Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002788.1 Hibiscus syriacus cultivar Beakdansim tig00005745_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: 59638
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5265 original size:3 final size:3
Alignment explanation
Indices: 5257--5282 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5247 AGTTAGTAAG
5257 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
5283 GAAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5801 original size:13 final size:14
Alignment explanation
Indices: 5775--5812 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
5765 ATTTGAAAAG
5775 AAATAATCAAGGAT-
1 AAATAAT-AAGGATC
5789 AAATAATAAGGATC
1 AAATAATAAGGATC
5803 AAATAGATAA
1 AAATA-ATAA
5813 ATTAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 12 0.55
15 4 0.18
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (14 bp):
AAATAATAAGGATC
Found at i:6315 original size:32 final size:31
Alignment explanation
Indices: 6260--6346 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 31
6250 TTTTAATCAT
*
6260 TAAAGTAAAAAAAA-TTAAATTAAAA-TATA
1 TAAAGTAAAAAAAATTTAAATTAAAAGGATA
*
6289 TAAAGTAAAAGAAAACTTTAAATTAAAAGGATT
1 TAAAGTAAAA-AAAA-TTTAAATTAAAAGGATA
*
6322 TAAATGTAAAAAAAATTAAAATTAA
1 TAAA-GTAAAAAAAATTTAAATTAA
6347 GGACCAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 10 0.20
30 4 0.08
32 20 0.40
33 10 0.20
34 6 0.12
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (31 bp):
TAAAGTAAAAAAAATTTAAATTAAAAGGATA
Found at i:7616 original size:17 final size:16
Alignment explanation
Indices: 7594--7672 Score: 63
Period size: 14 Copynumber: 4.7 Consensus size: 16
7584 AAATCAAAAA
7594 ATAATATTAATAATAAT
1 ATAATA-TAATAATAAT
7611 ATAATATAAT-A-AAT
1 ATAATATAATAATAAT
*
7625 ATAAAATAATAAATAAT
1 ATAATATAAT-AATAAT
* *
7642 ACTATAAAGAATATATATAT
1 A-TA-ATATAATA-ATA-AT
7662 ATAATATAATA
1 ATAATATAATA
7673 CGTACATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
14 12 0.24
15 1 0.02
16 5 0.10
17 10 0.20
18 9 0.18
19 11 0.22
20 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (16 bp):
ATAATATAATAATAAT
Found at i:7620 original size:22 final size:22
Alignment explanation
Indices: 7594--7672 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 22
7584 AAATCAAAAA
7594 ATAATATTAATAATAATATAAT
1 ATAATATTAATAATAATATAAT
7616 ATAATAAATATAA-AATAATA-AAT
1 ATAAT--AT-TAATAATAATATAAT
* * *
7639 AATACTATAAAGAAT-ATATATAT
1 -ATAATATTAATAATAATATA-AT
7662 ATAATA-TAATA
1 ATAATATTAATA
7673 CGTACATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
21 8 0.18
22 16 0.36
23 5 0.11
24 13 0.29
25 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (22 bp):
ATAATATTAATAATAATATAAT
Found at i:7642 original size:37 final size:37
Alignment explanation
Indices: 7581--7672 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 37
7571 GGTCCTAAAA
* * *
7581 AATAAATCAAAAAATAAT-ATTAATA-ATAATATAATAT
1 AATAAAT-ATAAAATAATAAATAATACATAA-AGAATAT
7618 AATAAATATAAAATAATAAATAATACTATAAAGAATAT
1 AATAAATATAAAATAATAAATAATAC-ATAAAGAATAT
* *
7656 -ATATATATAATATAATA
1 AATAAATATAAAATAATA
7673 CGTACATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
36 9 0.19
37 28 0.60
38 6 0.13
39 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (37 bp):
AATAAATATAAAATAATAAATAATACATAAAGAATAT
Found at i:7648 original size:34 final size:36
Alignment explanation
Indices: 7581--7648 Score: 95
Period size: 34 Copynumber: 1.9 Consensus size: 36
7571 GGTCCTAAAA
7581 AATAAATCAAAAAATAATATTAATAATAATATAATAT
1 AATAAATCAAAAAATAATA-TAATAATAATATAATAT
