Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002555.1 Hibiscus syriacus cultivar Beakdansim tig00005186_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: 118096
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:254 original size:23 final size:23
Alignment explanation
Indices: 211--254 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
201 CCTCAAATAC
211 AAAAGCAAAACCTAAAGTACACA
1 AAAAGCAAAACCTAAAGTACACA
234 AAAACGCATAAACC-AAA-TACA
1 AAAA-GCA-AAACCTAAAGTACA
255 AAAGTAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 8 0.42
24 6 0.32
25 5 0.26
ACGTcount: A:0.61, C:0.23, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAAGCAAAACCTAAAGTACACA
Found at i:1781 original size:2 final size:2
Alignment explanation
Indices: 1774--1798 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1764 CCTTCCTTTT
1774 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
1799 TTTAAATTTG
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:4489 original size:2 final size:2
Alignment explanation
Indices: 4482--4512 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4472 AATTATAAGC
4482 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 T
4513 GCTGTCAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14028 original size:75 final size:74
Alignment explanation
Indices: 13941--14131 Score: 247
Period size: 75 Copynumber: 2.5 Consensus size: 74
13931 CTTAATCGGT
* * * *
13941 TAAAATAAAATAGACGGTACCTATTATGTTAAACTACCTACCGGTTTGTTTGAAAGTTACTAATA
1 TAAAATAAAATAGACGCTACCTATTACGTTAAACTA-CTACCGGTTTATTTCAAAGTTACTAATA
14006 ATATAAACAG
65 ATATAAACAG
* * * ** *
14016 TAAAATAAAATAGGCGCTACCTATTACGTTAAAATATTCATTGGTTTATTTCAAGGTTACTAATA
1 TAAAATAAAATAGACGCTACCTATTACGTTAAACTACT-ACCGGTTTATTTCAAAGTTACTAATA
*
14081 ATGTAAACAG
65 ATATAAACAG
*
14091 TAAAATAAAATAGACACTACCTATTACGTTAAACTATCTAC
1 TAAAATAAAATAGACGCTACCTATTACGTTAAACTA-CTAC
14132 TCGACAATAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
74 1 0.01
75 96 0.98
76 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (74 bp):
TAAAATAAAATAGACGCTACCTATTACGTTAAACTACTACCGGTTTATTTCAAAGTTACTAATAA
TATAAACAG
Found at i:18965 original size:17 final size:17
Alignment explanation
Indices: 18943--18981 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
18933 TTATCAACAA
18943 AAAATATAAAA-ATATTT
1 AAAATATAAAATA-ATTT
*
18960 AAAATATACAATAATTT
1 AAAATATAAAATAATTT
18977 AAAAT
1 AAAAT
18982 TTTATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATAAAATAATTT
Found at i:21117 original size:130 final size:131
Alignment explanation
Indices: 20883--21134 Score: 418
Period size: 130 Copynumber: 1.9 Consensus size: 131
20873 TCGCTCCCCA
20883 AATTTTGGTTCATTGCAGAAGCTTGTGAATGCCCTTTGGGGGGAAGATGGGGGAGGTTGAAGAGA
1 AATTTTGGTTCATTGCAGAAGCTTGTGAATGCCCTTTGGGGGGAAGATGGGGGAGGTTGAAGAGA
20948 AAATAGCTAGTGATAATCTTTTTGTTTTCCAATTTCTTAATGATACAACTAGGGATTAGGTTCTC
66 AAATAGCTAGTGATAATCTTTTTGTTTTCCAATTTCTTAATGATACAACTAGGGATTAGGTTCTC
21013 G
131 G
* * *
21014 AATTTTGGTTCGTTGTAGAAGCTTGTGAATGCCCTTT-GGGGGAAGAT-GGGGAGGTTGAAGTGA
1 AATTTTGGTTCATTGCAGAAGCTTGTGAATGCCCTTTGGGGGGAAGATGGGGGAGGTTGAAGAGA
** * *
21077 AGAATATTTGGTGATAATCTTTTTGTTTTCCAATTTCTTAATGATACAGCTAGGGATT
66 A-AATAGCTAGTGATAATCTTTTTGTTTTCCAATTTCTTAATGATACAACTAGGGATT
21135 GGGTCCTTGA
Statistics
Matches: 113, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
129 16 0.14
130 62 0.55
131 35 0.31
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (131 bp):
AATTTTGGTTCATTGCAGAAGCTTGTGAATGCCCTTTGGGGGGAAGATGGGGGAGGTTGAAGAGA
AAATAGCTAGTGATAATCTTTTTGTTTTCCAATTTCTTAATGATACAACTAGGGATTAGGTTCTC
