Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005027.1 Hibiscus syriacus cultivar Beakdansim tig00011281_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: 192700
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3689 original size:18 final size:19
Alignment explanation
Indices: 3666--3722 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 19
3656 GTTCAGTATT
3666 TGTCCCGAATGACCACT-A
1 TGTCCCGAATGACCACTAA
3684 TGTCCCGAA-GAACCACTAGA
1 TGTCCCGAATG-ACCACTA-A
3704 TACGTCCCGAATGACCACT
1 T--GTCCCGAATGACCACT
3723 GGATACGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.03
18 15 0.45
20 2 0.06
22 14 0.42
23 1 0.03
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (19 bp):
TGTCCCGAATGACCACTAA
Found at i:3711 original size:40 final size:41
Alignment explanation
Indices: 3667--3756 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 41
3657 TTCAGTATTT
3667 GTCCCGAATGACCACT-AT-GTCCCGAAGAACCACTAGATA
1 GTCCCGAATGACCACTGATAGTCCCGAAGAACCACTAGATA
* *
3706 CGTCCCGAATGACCACTGGATACGTCCCGAAGGACCACTGGATA
1 -GTCCCGAATGACCACT-GATA-GTCCCGAAGAACCACTAGATA
3750 -TCCCGAA
1 GTCCCGAA
3757 GGACTAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
40 16 0.36
42 9 0.20
44 19 0.43
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (41 bp):
GTCCCGAATGACCACTGATAGTCCCGAAGAACCACTAGATA
Found at i:3713 original size:22 final size:21
Alignment explanation
Indices: 3685--3757 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 21
3675 TGACCACTAT
*
3685 GTCCCGAAGAACCACTAGATAC
1 GTCCCGAAG-ACCACTGGATAC
3707 GTCCCGAATGACCACTGGATAC
1 GTCCCGAA-GACCACTGGATAC
3729 GTCCCGAAGGACCACTGGATA-
1 GTCCCGAA-GACCACTGGATAC
3750 -TCCCGAAG
1 GTCCCGAAG
3758 GACTAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.02
20 7 0.15
22 39 0.81
23 1 0.02
ACGTcount: A:0.30, C:0.32, G:0.23, T:0.15
Consensus pattern (21 bp):
GTCCCGAAGACCACTGGATAC
Found at i:10579 original size:22 final size:22
Alignment explanation
Indices: 10551--10605 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
10541 TCAGTATTTG
10551 TCCCGAAGGACCACTGGATACA
1 TCCCGAAGGACCACTGGATACA
* *
10573 TCCCGAATGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACA
10595 TCCCGAAGGAC
1 TCCCGAAGGAC
10606 TAATATACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.15
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACA
Found at i:18532 original size:22 final size:23
Alignment explanation
Indices: 18502--18561 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
18492 GGGTGCATGA
*
18502 GGTATCGATACCCCC-TTGAATG
1 GGTACCGATACCCCCTTTGAATG
* *
18524 GGTACCGATTCCCCCTTTGAGTG
1 GGTACCGATACCCCCTTTGAATG
18547 GGTACCGATACCCCC
1 GGTACCGATACCCCC
18562 CAGGAGAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.18, C:0.33, G:0.23, T:0.25
Consensus pattern (23 bp):
GGTACCGATACCCCCTTTGAATG
Found at i:21283 original size:21 final size:21
Alignment explanation
Indices: 21259--21319 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
21249 TAGATTGCCC
21259 AGAGGGTACTGATACCCCCCA
1 AGAGGGTACTGATACCCCCCA
21280 AGAGGGTACTGATACCCCCCA
1 AGAGGGTACTGATACCCCCCA
*
21301 AGAGGGTACCGATACCCCC
1 AGAGGGTACTGATACCCCC
21320 ATATAAGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.28, C:0.34, G:0.25, T:0.13
Consensus pattern (21 bp):
AGAGGGTACTGATACCCCCCA
Found at i:27653 original size:5 final size:5
Alignment explanation
Indices: 27646--27679 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
27636 AGTAATGCCT
*
27646 CTCCT CTCCC CTCCC CTCCC CTCCC CTCCC CTCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC CTCCC CTCC
27680 AAACCCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (5 bp):
CTCCC
Found at i:32667 original size:3 final size:3
Alignment explanation
Indices: 32645--32683 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
32635 CGTTACAAGA
* * *
32645 AGG AGA AGG AGA ATG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
32684 TAATGTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.59, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:33905 original size:24 final size:25
Alignment explanation
Indices: 33873--33920 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
33863 AATTTATTTT
*
33873 CGTTTTCTTGA-AATTTTATAAATA
1 CGTTCTCTTGACAATTTTATAAATA
*
33897 CGTTCTCTTTACAATTTTATAAAT
1 CGTTCTCTTGACAATTTTATAAAT
33921 TTACCCATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (25 bp):
CGTTCTCTTGACAATTTTATAAATA
Found at i:38716 original size:2 final size:2
Alignment explanation
Indices: 38709--38737 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38699 AAAGGCTCAT
38709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38738 GGGACACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41078 original size:45 final size:45
Alignment explanation
Indices: 41013--41099 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
41003 TTTATTAATG
* * *
41013 GATTTTCCTATTGCAGAATAAA-TAATTATTATTATTGTTTTTTTA
1 GATTTTCCTACTGCAGAATAAATTAA-CATTATTATTGGTTTTTTA
* *
41058 GATTTTTCTACTGCATAATAAATTAACATTATTATTGGTTTT
1 GATTTTCCTACTGCAGAATAAATTAACATTATTATTGGTTTT
41100 CACTACTGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 33 0.92
46 3 0.08
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (45 bp):
GATTTTCCTACTGCAGAATAAATTAACATTATTATTGGTTTTTTA
Found at i:41591 original size:28 final size:28
Alignment explanation
Indices: 41526--41592 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
41516 AAGAACGCAA
*
