGGTATTATATGAACTGAATTAAGTAAATAGATTAG
ATTAGTATATAAATAAAATAATAGAAGTGATATATGTTTATAAGTATGACAGAGGTGATATGATC
TAGGTGAATATCATAGAATAAGGTGTAAGCTATATGATATAATATAAATG
Found at i:37374 original size:23 final size:23
Alignment explanation
Indices: 37341--37408 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
37331 AACCTTATAT
37341 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
37364 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
37387 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
37409 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:39541 original size:36 final size:36
Alignment explanation
Indices: 39501--39579 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
39491 TCGATCGGTC
* *
39501 TACCTAATTGACCAATCATTTCCATTAATGTATATT
1 TACCTAATTAACCAATCATTTCCATTAATGCATATT
39537 TACCTAATTAACCAATCATTTCCATTAATGCATATT
1 TACCTAATTAACCAATCATTTCCATTAATGCATATT
39573 TA-CTAAT
1 TACCTAAT
39580 CCCTAAATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (36 bp):
TACCTAATTAACCAATCATTTCCATTAATGCATATT
Found at i:43526 original size:20 final size:20
Alignment explanation
Indices: 43489--43526 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43479 ATCCTAATCC
*
43489 CTGATAATCTTTCATTCCCA
1 CTGATAATCTTACATTCCCA
*
43509 CTGATAATCTTACGTTCC
1 CTGATAATCTTACATTCC
43527 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.08, T:0.39
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:44651 original size:7 final size:7
Alignment explanation
Indices: 44639--44665 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
44629 TTAACCGGAA
44639 TTAAATT
1 TTAAATT
44646 TTAAATT
1 TTAAATT
44653 TTAAATT
1 TTAAATT
44660 TTAAAT
1 TTAAAT
44666 ATATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:45005 original size:180 final size:185
Alignment explanation
Indices: 44645--45038 Score: 590
Period size: 184 Copynumber: 2.2 Consensus size: 185
44635 GGAATTAAAT
* *
44645 TTTAAATTT-TAAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAAC
1 TTTAAATTTAAAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAAC
*
44709 TCAATTAATAAATTAAGATTCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAATGTA
66 TCAATTAATAAATTAAGATCCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAATGTA
44774 TATAAAATTTTTATTTTATAATTATATATTATCTAAATTAATTGTAAACTGTTTA
131 TATAAAATTTTTATTTTATAATTATATATTATCTAAATTAATTGTAAACTGTTTA
*
44829 TTTAAATTTAAAAATATTAAATATA-TATATATAACATATGGGCTCAGCCCAAACTATTTAAAAC
1 TTTAAATTTAAAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAAC
* * * *
44893 TCAATTAATAATTTAAGATCCAATAACTTTTACACCTAAATCAATATTAATTAATTAAAAAT-T-
66 TCAATTAATAAATTAAGATCCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAATGTA
* * *
44956 TATATAA-TTTT-TTTTATAATTATATATTATTTAAATTAATTAG-AAACTGTTTT
131 TATAAAATTTTTATTTTATAATTATATATTATCTAAATTAATT-GTAAACTGTTTA
* * *
45009 TTTGAA-TTAAAAATATTTAAT-TTTTATATA
1 TTTAAATTTAAAAATATTAAATATATTATATA
45039 AATTAGAAAA
Statistics
Matches: 193, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
178 1 0.01
179 20 0.10
180 43 0.22
181 5 0.03
182 6 0.03
183 1 0.01
184 104 0.54
185 13 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (185 bp):
TTTAAATTTAAAAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAAC
TCAATTAATAAATTAAGATCCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAATGTA
TATAAAATTTTTATTTTATAATTATATATTATCTAAATTAATTGTAAACTGTTTA
Found at i:50294 original size:103 final size:101
Alignment explanation
Indices: 49883--50439 Score: 643
Period size: 102 Copynumber: 5.4 Consensus size: 101
49873 AGCAAATATC
* * *
49883 AAATCTTATCTCACTTGAGATTGTTTTTCTTCAAAAAATAATTTGGTCTCGCTTGAGACAATTTC
1 AAAT-TTATCTCACTTGAGATTGTTTTTCTT-AAAACA-AATTTCGTCTCGCTTGAGACATTTTC
* * *
49948 CCTTGAAACATAAATTTTAAGATCGTTTCACTCAAAATAA
63 CCTTGAAACACAAATTTTAA-ATCGTTTCACTCGAAACAA
* * * *
49988 AAACTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCGTTTGAGATAGTTTT-TC
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCGCTTGAGACA-TTTTCCC
50052 TTGAAACACAAATTTTAAGATCGTTTCACTCGAAACAA
65 TTGAAACACAAATTTTAA-ATCGTTTCACTCGAAACAA
* * *
50090 AAATTTATCTCACTTGAGATTATTTTTCTTAAAACCAATTTCGTCTCGCTTAAGACAATTTT-CC
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCGCTTGAGAC-ATTTTCCC
* * *
50154 TTGAAATATAAATTTTGAAATAGTTTCACTCGAAACAA
65 TTGAAACACAAATTTT-AAATCGTTTCACTCGAAACAA
* * *
50192 ACATTTATCTCACTTGAGATTGTTTTTCTTAAAAACAAATTAT-GTCTCGCTAGAGATATTTTCC
1 AAATTTATCTCACTTGAGATTGTTTTTCTT-AAAACAAATT-TCGTCTCGCTTGAGACATTTTCC
* * * **
50256 CCTGAAATACAAATTTTAATTTTTTTTCACTCGAAACAA
64 CTTGAAACACAAATTTTAA-ATCGTTTCACTCGAAACAA
* * * * * *
50295 AAATTTATTTCATTTGAGATTATTTTTTCTTAAAACCAATTTAGTCTCGCTTGAGACAGTTTCCC
1 AAATTTATCTCACTTGAGATT-GTTTTTCTTAAAACAAATTTCGTCTCGCTTGAGACATTTTCCC
* *
50360 TTGAAACACCAATTTTGAAATTGTTTCACTCGAAACAA
65 TTGAAACACAAATTTT-AAATCGTTTCACTCGAAACAA
* * * * *
50398 AATTTTATCCCACATGAGATAGCTTTTCTTAAAACAAATTTC
1 AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTC
50440 TTTTCGTCTA
Statistics
Matches: 388, Mismatches: 54, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
102 194 0.50
103 154 0.40
104 37 0.10
105 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (101 bp):
AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTCGTCTCGCTTGAGACATTTTCCCT
TGAAACACAAATTTTAAATCGTTTCACTCGAAACAA
Found at i:50434 original size:205 final size:203
Alignment explanation
Indices: 49883--50439 Score: 715
Period size: 206 Copynumber: 2.7 Consensus size: 203
49873 AGCAAATATC
* ** *
49883 AAATCTTATCTCACTTGAGATTGTTTTTCTTCAAAAAATAATTTGGTCTCGCTTGAGACAATTTC
1 AAAT-TTATCTCACTTGAGATTATTTTTCTT--AAAACCAATTTAGTCTCGCTTGAGACAATTTC
* * * *
49948 CCTTGAAACATAAATTTT-AAGATCGTTTCACTCAAAATAAAAACTTATCTCACTTGAGATTGTT
63 CCTTGAAACATAAATTTTGAA-ATAGTTTCACTCGAAA-CAAAATTTATCTCACTTGAGATTGTT
* * * *
50012 TTTCTTAAAACAAATTTCGTCTCGTTTGAGATAGTTTTTCTTGAAACACAAATTTTAAGATCGTT
126 TTTCTTAAAACAAATTTCGTCTCGCTAGAGATAGTTTTCCCTGAAACACAAATTTTAAGATCGTT
50077 TCACTCGAAACAA
191 TCACTCGAAACAA
* * *
50090 AAATTTATCTCACTTGAGATTATTTTTCTTAAAACCAATTTCGTCTCGCTTAAGACAATTTTCCT
1 AAATTTATCTCACTTGAGATTATTTTTCTTAAAACCAATTTAGTCTCGCTTGAGACAATTTCCCT
*
50155 TGAAATATAAATTTTGAAATAGTTTCACTCGAAACAAACATTTATCTCACTTGAGATTGTTTTTC
66 TGAAACATAAATTTTGAAATAGTTTCACTCGAAACAAA-ATTTATCTCACTTGAGATTGTTTTTC
* ** **
50220 TTAAAAACAAATTAT-GTCTCGCTAGAGATA-TTTTCCCCTGAAATACAAATTTTAATTTTTTTT
130 TT-AAAACAAATT-TCGTCTCGCTAGAGATAGTTTT-CCCTGAAACACAAATTTTAAGATCGTTT
50283 CACTCGAAACAA
192 CACTCGAAACAA
* * *
50295 AAATTTATTTCATTTGAGATTATTTTTTCTTAAAACCAATTTAGTCTCGCTTGAGACAGTTTCCC
1 AAATTTATCTCACTTGAGATTA-TTTTTCTTAAAACCAATTTAGTCTCGCTTGAGACAATTTCCC
** * * * * *
50360 TTGAAACACCAATTTTGAAATTGTTTCACTCGAAACAAAATTTTATCCCACATGAGATAGCTTTT
65 TTGAAACATAAATTTTGAAATAGTTTCACTCGAAACAAAA-TTTATCTCACTTGAGATTGTTTTT
50425 CTTAAAACAAATTTC
129 CTTAAAACAAATTTC
50440 TTTTCGTCTA
Statistics
Matches: 308, Mismatches: 34, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
203 3 0.01
204 90 0.29
205 89 0.29
206 122 0.40
207 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (203 bp):
AAATTTATCTCACTTGAGATTATTTTTCTTAAAACCAATTTAGTCTCGCTTGAGACAATTTCCCT
TGAAACATAAATTTTGAAATAGTTTCACTCGAAACAAAATTTATCTCACTTGAGATTGTTTTTCT
TAAAACAAATTTCGTCTCGCTAGAGATAGTTTTCCCTGAAACACAAATTTTAAGATCGTTTCACT
CGAAACAA
Found at i:51271 original size:27 final size:26
Alignment explanation