G
Found at i:22940 original size:17 final size:17
Alignment explanation
Indices: 22918--22951 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22908 GAAATTCAAA
22918 GTGTTAGAAACGAATTT
1 GTGTTAGAAACGAATTT
22935 GTGTTAGAAACGAATTT
1 GTGTTAGAAACGAATTT
22952 AGAACATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (17 bp):
GTGTTAGAAACGAATTT
Found at i:25562 original size:2 final size:2
Alignment explanation
Indices: 25555--25580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25545 ACTGGAAAGA
25555 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
25581 GAATGGTTCG
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:29063 original size:21 final size:21
Alignment explanation
Indices: 29037--29081 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29027 GATTTCTGGG
* *
29037 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
29058 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
29079 CAA
1 CAA
29082 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:29549 original size:20 final size:22
Alignment explanation
Indices: 29509--29565 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
29499 TGAATGTGTG
*
29509 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
29531 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
29551 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
29566 TATGAATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:30133 original size:31 final size:31
Alignment explanation
Indices: 30095--30250 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
30085 AGGGTCGAGG
30095 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
30126 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
30157 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
30188 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
30219 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
30250 G
1 G
30251 GTCCTTCGGG
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 120 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:33416 original size:21 final size:21
Alignment explanation
Indices: 33379--33423 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33369 GATTTCTGGG
*
33379 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
33400 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
33421 CAA
1 CAA
33424 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:33888 original size:20 final size:22
Alignment explanation
Indices: 33848--33904 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
33838 TGAATGTGTG
*
33848 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
33870 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
33890 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
33905 TATGAATAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:34472 original size:31 final size:31
Alignment explanation
Indices: 34434--34589 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
34424 AGGGTCGAGG
*
34434 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
34465 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
34496 GTTTATCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
34527 GATTACCTAGGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
34558 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
34589 G
1 G
34590 GTCCTTCGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:36423 original size:15 final size:16
Alignment explanation
Indices: 36403--36433 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
36393 ATCTATCAAC
36403 TTCC-TTTTTTTGTTT
