Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001626.1 Hibiscus syriacus cultivar Beakdansim tig00003235_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: 73851
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:963 original size:15 final size:15
Alignment explanation
Indices: 943--981 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
933 ATGGCGTGGT
943 TGTTTAATGCTAATA
1 TGTTTAATGCTAATA
958 TGTTTAATGCTAATA
1 TGTTTAATGCTAATA
973 TGTTTAATG
1 TGTTTAATG
982 TGAAAGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.15, T:0.49
Consensus pattern (15 bp):
TGTTTAATGCTAATA
Found at i:1983 original size:20 final size:20
Alignment explanation
Indices: 1955--2000 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1945 AATATTTTTT
* *
1955 AATTGAAAAGAAAAAAC-AGA
1 AATTTAAAAAAAAAAACTA-A
1975 AATTTAAAAAAAAAAACTAA
1 AATTTAAAAAAAAAAACTAA
1995 AATTTA
1 AATTTA
2001 TGCAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
AATTTAAAAAAAAAAACTAA
Found at i:2961 original size:2 final size:2
Alignment explanation
Indices: 2954--2978 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2944 AGGTGATCAT
2954 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
2979 GTTTTAGAAA
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:7876 original size:26 final size:24
Alignment explanation
Indices: 7845--7904 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
7835 ACTTAAATTC
*
7845 ATAATATTTTTTATATATTAACTTA
1 ATAATATTTTTTAT-TATTAACCTA
* *
7870 TTAAATATATTTTATTATTAACCTA
1 AT-AATATTTTTTATTATTAACCTA
7895 ATAATATTTT
1 ATAATATTTT
7905 GGTGTATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.24
25 11 0.38
26 11 0.38
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (24 bp):
ATAATATTTTTTATTATTAACCTA
Found at i:13678 original size:15 final size:15
Alignment explanation
Indices: 13658--13688 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13648 GTCATCATCA
13658 ATTTGAATTTTGATG
1 ATTTGAATTTTGATG
13673 ATTTGAATTTTGATG
1 ATTTGAATTTTGATG
13688 A
1 A
13689 CGGATGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (15 bp):
ATTTGAATTTTGATG
Found at i:13791 original size:17 final size:17
Alignment explanation
Indices: 13769--13807 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
13759 CAGGCCGTAA
13769 ACACAGTTGAGCTTCAT
1 ACACAGTTGAGCTTCAT
13786 ACACAGTTGAGCTTCAT
1 ACACAGTTGAGCTTCAT
13803 ACACA
1 ACACA
13808 ATGTAGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (17 bp):
ACACAGTTGAGCTTCAT
Found at i:16722 original size:24 final size:24
Alignment explanation
Indices: 16688--16739 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16678 CCGAGCTATA
* * *
16688 CGAGGGCATCCGAGGGCATCCGTG
1 CGAGGGAATCCGAGGGCAGCCGAG
16712 CGAGGGAATCCGAGGGCAGCCGAG
1 CGAGGGAATCCGAGGGCAGCCGAG
16736 CGAG
1 CGAG
16740 CTATGCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.44, T:0.08
Consensus pattern (24 bp):
CGAGGGAATCCGAGGGCAGCCGAG
Found at i:16757 original size:23 final size:23
Alignment explanation
Indices: 16722--16786 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
16712 CGAGGGAATC
** *
16722 CGAGGGCAGCCGAGCGAGCTATG
1 CGAGGGCCTCCGAGCGAGCTATA
*
16745 CGAGGGCCTCCGAGCTAGCTATA
1 CGAGGGCCTCCGAGCGAGCTATA
16768 CGAGGGCCTCCGAGCGAGC
1 CGAGGGCCTCCGAGCGAGC
16787 GAGCAAGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.20, C:0.31, G:0.38, T:0.11
Consensus pattern (23 bp):
CGAGGGCCTCCGAGCGAGCTATA
Found at i:19399 original size:13 final size:13
