Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007051.1 Hibiscus syriacus cultivar Beakdansim tig00018280_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: 104280
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4000 original size:41 final size:41
Alignment explanation
Indices: 3955--4038 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
3945 TTCAAATAGT
* *
3955 TCAGTTAAACATCATTATCAACTATGGGTATCTTTTGTCAG
1 TCAGTCAAACATCATTATCAACTATGGGCATCTTTTGTCAG
* *
3996 TCAGTCATACATCATTATCAACTATGGGCATCTTTTGTTAG
1 TCAGTCAAACATCATTATCAACTATGGGCATCTTTTGTCAG
4037 TC
1 TC
4039 TAAACAACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (41 bp):
TCAGTCAAACATCATTATCAACTATGGGCATCTTTTGTCAG
Found at i:4056 original size:41 final size:41
Alignment explanation
Indices: 3970--4056 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
3960 TAAACATCAT
* ** * *
3970 TATCAACTATGGGTATCTTTTGTCAGTCAGTCATACATCAT
1 TATCAACTATGGGCATCTTTTGTCAGTCAAACATACATAAA
* *
4011 TATCAACTATGGGCATCTTTTGTTAGTCTAAACA-ACGTAAA
1 TATCAACTATGGGCATCTTTTGTCAGTC-AAACATACATAAA
4052 TATCA
1 TATCA
4057 TATTGGAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 35 0.92
42 3 0.08
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (41 bp):
TATCAACTATGGGCATCTTTTGTCAGTCAAACATACATAAA
Found at i:12760 original size:30 final size:30
Alignment explanation
Indices: 12726--12814 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 30
12716 ATTTCATTTT
* *
12726 TAATTTGACCCTAAATTTTAGATAAAATAC
1 TAATTTGACCATAAACTTTAGATAAAATAC
* * * ** *
12756 TAATTTGATCGTAAACTTTAAATAGTATAT
1 TAATTTGACCATAAACTTTAGATAAAATAC
* *
12786 TATTTTGACCATAAACTTTAGCTAAAATA
1 TAATTTGACCATAAACTTTAGATAAAATA
12815 TCAATTTAAC
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (30 bp):
TAATTTGACCATAAACTTTAGATAAAATAC
Found at i:13136 original size:16 final size:17
Alignment explanation
Indices: 13117--13154 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
13107 ATAATAAAAA
13117 TATATAATTTTT-TGTT
1 TATATAATTTTTATGTT
13133 TATAATAATTTTTATGTT
1 TAT-ATAATTTTTATGTT
13151 TATA
1 TATA
13155 ATATTAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 10 0.50
18 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TATATAATTTTTATGTT
Found at i:13142 original size:17 final size:18
Alignment explanation
Indices: 13120--13157 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
13110 ATAAAAATAT
13120 ATAATTTTT-TGTTTATA
1 ATAATTTTTATGTTTATA
13137 ATAATTTTTATGTTTATA
1 ATAATTTTTATGTTTATA
13155 ATA
1 ATA
13158 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
ATAATTTTTATGTTTATA
Found at i:13228 original size:26 final size:26
Alignment explanation
Indices: 13199--13254 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
13189 TATAATTTTC
13199 AATTATA-ATATAAATTTAGTTTTTGG
1 AATTATATAT-TAAATTTAGTTTTTGG
* * * *
13225 AATTCTTTATTTAATTTAGTTTTTTG
1 AATTATATATTAAATTTAGTTTTTGG
13251 AATT
1 AATT
13255 CTTTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (26 bp):
AATTATATATTAAATTTAGTTTTTGG
Found at i:13255 original size:26 final size:26
Alignment explanation
Indices: 13211--13262 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
13201 TTATAATATA
13211 AATTTAGTTTTTGGAATTCTTTATTT
1 AATTTAGTTTTTGGAATTCTTTATTT
*
13237 AATTTAGTTTTTTGAATTCTTTATTT
1 AATTTAGTTTTTGGAATTCTTTATTT
13263 TTAAAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (26 bp):
AATTTAGTTTTTGGAATTCTTTATTT
Found at i:14191 original size:3 final size:3
Alignment explanation
Indices: 14185--14227 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
14175 ATTTTTTTTC
14185 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
14228 GTTGTTTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16401 original size:26 final size:26
Alignment explanation
Indices: 16368--16454 Score: 165
Period size: 26 Copynumber: 3.3 Consensus size: 26
16358 CCAACCGTAC
16368 AAAAAATAAGTTATATATATCACATT
1 AAAAAATAAGTTATATATATCACATT
16394 AAAAAATAAGTTATATATATCACATT
1 AAAAAATAAGTTATATATATCACATT
*
16420 AAAAAATAAGTTATATATGTCACATT
1 AAAAAATAAGTTATATATATCACATT
16446 AAAAAATAA
1 AAAAAATAA
16455 TTAACGTCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 60 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (26 bp):
AAAAAATAAGTTATATATATCACATT