1 TTCCTTTTTTTTGTTT
36418 TTCCTTTTTTTTGTTT
1 TTCCTTTTTTTTGTTT
36434 CGAAGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (16 bp):
TTCCTTTTTTTTGTTT
Found at i:36874 original size:3 final size:3
Alignment explanation
Indices: 36866--36909 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
36856 TTTGGGTTTG
* **
36866 TAA TAA TAA T-A TAA TAA TAA TAT TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36910 AATTTATGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:36908 original size:24 final size:23
Alignment explanation
Indices: 36869--36914 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
36859 GGGTTTGTAA
*
36869 TAATAATATAATAATAATATTTT
1 TAATAATATAATAATAAAATTTT
36892 TAATAATAATAATAATAAAATTT
1 TAATAAT-ATAATAATAAAATTT
36915 ATGGGTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAATATAATAATAAAATTTT
Found at i:37684 original size:21 final size:21
Alignment explanation
Indices: 37658--37739 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
37648 GCCATATAGA
*
37658 ATGTCCCGAAGGACCACATAT
1 ATGTCCCGAAGGACCTCATAT
* ** *
37679 ATGTCCCGAAGAACCTTGTAGA
1 ATGTCCCGAAGGACCTCATA-T
* *
37701 ATTGTCTCGAATGACCTCATAT
1 A-TGTCCCGAAGGACCTCATAT
37723 ATGTCCCGAAGGACCTC
1 ATGTCCCGAAGGACCTC
37740 GTAGAACCCT
Statistics
Matches: 46, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
21 30 0.65
22 2 0.04
23 14 0.30
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
ATGTCCCGAAGGACCTCATAT
Found at i:37723 original size:44 final size:43
Alignment explanation
Indices: 37654--37745 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 43
37644 GAGTGCCATA
*
37654 TAGAATGTCCCGAAGGACCACATATATGTCCCGAAGAACCTTG
1 TAGAATGTCCCGAAGGACCACATATATGTCCCGAAGAACCTCG
* * * *
37697 TAGAATTGTCTCGAATGACCTCATATATGTCCCGAAGGACCTCG
1 TAGAA-TGTCCCGAAGGACCACATATATGTCCCGAAGAACCTCG
37741 TAGAA
1 TAGAA
37746 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 5 0.12
44 38 0.88
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (43 bp):
TAGAATGTCCCGAAGGACCACATATATGTCCCGAAGAACCTCG
Found at i:42992 original size:61 final size:61
Alignment explanation
Indices: 42893--43023 Score: 165
Period size: 61 Copynumber: 2.1 Consensus size: 61
42883 GTAGTGCTAA
* * * *
42893 ACCTACACTAACCTTACGCTCTAGTGCTAATCCAGATATGATACGTAGGGTTGTACCCACC
1 ACCTACACTAACCTTACACTCTAGTGCTAATCCAGATATGACACATAAGGTTGTACCCACC
* * ** *
42954 ACCTACACTAGA-TTTACACTCTAGTGCTAATCCGGATATGACACATAAGGTTGTGTCCTCC
1 ACCTACACTA-ACCTTACACTCTAGTGCTAATCCAGATATGACACATAAGGTTGTACCCACC
43015 ACCTACACT
1 ACCTACACT
43024 TAGTGTCCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
61 59 0.98
62 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (61 bp):
ACCTACACTAACCTTACACTCTAGTGCTAATCCAGATATGACACATAAGGTTGTACCCACC
Found at i:48229 original size:37 final size:37
Alignment explanation
Indices: 48158--48230 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
48148 AATTACCCCT
* * * *
48158 AACTAGGTACAACTAGGGTTGTTTGGTTATAGTGGCG
1 AACTAGGTACAACTAGGATTGTTTGATCACAGTGGCG
*
48195 AACTAGGTATAACTAGGATTGTTTGATCACAGTGGC
1 AACTAGGTACAACTAGGATTGTTTGATCACAGTGGC
48231 AGATGAAAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (37 bp):
AACTAGGTACAACTAGGATTGTTTGATCACAGTGGCG
Found at i:53072 original size:23 final size:24
Alignment explanation
Indices: 53037--53108 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 24
53027 CCACTAGGGG
*
53037 CTATGAATTTGTCCCGAATGAACA
1 CTATGAATATGTCCCGAATGAACA
*
53061 CTATGAA-ATGTCCCGAATGACCA
1 CTATGAATATGTCCCGAATGAACA
53084 CTAT--ATA--TCCCGAATG-AC-
1 CTATGAATATGTCCCGAATGAACA
53102 CTATGAA