Alignment explanation
Indices: 19381--19419 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
19371 ACTTCTAAAT
19381 TCACAGATTGTAA
1 TCACAGATTGTAA
19394 TCACAGATTGTAA
1 TCACAGATTGTAA
19407 TCACAGATTGTAA
1 TCACAGATTGTAA
19420 AATGTTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TCACAGATTGTAA
Found at i:21170 original size:6 final size:6
Alignment explanation
Indices: 21147--21198 Score: 61
Period size: 6 Copynumber: 8.7 Consensus size: 6
21137 AAAAAAGGAT
* * *
21147 AAAATA AATAATA AAAACA AAAACA AATA-A AAAATA AAAATA AAAATA
1 AAAATA AA-AATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
21195 AAAA
1 AAAA
21199 AGAATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
5 4 0.10
6 31 0.76
7 6 0.15
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:21174 original size:19 final size:19
Alignment explanation
Indices: 21147--21198 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
21137 AAAAAAGGAT
21147 AAAATAAATAATAAAAACA
1 AAAATAAATAATAAAAACA
* *
21166 AAAACAAAT-A-AAAAATA
1 AAAATAAATAATAAAAACA
21183 AAAATAAA-AATAAAAA
1 AAAATAAATAATAAAAA
21199 AGAATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 14 0.50
18 6 0.21
19 8 0.29
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (19 bp):
AAAATAAATAATAAAAACA
Found at i:21174 original size:23 final size:23
Alignment explanation
Indices: 21148--21207 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
21138 AAAAAGGATA
*
21148 AAATAAATAATAAAAACAAAAAC
1 AAATAAAAAATAAAAACAAAAAC
* *
21171 AAATAAAAAATAAAAATAAAAAT
1 AAATAAAAAATAAAAACAAAAAC
*
21194 AAA-AAAGAATAAAA
1 AAATAAAAAATAAAA
21208 TACTATATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 10 0.30
23 23 0.70
ACGTcount: A:0.82, C:0.03, G:0.02, T:0.13
Consensus pattern (23 bp):
AAATAAAAAATAAAAACAAAAAC
Found at i:21177 original size:16 final size:14
Alignment explanation
Indices: 21156--21207 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 14
21146 TAAAATAAAT
21156 AATAAAAACAAAAACA
1 AATAAAAA-AAAAA-A
*
21172 AAT-AAAAAATAAA
1 AATAAAAAAAAAAA
21185 AATAAAAATAAAAAA
1 AATAAAAA-AAAAAA
21200 GAATAAAA
1 -AATAAAA
21208 TACTATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 8 0.26
15 9 0.29
16 10 0.32
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.12
Consensus pattern (14 bp):
AATAAAAAAAAAAA
Found at i:21179 original size:29 final size:29
Alignment explanation
Indices: 21147--21207 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
21137 AAAAAAGGAT
21147 AAAATAAATAATAAAAACAAAAACA-AATAA
1 AAAATAAA-AATAAAAACAAAAA-AGAATAA
*
21177 AAAATAAAAATAAAAATAAAAAAGAATAA
1 AAAATAAAAATAAAAACAAAAAAGAATAA
21206 AA
1 AA
21208 TACTATATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.03
29 20 0.69
30 8 0.28
ACGTcount: A:0.82, C:0.03, G:0.02, T:0.13
Consensus pattern (29 bp):
AAAATAAAAATAAAAACAAAAAAGAATAA
Found at i:21328 original size:33 final size:31
Alignment explanation
Indices: 21274--21419 Score: 116
Period size: 33 Copynumber: 4.4 Consensus size: 31
21264 TTCAAAACCA
* *
21274 TATATTATATAATTTTAAAAAACGTTTTCAAAC
1 TATATT-TAT-ATTTTCAAAAACGTTTTAAAAC
21307 TATATGTTATAGTTTTCAAAAACGTTTTAAAAC
1 TATAT-TTATA-TTTTCAAAAACGTTTTAAAAC
* *
21340 TATA-TTATATGTTTCAAAAATGTTTTTTTAAAC
1 TATATTTATAT-TTTCAAAAACG--TTTTAAAAC
*
21373 TATATATTATATAAATTTC-AAAATGATTTTAAAAC
1 TATAT-TTATAT---TTTCAAAAACG-TTTTAAAAC
21408 TATATATTATAT
1 TATAT-TTATAT
21420 AAGTTTTCAA
Statistics
Matches: 97, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