41526 TAAGCCAACCTGAAACACATTACCTCCC
1 TAAGTCAACCTGAAACACATTACCTCCC
* * * * *
41554 CAAATTAACCTGAAACACATTATCTTCC
1 TAAGTCAACCTGAAACACATTACCTCCC
41582 TAAGTCAACCT
1 TAAGTCAACCT
41593 AAGCCTTATT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.33, G:0.06, T:0.24
Consensus pattern (28 bp):
TAAGTCAACCTGAAACACATTACCTCCC
Found at i:42846 original size:226 final size:220
Alignment explanation
Indices: 42588--43042 Score: 759
Period size: 226 Copynumber: 2.0 Consensus size: 220
42578 CGACCTGACA
* *
42588 CGACACGAAATAAAAAAAAATATTTTTATTCAATAAAAACATTGACTTAATTGAAAAAAAATATA
1 CGACCCGAAATAAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATA
*
42653 TATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTTGGGT
66 TATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATA-TTTTCGGGT
*
42718 CGGTCCGGT-TTTTTCACCCTAAACCCGACCCCGACCCGACCCGAATATCACACTTAAAAAAACC
130 C-G---GGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAA-C
42782 CGACCCGAACAAAATAAAGTTTCACCCGACC
190 CGACCCGAACAAAATAAAGTTTCACCCGACC
*
42813 CGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTAT
1 CGACCCGAAATAA-AAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATAT
*
42878 ATATAGAGGGGTATTATTGTAATTATTCCTAAATATGTAAGGTAAAATTATATATATTTTCGGGT
65 ATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGT
*
42943 CGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACCGACC
130 CGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGACC
* *
43008 TGACCAAAATAAAGTTTCACCCGACC
195 CGAACAAAATAAAGTTTCACCCGACC
43034 CGACCCGAA
1 CGACCCGAA
43043 TATATGAATT
Statistics
Matches: 219, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
221 42 0.19
222 51 0.23
224 1 0.00
225 21 0.10
226 104 0.47
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (220 bp):
CGACCCGAAATAAAAAAAAATATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATATA
TATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTC
GGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGACCC
GAACAAAATAAAGTTTCACCCGACC
Found at i:46885 original size:20 final size:20
Alignment explanation
Indices: 46860--46970 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
46850 CACCTGCACT
46860 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCATGC
*
46880 AATGCATCCATGCA-C-T-C
1 AATGCATCGATGCATCATGC
* *
46897 AA-ACATCGAATGCA-C-T-T
1 AATGCATCG-ATGCATCATGC
* *
46914 AGTGCATCGATACATCATGC
1 AATGCATCGATGCATCATGC
* * *
46934 CATACATCGATGCATCCTGC
1 AATGCATCGATGCATCATGC
*
46954 AATGCATCCATGCATCA
1 AATGCATCGATGCATCA
46971 AGGCTGCAAC
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
16 4 0.06
17 15 0.22
18 7 0.10
19 2 0.03
20 41 0.59
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (20 bp):
AATGCATCGATGCATCATGC
Found at i:49626 original size:29 final size:30
Alignment explanation
Indices: 49557--49615 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
49547 CAATTTAAGG
*
49557 CAAAATGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
*
49587 CAAAATATTTTTGGACTT-AATTAAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
49616 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:49946 original size:21 final size:21
Alignment explanation
Indices: 49917--49956 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
49907 TTTGAGTAGA
49917 AAAATCATCCCCAAGCGGCTCC
1 AAAATCATCCCCAA-CGGCTCC
49939 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
49957 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.35, C:0.40, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:53503 original size:14 final size:14
Alignment explanation
Indices: 53484--53511 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53474 CTGTTGTTAA
53484 AAATAATAATTCAT
1 AAATAATAATTCAT
53498 AAATAATAATTCAT
1 AAATAATAATTCAT
53512 TTGATCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAATAATTCAT
Found at i:61869 original size:20 final size:20
Alignment explanation
Indices: 61839--61883 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
61829 TATTTTATCC
61839 ATTTG-ACTTATTGGGCCAA
1 ATTTGCACTTATTGGGCCAA
61858 ATTTGCACTTATTGGGCCAA
1 ATTTGCACTTATTGGGCCAA
61878 ATTTGC
1 ATTTGC
61884 CCATTCATCC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTTGCACTTATTGGGCCAA
Found at i:62722 original size:20 final size:20
Alignment explanation
Indices: 62694--62732 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62684 TCCCATAAAA
*
62694 TAGATATAATTTATTTTTAT
1 TAGAAATAATTTATTTTTAT
62714 TAGAAATAATTTATTTTTA
1 TAGAAATAATTTATTTTTA
62733 ACAAATACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TAGAAATAATTTATTTTTAT
Found at i:65076 original size:20 final size:20
Alignment explanation
Indices: 65048--65098 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
65038 TACTTAACAA
* *
65048 TATCAGTATTGTTCTTGCAG
1 TATCGGTATTGTTCTTACAG
*
65068 TATCGGTATTGTTCTTATAG
1 TATCGGTATTGTTCTTACAG
65088 TATCGGTATTG
1 TATCGGTATTG
65099 CAGAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.47
Consensus pattern (20 bp):
TATCGGTATTGTTCTTACAG
Found at i:65430 original size:12 final size:12
Alignment explanation
Indices: 65413--65437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65403 TTTAGCACAA
65413 TAGTATCAGTAC
1 TAGTATCAGTAC
65425 TAGTATCAGTAC
1 TAGTATCAGTAC
65437 T
1 T
65438 GCATGAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TAGTATCAGTAC
Found at i:66733 original size:18 final size:19
Alignment explanation
Indices: 66707--66742 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