1 CTATGAA
53109 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.10
19 1 0.02
20 10 0.24
21 1 0.02
22 1 0.02
23 18 0.43
24 7 0.17
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (24 bp):
CTATGAATATGTCCCGAATGAACA
Found at i:53983 original size:12 final size:12
Alignment explanation
Indices: 53966--53993 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
53956 TCCTTTCTAA
53966 CTTCATTCAATT
1 CTTCATTCAATT
53978 CTTCATTCAATT
1 CTTCATTCAATT
53990 CTTC
1 CTTC
53994 TATTTTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (12 bp):
CTTCATTCAATT
Found at i:54690 original size:14 final size:14
Alignment explanation
Indices: 54671--54707 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
54661 AATTTTCACT
54671 GAACATATCAATAA
1 GAACATATCAATAA
54685 GAACATATCAATAA
1 GAACATATCAATAA
54699 GAACATATC
1 GAACATATC
54708 TTCTAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.16, G:0.08, T:0.22
Consensus pattern (14 bp):
GAACATATCAATAA
Found at i:57946 original size:64 final size:64
Alignment explanation
Indices: 57859--58000 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 64
57849 TCTTTAACAT
** * * *
57859 GTGCATCGATGCACTACTCATGCATTGATACACAAATCACCTTCGATGTTT-TTATTTTAAGGG
1 GTGCATCGATGCACTACTCATGCATCAATACACAAATCACATTCGATGTTTCTTATTTTAAAGA
* * * * ** *
57922 GATGCATCGATGCACTCCTTATGCATCAATGCACCAATTGCATTCGATGTTTCTTCTTTTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCAATACACAAATCACATTCGATGTTTCTTATTTTAAAGA
57987 GTGCATCGATGCAC
1 GTGCATCGATGCAC
58001 ATTCAATGTG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
63 1 0.02
64 54 0.83
65 10 0.15
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACTCATGCATCAATACACAAATCACATTCGATGTTTCTTATTTTAAAGA
Found at i:61122 original size:11 final size:11
Alignment explanation
Indices: 61106--61136 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61096 TGTATTAGCA
61106 TCAATCTGAAC
1 TCAATCTGAAC
61117 TCAATCTGAAC
1 TCAATCTGAAC
*
61128 TGAATCTGA
1 TCAATCTGA
61137 TATCAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (11 bp):
TCAATCTGAAC
Found at i:63903 original size:19 final size:19
Alignment explanation
Indices: 63879--63990 Score: 190
Period size: 19 Copynumber: 5.9 Consensus size: 19
63869 ATAGAATGAG
*
63879 TTGGAA-AGGCATTGGCAAC
1 TTGGAATAGGCA-TAGCAAC
63898 TTGGAATAGGCATAGCAAC
1 TTGGAATAGGCATAGCAAC
*
63917 TTGGAATAGGCATGGCAAC
1 TTGGAATAGGCATAGCAAC
63936 TTGGAATAGGCATAGCAAC
1 TTGGAATAGGCATAGCAAC
63955 TTGGAATAGGCATAGCAAC
1 TTGGAATAGGCATAGCAAC
63974 TTGGAATAGGCATAGCA
1 TTGGAATAGGCATAGCA
63991 TGTATCTTAT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
19 84 0.94
20 5 0.06
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (19 bp):
TTGGAATAGGCATAGCAAC
Found at i:66269 original size:33 final size:33
Alignment explanation
Indices: 66227--66317 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
66217 GTCGTTGGGG
66227 AAGTTTTTAAGTATTTGAATTTATCGAACTTGA
1 AAGTTTTTAAGTATTTGAATTTATCGAACTTGA
*
66260 AAGTTTTTAAGTATTTGAATTTATCGAACTTGG
1 AAGTTTTTAAGTATTTGAATTTATCGAACTTGA
* *
66293 AAGTATTTAAGTATTTCAA-TTATCG
1 AAGTTTTTAAGTATTTGAATTTATCG
66318 TAAACTTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.11
33 49 0.89
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
AAGTTTTTAAGTATTTGAATTTATCGAACTTGA
Found at i:76456 original size:14 final size:14
Alignment explanation
Indices: 76432--76464 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
76422 TATTAATCAA
76432 TTATA-ATATTTGT
1 TTATATATATTTGT
*
76445 TTATATATATTTTT
1 TTATATATATTTGT
76459 TTATAT
1 TTATAT