30 1 0.01
31 15 0.15
32 1 0.01
33 43 0.44
34 1 0.01
35 26 0.27
36 6 0.06
37 4 0.04
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (31 bp):
TATATTTATATTTTCAAAAACGTTTTAAAAC
Found at i:21408 original size:35 final size:35
Alignment explanation
Indices: 21221--21608 Score: 203
Period size: 37 Copynumber: 10.8 Consensus size: 35
21211 TATATGATAA
* * *
21221 AAAATG-TTTTAAAACTTTATATAATAT-GTATTTC
1 AAAATGATTTTAAAACTATATATTATATAAT-TTTC
* *
21255 AAAGAT-ATTTTCAAAACCATATATTATATAATTTTAA
1 AAA-ATGATTTT-AAAACTATATATTATATAATTTT-C
* * * *
21292 AAAACG-TTTTCAAACTATAT-GT-TATAGTTTTC
1 AAAATGATTTTAAAACTATATATTATATAATTTTC
* *
21324 AAAAACG-TTTTAAAAC--TATATTATAT--GTTTC
1 -AAAATGATTTTAAAACTATATATTATATAATTTTC
* * *
21355 AAAAATGTTTTTTTAAACTATATATTATATAAATTTC
1 -AAAATG-ATTTTAAAACTATATATTATATAATTTTC
21392 AAAATGATTTTAAAACTATATATTATATAAGTTTTC
1 AAAATGATTTTAAAACTATATATTATATAA-TTTTC
* *
21428 AAAATGGTTTTAAAAACTATATAATATAT-ATGGTTTC
1 AAAATGATTTT-AAAACTATATATTATATAAT--TTTC
** ** * * *
21465 AAAAAAAATTCAAAAATTATATAATATATATGTTTTC
1 -AAAATGATTTTAAAACTATATATTATATA-ATTTTC
*
21502 AAAAAATG-TTTTCAAAAACCATATATTATAT-ATTTTC
1 --AAAATGATTTT--AAAACTATATATTATATAATTTTC
* *
21539 AAAATGTTTTATTTTTAGAAAACCATATATTATATAGTTTTC
1 AAAATG----A-TTTT--AAAACTATATATTATATAATTTTC
* *
21581 AAAATGA-TTTCAAACTATATAATATATA
1 AAAATGATTTTAAAACTATATATTATATA
21609 TATATATATA
Statistics
Matches: 279, Mismatches: 43, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
31 13 0.05
32 1 0.00
33 33 0.12
34 19 0.07
35 53 0.19
36 46 0.16
37 55 0.20
38 12 0.04
39 15 0.05
41 21 0.08
42 11 0.04
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
AAAATGATTTTAAAACTATATATTATATAATTTTC
Found at i:21512 original size:13 final size:13
Alignment explanation
Indices: 21494--21519 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21484 TATAATATAT
21494 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
21507 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
21520 CCATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:31767 original size:21 final size:21
Alignment explanation
Indices: 31741--31783 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
31731 CTCGGGTTCC
31741 TCTTCGGAGGGTAACACTCCA
1 TCTTCGGAGGGTAACACTCCA
31762 TCTTCGGAGGGTAACACTCCA
1 TCTTCGGAGGGTAACACTCCA
31783 T
1 T
31784 TCTGATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (21 bp):
TCTTCGGAGGGTAACACTCCA
Found at i:38699 original size:77 final size:77
Alignment explanation
Indices: 38566--38735 Score: 227
Period size: 77 Copynumber: 2.2 Consensus size: 77
38556 TGCTCAGAAT
* * * *
38566 GAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTTAAATGATTTTGGCCCCGAGATTTCCAG
1 GAACCGATTCCCCCCATAGGAGGAACCAATTCCCCCCTAAAAGATTTTGGCCCCGAGAATTCCAG
38631 AATGCTCGGAGG
66 AATGCTCGGAGG
* *
38643 GAACCGATTCCCCTCATAGGAGGAACCAATTCCCCCCCTAAACAG-TTTT-GCTCCGAGAATTCC
1 GAACCGATTCCCCCCATAGGAGGAACCAATT-CCCCCCTAAA-AGATTTTGGCCCCGAGAATTCC
* *
38706 AGTATGCTCGGATG
64 AGAATGCTCGGAGG
*
38720 GAACCGATCCCCCCCA
1 GAACCGATTCCCCCCA
38736 AGGGGATACC
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 67 0.83
78 13 0.16
79 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (77 bp):
GAACCGATTCCCCCCATAGGAGGAACCAATTCCCCCCTAAAAGATTTTGGCCCCGAGAATTCCAG
AATGCTCGGAGG
Found at i:43035 original size:2 final size:2
Alignment explanation
Indices: 43028--43053 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43018 GAAACTTTGA
43028 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