* *
7618 AATAAAT-ATAAAATAATA-AATAATACTATAA
1 AATAAATCAAAAAATAATATAATAATAATATAA
7649 AGAATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 12 0.41
36 10 0.34
37 7 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (36 bp):
AATAAATCAAAAAATAATATAATAATAATATAATAT
Found at i:7722 original size:22 final size:22
Alignment explanation
Indices: 7680--7741 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 22
7670 ATACGTACAT
*
7680 TATATT-TATTTT-AAAATCTA
1 TATATTATATTTTCAAAAACTA
7700 TATATTATATTTTCAAAAACTA
1 TATATTATATTTTCAAAAACTA
*
7722 TATTATATATCTTTTCAAAA
1 TA-TAT-TATATTTTCAAAA
7742 CCCATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.17
21 6 0.17
22 9 0.25
23 3 0.08
24 12 0.33
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATTATATTTTCAAAAACTA
Found at i:7812 original size:75 final size:74
Alignment explanation
Indices: 7733--7892 Score: 178
Period size: 75 Copynumber: 2.1 Consensus size: 74
7723 ATTATATATC
* * * * * *
7733 TTTTCAAAACCCATTTTTTTAAAAACAACTATATT-TACGTTTTCAAAATCATTTTAAAAAATTG
1 TTTTCAAAA-ACATTTTTTTAAAAACAA-TACATTATACGTTTTCAAAACCACTTTAAAAAACTA
*
7797 TATATTACACG
64 TATATTACACA
* * * *
7808 TTTTCAGAAAACATTTTTTTTAAAACTATACATTATATGTTTTCAAAACCGCTTTAAAAAACTAT
1 TTTTCA-AAAACATTTTTTTAAAAACAATACATTATACGTTTTCAAAACCACTTTAAAAAACTAT
*
7873 ATATTATACA
65 ATATTACACA
7883 TTTTCAAAAA
1 TTTTCAAAAA
7893 ATATGTTTTC
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
74 9 0.13
75 59 0.83
76 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (74 bp):
TTTTCAAAAACATTTTTTTAAAAACAATACATTATACGTTTTCAAAACCACTTTAAAAAACTATA
TATTACACA
Found at i:7912 original size:75 final size:75
Alignment explanation
Indices: 7771--7913 Score: 173
Period size: 75 Copynumber: 1.9 Consensus size: 75
7761 CTATATTTAC
* * * * * * *
7771 GTTTTCAAAATCATTTTAAAAAATTGTATATTACACGTTTTCAGAAAACATTTTTTTTAAAACTA
1 GTTTTCAAAACCACTTTAAAAAACTATATATTACACATTTTCAGAAAACATTGTTTTCAAAACTA
7836 TACATTATAT
66 TACATTATAT
* *
7846 GTTTTCAAAACCGCTTTAAAAAACTATATATTATACATTTTCA-AAAA-ATATGTTTTCAAAACC
1 GTTTTCAAAACCACTTTAAAAAACTATATATTACACATTTTCAGAAAACAT-TGTTTTCAAAA-C
7909 TATAC
64 TATAC
7914 TATATACTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 2 0.04
74 13 0.23
75 42 0.74
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (75 bp):
GTTTTCAAAACCACTTTAAAAAACTATATATTACACATTTTCAGAAAACATTGTTTTCAAAACTA
TACATTATAT
Found at i:10066 original size:27 final size:27
Alignment explanation
Indices: 10028--10080 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
10018 GTCATCAAAA
10028 CTGAAAATTTCTGCACCAGATCTTTGT
1 CTGAAAATTTCTGCACCAGATCTTTGT
10055 CTGAAAATTTCTGCACCAGATCTTTG
1 CTGAAAATTTCTGCACCAGATCTTTG
10081 AACATCATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (27 bp):
CTGAAAATTTCTGCACCAGATCTTTGT
Found at i:12972 original size:2 final size:2
Alignment explanation
Indices: 12965--12993 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12955 TCAACTCAAC
12965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12994 CCTAAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16697 original size:65 final size:64
Alignment explanation
Indices: 16624--16782 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 64
16614 GAATAAATTG
*
16624 AACATCGAATGCATTTCATGCATCGATG-AACATACTATGCATCGATGCACTCAGAG-T-TTTAT
1 AACATCGAATGCATTTCATGCATCGATGCAACAGAC-ATGCATCGATGCACTCAG-GCTATTT-T
16686 GAA
63 G-A
* * * *
16689 AACGTCGAATGCATTTGATGCATCGATGCACCAGACATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCAACAGACATGCATCGATGCACTCAGGCTATTTTGA
16753 AACATCGAATGCATTTCATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
16783 TTCTTAGTGC
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 30 0.36
65 46 0.55
66 8 0.10
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCAACAGACATGCATCGATGCACTCAGGCTATTTTGA
Found at i:18202 original size:18 final size:18
Alignment explanation
Indices: 18181--18223 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
18171 CAAATTACAT
*
18181 AATTGAAAA-AAATATTAA
1 AATT-AAAACAAAAATTAA
*
18199 AATTAAAACAAAAATTAT
1 AATTAAAACAAAAATTAA
18217 AATTAAA
1 AATTAAA
18224 TTTCAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AATTAAAACAAAAATTAA
Found at i:18307 original size:39 final size:39
Alignment explanation
Indices: 18264--18374 Score: 136
Period size: 39 Copynumber: 2.8 Consensus size: 39
18254 TTTAAAAAAT
*
18264 AATTTAGAATATTA-ATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTATA-GTGAAATAATTTAAGAAATTAAG
* * *
18303 AATTTAGAATGTTATGGTGGCAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTATAGT-GAAATAATTTAAGAAATTAAG
* *
18342 AATTTATAATGTTATAGTGAAATAATTTGAGAA
1 AATTTAGAATGTTATAGTGAAATAATTTAAGAA
18375 TTATAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
38 3 0.05
39 55 0.90
40 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.17, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGTTATAGTGAAATAATTTAAGAAATTAAG
Found at i:21998 original size:41 final size:42
Alignment explanation
Indices: 21908--22188 Score: 171
Period size: 42 Copynumber: 6.8 Consensus size: 42
21898 AATTGATACT
* * * * *
21908 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATATAATTGACATA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATA-GAGTGATAAA
*
21951 TT-GCGGCGTTTTTA-TAAAAACGCCGCAATAGGGTGATAAA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * ** *
21991 TTAGCGGCGTTTATA-TCACAAACGCTTCAATAGA-TTATAAA
1 TTAGCGGCGTTTTTAGT-AAAAACGCCGCAATAGAGTGATAAA
* * ** * *
22032 TTTTGCGGCG-ATTTAGCCAAAACGCCGCAATATAGTGGTAAA
1 -TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * * ** * * *
22074 CTGGCAGCGTTTTTACCACAAACGCCACAATAGAAT-ATAAA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * * * * *
22115 TTTTGCAGCG-ATTGAGTAAAAACGCCGCAATAGAGCGGTAAA
1 -TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* **
22157 TTGGCGGCGTTTTTACAAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATA
22189 TATTACACAT
Statistics
Matches: 178, Mismatches: 51, Indels: 19
0.72 0.21 0.08
Matches are distributed among these distances:
40 7 0.04
41 83 0.47
42 86 0.48
43 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (42 bp):
TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
Found at i:22040 original size:42 final size:41
Alignment explanation
Indices: 21911--22188 Score: 102
Period size: 41 Copynumber: 6.7 Consensus size: 41
21901 TGATACTTTA
* * ** * *
21911 GCGGCGTTTTTAGTAAAAACGCTGCAATATAATTGACATA-TT
1 GCGGCGTTTATA-TAAAAACGCCGCAATAGGA-TGATAAATTT
* * *
21953 GCGGCGTTTTTATAAAAACGCCGCAATAGGGTGATAAATTA
1 GCGGCGTTTATATAAAAACGCCGCAATAGGATGATAAATTT
* ** *
21994 GCGGCGTTTATATCACAAACGCTTCAATA-GATTATAAATTTT
1 GCGGCGTTTATAT-AAAAACGCCGCAATAGGATGATAAA-TTT
*** * * * *
22036 GCGGCGATTTA-GCCAAAACGCCGCAATA-TAGTGGTAAACTG
1 GCGGCG-TTTATATAAAAACGCCGCAATAGGA-TGATAAATTT
* * * * * *
22077 GCAGCGTTTTTACCACAAACGCCACAATAGAAT-ATAAATTTT
1 GCGGCGTTTATA-TAAAAACGCCGCAATAGGATGATAAA-TTT
* * * * * *
22119 GCAGCGATTGA-GTAAAAACGCCGCAATA-GAGCGGTAAATTG
1 GCGGCG-TTTATATAAAAACGCCGCAATAGGA-TGATAAATTT
* *
22160 GCGGCGTTTTTACAAAAAACGCCGCAATA
1 GCGGCGTTTATA-TAAAAACGCCGCAATA
22189 TATTACACAT
Statistics