76465 TTTCACAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (14 bp):
TTATATATATTTGT
Found at i:79289 original size:12 final size:12
Alignment explanation
Indices: 79254--79282 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
79244 TCCATGTGGC
79254 ATTTACATGTTA
1 ATTTACATGTTA
79266 ATTTACATGTTA
1 ATTTACATGTTA
79278 ATTTA
1 ATTTA
79283 TGTGTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (12 bp):
ATTTACATGTTA
Found at i:80571 original size:2 final size:2
Alignment explanation
Indices: 80564--80607 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
80554 TTATTATTTC
80564 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80606 AT
1 AT
80608 TTACTATCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80636 original size:11 final size:11
Alignment explanation
Indices: 80620--80644 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80610 ACTATCATTT
80620 TTTCTATTTTA
1 TTTCTATTTTA
80631 TTTCTATTTTA
1 TTTCTATTTTA
80642 TTT
1 TTT
80645 TGTTGGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTATTTTA
Found at i:80711 original size:21 final size:22
Alignment explanation
Indices: 80651--80722 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 22
80641 ATTTTGTTGG
* *
80651 TTTGTATTTATTTATT-TATTG
1 TTTGTATTTATTTATTATTTTC
80672 TTTGTATATTA-TTATTATTTTC
1 TTTGTAT-TTATTTATTATTTTC
80694 TTTGT-TTTATTTATTATTTTC
1 TTTGTATTTATTTATTATTTTC
*
80715 CTT-TATTT
1 TTTGTATTT
80723 TTACTTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.09
21 29 0.66
22 11 0.25
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.72
Consensus pattern (22 bp):
TTTGTATTTATTTATTATTTTC
Found at i:80732 original size:22 final size:21
Alignment explanation
Indices: 80683--80742 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
80673 TTGTATATTA
*
80683 TTATTATTTTCTTTGTTTTAT
1 TTATTATTTTCTTTGTTTTAC
*
80704 TTATTATTTTCCTTTATTTTTAC
1 TTATTATTTT-CTTT-GTTTTAC
80727 TT-TTA-TTTCTTT-TTTT
1 TTATTATTTTCTTTGTTTT
80743 CTCTTTATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 4 0.11
20 4 0.11
21 13 0.37
22 7 0.20
23 7 0.20
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (21 bp):
TTATTATTTTCTTTGTTTTAC
Found at i:80733 original size:29 final size:29
Alignment explanation
Indices: 80698--80825 Score: 86
Period size: 29 Copynumber: 4.4 Consensus size: 29
80688 ATTTTCTTTG
80698 TTTTATTTATTATTTTC-CTTTATTTTTA
1 TTTTATTTATTATTTTCTCTTTATTTTTA
* * **
80726 CTTTTATTTCTTTTTTTCTCTTTATCGTTA
1 -TTTTATTTATTATTTTCTCTTTATTTTTA
* * *
80756 TTTTACTTATTTTATTTACTTTTTATATCTTTA
1 TTTTA-TT-TATTATTTTCTCTTTAT-T-TTTA
* *
80789 CTTTATCTT-TT-TATT-TCTTTA-TTTTA
1 TTTTAT-TTATTATTTTCTCTTTATTTTTA
80815 TTTTATTTATT
1 TTTTATTTATT
80826 TCATTAGTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
25 2 0.03
26 11 0.14
27 1 0.01
29 25 0.32
30 13 0.17
31 15 0.19
32 2 0.03
33 8 0.10
ACGTcount: A:0.16, C:0.10, G:0.01, T:0.73
Consensus pattern (29 bp):
TTTTATTTATTATTTTCTCTTTATTTTTA
Found at i:80814 original size:21 final size:21
Alignment explanation
Indices: 80766--80859 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
80756 TTTTACTTAT
*
80766 TTTA-TTTA-CTTTTTATATC
1 TTTATTTTATCTTTTTATTTC
*
80785 TTTACTTTATCTTTTTATTTC
1 TTTATTTTATCTTTTTATTTC
*
80806 TTTATTTTATTTTATTTATTTC
1 TTTATTTTATCTT-TTTATTTC
*
80828 ATTAGTTTT-T-TATTTTATTTTC
1 TTTA-TTTTATCT-TTTTA-TTTC
*
80850 TCTATTTTAT
1 TTTATTTTAT
80860 TTATTTTCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
19 4 0.06
20 4 0.06
21 30 0.48
22 20 0.32
23 4 0.06
ACGTcount: A:0.18, C:0.09, G:0.01, T:0.72
Consensus pattern (21 bp):
TTTATTTTATCTTTTTATTTC