43054 TGTAAAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43725 original size:25 final size:26
Alignment explanation
Indices: 43697--43752 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
43687 GCTTTGTTCC
43697 AAAATT-AATAATACATTAGATAT-TT
1 AAAATTGAATAATA-ATTAGATATGTT
* *
43722 AAAATTGAGTAATAATTAGATGTGTT
1 AAAATTGAATAATAATTAGATATGTT
43748 AAAAT
1 AAAAT
43753 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (26 bp):
AAAATTGAATAATAATTAGATATGTT
Found at i:44299 original size:38 final size:39
Alignment explanation
Indices: 44237--44328 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 39
44227 TTTTTTTTCA
*
44237 AAACTAAAAATTAAATTTTGAATGGT-GG-TACTAAAATG
1 AAAC-AAAAACTAAATTTTGAATGGTGGGATACTAAAATG
* *
44275 AAACAAAAACTAAAGTTTTTAATGGTGGGATGCTAAAATG
1 AAACAAAAACTAAA-TTTTGAATGGTGGGATACTAAAATG
44315 AAACAAAAACTAAA
1 AAACAAAAACTAAA
44329 CTTTATATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
37 9 0.19
38 14 0.29
39 2 0.04
40 23 0.48
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (39 bp):
AAACAAAAACTAAATTTTGAATGGTGGGATACTAAAATG
Found at i:45687 original size:37 final size:36
Alignment explanation
Indices: 45612--45687 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
45602 TTTTTATATT
*
45612 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
45648 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
45685 TTT
1 TTT
45688 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:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:50070 original size:19 final size:18
Alignment explanation
Indices: 50048--50106 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
50038 TAAACAATTA
50048 AATTAATATATTTTATAAT
1 AATTAATATATTTT-TAAT
**
50067 AATTTTTATATTTTTAAT
1 AATTAATATATTTTTAAT
50085 AATTAGATAATATTATTTAAT
1 AATTA-AT-ATATT-TTTAAT
50106 A
1 A
50107 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.24
19 13 0.39
20 5 0.15
21 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTAATATATTTTTAAT
Found at i:51128 original size:33 final size:33
Alignment explanation
Indices: 51086--51160 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
51076 CCGAGGCCAT
* *
51086 CCGAACGAGCTATGCGAGGGCATCCGAGGGTAA-
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGG-AAG
*
51119 CCGAGCGAGCTATGCGATGGAATCCGAGGGAAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
51152 CCGAGCGAG
1 CCGAGCGAG
51161 GGTAGGTCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.27, C:0.24, G:0.39, T:0.11
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
Found at i:51197 original size:29 final size:29
Alignment explanation
Indices: 51164--51219 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
51154 GAGCGAGGGT
*
51164 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
51193 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
51220 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:51321 original size:29 final size:29
Alignment explanation
Indices: 51278--51334 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
51268 GAGCAAGGGT
51278 AGGTCGCCCGAAGTGCATGGCGACCTACA
1 AGGTCGCCCGAAGTGCATGGCGACCTACA
*
51307 AGGTCGCCC-AGAGTGCATTGCGACCTAC
1 AGGTCGCCCGA-AGTGCATGGCGACCTAC
51335 GGCCAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.23, C:0.32, G:0.30, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGAAGTGCATGGCGACCTACA
Found at i:63453 original size:17 final size:17
Alignment explanation
