Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006799.1 Hibiscus syriacus cultivar Beakdansim tig00017248_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: 50747
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1926 original size:34 final size:33
Alignment explanation
Indices: 1888--1959 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
1878 CTCTTTATTC
*
1888 TTTTCTTTGT-TTTTTCCTTTTTCTCTTGCCTTTT
1 TTTTC-TTGTATTTTGCCTTTTTCTCTT-CCTTTT
* * *
1922 TTTTCTTGTATTTTGCTTTTTTTTCTTCGTTTT
1 TTTTCTTGTATTTTGCCTTTTTCTCTTCCTTTT
1955 TTTTC
1 TTTTC
1960 CTCTTGCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (33 bp):
TTTTCTTGTATTTTGCCTTTTTCTCTTCCTTTT
Found at i:4480 original size:21 final size:20
Alignment explanation
Indices: 4455--4498 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
4445 AAATTTGTTC
*
4455 TTAAACTAATTTAC-AAATAAT
1 TTAAAATAA-TTACTAAAT-AT
4476 TTAAAATAATTACTAAATAT
1 TTAAAATAATTACTAAATAT
4496 TTA
1 TTA
4499 TGATTAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAATAATTACTAAATAT
Found at i:5025 original size:81 final size:81
Alignment explanation
Indices: 4906--5290 Score: 429
Period size: 81 Copynumber: 4.8 Consensus size: 81
4896 GCATTTACTT
* * * **
4906 TTCATCTAACTTGCATGATTGACA-CTTGTCTGCCAAATGCACAATTAGGGCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTT-TATGCCAAATGCACAGCTAGGGCATTTATCTTTTAC
4970 TCAACGGTCTTTAACCG
65 TCAACGGTCTTTAACCG
* * *
4987 TTCACCTAACTGGCATAATTGACACCTTTATGCTAAATGCACAGCTAGGACATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAGCTAGGGCATTTATCTTTTACT
* *
5052 CAACGGTCTGTAATCG
66 CAACGGTCTTTAACCG
* * * **
5068 --CATCTAGCTGGCATAATTGACACATTTATGCCAAAGGCACAGCTAGTTCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAGCTAGGGCATTTATCTTTTACT
* * *
5131 CAATGATCTTTAACCA
66 CAACGGTCTTTAACCG
* * * * *
5147 TTCATCTAACTGGCATAATTGACAACTTTCTGCCAAATGTAGACCTA-GGCAATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAGCTAGGGC-ATTTATCTTTTAC
* **
5211 TCAATGGTCTTTAACAT
65 TCAACGGTCTTTAACCG
* * * * *
5228 TTCATCTAACTGGCATAATTTACACCTTTTTGTCAAATGCACAGTTA-GGCTATTTATCATTTA
1 TTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAGCTAGGGC-ATTTATCTTTTA
5291 TTTTAGAACA
Statistics
Matches: 255, Mismatches: 45, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
79 67 0.26
80 1 0.00
81 184 0.72
82 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGCACAGCTAGGGCATTTATCTTTTACT
CAACGGTCTTTAACCG
Found at i:5128 original size:160 final size:162
Alignment explanation
Indices: 4908--5271 Score: 430
Period size: 160 Copynumber: 2.3 Consensus size: 162
4898 ATTTACTTTT
* * * * ** **
4908 CATCTAACTTGCATGATTGACAC-TTGTCTGCCAAATGCACAATTAGGGCATTTATCTTTTACTC
1 CATCTAACTGGCATAATTGACACATT-TATGCCAAAGGCACAGCTAGTTCATTTATCTTTTACTC
* * * * *
4972 AACGGTCTTTAACCGTTCACCTAACTGGCATAATTGACACCTTTATGCTAAATGCACAGCTAGG-
65 AACGATCTTTAACCATTCACCTAACTGGCATAATTGACAACTTTATGCCAAATGCACACCTAGGC
5036 ACATTTATCTTTTACTCAACGGTCTGT-A-ATCG
130 A-ATTTATCTTTTACTCAACGGTCTGTAACATCG
*
5068 CATCTAGCTGGCATAATTGACACATTTATGCCAAAGGCACAGCTAGTTCATTTATCTTTTACTCA
1 CATCTAACTGGCATAATTGACACATTTATGCCAAAGGCACAGCTAGTTCATTTATCTTTTACTCA
* * * * *
5133 ATGATCTTTAACCATTCATCTAACTGGCATAATTGACAACTTTCTGCCAAATGTAGACCTAGGCA
66 ACGATCTTTAACCATTCACCTAACTGGCATAATTGACAACTTTATGCCAAATGCACACCTAGGCA
* * **
5198 ATTTATCTTTTACTCAATGGTCTTTAACATTT
131 ATTTATCTTTTACTCAACGGTCTGTAACATCG
* * * * *
5230 CATCTAACTGGCATAATTTACACCTTTTTGTCAAATGCACAG
1 CATCTAACTGGCATAATTGACACATTTATGCCAAAGGCACAG
5272 TTAGGCTATT
Statistics
Matches: 171, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
160 129 0.75
161 4 0.02
162 38 0.22