Found at i:85084 original size:29 final size:29
Alignment explanation
Indices: 85042--85122 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
85032 TTCCATATGT
85042 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
85070 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
85099 TCATGTAGCTCATGTCATATTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
85123 ATATCACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:85604 original size:64 final size:64
Alignment explanation
Indices: 85536--85661 Score: 150
Period size: 64 Copynumber: 2.0 Consensus size: 64
85526 GTGTATAAAA
* * * *
85536 TGCATTCAATG-TTTTATTATT-AATGGGATGCATCGATGCA-TGCCTTATGCATCGATGCACTA
1 TGCATTCAATGTTTTTATT-TTAAAAGAG-TGCATCGATGCACT-ACATATGCATCGATGCACTA
85598 AT
63 AT
* *
85600 TGCATTCGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACATGTGCATCGATGCACTA
1 TGCATTCAATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACATATGCATCGATGCACTA
85662 CCTGTGCATC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
64 41 0.77
65 12 0.23
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (64 bp):
TGCATTCAATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACATATGCATCGATGCACTAAT
Found at i:85651 original size:19 final size:19
Alignment explanation
Indices: 85627--85671 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
85617 TTTTAAAAGA
85627 GTGCATCGATGCACTACAT
1 GTGCATCGATGCACTACAT
*
85646 GTGCATCGATGCACTACCT
1 GTGCATCGATGCACTACAT
85665 GTGCATC
1 GTGCATC
85672 AATACACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCACTACAT
Found at i:103878 original size:15 final size:15
Alignment explanation
Indices: 103854--103887 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
103844 TCGTAGGACC
103854 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
103869 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
103884 ACTA
1 ACTA
103888 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:104462 original size:64 final size:63
Alignment explanation
Indices: 104393--104549 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 63
104383 TAATGAAGGT
* **
104393 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
104456 G
63 G
* * *
104457 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
*
104520 AGTGCATCGATGCACTACATGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
104550 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 67 0.85
65 9 0.11
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:106128 original size:99 final size:99
Alignment explanation
Indices: 105950--106146 Score: 297
Period size: 99 Copynumber: 2.0 Consensus size: 99
105940 ATATTTTATA
* *
105950 TATACAATAAAGCTTGAGTTATCCATATAGAGAAATTGGTTAAACGCCCCAACTTTATGGATAAG
1 TATACAATAAAGCTTGAATCATCCATATAGAGAAATTGGTTAAACGCCCCAACTTTATGGATAAG
* * *
106015 ATTCAGCTAGCCTGATAAAGTTGATTATAATATC
66 ATTCAACTAACCTGATAAAGGTGATTATAATATC
* * **
106049 TATACAATAAAGCTTGAATCATCCCA-CTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 TATACAATAAAGCTTGAATCAT-CCATATAGAGAAATTGGTTAAACGCCCCAACTTTATGGATAA
106113 GATTCAACTAACCTGATAAAGGTGATTATAATAT
65 GATTCAACTAACCTGATAAAGGTGATTATAATAT
106147 TGAGATGTCC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 85 0.97
100 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (99 bp):
TATACAATAAAGCTTGAATCATCCATATAGAGAAATTGGTTAAACGCCCCAACTTTATGGATAAG
ATTCAACTAACCTGATAAAGGTGATTATAATATC
Found at i:107292 original size:147 final size:146
Alignment explanation
Indices: 107060--107520 Score: 692
Period size: 145 Copynumber: 3.2 Consensus size: 146
107050 GATGGTGGTT