66697 TTTAAATAGA
66707 AAACACAAAA-TTTGAAAT
1 AAACACAAAACTTTGAAAT
*
66725 AAACCCAAAACTTTGAAA
1 AAACACAAAACTTTGAAA
66743 ACCTTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (19 bp):
AAACACAAAACTTTGAAAT
Found at i:67979 original size:21 final size:21
Alignment explanation
Indices: 67953--68002 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
67943 GTCAGGTTCG
67953 GGTCGGGTGAAATCTTGTTTT
1 GGTCGGGTGAAATCTTGTTTT
67974 GGTCGGGTGAAATCTTGTTTT
1 GGTCGGGTGAAATCTTGTTTT
*
67995 GGTTGGGT
1 GGTCGGGT
68003 CGAGTCTCGA
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:0.12, C:0.08, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTCGGGTGAAATCTTGTTTT
Found at i:68003 original size:26 final size:24
Alignment explanation
Indices: 67947--68004 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 24
67937 TATTGGGTCA
67947 GGTTCGGGTCGGGTGAAATCTTGTT
1 GGTT-GGGTCGGGTGAAATCTTGTT
67972 --TT-GGTCGGGTGAAATCTTGTTTT
1 GGTTGGGTCGGGTGAAATCTTG--TT
67995 GGTTGGGTCG
1 GGTTGGGTCG
68005 AGTCTCGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
21 17 0.61
23 4 0.14
25 2 0.07
26 5 0.18
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (24 bp):
GGTTGGGTCGGGTGAAATCTTGTT
Found at i:75322 original size:23 final size:23
Alignment explanation
Indices: 75304--75364 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
75294 CTCGTATAAA
75304 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
75327 TGCACCGAAGTGTCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
75350 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
75365 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:75621 original size:30 final size:31
Alignment explanation
Indices: 75587--75646 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
75577 TATTGTATAG
75587 ACATATAAT-TTCCAT-ACCTTTATCACATAA
1 ACATATAATGTTCCATCA-CTTTATCACATAA
75617 ACATATAATGTTCCATCACTTTATCACATA
1 ACATATAATGTTCCATCACTTTATCACATA
75647 TCTTATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 9 0.32
31 18 0.64
32 1 0.04
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (31 bp):
ACATATAATGTTCCATCACTTTATCACATAA
Found at i:80419 original size:18 final size:18
Alignment explanation
Indices: 80392--80426 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
80382 CTGGTTCCTT
*
80392 CCTCTACCTCTTCCTCTA
1 CCTCTACCTCGTCCTCTA
*
80410 CCTCTTCCTCGTCCTCT
1 CCTCTACCTCGTCCTCT
80427 CTGTGAGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.51, G:0.03, T:0.40
Consensus pattern (18 bp):
CCTCTACCTCGTCCTCTA
Found at i:80426 original size:12 final size:12
Alignment explanation
Indices: 80389--80419 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
80379 AGACTGGTTC
80389 CTTCCTCTACCT
1 CTTCCTCTACCT
80401 CTTCCTCTACCT
1 CTTCCTCTACCT
80413 CTTCCTC
1 CTTCCTC
80420 GTCCTCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.52, G:0.00, T:0.42
Consensus pattern (12 bp):
CTTCCTCTACCT
Found at i:82313 original size:23 final size:23
Alignment explanation
Indices: 82255--82306 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
82245 CTCGTATAAA
*
82255 TGCACCGAAATGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
82278 TGTACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
82301 TGCACC
1 TGCACC
82307 ATAGTGCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:82582 original size:31 final size:30
Alignment explanation
Indices: 82538--82597 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
82528 TATTGTATAG
82538 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
82568 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
82598 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:85828 original size:18 final size:18
Alignment explanation
Indices: 85805--85854 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
85795 GGTTCTACGC
85805 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
85823 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
85841 GGTCCTACGGGACA
1 GGTCCTTCGGGACA
85855 AATTCTACGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.24
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:88352 original size:75 final size:75
Alignment explanation
Indices: 88273--88474 Score: 262
Period size: 75 Copynumber: 2.7 Consensus size: 75
88263 AAAATTTTCA
* *
88273 AAAATTTTAGGGTGGAAACCATCAATAAAATGGGTC-ACTAATTGAAGAAAATTCAGATTTCAGG
1 AAAATTTTAGGGTGGAAACCATCAATAAAATTGG-CGACTAATCGAAGAAAATTCAGATTTCAGG
88337 GTAGACAAAAT
65 GTAGACAAAAT
** * *
88348 AAAATTTTAGGGTGGGTACCATCAATAAAATTGGCGACTAATCGAAGAAAAATCAGATTTCATGG
1 AAAATTTTAGGGTGGAAACCATCAATAAAATTGGCGACTAATCGAAGAAAATTCAGATTTCAGGG
* *
88413 TGGACACAAT
66 TAGACAAAAT
*** * * *
88423 ATTTTTTTATGGTGTACACCATCAATAAAATTGGCGACTAATCGAAGAAAAT
1 AAAATTTTAGGGTGGAAACCATCAATAAAATTGGCGACTAATCGAAGAAAAT
88475 CCAAATTTTA
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 1 0.01
75 109 0.99
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (75 bp):
AAAATTTTAGGGTGGAAACCATCAATAAAATTGGCGACTAATCGAAGAAAATTCAGATTTCAGGG
TAGACAAAAT
Found at i:89197 original size:17 final size:17
Alignment explanation
Indices: 89162--89207 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
89152 ATACAATTGA
* *
89162 AAATATTTCTTATTTTT
1 AAATATTTATTATTATT
89179 AAATATTT-TTATTAATT
1 AAATATTTATTATT-ATT
89196 -AATATTTATTAT
1 AAATATTTATTAT
89208 ATAGTGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTATTATTATT
Found at i:91520 original size:235 final size:235
Alignment explanation
