Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001263.1 Hibiscus syriacus cultivar Beakdansim tig00002481_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: 77374
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:214 original size:13 final size:14
Alignment explanation
Indices: 196--224 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
186 CAATTATGGA
196 TTTTCTT-TCCTTT
1 TTTTCTTCTCCTTT
209 TTTTCTTCTCCTTT
1 TTTTCTTCTCCTTT
223 TT
1 TT
225 GAATAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTCTCCTTT
Found at i:598 original size:2 final size:2
Alignment explanation
Indices: 591--628 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
581 GTTTAAATTA
591 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
629 CTCAATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:776 original size:2 final size:2
Alignment explanation
Indices: 771--796 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
761 TTTCTAAATT
771 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
797 GTTAAAATAA
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:1968 original size:29 final size:31
Alignment explanation
Indices: 1904--1969 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
1894 ATGAATAGTG
*
1904 ATTTTAGTATTTTTAATATATATTCTTAATT
1 ATTTTAGTATATTTAATATATATTCTTAATT
* * *
1935 CTTTTAGTA-ATTTAATTTA-ATTTTTAATT
1 ATTTTAGTATATTTAATATATATTCTTAATT
1964 ATTTTA
1 ATTTTA
1970 TATTTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 14 0.47
30 8 0.27
31 8 0.27
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (31 bp):
ATTTTAGTATATTTAATATATATTCTTAATT
Found at i:1974 original size:22 final size:22
Alignment explanation
Indices: 1945--1998 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1935 CTTTTAGTAA
1945 TTTA-ATTTAATTTTTAATTAT
1 TTTATATTTAATTTTTAATTAT
*
1966 TTTATATTTATTTTTTAATTAT
1 TTTATATTTAATTTTTAATTAT
1988 TTTATATTTAA
1 TTTATATTTAA
1999 AATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATATTTAATTTTTAATTAT
Found at i:1978 original size:11 final size:11
Alignment explanation
Indices: 1945--1997 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
1935 CTTTTAGTAA
1945 TTTA-ATTTAAT
1 TTTATATTT-AT
*
1956 TTT-TAATTAT
1 TTTATATTTAT
1966 TTTATATTTAT
1 TTTATATTTAT
* *
1977 TTTTTAATTAT
1 TTTATATTTAT
1988 TTTATATTTA
1 TTTATATTTA
1998 AAATATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 5 0.15
11 29 0.85
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATATTTAT
Found at i:2083 original size:30 final size:29
Alignment explanation
Indices: 2019--2088 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
2009 TATTTTTTCT
*
2019 AAAAAATC-ATTAAGCTCTTGAACTATTT
1 AAAAAATCAATTAAGCTCTTGAACTATTC
2047 AAAAAATCAACTTAA-CTCTTGAACTCGA-TC
1 AAAAAATCAA-TTAAGCTCTTGAACT--ATTC
2077 AAAAAATCAATT
1 AAAAAATCAATT
2089 TAGCCCATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 8 0.22
29 13 0.35
30 15 0.41
31 1 0.03
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAAATCAATTAAGCTCTTGAACTATTC
Found at i:6794 original size:75 final size:72
Alignment explanation
Indices: 6673--6823 Score: 275
Period size: 75 Copynumber: 2.1 Consensus size: 72
6663 CTATATGCAC