Indices: 63427--63460 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63417 AGATAACGTG
63427 TTTTAATAAAATATATT
1 TTTTAATAAAATATATT
* *
63444 TTTTATTAAAATTTATT
1 TTTTAATAAAATATATT
63461 ATCAAGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAATAAAATATATT
Found at i:68425 original size:29 final size:30
Alignment explanation
Indices: 68351--68434 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 30
68341 TTAATAGAGT
*
68351 AAAATAAATTATT-AGAATTTGAATTATTAA
1 AAAATAAATTATTGA-AATTTGAATTATAAA
* *
68381 AAAATTAATTAGTGAAATTTGAATT-TAAA
1 AAAATAAATTATTGAAATTTGAATTATAAA
*
68410 AAAATGAATTATTGAAATTTGAATT
1 AAAATAAATTATTGAAATTTGAATT
68435 CTGGAAATAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
29 26 0.54
30 21 0.44
31 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (30 bp):
AAAATAAATTATTGAAATTTGAATTATAAA
Found at i:68434 original size:15 final size:15
Alignment explanation
Indices: 68357--68434 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
68347 GAGTAAAATA
*
68357 AATTATTAGAATTTG
1 AATTATTAAAATTTG
*
68372 AATTATTAAAAAATT-
1 AATTATT-AAAATTTG
* *
68387 AATTAGTGAAATTTG
1 AATTATTAAAATTTG
* **
68402 AATT-TAAAAAAATG
1 AATTATTAAAATTTG
*
68416 AATTATTGAAATTTG
1 AATTATTAAAATTTG
68431 AATT
1 AATT
68435 CTGGAAATAA
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
14 14 0.30
15 27 0.59
16 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
AATTATTAAAATTTG
Found at i:68465 original size:14 final size:14
Alignment explanation
Indices: 68448--68482 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
68438 GAAATAAATT
68448 ATATTTTTTAAAAA
1 ATATTTTTTAAAAA
*
68462 ATATTTTTTAGAAA
1 ATATTTTTTAAAAA
*
68476 ATGTTTT
1 ATATTTT
68483 CCGTAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
ATATTTTTTAAAAA
Found at i:68687 original size:18 final size:19
Alignment explanation
Indices: 68664--68700 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
68654 ATTTTAAAAA
68664 TATTAAA-AATATTTTTAT
1 TATTAAATAATATTTTTAT
*
68682 TATTAAATATTATTTTTAT
1 TATTAAATAATATTTTTAT
68701 AATTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTAAATAATATTTTTAT
Found at i:68846 original size:23 final size:23
Alignment explanation
Indices: 68797--68846 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
68787 GTGTTATATT
**
68797 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
68820 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
68843 ATAT
1 ATAT
68847 AGATTATTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:68928 original size:26 final size:25
Alignment explanation
Indices: 68896--68951 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
68886 TATTAAATAT
68896 ATAAAAAATTAT-TATATATTTATTAAA
1 ATAAAAAA-TATCT-TATA-TTATTAAA
*
68923 ATAAAAAATATCTTATATTATTATA
1 ATAAAAAATATCTTATATTATTAAA
68948 ATAA
1 ATAA
68952 TTGATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 11 0.41
26 7 0.26
27 9 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATAAAAAATATCTTATATTATTAAA
Found at i:69011 original size:26 final size:26
Alignment explanation
Indices: 68836--69021 Score: 90
Period size: 26 Copynumber: 7.2 Consensus size: 26
68826 TAAATATCTT
*
68836 TATTAAAATATAGAT-TATTA-GATTAA
1 TATTAAAATATA-ATATATTATTA-TAA
68862 TATTAAATATATAA-ATA-TATTCAT--
1 TATTAAA-ATATAATATATTATT-ATAA
* *
68886 TATTAAATATATAAAAAATTATTATATA
1 TATTAAA-ATATAATATATTATTATA-A
* * * *
68914 TTTATTAAAATAAAAAATA-TCTTATAT
1 --TATTAAAATATAATATATTATTATAA
* * *