Indices: 51199--51292 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 26
51189 ATGAAAAAGA
*
51199 AAAAATGAGAAAAATTGAAAAATTGAAAG-
1 AAAAA-GAG-AAAATTGAAAAA-T-AGAGT
51228 AAGAAAGAAGAAAATTGAATAAA-AGAGT
1 AA-AAAG-AGAAAATTGAA-AAATAGAGT
51256 GAAAAAGAGAAAATTGAAAAATAGAGT
1 -AAAAAGAGAAAATTGAAAAATAGAGT
*
51283 AAAAAAAGAA
1 AAAAAGAGAA
51293 TAAATAAATG
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
26 12 0.21
27 19 0.33
28 4 0.07
29 14 0.25
30 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (26 bp):
AAAAAGAGAAAATTGAAAAATAGAGT
Found at i:52695 original size:8 final size:8
Alignment explanation
Indices: 52678--52708 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
52668 TTTCGTCCGA
52678 TTTA-TAT
1 TTTATTAT
52685 TTTATTAT
1 TTTATTAT
52693 TTTATTAT
1 TTTATTAT
52701 TTTATTAT
1 TTTATTAT
52709 AGTATGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTATTAT
Found at i:62533 original size:20 final size:20
Alignment explanation
Indices: 62508--62554 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
62498 CTGTCAAACT
62508 GTATTTGAGAAAATAAAGGA
1 GTATTTGAGAAAATAAAGGA
62528 GTATTTGAGAAAATAAAGGA
1 GTATTTGAGAAAATAAAGGA
62548 GTATTTG
1 GTATTTG
62555 TCTCACACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.30
Consensus pattern (20 bp):
GTATTTGAGAAAATAAAGGA
Found at i:64919 original size:15 final size:15
Alignment explanation
Indices: 64887--64943 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
64877 CTTAAATTGA
*
64887 AAAAATGAAAAGAAAG
1 AAAAATGAAAA-AGAG
*
64903 AAAAAGGAAAAAGAG
1 AAAAATGAAAAAGAG
*
64918 AAAAA--AGAAAGAG
1 AAAAATGAAAAAGAG
64931 -AAAATGAAAAAGA
1 AAAAATGAAAAAGA
64944 AAGAAGGTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 4 0.11
13 7 0.20
14 6 0.17
15 8 0.23
16 10 0.29
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (15 bp):
AAAAATGAAAAAGAG
Found at i:64940 original size:26 final size:25
Alignment explanation
Indices: 64894--64945 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
64884 TGAAAAAATG
64894 AAAAGAAAGAAAAAGGAAAAAGAGAA
1 AAAAGAAAGAAAAAGGAAAAA-AGAA
*
64920 AAAAGAAAGAGAAAATG-AAAAAGAA
1 AAAAGAAAGA-AAAAGGAAAAAAGAA
64945 A
1 A
64946 GAAGGTGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 14 0.58
27 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (25 bp):
AAAAGAAAGAAAAAGGAAAAAAGAA
Found at i:64946 original size:22 final size:23
Alignment explanation
Indices: 64888--64948 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
64878 TTAAATTGAA
64888 AAAATG-AAAAGAAAGAAAAAGG
1 AAAATGAAAAAGAAAGAAAAAGG
* * *
64910 AAAAAGAGAAA-AAAGAAAGA-G
1 AAAATGAAAAAGAAAGAAAAAGG
64931 AAAATGAAAAAGAAAGAA
1 AAAATGAAAAAGAAAGAA
64949 GGTGGGTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 10 0.31
22 19 0.59
23 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.03
Consensus pattern (23 bp):
AAAATGAAAAAGAAAGAAAAAGG
Found at i:65345 original size:39 final size:39
Alignment explanation
Indices: 65301--65376 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
65291 CCCTCCATCC
* *
65301 AGCAGCCCCTCCACGCATCATTTCCAGCAGCTTCCAGGG
1 AGCAGCCCCTCCACGCATCAGTTACAGCAGCTTCCAGGG
* *
65340 AGCAGCCCTTCCACGCATCAGTTACAGTAGCTTCCAG
1 AGCAGCCCCTCCACGCATCAGTTACAGCAGCTTCCAG
65377 CACTGCCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (39 bp):
AGCAGCCCCTCCACGCATCAGTTACAGCAGCTTCCAGGG
Found at i:66533 original size:29 final size:30
Alignment explanation
Indices: 66500--66556 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
66490 GGTTGTAAAT
66500 TTTAATATTT-TATATTTTAATC-CTATTAC
1 TTTAAT-TTTATATATTTTAATCACTATTAC
* *
66529 TTTAATTTTATATGTTTTAGTCACTATT
1 TTTAATTTTATATATTTTAATCACTATT
66557 TAATTACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTAATTTTATATATTTTAATCACTATTAC
Found at i:66664 original size:2 final size:2
Alignment explanation
Indices: 66645--66752 Score: 198
Period size: 2 Copynumber: 54.0 Consensus size: 2
66635 TATATTATTC
* *
66645 AT AT AA AT AT AA 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 AT AT AT
66687 AT AT AT 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 AT AT AT
66729 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
66753 GTTTAACTAA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 102 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71886 original size:10 final size:10
Alignment explanation
Indices: 71871--71895 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
71861 ATTATACTTG
71871 AAAAAAAAGA
1 AAAAAAAAGA
71881 AAAAAAAAGA
1 AAAAAAAAGA
71891 AAAAA
1 AAAAA
71896 TTGAACCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:72390 original size:32 final size:32
Alignment explanation
Indices: 72349--72410 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
72339 GTCAGACACA
* * *
72349 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAATATCTCTACAAGATAAGCATAACAACG
72381 AGAAATATCTCTACAAGATAAGCATAACAA
1 AGAAATATCTCTACAAGATAAGCATAACAA
72411 TAATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (32 bp):
AGAAATATCTCTACAAGATAAGCATAACAACG
Found at i:74120 original size:73 final size:73
Alignment explanation
Indices: 73945--74267 Score: 457
Period size: 73 Copynumber: 4.4 Consensus size: 73
73935 CTATTTCCAA
* * * * * *
73945 CATCCGTAAGCCCTGCAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGA--TCTT--A
*
74010 AACCCTCAGGGT
62 AAGCCTCAGGGT
* *
74022 CGTCTGTAAGACCTACAGTGCATGATGTTCTCAAAAAGCCTTCAGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATCTTAAAGC
74087 CTCAGGGT
66 CTCAGGGT
* ** * *
74095 CATCTGTAAGACCTATAGTGCATGATACTTTCAAAAAGCCTTCATGAGCTTTTTGTTCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATCTTAAAGC
74160 CTCAGGGT
66 CTCAGGGT
*
74168 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCCGGAGCTTTTTGATCTTAAAGC
1 CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATCTTAAAGC
74233 CTCAGGGT
66 CTCAGGGT
* *
74241 CATCTGTAAGCCCTACAGTGCAAGATG
1 CATCTGTAAGACCTACAGTGCATGATG
74268 ATAAGACCTC
Statistics
Matches: 222, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
73 170 0.77
75 3 0.01
77 49 0.22
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (73 bp):
CATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATCTTAAAGC
CTCAGGGT
Found at i:74589 original size:123 final size:124
Alignment explanation
Indices: 74432--74757 Score: 426
Period size: 124 Copynumber: 2.6 Consensus size: 124
74422 ATTAGCGTTG
* * * *
74432 CCAGAGAAAGTTCATAATGAGAATAATTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
1 CCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
* *
74497 CTTGTTCAACCTTTTGCATGACT-C-TATCACAAAAGGAGATAGATCAACACCAACT-TTT
66 CTTGTTCAACCTTTTGCATGACTCCATATC-CAAAAAGAGATAGAGCAACA-CAACTATTT
* *
74555 CCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGTAA-AAGGAAGTTCATAATGAGAACA
1 CCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAA-GAAGTTCATAATGAGAAGA
* * * *
74619 ACTTGTTCAACCTTTTGCTTGACTCCATTTCCAAAAAGAGATAGAGCAACAGAGCTATTT
65 ACTTGTTCAACCTTTTGCATGACTCCATATCCAAAAAGAGATAGAGCAACACAACTATTT
*** * * * *
74679 CCAGGTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGGAAAAAGTTCATAATGATAAGAA
1 CCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
74744 CTTGTTCAACCTTT
66 CTTGTTCAACCTTT
74758 CATTGATTCA
Statistics
Matches: 177, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
122 2 0.01
123 81 0.46
124 89 0.50
