Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003405.1 Hibiscus syriacus cultivar Beakdansim tig00007176_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: 91233
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3706 original size:19 final size:20
Alignment explanation
Indices: 3672--3942 Score: 96
Period size: 20 Copynumber: 13.6 Consensus size: 20
3662 AAATGACCAA
* *
3672 CAAATTCGCGACGCGATCT-
1 CAAATTCGCAACGCGAACTC
*
3691 CAAATTCGCAATGCGAACTC
1 CAAATTCGCAACGCGAACTC
* * * *
3711 CAATTTCGCAACACGAATATG
1 CAAATTCGCAACGCGAA-CTC
* * * *
3732 TAAA-TCGCAACACAAAAGT-
1 CAAATTCGCAACGC-GAACTC
* *
3751 CAAATTCTCAACGCGATAGT-
1 CAAATTCGCAACGCGA-ACTC
* *
3771 CAAATTCGCAACGAGATAGT-
1 CAAATTCGCAACGCGA-ACTC
*
3791 CAAATTCGCAACGCGAATCTG
1 CAAATTCGCAACGCGAA-CTC
** *
3812 TGAA-TCGCAACGCGAATCTG
1 CAAATTCGCAACGCGAA-CTC
* * *
3832 TAAA-TCGCAACGCGAATTTG
1 CAAATTCGCAACGCGAA-CTC
* * *
3852 TAAA-TCGCAACACAGAAGT-
1 CAAATTCGCAACGC-GAACTC
*
3871 CAAATTCGCAACGCGATAGT-
1 CAAATTCGCAACGCGA-ACTC
* *
3891 CAAATTCGCAACGCGGAATTT
1 CAAATTCGCAACGC-GAACTC
* * *
3912 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAACTC
3931 CAAATTCGCAAC
1 CAAATTCGCAAC
3943 TGAATTTCGA
Statistics
Matches: 210, Mismatches: 30, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
19 44 0.21
20 142 0.68
21 24 0.11
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:3780 original size:40 final size:39
Alignment explanation
Indices: 3715--3902 Score: 152
Period size: 40 Copynumber: 4.7 Consensus size: 39
3705 GAACTCCAAT
*
3715 TTCGCAACACGAATATGTAAATCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATA-GTAAATCGCAACACAAAAGTCAAA
* * *
3755 TTCTCAACGCG-ATAGTCAAATTCGCAACGA-GATAGTCAAA
1 TTCGCAACGCGAATAGT-AAA-TCGCAAC-ACAAAAGTCAAA
* * * **
3795 TTCGCAACGCGAATCTGTGAATCGCAACGCGAATCTGT-AAA
1 TTCGCAACGCGAAT-AGTAAATCGCAACAC-AA-AAGTCAAA
* *
3836 -TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAA-TAGTAAATCGCAACACAAAAGTCAAA
3875 TTCGCAACGCG-ATAGTCAAATTCGCAAC
1 TTCGCAACGCGAATAGT-AAA-TCGCAAC
3903 GCGGAATTTC
Statistics
Matches: 118, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
38 7 0.06
39 14 0.12
40 83 0.70
41 10 0.08
42 4 0.03
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (39 bp):
TTCGCAACGCGAATAGTAAATCGCAACACAAAAGTCAAA
Found at i:3799 original size:80 final size:79
Alignment explanation
Indices: 3672--3822 Score: 187
Period size: 80 Copynumber: 1.9 Consensus size: 79
3662 AAATGACCAA
* * * *
3672 CAAATTCGCGACGCGATCTCAAATTCGCAATGCGAACTCCAATTTCGCAACACGAATATGTAAAT
1 CAAATTCGCAACGCGATCTCAAATTCGCAACGAGAACTCCAAATTCGCAACACGAATATGTAAAT
3737 CGCAACACAAAAGT
66 CGCAACACAAAAGT
* * * * * *
3751 CAAATTCTCAACGCGATAGTCAAATTCGCAACGAGATAGT-CAAATTCGCAACGCGAATCTGTGA
1 CAAATTCGCAACGCGAT-CTCAAATTCGCAACGAGA-ACTCCAAATTCGCAACACGAATATGTAA
3815 ATCGCAAC
64 ATCGCAAC
3823 GCGAATCTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
79 15 0.25
80 43 0.72
81 2 0.03
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (79 bp):
CAAATTCGCAACGCGATCTCAAATTCGCAACGAGAACTCCAAATTCGCAACACGAATATGTAAAT
CGCAACACAAAAGT
Found at i:3934 original size:60 final size:59
Alignment explanation
Indices: 3690--4000 Score: 171
Period size: 60 Copynumber: 5.2 Consensus size: 59
3680 CGACGCGATC
* * * * * **
3690 TCAAATTCGCAATGCGA-ACTCCAATTTCGCAACACGAATATGT-AAA-TCGCAACACAAAAG
1 TCAAATTCGCAACGCGATAGT-CAAATTCGCAACGCGAAT-T-TCAAATTCGCAACA-GAATT
* * * *
3750 TCAAATTCTCAACGCGATAGTCAAATTCGCAACGAG-ATAGTCAAATTCGCAACGCGAATCT
1 TCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAT-TTCAAATTCGCAAC-AGAAT-T
* * * *
3811 GT-GAA-TCGCAACGCGAATCTGT-AAA-TCGCAACGCGAATTTGTAAA-TCGCAACACAGAA-G
1 -TCAAATTCGCAACGCG-AT-AGTCAAATTCGCAACGCGAATTT-CAAATTCGC-A-ACAGAATT
*
3870 TCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACGCGATAGTCAAATTCGCAACGC-GAATTTCAAATTCGCAACAGAATT
* * * ** * *
3930 TCAAATTCGCAAC-TGA-ATTTCGAATTCGCAACTAGATTTTCGAATTCGCAACACGAATT
1 TCAAATTCGCAACGCGATA-GTCAAATTCGCAACGCGAATTTCAAATTCGCAACA-GAATT
*
3989 T-AATTTCGCAAC
1 TCAAATTCGCAAC
4001 AGGTTTTAGT
Statistics
Matches: 197, Mismatches: 33, Indels: 44
0.72 0.12 0.16
Matches are distributed among these distances:
58 31 0.16
59 38 0.19
60 95 0.48
61 28 0.14
62 5 0.03
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (59 bp):
TCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAATTTCAAATTCGCAACAGAATT
Found at i:3957 original size:38 final size:39
Alignment explanation
Indices: 3890--4000 Score: 127
Period size: 39 Copynumber: 2.8 Consensus size: 39
3880 AACGCGATAG
3890 TCAAATTCGCAACGCGGAATTTCAAATTCGCAACT-GAATT