Matches: 172, Mismatches: 50, Indels: 28
0.69 0.20 0.11
Matches are distributed among these distances:
40 11 0.06
41 77 0.45
42 77 0.45
43 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
GCGGCGTTTATATAAAAACGCCGCAATAGGATGATAAATTT
Found at i:22040 original size:83 final size:83
Alignment explanation
Indices: 21951--22188 Score: 271
Period size: 83 Copynumber: 2.9 Consensus size: 83
21941 AATTGACATA
* * * * *
21951 TTGCGGCGTTTTTA-TAAAAACGCCGCAATAGGGTGATAAATTAGCGGCGTTTATATCACAAACG
1 TTGCGGCG-ATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACG
** *
22015 CTTCAATAGATTATAAATT
65 CCACAATAGAATATAAATT
** * * * *
22034 TTGCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTACCACAAACGC
1 TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
22099 CACAATAGAATATAAATT
66 CACAATAGAATATAAATT
* * * * * *
22117 TTGCAGCGATTGAGTAAAAACGCCGCAATAGAGCGGTAAATTGGCGGCGTTTTTACAAAAAACGC
1 TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
*
22182 CGCAATA
66 CACAATA
22189 TATTACACAT
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 4 0.03
83 125 0.97
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (83 bp):
TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
CACAATAGAATATAAATT
Found at i:25566 original size:21 final size:21
Alignment explanation
Indices: 25548--25633 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
25538 ATGAAGCAAG
*
25548 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
25569 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
25590 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
25611 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
25632 GG
1 GG
25634 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:25634 original size:21 final size:21
Alignment explanation
Indices: 25556--25648 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
25546 AGGGAAACAG
* *
25556 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
25578 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
25598 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
25619 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
25640 AGAGAGAAG
1 AGAGAGAAG
25649 TAATATATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:26118 original size:43 final size:43
Alignment explanation
Indices: 25986--26209 Score: 147
Period size: 43 Copynumber: 5.2 Consensus size: 43
25976 CATACAGTTA
* * * *
25986 GCGGCGTTTTTGATA-AAAACGCCGCAAAATCTCAATACATATT
1 GCGGCGTTTTTG-TAGAAAACGCCGCTAAATATCAACACCTATT
* * * * * ** *
26029 CGCAGCG--TTTGTAAGAAAACGCCGGTAAAAATAAAAATATACT
1 -GCGGCGTTTTTGT-AGAAAACGCCGCTAAATATCAACACCTATT
*
26072 GCGGCGTTTTTGTAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTTTGTAGAAAACGCCGCTAAATATCAAC-ACCTATT
* * *
26115 GCGGCG--TTTGTATGCCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTTTTGTA-G-AAAACGCCGCTAAATATCAACACCTATT
** * *
26158 GCGGCGTTTTAAT-GATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTTGTAGA-AAACGCCGCTAAATATCAACACCTATT
*
26201 GCGTCGTTT
1 GCGGCGTTT
26210 GTTGAACAAT
Statistics
Matches: 141, Mismatches: 28, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
41 7 0.05
42 12 0.09
43 108 0.77
44 11 0.08
45 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTTTGTAGAAAACGCCGCTAAATATCAACACCTATT
Found at i:30697 original size:64 final size:64
Alignment explanation
Indices: 30542--30702 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 64
30532 AATTAAATTG
* * *
30542 AACATCGAATGCATTTCATGCATCGTTGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCAC-TACCATGCACCGATGCACTCAGGATTTTATGAA