125 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (124 bp):
CCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCATGACTCCATATCCAAAAAGAGATAGAGCAACACAACTATTT
Found at i:74924 original size:139 final size:139
Alignment explanation
Indices: 74685--75030 Score: 471
Period size: 139 Copynumber: 2.5 Consensus size: 139
74675 ATTTCCAGGT
* * * *
74685 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGGAAAAAGTTCATAATGATAAGAACTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * *
74750 CAACCTTTCATTGATTCATCTCATATGGAATTGAATGAAAGAAAAACCTCATTTGAGGATCAATA
66 CAACCTTACATTAATTCATCACATATGGAATTGAAT-AAACAAAAACCTCATTTGAAGATCAATA
*
74815 TTTTCAG-AG
130 TTTCCAGAAG
* *
74824 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTATAATAAGAAGAATTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * ** * *
74889 CAACCTTACCTTAATTCATCACATATGGAGTTGAATCAACAAATCCCTCTTTTGAAGATCAGTAT
66 CAACCTTACATTAATTCATCACATATGGAATTGAATAAACAAAAACCTCATTTGAAGATCAATAT
74954 TTCCAGAAG
131 TTCCAGAAG
* * *
74963 G-AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
75027 CAAC
66 CAAC
75031 TTTTTGCTAG
Statistics
Matches: 182, Mismatches: 24, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
138 89 0.49
139 93 0.51
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (139 bp):
GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTACATTAATTCATCACATATGGAATTGAATAAACAAAAACCTCATTTGAAGATCAATAT
TTCCAGAAG
Found at i:75073 original size:138 final size:137
Alignment explanation
Indices: 74674--75030 Score: 339
Period size: 138 Copynumber: 2.6 Consensus size: 137
74664 GCAACAGAGC
* * * *
74674 TATTTCCAG-GTGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGGAAA-AAGTTCATAATG
1 TATTTCCAGAG-GAAGTTCATAATGAGAAGAACTCATCTGAAAAAGA-AAAAGAAGTTCATAATA
* * * * * * * * * *
74737 ATAAGAACTTGTTCAACCTTTCATTGATTCATCTCATATGGAATTGAATGAAA-GAA-AA-ACCT
64 AGAAGAATTTGTTCAACCTTACCTTAATTCATCACAGA-AGAA--G-AT-AAATCAACAATCCCT
*
74799 CATTTGAGGATCAA
124 CATTTGAAGATCAA
* * * * *
74813 TATTTTCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTTATAATAAG
1 TATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAAAGAAGTTCATAATAAG
* * * * * *
74878 AAGAATTTGTTCAACCTTACCTTAATTCATCACATATGGAGTTGAATCAACAAATCCCTCTTTTG
66 AAGAATTTGTTCAACCTTACCTTAATTCATCACAGAAGAAGATAAATCAAC-AATCCCTCATTTG
*
74943 AAGATCAG
130 AAGATCAA
*
74951 TATTTCCAGAAGG-AGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAAAGAAGTTCATAATGA
1 TATTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAAAGAAGTTCATAATAA
75015 GAAGAATTTGTTCAAC
65 GAAGAATTTGTTCAAC
75031 TTTTTGCTAG
Statistics
Matches: 185, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
134 2 0.01
135 3 0.02
136 1 0.01
137 2 0.01
138 88 0.48
139 88 0.48
140 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (137 bp):
TATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAAAAGAAAAAGAAGTTCATAATAAG
AAGAATTTGTTCAACCTTACCTTAATTCATCACAGAAGAAGATAAATCAACAATCCCTCATTTGA
AGATCAA
Found at i:75323 original size:39 final size:39
Alignment explanation
Indices: 75279--75355 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
75269 CCCTCCATCC
*
75279 AGCAGCCCCTCCACGCATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACGCATCAGTTCCAGCAGCTTCCAGCG
* *
75318 AGCAGCCCCTCCATGCATCAGTTGCAGCAGCTTCCAGC
1 AGCAGCCCCTCCACGCATCAGTTCCAGCAGCTTCCAGC
75356 ACTGTCAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.21, C:0.42, G:0.19, T:0.18
Consensus pattern (39 bp):
AGCAGCCCCTCCACGCATCAGTTCCAGCAGCTTCCAGCG
Found at i:76500 original size:29 final size:30
Alignment explanation
Indices: 76467--76523 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
76457 GGTTGTAAAT
76467 TTTAATATTT-TATATTTTAATC-CTATTAC
1 TTTAAT-TTTATATATTTTAATCACTATTAC
* *
76496 TTTAATTTTATATGTTTTAGTCACTATT
1 TTTAATTTTATATATTTTAATCACTATT
76524 TAATTGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 16 0.67
30 5 0.21
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (30 bp):
TTTAATTTTATATATTTTAATCACTATTAC
Found at i:76625 original size:2 final size:2
Alignment explanation
Indices: 76612--76643 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
76602 TATATTATTC
*
76612 AT AT AA 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
76644 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:76648 original size:2 final size:2
Alignment explanation
Indices: 76643--76669 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
76633 TATATATATA
76643 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
76670 AACTAATAAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:79223 original size:27 final size:27
Alignment explanation
Indices: 79193--79250 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
79183 CAACACACAA
79193 AAACACACAAGAAATCACACGAAGAGG
1 AAACACACAAGAAATCACACGAAGAGG
* *
79220 AAACGCTCAAGAAATCACACGAAGAGG
1 AAACACACAAGAAATCACACGAAGAGG
79247 AAAC
1 AAAC
79251 GCTTAAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.53, C:0.22, G:0.19, T:0.05
Consensus pattern (27 bp):
AAACACACAAGAAATCACACGAAGAGG
Found at i:79251 original size:27 final size:27
Alignment explanation
Indices: 79200--79263 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
79190 CAAAAACACA
79200 CAAGAAATCACACGAAGAGGAAACGCT
1 CAAGAAATCACACGAAGAGGAAACGCT
79227 CAAGAAATCACACGAAGAGGAAACGCT
1 CAAGAAATCACACGAAGAGGAAACGCT
*
79254 TAAGAAATCA
1 CAAGAAATCA
79264 AAGCATTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.50, C:0.20, G:0.20, T:0.09
Consensus pattern (27 bp):
CAAGAAATCACACGAAGAGGAAACGCT
Found at i:79992 original size:28 final size:30
Alignment explanation
Indices: 79944--80002 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 30
79934 CTATTATATG
*
79944 TATATATATTTTGTATCATTATTTTATTTA
1 TATATATATTTTGTATCATTATTTCATTTA
79974 TATATATATATTT-T-T-ATTATTTCATTTA
1 TATATATAT-TTTGTATCATTATTTCATTTA
80002 T
1 T
80003 TTATTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 13 0.48
29 1 0.04
30 10 0.37
31 3 0.11
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (30 bp):
TATATATATTTTGTATCATTATTTCATTTA
Found at i:80087 original size:2 final size:2
Alignment explanation
Indices: 80082--80117 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
80072 TTTTATATGC
80082 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
80118 TTTTTCCTTT
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:80548 original size:14 final size:14
Alignment explanation
Indices: 80528--80561 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
80518 TCGATTGCTC
*
80528 CTTTTATTTTCTTT
1 CTTTTATTTTATTT
*
80542 GTTTTATTTTATTT
1 CTTTTATTTTATTT
80556 CTTTTA
1 CTTTTA
80562 ATTCTTCAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.76
Consensus pattern (14 bp):
CTTTTATTTTATTT
Found at i:80974 original size:19 final size:19
Alignment explanation
Indices: 80947--80985 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
80937 ACATCGAATG
*
80947 CATTTCATGCATCGATGCA
1 CATTCCATGCATCGATGCA
80966 CATTCCATGCATCGATGCA
1 CATTCCATGCATCGATGCA
80985 C
1 C
80986 TGAGGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (19 bp):
CATTCCATGCATCGATGCA
Found at i:81005 original size:65 final size:63
Alignment explanation
Indices: 80886--81095 Score: 228
Period size: 65 Copynumber: 3.3 Consensus size: 63
80876 TTTTTCATAG
* * * **