1 TCAAATTCGCAA--CGGAATTTCAAATTCGCAACTAGAATT
* * *
3930 TCAAATTCGCAACTGAATTTCGAATTCGCAACTAGATTT
1 TCAAATTCGCAACGGAATTTCAAATTCGCAACTAGAATT
* * *
3969 TCGAATTCGCAACACGAATTT-AATTTCGCAAC
1 TCAAATTCGCAAC-GGAATTTCAAATTCGCAAC
4001 AGGTTTTAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 19 0.31
39 25 0.40
40 18 0.29
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (39 bp):
TCAAATTCGCAACGGAATTTCAAATTCGCAACTAGAATT
Found at i:3972 original size:20 final size:19
Alignment explanation
Indices: 3890--4000 Score: 125
Period size: 19 Copynumber: 5.7 Consensus size: 19
3880 AACGCGATAG
*
3890 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
3911 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
3930 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
3949 TCGAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
3969 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
3989 T-AATTTCGCAAC
1 TCAAATTCGCAAC
4001 AGGTTTTAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
19 47 0.58
20 22 0.27
21 12 0.15
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:4001 original size:19 final size:19
Alignment explanation
Indices: 3974--4020 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3964 GATTTTCGAA
3974 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
3993 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
4011 TTCGCAACAC
1 TTCGCAACAC
4021 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:4965 original size:24 final size:24
Alignment explanation
Indices: 4933--4986 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
4923 GTATTCGAAA
4933 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
4957 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
4981 TTTGAT
1 TTTGAT
4987 GATGTGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:5790 original size:18 final size:18
Alignment explanation
Indices: 5767--5802 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5757 AAGCAAAAGG
5767 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
5785 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
5803 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:6164 original size:20 final size:20
Alignment explanation
Indices: 6139--6223 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
6129 AAATTGCAAC
6139 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* *
6159 GCGAATTTGACTATCGC--A
1 GCGAATTTGACTTTCGCGTT
* *
6177 ACG--CTT-A-TTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
*
6193 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCGCGTT
6213 GCGAATTTGAC
1 GCGAATTTGAC
6224 AAAATCGCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
14 5 0.10
15 1 0.02
16 4 0.08
18 4 0.08
19 1 0.02
20 35 0.70
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:6436 original size:50 final size:52
Alignment explanation
Indices: 6331--6441 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 52
6321 ATCAACTTTT
6331 ACAAATCAATTAAACAAGTAAAAAAATAATTCTTATTTACACATCAAATTAA
1 ACAAATCAATTAAACAAGTAAAAAAATAATTCTTATTTACACATCAAATTAA
* * * * * *
6383 ACAAATCAATTAAACATG-CAAAAAATAATTGTTATTTCCTCTTC-AATTAA
1 ACAAATCAATTAAACAAGTAAAAAAATAATTCTTATTTACACATCAAATTAA
6433 ACAAATCAA
1 ACAAATCAA
6442 CTTTCAATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 15 0.28
51 21 0.40
52 17 0.32
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (52 bp):
ACAAATCAATTAAACAAGTAAAAAAATAATTCTTATTTACACATCAAATTAA
Found at i:7844 original size:21 final size:21
Alignment explanation
Indices: 7820--7914 Score: 99
Period size: 20 Copynumber: 4.6 Consensus size: 21
7810 GGGCGAGACA
* *
7820 TCTTGAATGATGACAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
*
7841 TCTTGAA--ACTGGGAGGGGCC
1 TCTTGAACGA-TGAGAGGGGCC
*
7861 TCTTCG-ATGATGAGAGGGGCC
1 TCTT-GAACGATGAGAGGGGCC
*
7882 TCTTGAACGAT-AGAGGTGCC
1 TCTTGAACGATGAGAGGGGCC
7902 TCTTGAACGATGA
1 TCTTGAACGATGA
7915 TAGGTGCATC
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.02
20 34 0.54
21 27 0.43
22 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGGGCC
Found at i:7914 original size:41 final size:41
Alignment explanation
Indices: 7820--7914 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
7810 GGGCGAGACA
*
7820 TCTTGAATGATGACAGGGGCCTCTTGAAACTGGGAGGGGCC
1 TCTTGAATGATGACAGGGGCCTCTTGAAACTGAGAGGGGCC
* *
7861 TCTTCG-ATGATGAGAGGGGCCTCTTG-AAC-GATAGAGGTGCC
1 TCTT-GAATGATGACAGGGGCCTCTTGAAACTG--AGAGGGGCC
*
7902 TCTTGAACGATGA
1 TCTTGAATGATGA
7915 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
39 1 0.02
40 4 0.09
41 40 0.87
42 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (41 bp):