Indices: 91057--91524 Score: 920
Period size: 235 Copynumber: 2.0 Consensus size: 235
91047 TTTCGTTTTA
91057 TCCCTTGCTGTCTCTAGGAACTGGATGTCGAGACAAGTCGACGTTAATAACGCGTTTCTTAACGG
1 TCCCTTGCTGTCTCTAGGAACTGGATGTCGAGACAAGTCGACGTTAATAACGCGTTTCTTAACGG
91122 TGGTCTTGATGAAGACGTTTACATACAATAGCCATCGGGGTTTGAATGTTAGACTGCTGACGGCA
66 TGGTCTTGATGAAGACGTTTACATACAATAGCCATCGGGGTTTGAATGTTAGACTGCTGACGGCA
91187 TTGAGTTAGTTTGTAAGTTGCAAAGAGCTCTTTATGGGCCGAGTCAAGCGTCATTGTTTATTCTG
131 TTGAGTTAGTTTGTAAGTTGCAAAGAGCTCTTTATGGGCCGAGTCAAGCGTCATTGTTTATTCTG
91252 AACAAGAATGGCGTTCGCACGTACATGTTAGTTTACGTTT
196 AACAAGAATGGCGTTCGCACGTACATGTTAGTTTACGTTT
91292 TCCCTTGCTGTCTCTAGGAACTGGATGTCGAGACAAGTCGACGTTAATAACGCGTTTCTTAACGG
1 TCCCTTGCTGTCTCTAGGAACTGGATGTCGAGACAAGTCGACGTTAATAACGCGTTTCTTAACGG
91357 TGGTCTTGATGAAGACGTTTACATACAATAGCCATCGGGGTTTGAATGTTAGACTGCTGACGGCA
66 TGGTCTTGATGAAGACGTTTACATACAATAGCCATCGGGGTTTGAATGTTAGACTGCTGACGGCA
91422 TTGAGTTAGTTTGTAAGTTGCAAAGAGCTC-TTATGGGCCGAGTCAAGCGTCATTGTTTATTCTG
131 TTGAGTTAGTTTGTAAGTTGCAAAGAGCTCTTTATGGGCCGAGTCAAGCGTCATTGTTTATTCTG
91486 AACAAGAATGGCGTTCGCACGTACATGTTTAGTTTACGT
196 AACAAGAATGGCGTTCGCACGTACATG-TTAGTTTACGT
91525 AGACGATATT
Statistics
Matches: 232, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
234 61 0.26
235 171 0.74
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (235 bp):
TCCCTTGCTGTCTCTAGGAACTGGATGTCGAGACAAGTCGACGTTAATAACGCGTTTCTTAACGG
TGGTCTTGATGAAGACGTTTACATACAATAGCCATCGGGGTTTGAATGTTAGACTGCTGACGGCA
TTGAGTTAGTTTGTAAGTTGCAAAGAGCTCTTTATGGGCCGAGTCAAGCGTCATTGTTTATTCTG
AACAAGAATGGCGTTCGCACGTACATGTTAGTTTACGTTT
Found at i:102324 original size:11 final size:11
Alignment explanation
Indices: 102290--102330 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
102280 TTAGTTAAGT
*
102290 TTTATTTTATA
1 TTTATTATATA
102301 TTT-TTAT-TCA
1 TTTATTATAT-A
102311 TTTATTATATA
1 TTTATTATATA
102322 TTTATTATA
1 TTTATTATA
102331 CTTAAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 1 0.04
10 7 0.27
11 17 0.65
12 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTATATA
Found at i:102533 original size:15 final size:14
Alignment explanation
Indices: 102490--102535 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
102480 TTTGTAATTA
102490 TTTATTAAAAT-TT
1 TTTATTAAAATATT
102503 TTTGATTAAAATTATT
1 TTT-ATTAAAA-TATT
102519 TTTATATAAAATATT
1 TTTAT-TAAAATATT
102534 TT
1 TT
102536 ATTTCATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.10
14 7 0.24
15 9 0.31
16 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTATTAAAATATT
Found at i:102537 original size:14 final size:13
Alignment explanation
Indices: 102490--102538 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
102480 TTTGTAATTA
*
102490 TTTATTAAAATTT
1 TTTATTAAAATAT
102503 TTTGATTAAAATTATT
1 TTT-ATTAAAA-TA-T
102519 TTTATATAAAATAT
1 TTTAT-TAAAATAT
102533 TTTATT
1 TTTATT
102539 TCATGTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
13 4 0.13
14 13 0.42
15 5 0.16
16 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TTTATTAAAATAT
Found at i:102676 original size:32 final size:30
Alignment explanation
Indices: 102617--102676 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 30
102607 TATTTAAAAC
*
102617 ATAAATTATATAATTTAAAATTGAAAGAAT
1 ATAAATTATAAAATTTAAAATTGAAAGAAT
102647 ATAAATTTATAAAGATTTCAAAA-TGAAAGA
1 ATAAA-TTATAAA-ATTT-AAAATTGAAAGA
102677 GATTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.19
31 6 0.23
32 11 0.42
33 4 0.15
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (30 bp):
ATAAATTATAAAATTTAAAATTGAAAGAAT
Found at i:104486 original size:2 final size:2
Alignment explanation
Indices: 104442--104471 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
104432 CCAAAATCCA
104442 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
104472 CAAAACTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107707 original size:2 final size:2
Alignment explanation
Indices: 107700--107726 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
107690 ACCTTTACAA
107700 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 A
107727 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:107831 original size:31 final size:32
Alignment explanation
Indices: 107772--107844 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
107762 ACTAGGTAAC
** *
107772 GGGTCAAATTGATATTTTTTTCTAAAATTTAA
1 GGGTCAAATTGATATTTTTACCTAAAATTCAA
* *
107804 GGGTCAATTTGATA-TTTTACCTAAAATTCAG
1 GGGTCAAATTGATATTTTTACCTAAAATTCAA
107835 GGGTCAAATT
1 GGGTCAAATT
107845 AAAAAGTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 22 0.63
32 13 0.37
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (32 bp):
GGGTCAAATTGATATTTTTACCTAAAATTCAA
Found at i:107952 original size:31 final size:31
Alignment explanation
Indices: 107912--107981 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
107902 ACACTGATCG
**
107912 AAATATTATAAATAT-ATAATGTAAGTGACCA
1 AAATATTATAAA-ATGATAACATAAGTGACCA
* *
107943 AAATGTTATAAAATGATAACATAAGTGACTA
1 AAATATTATAAAATGATAACATAAGTGACCA
*
107974 AAAAATTA
1 AAATATTA
107982 CTTTTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.30
Consensus pattern (31 bp):
AAATATTATAAAATGATAACATAAGTGACCA
Found at i:110540 original size:15 final size:16
Alignment explanation
Indices: 110514--110544 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
110504 AGGTGGGGTT
110514 TTTTTAAGAAAAAATA
1 TTTTTAAGAAAAAATA
110530 TTTTTAA-AAAAAATA
1 TTTTTAAGAAAAAATA
110545 AATTCTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTTTTAAGAAAAAATA
Found at i:111508 original size:38 final size:38
Alignment explanation
Indices: 111466--111541 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
111456 CCAACAAAAG
111466 AAAGAAAAATTATTCCACCAAAATAAAGCATTGGTAAT
1 AAAGAAAAATTATTCCACCAAAATAAAGCATTGGTAAT
111504 AAAGAAAAATTATTCCACCAAAATAAAGCATTGGTAAT
1 AAAGAAAAATTATTCCACCAAAATAAAGCATTGGTAAT
111542 GTGTGATCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (38 bp):
AAAGAAAAATTATTCCACCAAAATAAAGCATTGGTAAT
Found at i:127991 original size:7 final size:7
Alignment explanation
Indices: 127981--128024 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
127971 AATTTTAATT
127981 TTTTTTA
1 TTTTTTA
127988 TTTTTTA
1 TTTTTTA
127995 TTTTTTA
1 TTTTTTA
128002 TTTTTTA
1 TTTTTTA
128009 TTTTTTA
1 TTTTTTA
128016 TTTTTTA
1 TTTTTTA
128023 TT
1 TT
128025 AAAATATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTA
Found at i:132943 original size:31 final size:31
Alignment explanation
Indices: 132905--133029 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
132895 AGGGTCGAGG
*
132905 GTTTACCTATGTTCTTCGAGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
132936 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
132967 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
132998 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
133029 G
1 G
133030 GTCATTCGGG
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:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:137723 original size:74 final size:76
Alignment explanation
Indices: 137573--137748 Score: 239
Period size: 75 Copynumber: 2.3 Consensus size: 76
137563 GATACCCCCT
* * * ** *
137573 TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAACTGTTTAGGGGGGAATC
1 TGGGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAACAAAACCATTCAGGGGGGAATC
137638 AGTTCCTCCTA
66 AGTTCCTCCTA
* *
137649 T-GGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAGCCAAACCATTCA-GGGGGAATC
1 TGGGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAACAAAACCATTCAGGGGGGAATC
*
137712 GGTTCCTCCTA
66 AGTTCCTCCTA
* *
137723 TGGGGGGAATCAGTTCCCTCTGAGCA
1 TGGGGGGAATCGGTTCCCTCCGAGCA
137749 ATCTGGAATT
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 20 0.23
75 67 0.76
76 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (76 bp):
TGGGGGGAATCGGTTCCCTCCGAGCATAATGGAAATCTCGGAACAAAACCATTCAGGGGGGAATC
AGTTCCTCCTA
Found at i:146807 original size:74 final size:75
Alignment explanation
Indices: 146706--146911 Score: 274
Period size: 75 Copynumber: 2.8 Consensus size: 75
146696 CCGTTGAACA
* * *
146706 AGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
** *
146770 AAAACTGTTT
66 AAAACCATTC
* * *
146780 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
*
146844 CCAAACCATTC
65 CAAAACCATTC
*
146855 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
146912 TTTGGCTTTG
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 22 0.19
75 92 0.80
76 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (75 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
AAAACCATTC
Found at i:153089 original size:21 final size:21
Alignment explanation
Indices: 153041--153102 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 21
153031 CCCCCCATGA
153041 GGGAACCGATTCCCCCCTTTGAAG
1 GGGAACCGATTCCCCCC--T-AAG
153065 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTA-AG
* *
153086 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
153103 CTGGGGTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 17 0.49
24 17 0.49
ACGTcount: A:0.23, C:0.39, G:0.24, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTAAG
Found at i:154733 original size:12 final size:12
Alignment explanation
Indices: 154716--154744 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
154706 AGATGAGCCT
154716 GAGCAGCCCGAG
1 GAGCAGCCCGAG
154728 GAGCAGCCCGAG
1 GAGCAGCCCGAG
154740 GAGCA
1 GAGCA
154745 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:155095 original size:24 final size:23
Alignment explanation
Indices: 155045--155117 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
155035 GCTTCAACTT
* *
155045 TTTGGATTGTTTGATTTTATGAC
1 TTTGGATTGTTTGATGTTATGAA
155068 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTATGAA
*
155092 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTATGAA
155115 TTT
1 TTT
155118 ATGGATGATG
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 1 0.02
22 2 0.05
23 12 0.28
24 12 0.28
25 12 0.28
26 4 0.09
ACGTcount: A:0.18, C:0.01, G:0.25, T:0.56
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTATGAA
Found at i:156664 original size:76 final size:77
Alignment explanation
Indices: 156580--156743 Score: 240
Period size: 76 Copynumber: 2.1 Consensus size: 77
156570 TGCATATATA
* *
156580 TATATATATATACTTATCATTGATCAATGATATATGTATATATATATGATGTATATACATAAGTA
1 TATATATATATACTTATCATTAATCAATGATATATGTACATATATATGATGTATATACATAAGTA
*
156645 TGAATATAAGTT
66 TAAATATAAGTT
* * * *
156657 TA-ATATATATACTTATCATTAATCATTGATGTATGTACATATGTATGATGTATGTACATAAGTA
1 TATATATATATACTTATCATTAATCAATGATATATGTACATATATATGATGTATATACATAAGTA
*
156721 TAAATATAATTT
66 TAAATATAAGTT
*
156733 TATTTATATAT
1 TATATATATAT
156744 TGAAATAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 68 0.88
77 9 0.12
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (77 bp):
TATATATATATACTTATCATTAATCAATGATATATGTACATATATATGATGTATATACATAAGTA
TAAATATAAGTT
Found at i:156707 original size:19 final size:19