68941 TATTATAATAATTGATTATTTTATTATAA
1 TATTAAAAT-A-T-AATATATTATTATAA
68970 TATTAAAATATAATATATTATTATAAA
1 TATTAAAATATAATATATTATTAT-AA
68997 TATT--AATA-AATATATT-TTA-AA
1 TATTAAAATATAATATATTATTATAA
69018 TATT
1 TATT
69022 TTAATAATTA
Statistics
Matches: 128, Mismatches: 16, Indels: 37
0.71 0.09 0.20
Matches are distributed among these distances:
21 6 0.05
23 3 0.02
24 22 0.17
25 18 0.14
26 27 0.21
27 13 0.10
28 10 0.08
29 22 0.17
30 7 0.05
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.47
Consensus pattern (26 bp):
TATTAAAATATAATATATTATTATAA
Found at i:69017 original size:21 final size:20
Alignment explanation
Indices: 68970--69021 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
68960 TTTATTATAA
*
68970 TATTA-AAATA-TAATATAT
1 TATTATAAATATTAATAAAT
68988 TATTATAAATATTAATAAAT
1 TATTATAAATATTAATAAAT
*
69008 ATATTTTAAATATT
1 -TATTATAAATATT
69022 TTAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 5 0.17
20 7 0.24
21 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTATAAATATTAATAAAT
Found at i:69025 original size:23 final size:23
Alignment explanation
Indices: 68957--69074 Score: 71
Period size: 24 Copynumber: 4.7 Consensus size: 23
68947 AATAATTGAT
68957 TATTTTATTATAATATTAAAATATAATA
1 TATTTTA-TA-AATATT--AATA-AATA
68985 TATTATTATAAATATTAATAAATA
1 TATT-TTATAAATATTAATAAATA
* *
69009 TATTTTA-AATATTTTAATAATTAA
1 TATTTTATAA-ATATTAATAAAT-A
*
69033 TATTTTGATGAAA-ATGATATTAAA-A
1 TATTTT-AT-AAATAT--TAATAAATA
*
69058 TATTTTATTAATATTAA
1 TATTTTATAAATATTAA
69075 ATTCATAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
22 4 0.05
23 15 0.20
24 19 0.26
25 13 0.18
26 1 0.01
27 13 0.18
28 6 0.08
29 3 0.04
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TATTTTATAAATATTAATAAATA
Found at i:69291 original size:42 final size:42
Alignment explanation
Indices: 69235--69329 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
69225 TTCCTCCAAC
* * *
69235 CAAACACTGGAAAACATTCTCCGGAAAACGAATTACTTGAAA
1 CAAACACGGGAAAACATTCTCCGAAAAACGAATTACATGAAA
*
69277 CAAACACGGGAAAACATTTTCCGAAAAACGAATTACATGAAA
1 CAAACACGGGAAAACATTCTCCGAAAAACGAATTACATGAAA
69319 CAAACACGGGA
1 CAAACACGGGA
69330 TTTCAGGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (42 bp):
CAAACACGGGAAAACATTCTCCGAAAAACGAATTACATGAAA
Found at i:70882 original size:18 final size:18
Alignment explanation
Indices: 70855--70890 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
70845 TTAATTTACG
* *
70855 ATTGTGATTTTAAATATT
1 ATTGTAATTTAAAATATT
70873 ATTGTAATTTAAAATATT
1 ATTGTAATTTAAAATATT
70891 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTGTAATTTAAAATATT
Found at i:71882 original size:14 final size:15
Alignment explanation
Indices: 71845--71887 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
71835 TTCTTTTATC
71845 TAAATAAATAAAA-A
1 TAAATAAATAAAATA
* *
71859 TCAATTAATAAAATA
1 TAAATAAATAAAATA
71874 -AAATAAATAAAATA
1 TAAATAAATAAAATA
71888 CCAAAATTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 23 0.96
15 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATAAATAAAATA
Found at i:72991 original size:20 final size:20
Alignment explanation
Indices: 72963--73003 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
72953 ATCAGATTGT
72963 CCAGCGGGTACAGATTCCCC
1 CCAGCGGGTACAGATTCCCC
* *
72983 CCAGGGGGTACCGATTCCCC
1 CCAGCGGGTACAGATTCCCC
73003 C
1 C
73004 TGTCTAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.41, G:0.27, T:0.15
Consensus pattern (20 bp):
CCAGCGGGTACAGATTCCCC
Done.