* * * *
30607 AACATCGAATGCATTTGATGCATCGATGCACTAGCCATGCATCGATTCACTCTGGCTATTT-TG-
1 AACATCGAATGCATTTGATGCATCGATGCACTA-CCATGCACCGATGCACTCAGGAT-TTTATGA
30670 A
64 A
* *
30671 AACATCGAATGCACTTGATGCGTCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACT
30703 CTTAGTGCAC
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 33 0.39
65 49 0.58
66 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTACCATGCACCGATGCACTCAGGATTTTATGAA
Found at i:37455 original size:2 final size:2
Alignment explanation
Indices: 37448--37474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37438 TAGCTTAAGC
37448 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
37475 CAATTGGCTA
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:37570 original size:17 final size:17
Alignment explanation
Indices: 37548--37583 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
37538 AAAAAAGGGG
37548 AGAAATGTTATGTTTTA
1 AGAAATGTTATGTTTTA
37565 AGAAATGTTATGTTTTA
1 AGAAATGTTATGTTTTA
37582 AG
1 AG
37584 GGAGAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.44
Consensus pattern (17 bp):
AGAAATGTTATGTTTTA
Found at i:37594 original size:21 final size:20
Alignment explanation
Indices: 37545--37596 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 20
37535 AACAAAAAAG
37545 GGGAGAAATGTTATGTTTTAA
1 GGGAG-AATGTTATGTTTTAA
37566 --GA-AATGTTATGTTTTAA
1 GGGAGAATGTTATGTTTTAA
37583 GGGAGAAGTGTTAT
1 GGGAGAA-TGTTAT
37597 AGTAAGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 15 0.56
19 4 0.15
20 2 0.07
21 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.38
Consensus pattern (20 bp):
GGGAGAATGTTATGTTTTAA
Found at i:38052 original size:65 final size:64
Alignment explanation
Indices: 37933--38143 Score: 216
Period size: 65 Copynumber: 3.3 Consensus size: 64
37923 TTTTTCAGAG
* * * *
37933 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CTAGCCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
37995 ATT
62 ATT
* * *
37998 TCATGCATCGATGCACATA-CCATGCA-CTGATGCACTGAGGATTTTTTGAAAACATCGAATGCA
1 TGATGCATCGATGCAC-TAGCCATGCATC-GATGCACTCAGGATATTTTG-AAACATCGAATGCA
*
38061 TA
63 TT
* * * *
38063 TGATGCATGGATGCACTAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
38127 TGATGCATCGATGCACT
1 TGATGCATCGATGCACT
38144 TTTAGTGCAC
Statistics
Matches: 122, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
63 4 0.03
64 47 0.39
65 68 0.56
66 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACTAGCCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:38158 original size:64 final size:63
Alignment explanation
Indices: 37983--38162 Score: 200
Period size: 65 Copynumber: 2.8 Consensus size: 63
37973 AATTAAATTG
* * * *
37983 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACTGATGCACTGAGGATTTTTTGAA
1 AACATCGAATGCA-TTGATGCATCGATGCAC-TACCATGCACCGATGCACTCAGGATATTTTGAA
* * * *
38048 AACATCGAATGCATATGATGCATGGATGCACTAGCCATGCATCGATGCACTCTGGCTATTTTG-A
1 AACATCGAATGCAT-TGATGCATCGATGCACTA-CCATGCACCGATGCACTCAGGATATTTTGAA
***
38112 AACATCGAATGCACTTGATGCATCGATGCACTTTTAGTGCACCGATGCACT
1 AACATCGAATGCA-TTGATGCATCGATGCACTACCA-TGCACCGATGCACT
38163 AAGGGTCCAA
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 46 0.47
65 51 0.52
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTGATGCATCGATGCACTACCATGCACCGATGCACTCAGGATATTTTGAA
Found at i:39182 original size:20 final size:20
Alignment explanation
Indices: 39149--39200 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
39139 TAAATCTAGA
39149 AAATTAAA-AATAATGAAAC-
1 AAATTAAATAATAAT-AAACT