Alignment explanation
Indices: 156683--156721 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
156673 CATTAATCAT
*
156683 TGATGTATGTACATATGTA
1 TGATGTATGTACATAAGTA
156702 TGATGTATGTACATAAGTA
1 TGATGTATGTACATAAGTA
156721 T
1 T
156722 AAATATAATT
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:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (19 bp):
TGATGTATGTACATAAGTA
Found at i:156926 original size:2 final size:2
Alignment explanation
Indices: 156919--156943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
156909 TACATAAACT
156919 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
156944 CATTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:157443 original size:18 final size:18
Alignment explanation
Indices: 157406--157442 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
157396 TGTTTCTTTT
157406 AATCAATTTCCCTTCAAA
1 AATCAATTTCCCTTCAAA
157424 AATCAATTTCCC-TCAAA
1 AATCAATTTCCCTTCAAA
157441 AA
1 AA
157443 AAACATTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (18 bp):
AATCAATTTCCCTTCAAA
Found at i:157450 original size:18 final size:18
Alignment explanation
Indices: 157410--157452 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
157400 TCTTTTAATC
**
157410 AATTTCCCTTCAAAAATC
1 AATTTCCCTTCAAAAAAA
157428 AATTTCCC-TCAAAAAAA
1 AATTTCCCTTCAAAAAAA
157445 ACATTTCC
1 A-ATTTCC
157453 TTTAAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTTCCCTTCAAAAAAA
Found at i:157541 original size:25 final size:24
Alignment explanation
Indices: 157500--157546 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
157490 CTTTTATATA
157500 TATATTTTAAAATTTTAAATTAAAT
1 TATATTTTAAAATTTT-AATTAAAT
*
157525 TATA-TTTAAATTATTTAATTAA
1 TATATTTTAAAAT-TTTAATTAA
157547 CTATTACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATTTTAAAATTTTAATTAAAT
Found at i:157590 original size:15 final size:16
Alignment explanation
Indices: 157549--157590 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
157539 TTAATTAACT
*
157549 ATTACATTAAAAATAA
1 ATTAAATTAAAAATAA
157565 ATTAAACTTAAAAA-AA
1 ATTAAA-TTAAAAATAA
*
157581 TTTAAATTAA
1 ATTAAATTAA
157591 TTTTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 12 0.52
17 7 0.30
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTAAATTAAAAATAA
Found at i:158690 original size:15 final size:15
Alignment explanation
Indices: 158667--158711 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
158657 TATGACATTT
158667 ATTATTATTTTATTA
1 ATTATTATTTTATTA
*
158682 ATTAATATTTTATTA
1 ATTATTATTTTATTA
158697 A-TATTATTTTTATTA
1 ATTATTA-TTTTATTA
158712 CCCCATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTATTATTTTATTA
Found at i:160536 original size:212 final size:210
Alignment explanation
Indices: 160149--160535 Score: 665
Period size: 212 Copynumber: 1.8 Consensus size: 210
160139 GGGTGAAAAT
* *
160149 ACCCGATCTGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAAAAATTACAATAATAC
1 ACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAAAAATTACAATAATAC
160214 CCCTCTATATATAATTTTTTTTCAATTAAATCACTGTTTTTATTGAATAAAAATAATTTTTTTAT
66 CCCTCTATATATAATTTTTTTTCAATTAAATCACTGTTTTTATTGAATAAAAATAATTTTTTTAT
160279 TATTTCAGGTCGAGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTT
131 TATTTCA-G-CGAGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTT
160344 AGGGTGAAAAATACCCG
194 AGGGTGAAAAATACCCG
*
160361 ACCCGACCCGACCTGAAAAAATATATAATTTTACCTTATATATTTAGGAAAAATTACAATAATAC
1 ACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAAAAATTACAATAATAC
*
160426 CCCTCTATATATAATTTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAA-TTTTTTA
66 CCCTCTATATATAATTTTTTTT-CAATTAAATCACTGTTTTTATTGAATAAAAATAATTTTTTTA
* *
160490 TTATTTC-G-G-GTCGAGTTTCTAATTCATATATTCGGGTTGGGTCGGG
130 TTATTTCAGCGAGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGG
160536 TGGAACTTTA
Statistics
Matches: 168, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
207 35 0.21
208 1 0.01
210 1 0.01
212 98 0.58
213 33 0.20
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (210 bp):
ACCCGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAAAAATTACAATAATAC
CCCTCTATATATAATTTTTTTTCAATTAAATCACTGTTTTTATTGAATAAAAATAATTTTTTTAT
TATTTCAGCGAGTCGAATTTCTAATTCATATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTTAG
GGTGAAAAATACCCG
Found at i:160802 original size:257 final size:263
Alignment explanation
Indices: 160310--160817 Score: 812
Period size: 257 Copynumber: 1.9 Consensus size: 263
160300 TCTAATTCAT
160310 ATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGACCT
1 ATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTTAGGGTGAAAAAT---C-ACCCGACCCGA-C-
*
160375 GAAAAAATATATAATTTTACCTTATATATTTAGGAAAAATTACAATAATACCCCTCTATATATAA
60 -AAAAAATATATAATTTTACATTATATATTTAGGAAAAATTACAATAATACCCCTCTATATATAA
*
160440 TTTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTATTATTTCGGGTCGAG
124 TTTTTTTTCCAATTAAGTCACTGTTTTTATTCAATAAAAATAATTTTTTATTATTTCGGGTCGAG
* * *
160505 TTTCTAATTCATATATTCGGGTTGGGTCGGGTGGAACTTTATTTTGGTCGGGTCGGGTCGGTTTT
189 TTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTT
160570 TTTAATTGTG
254 TTTAATTGTG
*
160580 ATATTTGGGTCGGGTC-GGGTCGGGTTCGGGTTTAGGGTGAAAAAT-ACCCGACCC-A-AAAAAA
1 ATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTTAGGGTGAAAAATCACCCGACCCGACAAAAAA
* *
160641 TATATAATTTTACATTATATATTTAGGAATAATTACAATAATATCCCTCTATATATAA-TTTTTT
66 TATATAATTTTACATTATATATTTAGGAAAAATTACAATAATACCCCTCTATATATAATTTTTTT