80886 TGATGCACCGATGCACCAATTCATGCATCGATGCAC-CATGAAATAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-G-GATATTTTGAAACATCGAATGCA
80949 TT
62 TT
* * *
80951 TCATGCATCGATGCACATTCCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
81015 T
63 T
* * *
81016 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
81080 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
81096 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 48 0.39
65 65 0.52
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:81095 original size:17 final size:19
Alignment explanation
Indices: 81067--81115 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
81057 TATTTTGAAA
81067 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
81085 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
81104 CACCGATGCACT
1 CATCGATGCACT
81116 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:86975 original size:23 final size:22
Alignment explanation
Indices: 86907--86984 Score: 104
Period size: 23 Copynumber: 3.5 Consensus size: 22
86897 CACCTAATAA
86907 TGCATCGATGCATCCTTGAATG
1 TGCATCGATGCATCCTTGAATG
* * *
86929 TGCATCGATACA-CCATGAAGG
1 TGCATCGATGCATCCTTGAATG
*
86950 TGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCAT-CCTTGAATG
86973 TGCATCGATGCA
1 TGCATCGATGCA
86985 CAAGGTCATG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 17 0.37
22 11 0.24
23 18 0.39
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:87002 original size:43 final size:42
Alignment explanation
Indices: 86910--87007 Score: 99
Period size: 44 Copynumber: 2.3 Consensus size: 42
86900 CTAATAATGC
* * *
86910 ATCGATGCATCCTTGAATGTGCATCGATACACCATGAAGGTGC
1 ATCGATGCATCCTTGAATGTGCATCGATACACAAGGAA-GTGA
* * *
86953 ACCGATGCATGCCTTGAATGTGCATCGATGCACAAGGTCA-TGA
1 ATCGATGCAT-CCTTGAATGTGCATCGATACACAAGG-AAGTGA
*
86996 ATCGATGTATCC
1 ATCGATGCATCC
87008 GTCGGGTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
42 2 0.04
43 19 0.42
44 23 0.51
45 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (42 bp):
ATCGATGCATCCTTGAATGTGCATCGATACACAAGGAAGTGA
Found at i:88563 original size:21 final size:21
Alignment explanation
Indices: 88521--88564 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
88511 ACTCCGGGAG
* *
88521 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
88542 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
88563 CT
1 CT
88565 CCTCCGGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:89004 original size:25 final size:24
Alignment explanation
Indices: 88959--89008 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 24
88949 ATTTGGATGC
88959 TTGGTTGATTTAACTTATTATATAT
1 TTGGTTGATTTAACTTATTAT-TAT
88984 TTGGTTTGATTTTAACTTTATTATT
1 TTGG-TTGA-TTTAAC-TTATTATT
89009 TTGAGCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 7 0.32
28 7 0.32
ACGTcount: A:0.24, C:0.04, G:0.12, T:0.60
Consensus pattern (24 bp):
TTGGTTGATTTAACTTATTATTAT
Found at i:89793 original size:19 final size:19
Alignment explanation
Indices: 89763--89815 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
89753 AAACATCGAA
*
89763 TGCACTTGATGCACTTTTAG
1 TGCAC-TGATGCACTCTTAG
89783 TGCACTGATGCACTCTTAG
1 TGCACTGATGCACTCTTAG
*
89802 TGCACCGATGCACT
1 TGCACTGATGCACT
89816 AAGGGTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (19 bp):
TGCACTGATGCACTCTTAG
Found at i:91430 original size:29 final size:29
Alignment explanation
Indices: 91370--91430 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
91360 TGTCCTTTTC
** * *
91370 TTTTATTTTGATTTGGTCTCACTATTTTA
1 TTTTATTTCAATTTGGTCCCACTATTTAA
91399 TTTTATTTCAATTTGGTCACCACT-TTTAA
1 TTTTATTTCAATTTGGTC-CCACTATTTAA
91428 TTT
1 TTT
91431 GTTATTACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.20, C:0.13, G:0.08, T:0.59
Consensus pattern (29 bp):
TTTTATTTCAATTTGGTCCCACTATTTAA
Found at i:99068 original size:12 final size:13
Alignment explanation
Indices: 99045--99073 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
99035 AACAAATATG
99045 AAATTATAAATTT
1 AAATTATAAATTT
99058 AAATT-TAAATTT
1 AAATTATAAATTT
99070 AAAT
1 AAAT
99074 AAATTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTATAAATTT
Found at i:99762 original size:21 final size:21
Alignment explanation
Indices: 99712--99765 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
99702 CCATAACAGG
*
99712 GGGTATCAATACCCCTTCAAA
1 GGGTATCAGTACCCCTTCAAA
* *
99733 GTGTATCAGTTCCCCTTCAAA
1 GGGTATCAGTACCCCTTCAAA
99754 GGGTATCAGTAC
1 GGGTATCAGTAC
99766 TTCCTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
GGGTATCAGTACCCCTTCAAA
Found at i:99842 original size:19 final size:19
Alignment explanation
Indices: 99818--99874 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
99808 TTGGAGCCTT
99818 GGGTATGGATACCCAGTAG
1 GGGTATGGATACCCAGTAG
*
99837 GGGTATCGATACCCAG-A-
1 GGGTATGGATACCCAGTAG
99854 ---TATGGATACCCA-TAG
1 GGGTATGGATACCCAGTAG
99869 GGGTAT
1 GGGTAT
99875 CAGTACCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 12 0.39
18 4 0.13
19 15 0.48
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.23
Consensus pattern (19 bp):
GGGTATGGATACCCAGTAG
Found at i:99929 original size:22 final size:22
Alignment explanation
Indices: 99904--99948 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
99894 GATGTTTGAG
*
99904 CAATCATAGGGGTATTGATACC
1 CAATCATAGGGGTATCGATACC
99926 CAATCATAGGGGTATCGATACC
1 CAATCATAGGGGTATCGATACC
99948 C
1 C
99949 TGGTATGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (22 bp):
CAATCATAGGGGTATCGATACC
Found at i:101051 original size:22 final size:21
Alignment explanation
Indices: 101011--101051 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
101001 AATTTGAGCC
*
101011 TTCATGGGGTATTGATACCCA
1 TTCATGGGGTATCGATACCCA
*
101032 TTCATAGGGGTATCGGTACC
1 TTCAT-GGGGTATCGATACC
101052 TCTTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (21 bp):
TTCATGGGGTATCGATACCCA
Found at i:101295 original size:21 final size:19
Alignment explanation
Indices: 101267--101324 Score: 73
Period size: 18 Copynumber: 3.0 Consensus size: 19
101257 TGTTTAATGA
101267 AAAAGATACCAATTGCTTAC
1 AAAAGATACCAATTG-TTAC
*
101287 AAAATGATATCAATTGTTA-
1 AAAA-GATACCAATTGTTAC
*
101306 AAAAAATACCAATTGTTAC
1 AAAAGATACCAATTGTTAC
101325 CAATTGTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
20 7 0.21
21 10 0.30
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (19 bp):
AAAAGATACCAATTGTTAC
Found at i:103876 original size:22 final size:22
Alignment explanation
Indices: 103842--103883 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
103832 TTTAATATCA
*
103842 ATACCCATGCATAGGAGTATTG
1 ATACACATGCATAGGAGTATTG
* *
103864 ATACACATTCATAGGGGTAT
1 ATACACATGCATAGGAGTAT
103884 CGGTACCTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (22 bp):
ATACACATGCATAGGAGTATTG
Found at i:106611 original size:33 final size:34
Alignment explanation
Indices: 106574--106644 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
106564 CCTTTACAAC
* *
106574 TCCCTAG-TTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGAGATAAACTAGAACCTT
* * *
106607 TCCCTAGCTTTTACACGAGCTTAGCTAGAACCTT
1 TCCCTAGCTTTTACACGAGATAAACTAGAACCTT
106641 TCCC
1 TCCC
106645 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGAGATAAACTAGAACCTT
Found at i:107340 original size:2 final size:2
Alignment explanation
Indices: 107331--107464 Score: 74
Period size: 2 Copynumber: 70.5 Consensus size: 2