39168 AAATTAAATAATAATAAACT
1 AAATTAAATAATAATAAACT
*
39188 TAATTAAAATAAT
1 AAATT-AAATAAT
39201 TAAAATAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.41
20 10 0.34
21 7 0.24
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (20 bp):
AAATTAAATAATAATAAACT
Found at i:39222 original size:25 final size:25
Alignment explanation
Indices: 39188--39263 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
39178 ATAATAAACT
*
39188 TAATTAAAATAATTAAAATAACAAA
1 TAATAAAAATAATTAAAATAACAAA
* *
39213 TAATAAAAATAGTTAAAGA-ACCAAA
1 TAATAAAAATAATTAAA-ATAACAAA
*
39238 -AATATAAAGAAAATTAAAATATACAA
1 TAATA-AAA-ATAATTAAAATA-ACAA
39264 GGATCTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
24 4 0.10
25 24 0.60
26 9 0.22
27 3 0.08
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.24
Consensus pattern (25 bp):
TAATAAAAATAATTAAAATAACAAA
Found at i:43666 original size:35 final size:36
Alignment explanation
Indices: 43626--43812 Score: 177
Period size: 36 Copynumber: 5.2 Consensus size: 36
43616 AATAATTTTA
* * *
43626 AATATAT-ATTTTTTAAAACGGTTTTAAAAACGTAT
1 AATATATGATTTTTTAAAACAGTTTTGAAAACATAT
*
43661 AATATATGATTTTTTAAAACAGTTTTGAAAACGTAT
1 AATATATGATTTTTTAAAACAGTTTTGAAAACATAT
* * * *
43697 ATTATATAATTTTTT-AAACATTTTTGAAAATATAT
1 AATATATGATTTTTTAAAACAGTTTTGAAAACATAT
*
43732 AATATA--ATTTTTGAAAAC-GCATTTTGGAAAACATAT
1 AATATATGATTTTTTAAAACAG--TTTT-GAAAACATAT
** * *
43768 AATATATGATTTTAAAAAAAATATTTTTGAAAACATAT
1 AATATATGATTTT--TTAAAACAGTTTTGAAAACATAT
43806 AATATAT
1 AATATAT
43813 AGTTTCTTTG
Statistics
Matches: 127, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
33 6 0.05
34 4 0.03
35 33 0.26
36 54 0.43
38 22 0.17
39 4 0.03
40 4 0.03
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
AATATATGATTTTTTAAAACAGTTTTGAAAACATAT
Found at i:43710 original size:71 final size:70
Alignment explanation
Indices: 43626--43785 Score: 162
Period size: 71 Copynumber: 2.3 Consensus size: 70
43616 AATAATTTTA
* * * *
43626 AATATATATTTTTTAAAACGGTTTTAAAAACGTATAATATATGATTTTTTAAAAC-AGTTTT-GA
1 AATATATAATTTTTAAAACAGTTTTAAAAACATATAATATA--ATTTTTGAAAACGA-TTTTGGA
*
43689 AAACGTAT
63 AAACATAT
* * * * *
43697 ATTATATAATTTTTTAAACATTTTTGAAAATATATAATATAATTTTTGAAAACGCATTTTGGAAA
1 AATATATAATTTTTAAAACAGTTTTAAAAACATATAATATAATTTTTGAAAACG-ATTTTGGAAA
43762 ACATAT
65 ACATAT
* *
43768 AATATATGATTTTAAAAA
1 AATATATAATTTTTAAAA
43786 AAATATTTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
69 11 0.15
70 4 0.06
71 57 0.79
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (70 bp):
AATATATAATTTTTAAAACAGTTTTAAAAACATATAATATAATTTTTGAAAACGATTTTGGAAAA
CATAT
Found at i:45718 original size:20 final size:20
Alignment explanation
Indices: 45693--45750 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
45683 TAGTTGGTGC
*
45693 TTGATTCTGTTTTATATTGT
1 TTGATTCTGTTTGATATTGT
*
45713 TTGATTCTGTTTGATATTGG
1 TTGATTCTGTTTGATATTGT
* **
45733 TTGCTTCTACTTGATATT
1 TTGATTCTGTTTGATATT
45751 TGTAAGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.09, G:0.17, T:0.59
Consensus pattern (20 bp):
TTGATTCTGTTTGATATTGT
Found at i:45867 original size:23 final size:23
Alignment explanation
Indices: 45837--45966 Score: 226
Period size: 23 Copynumber: 5.7 Consensus size: 23
45827 TGCTTTCTTA
45837 ATGC-ATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCTGAATTG
45859 ATGCAATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCTGAATTG
45882 ATGCAATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCTGAATTG
45905 ATGCAATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCTGAATTG
45928 ATGCAATGATGCTTGCTGAATTG