6673 ATATGATTTAACTGAATTAGTACAGTATTTATCAAGATGAAAATTCTATATGAAACATAAATTAA
1 ATATGATTTAACTGAATTAGTACAGTATTTATCAAGATGAAAATTCTATATG-AACATAAATTAA
6738 TTACATTG
65 TTACATTG
6746 ATATGATTTAACTGAATTAGTATACAGTATTTATCAAGATGAAAATTCTATATGAACATAAATTA
1 ATATGATTTAACTGAATTAG--TACAGTATTTATCAAGATGAAAATTCTATATGAACATAAATTA
6811 ATTACATTG
64 ATTACATTG
6820 ATAT
1 ATAT
6824 CATATCTTAA
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
73 20 0.26
74 24 0.32
75 32 0.42
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (72 bp):
ATATGATTTAACTGAATTAGTACAGTATTTATCAAGATGAAAATTCTATATGAACATAAATTAAT
TACATTG
Found at i:10105 original size:16 final size:17
Alignment explanation
Indices: 10074--10110 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
10064 TAAAATGGTG
10074 TTAA-ATTATCTAGATT
1 TTAATATTATCTAGATT
10090 TTAATATTATCT-GATT
1 TTAATATTATCTAGATT
*
10106 ATAAT
1 TTAAT
10111 TTAAAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
TTAATATTATCTAGATT
Found at i:21917 original size:160 final size:157
Alignment explanation
Indices: 21651--21966 Score: 542
Period size: 160 Copynumber: 2.0 Consensus size: 157
21641 TTGCCTCTAG
*
21651 GTTTTTGAAAAGATAAAAGGACTAATTAAGACAAGCCGCGTTTCTACCACAGAACAATTAGCAGA
1 GTTTTTGAAAAGATAAAAGGACTAATTAAGACAAGCCACGTTTCTACCACAGAACAATTAGCAGA
* *
21716 CATCTTCATAGAGTCTCTGAGTGTGAAGCAGCACAAGTGTTTAATGTCCAAGTTAGGGGTTAGAG
66 CATCTTCATAGAGTCTCCGAGTGTGAAGCAGCACAAGTGTTTAATGTCCAAGTTAGGGGTTAGAA
21781 ATATATTTAAACCTCCAACTTAAGAGT
131 ATATATTTAAACCTCCAACTTAAGAGT
* *
21808 GTTTTTGAAAAGATACAAGAATGACTAATTAAGACAAGCCACGTTTCTACCCCAGAACAATTAGC
1 GTTTTTGAAAAGAT--AA-AAGGACTAATTAAGACAAGCCACGTTTCTACCACAGAACAATTAGC
**
21873 AGACATCTTCATAGAGTCTCCGAGTGTGAAGCAGCATGAGTGTTTAATGTCCAAGTTAGGGGTTA
63 AGACATCTTCATAGAGTCTCCGAGTGTGAAGCAGCACAAGTGTTTAATGTCCAAGTTAGGGGTTA
21938 GAAATATATTTAAACCTCCAACTTAAGAG
128 GAAATATATTTAAACCTCCAACTTAAGAG
21967 AGTGTTAAAA
Statistics
Matches: 149, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
157 14 0.09
159 2 0.01
160 133 0.89
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (157 bp):
GTTTTTGAAAAGATAAAAGGACTAATTAAGACAAGCCACGTTTCTACCACAGAACAATTAGCAGA
CATCTTCATAGAGTCTCCGAGTGTGAAGCAGCACAAGTGTTTAATGTCCAAGTTAGGGGTTAGAA
ATATATTTAAACCTCCAACTTAAGAGT
Found at i:28670 original size:18 final size:18
Alignment explanation
Indices: 28647--28682 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28637 ATTAAACAAC
28647 TGTGTTTAGTATTTTCAA
1 TGTGTTTAGTATTTTCAA
28665 TGTGTTTAGTATTTTCAA
1 TGTGTTTAGTATTTTCAA
28683 GAGAATGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (18 bp):
TGTGTTTAGTATTTTCAA
Found at i:29102 original size:3 final size:3
Alignment explanation
Indices: 29096--29187 Score: 94
Period size: 3 Copynumber: 29.0 Consensus size: 3
29086 CCTCCTCCTC
*
29096 CTT CTT CATT CTTT CTT CATG CTT CTT CTT CTT CTT CTT CTT CTT CTTT
1 CTT CTT C-TT C-TT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT C-TT
* * * *
29145 CTT CCT ATT CTT CTT CTTT CTT CCT ATT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT
29188 TCTTTATATA
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
3 60 0.81
4 14 0.19