107321 ATAAAATAAT
*
107331 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * ** *
107371 TA TA TA TA -A TG TA CA T- TA TA CTA -A TG CA TA CG T- TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
107410 TA -A GTA TA TA CT- TA T- TA TA TA TA TA CT- TT 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
107449 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
107465 GTATGATGAA
Statistics
Matches: 101, Mismatches: 16, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
1 11 0.11
2 85 0.84
3 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:119168 original size:21 final size:21
Alignment explanation
Indices: 119143--119202 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
119133 ATTTTAACCT
119143 AAAGGGATCGATCCTTTTAGA
1 AAAGGGATCGATCCTTTTAGA
119164 AAAGGGATCGATCCTTTTAGA
1 AAAGGGATCGATCCTTTTAGA
*
119185 AAAGGGATCGATCTTTTT
1 AAAGGGATCGATCCTTTT
119203 CTGGAAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (21 bp):
AAAGGGATCGATCCTTTTAGA
Found at i:120725 original size:23 final size:23
Alignment explanation
Indices: 120694--120737 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
120684 TGTCAACATC
* * *
120694 CTTCTTCTTCTTGTTTTTCTTTT
1 CTTCATCTTCTTCTTGTTCTTTT
120717 CTTCATCTTCTTCTTGTTCTT
1 CTTCATCTTCTTCTTGTTCTT
120738 CCTCCTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.25, G:0.05, T:0.68
Consensus pattern (23 bp):
CTTCATCTTCTTCTTGTTCTTTT
Found at i:122434 original size:2 final size:2
Alignment explanation
Indices: 122427--122465 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
122417 AAAGTATGTA
* *
122427 TG TG TG TG TA TG TG TG TG TG TG TG TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
122466 ACTTATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:122438 original size:10 final size:10
Alignment explanation
Indices: 122423--122466 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
122413 CAGAAAAGTA
122423 TGTATGTGTG
1 TGTATGTGTG
122433 TGTATGTGTG
1 TGTATGTGTG
* *
122443 TGTGTGTGTA
1 TGTATGTGTG
*
122453 TGTGTGTGTG
1 TGTATGTGTG
122463 TGTA
1 TGTA
122467 CTTATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.09, C:0.00, G:0.41, T:0.50
Consensus pattern (10 bp):
TGTATGTGTG
Found at i:122439 original size:14 final size:14
Alignment explanation
Indices: 122420--122466 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
122410 CAACAGAAAA
122420 GTATGTATGTGTGT
1 GTATGTATGTGTGT
122434 GTATG--TGTGTGT
1 GTATGTATGTGTGT
*
122446 GTGTGTATGTGTGT
1 GTATGTATGTGTGT
*
122460 GTGTGTA
1 GTATGTA
122467 CTTATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.37
14 19 0.63
ACGTcount: A:0.11, C:0.00, G:0.40, T:0.49
Consensus pattern (14 bp):
GTATGTATGTGTGT
Found at i:122448 original size:16 final size:16
Alignment explanation
Indices: 122427--122465 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
122417 AAAGTATGTA
122427 TGTGTGTGTATGTGTG
1 TGTGTGTGTATGTGTG
122443 TGTGTGTGTATGTGTG
1 TGTGTGTGTATGTGTG
122459 TGTGTGT
1 TGTGTGT
122466 ACTTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.05, C:0.00, G:0.44, T:0.51
Consensus pattern (16 bp):
TGTGTGTGTATGTGTG
Found at i:122513 original size:2 final size:2
Alignment explanation
Indices: 122506--122610 Score: 80
Period size: 2 Copynumber: 54.0 Consensus size: 2
122496 AAAATATTAT
*
122506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
122547 GTA TA AA GTA TA -A GTA TA TA TG TA TA -A GTA TA T- TA -A TA TA
1 -TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* *
122587 AA T- TA T- TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
122611 CATACATTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
1 7 0.08
2 72 0.87
3 4 0.05
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:122690 original size:32 final size:32
Alignment explanation
Indices: 122575--122696 Score: 99
Period size: 32 Copynumber: 3.8 Consensus size: 32
122565 TATGTATAAG
* *
122575 TATATTAATATAAATTATTAAA-TA-TATATA
1 TATATAAATATAAATTATTAAAGTATTAAATA
* * * * *
122605 TATATACATACATTAATAAATTGAAGTATTGAAGTA
1 TATATA-A-ATATAAAT-TATTAAAGTATT-AAATA
* *
122641 TATAT--ATAAAAAGTATTAAAGTATTAAATA
1 TATATAAATATAAATTATTAAAGTATTAAATA
122671 TATATAAATATAAATTATTAAAGTAT
1 TATATAAATATAAATTATTAAAGTAT
122697 ATATAAATAA
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
30 14 0.21
31 11 0.16
32 27 0.40
33 5 0.07
34 2 0.03
35 1 0.01
36 8 0.12
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (32 bp):
TATATAAATATAAATTATTAAAGTATTAAATA
Found at i:122703 original size:25 final size:25
Alignment explanation
Indices: 122642--122705 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
122632 ATTGAAGTAT
*
122642 ATATATAAAAAGTATTAAAGTATTAA
1 ATATATATAAA-TATTAAAGTATTAA
*
122668 ATATATATAAATA-TAAATTATTAA
1 ATATATATAAATATTAAAGTATTAA
122692 AGTATATATAAATA
1 A-TATATATAAATA
122706 AATTATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 11 0.31
25 14 0.40
26 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
ATATATATAAATATTAAAGTATTAA
Found at i:122706 original size:23 final size:24
Alignment explanation
Indices: 122642--122717 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 24
122632 ATTGAAGTAT
* *
122642 ATATATAAAAAGTATTAAAGTATTAA
1 ATATATATAAA-TA-TAAATTATTAA
122668 ATATATATAAATATAAATTATTAA
1 ATATATATAAATATAAATTATTAA
*
122692 AGTATATAT-AA-ATAAATTATAAA
1 A-TATATATAAATATAAATTATTAA
122715 ATA
1 ATA
122718 CATAGGATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.04
23 12 0.26
24 13 0.28
25 9 0.20
26 10 0.22
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
ATATATATAAATATAAATTATTAA
Found at i:123470 original size:83 final size:83
Alignment explanation
Indices: 123379--123535 Score: 228
Period size: 83 Copynumber: 1.9 Consensus size: 83
123369 CCTAAACCTA
*
123379 AATCTCAAATCCCAAACATTATTCATCCCCTATTCCTCTTCTTTAAAT-AAGACTCTT-CCTCTT
1 AATCTCAAATCCCAAACATTATTCATCCCCTATTCCTCTTCTCT-AATCAAGACTCTTCCCT-TT
*
123442 CCCCTTTTTCTATTTCCCAT
64 CCCCTTCTTCTATTTCCCAT
* * * *
123462 AATCTCAAATCCCAAACATTATTTATCTCTTATTCCTCTTCTCTAATCGAGACTCTTCCCTTTCC
1 AATCTCAAATCCCAAACATTATTCATCCCCTATTCCTCTTCTCTAATCAAGACTCTTCCCTTTCC
123527 CCTTCTTCT
66 CCTTCTTCT
123536 TCTTCTGTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 3 0.05
83 60 0.91
84 3 0.05
ACGTcount: A:0.23, C:0.34, G:0.02, T:0.41
Consensus pattern (83 bp):
AATCTCAAATCCCAAACATTATTCATCCCCTATTCCTCTTCTCTAATCAAGACTCTTCCCTTTCC
CCTTCTTCTATTTCCCAT
Found at i:128971 original size:24 final size:25
Alignment explanation
Indices: 128933--128980 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
128923 CAATAACTAA
128933 ATTATATAATAAAATTATTT-TAATG
1 ATTATATAATAAAATT-TTTATAATG
*
128958 ATTA-ATAATTAAATTTTTATAAT
1 ATTATATAATAAAATTTTTATAAT
128981 ATAAGGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTATATAATAAAATTTTTATAATG
Found at i:134446 original size:2 final size:2
Alignment explanation
Indices: 134439--134473 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
134429 ATCCAAAATA
134439 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
134474 CAACAGTCAT
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:135684 original size:16 final size:16
Alignment explanation
Indices: 135663--135694 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
135653 TATGTCAGTT
135663 TTGATGCCAAAAAAAA
1 TTGATGCCAAAAAAAA
135679 TTGATGCCAAAAAAAA
