Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009037.1 Hibiscus syriacus cultivar Beakdansim tig00112444_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: 144382
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:4768 original size:21 final size:21
Alignment explanation
Indices: 4742--4803 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
4732 TTTTGGTGCA
*
4742 GAGGGAATCGATTCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
4763 GAGGGAACCGATT-CCCCTTT
1 GAGGGAACCGATTCCCCCCCT
4783 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
4804 ACAGGGAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 6 0.18
21 13 0.38
22 11 0.32
23 4 0.12
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:8300 original size:14 final size:14
Alignment explanation
Indices: 8262--8300 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
8252 CTAGATCGTG
*
8262 AACCCTAAACCTTT
1 AACCCTAAACCTTC
* *
8276 AACCTTCAACCTTC
1 AACCCTAAACCTTC
8290 AACCCTAAACC
1 AACCCTAAACC
8301 ATAAACTATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTAAACCTTC
Found at i:8375 original size:19 final size:20
Alignment explanation
Indices: 8330--8391 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
8320 TATAGTACAT
* * *
8330 GTATGTATAAACCATGTATA
1 GTATATATAAACTATATATA
8350 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
* *
8370 -TATATATAAACTTTATAAA
1 GTATATATAAACTATATATA
8389 GTA
1 GTA
8392 AATTACTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:8478 original size:49 final size:49
Alignment explanation
Indices: 8375--8478 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
8365 ATATATATAT
* * ** **
8375 ATAAACTTTATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAACC
*
8424 ATAAACTATATAAAGT-AATAAAATATATAGTTTATAGAAACCCTAAACC
1 ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACT-AACC
*
8473 CTAAAC
1 ATAAAC
8479 CAAAAATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 24 0.52
49 22 0.48
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAATATATAGTTTATAGAAACACTAACC
Found at i:8903 original size:2 final size:2
Alignment explanation
Indices: 8891--8945 Score: 67
Period size: 2 Copynumber: 27.0 Consensus size: 2
8881 ATAAACCAAG
* *
8891 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA -A CA TA TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8934 TA TA TA TA TA TA
1 TA TA TA TA TA TA
8946 AAGTAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.02
2 43 0.91
3 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:8918 original size:17 final size:17
Alignment explanation
Indices: 8891--8945 Score: 71
Period size: 15 Copynumber: 3.4 Consensus size: 17
8881 ATAAACCAAG
8891 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
8909 TATATATATAT-AAC-A
1 TATATATATATAAACTA
*
8924 TATATATATATATA-TA
1 TATATATATATAAACTA
8940 TATATA
1 TATATA
8946 AAGTAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 12 0.35
16 11 0.32
17 7 0.21
18 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:9039 original size:7 final size:7
Alignment explanation
Indices: 9029--9093 Score: 58
Period size: 7 Copynumber: 9.3 Consensus size: 7
9019 TAGTTTATAG
9029 AAACCCT
1 AAACCCT
9036 AAACCCT
1 AAACCCT
9043 AAACCCT
1 AAACCCT
**
9050 AAACTTT
1 AAACCCT
*
9057 AAACCTT
1 AAACCCT
**
9064 AAATACT
1 AAACCCT
*
9071 AACCCCT
1 AAACCCT
*
9078 AAACCAT
1 AAACCCT
*
9085 AAACTCT
1 AAACCCT
9092 AA
1 AA
9094 TATAAATGGA
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:9446 original size:20 final size:19
Alignment explanation
Indices: 9414--9472 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 19
9404 ATTTTAATTA
*
9414 ATAT-GTATGTATAAACCAT
1 ATATAGTATATATAAACC-T
*
9433 GTATAGTATATATAAA-CT
1 ATATAGTATATATAAACCT
9451 ATATA-TATATATAAA-CT
1 ATATAGTATATATAAACCT
9468 ATATA
1 ATATA
9473 AAGTAAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.47
18 5 0.14
19 4 0.11
20 10 0.28
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (19 bp):
ATATAGTATATATAAACCT
Found at i:9453 original size:9 final size:9
Alignment explanation
Indices: 9441--9474 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
9431 ATGTATAGTA
9441 TATATAAAC
1 TATATAAAC
*
9450 TATATATA-
1 TATATAAAC
9458 TATATAAAC
1 TATATAAAC
9467 TATATAAA
1 TATATAAA
9475 GTAAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (9 bp):
TATATAAAC
Found at i:9461 original size:17 final size:18
Alignment explanation
Indices: 9434--9472 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
9424 ATAAACCATG
9434 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
9452 TATA-TATATATAAACTA
1 TATAGTATATATAAACTA
9469 TATA
1 TATA
9473 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:9886 original size:15 final size:15
Alignment explanation
Indices: 9863--9912 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
9853 ACCTAATTAA
* *
9863 TTATGTTTATATAAT
1 TTATATTTAAATAAT
9878 TTATATTTAAATAAT
1 TTATATTTAAATAAT
9893 TT-TA-TTAAATAATT
1 TTATATTTAAATAA-T
9907 TTATAT
1 TTATAT
9913 AATATGTATC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 8 0.27
14 5 0.17
15 17 0.57
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATATTTAAATAAT
Found at i:9916 original size:13 final size:13
Alignment explanation
Indices: 9873--9910 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
9863 TTATGTTTAT
9873 ATAATTTATATTTAA
1 ATAATTT-TA-TTAA
9888 ATAATTTTATTAA
1 ATAATTTTATTAA
9901 ATAATTTTAT
1 ATAATTTTAT
9911 ATAATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.61
14 2 0.09
15 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATAATTTTATTAA
Found at i:9997 original size:2 final size:2
Alignment explanation
Indices: 9950--9988 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
9940 ATATGTAAAC
*
9950 TA TA TA TA -A AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9989 AACTATATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:10082 original size:7 final size:7
Alignment explanation
Indices: 10072--10132 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
10062 TAGTTTATAG
10072 AAACCTT
1 AAACCTT
10079 AAACCTT
1 AAACCTT
*
10086 AAACCCT
1 AAACCTT
* *
10093 AAATCAT
1 AAACCTT
*
10100 AAACCCT
1 AAACCTT
10107 AAATCC-T
1 AAA-CCTT
*
10114 AAACTTT
1 AAACCTT
*
10121 AAACCAT
1 AAACCTT
10128 AAACC
1 AAACC
10133 ATAATGTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
6 1 0.02
7 41 0.93
8 2 0.05
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACCTT
Found at i:10095 original size:14 final size:14
Alignment explanation
Indices: 10072--10132 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
10062 TAGTTTATAG
* *
10072 AAACCTTAAACCTT
1 AAACCCTAAACCAT
*
10086 AAACCCTAAATCAT
1 AAACCCTAAACCAT
10100 AAACCCTAAATCC-T
1 AAACCCTAAA-CCAT
**
10114 AAACTTTAAACCAT
1 AAACCCTAAACCAT
10128 AAACC
1 AAACC
10133 ATAATGTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 2 0.05
14 35 0.92
15 1 0.03
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:10123 original size:21 final size:20
Alignment explanation
Indices: 10076--10132 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
10066 TTATAGAAAC
*
10076 CTTAAACCTTAAACCCTAAA
1 CTTAAACCATAAACCCTAAA
* * *
10096 TCATAAACCCTAAATCCTAAA