ACGTcount: A:0.04, C:0.32, G:0.01, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:29132 original size:19 final size:19
Alignment explanation
Indices: 29097--29187 Score: 109
Period size: 19 Copynumber: 4.9 Consensus size: 19
29087 CTCCTCCTCC
29097 TTCTTCATTCTTTCTTC--A
1 TTCTTC-TTCTTTCTTCTTA
* *
29115 TGCTTCTTC-TTCTTCTTC
1 TTCTTCTTCTTTCTTCTTA
*
29133 TTCTTCTTCTTTCTTCCTA
1 TTCTTCTTCTTTCTTCTTA
*
29152 TTCTTCTTCTTTCTTCCTA
1 TTCTTCTTCTTTCTTCTTA
29171 TTCTTCTTC-TTCTTCTT
1 TTCTTCTTCTTTCTTCTT
29188 TCTTTATATA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
16 6 0.09
17 3 0.05
18 20 0.31
19 35 0.55
ACGTcount: A:0.04, C:0.31, G:0.01, T:0.64
Consensus pattern (19 bp):
TTCTTCTTCTTTCTTCTTA
Found at i:29188 original size:25 final size:24
Alignment explanation
Indices: 29121--29191 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 24
29111 TTCATGCTTC
29121 TTCTTCTTCTTCTTC-TTCTT-CT
1 TTCTTCTTCTTCTTCTTTCTTCCT
29143 TTCTTCCTATTCTTCTTCTTTCTTCCT
1 TTCTT-C--TTCTTCTTCTTTCTTCCT
29170 ATTCTTCTTCTTCTTCTTTCTT
1 -TTCTTCTTCTTCTTCTTTCTT
29192 TATATATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.12
23 1 0.02
25 24 0.56
26 5 0.12
27 3 0.07
28 5 0.12
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (24 bp):
TTCTTCTTCTTCTTCTTTCTTCCT
Found at i:35997 original size:30 final size:31
Alignment explanation
Indices: 35958--36045 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
35948 ATTTGATTCT
* *
35958 TGAACTTTAGATATAATAAT-ATTTTGA-CCC
1 TGAACTTTAGATAAAAT-ATCATTTTGATCAC
*
35988 TGAATTTTAGATAAAATATCATTTTGATCAC
1 TGAACTTTAGATAAAATATCATTTTGATCAC
* *
36019 TGAACTTTAGATAATATATCAATTTGA
1 TGAACTTTAGATAAAATATCATTTTGA
36046 CTAATTTAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.04
30 22 0.44
31 26 0.52
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (31 bp):
TGAACTTTAGATAAAATATCATTTTGATCAC
Found at i:39015 original size:14 final size:14
Alignment explanation
Indices: 38998--39025 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38988 ATCATAACAA
38998 AATTATATAACTAT
1 AATTATATAACTAT
39012 AATTATATAACTAT
1 AATTATATAACTAT
39026 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:41996 original size:13 final size:13
Alignment explanation
Indices: 41978--42002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41968 TCGAATATAC
41978 TTAGAAAATCTTT
1 TTAGAAAATCTTT
41991 TTAGAAAATCTT
1 TTAGAAAATCTT
42003 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:42173 original size:17 final size:17
Alignment explanation
Indices: 42151--42187 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42141 ACTTCTCCCC
42151 TTTAAAACATTTTAACA
1 TTTAAAACATTTTAACA
42168 TTTAAAACATTTTAACA
1 TTTAAAACATTTTAACA
42185 TTT
1 TTT
42188 CTCCCCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAAAACATTTTAACA
Found at i:44043 original size:21 final size:22
Alignment explanation
Indices: 44014--44067 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
44004 AGTGGGGGGT
*
44014 ATCGATTCCC-TC-AAGGACGGA
1 ATCGGTTCCCATCAAAGG-CGGA
*
44035 ATCGGTTCCCATTCAAAGGGGGA
1 ATCGGTTCCCA-TCAAAGGCGGA
44058 ATCGGTTCCC
1 ATCGGTTCCC
44068 CTTCAAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
23 15 0.54
24 4 0.14
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (22 bp):