TCTTGAATGATGACAGGGGCCTCTTGAAACTGAGAGGGGCC
Found at i:10771 original size:20 final size:20
Alignment explanation
Indices: 10691--10777 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
10681 TGTGTTTCGC
* * *
10691 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
10711 ATTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
10731 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
10751 GTTGCGAATTTGA-TTTCTGT
1 GTTGCGAATTTGACTTT-TGT
10771 GTTGCGA
1 GTTGCGA
10778 TTTACAAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 3 0.05
20 58 0.95
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:10794 original size:20 final size:20
Alignment explanation
Indices: 10771--10817 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
10761 TGATTTCTGT
*
10771 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTCGC
*
10791 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
10811 GTTGCGA
1 GTTGCGA
10818 AATTGGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:10795 original size:40 final size:40
Alignment explanation
Indices: 10691--10797 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
10681 TGTGTTTCGC
* *
10691 GTTGCGAATTTGAC-TATCGCATTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACAT-TTGCGTTGCGAATTTGACTTTTGT
* *
10731 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGA-TTTCTGT
1 GTTGCGAATTTGACATTTGCGTTGCGAATTTGACTTT-TGT
10771 GTTGCG-ATTT-ACAAATTTGCGTTGCGA
1 GTTGCGAATTTGAC--ATTTGCGTTGCGA
10798 TTTACAGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
38 2 0.03
39 7 0.12
40 48 0.83
41 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (40 bp):
GTTGCGAATTTGACATTTGCGTTGCGAATTTGACTTTTGT
Found at i:10858 original size:20 final size:20
Alignment explanation
Indices: 10807--10862 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
10797 ATTTACAGAT
*
10807 TCGCGTTGCGAAATTGGAAA
1 TCGCGTTGCGAAATTTGAAA
* * *
10827 TTGGGTTGCGAAATTTGAGA
1 TCGCGTTGCGAAATTTGAAA
*
10847 TCGCGTTACG-AATTTG
1 TCGCGTTGCGAAATTTG
10863 TTGGTCATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.32
Consensus pattern (20 bp):
TCGCGTTGCGAAATTTGAAA
Found at i:13191 original size:44 final size:44
Alignment explanation
Indices: 13069--13400 Score: 300
Period size: 43 Copynumber: 7.6 Consensus size: 44
13059 GCTGATGTTG
* * * *
13069 GCGGCGTTTGTGATATAAAAACGCCGCAAAAAGTCAAGATCTATA
1 GCGGCGTTTTTG-GATACAAACGCCGCAAAAGGTCAAGATCTATA
* * * *
13114 GAGGCGTTTTTGGA-ACAAACGTCGCAAAATGTCGAGATCTATA
1 GCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAGATCTATA
* * * *
13157 GCGGCGTTTTTGGATACAAACGCCGCAAAATGTCGAGTTCTCTA
1 GCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAGATCTATA
* ** * *
13201 GCGGTGTTTTTTCCA-A-AAACGCCGCAAAAGGT-TAGATATATA
1 GCGGCG-TTTTTGGATACAAACGCCGCAAAAGGTCAAGATCTATA
** * *
13243 GTAGCGTTATTGGATACAAACGCCACAAAAGGTCAAGATCTATA
1 GCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAGATCTATA
* * * * * *
13287 GCGG-GTTTTTGGAAAAAAAAATGCCGCAAAAGGT-TAGTTATATA
1 GCGGCGTTTTTGG--ATACAAACGCCGCAAAAGGTCAAGATCTATA
* *
13331 GTGGCATTTTTTGGATACAAACGCCGCAAAAGGTC-AGATCTATA
1 GCGGC-GTTTTTGGATACAAACGCCGCAAAAGGTCAAGATCTATA
*
13375 GCGGCGTTTTTGGATATAAACGCCGC
1 GCGGCGTTTTTGGATACAAACGCCGC
13401 TAATTACCAT
Statistics
Matches: 229, Mismatches: 48, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
41 5 0.02
42 10 0.04
43 94 0.41
44 81 0.35
45 32 0.14
46 7 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (44 bp):
GCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAGATCTATA
Found at i:23036 original size:28 final size:28
Alignment explanation
Indices: 22995--23059 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
22985 TTATAGAAAT
* * *
22995 TAGGGACCTCATTATAAATATAAAAAAC
1 TAGGGCCCTAATTATAAATACAAAAAAC
* *
23023 TGGGGCCCTAATTATAAATACAAAAAAT
1 TAGGGCCCTAATTATAAATACAAAAAAC
23051 TAGGGCCCT
1 TAGGGCCCT
23060 GAGCGGTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (28 bp):
TAGGGCCCTAATTATAAATACAAAAAAC
Found at i:23811 original size:20 final size:22
Alignment explanation
Indices: 23788--23828 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
23778 TATTTTCATA
23788 TTAAAAATAA-TAT-TATATTT
1 TTAAAAATAATTATATATATTT
23808 TTAAAAATAATTATATATATT
1 TTAAAAATAATTATATATATT
23829 AGTTATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 3 0.16
22 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAAAAATAATTATATATATTT
Found at i:30733 original size:28 final size:30
Alignment explanation
Indices: 30678--30733 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30668 CAAAAATTGA