1 -CTTAAACCATAAACCCTAAA
10117 CTTTAAACCATAAACC
1 C-TTAAACCATAAACC
10133 ATAATGTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (20 bp):
CTTAAACCATAAACCCTAAA
Found at i:10323 original size:23 final size:23
Alignment explanation
Indices: 10296--10344 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
10286 TTATTTTTTC
10296 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATT-AACTATATTAA
10319 TTTATATAAATTAACTATATTAA
1 TTTATATAAATTAACTATATTAA
10342 TTT
1 TTT
10345 TCCATTACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATATAAATTAACTATATTAA
Found at i:15685 original size:67 final size:67
Alignment explanation
Indices: 15577--15711 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
15567 AAGATGGATC
*
15577 GTTTTACATGCTGAGAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
1 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
15642 AT
66 AT
*
15644 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATGTTGGTGTTTACT
1 GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
15709 AT
66 AT
15711 G
1 G
15712 CAGATTATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (67 bp):
GTTTTACATGCTGAAAGGAAACAATCAGAGAGAACCACTTATCGGAGAAGATATTGGTGTTTACT
AT
Found at i:16822 original size:43 final size:43
Alignment explanation
Indices: 16775--16906 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
16765 ACAAATGCTG
* * * *
16775 CTAAAATTCATTATATATAGTGGCATTTTTTAC-TGAAACATCA
1 CTAAAAGTCATTATATATAGTGGCGTTTTTCACGT-AAACACCA
* * * *
16818 CTAAAGGTCATGATATATAGTGGCGTTTTACACGTAAACGCCA
1 CTAAAAGTCATTATATATAGTGGCGTTTTTCACGTAAACACCA
**
16861 CTAAAAGTCA-TATATATAGTGGCGTTTTTCACACAAACACCA
1 CTAAAAGTCATTATATATAGTGGCGTTTTTCACGTAAACACCA
16903 CTAA
1 CTAA
16907 GTTTAATTGA
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
42 31 0.42
43 42 0.57
44 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (43 bp):
CTAAAAGTCATTATATATAGTGGCGTTTTTCACGTAAACACCA
Found at i:24871 original size:19 final size:19
Alignment explanation
Indices: 24847--24884 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24837 ATACTACTAT
24847 GTATAGGGGTATCGATACC
1 GTATAGGGGTATCGATACC
24866 GTATAGGGGTATCGATACC
1 GTATAGGGGTATCGATACC
24885 ACTTTGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
GTATAGGGGTATCGATACC
Found at i:27001 original size:13 final size:13
Alignment explanation
Indices: 26985--27009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26975 TGAAAACTAT
26985 TTTGAAAAATAAG
1 TTTGAAAAATAAG
26998 TTTGAAAAATAA
1 TTTGAAAAATAA
27010 TAGTTCGTAT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (13 bp):
TTTGAAAAATAAG
Found at i:36455 original size:16 final size:18
Alignment explanation
Indices: 36435--36473 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
36425 AAATTCCAGA
36435 ATACCGAAAT-GGTATCG
1 ATACCGAAATGGGTATCG
*
36452 -TACCGAAGTGGGTATCG
1 ATACCGAAATGGGTATCG
36469 ATACC
1 ATACC
36474 ATAGAATGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.23
Consensus pattern (18 bp):
ATACCGAAATGGGTATCG
Found at i:36507 original size:20 final size:20
Alignment explanation
Indices: 36478--36515 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36468 GATACCATAG
*
36478 AATGGAAGTATCGATACTGT
1 AATGGAAGTACCGATACTGT
*
36498 AATGGGAGTACCGATACT
1 AATGGAAGTACCGATACT
36516 AATGAGCTTG
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:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (20 bp):
AATGGAAGTACCGATACTGT
Found at i:37098 original size:21 final size:22
Alignment explanation
Indices: 37048--37099 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
37038 GTTGAGGGTT
37048 CTATGTGGTTCTTCGGGACAAA
1 CTATGTGGTTCTTCGGGACAAA
37070 GCTATGTGG-TCTTTCGGGACAAA
1 -CTATGTGGTTC-TTCGGGACAAA
37093 -TATGTGG
1 CTATGTGG
37100 CACTTCGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.25
22 2 0.07
23 19 0.68
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (22 bp):
CTATGTGGTTCTTCGGGACAAA
Found at i:37106 original size:21 final size:21
Alignment explanation
Indices: 37048--37106 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
37038 GTTGAGGGTT
*
37048 CTATGTGGTTCTTCGGGACAAA
1 CTATGTGG-CCTTCGGGACAAA
*
37070 GCTATGTGGTCTTTCGGGACAAA
1 -CTATGTGG-CCTTCGGGACAAA
37093 -TATGTGGCACTTCG
1 CTATGTGGC-CTTCG
37107 TTGCAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 11 0.34
23 20 0.62
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (21 bp):
CTATGTGGCCTTCGGGACAAA
Found at i:43102 original size:7 final size:7
Alignment explanation
Indices: 43081--43115 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
43071 CCAAAAGGAA
43081 ATTAAAT
1 ATTAAAT
*
43088 A-AAAAT
1 ATTAAAT
43094 ATTAAAT
1 ATTAAAT
43101 ATTAAAT
1 ATTAAAT
43108 ATTAAAT
1 ATTAAAT
43115 A
1 A
43116 AACCAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
ATTAAAT
Found at i:43208 original size:27 final size:27
Alignment explanation
Indices: 43178--43234 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
43168 TAAATAATCA
* * *
43178 ATAATAATAATAAATATGTATATGTAT
1 ATAAAAATAATAAATATATATATATAT
*
43205 ATAAAAATAATATATATATATATATAT
1 ATAAAAATAATAAATATATATATATAT
43232 ATA
1 ATA
43235 TATGAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
ATAAAAATAATAAATATATATATATAT
Found at i:43219 original size:2 final size:2
Alignment explanation
Indices: 43191--43237 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
43181 ATAATAATAA
* * * *
43191 AT AT GT AT AT GT AT AT AA AA AT A- 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
43232 AT AT AT
1 AT AT AT
43238 GAAATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:44413 original size:3 final size:3
Alignment explanation
Indices: 44405--44432 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
44395 AAAAGAAATA
44405 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
44433 TAGCGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44474 original size:32 final size:31
Alignment explanation
Indices: 44438--44513 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
44428 TAATATAGCG
* * *
44438 TATATAATATATAAAAATATTTTTTAAAACTA
1 TATATTATATATAAAAAT-GTTTTCAAAACTA
*
44470 TATATTATACT-TAAAAATGTTTTCAAAGCTA
1 TATATTATA-TATAAAAATGTTTTCAAAACTA
44501 TATATTATATATA
1 TATATTATATATA
44514 GTTTTCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.03
31 21 0.55
32 15 0.39
33 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (31 bp):
TATATTATATATAAAAATGTTTTCAAAACTA
Found at i:44590 original size:71 final size:71
Alignment explanation
Indices: 44463--44675 Score: 210
Period size: 71 Copynumber: 3.0 Consensus size: 71
44453 AATATTTTTT
* * * * *
44463 AAAACTATATATTATA-CTTAAAAATGTTTTCAAAGCTATATATTATATATAGTTTTCAAAAATG
1 AAAACTATACATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAAGTTTTCAAAAATG
44527 -ATTTA
66 TATTTA
* *
44532 AAAA-TATA-A-TATAAGTTTTTCAAAATGTTTTTTAAAACTATATATTATATAAATTTTTCAAA
1 AAAACTATACATTAT-A--TTTTCAAAATG-TTTTCAAAACTATATATTATATAAAGTTTTCAAA
*
44594 AATGTTTTTTTA
62 AATG--TATTTA
* * *
44606 AAAACTATACATTATATTTTCAAAATGATTTCAAAAATATATATTATAT-AA-CTTTC-AAAATG
1 AAAACTATACATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAAGTTTTCAAAAATG
44668 T-TTTA
66 TATTTA
44673 AAA
1 AAA
44676 CTTATATATT
Statistics