ATCGGTTCCCATCAAAGGCGGA
Found at i:44078 original size:22 final size:23
Alignment explanation
Indices: 44032--44078 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
44022 CCTCAAGGAC
44032 GGAATCGGTTCCCATTCAAAGGG
1 GGAATCGGTTCCCATTCAAAGGG
*
44055 GGAATCGGTTCCCCTTC-AAGGG
1 GGAATCGGTTCCCATTCAAAGGG
44077 GG
1 GG
44079 TATCAATTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.21
Consensus pattern (23 bp):
GGAATCGGTTCCCATTCAAAGGG
Found at i:44088 original size:22 final size:23
Alignment explanation
Indices: 44040--44089 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
44030 ACGGAATCGG
**
44040 TTCCCATTCAAAGGGGGAATCGG
1 TTCCCATTCAAAGGGGGAATCAA
* *
44063 TTCCCCTTC-AAGGGGGTATCAA
1 TTCCCATTCAAAGGGGGAATCAA
44085 TTCCC
1 TTCCC
44090 TCTGTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
TTCCCATTCAAAGGGGGAATCAA
Found at i:56716 original size:20 final size:20
Alignment explanation
Indices: 56670--56735 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
56660 AATTAAATTC
*
56670 TTATTTTTATTGAATAACAATA
1 TTATTTTT-TT-AATAAAAATA
56692 -T-TTTTTTTAATAAAAATA
1 TTATTTTTTTAATAAAAATA
* *
56710 TTATTTTTTAAATAAATATA
1 TTATTTTTTTAATAAAAATA
56730 TTATTT
1 TTATTT
56736 CGGGTCGATC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 9 0.23
19 3 0.08
20 26 0.67
21 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATTTTTTTAATAAAAATA
Found at i:58866 original size:19 final size:19
Alignment explanation
Indices: 58842--58888 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
58832 TTGATTCATA
58842 TCAATGCAGCAAAAGTTGC
1 TCAATGCAGCAAAAGTTGC
58861 TCAATGCAGCAAAAGTTGC
1 TCAATGCAGCAAAAGTTGC
58880 TCAATGCAG
1 TCAATGCAG
58889 TATCTCCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
TCAATGCAGCAAAAGTTGC
Found at i:60624 original size:14 final size:15
Alignment explanation
Indices: 60605--60634 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
60595 CCAAAGTCCA
60605 ATCATAACAAA-AAT
1 ATCATAACAAACAAT
60619 ATCATAACAAACAAT
1 ATCATAACAAACAAT
60634 A
1 A
60635 ATAGGACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.17, G:0.00, T:0.20
Consensus pattern (15 bp):
ATCATAACAAACAAT
Found at i:61187 original size:10 final size:10
Alignment explanation
Indices: 61172--61209 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
61162 CTTTGCCTAC
61172 GAGAGAGAAA
1 GAGAGAGAAA
61182 GAGAGAG-AA
1 GAGAGAGAAA
*
61191 G-GGGAGAAA
1 GAGAGAGAAA
61200 GAGAGAGAAA
1 GAGAGAGAAA
61210 ATTCTCTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.17
9 6 0.25
10 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (10 bp):
GAGAGAGAAA
Found at i:62026 original size:3 final size:3
Alignment explanation
Indices: 62011--62082 Score: 112
Period size: 3 Copynumber: 24.3 Consensus size: 3
62001 AAATGTAAAT
*
62011 ATA ATA TTA ATA ATA ATA A-A AGTA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
62055 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
62083 ATTAAAATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 4 0.06
3 58 0.91
4 2 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:62090 original size:6 final size:5
Alignment explanation
Indices: 62019--62094 Score: 53