* *
160705 T-CAATTAAGTCACTGTTTTTATTCAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAA
131 TCCAATTAAGTCACTGTTTTTATTCAATAAAAATAATTTTTTATTATTTCGGGTCGAGTTTCTAA
*
160769 TTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCTGGTCGG
196 TTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG
160818 ATCGAGTCTC
Statistics
Matches: 227, Mismatches: 11, Indels: 13
0.90 0.04 0.05
Matches are distributed among these distances:
257 105 0.46
258 7 0.03
259 61 0.27
263 1 0.00
264 9 0.04
269 29 0.13
270 15 0.07
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (263 bp):
ATATTCGGGTCGGGTCGGGGTCGGGTTCGGGTTTAGGGTGAAAAATCACCCGACCCGACAAAAAA
TATATAATTTTACATTATATATTTAGGAAAAATTACAATAATACCCCTCTATATATAATTTTTTT
TCCAATTAAGTCACTGTTTTTATTCAATAAAAATAATTTTTTATTATTTCGGGTCGAGTTTCTAA
TTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAATT
GTG
Found at i:161197 original size:18 final size:18
Alignment explanation
Indices: 161170--161218 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
161160 AATTCCTGAC
*
161170 AGATTCCAATTCCTTCAT
1 AGATTTCAATTCCTTCAT
161188 AGATTTCAATTCCTTCAT
1 AGATTTCAATTCCTTCAT
*
161206 AAATTTCAATTCC
1 AGATTTCAATTCC
161219 CTCAGAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (18 bp):
AGATTTCAATTCCTTCAT
Found at i:172543 original size:20 final size:20
Alignment explanation
Indices: 172518--172559 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
172508 TCAACACCCC
172518 ATGAGATGACATGGCAAATT
1 ATGAGATGACATGGCAAATT
172538 ATGAGATGACATGGCAAATT
1 ATGAGATGACATGGCAAATT
172558 AT
1 AT
172560 ATTAGTACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (20 bp):
ATGAGATGACATGGCAAATT
Found at i:173221 original size:78 final size:76
Alignment explanation
Indices: 173071--173341 Score: 325
Period size: 75 Copynumber: 3.5 Consensus size: 76
173061 TGGTGCTTAA
* * * * *
173071 ATGGATGGATTTGGTTTAACCATTGTTCGTAGATTTTGGGCTT-TGGGTTTGGTTTAGTCGCTGA
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGGATTTTGGGGTTGTGGGTTT-GTTTAGTCACTGA
173135 TGGTGGTGGTGGC
65 T-GTGGTGGTGGC
* * *
173148 ATGGACGAACTTGGTTTAACCATCGTTGGTGGATTTTGGGGTTGTGGGTTTAGTTTAGTCACTGA
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGGATTTTGGGGTTGTGGGTTT-GTTTAGTCACTGA
173213 TAGTGGTGGT---
65 T-GTGGTGGTGGC
* * * **
173223 ATGGACGGATTTGATTTAACTATTGTTGGTGAATTTTGGGAATGTGGGTTTGATTTAGTCACTGA
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGGATTTTGGGGTTGTGGGTTTG-TTTAGTCACTGA
173288 TGATGGTGGTGGC
65 TG-TGGTGGTGGC
* *
173301 ATGTACGGATTTGGTTTAACCATGGTTGGTGGATTTTGGGG
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGGATTTTGGGG
173342 ACGAATTTGA
Statistics
Matches: 164, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
74 2 0.01
75 63 0.38
77 36 0.22
78 63 0.38
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (76 bp):
ATGGACGGATTTGGTTTAACCATTGTTGGTGGATTTTGGGGTTGTGGGTTTGTTTAGTCACTGAT
GTGGTGGTGGC
Found at i:173259 original size:75 final size:74
Alignment explanation
Indices: 173071--173341 Score: 285
Period size: 78 Copynumber: 3.6 Consensus size: 74
173061 TGGTGCTTAA
* * * *
173071 ATGGATGGATTTGGTTTAACCATTGTTCGT-AGATTTTGGGCTT-TGGGTTTGGTTTAGTCGCTG
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGA-ATTTTGGGGTTGTGGGTTT-GTTTAGTCACTG
*
173134 ATGGTGGTGGT
64 ATAGTGGTGGT
* * * *
173145 GGCATGGACGAACTTGGTTTAACCATCGTTGGTGGATTTTGGGGTTGTGGGTTTAGTTTAGTCAC
1 ---ATGGACGGATTTGGTTTAACCATTGTTGGTGAATTTTGGGGTTGTGGGTTT-GTTTAGTCAC
173210 TGATAGTGGTGGT
62 TGATAGTGGTGGT
* * **
173223 ATGGACGGATTTGATTTAACTATTGTTGGTGAATTTTGGGAATGTGGGTTTGATTTAGTCACTGA
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGAATTTTGGGGTTGTGGGTTTG-TTTAGTCACTGA
*
173288 TGATGGTGGTGGC
65 T-A--GTGGTGGT
* * *
173301 ATGTACGGATTTGGTTTAACCATGGTTGGTGGATTTTGGGG
1 ATGGACGGATTTGGTTTAACCATTGTTGGTGAATTTTGGGG
173342 ACGAATTTGA
Statistics
Matches: 163, Mismatches: 25, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
74 1 0.01
75 56 0.34
76 1 0.01
77 35 0.21
78 70 0.43
ACGTcount: A:0.17, C:0.08, G:0.35, T:0.40
Consensus pattern (74 bp):
ATGGACGGATTTGGTTTAACCATTGTTGGTGAATTTTGGGGTTGTGGGTTTGTTTAGTCACTGAT
AGTGGTGGT
Found at i:173429 original size:113 final size:115
Alignment explanation
Indices: 173225--173453 Score: 322
Period size: 113 Copynumber: 2.0 Consensus size: 115
173215 GTGGTGGTAT
* * * * *
173225 GGACGGATTTGATTTAACTATTGTTGGTGAATTTTGGGAATGTGGGTTTGATTTAGTCACTGATG
1 GGACGAATTTGATTTAACCATTATTGGTGAATTTTGGGAATCTGAGTTTGATTTAGTCACTGATG
* * *
173290 ATGGTGGTGGCATGTACGGATTTGGTTTAACCATGGTTGGTGGATTTTGG
66 ATGGTGGTGACATGGACGAATTTGGTTTAACCATGGTTGGTGGATTTTGG
173340 GGACGAATTTGATTTAACCATTATTGGT-AGATTTTGGG-A-CTGAGTTT-AGTTTAGTCACTGA
1 GGACGAATTTGATTTAACCATTATTGGTGA-ATTTTGGGAATCTGAGTTTGA-TTTAGTCACTGA
* *
173401 TGATGGTGGTGACATGGACGAATTTGGTTTAATCATTGTTGGTGGATTTTGG
64 TGATGGTGGTGACATGGACGAATTTGGTTTAACCATGGTTGGTGGATTTTGG
173453 G
1 G
173454 TTGTGGGTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
112 1 0.01
113 66 0.65
114 2 0.02
115 33 0.32
ACGTcount: A:0.21, C:0.07, G:0.32, T:0.40
Consensus pattern (115 bp):
GGACGAATTTGATTTAACCATTATTGGTGAATTTTGGGAATCTGAGTTTGATTTAGTCACTGATG
ATGGTGGTGACATGGACGAATTTGGTTTAACCATGGTTGGTGGATTTTGG
Found at i:173473 original size:190 final size:188
Alignment explanation
Indices: 173150--173515 Score: 467
Period size: 190 Copynumber: 1.9 Consensus size: 188
173140 GTGGTGGCAT
* * * ** *
173150 GGACGAACTTGGTTTAACCATCGTTGGTGGATTTTGGGGTTGTGGGTTTAGTTTAGTCACTGATA
1 GGACGAACTTGATTTAACCATCATTGGTAGATTTTGGGGTACTGAGTTTAGTTTAGTCACTGATA