Matches: 122, Mismatches: 11, Indels: 24
0.78 0.07 0.15
Matches are distributed among these distances:
66 3 0.02
67 9 0.07
68 5 0.04
69 4 0.03
70 14 0.11
71 38 0.31
72 2 0.02
73 19 0.16
74 19 0.16
75 4 0.03
76 2 0.02
77 3 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (71 bp):
AAAACTATACATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAAGTTTTCAAAAATG
TATTTA
Found at i:44662 original size:35 final size:35
Alignment explanation
Indices: 44483--44703 Score: 152
Period size: 35 Copynumber: 6.1 Consensus size: 35
44473 ATTATACTTA
* **
44483 AAAATGTTTTCAAAGCTATATATTATATATAGTTTTC
1 AAAATGTTTTTAAAAATATATATTATATA-A-TTTTC
* *
44520 AAAAATG-ATTTAAAAATATA-A-TATA-AGTTTTTC
1 -AAAATGTTTTTAAAAATATATATTATATA-ATTTTC
*
44553 AAAATGTTTTTTAAAACTATATATTATATAAATTTTTC
1 AAAATG-TTTTTAAAAATATATATTATAT-AA-TTTTC
*
44591 AAAAATGTTTTTTTAAAAACTATACA-T-TAT-ATTTTC
1 -AAAATG--TTTTTAAAAA-TATATATTATATAATTTTC
* * *
44627 AAAATGATTTCAAAAATATATATTATATAACTTTC
1 AAAATGTTTTTAAAAATATATATTATATAATTTTC
*
44662 AAAATG-TTTTAAAACTTATATATTGTATATAAGTTTTC
1 AAAATGTTTTTAAAA-ATATATA-T-TATATAA-TTTTC
44700 AAAA
1 AAAA
44704 ACATTAACTA
Statistics
Matches: 148, Mismatches: 18, Indels: 34
0.74 0.09 0.17
Matches are distributed among these distances:
32 11 0.07
33 14 0.09
34 22 0.15
35 28 0.19
36 11 0.07
37 17 0.11
38 20 0.14
39 9 0.06
40 11 0.07
41 5 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (35 bp):
AAAATGTTTTTAAAAATATATATTATATAATTTTC
Found at i:45449 original size:84 final size:86
Alignment explanation
Indices: 45319--45499 Score: 260
Period size: 84 Copynumber: 2.1 Consensus size: 86
45309 CTGAATGGAA
* * * *
45319 TCGAACTCGAAAGGTCTTTGGTAGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATG
1 TCGAACTCGAAAGGTCTTTGGTAGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
45384 TG-CCTTTGAGCTGAGCGTAG
66 TGCCCTTTGAGCTGAGCGTAG
* * * *
45404 TCGAACTCGAAA-GTCTCTT-GTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAGATGAT
1 TCGAACTCGAAAGGTCT-TTGGTAGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGAT
45467 GTGCCCTTTGAGCTGAGCGTAG
65 GTGCCCTTTGAGCTGAGCGTAG
45489 TCGAACTCGAA
1 TCGAACTCGAA
45500 GGTATCGTGT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
84 43 0.50
85 43 0.50
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (86 bp):
TCGAACTCGAAAGGTCTTTGGTAGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
TGCCCTTTGAGCTGAGCGTAG
Found at i:45571 original size:27 final size:28
Alignment explanation
Indices: 45509--45577 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 28
45499 AGGTATCGTG
*
45509 TTTCAAGAGAAACATTTTCAAAGGGGTTT
1 TTTCAAGAGAAACAATTTCAAA-GGGTTT
45538 TTTCAAGAGAAACAATTTCAAA-GGTTT
1 TTTCAAGAGAAACAATTTCAAAGGGTTT
45565 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
45578 TGTCTCAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 18 0.46
29 21 0.54
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (28 bp):
TTTCAAGAGAAACAATTTCAAAGGGTTT
Found at i:45681 original size:36 final size:36
Alignment explanation
Indices: 45565--45797 Score: 254
Period size: 36 Copynumber: 6.4 Consensus size: 36
45555 TCAAAGGTTT
*
45565 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* *
45602 TTTCAAGGGAAACTGTTTCAA-AGATTGACAAAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGA--GAC--AAAATTTG
* *
45641 TTTCAA-AGGAAACTGTCTCAAGGGAGACGAAATTTG
1 TTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATTTG
* * * *
45677 TTTCAAGTGAAACTGTCTCAAGGGAGGCGAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
45713 TTTTAAGGGAAATTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
45749 TTTCAAGAGAATCTGTCTCAAGAGAGACAAATTTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
45785 TTTCAAGAAAAAC
1 TTTCAAGAGAAAC
45798 AATCTCAAAG
Statistics
Matches: 166, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
36 113 0.68
37 19 0.11
38 6 0.04
39 22 0.13
40 6 0.04
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:45804 original size:36 final size:36
Alignment explanation
Indices: 45728--45805 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
45718 AGGGAAATTG
* * * **
45728 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAATCTG
1 TCTCAAGAGAGACAAAATTTATTTCAAGAAAAACAA
*
45764 TCTCAAGAGAGACAAATTTTATTTCAAGAAAAACAA
1 TCTCAAGAGAGACAAAATTTATTTCAAGAAAAACAA
45800 TCTCAA
1 TCTCAA
45806 AGGTTTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTATTTCAAGAAAAACAA
Found at i:45805 original size:108 final size:110
Alignment explanation
Indices: 45565--45797 Score: 296
Period size: 108 Copynumber: 2.1 Consensus size: 110
45555 TCAAAGGTTT
*
45565 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTTTCAAAGATTGA
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAAGA-TGA
* *
45630 CAAAAAATTTGTTTCAAAGGAAACTGTCTCAAGGGAGACGAAATTTG
65 C-AAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACGAAATTTA
* * * * *
45677 TTTCAAGTGAAACTGTCTCAAGGGAGGCGAAA-TTTGTTTTAAGGGAAATTGTCTCAAGAGA-GA
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAA-AGATGA
*
45740 C-AAAATTTGTTTC-AAGAGAATCTGTCTCAAGAGAGAC-AAATTTTA
65 CAAAAATTTGTTTCAAAG-GAAACTGTCTCAAGAGAGACGAAA-TTTA
*
45785 TTTCAAGAAAAAC
1 TTTCAAGAGAAAC
45798 AATCTCAAAG
Statistics
Matches: 107, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
107 6 0.06
108 44 0.41
110 3 0.03
111 22 0.21
112 32 0.30
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (110 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAAGATGAC
AAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACGAAATTTA
Found at i:46016 original size:84 final size:84
Alignment explanation
Indices: 45801--46412 Score: 642
Period size: 84 Copynumber: 7.4 Consensus size: 84
45791 GAAAAACAAT
* * * * *
45801 CTCAAAGGT-TTTTGTTGACAGATAACTCC-TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 CTCAAAGGTCTTTGGTTGGCAGATAAC-CCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CC
* * * * *
45864 TCGGAGCTGAGTGGAATCAAA
64 TTGGAGCTGAGCGTAGTCGAA
** * * * * * *
45885 CTCAGGGGTC--T--TTGGCAAACAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
1 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
45946 GGAGCTGAGCGTAGTCGAA
66 GGAGCTGAGCGTAGTCGAA
* * *
45965 CTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCGT
1 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-T
46030 T-GAGCTGAGCGTAGTCGAA
65 TGGAGCTGAGCGTAGTCGAA
** * * * *
46049 CTCAAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCC
1 CTCAAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CC
* * * *
46113 TCGAAGCTGAGTGTAATCGAA
64 TTGGAGCTGAGCGTAGTCGAA
** * * *
46134 CTCAGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
1 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-T
46195 T-GAGCTGAGCGTAGTCGAA
65 TGGAGCTGAGCGTAGTCGAA
* * * * *
46214 CTCAAAGGTCTTTTGTTGGTAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTT
1 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
46279 GGAGCTGAGCGTAGTCGAA
66 GGAGCTGAGCGTAGTCGAA
* * *
46298 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCCTT
1 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
46363 GGAGCTGAGCGTAGTCGAA
66 GGAGCTGAGCGTAGTCGAA
* * *
46382 CTCGAAGGTCTTT-G-TGGCAGGTAGCCCTTCT
1 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCT
46413 GGCCTTGAGC
Statistics
Matches: 440, Mismatches: 71, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
80 53 0.12
81 70 0.16
82 18 0.04
83 4 0.01
84 263 0.60
85 32 0.07
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (84 bp):
CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAA
Found at i:46170 original size:165 final size:166
Alignment explanation
Indices: 45812--46394 Score: 610
Period size: 165 Copynumber: 3.5 Consensus size: 166
45802 TCAAAGGTTT
* * * * * * * *
45812 TTGTTGACAGATAACTCC-TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGGAGCTGAGT
1 TTGTTGGCAGATAAC-CCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCGT-TGAGCTGAGC
* * * ** * * * *
45876 GGAATCAAACTCAGGGGTC-TTTGG-CA-A-ACAGCCCTTCTCGACTTAAGCTATACTGCAAATG
64 GTAGTCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATG
* * * * *
45937 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
129 ATATGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC
* *
45975 TTTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCGTTGAGCTGAGC
1 -TT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCGTTGAGCTGAGC
* * * *
46040 GTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
64 GTAGTCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATG
* *
46105 ATGA-GCCCTCGAAGCTGAGTGTAATCGAACTC-AGGGGTC
129 AT-ATG-CCTCGAAGCTGAGCGTAATCGAACTCGA-AGGTC
* * * *
46144 -T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGT
1 TTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCGTTGAGCTGAGCGT
* *** *
46207 AGTCGAACTCAAAGGTCTTTTGTTGGTAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGAT
66 AGTCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
* * *
46272 ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
131 ATGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC
*
46308 TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAG
1 -TT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCGTT-GAGCTGAG
*
46372 CGTAGTCGAACTCGAAGGTCTTT
63 CGTAGTCGAACTCAAAGGTCTTT
46395 GTGGCAGGTA
Statistics
Matches: 349, Mismatches: 54, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
164 53 0.15
165 159 0.46
166 3 0.01
167 4 0.01
168 104 0.30
169 26 0.07
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (166 bp):
TTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCGTTGAGCTGAGCGT
AGTCGAACTCAAAGGTCTTTTGGTCACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
ATGCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTC
Found at i:46256 original size:249 final size:249
Alignment explanation
Indices: 45801--46434 Score: 906
Period size: 249 Copynumber: 2.5 Consensus size: 249
45791 GAAAAACAAT
* *
45801 CTCAAAGGT-TTTTGTTGACAGATAACTCC-TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 CTCAAAGGTCTTTTGGTGACAGATAAC-CCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCC
* * * * *
45864 TCGGAGCTGAGTGGAATCAAACTCAGGGGTCTTTGGCAAACAGCCCTTCTCGACTTAAGCTATAC
65 TCGGAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
45929 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCC
130 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCC
45994 TTCTAGACTTAAGTTGTGCTGCAAATGATATGCCGTT-GAGCTGAGCGTAGTCGAA
195 TTCTAGACTTAAGTTGTGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAA
*
46049 CTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCT
1 CTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCT
*
46114 CGAAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
66 CGGAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
* *
46179 GCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGTAGACAACCC
131 GCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCC
46243 TTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
195 TTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
* * * * * *
46298 CTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGAT-ATG-C
1 CTCAAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGA-GCC
* * * * * * * *
46360 CTTGGAGCTGAGCGTAGTCGAACTC-GAAGGTCTTTGTGGCAGGTAGCCCTTCTGGCCTTGAGCT
64 CTCGGAGCTGAGTGTAATCGAACTCAG-GGGTC-TT-TGGCAGATAGCCCTTCTCGACTTAAGCT
*
46424 AAGCTGCAAAT
126 ATGCTGCAAAT
46435 AGTTTGTTTA
Statistics
Matches: 349, Mismatches: 28, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
247 1 0.00
248 45 0.13
249 267 0.77
250 36 0.10
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (249 bp):
CTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGAGCCCT
CGGAGCTGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCT
GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCT
TCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
Found at i:49808 original size:19 final size:19
Alignment explanation
Indices: 49784--49829 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
49774 AGTTAATGTG
49784 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
49803 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
49822 AATGCAAA
1 AATGCAAA
49830 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:51605 original size:20 final size:21
Alignment explanation
Indices: 51580--51632 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
51570 GGAATAAAAG
**
51580 AATAAACCAAAAGGAA-ATTA
1 AATAAACCAAAAAAAATATTA
51600 AATAAA--AATAAAAAATATTA
1 AATAAACCAA-AAAAAATATTA
51620 AATAAACCAAAAA
1 AATAAACCAAAAA
51633 TGTATGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.07
19 4 0.15
20 16 0.59
21 3 0.11
22 2 0.07
ACGTcount: A:0.72, C:0.08, G:0.04, T:0.17
Consensus pattern (21 bp):
AATAAACCAAAAAAAATATTA
Found at i:52902 original size:3 final size:3
Alignment explanation
Indices: 52894--52934 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
52884 AATGAAAAGA
52894 AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
52935 TATAGCGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:52954 original size:9 final size:10
Alignment explanation
Indices: 52895--52938 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
52885 ATGAAAAGAA
*
52895 ATAATAATAA
1 ATAATAATAT
52905 ATAATAATA-
1 ATAATAATAT
52914 ATAATAATAAT
1 ATAATAAT-AT
52925 AATAATAATAT
1 -ATAATAATAT
52936 ATA
1 ATA
52939 GCGTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.26
10 13 0.42
11 2 0.06
12 8 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAATAATAT
Found at i:53196 original size:37 final size:36
Alignment explanation
Indices: 53127--53207 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 36
53117 TACATTATAT
53127 TTTCAAAATGATTTCAAAAATATATATTATATAA-C
1 TTTCAAAATGATTTCAAAAATATATATTATATAAGC
* * *
53162 TTTCAAAATG-TTTTAAAACTTATATATTGTATATAAGT
1 TTTCAAAATGATTTCAAAA-ATATATA-T-TATATAAGC
53200 TTTCAAAA
1 TTTCAAAA
53208 ACATTAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 7 0.18
35 16 0.41
36 1 0.03
37 7 0.18
38 8 0.21
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (36 bp):
TTTCAAAATGATTTCAAAAATATATATTATATAAGC
Found at i:61919 original size:30 final size:29
Alignment explanation
Indices: 61880--61955 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
61870 CCTCTTGTTA
* *
61880 AAATCCAAATATCATATTATA-ATTTTATT
1 AAATACAAATATCATATTATACATTTTA-G
*
61909 AAAGTACAAATATCACATTATACATTTTAG
1 AAA-TACAAATATCATATTATACATTTTAG