Period size: 6 Copynumber: 13.4 Consensus size: 5
62009 ATATAATATT
*
62019 AATAA TAATAA AAGTAA TATAA TAATAA TAATAA TAATAA TAATAA TAATAA
1 AATAA -AATAA AA-TAA AATAA -AATAA -AATAA -AATAA -AATAA -AATAA
*
62071 TAATAA TAATAA ATTAA AATAA AA
1 -AATAA -AATAA AATAA AATAA AA
62095 AAGACCCGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
5 15 0.23
6 49 0.77
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (5 bp):
AATAA
Found at i:62492 original size:134 final size:134
Alignment explanation
Indices: 62330--62632 Score: 446
Period size: 134 Copynumber: 2.3 Consensus size: 134
62320 GGATGAAAAT
* * * *
62330 GCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGTAGGGTGATAACTCGGTTCCTACGCGATG
1 GCTCATATGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATG
* *
62395 AGGATGGCTGGTTATCTAGGGGTGACACAGCTCCTACGTGATGAAGAGATCTGGCCGGTGGATGA
66 AGGACGGCTGGTTATCTAGGGGTGACACAGCTCCTACATGATGAAGAGATCTGGCCGGTGGATGA
62460 CACG
131 CACG
*
62464 GCTCATATGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATG
1 GCTCATATGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATG
* * * * * **
62529 AGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACATGATGAGGAGGTCTGTTCGGTGGATGA
66 AGGACGGCTGGTTATCTAGGGGTGACACAGCTCCTACATGATGAAGAGATCTGGCCGGTGGATGA
62594 CACG
131 CACG
* *
62598 GCTTATACT-TGATGAAGAGTTCTGGCCATCTTTAG
1 GCTCATA-TGTGATGAAGAGTTCTGGTCATCTTTAG
62633 TGATTATGGT
Statistics
Matches: 152, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
134 151 0.99
135 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (134 bp):
GCTCATATGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGCGATAACACGGTTCCTACGCGATG
AGGACGGCTGGTTATCTAGGGGTGACACAGCTCCTACATGATGAAGAGATCTGGCCGGTGGATGA
CACG
Found at i:63283 original size:29 final size:30
Alignment explanation
Indices: 63242--63304 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
63232 AGAGACAAAA
*
63242 TTTTGTTTCC-AAAGAAACCGACTCAAAGAT
1 TTTTGTTTCCAAAAGAAA-CAACTCAAAGAT
*
63272 TTTTGTTT-CAAAAGAAACAACTCAAATAT
1 TTTTGTTTCCAAAAGAAACAACTCAAAGAT
63301 TTTT
1 TTTT
63305 TTCACGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (30 bp):
TTTTGTTTCCAAAAGAAACAACTCAAAGAT
Found at i:63305 original size:30 final size:30
Alignment explanation
Indices: 63242--63304 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
63232 AGAGACAAAA
* *
63242 TTTTGTTTCCAAAGAAACCGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACCAACTCAAAGAT
*
63272 TTTTGTTTCAAAAGAAA-CAACTCAAATAT
1 TTTTGTTTCAAAAGAAACCAACTCAAAGAT
63301 TTTT
1 TTTT
63305 TTCACGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACCAACTCAAAGAT
Found at i:63339 original size:92 final size:94
Alignment explanation
Indices: 63161--63576 Score: 298
Period size: 94 Copynumber: 4.5 Consensus size: 94
63151 TTTTGTTAGT
* * *
63161 AGAAACAAACTCAAAGA-TTTTTTTCAAAATGAGCATACTCAAAGATTTGTTTCAAGAGAAAATG
1 AGAAACAGACTCAAAGATTTTTTTTCAAAATGAACATACTCAAAGATTTGTTTCAAGAGAAAATA
* *
63225 TCTCAAGAGAGACAAAATTTTGTTTCCAA
66 TCTCAAGAGAGACAAAACTTTGTTTCAAA
* * * * *
63254 AGAAACCGACTCAAAGATTTTTGTTTCAAAA-GAAACA-ACTCAAATATTTTTTTC-A-CGAAAT
1 AGAAACAGACTCAAAGATTTTT-TTTCAAAATG-AACATACTCAAAGATTTGTTTCAAGAGAAAA