Found at i:16646 original size:17 final size:16
Alignment explanation
Indices: 16621--16655 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
16611 CAATATTCGA
*
16621 TAAATTAATAATCTTTT
1 TAAAATAATAAT-TTTT
16638 TAAAATAATAATTTTT
1 TAAAATAATAATTTTT
16654 TA
1 TA
16656 TTTTAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAAATAATAATTTTT
Found at i:17236 original size:11 final size:9
Alignment explanation
Indices: 17203--17232 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
17193 GCATATATAC
17203 GGGAAGAGG
1 GGGAAGAGG
17212 GGGAAGAGG
1 GGGAAGAGG
17221 GGGAAGAGG
1 GGGAAGAGG
17230 GGG
1 GGG
17233 GGAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (9 bp):
GGGAAGAGG
Found at i:18937 original size:2 final size:2
Alignment explanation
Indices: 18930--18955 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18920 CTAATTATCT
18930 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
18956 ATAATAATAA
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):
TA
Found at i:21368 original size:21 final size:21
Alignment explanation
Indices: 21326--21368 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21316 TTTCTGGGCT
*
21326 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
21347 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
21368 A
1 A
21369 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:21421 original size:20 final size:20
Alignment explanation
Indices: 21396--21433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21386 GAATGCTAGA
*
21396 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
21416 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
21434 TAATAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:22140 original size:103 final size:103
Alignment explanation
Indices: 21915--22132 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
21905 GTAGAGGGTC
* *
21915 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
21980 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
22018 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
22083 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
22121 TATGTGGTCCTT
1 TATGTGGTCCTT
22133 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:22183 original size:23 final size:23
Alignment explanation
Indices: 22149--22211 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
22139 ATTATTATAT
*
22149 GGCACTAC-GGTGCAATTCTACGC
1 GGCACT-CTGGTGCAATTCTAAGC
* *
22172 GGCACTCTGGTGTAATTCTAAGT
1 GGCACTCTGGTGCAATTCTAAGC
22195 GGCACT-TAGGTGCAATT
1 GGCACTCT-GGTGCAATT
22212 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 2 0.06
23 32 0.94
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTAAGC
Found at i:33107 original size:2 final size:2
Alignment explanation
Indices: 33100--33128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33090 TTATTCTTAA
33100 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
33129 AGGTAAAATT
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:33597 original size:2 final size:2
Alignment explanation
Indices: 33590--33616 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33580 TAGCTCAGAT
33590 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
33617 GAACCTGTTT
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:35979 original size:24 final size:23
Alignment explanation
Indices: 35952--36007 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
35942 TGATGTTCAA
*
35952 TATAAATTAACATTATATTTTTAT
1 TATAAATTAA-AATATATTTTTAT
* *
35976 TATAAACTAAAATATTTTTTTAT
1 TATAAATTAAAATATATTTTTAT
35999 TATGAAATT
1 TAT-AAATT
36008 TTTTATCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (23 bp):
TATAAATTAAAATATATTTTTAT
Found at i:40174 original size:2 final size:2
Alignment explanation
Indices: 40167--40195 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40157 TTATTTTTAA
40167 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
40196 AGGTAAAATT
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:40664 original size:2 final size:2
Alignment explanation
Indices: 40657--40693 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40647 TAGCTCAGAT
40657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40694 GAACCTGTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45001 original size:36 final size:36