*
61939 AAATACATATATCATAT
1 AAATACAAATATCATAT
61956 GAGATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.38
30 19 0.47
31 6 0.15
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (29 bp):
AAATACAAATATCATATTATACATTTTAG
Found at i:63992 original size:20 final size:21
Alignment explanation
Indices: 63959--64000 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
63949 TAATAAGTAA
63959 GATCTTTTTCCAACTCGTGAT
1 GATCTTTTTCCAACTCGTGAT
*
63980 GATCTTTTT-CAACTCTTGAT
1 GATCTTTTTCCAACTCGTGAT
64000 G
1 G
64001 CAAAACCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.45
Consensus pattern (21 bp):
GATCTTTTTCCAACTCGTGAT
Found at i:68608 original size:2 final size:2
Alignment explanation
Indices: 68601--68639 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
68591 CTGAAGGTAT
68601 TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
68640 CCTCCCTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:68746 original size:2 final size:2
Alignment explanation
Indices: 68735--68771 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
68725 TATACACTGC
68735 AT AT -T 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
68772 GATTATGGGA
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):
AT
Found at i:69244 original size:2 final size:2
Alignment explanation
Indices: 69237--69268 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
69227 ATGTTAAATC
69237 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
69269 GATCATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69725 original size:38 final size:38
Alignment explanation
Indices: 69683--69769 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
69673 CATTTGAACC
* *
69683 AAATATACTAATAAAATAACTTCAAAACACTGTAATCA
1 AAATATACTAATAAAACAACTTCAAAACACTATAATCA
* * * *
69721 AAATATACCATTAAAACAACTTCAAATCAGTATAATCA
1 AAATATACTAATAAAACAACTTCAAAACACTATAATCA
69759 AAATATACTAA
1 AAATATACTAA
69770 GATTAATGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.26
Consensus pattern (38 bp):
AAATATACTAATAAAACAACTTCAAAACACTATAATCA
Found at i:76950 original size:29 final size:29
Alignment explanation
Indices: 76883--77019 Score: 125
Period size: 29 Copynumber: 4.7 Consensus size: 29
76873 AAATCTTAAT
*
76883 ATTTAAAAGTATATTTT-ATTTT-TTCTTA
1 ATTTAAAAATATATTTTAATTTTATT-TTA
* * * *
76911 ACTTATTAAATATATTTTATTTTTAATTTA
1 ATTTA-AAAATATATTTTAATTTTATTTTA
* *
76941 ATTTAAAAATATATTTTAATATCATTTTA
1 ATTTAAAAATATATTTTAATTTTATTTTA
* * *
76970 AATTAAAAATATATATTAATCTTATTTTA
1 ATTTAAAAATATATTTTAATTTTATTTTA
*
76999 TTTTTAAAAAATATATTTTAA
1 -ATTT-AAAAATATATTTTAA
77020 ATTAAAGTCA
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
28 4 0.05
29 54 0.63
30 13 0.15
31 15 0.17
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (29 bp):
ATTTAAAAATATATTTTAATTTTATTTTA
Found at i:77089 original size:45 final size:48
Alignment explanation
Indices: 77040--77182 Score: 141
Period size: 45 Copynumber: 2.9 Consensus size: 48
77030 CATATTAAAA
77040 TTAAAAATATATTTTATCTTAATTT-A-TTAAATATATTTTTTTAAT-
1 TTAAAAATATATTTTATCTTAATTTAATTTAAATATATTTTTTTAATC
* * *
77085 TTAAAAATATAGTTTAGACTT-ATTTAATTTAAATATATTTATTTTTATC
1 TTAAAAATATATTTTA-TCTTAATTTAATTTAAATATATTT-TTTTAATC
* *
77134 TTACTTATGAAATATATTTTATTTTAATTTCATTTTAAATATATTTTTT
1 TTA---A--AAATATATTTTATCTTAATTT-AATTTAAATATATTTTTT
77183 AAAAATTAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
45 19 0.24
46 4 0.05
47 12 0.15
48 6 0.08
49 3 0.04
52 1 0.01
53 2 0.03
54 18 0.23
55 14 0.18
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (48 bp):
TTAAAAATATATTTTATCTTAATTTAATTTAAATATATTTTTTTAATC
Found at i:77256 original size:23 final size:24
Alignment explanation
Indices: 77221--77284 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
77211 CTTTAAGTTA
* * *
77221 AAATAATATTAAAATATATTT-TT
1 AAATAAAAATAAAATATATTTAAT
77244 AAATAAAAATAAAATATATTTAAT
1 AAATAAAAATAAAATATATTTAAT
*
77268 AAGTTAAAAATAAAATA
1 AA-ATAAAAATAAAATA
77285 AAATATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 19 0.54
24 3 0.09
25 13 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATAAAAATAAAATATATTTAAT
Found at i:80756 original size:21 final size:21
Alignment explanation
Indices: 80707--80756 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
80697 TTAGTTGAGA
*
80707 AAAGATCGTTAGAACTCACCT
1 AAAGATCTTTAGAACTCACCT
80728 AAAGATCTTTAGAACTCACCT
1 AAAGATCTTTAGAACTCACCT
80749 AAAGATCT
1 AAAGATCT
80757 GGTCTCGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (21 bp):
AAAGATCTTTAGAACTCACCT
Found at i:82028 original size:20 final size:20
Alignment explanation
Indices: 81999--82044 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
81989 TACTAAGCAT
*
81999 ATTGAGTAGCAAGAAGGCTG
1 ATTGACTAGCAAGAAGGCTG
82019 ATTGACTAGCAAGAAGGCTG
1 ATTGACTAGCAAGAAGGCTG
82039 ATTGAC
1 ATTGAC
82045 AGGTGATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (20 bp):
ATTGACTAGCAAGAAGGCTG
Found at i:82274 original size:21 final size:21
Alignment explanation
Indices: 82249--82345 Score: 133
Period size: 21 Copynumber: 4.6 Consensus size: 21
82239 TCATACCAAG
*
82249 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCACAAA
*
82270 GACGAGAAGATCATTCACAAA
1 GACGAGAAGACCATTCACAAA
*
82291 GACGAGAAGACCATTCACAAG
1 GACGAGAAGACCATTCACAAA
* *
82312 GACGAGAAGATCATTCATAAA
1 GACGAGAAGACCATTCACAAA
82333 GAC-ATGAAGACCA
1 GACGA-GAAGACCA
82346 CTTCTCACTG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 1 0.01
21 66 0.99
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (21 bp):
GACGAGAAGACCATTCACAAA
Found at i:82296 original size:42 final size:42
Alignment explanation
Indices: 82249--82345 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
82239 TCATACCAAG
*
82249 GACGAGAAGACCATTCATAAAGACGAGAAGATCATTCACAAA
1 GACGAGAAGACCATTCACAAAGACGAGAAGATCATTCACAAA
* *
82291 GACGAGAAGACCATTCACAAGGACGAGAAGATCATTCATAAA
1 GACGAGAAGACCATTCACAAAGACGAGAAGATCATTCACAAA
82333 GAC-ATGAAGACCA
1 GACGA-GAAGACCA
82346 CTTCTCACTG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
41 1 0.02
42 50 0.98
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (42 bp):
GACGAGAAGACCATTCACAAAGACGAGAAGATCATTCACAAA
Found at i:86859 original size:36 final size:36
Alignment explanation
Indices: 86819--87341 Score: 276
Period size: 37 Copynumber: 14.1 Consensus size: 36
86809 AGCAAAGTCA
* *
86819 ATCTTAATCCTTCACCAGAGAGTAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGCAATCC
*
86855 ATCTTAAGCCTTCACC-GAAGAATAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCAG-AGAATAGTGAAGC-AATCC
* *
86892 ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGC-AATCC
* *
86929 ATTTTAAGCCTTCACC-GAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCAG-AGAATAGTGAAGC-AATCC
* * * *** * *
86966 ATCAGTAAGCCTTCCGAACATGATGATTAAGT-CCTCAAGGCA
1 ATC-TTAAGCCTT-C-ACCA-GA-GAAT-AGTGAAGCAA-TCC
* *
87008 ATCTTAAGCCTTCACCTGAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGCAATCC
*** * *
87044 ATCTTAAGCCTTCATTTGAGAATAGTGAAACAAATCA
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGC-AATCC
* * *
87081 ATCTTAAGCCTTCACTAGAGATTAGTGAAAC-A-CC
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGCAATCC
* * * * *