63315 TATCTCAAGAGAGACAAAACTTTGTTTCAAA
64 TATCTCAAGAGAGACAAAACTTTGTTTCAAA
* ** * ** * ** *
63346 AGAAATAGACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGACAAA-ACTTTGTTTCAAAAGAA
1 AGAAACAGACTCAAAGATTTTTTTTC-AAAATG-AAC-ATACTCAAAGA-TTTGTTTCAAGAGAA
* *
63409 ACAGA-CTC-A-A-AG-----A-TTTTTTTCAAA
62 A-ATATCTCAAGAGAGACAAAACTTTGTTTCAAA
* * *
63433 AGAAACA-ACTCAAAGATTTTTATTCAAAAGGAACAGACTCAAAGATTTTGTTTCAAGAGAAACA
1 AGAAACAGACTCAAAGATTTTTTTTCAAAATGAACATACTCAAAGA-TTTGTTTCAAGAGAAA-A
* * *
63497 AATCTCAAGAGAGACAAAA-TTCGTTTCAAG
64 TATCTCAAGAGAGACAAAACTTTGTTTCAAA
* * *
63527 AGAAAC-GACTCAAAGATGGTTTGTTTCAAGA-GAAACAAACTCAAAGATTT
1 AGAAACAGACTCAAAGAT--TTTTTTTCAAAATG-AACATACTCAAAGATTT
63577 TGTATTTTGA
Statistics
Matches: 252, Mismatches: 45, Indels: 50
0.73 0.13 0.14
Matches are distributed among these distances:
84 7 0.03
85 20 0.08
86 16 0.06
87 22 0.09
88 2 0.01
89 2 0.01
90 2 0.01
91 7 0.03
92 49 0.19
93 20 0.08
94 58 0.23
95 17 0.07
96 29 0.12
97 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.28
Consensus pattern (94 bp):
AGAAACAGACTCAAAGATTTTTTTTCAAAATGAACATACTCAAAGATTTGTTTCAAGAGAAAATA
TCTCAAGAGAGACAAAACTTTGTTTCAAA
Found at i:63428 original size:61 final size:63
Alignment explanation
Indices: 63273--63430 Score: 254
Period size: 59 Copynumber: 2.6 Consensus size: 63
63263 CTCAAAGATT
*
63273 TTTGTTTCAAAAGAAACA-ACTCAAATATTTTTTTCACGAAATTATCTCAAGAGAGACAAAAC
1 TTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTCACGAAATTATCTCAAGAGAGACAAAAC
* *
63335 TTTGTTTCAAAAGAAATAGACTCAAAGA--TTTTTCACGAAATTGTCTC-A-AGAGACAAAAC
1 TTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTCACGAAATTATCTCAAGAGAGACAAAAC
63394 TTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTCA
1 TTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTCA
63431 AAAGAAACAA
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
59 38 0.43
60 1 0.01
61 25 0.28
62 17 0.19
63 8 0.09
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (63 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTCACGAAATTATCTCAAGAGAGACAAAAC
Found at i:63487 original size:29 final size:28
Alignment explanation
Indices: 63398--63496 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 28
63388 CAAAACTTTG
63398 TTTCAAAAGAAACAGACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
63426 TTTCAAAAGAAACA-ACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
*
63453 TATTCAAAAGGAACAGACTCAAAGATTTT
1 T-TTCAAAAGAAACAGACTCAAAGATTTT
*
63482 GTTTCAAGAGAAACA
1 -TTTCAAAAGAAACA
63497 AATCTCAAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.22
28 26 0.40
29 24 0.37
30 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:63506 original size:29 final size:28
Alignment explanation
Indices: 63398--63504 Score: 144
Period size: 29 Copynumber: 3.8 Consensus size: 28
63388 CAAAACTTTG
*
63398 TTTCAAAAGAAACAGACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
63426 TTTCAAAAGAAAC-AACTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
63453 TATTCAAAAGGAACAGACTCAAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
63482 GTTTCAAGAGAAACAAATCTCAA
1 -TTTCAAAAGAAACAAA-CTCAA
63505 GAGAGACAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.20