1 ATGCAATGATGCTTGCTGAATTG
* * *
45951 GTACAGTGATGCTTGC
1 ATGCAATGATGCTTGC
45967 CGGTTGCTGC
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
22 4 0.04
23 100 0.96
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.35
Consensus pattern (23 bp):
ATGCAATGATGCTTGCTGAATTG
Found at i:46568 original size:19 final size:19
Alignment explanation
Indices: 46537--46583 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
46527 AATAACATTT
*
46537 ATAATAT-AAGAATTATAA
1 ATAATATAAAGAATTAGAA
*
46555 ATAATATAAAGAATTGGAA
1 ATAATATAAAGAATTAGAA
*
46574 TTAATATAAA
1 ATAATATAAA
46584 AACCAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (19 bp):
ATAATATAAAGAATTAGAA
Found at i:46690 original size:27 final size:26
Alignment explanation
Indices: 46649--46699 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
46639 TAATCATAGT
*
46649 AATTTAATTATCATAAGTT-TATTATA
1 AATTTAAGTATCATAA-TTATATTATA
46675 AATTTAAAGTATCATAATTATATTA
1 AATTT-AAGTATCATAATTATATTA
46700 ATTGTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (26 bp):
AATTTAAGTATCATAATTATATTATA
Found at i:47317 original size:21 final size:21
Alignment explanation
Indices: 47293--47332 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47283 TTTATAAATA
*
47293 ATATAAAATAATATATATTAT
1 ATATAAAATAATAAATATTAT
* *
47314 ATATTAAATATTAAATATT
1 ATATAAAATAATAAATATT
47333 TTTTGGTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAAAATAATAAATATTAT
Found at i:48096 original size:18 final size:18
Alignment explanation
Indices: 48075--48110 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
48065 ACTAAAAGTT
48075 AAACATCAACTGGATTGA
1 AAACATCAACTGGATTGA
*
48093 AAACATCAACTTGATTGA
1 AAACATCAACTGGATTGA
48111 TTTAAGTGGT
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:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (18 bp):
AAACATCAACTGGATTGA
Found at i:49650 original size:18 final size:18
Alignment explanation
Indices: 49623--49663 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49613 AGGGGCACTT
*
49623 CACT-TATCCCGAAGGGC
1 CACTATATCCCGAAGGAC
49640 CACTATATCCCGAAGGAC
1 CACTATATCCCGAAGGAC
49658 CACTAT
1 CACTAT
49664 CCATATGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
CACTATATCCCGAAGGAC
Found at i:50021 original size:16 final size:17
Alignment explanation
Indices: 50002--50034 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49992 GACCTACAAC
50002 ACATAT-ATCATATTAA
1 ACATATGATCATATTAA
*
50018 ACATATGCTCATATTAA
1 ACATATGATCATATTAA
50035 TGAATTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36
Consensus pattern (17 bp):
ACATATGATCATATTAA
Found at i:50420 original size:53 final size:53
Alignment explanation
Indices: 50357--50476 Score: 222
Period size: 53 Copynumber: 2.3 Consensus size: 53
50347 TTCCCTAGCT
50357 ATGGTATCGATACCAAGTATGGGTATCGATACCCAAATTACATTCGATATTTC
1 ATGGTATCGATACCAAGTATGGGTATCGATACCCAAATTACATTCGATATTTC
*
50410 ATGGTATCGATACCAAGTATGGGTATCGATACCCAAATTGCATTCGATATTTC
1 ATGGTATCGATACCAAGTATGGGTATCGATACCCAAATTACATTCGATATTTC
*
50463 CTGGTATCGATACC
1 ATGGTATCGATACC
50477 TTCCTTATGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (53 bp):
ATGGTATCGATACCAAGTATGGGTATCGATACCCAAATTACATTCGATATTTC
Found at i:55710 original size:15 final size:16
Alignment explanation
Indices: 55690--55719 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55680 GGAAGAAGAT
55690 AAAAAAGA-AAGAGGG
1 AAAAAAGACAAGAGGG
55705 AAAAAAGACAAGAGG
1 AAAAAAGACAAGAGG
55720 TGTGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (16 bp):
AAAAAAGACAAGAGGG
Done.