87115 ACCTTGATCATTCA-CAGAAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAG-AGAATAGTGAAGCAATCC
* * * * * *
87151 ATCTGAAACATTCACCGGAGAATAGTGAATCAACTCA
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGCAA-TCC
* *
87188 ATCTTAAGCCTTTACC-GAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCAG-AGAATAGTGAAGC-AATCC
** * * *** * *
87225 ATCAGCAAGCCTTCTGAGCATGATGATTAAGT-CCTCAAGGCA
1 ATC-TTAAGCCTTC--ACCA-GA-GAAT-AGTGAAGCAA-TCC
* *
87267 ATCTTAAGCCTTCACCTGA-AAGGAGTGAAGCAATTCC
1 ATCTTAAGCCTTCACCAGAGAA-TAGTGAAGCAA-TCC
*
87304 ATCTTAAGCCTTCA-CA-AGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCAGAGAATAGTGAAGC-AATCC
87339 ATC
1 ATC
87342 AGTAAGTCTT
Statistics
Matches: 374, Mismatches: 80, Indels: 67
0.72 0.15 0.13
Matches are distributed among these distances:
33 2 0.01
34 22 0.06
35 18 0.05
36 95 0.25
37 159 0.43
38 22 0.06
39 5 0.01
40 5 0.01
41 22 0.06
42 18 0.05
43 6 0.02
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAGAGAATAGTGAAGCAATCC
Found at i:86905 original size:37 final size:37
Alignment explanation
Indices: 86809--87223 Score: 309
Period size: 37 Copynumber: 11.2 Consensus size: 37
86799 ATGAGATTGG
* *
86809 AGCAAAGTCAATCTTAATCCTTCACC-AGAGAGTAGTGA
1 AGCAAA-TCAATCTTAAGCCTTCACCGA-AGAATAGTGA
*
86847 AGC-AATCCATCTTAAGCCTTCACCGAAGAATAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAATAGTGA
86883 AGCAAATCAATCTTAAGCCTTCACCTG-AGAATAGTGA
1 AGCAAATCAATCTTAAGCCTTCACC-GAAGAATAGTGA
* *
86920 AGCAAATCAATTTTAAGCCTTCACCGAAGAGTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAATAGTGA
* * * *
86957 AGCAAATCCATCAGTAAGCCTT--CCGAA-CATGATGATTA
1 AGCAAATCAATC-TTAAGCCTTCACCGAAGAAT-A-G-TGA
**
86995 AGTCCTCAAGGCAATCTTAAGCCTTCACCTG-AGAATAGTGA
1 AG----CAAATCAATCTTAAGCCTTCACC-GAAGAATAGTGA
* **
87036 AGCAAA-CCATCTTAAGCCTTCATTTG-AGAATAGTGA
1 AGCAAATCAATCTTAAGCCTTCA-CCGAAGAATAGTGA
* * *
87072 AACAAATCAATCTTAAGCCTTCA-CTAGAGATTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGA-AGAATAGTGA
* * * * * * *
87109 A--ACA-CCACCTTGATCATTCACAGAAGAATAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAATAGTGA
* * * * *
87143 AGCAAA-CCATCTGAAACATTCACCGGAGAATAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAATAGTGA
* * * *
87179 ATCAACTCAATCTTAAGCCTTTACCGAAGAGTAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAGAATAGTGA
87216 AGCAAATC
1 AGCAAATC
87224 CATCAGCAAG
Statistics
Matches: 299, Mismatches: 54, Indels: 49
0.74 0.13 0.12
Matches are distributed among these distances:
34 21 0.07
35 4 0.01
36 97 0.32
37 134 0.45
38 16 0.05
41 12 0.04
42 8 0.03
43 4 0.01
44 3 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (37 bp):
AGCAAATCAATCTTAAGCCTTCACCGAAGAATAGTGA
Found at i:87812 original size:214 final size:215
Alignment explanation
Indices: 87337--88287 Score: 1541
Period size: 216 Copynumber: 4.4 Consensus size: 215
87327 TGAAGCAAAT
87337 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
87402 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCA-ATGAATTTGAAAA
* * *
87467 TGAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTC
130 TGAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAAAATGCGATTTTCAAAATTTC
* *
87532 ATAATTTATAAGGCATTCGGG
195 ACAATTTATAAGTCATTCGGG
*
87553 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* * *
87618 GATGATAAGTCCTTCGGGCTATCCATAAGACCTTCGGGTAGGATATTTTCATTGAATTTGAAAAT
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATGAATTTGAAAAT
* * *
87683 G-AAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAAAAAGCGATTATCAAAAATTCA
131 GAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAAAATGCGATTTTCAAAATTTCA
*
87747 CAATTTATAAGTCCTTCGGG
196 CAATTTATAAGTCATTCGGG
* * *
87767 CCATCAGTAAGTCTTTCGAGTATGATACTTAAATCCTTAGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
87832 GATGATAAGTCCTTCGGGCCGTCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAA
66 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTC-AATGAATTTG-AAA
*
87897 ATG-AAAGAATGATGTTTTAAGAAGATGAAATTTTTGAAAAC-AAATAATGCGATTTTCAAAATT
129 ATGAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAA-AATGCGATTTTCAAAATT
*
87960 TCACAATTTATAAGACATTCGGG
193 TCACAATTTATAAGTCATTCGGG
*
87983 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGTCATCTAG-AAGCCTTTAGAGCA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCT-GTAAGCCTTTAGAGCA
* *
88047 AGATGATAAGTCCTTCGGGCCGTCCATAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAA
65 AGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATGAATTTGAAAA
* *
88112 TGAAAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAGAATGTGATTTTCAAAATT
130 TG--AAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAAAATGCGATTTTCAAAATT
* *
88177 TCACAATTTATAAGTCCTTTGGG
193 TCACAATTTATAAGTCATTCGGG
* *
88200 CCATCAGTAAGTTTTTCGAGCATGATGCTTAAACCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
1 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
*
88265 GATGATAAGTCCTTCGGACCATC
66 GATGATAAGTCCTTCGGGCCATC
88288 AGTAAGTCTT
Statistics
Matches: 684, Mismatches: 42, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
214 188 0.27
215 34 0.05
216 304 0.44
217 156 0.23
218 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (215 bp):
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCAATGAATTTGAAAAT
GAAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACGAAAAATGCGATTTTCAAAATTTCA
CAATTTATAAGTCATTCGGG
Found at i:88293 original size:41 final size:41
Alignment explanation
Indices: 88186--88310 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 41
88176 TTCACAATTT
* *
88186 ATAAGTCCTTTGGGCCATCAGTAAGTTTTTCGAGCATGATG
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
* ** * * * * *
88227 CTTAAACCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG
1 -ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
*
88269 ATAAGTCCTTCGGACCATCAGTAAGTC-TTCGAGCATGATG
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
88309 AT
1 AT
88311 TAAATCTTTC
Statistics
Matches: 64, Mismatches: 19, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
40 13 0.20
41 20 0.31
42 31 0.48
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (41 bp):
ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
Found at i:88322 original size:41 final size:41
Alignment explanation
Indices: 88191--88322 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 41
88181 AATTTATAAG
* * * *
88191 TCCTTTGGGCCATCAGTAAGTTTTTCGAGCATGATGCTTAAA
1 TCCTTCGGACCATCAGTAAG-TCTTCGAGCATGATGATTAAA
* ** * * * * *
88233 CCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA-TAAG
1 TCCTTCGGACCATCAGTAAGTC-TTCGAGCATGATGATTAAA
88274 TCCTTCGGACCATCAGTAAGTCTTCGAGCATGATGATTAAA
1 TCCTTCGGACCATCAGTAAGTCTTCGAGCATGATGATTAAA
*
88315 TCTTTCGG
1 TCCTTCGG
88323 GTAATTTGTA
Statistics
Matches: 69, Mismatches: 19, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
40 12 0.17
41 30 0.43
42 27 0.39
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (41 bp):
TCCTTCGGACCATCAGTAAGTCTTCGAGCATGATGATTAAA
Found at i:88324 original size:82 final size:83
Alignment explanation
Indices: 88186--88338 Score: 227
Period size: 82 Copynumber: 1.9 Consensus size: 83
88176 TTCACAATTT
* * * * *
88186 ATAAGTCCTTTGGGCCATCAGTAAGTTTTTCGAGCATGATGCTTAAACCCTTCGGGTCATCTGTA