28 24 0.35
29 25 0.36
30 6 0.09
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:64987 original size:11 final size:11
Alignment explanation
Indices: 64973--65058 Score: 69
Period size: 11 Copynumber: 8.1 Consensus size: 11
64963 TGCTTTTGTC
64973 TTCTTTTTCTT
1 TTCTTTTTCTT
64984 TTCTTTTTCTT
1 TTCTTTTTCTT
64995 TAT-TGTTTTCTT
1 T-TCT-TTTTCTT
65007 TT-TTTTTC-T
1 TTCTTTTTCTT
65016 TTCTTTGTT-TT
1 TTCTTT-TTCTT
*
65027 TTC--TTT-GT
1 TTCTTTTTCTT
65035 TTCTTTTTCTT
1 TTCTTTTTCTT
*
65046 TGCTTTTGTCTT
1 TTCTTTT-TCTT
65058 T
1 T
65059 GTTTCTTTCT
Statistics
Matches: 63, Mismatches: 3, Indels: 17
0.76 0.04 0.20
Matches are distributed among these distances:
8 6 0.10
9 4 0.06
10 11 0.17
11 28 0.44
12 14 0.22
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:65003 original size:23 final size:23
Alignment explanation
Indices: 64977--65040 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
64967 TTTGTCTTCT
64977 TTTTCTTTTCTTTTTCTTT-ATTG
1 TTTTCTTTT-TTTTTCTTTCATTG
*
65000 TTTTCTTTTTTTTTCTTTCTTTG
1 TTTTCTTTTTTTTTCTTTCATTG
*
65023 TTTT-TTCTTTGTTTCTTT
1 TTTTCTT-TTTTTTTCTTT
65041 TTCTTTGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.30
23 26 0.70
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (23 bp):
TTTTCTTTTTTTTTCTTTCATTG
Found at i:65028 original size:15 final size:14
Alignment explanation
Indices: 64973--65066 Score: 75
Period size: 15 Copynumber: 6.4 Consensus size: 14
64963 TGCTTTTGTC
64973 TTCTTTTTCTTTTCT
1 TTCTTTTT-TTTTCT
*
64988 TT-TTCTTTATTGT-T
1 TTCTT-TTT-TTTTCT
65002 TTCTTTTTTTTTCT
1 TTCTTTTTTTTTCT
65016 TTCTTTGTTTTTTCT
1 TTCTTT-TTTTTTCT
* *
65031 TTGTTTCTTTTTCT
1 TTCTTTTTTTTTCT
* *
65045 TTGCTTTTGTCTTTGT
1 TT-CTTTT-TTTTTCT
65061 TTCTTT
1 TTCTTT
65067 CTCTTTGCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
13 3 0.05
14 24 0.38
15 30 0.47
16 7 0.11
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.79
Consensus pattern (14 bp):
TTCTTTTTTTTTCT
Found at i:65051 original size:19 final size:19
Alignment explanation
Indices: 65015--65062 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
65005 TTTTTTTTTC
*
65015 TTTCTTTGTTTTTTCTTTG
1 TTTCTTTGTTTTTGCTTTG
65034 TTTCTTT-TTCTTTGCTTT-
1 TTTCTTTGTT-TTTGCTTTG
*
65052 TGTCTTTGTTT
1 TTTCTTTGTTT
65063 CTTTCTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.77
Consensus pattern (19 bp):
TTTCTTTGTTTTTGCTTTG
Found at i:65059 original size:26 final size:26
Alignment explanation
Indices: 64983--65074 Score: 109
Period size: 26 Copynumber: 3.6 Consensus size: 26
64973 TTCTTTTTCT
*
64983 TTTCTTTTTCTTT-ATTGTTTTCTTT-
1 TTTCTTTTTCTTTGCTT-TTTTCTTTG
*
65008 TTTTTTCTTTCTTTG-TTTTTTCTTTG
1 TTTCTT-TTTCTTTGCTTTTTTCTTTG
*
65034 TTTCTTTTTCTTTGCTTTTGTCTTTG
1 TTTCTTTTTCTTTGCTTTTTTCTTTG
*
65060 TTTCTTTCTCTTTGC
1 TTTCTTTTTCTTTGC
65075 ATATGGTTCA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
25 21 0.36
26 38 0.64
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (26 bp):
TTTCTTTTTCTTTGCTTTTTTCTTTG
Found at i:65064 original size:34 final size:33
Alignment explanation
Indices: 64954--65066 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 33
64944 GAGGGACTCA
*
64954 TTGTCTTTG-TGCTTTTGTCTTCTTTTTCTTTTCTT