* *
30678 TTAGTGATTAAAATGTAAATTTGTGGAAGT
1 TTAGTGATTAAAATGAAAAATTGTGGAAGT
30708 TTAGTGATTAAAAT-AAAAATT-TGGAA
1 TTAGTGATTAAAATGAAAAATTGTGGAA
30734 AAATTTAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 5 0.21
30 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.38
Consensus pattern (30 bp):
TTAGTGATTAAAATGAAAAATTGTGGAAGT
Found at i:30741 original size:30 final size:30
Alignment explanation
Indices: 30678--30741 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
30668 CAAAAATTGA
** * *
30678 TTAGTGATTAAAATGTAAATTTGTGGAAGT
1 TTAGTGATTAAAATAAAAATTTGTGAAAAT
30708 TTAGTGATTAAAATAAAAATTTG-GAAAAAT
1 TTAGTGATTAAAATAAAAATTTGTG-AAAAT
30738 TTAG
1 TTAG
30742 GGACCAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (30 bp):
TTAGTGATTAAAATAAAAATTTGTGAAAAT
Found at i:32641 original size:11 final size:11
Alignment explanation
Indices: 32625--32652 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
32615 AGTCTTAAAA
32625 AAATATTGAAT
1 AAATATTGAAT
32636 AAATATTGAAT
1 AAATATTGAAT
32647 AAATAT
1 AAATAT
32653 GAGTGTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (11 bp):
AAATATTGAAT
Found at i:33269 original size:23 final size:23
Alignment explanation
Indices: 33239--33297 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
33229 TGGGTACTTC
*
33239 TGTATCAGTGTTTTATGCACTCT
1 TGTATCAGTGTATTATGCACTCT
* *
33262 TGTATCAGTGCCATTGTGCACTCT
1 TGTATCAGTG-TATTATGCACTCT
*
33286 TGAATCAGTGTA
1 TGTATCAGTGTA
33298 ATTGTGGACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 11 0.37
24 19 0.63
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (23 bp):
TGTATCAGTGTATTATGCACTCT
Found at i:33286 original size:24 final size:24
Alignment explanation
Indices: 33254--33379 Score: 98
Period size: 24 Copynumber: 5.3 Consensus size: 24
33244 CAGTGTTTTA
*
33254 TGCACTCTTGTATCAGTGCCATTG
1 TGCACTCTTGTATCAGTGCAATTG
* *
33278 TGCACTCTTGAATCAGTGTAATTG
1 TGCACTCTTGTATCAGTGCAATTG
* *
33302 TGGACT-TCTGTATTAGTGCGAA-TG
1 TGCACTCT-TGTATCAGTGC-AATTG
** * *
33326 CACACTCCTGTAT-AGTGCAACTG
1 TGCACTCTTGTATCAGTGCAATTG
* *
33349 TGCACTCCTGTATTAGTGCAACTT-
1 TGCACTCTTGTATCAGTGCAA-TTG
33373 TGCACTC
1 TGCACTC
33380 CCGAAATTAG
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
22 2 0.02
23 19 0.23
24 58 0.71
25 3 0.04
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (24 bp):
TGCACTCTTGTATCAGTGCAATTG
Found at i:33343 original size:23 final size:24
Alignment explanation
Indices: 33309--33371 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
33299 TTGTGGACTT
33309 CTGTATTAGTGCGAA-TGCACACTC
1 CTGTATTAGTGC-AACTGCACACTC
**
33333 CTGTA-TAGTGCAACTGTGCACTC
1 CTGTATTAGTGCAACTGCACACTC
33356 CTGTATTAGTGCAACT
1 CTGTATTAGTGCAACT
33372 TTGCACTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 2 0.06
23 18 0.51
24 15 0.43
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (24 bp):
CTGTATTAGTGCAACTGCACACTC
Found at i:39159 original size:37 final size:36
Alignment explanation
Indices: 39084--39159 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
39074 TTTTTATATT
*
39084 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAAATATTATCAA
* *
39120 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATATAAATATTAT-CAA
39157 TTT
1 TTT
39160 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAATTATATAAATATTATCAA
Found at i:39503 original size:2 final size:2
Alignment explanation
Indices: 39461--39487 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39451 TAACTACAAT
39461 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39488 TAACTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41468 original size:22 final size:23
Alignment explanation
Indices: 41442--41493 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
41432 TTGAAAAACG
* *
41442 ATTTTGAG-CTCTCAAAAATAAA
1 ATTTTAAGTCTCTCAAAAAGAAA
* *
41464 ATTTTAAGTTTTTCAAAAAGAAA
1 ATTTTAAGTCTCTCAAAAAGAAA
41487 ATTTTAA
1 ATTTTAA
41494 TTTGAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (23 bp):
ATTTTAAGTCTCTCAAAAAGAAA
Found at i:43309 original size:21 final size:21
Alignment explanation
Indices: 43284--43342 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
43274 CTTAAGGAAT
43284 TTTAATTCCTTGTCAAAAGCA
1 TTTAATTCCTTGTCAAAAGCA
*
43305 TTTAA-T-C-TG--AATA--A
1 TTTAATTCCTTGTCAAAAGCA
43319 TTTAATTCCTTGTCAAAAGCA
1 TTTAATTCCTTGTCAAAAGCA
43340 TTT
1 TTT
43343 TATCCGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
14 6 0.21
15 1 0.03
16 4 0.14
17 2 0.07
18 2 0.07
19 4 0.14
20 1 0.03
21 9 0.31
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (21 bp):