1 ATAAGTCCTTCGGACCATCAGTAAGTTCTTCGAGCATGATGATTAAACCCTTCGGGTAATCTGTA
88251 AGCCTTTAGAGCAAGATG
66 AGCCTTTAGAGCAAGATG
* * *
88269 ATAAGTCCTTCGGACCATCAGTAAG-TCTTCGAGCATGATGATTAAATCTTTCGGGTAATTTGTA
1 ATAAGTCCTTCGGACCATCAGTAAGTTCTTCGAGCATGATGATTAAACCCTTCGGGTAATCTGTA
88333 AGCCTT
66 AGCCTT
88339 CACTAAAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
82 39 0.63
83 23 0.37
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (83 bp):
ATAAGTCCTTCGGACCATCAGTAAGTTCTTCGAGCATGATGATTAAACCCTTCGGGTAATCTGTA
AGCCTTTAGAGCAAGATG
Found at i:88490 original size:57 final size:58
Alignment explanation
Indices: 88368--88519 Score: 179
Period size: 57 Copynumber: 2.7 Consensus size: 58
88358 AGAGTCACAT
* * * * *
88368 CAGAAGATTTCTCGAGTTCTATACTCCTTGAAAGGAAT-AGGGAGCGAACCCATTTTT
1 CAGAAGATTTCTCGAGTTCTATACTCCCTGAAAGGAATAAGGGAGCGAAACAAGTTTG
* *
88425 CAGGAGATTTCTTGAGTTCTATACTCCCTGAAAGGAATAAGGGAGC-AAACAAGTTTG
1 CAGAAGATTTCTCGAGTTCTATACTCCCTGAAAGGAATAAGGGAGCGAAACAAGTTTG
*
88482 CTGAAGATTAT-TCGAG-TCTTATACTCCCTGAAA-GAATA
1 CAGAAGATT-TCTCGAGTTC-TATACTCCCTGAAAGGAATA
88520 GAGAGCATAG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
56 7 0.09
57 67 0.82
58 8 0.10
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (58 bp):
CAGAAGATTTCTCGAGTTCTATACTCCCTGAAAGGAATAAGGGAGCGAAACAAGTTTG
Found at i:88553 original size:55 final size:54
Alignment explanation
Indices: 88438--88574 Score: 125
Period size: 55 Copynumber: 2.5 Consensus size: 54
88428 GAGATTTCTT
* * *
88438 GAGTTCTATACTCCCTGAAAGGAATAAGGGAGCAAACAAGTTTGCTGAAGATTATTC
1 GAGTT-TATACTCCCTGAAA-GAAT-AGAGAGCAAACAAGTTTGATGAAGATTATGC
* * * *
88495 GAGTCTTATACTCCCTGAAAGAATAGAGAGCATAGACGTTT-ATGGAAGATTGTGC
1 GAGT-TTATACTCCCTGAAAGAATAGAGAGCAAACAAGTTTGAT-GAAGATTATGC
* *
88550 GAGTTTCATGCACCCTGAAA-AATAG
1 GAGTTT-ATACTCCCTGAAAGAATAG
88575 GGAGTGAACC
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
54 8 0.12
55 37 0.54
56 4 0.06
57 18 0.26
58 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (54 bp):
GAGTTTATACTCCCTGAAAGAATAGAGAGCAAACAAGTTTGATGAAGATTATGC
Found at i:97739 original size:3 final size:3
Alignment explanation
Indices: 97733--97789 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
97723 TTTTTACTCA
*
97733 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
97781 TA- TAT TAT T
1 TAT TAT TAT T
97790 TAAAATTACA
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:98275 original size:15 final size:15
Alignment explanation
Indices: 98234--98269 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
98224 GAGAGAGAAA
98234 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
98249 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
98264 AAAGAA
1 AAAGAA
98270 GGGAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:99149 original size:13 final size:13
Alignment explanation
Indices: 99133--99178 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
99123 ATATAATAAA
99133 TAAATATTTATTT
1 TAAATATTTATTT
*
99146 TAAATAAATTATTT
1 TAAAT-ATTTATTT
99160 T-AATATTTATTT
1 TAAATATTTATTT
*
99172 TTAATAT
1 TAAATAT
99179 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:99808 original size:6 final size:7
Alignment explanation
Indices: 99787--99811 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
99777 TGTCTCCATT
99787 AATTAAA
1 AATTAAA
99794 AATTAAA
1 AATTAAA
99801 AATTAAA
1 AATTAAA
99808 AATT
1 AATT
99812 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:110848 original size:16 final size:16
Alignment explanation
Indices: 110822--110866 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
110812 TTTGAATACA
*
110822 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
110839 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
110854 ATTCAATTTATTT
1 ATTCAATTTATTT
110867 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:111737 original size:82 final size:82
Alignment explanation
Indices: 111590--111988 Score: 764
Period size: 82 Copynumber: 4.9 Consensus size: 82
111580 ATATCCTAGT
* *
111590 CCAAACATTAAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
111655 TGATCTGGTTTGGTAAA
66 TGATCTGGTTTGGTAAA
*
111672 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAGGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
111737 TGATCTGGTTTGGTAAA
66 TGATCTGGTTTGGTAAA
111754 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
111819 TGATCTGGTTTGGTAAA
66 TGATCTGGTTTGGTAAA
111836 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
111901 TGATCTGGTTTGGTAAA
66 TGATCTGGTTTGGTAAA
111918 CCAATCATTGAATTTAGAAGAT-AATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
111982 TGATCTG
66 TGATCTG
111989 ATTCGGTAGG
Statistics
Matches: 313, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
81 49 0.16
82 264 0.84
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (82 bp):
CCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGTAAA
Found at i:113055 original size:112 final size:112
Alignment explanation
Indices: 112725--113491 Score: 1263
Period size: 112 Copynumber: 6.8 Consensus size: 112
112715 ATTCAAATCT
*
112725 ATCATTTGATGGATTATCTTTT-CCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTAT-TTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
112789 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACATTTTATTTGAATTC
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
* * *
112837 ATCAAATTGATGGATTAGCTTTT-CCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGAAGG
1 ATC-ACTTGATGGATTA-TTTTTGCCAGAGAA-GTTCATAATGAGAAGAA--C-TCATCTGAAGA
112901 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
60 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
112954 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
113019 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
113066 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
113131 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
113178 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
*
113243 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
113290 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
113355 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TGCTCAAATC
65 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAT-CTGAATTC
* * ** *
113403 TATTACTTGATGGGTTATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 -ATCACTTGATGGATTATTTTTGCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
113468 AG-AGAAAGTTCATAATGAGAAGAA
64 AGAAG-AAGTTCATAATGAGAAGAA
113492 CTCATCAAAA
Statistics
Matches: 628, Mismatches: 16, Indels: 20
0.95 0.02 0.03
Matches are distributed among these distances:
112 318 0.51
113 107 0.17
114 97 0.15
115 21 0.03
116 21 0.03
117 64 0.10
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (112 bp):
ATCACTTGATGGATTATTTTTGCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATCTGAATTC
Found at i:113751 original size:3 final size:3
Alignment explanation
Indices: 113745--113802 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
113735 TTTTTACTCA
113745 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
113793 TAT TAT TAT T
1 TAT TAT TAT T
113803 TAAAATTACA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:114288 original size:15 final size:15
Alignment explanation