1 TTGTCTTTGTTTC-TTTGT-TTCTTTTTC-TTTCTT
* * *
64989 TT-TCTTTATTGT-TTTCTTTTTTTTTCTTTC-T
1 TTGTCTTTGTT-TCTTTGTTTCTTTTTCTTTCTT
65020 TTG--TTT-TTTCTTTGTTTCTTTTTCTTTGCTT
1 TTGTCTTTGTTTCTTTGTTTCTTTTTCTTT-CTT
65051 TTGTCTTTGTTTCTTT
1 TTGTCTTTGTTTCTTT
65067 CTCTTTGCAT
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
28 1 0.02
29 17 0.27
30 4 0.06
31 7 0.11
32 4 0.06
33 11 0.17
34 16 0.25
35 3 0.05
ACGTcount: A:0.01, C:0.14, G:0.09, T:0.76
Consensus pattern (33 bp):
TTGTCTTTGTTTCTTTGTTTCTTTTTCTTTCTT
Found at i:65073 original size:14 final size:13
Alignment explanation
Indices: 65000--65073 Score: 64
Period size: 14 Copynumber: 5.7 Consensus size: 13
64990 TTCTTTATTG
* *
65000 TTTTCTTTTTTTT
1 TTTTCTTTGTTTC
65013 TCTTTCTTTG-TT-
1 T-TTTCTTTGTTTC
65025 TTTTCTTTGTTTC
1 TTTTCTTTGTTTC
*
65038 TTTTTCTTTGCTT-
1 -TTTTCTTTGTTTC
*
65051 TTGTCTTTGTTTC
1 TTTTCTTTGTTTC
65064 TTTCTCTTTG
1 TTT-TCTTTG
65074 CATATGGTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
11 8 0.16
12 13 0.26
13 5 0.10
14 24 0.48
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (13 bp):
TTTTCTTTGTTTC
Found at i:65665 original size:20 final size:20
Alignment explanation
Indices: 65627--65665 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65617 GGATAAATGC
*
65627 AATGTTTCAATGTCACAAAG
1 AATGTTTCAAGGTCACAAAG
*
65647 AATGTTTCAAGGTCTCAAA
1 AATGTTTCAAGGTCACAAA
65666 AAGAGGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTTTCAAGGTCACAAAG
Found at i:67976 original size:16 final size:18
Alignment explanation
Indices: 67952--67989 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
67942 ACGTCTTTCT
67952 AAATAA-TTTTAAGA-AA
1 AAATAATTTTTAAGACAA
*
67968 AAATCATTTTTAAGACAA
1 AAATAATTTTTAAGACAA
67986 AAAT
1 AAAT
67990 GGTCTACGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATAATTTTTAAGACAA
Found at i:70354 original size:3 final size:3
Alignment explanation
Indices: 70340--70399 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
70330 AATGTAAATG
*
70340 TAA TAT TAA TAA TAA TAA -AA GTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* *
70385 TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA
70400 AAAAGATCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:72104 original size:20 final size:20
Alignment explanation
Indices: 72065--72103 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
72055 TTGTGATTTA
*
72065 GGATTTGTGATATAATTTTT
1 GGATTTGAGATATAATTTTT
72085 GGATTTGAG-TATAATTTTT
1 GGATTTGAGATATAATTTTT
72104 TAAGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.54
Consensus pattern (20 bp):
GGATTTGAGATATAATTTTT
Found at i:75812 original size:31 final size:30
Alignment explanation
Indices: 75777--75850 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
75767 TGATACCTGC
*
75777 ACTTTGAAAAAATATCTAATGTGATGCTTAT
1 ACTTTGATAAAATATCT-ATGTGATGCTTAT
** * *
75808 ACTTT--TAAAAGGTCTATGTGGTGCTTGT
1 ACTTTGATAAAATATCTATGTGATGCTTAT
75836 ACTTTGATAAAATAT
1 ACTTTGATAAAATAT
75851 TCAATGCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
28 16 0.47
29 7 0.21
30 6 0.18
31 5 0.15
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (30 bp):
ACTTTGATAAAATATCTATGTGATGCTTAT
Done.