1 TTGATGCCAAAAAAAA
135695 ACACAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (16 bp):
TTGATGCCAAAAAAAA
Found at i:146755 original size:17 final size:17
Alignment explanation
Indices: 146733--146766 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
146723 ATAATTGAGA
*
146733 TTTTTATTTTTAAAATT
1 TTTTTATCTTTAAAATT
*
146750 TTTTTATCTTTACAATT
1 TTTTTATCTTTAAAATT
146767 GAGATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATCTTTAAAATT
Found at i:146896 original size:42 final size:43
Alignment explanation
Indices: 146775--147458 Score: 563
Period size: 43 Copynumber: 16.3 Consensus size: 43
146765 TTGAGATTTT
* * * * *
146775 TAATTTTTGTAATCTCACTATTTATCTTTATAATTGATACCTC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* * *
146818 TAATTTTTTTCAATCTTACTTTTTACATTTATAATTGAGACCCT
1 TAATTTTTTT-AATCTCACTTTTTACCTTTATAATTGAGACCCC
* * * *
146862 TAATTTTGTTATTC-CAATTTTTACCTTTATAATTGAGGCCCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* * * * * *
146904 TAACTTTTTTCATCTCATTTTTTACTTTTTATAGTTGATG-CCTC
1 TAATTTTTTTAATCTCACTTTTTAC-CTTTATAATTGA-GACCCC
* * * *
146948 TAATTTTTTCAATCTCACTTTCTACCTTTATGATTGA-AGCTCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGA-CCCC
* * *
146991 TATTTTTTTTATTATCACTTTTTACCTTTATAATTGAGACCCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
147034 TAA------T--T-T---TTTTTACCTTTATAATTGAGACCCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* * * *
147065 T-ATTTTTTTAATCTTACTTTCTAGCTTTAAAATTGA-AGCCCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGA-CCCC
* * * ***
147107 TAATTTTTTTAATCTCACTTTTTACCTTTATAACTAAGGCTTT
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* * * *
147150 TAATCTTTTTCATCTCACTTTTTACC--T-T--TTGAGGCCCT
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* *
147188 TAATTTTTTTCAATTTCACTTTTTACCTTTATAATTGAAACCCC
1 TAATTTTTTT-AATCTCACTTTTTACCTTTATAATTGAGACCCC
* * * * *
147232 TAATTTTTTTCGATCTCGCCTTTTACCTTTATAATTGA-AGTCTC
1 TAATTTTTTT-AATCTCACTTTTTACCTTTATAATTGAGA-CCCC
** * * *
147276 TAATTTTTTTAATCTCACTTTTTATATTTATAACTGAGGCCCT
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* ** *
147319 TAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCA
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* *
147362 TAA-TTTTTTAATCTCATTTTTTACCTTTATAATTAAG-CCCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* * *
147403 TAATTTTTTTAATCTCACTTTTTAGCTTTACAATTGAGGCCCC
1 TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
* *
147446 CAATTTTTCTAAT
1 TAATTTTTTTAAT
147459 TCAACCTTTT
Statistics
Matches: 510, Mismatches: 99, Indels: 64
0.76 0.15 0.10
Matches are distributed among these distances:
30 1 0.00
31 26 0.05
34 1 0.00
35 1 0.00
36 1 0.00
37 1 0.00
38 16 0.03
39 15 0.03
40 1 0.00
41 8 0.02
42 116 0.23
43 200 0.39
44 122 0.24
45 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.50
Consensus pattern (43 bp):
TAATTTTTTTAATCTCACTTTTTACCTTTATAATTGAGACCCC
Found at i:147044 original size:31 final size:30
Alignment explanation
Indices: 147009--147073 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 30
146999 TTATTATCAC
147009 TTTTTACCTTTATAATTGAGACCCCTAATTT
1 TTTTTACCTTTATAATTGAGACCCCT-ATTT
147040 TTTTTACCTTTATAATTGAGACCCCTATTT
1 TTTTTACCTTTATAATTGAGACCCCTATTT
147070 TTTT
1 TTTT
147074 AATCTTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.52
Consensus pattern (30 bp):
TTTTTACCTTTATAATTGAGACCCCTATTT
Found at i:147107 original size:73 final size:74
Alignment explanation
Indices: 146970--147116 Score: 185
Period size: 73 Copynumber: 2.0 Consensus size: 74
146960 TCTCACTTTC
* * * * *
146970 TACCTTTATGATTGAAGCTCCTATTTTTTTTATTATCACTTTTTACCTTTATAATTGAGACCCCT
1 TACCTTTATAATTGAAGCCCCTATTTTTTTAATTATCACTTTCTACCTTTAAAATTGAGACCCCT
147035 AATTTTTTT
66 AATTTTTTT
*
147044 TACCTTTATAATTG-AGACCCCTATTTTTTTAATCT-T-ACTTTCTAGCTTTAAAATTGA-AGCC
1 TACCTTTATAATTGAAG-CCCCTATTTTTTTAAT-TATCACTTTCTACCTTTAAAATTGAGA-CC
147105 CCTAATTTTTTT
63 CCTAATTTTTTT
147117 AATCTCACTT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
72 1 0.02
73 34 0.53
74 28 0.44
75 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.50
Consensus pattern (74 bp):
TACCTTTATAATTGAAGCCCCTATTTTTTTAATTATCACTTTCTACCTTTAAAATTGAGACCCCT
AATTTTTTT
Found at i:147159 original size:44 final size:43
Alignment explanation
Indices: 147040--147537 Score: 400
Period size: 43 Copynumber: 11.7 Consensus size: 43
147030 CCCCTAATTT
* * *
147040 TTTTTACCTTTATAATTGAGACCCCT-ATTTTTTTAATCTTAC
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTCAC
* * *
147082 TTTCTAGCTTTAAAATTGAA-GCCCCTAATTTTTTTAATCTCAC
1 TTTTTACCTTTATAATT-AAGGCCCCTAATTTTTTTAATCTCAC
* *** * *
147125 TTTTTACCTTTATAACTAAGGCTTTTAATCTTTTTCATCTCAC
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTCAC
* * *
147168 TTTTTACC--T-T--TTGAGGCCCTTAATTTTTTTCAATTTCAC
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTT-AATCTCAC
* * *
147207 TTTTTACCTTTATAATTGAA-ACCCCTAATTTTTTTCGATCTCGC
1 TTTTTACCTTTATAATT-AAGGCCCCTAATTTTTTT-AATCTCAC
* * *
147251 CTTTTACCTTTATAATTGAA-GTCTCTAATTTTTTTAATCTCAC
1 TTTTTACCTTTATAATT-AAGGCCCCTAATTTTTTTAATCTCAC
** * * * *
147294 TTTTTATATTTATAACTGAGGCCCTTAATTTTTTCAATCTCAC
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTCAC
* * * *
147337 TTTTTACCTTTATAATTGAGGTCCATAA-TTTTTTAATCTCAT
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTCAC
147379 TTTTTACCTTTATAATTAA-GCCCCTAATTTTTTTAATCTCAC
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTCAC
* * * * *
147421 TTTTTAGCTTTACAATTGAGGCCCCCAATTTTTCTAAT-TCAAC
1 TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTC-AC
* * * * *
147464 CTTTTA-CTTTCATAACTT-ACGCTCCC-AATTCTTCTAATC-CAA
1 TTTTTACCTTT-ATAA-TTAAGGC-CCCTAATTTTTTTAATCTCAC
*
147506 TCTTTTACTTTTATAACTT-AGGCCCCTAATTT
1 T-TTTTACCTTTATAA-TTAAGGCCCCTAATTT
147538 AATCATTTTT
Statistics
Matches: 367, Mismatches: 68, Indels: 41
0.77 0.14 0.09
Matches are distributed among these distances:
38 15 0.04
39 14 0.04
40 1 0.00
41 8 0.02
42 92 0.25
43 176 0.48
44 60 0.16
45 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (43 bp):
TTTTTACCTTTATAATTAAGGCCCCTAATTTTTTTAATCTCAC
Found at i:147159 original size:116 final size:116
Alignment explanation
Indices: 146950--147413 Score: 290
Period size: 116 Copynumber: 3.8 Consensus size: 116
146940 GATGCCTCTA
** * * *
146950 ATTTTTTCAATCTCACTTTCTACCTTTATGATTGAAGCTCCTATTTTTTTTATTATCACTTTTTA
1 ATTTTTTCAATCTCACTTTCTACCTTTAAAATTGAAGCCCCTAATTTTTTTAATATCACTTTTTA
* * *
147015 CCTTTATAATTGAGACCCCTAATTTTTTTTACCTTTATAATTGAGACCCCT
66 CCTTTATAACTAAGACCCCTAATCTTTTTTACCTTTATAATTGAGACCCCT
* * * *
147066 ATTTTTTTAATCTTACTTTCTAGCTTTAAAATTGAAGCCCCTAATTTTTTTAATCTCACTTTTTA
1 ATTTTTTCAATCTCACTTTCTACCTTTAAAATTGAAGCCCCTAATTTTTTTAATATCACTTTTTA
* *** * * * * *
147131 CCTTTATAACTAAGGCTTTTAATCTTTTTCATCTCACTTTTTACCTTTTGAGGCCCTT
66 CCTTTATAACTAAGACCCCTAATCTTTTT--T-AC-CTTTATA---ATTGAGACCCCT
* * * * * * * *
147189 AATTTTTTTCAATTTCACTTTTTACCTTTATAATTGAAACCCCTAATTTTTTTCGATCTCGCCTT
1 -A-TTTTTTCAATCTCACTTTCTACCTTTAAAATTGAAGCCCCTAATTTTTTT-AATATCACTTT
* * * *
147254 TTACCTTTATAATTGAAG-TCTCTAAT-TTTTTTAATCTCACTTTTTATATTTATAACTGAGGCC
63 TTACCTTTATAACT-AAGACCCCTAATCTTTTTT-A---C-C--TTTATA---AT---TGAGACC
*
147317 CTT
114 CCT
* * * * * * *
147320 AATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGGTCCATAA-TTTTTTAATCTCATTTTTT