Indices: 114247--114282 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
114237 GAGAGAGAAA
114247 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
114262 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
114277 AAAGAA
1 AAAGAA
114283 TGGAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:115162 original size:13 final size:13
Alignment explanation
Indices: 115146--115191 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
115136 ATATAATAAA
115146 TAAATATTTATTT
1 TAAATATTTATTT
*
115159 TAAATAAATTATTT
1 TAAAT-ATTTATTT
115173 T-AATATTTATTT
1 TAAATATTTATTT
*
115185 TTAATAT
1 TAAATAT
115192 CGAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:118836 original size:26 final size:26
Alignment explanation
Indices: 118789--118918 Score: 93
Period size: 26 Copynumber: 4.9 Consensus size: 26
118779 TTAATAATTT
* *
118789 TCAAATAAATTTGTGTTTGATTAACGG
1 TCAAATAATTTTG-GTTCGATTAACGG
*
118816 TCAAATAATTTTGGTTCGATTAATGG
1 TCAAATAATTTTGGTTCGATTAACGG
* * * * * ***
118842 TTAAAGAAAAAATTCGGTT--AATAATTT
1 -T-CA-AATAATTTTGGTTCGATTAACGG
118869 TCAAATAAATTTTGGTTCGATTAACGG
1 TCAAAT-AATTTTGGTTCGATTAACGG
*
118896 TCAAATAATTTTGATTCGATTAA
1 TCAAATAATTTTGGTTCGATTAA
118919 TTTTAAAGAA
Statistics
Matches: 78, Mismatches: 19, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
24 2 0.03
25 9 0.12
26 28 0.36
27 28 0.36
28 1 0.01
29 10 0.13
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (26 bp):
TCAAATAATTTTGGTTCGATTAACGG
Found at i:118905 original size:80 final size:79
Alignment explanation
Indices: 118772--119035 Score: 314
Period size: 80 Copynumber: 3.2 Consensus size: 79
118762 TTATTCGGTT
*
118772 AATTCGGTTAATAATTTTCAAATAAA-TTTGTGTTTGATTAACGGTCAAATAATTTTGGTTCGAT
1 AATTCGGTTAATAATTTTCAAATAAATTTTG-GTTCGATTAACGGTCAAATAATTTTGGTTCGAT
118836 TAATGGTTAAAGAAAA
65 TAAT-GTTAAAGAAAA
*
118852 AATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGATTCGATT
1 AATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGGTTCGATT
*
118917 AATTTTAAAGAAAA
66 AATGTTAAAGAAAA
** *
118931 AATTCGGTTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATA
1 AATTCGGTTAA--TAATT---TTCA-AA---T-AAAT---TTT-GGTTCGATTAACGGTCAAATA
118996 ATTTTGGTTCGATTAATGTTAAAGAAAA
52 ATTTTGGTTCGATTAATGTTAAAGAAAA
*
119024 AATTTGGTTAAT
1 AATTCGGTTAAT
119036 TTAGTTCGAT
Statistics
Matches: 160, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
79 21 0.13
80 61 0.38
81 7 0.04
84 3 0.02
85 2 0.01
88 1 0.01
89 4 0.03
91 1 0.01
92 3 0.02
93 57 0.36
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.41
Consensus pattern (79 bp):
AATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGGTTCGATT
AATGTTAAAGAAAA
Found at i:119087 original size:92 final size:93
Alignment explanation
Indices: 118854--119088 Score: 391
Period size: 93 Copynumber: 2.5 Consensus size: 93
118844 AAAGAAAAAA
*
118854 TTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGTCAAATAATTTTGATTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGATTCGATTAA
* *
118919 TTTTAAAGAAAAAATTCGGTTAATTTGG
66 TGTTAAAGAAAAAATTCGGTTAATTTAG
*
118947 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGATTCGATTAA
*
119012 TGTTAAAGAAAAAATTTGGTTAATTTAG
66 TGTTAAAGAAAAAATTCGGTTAATTTAG
* * *
119040 TTCGATTAAT-ATTTTAAAATAAATTTCGGTTCGATTAACGGTTAAATAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAA
119089 AAAATATTTA
Statistics
Matches: 134, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
92 37 0.28
93 97 0.72
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (93 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTTGATTCGATTAA
TGTTAAAGAAAAAATTCGGTTAATTTAG
Found at i:121285 original size:13 final size:14
Alignment explanation
Indices: 121267--121299 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
121257 TTTTTTAGAT
*
121267 TCGGGTCGAC-GGG
1 TCGGGTCAACTGGG
121280 TCGGGTCAACTGGG
1 TCGGGTCAACTGGG
121294 TCGGGT
1 TCGGGT
121300 AATTTTGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.09, C:0.21, G:0.48, T:0.21
Consensus pattern (14 bp):
TCGGGTCAACTGGG
Found at i:124567 original size:35 final size:35
Alignment explanation
Indices: 124518--124588 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
124508 GTTAAAACCT
*
124518 ATATTAATATACTAAATTAAAAGCAGGGCTCATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGCTCATAA
* *
124553 ATATTAATAAACTAAATTAGAAGCAGGGCTTATAA
1 ATATTAATAAACTAAATTAAAAGCAGGGCTCATAA
124588 A
1 A
124589 CTTATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (35 bp):
ATATTAATAAACTAAATTAAAAGCAGGGCTCATAA
Found at i:126022 original size:23 final size:23
Alignment explanation
Indices: 125996--126056 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
125986 CTCGTATAAC
* *
125996 TGCACCAAAGTGTCACGTAGAAT
1 TGCACCAAAGTGCCACATAGAAT
** *
126019 TGCACCGGAGTGCCGCATAGAAT
1 TGCACCAAAGTGCCACATAGAAT
**
126042 TGCACCGGAGTGCCA
1 TGCACCAAAGTGCCA
126057 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCAAAGTGCCACATAGAAT
Found at i:127595 original size:21 final size:21
Alignment explanation
Indices: 127553--127634 Score: 137
Period size: 21 Copynumber: 3.9 Consensus size: 21
127543 TTCACTTGAG
*
127553 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
127575 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
*
127596 GGGTATCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
127617 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
127635 CCCAGAAATC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 43 0.75
22 14 0.25
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:127616 original size:42 final size:43
Alignment explanation
Indices: 127553--127634 Score: 157
Period size: 42 Copynumber: 1.9 Consensus size: 43
127543 TTCACTTGAG
127553 GGGTATCGATTCCCCATTGAATGGGTACCGATTCCCCTTGAAT
1 GGGTATCGATTCCCCATTGAATGGGTACCGATTCCCCTTGAAT
127596 GGGTATCGATTCCCC-TTGAATGGGTACCGATTCCCCTTG
1 GGGTATCGATTCCCCATTGAATGGGTACCGATTCCCCTTG
127635 CCCAGAAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
42 24 0.62
43 15 0.38
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.30
Consensus pattern (43 bp):
GGGTATCGATTCCCCATTGAATGGGTACCGATTCCCCTTGAAT
Found at i:133030 original size:30 final size:30
Alignment explanation
Indices: 132995--133062 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
132985 TGGGATGATT
*
132995 TTGAAGCTAAATGGGTTAGGGTATTTGTTG
1 TTGAAGCTAAATGGGTTAGGGTATTTATTG
133025 TTGAAGCTAAATGGGTTAGGGTATTTATTG
1 TTGAAGCTAAATGGGTTAGGGTATTTATTG
133055 TTGAAGCT
1 TTGAAGCT
133063 TAAGGACTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.25, C:0.04, G:0.31, T:0.40
Consensus pattern (30 bp):
TTGAAGCTAAATGGGTTAGGGTATTTATTG
Found at i:137420 original size:38 final size:37
Alignment explanation
Indices: 137340--137422 Score: 148
Period size: 37 Copynumber: 2.2 Consensus size: 37
137330 ATTTTATGGT
*
137340 TTTTAATTATATATGTTATGACTTGTGATTTTATACC
1 TTTTAATAATATATGTTATGACTTGTGATTTTATACC
137377 TTTTAATAATATATGTTATGACTTGTGATATTTATACC
1 TTTTAATAATATATGTTATGACTTGTGAT-TTTATACC
137415 TTTTAATA
1 TTTTAATA
137423 TTGTAAACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 28 0.64
38 16 0.36
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (37 bp):
TTTTAATAATATATGTTATGACTTGTGATTTTATACC
Done.