TTTAATTCCTTGTCAAAAGCA
Found at i:43328 original size:35 final size:35
Alignment explanation
Indices: 43284--43356 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
43274 CTTAAGGAAT
*
43284 TTTAATTCCTTGTCAAAAGCATTTAATCTGAATAA
1 TTTAATTCCTTGTCAAAAGCATTTAATCCGAATAA
*
43319 TTTAATTCCTTGTCAAAAGCATTTTATCCGAATAA
1 TTTAATTCCTTGTCAAAAGCATTTAATCCGAATAA
43354 TTT
1 TTT
43357 CACACCAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (35 bp):
TTTAATTCCTTGTCAAAAGCATTTAATCCGAATAA
Found at i:51305 original size:6 final size:7
Alignment explanation
Indices: 51296--51349 Score: 53
Period size: 6 Copynumber: 7.9 Consensus size: 7
51286 AAATTAAATT
51296 TATTA-A
1 TATTATA
51302 TATTATA
1 TATTATA
51309 TA-TATA
1 TATTATA
51315 TATATATA
1 TAT-TATA
51323 TATATATA
1 TAT-TATA
51331 TAATTAT-
1 T-ATTATA
51338 TATTAT-
1 TATTATA
51344 TATTAT
1 TATTAT
51350 TTTTAATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
6 22 0.50
7 4 0.09
8 16 0.36
9 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATTATA
Found at i:51312 original size:2 final size:2
Alignment explanation
Indices: 51301--51332 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
51291 AAATTTATTA
51301 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51333 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51397 original size:13 final size:13
Alignment explanation
Indices: 51361--51397 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
51351 TTTAATATTT
*
51361 ATCGGGGCGGATA
1 ATCGGGGCGGGTA
*
51374 ATCAGGGCGGGTA
1 ATCGGGGCGGGTA
51387 ATCGGGGCGGG
1 ATCGGGGCGGG
51398 GATTACCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.51, T:0.14
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:51455 original size:36 final size:36
Alignment explanation
Indices: 51408--51490 Score: 157
Period size: 36 Copynumber: 2.3 Consensus size: 36
51398 GATTACCAAA
51408 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
1 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
*
51444 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTT
1 CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
51480 CCCGTCCCCGT
1 CCCGTCCCCGT
51491 TTAATTCGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.14, C:0.41, G:0.14, T:0.30
Consensus pattern (36 bp):
CCCGTCCCCGTCCCCGTTTAACATAAACGGTTTTTC
Found at i:52059 original size:2 final size:2
Alignment explanation
Indices: 52052--52087 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
52042 GAAATAATAC
* *
52052 AT AT AT AT AT AT AT AC AT AC 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
52088 TGATTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:52073 original size:20 final size:20
Alignment explanation
Indices: 52048--52086 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
52038 GTTTGAAATA
52048 ATACATATATATATATATAC
1 ATACATATATATATATATAC
52068 ATACATATATATATATATA
1 ATACATATATATATATATA
52087 TTGATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
ATACATATATATATATATAC
Found at i:54750 original size:36 final size:37
Alignment explanation
Indices: 54679--54762 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
54669 ATCCCATTAT
54679 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATCTACCAAACTTTGAAAAAC
* * * *
54715 TATTTTTCAAATAAATATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAACAAACATCTACCAAACTTTGAAAAAC
54751 CATTTTTTCAAA
1 CA-TTTTTCAAA
54763 GTTGGTTACC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.32
37 28 0.68
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (37 bp):
CATTTTTCAAACAAACATCTACCAAACTTTGAAAAAC
Found at i:55332 original size:25 final size:25
Alignment explanation
Indices: 55304--55354 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
55294 GTCAACATTT
55304 CCGGCTAAGTCAGCATCTACATAGC
1 CCGGCTAAGTCAGCATCTACATAGC
55329 CCGGCTAAGTCAGCATCTACATAGC
1 CCGGCTAAGTCAGCATCTACATAGC
55354 C
1 C
55355 TATTAGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (25 bp):
CCGGCTAAGTCAGCATCTACATAGC
Found at i:59352 original size:36 final size:38
Alignment explanation
Indices: 59284--59365 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 38
59274 CCCATTATCA
* *
59284 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA-T
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATT
*
59320 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATT
59357 TTTTCAAAG
1 TTTTCAAAG
59366 TTGGTTACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
36 11 0.27
37 30 0.73
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (38 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACCATT
Found at i:61647 original size:7 final size:7
Alignment explanation
Indices: 61637--61666 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
61627 AAATGAGTTC
61637 TGTGTGT
1 TGTGTGT
61644 TGTGTGT
1 TGTGTGT
61651 TGTGTGAT
1 TGTGTG-T
61659 TGTGTGT
1 TGTGTGT
61666 T
1 T
61667 TTTTTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.03, C:0.00, G:0.40, T:0.57
Consensus pattern (7 bp):
TGTGTGT
Found at i:62887 original size:19 final size:20
Alignment explanation
Indices: 62857--62894 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
62847 CCTTACATTT
62857 TGCATATGCATTTTACTTTC
1 TGCATATGCATTTTACTTTC
62877 TGCAT-TGCATTTTACTTT
1 TGCATATGCATTTTACTTT
62895 TCGCAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (20 bp):
TGCATATGCATTTTACTTTC
Found at i:62904 original size:19 final size:19
Alignment explanation
Indices: 62849--62905 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
62839 TATCAACCCC
62849 TTACATTTT-GCATATGCATT
1 TTAC-TTTTCGCA-ATGCATT
*
62869 TTAC-TTTCTGCATTGCATT
1 TTACTTTTC-GCAATGCATT
62888 TTACTTTTCGCAATGCAT
1 TTACTTTTCGCAATGCAT
62906 GTTATCCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 3 0.09
19 18 0.56
20 11 0.34
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (19 bp):
TTACTTTTCGCAATGCATT
Found at i:63792 original size:2 final size:2
Alignment explanation
Indices: 63785--63886 Score: 128
Period size: 2 Copynumber: 54.5 Consensus size: 2
63775 TTTCCTCGAT
63785 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
63827 TA TA TA TA TA TA TA TG TA TA TA TA -A TA T- TT TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63866 TA TA T- TA -A T- TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
63887 TGGGATCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
1 7 0.08
2 82 0.92
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:67739 original size:134 final size:131
Alignment explanation
Indices: 67524--67843 Score: 410
Period size: 134 Copynumber: 2.4 Consensus size: 131
67514 ATATGATCTC
* * * * * *
67524 CCCTAAAGAGTAGTGGAGCAGATCCTCTTTATTTT-GGATTTGGTATTCTTGAAGAGAGGTGAAG
1 CCCTAAAGAGTAGTGGAGCATATCCT-TTT-TTTTCAGATTTGGTCTTCCTGAAAAGAAGTGAAG
* *
67588 CAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACAAAATGGATC-AAAAATTTTCGAGTCTG
64 CAAATCAAGTTCGATTCAATATTCCCTGAAGAGCAACAAAATGGATCAAAAAAATTT-GAGTCTG
67652 ATATT
128 ATA-T
*
67657 TCCTAAAGAGTAGTGGAGCATATCCTTATTTTTCTCAGATTTGGTCTTCCTGAAAAGAAGTGAAG
1 CCCTAAAGAGTAGTGGAGCATATCCTT-TTTTT-TCAGATTTGGTCTTCCTGAAAAGAAGTGAAG
* * *
67722 CAAATCAAGTTCGATTCAATATTCCTTGAAGAGCAGCAAAGTGGATCGAAAAAAATTTGAGTCTG
64 CAAATCAAGTTCGATTCAATATTCCCTGAAGAGCAACAAAATGGATC-AAAAAAATTTGAGTCTG
67787 ATAT
128 ATAT
* **
67791 CCCATAAAGAGTAGTGGAGCATATCCTCCTACTTTCAGATTTGGTCTTCCTGA
1 CCC-TAAAGAGTAGTGGAGCATATCCT-TTTTTTTCAGATTTGGTCTTCCTGA
67844 GGAGCAGCGA
Statistics
Matches: 164, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
132 4 0.02
133 27 0.16
134 89 0.54
135 36 0.22
136 8 0.05
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (131 bp):
CCCTAAAGAGTAGTGGAGCATATCCTTTTTTTTCAGATTTGGTCTTCCTGAAAAGAAGTGAAGCA
AATCAAGTTCGATTCAATATTCCCTGAAGAGCAACAAAATGGATCAAAAAAATTTGAGTCTGATA
T
Found at i:67892 original size:134 final size:135
Alignment explanation
Indices: 67524--67906 Score: 391
Period size: 134 Copynumber: 2.9 Consensus size: 135
67514 ATATGATCTC
* * ** * * * * *
67524 CCCTAAAGAGTAGTGGAGCAGATCCTCTTTA-TT-TTGGATTTGGTATTCTTGAAGAGAGGTGAA
1 CCCTAAAGAGTAGTGGAGCATATCCTC-ATACTTCTCAGATTTGGTCTTCCTGAAAAGAAGCGAA
* * * *
67587 GCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACAAAATGGATC-AAAAATTTTCGAGTCT
65 GCAAATCAACTTCGATTCAATCTTCCCTGAAGAGCAGCAAAGTGGATCAAAAAAATTTCGAGTCT
67651 GATATT
130 GATATT
* * ** *
67657 TCCTAAAGAGTAGTGGAGCATATCCTTATTTTTCTCAGATTTGGTCTTCCTGAAAAGAAGTGAAG
1 CCCTAAAGAGTAGTGGAGCATATCCTCATACTTCTCAGATTTGGTCTTCCTGAAAAGAAGCGAAG
* * *
67722 CAAATCAAGTTCGATTCAATATTCCTTGAAGAGCAGCAAAGTGGATCGAAAAAAATTT-GAGTCT
66 CAAATCAACTTCGATTCAATCTTCCCTGAAGAGCAGCAAAGTGGATC-AAAAAAATTTCGAGTCT
67786 GATA-T
130 GATATT
* ** *
67791 CCCATAAAGAGTAGTGGAGCATATCCTCCTACTT-TCAGATTTGGTCTTCCTGAGGAGCAGCGAA
1 CCC-TAAAGAGTAGTGGAGCATATCCTCATACTTCTCAGATTTGGTCTTCCTGAAAAGAAGCGAA
** * * * ** * *
67855 GTGAATCGACTTTGATTCAACCTTCCCTGTGGAGCAGCGAAGTGAATCAAAA
65 GCAAATCAACTTCGATTCAATCTTCCCTGAAGAGCAGCAAAGTGGATCAAAA
67907 TTTTCCAAAT
Statistics
Matches: 208, Mismatches: 37, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
132 1 0.00
133 30 0.14
134 133 0.64
135 36 0.17
136 8 0.04
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (135 bp):