1 -ATTTTTTCAATCTCACTTTCTACCTTTAAAATTGAAGCCCCTAATTTTTTTAATATCACTTTTT
*
147384 ACCTTTATAATTAAG-CCCCTAAT-TTTTTTA
65 ACCTTTATAACTAAGACCCCTAATCTTTTTTA
147414 ATCTCACTTT
Statistics
Matches: 277, Mismatches: 52, Indels: 28
0.78 0.15 0.08
Matches are distributed among these distances:
116 78 0.28
118 1 0.00
119 1 0.00
120 6 0.02
123 10 0.04
124 1 0.00
125 48 0.17
126 30 0.11
127 18 0.06
128 28 0.10
129 6 0.02
130 38 0.14
131 12 0.04
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (116 bp):
ATTTTTTCAATCTCACTTTCTACCTTTAAAATTGAAGCCCCTAATTTTTTTAATATCACTTTTTA
CCTTTATAACTAAGACCCCTAATCTTTTTTACCTTTATAATTGAGACCCCT
Found at i:147178 original size:21 final size:20
Alignment explanation
Indices: 147112--147179 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
147102 GCCCCTAATT
147112 TTTTTAATCTCACTTTTTACC
1 TTTTT-ATCTCACTTTTTACC
* * * * *
147133 TTTATAACTAAGGCTTTTAATC
1 TTTTTATCTCA--CTTTTTACC
147155 TTTTTCATCTCACTTTTTACC
1 TTTTT-ATCTCACTTTTTACC
147176 TTTT
1 TTTT
147180 GAGGCCCTTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
22 11 0.32
23 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTATCTCACTTTTTACC
Found at i:147336 original size:169 final size:169
Alignment explanation
Indices: 147040--147480 Score: 522
Period size: 169 Copynumber: 2.6 Consensus size: 169
147030 CCCCTAATTT
* *
147040 TTTTTACCTTTATAATTGAGACCCCT-ATTTTTTTAATCTTA-CTTTCTAGCTTTAAAATTGAAG
1 TTTTTACCTTTATAATTGAAACCCCTAATTTTTTTAATCTCACCTTT-TAGCTTTAAAATTGAAG
* **
147103 CCCCTAATTTTTTTAATCTCACTTTTTACCTTTATAACTAAGGCTTTTAATCTTTTTCATCTCAC
65 CCCCTAATTTTTTTAATCTCACTTTTTACATTTATAACTAAGGCCCTTAATCTTTTTCATCTCAC
* *
147168 TTTTTACC-T-T-TTGAGGCCCTTAATTTTTTTCAATTTCAC
130 TTTTTACCTTATATTGAGGCCCATAA-TTTTTT-AATCTCAC
* * * *
147207 TTTTTACCTTTATAATTGAAACCCCTAATTTTTTTCGATCTCGCCTTTTACCTTTATAATTGAAG
1 TTTTTACCTTTATAATTGAAACCCCTAATTTTTTT-AATCTCACCTTTTAGCTTTAAAATTGAAG
* * * *
147272 TCTCTAATTTTTTTAATCTCACTTTTTATATTTATAACTGAGGCCCTTAAT-TTTTTCAATCTCA
65 CCCCTAATTTTTTTAATCTCACTTTTTACATTTATAACTAAGGCCCTTAATCTTTTTC-ATCTCA
* *
147336 CTTTTTACCTTTATAATTGAGGTCCATAATTTTTTAATCTCAT
129 CTTTTTACC-TTAT-ATTGAGGCCCATAATTTTTTAATCTCAC
* * * *
147379 TTTTTACCTTTATAATT-AAGCCCCTAATTTTTTTAATCTCACTTTTTAGCTTTACAATTGAGGC
1 TTTTTACCTTTATAATTGAAACCCCTAATTTTTTTAATCTCACCTTTTAGCTTTAAAATTGAAGC
* * *
147443 CCCCAATTTTTCTAAT-TCAACCTTTTAC-TTTCATAACT
66 CCCTAATTTTTTTAATCTC-ACTTTTTACATTT-ATAACT
147481 TACGCTCCCA
Statistics
Matches: 233, Mismatches: 30, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
167 25 0.11
168 14 0.06
169 83 0.36
170 53 0.23
171 17 0.07
172 24 0.10
173 6 0.03
174 11 0.05
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.49
Consensus pattern (169 bp):
TTTTTACCTTTATAATTGAAACCCCTAATTTTTTTAATCTCACCTTTTAGCTTTAAAATTGAAGC
CCCTAATTTTTTTAATCTCACTTTTTACATTTATAACTAAGGCCCTTAATCTTTTTCATCTCACT
TTTTACCTTATATTGAGGCCCATAATTTTTTAATCTCAC
Found at i:150308 original size:31 final size:31
Alignment explanation
Indices: 150270--150425 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
150260 AGGGTCGAGG
150270 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
150301 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
150332 GTTTACCTATGTTCTTCGGGATATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
150363 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
150394 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
150425 G
1 G
150426 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:154405 original size:31 final size:31
Alignment explanation
Indices: 154367--154491 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
154357 AGGGTCGAGG
154367 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
154398 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
154429 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
154460 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
154491 G
1 G
154492 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:158490 original size:31 final size:31
Alignment explanation
Indices: 158452--158576 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
158442 AGGGTCGAGG
* *
158452 GTTTACCTATGTTCTTCGTGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
158483 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
158514 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
158545 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
158576 G
1 G
158577 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:158864 original size:17 final size:18
Alignment explanation
Indices: 158838--158871 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
158828 AATGATGATG
158838 ATGATATATGTT-TATGT
1 ATGATATATGTTATATGT
*
158855 ATGATTTATGTTATATG
1 ATGATATATGTTATATG
158872 AAATATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
ATGATATATGTTATATGT
Found at i:164795 original size:23 final size:22
Alignment explanation
Indices: 164768--164816 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
164758 GTCGGAGTGT
* *
164768 GGCGGAGGATGGCTGACGGCGGC
1 GGCGGAGG-TGGCGGACGACGGC
164791 GGC-G-GGTGGCGGACGACGGC
1 GGCGGAGGTGGCGGACGACGGC
164811 GGCGGA
1 GGCGGA
164817 CAACTAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
20 15 0.68
21 3 0.14
22 1 0.05
23 3 0.14
ACGTcount: A:0.12, C:0.22, G:0.59, T:0.06
Consensus pattern (22 bp):
GGCGGAGGTGGCGGACGACGGC
Found at i:164800 original size:20 final size:20
Alignment explanation
Indices: 164777--164815 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
164767 TGGCGGAGGA
* *
164777 TGGCTGACGGCGGCGGCGGG
1 TGGCGGACGACGGCGGCGGG
164797 TGGCGGACGACGGCGGCGG
1 TGGCGGACGACGGCGGCGG
164816 ACAACTAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.26, G:0.59, T:0.08
Consensus pattern (20 bp):
TGGCGGACGACGGCGGCGGG
Found at i:166189 original size:14 final size:14
Alignment explanation
Indices: 166170--166217 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
166160 TGAGAATGTT
166170 TCTTTATTCTTTTC
1 TCTTTATTCTTTTC
***
166184 TCTTTAAAATTTTC
1 TCTTTATTCTTTTC
166198 -CTTTTATTCTTTTC
1 TC-TTTATTCTTTTC
166212 TCTTTA
1 TCTTTA
166218 AAATTTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTATTCTTTTC
Found at i:166224 original size:14 final size:14
Alignment explanation
Indices: 166179--166241 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
166169 TTCTTTATTC
166179 TTTTCTCTTTAAAA
1 TTTTCTCTTTAAAA
***
166193 TTTTC-CTTTTATTC
1 TTTTCTC-TTTAAAA
166207 TTTTCTCTTTAAAA
1 TTTTCTCTTTAAAA
*
166221 TTTTTCATTTTTAAAA
1 -TTTTC-TCTTTAAAA
166237 TTTTC
1 TTTTC
166242 CGATGCAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
13 1 0.03
14 18 0.47
15 11 0.29
16 8 0.21
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTCTCTTTAAAA
Found at i:172566 original size:20 final size:19
Alignment explanation
Indices: 172529--172589 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 19
172519 GTATCGATCC
*
172529 AAAATGAT-ATACCAGGTAA
1 AAAATGATAAAACC-GGTAA
172548 AAATATGATAAAACCGGTAA
1 AAA-ATGATAAAACCGGTAA
172568 CAAAATGATAAAACCGGTAA
1 -AAAATGATAAAACCGGTAA
172588 AA
1 AA
172590 CGTTACCGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 26 0.68
21 7 0.18
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAATGATAAAACCGGTAA
Found at i:172658 original size:180 final size:182
Alignment explanation
Indices: 172336--172803 Score: 646
Period size: 181 Copynumber: 2.6 Consensus size: 182