Alignment explanation
Indices: 44961--45033 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
44951 TGGCGTCTTG
44961 AAAATGGTTTGCAATAGCATTAACACCCCACCACCT
1 AAAATGGTTTGCAATAGCATTAACACCCCACCACCT
44997 AAAATGGTTTGCAATAGCATTAACACCCCACCACCT
1 AAAATGGTTTGCAATAGCATTAACACCCCACCACCT
45033 A
1 A
45034 CCGCAAGCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (36 bp):
AAAATGGTTTGCAATAGCATTAACACCCCACCACCT
Found at i:61711 original size:13 final size:13
Alignment explanation
Indices: 61690--61748 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
61680 ATTTTGTTAG
61690 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
61703 TATTGTA-TTATT
1 TATTTTATTTAAT
* *
61715 TAATTTAATT-AT
1 TATTTTATTTAAT
61727 T-TTTTATTTAAT
1 TATTTTATTTAAT
61739 TATTTTATTT
1 TATTTTATTT
61749 TTTTTGCAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
11 6 0.17
12 14 0.39
13 16 0.44
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:61727 original size:16 final size:16
Alignment explanation
Indices: 61694--61742 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
61684 TGTTAGTATT
*
61694 TTATTTAA-TTATTGTA
1 TTATTTAATTTAAT-TA
61710 TTATTTAATTTAATTA
1 TTATTTAATTTAATTA
*
61726 TT-TTTTATTTAATTA
1 TTATTTAATTTAATTA
61741 TT
1 TT
61743 TTATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 14 0.47
16 12 0.40
17 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTTAATTTAATTA
Found at i:61751 original size:20 final size:20
Alignment explanation
Indices: 61690--61739 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 20
61680 ATTTTGTTAG
* *
61690 TATTTTATTTAATTATTGTAT
1 TATTTAATTTAATTATT-TTT
61711 TATTTAATTTAATTATTTTT
1 TATTTAATTTAATTATTTTT
61731 TATTTAATT
1 TATTTAATT
61740 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTTAATTTAATTATTTTT
Found at i:62035 original size:28 final size:28
Alignment explanation
Indices: 62003--62066 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
61993 ATAACTGCAA
*
62003 AAAAATA-AAAATAATTAAATAAAATAAT
1 AAAAATATAAAATAATAAAAT-AAATAAT
* *
62031 AAAAA-ATTAAATAATAAAATAATTAAT
1 AAAAATATAAAATAATAAAATAAATAAT
62058 ACAAAATAT
1 A-AAAATAT
62067 GATTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 8 0.27
28 20 0.67
29 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAATATAAAATAATAAAATAAATAAT
Found at i:82841 original size:112 final size:113
Alignment explanation
Indices: 82625--82847 Score: 310
Period size: 112 Copynumber: 2.0 Consensus size: 113
82615 CGATTTCGGG
* *
82625 ACAATAATAGTGACGTTTTTTTTTGAAAAAAACGTCGCAATAGGTCCATCTATAGTGTGTTTATT
1 ACAATAATAGTGACG--TTTTTTTGAAAAAAACGTCACAATAGATCCATCTATAGTGTGTTTATT
* *
82690 AAAAAACACCACTATATATATATATTTGTTTGGGGCATTTTTGGGGCTGC
64 AAAAAACACCACTATATATATATATTTGTTTAGGCCATTTTTGGGGCTGC
* *
82740 ACAATAATAGTGGCG-TTTTTTGAAAAAAACGTCACAATAGATCCATCTATAGTGGTGTTTATTG
1 ACAATAATAGTGACGTTTTTTTGAAAAAAACGTCACAATAGATCCATCTATAGT-GTGTTTATTA
*
82804 AAAAACGCCA-T-TATATATATACTTT-TTTAAGGCCATTTTTGGGG
65 AAAAACACCACTATATATATATA-TTTGTTT-AGGCCATTTTTGGGG
82848 GTATGCTCAG
Statistics
Matches: 98, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
111 13 0.13
112 53 0.54
113 18 0.18
115 14 0.14
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (113 bp):
ACAATAATAGTGACGTTTTTTTGAAAAAAACGTCACAATAGATCCATCTATAGTGTGTTTATTAA
AAAACACCACTATATATATATATTTGTTTAGGCCATTTTTGGGGCTGC
Found at i:87557 original size:28 final size:30
Alignment explanation
Indices: 87526--87586 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 30
87516 AAATATTTAT
87526 AATTTAAA-ATACAAAA-A-AAATTTAAA-TA
1 AATTTAAATATA-AAAATATAAA-TTAAATTA
87554 AA-TTAAATATAAAAATATAAATTAAATTA
1 AATTTAAATATAAAAATATAAATTAAATTA
87583 AATT
1 AATT
87587 ACTAAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
27 9 0.32
28 11 0.39
29 7 0.25
30 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (30 bp):
AATTTAAATATAAAAATATAAATTAAATTA
Found at i:87579 original size:24 final size:25
Alignment explanation
Indices: 87541--87594 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
87531 AAAATACAAA
*
87541 AAAAATTTAAATAAATTAAA-TA-T
1 AAAAATATAAATAAATTAAATTACT
87564 AAAAATATAAATTAAATTAAATTACT
1 AAAAATATAAA-TAAATTAAATTACT
87590 AAAAA
1 AAAAA
87595 CTAAAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.37