* * * *
107060 GCTCAACTTCACAACGAATGAGTGTCTGTCAATAACAACTTTCCAGTTTCATTCAGAGTCAATTT
1 GCTCAACTTCACAGCGAAGGAGCGTCTGTCAAAAACAACTTTCCAGTTTCATTCAGAGTCAATTT
* * * *
107125 CAACTTCACGGTGAAGGATATTGAACTCGAAACAACACAAGATTGGATTTCAACTTCACAACGAA
66 CAACTTCACGGCGAATGATATTGGACTCGAAACAACACAAGATTGGATTTTAACTTCACAACGAA
*
107190 TGATATGCAATTCAAA
131 TGATATCCAATTCAAA
* *
107206 GCTCAACTTCACAGTGAAGGAGCGTCTGTCAACAAATAACTTTCCAGTTTCATTCAGAGTCAATT
1 GCTCAACTTCACAGCGAAGGAGCGTCTGTCAA-AAACAACTTTCCAGTTTCATTCAGAGTCAATT
* *
107271 TCAACTTCACGGCGAATGATATTGGAGTCGAAACAACACAAGATTGGATTTTAACTT--CAACTA
65 TCAACTTCACGGCGAATGATATTGGACTCGAAACAACACAAGATTGGATTTTAACTTCACAACGA
*
107334 ATGAAATCCAATTCAAA
130 ATGATATCCAATTCAAA
*
107351 GCTCAACTTCACAGCGAAGGAGCGTCTGACAATAAACAACTTTCCAGTTTCATTCAGAGTCAATT
1 GCTCAACTTCACAGCGAAGGAGCGTCTGTCAA-AAACAACTTTCCAGTTTCATTCAGAGTCAATT
* * * *
107416 TCAAATTCACAGCGAATGATATTGGACTCGAAACAACGCAAGATTGGATTTTAACATCACAACGA
65 TCAACTTCACGGCGAATGATATTGGACTCGAAACAACACAAGATTGGATTTTAACTTCACAACGA
*
107481 ATGATATCCAATTTAAA
130 ATGATATCCAATTCAAA
* *
107498 GCTCAACTTCACAACGAATGAGC
1 GCTCAACTTCACAGCGAAGGAGC
107521 CATTCACGAT
Statistics
Matches: 284, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
145 133 0.47
146 28 0.10
147 123 0.43
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (146 bp):
GCTCAACTTCACAGCGAAGGAGCGTCTGTCAAAAACAACTTTCCAGTTTCATTCAGAGTCAATTT
CAACTTCACGGCGAATGATATTGGACTCGAAACAACACAAGATTGGATTTTAACTTCACAACGAA
TGATATCCAATTCAAA
Found at i:107685 original size:65 final size:63
Alignment explanation
Indices: 107574--107748 Score: 221
Period size: 65 Copynumber: 2.8 Consensus size: 63
107564 AGCAGCAATA
* *
107574 TACTCGAGATTGGATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAAC
1 TACTC-AGATTGGATTTCAACTTCACAACGAATGATATCTAACTCAAAGCCAATTTGGTAAAAC
* * * *
107638 TTACTCAAGATTGGATTTCAACTTCACGACGAAGGATATCTAGCTCAAAACCAATTTGGTAAAAC
1 -TACTC-AGATTGGATTTCAACTTCACAACGAATGATATCTAACTCAAAGCCAATTTGGTAAAAC
* * *
107703 AATTC---TTGGATTTCAACTTCACAACGAATGATATCTAATTCAAAGC
1 TACTCAGATTGGATTTCAACTTCACAACGAATGATATCTAACTCAAAGC
107749 TCAACTTCAC
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
60 36 0.38
64 3 0.03
65 57 0.59
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (63 bp):
TACTCAGATTGGATTTCAACTTCACAACGAATGATATCTAACTCAAAGCCAATTTGGTAAAAC
Found at i:108124 original size:85 final size:85
Alignment explanation
Indices: 107886--108224 Score: 455
Period size: 85 Copynumber: 4.0 Consensus size: 85
107876 TGCAGTAAAA
* * * * *
107886 CTCAAGGAGAGAAGGGTTATCTGTCATCAAATACCTTCAAGTTCGATTGCACTCAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGC
* *
107951 ACATCAAATTTACAGCATAG
66 ATATCAAATTTACAACATAG
* * *
107971 CTCAAGGCGAGAATGGTTATCTGTTAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGG
1 CTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGG
108036 CATATCAAATTTACAACATAG
65 CATATCAAATTTACAACATAG
* * *
108057 CTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCAAGTTCGATTACATTCAACTCAAAGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGC
* * *
108122 ATATCCAATTTACAGCATAA
66 ATATCAAATTTACAACATAG
* * * * *
108142 CTCAAGGCGAGAAGGATTATCTATCAGCAAA-ACCTTCGAGTTCGATTACATTCAGCTCAAGGGC
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGC
* *
108206 ATGTCAAATTCACAACATA
66 ATATCAAATTTACAACATA
108225 ACTTAAGTTG
Statistics
Matches: 222, Mismatches: 31, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
84 45 0.20
85 101 0.45
86 76 0.34
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (85 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACATTCAGCTCAAAGGC
ATATCAAATTTACAACATAG
Found at i:110157 original size:15 final size:15
Alignment explanation
Indices: 110121--110158 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
110111 ATTATTCTTA
110121 TTATTATTTCTTTCT
1 TTATTATTTCTTTCT
*
110136 TTCTTATTTCTGTT-T
1 TTATTATTTCT-TTCT
110151 TTATTATT
1 TTATTATT
110159 ATTATTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.74
Consensus pattern (15 bp):
TTATTATTTCTTTCT
Found at i:110223 original size:11 final size:11
Alignment explanation
Indices: 110190--110227 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
110180 ATTTACTATC
*
110190 ATTTT-TTTCT
1 ATTTTATTTTT
110200 ATTTTATTTTTT
1 ATTTTA-TTTTT
110212 ATTTTATTTTT
1 ATTTTATTTTT
110223 ATTTT
1 ATTTT
110228 TTGGTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 10 0.40
12 10 0.40
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:110224 original size:18 final size:18
Alignment explanation
Indices: 110201--110292 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 18
110191 TTTTTTTCTA
110201 TTTTATTTTTTATTTTAT
1 TTTTATTTTTTATTTTAT
*
110219 TTTTATTTTTTGGTTTGTATT
1 TTTTATTTTTT-ATTT-TA-T
110240 TATTTATTTATTGTATTATTAT
1 T-TTTATTT-TT-TATT-TTAT
* *
110262 TATTATTTTCTTTGTTTTAT
1 TTTTA-TTT-TTTATTTTAT
110282 TTATTATTTTT
1 TT-TTATTTTT
110293 CCTTTATCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
18 11 0.19
19 5 0.08
20 10 0.17
21 11 0.19
22 14 0.24
23 6 0.10
24 2 0.03
ACGTcount: A:0.17, C:0.01, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTATTTTTTATTTTAT
Found at i:110276 original size:23 final size:23
Alignment explanation
Indices: 110250--110297 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
110240 TATTTATTTA
*
110250 TTGTATTA-TTATTATTATTTTCT
1 TTGTATTATTTATTATT-TTTCCT
*
110273 TTGTTTTATTTATTATTTTTCCT
1 TTGTATTATTTATTATTTTTCCT
110296 TT
1 TT
110298 ATCTTTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (23 bp):
TTGTATTATTTATTATTTTTCCT
Found at i:110304 original size:24 final size:23
Alignment explanation
Indices: 110258--110313 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
110248 TATTGTATTA
* * *
110258 TTATTATTATTTTCTTTGTTTTAT
1 TTATTATT-TTTCCTTTATTTTAC
110282 TTATTATTTTTCCTTTATCTTTAC
1 TTATTATTTTTCCTTTAT-TTTAC
110306 TT-TTATTT
1 TTATTATTT
110314 CTTTTATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (23 bp):
TTATTATTTTTCCTTTATTTTAC
Found at i:110351 original size:14 final size:14
Alignment explanation
Indices: 110332--110440 Score: 57
Period size: 14 Copynumber: 7.4 Consensus size: 14
110322 CTCATTATCG
110332 TTATTTTACTTATT
1 TTATTTTACTTATT
110346 TTA-TTTACTT-TT
1 TTATTTTACTTATT
110358 TTATCTTTACTTTATCT
1 TTAT-TTTAC-TTAT-T
*
110375 TT-TTATTTCGTTATT
1 TTATT-TTAC-TTATT
110390 TTATTTT-CTTTATT
1 TTATTTTAC-TTATT
* **
110404 TCATTCGTTTTTTTATT
1 TTA-T--TTTACTTATT
110421 TTATTTT-CTCTATT
1 TTATTTTACT-TATT
110435 TTATTT
1 TTATTT
110441 ATTTTCATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
12 5 0.07
13 8 0.11
14 29 0.38
15 9 0.12
16 12 0.16
17 13 0.17
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (14 bp):
TTATTTTACTTATT
Found at i:110443 original size:18 final size:18
Alignment explanation
Indices: 110414--110459 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
110404 TCATTCGTTT
110414 TTTTATTTTATTTTC-TCTA
1 TTTTA-TTTATTTTCAT-TA
110433 TTTTATTTATTTTCATTA
1 TTTTATTTATTTTCATTA
110451 TTTT-TTTAT
1 TTTTATTTAT
110460 GTAACCCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 15 0.58
19 6 0.23
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTATTTTCATTA
Done.