172326 GATCCAAATT
* * * * * *
172336 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACC-GT-AC----CGGTA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* * * * * *
172395 AAGCGCCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
66 AA--ACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
*
172460 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTT-A
129 TCGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
172513 AAAAATGTATCGATCCAAAATGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
172578 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
172642 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
172694 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
* *
172759 AAACCGGTAAAATGATACCAGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
172804 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
177 45 0.17
178 2 0.01
179 2 0.01
180 64 0.25
181 141 0.54
183 5 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (182 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:172747 original size:20 final size:19
Alignment explanation
Indices: 172710--172770 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
172700 ATATCGATCC
* * *
172710 AAAACGATATAACAGGTAA
1 AAAATGATAAAACCGGTAA
*
172729 AAATATGATAAAACCGGTATC
1 AAA-ATGATAAAACCGGTA-A
172750 AAAATGATAAAACCGGTAA
1 AAAATGATAAAACCGGTAA
172769 AA
1 AA
172771 TGATACCAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAATGATAAAACCGGTAA
Found at i:172772 original size:17 final size:19
Alignment explanation
Indices: 172733--172775 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
172723 AGGTAAAAAT
172733 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
172753 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
172770 ATGATA
1 ATGATA
172776 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:174999 original size:21 final size:21
Alignment explanation
Indices: 174973--175037 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
174963 AAGACAATCA
*
174973 AGAGTCGAAGATAAACTTGAT
1 AGAGTCGAAGATAAACTTGAG
*
174994 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGATAAACTTGAG
*
175015 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATAAACTTGAG
175036 AG
1 AG
175038 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGATAAACTTGAG
Found at i:175113 original size:33 final size:33
Alignment explanation
Indices: 175071--175136 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
175061 AAATAGATGG
*
175071 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
175104 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
175137 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:176953 original size:19 final size:19
Alignment explanation
Indices: 176929--176996 Score: 109
Period size: 19 Copynumber: 3.6 Consensus size: 19
176919 AATGTAGGGT
*
176929 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
176948 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
*
176967 TATTTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
*
176986 TATTTTTGTAT
1 TAATTTTGTAT
176997 GTGAATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:177461 original size:200 final size:200
Alignment explanation
Indices: 177118--178072 Score: 1592
Period size: 200 Copynumber: 4.9 Consensus size: 200
177108 TATGGCCAAA
* *
177118 AGGGTGCAACAATAAAGTGTCGAACCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
* *
177183 AAAGTATAATGTAATATGTAATTTTCCAATCTAACTGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
177248 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
177313 AAAAC
196 AAAAC
* **
177318 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTTGATCCCAAAAACATCGAAACCTT
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
*
177383 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
*
177448 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATAGTTTTTGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
177513 AAAAC
196 AAAAC
*
177518 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCTATCCCAAAAACATCGAAACCCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
*
177583 AAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
**
177648 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTAATTGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
177713 AAAAC
196 AAAAC
177718 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
*
177783 AAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAAGTATACCGGTTTTATGAGAGAA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
177848 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
177913 AAAAC
196 AAAAC
* * *
177918 AGGGTGCAACCATAAAGTGTCGATCC-----CAAAAA----C-AT--C--GAA-A-C----CCAA
1 AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
* *
177963 A-AGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGCA
66 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
178027 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATT
131 TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATT
178073 AATTTAAATA
Statistics
Matches: 726, Mismatches: 29, Indels: 21
0.94 0.04 0.03
Matches are distributed among these distances:
179 106 0.15
180 4 0.01
184 1 0.00
185 1 0.00
186 2 0.00
188 1 0.00
190 2 0.00
191 1 0.00
195 5 0.01
200 603 0.83
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (200 bp):
AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTTGTCCAGAATGAATGG
AAAAC
Found at i:179544 original size:6 final size:6
Alignment explanation
Indices: 179533--179620 Score: 68
Period size: 6 Copynumber: 14.7 Consensus size: 6
179523 CAAGCGGTCA
* * * * *
179533 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * * *
179581 CTGACG ATGAAG ATGATG ACGATG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
179621 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:179570 original size:3 final size:3
Alignment explanation
Indices: 179550--179624 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
179540 TGAAGCTGAC
* * * * * * *
179550 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
179598 GAC GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
179625 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.07, G:0.33, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:179585 original size:36 final size:36
Alignment explanation
Indices: 179533--179614 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
179523 CAAGCGGTCA
*
179533 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
* *
179569 ATGACGATGAAGCTGACGATGAAGATGATGACGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
*
179605 ATGATGATGA
1 ATGAAGATGA
179615 TGATGATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.21
Consensus pattern (36 bp):
ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
Found at i:179624 original size:12 final size:12
Alignment explanation
Indices: 179533--179620 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
179523 CAAGCGGTCA
*
179533 ATGAAGATGAAG
1 ATGACGATGAAG
*
179545 CTGACGATGAAG
1 ATGACGATGAAG
*
179557 ATGACGATGATG
1 ATGACGATGAAG
179569 ATGACGATGAAG
1 ATGACGATGAAG
*
179581 CTGACGATGAAG
1 ATGACGATGAAG
* * *
179593 ATGATGACGATG
1 ATGACGATGAAG
* *
179605 ATGATGATGATG
1 ATGACGATGAAG
179617 ATGA
1 ATGA
179621 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Done.