CCCTAAAGAGTAGTGGAGCATATCCTCATACTTCTCAGATTTGGTCTTCCTGAAAAGAAGCGAAG
CAAATCAACTTCGATTCAATCTTCCCTGAAGAGCAGCAAAGTGGATCAAAAAAATTTCGAGTCTG
ATATT
Found at i:70088 original size:35 final size:39
Alignment explanation
Indices: 70039--70109 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 39
70029 TAATATATAT
70039 ATATATATAGTATAATTTTT-GAAAAT-ATTTTTAAAAA
1 ATATATATAGTATAATTTTTAGAAAATGATTTTTAAAAA
*
70076 ATATA-ATA-TATAATTTTTAGAAAATGGTTTTTAA
1 ATATATATAGTATAATTTTTAGAAAATGATTTTTAA
70110 TGATCGATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 10 0.32
36 9 0.29
37 12 0.39
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (39 bp):
ATATATATAGTATAATTTTTAGAAAATGATTTTTAAAAA
Found at i:73796 original size:99 final size:100
Alignment explanation
Indices: 73681--73884 Score: 320
Period size: 99 Copynumber: 2.0 Consensus size: 100
73671 TTATAATATT
* * * * * **
73681 ATATGTATACAGTAAAGATTGAGTTGTCCCTCTAGAGCAATTTGTTAAATTCCCCGGCTTTATGG
1 ATATTTATACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACTCCCCAACTTTATGG
*
73746 ATAAGATTCAGCTAGCCTGATAAAGGTGA-TTATA
66 ATAAAATTCAGCTAGCCTGATAAAGGTGATTTATA
*
73780 ATATTTATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACTCCCCAACTTTATGG
1 ATATTTATACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACTCCCCAACTTTATGG
73845 ATAAAATTCAGCTAGCCTGATAAAGGTGATTTATA
66 ATAAAATTCAGCTAGCCTGATAAAGGTGATTTATA
73880 ATATT
1 ATATT
73885 GAGGTGTCCC
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 85 0.89
100 10 0.11
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (100 bp):
ATATTTATACAATAAAGATTGAGTTGTCCCTCTAAAGCAATTGGTTAAACTCCCCAACTTTATGG
ATAAAATTCAGCTAGCCTGATAAAGGTGATTTATA
Found at i:75097 original size:85 final size:85
Alignment explanation
Indices: 74948--75553 Score: 623
Period size: 85 Copynumber: 7.1 Consensus size: 85
74938 TAAAGGAGCT
* * * *
74948 ATTTACAGCATAGCTCAAGGCGAGAATGATAATATCTGTCAATAAAAACCTTCGAGTTCAATTAC
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGT--TATCTGTCAACAAAAACCTTCGAGTTCGATTAC
75013 ATTCAGCTCAAGGGCATATCAA
64 ATTCAGCTCAAGGGCATATCAA
* * ** * *
75035 ATTTATAGCATAGCTCAAGGCGAGAAAGACTATCTGTTAACGAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
75100 TCAACTCAAAGACATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * * *
75120 ATTTACAACATAACTTAAGGCTAGAAGGGTTATCT-TCCAGC-AAAACCTTCGAGTTCGATTATA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGT-CAACAAAAACCTTCGAGTTCGATTACA
* * * *
75183 TTCACCTCATGGACATATTAA
65 TTCAGCTCAAGGGCATATCAA
* * * *
75204 ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCAGCCAGC-AAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* *
75268 TCAGCTCAATGACATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * *
75288 ATTTATAGCATAACTCAAGGCGATAAGGGTTAACTGTCAATAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
75353 TCAGCTCAAGGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * *
75373 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATTTGTCAACAAAAAACCTTCAAGTTTGATT-CA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAAACCTTCGAGTTCGATTAC-
* * ** *
75437 ATTTAGTTCAAGGGCA-GCCGA
64 ATTCAGCTCAAGGGCATATCAA
* * ** * * * *
75458 ATTTACAGCATAGCTTAAGTCGAGAAGGACTATCTATCAACAAAATCCTTTGAGATT-GATTCCA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAG-TTCGATTACA
* **
75522 TTTAGCTCAAGGGCA-GCCAA
65 TTCAGCTCAAGGGCATATCAA
*
75542 ATTTACAACATA
1 ATTTACAGCATA
75554 ACTAAAGACA
Statistics
Matches: 443, Mismatches: 69, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
84 190 0.43
85 194 0.44
86 32 0.07
87 27 0.06
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (85 bp):
ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGGCATATCAA
Found at i:77899 original size:25 final size:23
Alignment explanation
Indices: 77871--77937 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 23
77861 ATTCATAATA
77871 TTTTATATATATTAACTTAAAATG
1 TTTT-TATATATTAACTTAAAATG
77895 TTTTT-TATATTAACTTATTAAATG
1 TTTTTATATATTAACTTA--AAATG
77919 TATTTTAT-TATTAACTTAA
1 T-TTTTATATATTAACTTAA
77938 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
22 12 0.31
23 2 0.05
24 10 0.26
25 14 0.36
26 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTTTATATATTAACTTAAAATG
Found at i:77943 original size:27 final size:24
Alignment explanation
Indices: 77878--77936 Score: 86
Period size: 22 Copynumber: 2.5 Consensus size: 24
77868 ATATTTTATA
*
77878 TATATTAACTTA--AAATGTTTTT
1 TATATTAACTTATTAAATGTATTT
77900 TATATTAACTTATTAAATGTATTT
1 TATATTAACTTATTAAATGTATTT
77924 TATTATTAACTTA
1 TA-TATTAACTTA