24 9 0.33
25 2 0.07
26 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAATATAAATAAATTAAATTACT
Found at i:87828 original size:24 final size:24
Alignment explanation
Indices: 87795--87842 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
87785 AAGTCAATTG
87795 ATATATATTTATAATAAATTTTATTT
1 ATATAT-TTTA-AATAAATTTTATTT
*
87821 ATATATTTTAAATATATTTTAT
1 ATATATTTTAAATAAATTTTAT
87843 GTTAGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATATTTTAAATAAATTTTATTT
Found at i:87830 original size:13 final size:12
Alignment explanation
Indices: 87795--87842 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
87785 AAGTCAATTG
87795 ATATATATTTATA
1 ATATAT-TTTATA
* *
87808 ATAAATTTTATTT
1 ATATATTTTA-TA
87821 ATATATTTTA-A
1 ATATATTTTATA
87832 ATATATTTTAT
1 ATATATTTTAT
87843 GTTAGATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 10 0.34
12 4 0.14
13 15 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTTTATA
Found at i:88991 original size:24 final size:24
Alignment explanation
Indices: 88950--88995 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
88940 TCAATATTTG
*
88950 AAATTTAATTTAATTATAACATAA
1 AAATTTAATTGAATTATAACATAA
88974 AAATTTAATTCGAA-TATAACAT
1 AAATTTAATT-GAATTATAACAT
88996 TAAATATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATTTAATTGAATTATAACATAA
Found at i:89009 original size:32 final size:31
Alignment explanation
Indices: 88973--89034 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
88963 TTATAACATA
* *
88973 AAAATTTAATTCGAATATAACATTAAATATCT
1 AAAATGTAATTCAAATATAAC-TTAAATATCT
* *
89005 AAAATGTATTTCAAATATAACTTTAATATC
1 AAAATGTAATTCAAATATAACTTAAATATC
89035 GATGAAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAATGTAATTCAAATATAACTTAAATATCT
Found at i:92037 original size:12 final size:12
Alignment explanation
Indices: 92020--92045 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
92010 TTTTTCACTA
92020 TTGGAGTAAACG
1 TTGGAGTAAACG
92032 TTGGAGTAAACG
1 TTGGAGTAAACG
92044 TT
1 TT
92046 CTAGAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (12 bp):
TTGGAGTAAACG
Found at i:95014 original size:11 final size:11
Alignment explanation
Indices: 94998--95039 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
94988 GAATAAACAT
94998 TCTAGAATGAA
1 TCTAGAATGAA
* *
95009 TCTAGAAACG-T
1 TCTAG-AATGAA
95020 TCTAGAATGAA
1 TCTAGAATGAA
95031 TCTAGAATG
1 TCTAGAATG
95040 CTGATGCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (11 bp):
TCTAGAATGAA
Found at i:95022 original size:22 final size:22
Alignment explanation
Indices: 94992--95037 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
94982 ACGTTGGAAT
94992 AAACATTCTAGAATGAATCTAG
1 AAACATTCTAGAATGAATCTAG
*
95014 AAACGTTCTAGAATGAATCTAG
1 AAACATTCTAGAATGAATCTAG
95036 AA
1 AA
95038 TGCTGATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (22 bp):
AAACATTCTAGAATGAATCTAG
Found at i:102130 original size:3 final size:3
Alignment explanation
Indices: 102122--102153 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
102112 ACACAGTCAT
102122 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
102154 TGGCGGGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:103037 original size:116 final size:115
Alignment explanation
Indices: 102824--103062 Score: 320
Period size: 116 Copynumber: 2.1 Consensus size: 115
102814 TATATATAGA
* **
102824 CATGAATAAAAAAGCTCATGTATATACATTTAAGTATCTATTGCCACACCTCGCCTCACCGAGCA
1 CATGAATAAAAAAGCTCATGTATATACATATAAGTATCTAGAGCCACACCTCGCCTCACCGAGCA
* * *
102889 TCCCAATAAGTAGGCTTGAAACAAGTTATCTAAATCAACACCAAAACTCT
66 TCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACTCT
* *
102939 CATGAATACAAAAA-CTCAATGTATATACATATAAGTTTCTAGAGCCACACCTCGCCTCGCCTG-
1 CATGAATA-AAAAAGCTC-ATGTATATACATATAAGTATCTAGAGCCACACCTCGCCTCACC-GA
** * *
103002 GTGTCCCAACAAGTAGGCTCGAAACAAATTCTCTAAATCAACACCAAGACTCT
63 GCATCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACTCT
103055 CAATGAAT
1 C-ATGAAT
103063 TCAGTTTCAC
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
115 11 0.10
116 90 0.83
117 7 0.06
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (115 bp):
CATGAATAAAAAAGCTCATGTATATACATATAAGTATCTAGAGCCACACCTCGCCTCACCGAGCA
TCCCAACAAGTAGGCTCGAAACAAATTATCTAAATCAACACCAAAACTCT
Done.