*
173215 GTGGTGGTATGGACGGATTTGATTTAACTATTGTTGGTGAATTTTGGGAATGTGGGTTTGATTTA
66 GTGGTGGTATGGACGAATTTGATTTAACTATTGTTGGTGAATTTTGGGAATGTGGGTTTGATTTA
173280 GTCACTGATGATGGTGGTGGCAT-GTACGGATTTGGTTTAACCA-TGGTTGGTGGATTTTGG
131 GTCA-T--TGATGGTGGTGGCATAG-ACGGATTTGGTTTAACCATTGGTTGGTGGATTTTGG
* *
173340 GGACGAATTTGATTTAACCATTATTGGTAGATTTT-GGG-ACTGAGTTTAGTTTAGTCACTGAT-
1 GGACGAACTTGATTTAACCATCATTGGTAGATTTTGGGGTACTGAGTTTAGTTTAGTCACTGATA
* * *
173402 GATGGTGGTGACATGGACGAATTTGGTTTAA-TCATTGTTGGTGGATTTTGGG-TTGTGGGTTTG
66 G-TGGTGGT---ATGGACGAATTTGATTTAACT-ATTGTTGGTGAATTTTGGGAATGTGGGTTTG
* * *
173465 GTTTAGTCATTGATGGTGGTGGTATAGACGTATTTGGTTTAACCATTGGTT
126 ATTTAGTCATTGATGGTGGTGGCATAGACGGATTTGGTTTAACCATTGGTT
173516 TGGCTTAGTT
Statistics
Matches: 154, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
187 32 0.21
188 34 0.22
189 4 0.03
190 49 0.32
191 35 0.23
ACGTcount: A:0.19, C:0.08, G:0.33, T:0.40
Consensus pattern (188 bp):
GGACGAACTTGATTTAACCATCATTGGTAGATTTTGGGGTACTGAGTTTAGTTTAGTCACTGATA
GTGGTGGTATGGACGAATTTGATTTAACTATTGTTGGTGAATTTTGGGAATGTGGGTTTGATTTA
GTCATTGATGGTGGTGGCATAGACGGATTTGGTTTAACCATTGGTTGGTGGATTTTGG
Found at i:173505 original size:74 final size:75
Alignment explanation
Indices: 173341--173512 Score: 204
Period size: 76 Copynumber: 2.3 Consensus size: 75
173331 GGATTTTGGG
* *
173341 GACGAATTTGATTTAACCATTATTGGTAGATTTTGGGACTGAGTTTAGTTTAGTCACTGATGATG
1 GACGAATTTGGTTTAACCATTGTTGGTAGATTTTGGGACTGAGTTTAGTTTAGTCACT-ATGATG
*
173406 GTGGTGACATG
65 GTGGTGACATA
* * ** * *
173417 GACGAATTTGGTTTAATCATTGTTGGTGGATTTTGGGTTGTGGGTTTGGTTTAGTCA-T-TGATG
1 GACGAATTTGGTTTAACCATTGTTGGTAGATTTTGGG-ACTGAGTTTAGTTTAGTCACTATGATG
**
173480 GTGGTGGTATA
65 GTGGTGACATA
*
173491 GACGTATTTGGTTTAACCATTG
1 GACGAATTTGGTTTAACCATTG
173513 GTTTGGCTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
74 33 0.40
76 34 0.41
77 15 0.18
ACGTcount: A:0.21, C:0.08, G:0.30, T:0.41
Consensus pattern (75 bp):
GACGAATTTGGTTTAACCATTGTTGGTAGATTTTGGGACTGAGTTTAGTTTAGTCACTATGATGG
TGGTGACATA
Found at i:177949 original size:25 final size:25
Alignment explanation
Indices: 177915--177965 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
177905 TTGTTTAAGC
177915 AAGTATTGAGTTCGAGATCTTGTGT
1 AAGTATTGAGTTCGAGATCTTGTGT
*
177940 AAGTATTGAGTTCGAGGTCTTGTGT
1 AAGTATTGAGTTCGAGATCTTGTGT
177965 A
1 A
177966 TATAGAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (25 bp):
AAGTATTGAGTTCGAGATCTTGTGT
Found at i:183144 original size:24 final size:24
Alignment explanation
Indices: 183117--183170 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
183107 GTGGAGATTT
183117 GTTGGTTTTTTGGCAAAGTCCCAC
1 GTTGGTTTTTTGGCAAAGTCCCAC
* *
183141 GTT-GTTTTTTGGTAAAGTCTCAC
1 GTTGGTTTTTTGGCAAAGTCCCAC
*
183164 ATTGGTT
1 GTTGGTT
183171 GTGTATAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.44
Consensus pattern (24 bp):
GTTGGTTTTTTGGCAAAGTCCCAC
Found at i:183999 original size:17 final size:17
Alignment explanation
Indices: 183977--184021 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
183967 TCTCTTAAAA
183977 ATTTTAAATTATTATAT
1 ATTTTAAATTATTATAT
*
183994 ATTTTAATATT-TTATGT
1 ATTTTAA-ATTATTATAT
*
184011 ATTTTTAATTA
1 ATTTTAAATTA
184022 ATACTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 3 0.12
17 18 0.75
18 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:184092 original size:25 final size:25
Alignment explanation
Indices: 184033--184081 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
184023 TACTTTTTTT
*
184033 TATTTCTTAAAATTTTATAAGTTTA
1 TATTTCTTAAAATTTTATAAATTTA
184058 TATTTCTTAAAATTTTATAAATTT
1 TATTTCTTAAAATTTTATAAATTT
184082 TCTCTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTTCTTAAAATTTTATAAATTTA
Found at i:188848 original size:37 final size:37
Alignment explanation
Indices: 188786--188887 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 37
188776 TGATATGGAA
* *
188786 ATTACTACATTGTTTC-GCCAGTTGATTAAAATGTCCT
1 ATTACTACATTG-TTCAGCAAATTGATTAAAATGTCCT
188823 ATTACTACATTGTTCAGCAAATTG------A--TCCT
1 ATTACTACATTGTTCAGCAAATTGATTAAAATGTCCT
*
188852 ATTACTACATTGTTCAGCAAATTGATTAAAGTGTCC
1 ATTACTACATTGTTCAGCAAATTGATTAAAATGTCC
188888 ATCGAGTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
29 28 0.53
31 1 0.02
36 3 0.06
37 21 0.40
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (37 bp):
ATTACTACATTGTTCAGCAAATTGATTAAAATGTCCT
Found at i:188854 original size:29 final size:29
Alignment explanation
Indices: 188819--188877 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
188809 GATTAAAATG
188819 TCCTATTACTACATTGTTCAGCAAATTGA
1 TCCTATTACTACATTGTTCAGCAAATTGA
188848 TCCTATTACTACATTGTTCAGCAAATTGA
1 TCCTATTACTACATTGTTCAGCAAATTGA
188877 T
1 T
188878 TAAAGTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (29 bp):
TCCTATTACTACATTGTTCAGCAAATTGA
Found at i:189628 original size:29 final size:31
Alignment explanation
Indices: 189560--189645 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 31
189550 TATGAGTAGT
189560 CCTTTAATAATAAATATTAGAA-AAAAATTGAA
1 CCTTTAATAATAAATATTAGAATAAAAA-T-AA
* *
189592 CCTATAATAATAAGTATTAGAATAAAAA-AA
1 CCTTTAATAATAAATATTAGAATAAAAATAA
*
189622 -CTTTAATAATAAATATTAAAATAA
1 CCTTTAATAATAAATATTAGAATAA
189646 TTGAGTCCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
29 21 0.44
30 2 0.04
32 20 0.42
33 5 0.10
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.31
Consensus pattern (31 bp):
CCTTTAATAATAAATATTAGAATAAAAATAA
Done.