77937 ATTTAAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 12 0.36
24 11 0.33
25 10 0.30
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.54
Consensus pattern (24 bp):
TATATTAACTTATTAAATGTATTT
Found at i:77949 original size:27 final size:26
Alignment explanation
Indices: 77897--78001 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 26
77887 TTAAAATGTT
* **
77897 TTTTATATTAACTT-A-TTAAATGTA
1 TTTTATTTTAACTTAATTTAAAAATA
77921 TTTTATTATTAACTTAATTTAAAAATA
1 TTTTATT-TTAACTTAATTTAAAAATA
***
77948 TTTTAATTTTGTTTTAATTTAAAAATATA
1 TTTT-ATTTTAACTTAATTT-AAAA-ATA
*
77977 TTTTATGTTAAAACTTAATTTAAAA
1 TTTTAT-TT-TAACTTAATTTAAAA
78002 GTATGACTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
24 6 0.10
25 7 0.11
26 1 0.02
27 20 0.32
28 9 0.14
29 13 0.21
30 7 0.11
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (26 bp):
TTTTATTTTAACTTAATTTAAAAATA
Found at i:78179 original size:31 final size:31
Alignment explanation
Indices: 78123--78182 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
78113 ACATCCTAGC
***
78123 TAAATAAAAACAAAAGTGGTTATATCTTAAT
1 TAAATAAAAACAAAAGTGACCATATCTTAAT
*
78154 TAAATAAAAACAAAATTGACCATATCTTA
1 TAAATAAAAACAAAAGTGACCATATCTTA
78183 TTTTATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (31 bp):
TAAATAAAAACAAAAGTGACCATATCTTAAT
Found at i:78645 original size:2 final size:2
Alignment explanation
Indices: 78638--78674 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
78628 AAAAATCTAG
78638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78675 GTATCAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:84177 original size:33 final size:32
Alignment explanation
Indices: 84116--84185 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 32
84106 CCTTACAAAC
**
84116 TCCCTAGTTTTTGCGGACTAAACTAGAACCTT
1 TCCCTAGTTTTCACGGACTAAACTAGAACCTT
* *
84148 TCCCTAGCTTTTCACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTCACGGACTAAACTAGAACCTT
84181 TCCCT
1 TCCCT
84186 TTACAAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTCACGGACTAAACTAGAACCTT
Found at i:85693 original size:51 final size:48
Alignment explanation
Indices: 85619--85723 Score: 167
Period size: 51 Copynumber: 2.1 Consensus size: 48
85609 TTCACATCAC
85619 TCATATAAACATAGCATCGTGTAACGTTCTCATA-AAACACATATGAG
1 TCATATAAACATAGCATCGTGTAACGTTCTCATAGAAACACATATGAG
85666 TCATATAACTACATAGCATATCGTGTAACGTTCTCATAGAAACACATATGAG
1 TCATATAA--ACATAGC--ATCGTGTAACGTTCTCATAGAAACACATATGAG
85718 TCATAT
1 TCATAT
85724 CACTTTCACA
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
47 8 0.15
49 7 0.13
51 19 0.36
52 19 0.36
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (48 bp):
TCATATAAACATAGCATCGTGTAACGTTCTCATAGAAACACATATGAG
Found at i:86284 original size:63 final size:63
Alignment explanation
Indices: 86211--86331 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
86201 CACCACACCC
*
86211 TGCATCGATGCAT-AAAT-CCTATTCGATGTTTACA-TTTAAGAGAGTGCATCGATGCACTAATT
1 TGCATCGATGC-TCAAATGCC-ATTCGATGTTTACATTTTAA-AGAGTACATCGATGCACTAATT
86273 G
63 G
** *
86274 TGCATCGATGCTCTGATGGCATTCGATGTTTACATTTTAAAGAGTACATCGATGCACT
1 TGCATCGATGCTCAAATGCCATTCGATGTTTACATTTTAAAGAGTACATCGATGCACT
86332 TCAGGTGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
62 1 0.02
63 44 0.86
64 6 0.12
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
TGCATCGATGCTCAAATGCCATTCGATGTTTACATTTTAAAGAGTACATCGATGCACTAATTG
Found at i:87228 original size:21 final size:21
Alignment explanation
Indices: 87204--87276 Score: 128
Period size: 21 Copynumber: 3.5 Consensus size: 21
87194 CCGTTGATCA
87204 GGGGGAATCGATACCCCATTG
1 GGGGGAATCGATACCCCATTG
*
87225 GGGGGAATCGATACCCTATTG
1 GGGGGAATCGATACCCCATTG
*
87246 GGGGGAATCGATACCCCCTTG
1 GGGGGAATCGATACCCCATTG
87267 GGGGGAATCG
1 GGGGGAATCG
87277 GTTCCCTCCG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGATACCCCATTG
Found at i:88770 original size:19 final size:19
Alignment explanation
Indices: 88746--88791 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
88736 TAAATCATTT
88746 TTTCAAAAT-TCATTTTGGC
1 TTTCAAAATCT-ATTTTGGC
* *
88765 TTTCAAAATCTATTTTTGT
1 TTTCAAAATCTATTTTGGC
88784 TTTCAAAA
1 TTTCAAAA
88792 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTATTTTGGC
Found at i:90926 original size:17 final size:17
Alignment explanation
Indices: 90904--90945 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
90894 AGTATTAAAT
90904 TAAAGTTGTAACAAGGG
1 TAAAGTTGTAACAAGGG
90921 TAAAGTTGTAACAAGGG
1 TAAAGTTGTAACAAGGG
*
90938 AAAAGTTG
1 TAAAGTTG
90946 AGGACTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (17 bp):
TAAAGTTGTAACAAGGG
Done.