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (162 bp):
CATCTAACTGGCATAATTGACACATTTATGCCAAAGGCACAGCTAGTTCATTTATCTTTTACTCA
ACGATCTTTAACCATTCACCTAACTGGCATAATTGACAACTTTATGCCAAATGCACACCTAGGCA
ATTTATCTTTTACTCAACGGTCTGTAACATCG
Found at i:6022 original size:20 final size:20
Alignment explanation
Indices: 5997--6051 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5987 TCTGTGATCA
5997 ATGGTATCGATACCATCCTC
1 ATGGTATCGATACCATCCTC
*
6017 ATGGTATAGATACTC-TCCTC
1 ATGGTATCGATAC-CATCCTC
*
6037 TTGGTATCGATACCA
1 ATGGTATCGATACCA
6052 CTTGAATCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGGTATCGATACCATCCTC
Found at i:7217 original size:46 final size:44
Alignment explanation
Indices: 7163--7250 Score: 131
Period size: 46 Copynumber: 2.0 Consensus size: 44
7153 TTGAAAAAGC
* *
7163 CTGAGTGCATTGATGCATGGTCTTGTGCATCAATGCATCAAATGCA
1 CTGAGTGCATCGATGCATGGT-ATGTGCATCAATGCAT-AAATGCA
*
7209 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAATG
1 CTGAGTGCATCGATGCATGGTATGTGCATCAATGCATAAATG
7251 TATTCGATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 5 0.13
45 14 0.36
46 20 0.51
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (44 bp):
CTGAGTGCATCGATGCATGGTATGTGCATCAATGCATAAATGCA
Found at i:7297 original size:20 final size:20
Alignment explanation
Indices: 7272--7309 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7262 TGAAAAATTA
7272 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
7292 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
7310 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:15840 original size:19 final size:19
Alignment explanation
Indices: 15816--15867 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
15806 AAAAGCATGA
15816 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
15835 GTGCATCGATGCATGGTAT
1 GTGCATCGATGCATGGTAT
15854 GTGCATCGATGCAT
1 GTGCATCGATGCAT
15868 AAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTAT
Found at i:21961 original size:13 final size:13
Alignment explanation
Indices: 21943--21967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21933 TATATATGTG
21943 TTTAACATAAACA
1 TTTAACATAAACA
21956 TTTAACATAAAC
1 TTTAACATAAAC
21968 TGAAAGATAA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTAACATAAACA
Found at i:22891 original size:22 final size:22
Alignment explanation
Indices: 22822--22892 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 22
22812 AGAGTTAATT
*
22822 AAATATATGTTTTAA-TAATCTTG
1 AAATATA-GATTTAATTAAT-TTG
*
22845 AATATTTA-ATTTCAATTAA-TT-
1 AA-ATATAGATTT-AATTAATTTG
22866 AAATATAGATTTAATTAATTTG
1 AAATATAGATTTAATTAATTTG
22888 AAATA
1 AAATA
22893 ATAAAATCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
20 10 0.26
21 8 0.21
22 10 0.26
23 4 0.10
24 7 0.18
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (22 bp):
AAATATAGATTTAATTAATTTG
Found at i:22968 original size:90 final size:90
Alignment explanation
Indices: 22847--23024 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
22837 TAATCTTGAA
* * *
22847 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
22912 TAGCGTAACTTGGATATAAAAGGAT
66 TAGCGTAACTTGGATATAAAAGGAT
22937 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
* *
23002 TAGGGTAACTTGGCTATAAAAGG
66 TAGCGTAACTTGGATATAAAAGG
23025 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGCGTAACTTGGATATAAAAGGAT
Found at i:28769 original size:93 final size:93
Alignment explanation
Indices: 28631--29421 Score: 863
Period size: 93 Copynumber: 8.5 Consensus size: 93
28621 TAAATTCCAA
** *
28631 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTTTGTAAACATAAAAGTGTTTAGTTAA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
* * *
28696 GACATTCCAACGTTATTCAAACTTCTAA
66 GACATTTCAACGCTATTCAAACTTCTAT
* * *
28724 CCATTAATGTAACAACTTGAATAAGATAACTTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
* *
28789 GACATTTCAACGTTATTCAAACTTCCAT
66 GACATTTCAACGCTATTCAAACTTCTAT
* ** **
28817 CCATTAATGTAACAACTTGAATAAGTTAACCTCTTTAGTTTGTAAATGTCAAAGTGTTTAGTTAA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
** * *
28882 GACATTTCAATACTATTCAAACTTCCAC
66 GACATTTCAACGCTATTCAAACTTCTAT
* * * * *
28910 CCATTAATTTAACAACTTGGATAAGCTAAACTCTTTAATCCATAAACATCAAAGTGTTTAGTTAA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
* * * *
28975 TACATTTCAACGCTACTCAGACTTTCAAT
66 GACATTTCAACGCTATTCAAAC-TTCTAT
* * * * * * *
29004 -CATTAATGTGACAACTTTGATAAGTTAACATCCTTACTACATAAACATCAAAGTGTTTAGTTAA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
* * * *
29068 TACATTTCAACGATATTCAAACTACCAT
66 GACATTTCAACGCTATTCAAACTTCTAT
* * * * * *
29096 CCATTATTGTAACAACTTGGATAAGTTAACCTCTTTCGTCTGTAACCATCAAAGTGTTTATTTAC
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
* *
29161 GTCATTTCAACCCTATTCAAACTT-TCAT
66 GACATTTCAACGCTATTCAAACTTCT-AT
* * * * * * * *
29189 CAATTAATGTAAAAACTTGGATAATTTAACCTCCTTACTTCATAAATATCAAAGTGTTTAGTTAA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
*
29254 GACATTTCAACGTTATTCAAACTT-TCAT
66 GACATTTCAACGCTATTCAAACTTCT-AT
* * * ** * * **
29282 GCATTATTGTTAA-AATTTTCATAGGTTAACCTCTTTTGTCCGTAAATGTCAAAGTGTTTAGTTA
1 CCATTAATG-TAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTA
**
29346 AGACATTTCAATACTATTCAAACTTCTAT
65 AGACATTTCAACGCTATTCAAACTTCTAT
* * * *
29375 CCATTAATGTAACAA-TTGGATAATTTAACCTCCTCAGTCTGTAAACA
1 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACA
29422 ACTTGTAGAA
Statistics
Matches: 577, Mismatches: 115, Indels: 13
0.82 0.16 0.02
Matches are distributed among these distances:
92 29 0.05
93 540 0.94
94 8 0.01
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (93 bp):
CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAA
GACATTTCAACGCTATTCAAACTTCTAT
Found at i:29131 original size:279 final size:279
Alignment explanation
Indices: 28625--29421 Score: 985
Period size: 279 Copynumber: 2.9 Consensus size: 279
28615 TTATTTTAAA
* ** *
28625 TTCCAACCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTTTGTAAACATAAAAGTGTTT
1 TTCCAACCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAATTCATAAACATCAAAGTGTTT
* * *
28690 AGTTAAGACATTCCAACGTTATTCAAAC-TTCTAACCATTAATGTAACAAC-TTGAATAAGATAA
66 AGTTAAGACATTTCAACGTTATTCAAACTTTC-AATCATTAATGTAACAACTTTG-ATAAGTTAA
* *
28753 CTTCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAAGACATTTCAACGTTATTCAAACTTCCATC
129 CATCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAAGACATTTCAACGATATTCAAACTTCCATC
* * **
28818 CATTAATGTAACAACTTGAATAAGTTAACCTCTTTAGTTTGTAAATGTCAAAGTGTTTAGTTAAG
194 CATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCTGTAAACATCAAAGTGTTTAGTTAAG
*
28883 ACATTTCAATACTATTCAAAC
259 ACATTTCAACACTATTCAAAC
* * * * *
28904 TTCCACCCATTAATTTAACAACTTGGATAAGCTAAACTCTTTAATCCATAAACATCAAAGTGTTT
1 TTCCAACCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAATTCATAAACATCAAAGTGTTT
* * * * *
28969 AGTTAATACATTTCAACGCTACTCAGACTTTCAATCATTAATGTGACAACTTTGATAAGTTAACA
66 AGTTAAGACATTTCAACGTTATTCAAACTTTCAATCATTAATGTAACAACTTTGATAAGTTAACA
* * * * * *
29034 TCCTTACTACATAAACATCAAAGTGTTTAGTTAATACATTTCAACGATATTCAAACTACCATCCA
131 TCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAAGACATTTCAACGATATTCAAACTTCCATCCA
* * * * * *
29099 TTATTGTAACAACTTGGATAAGTTAACCTCTTTCGTCTGTAACCATCAAAGTGTTTATTTACGTC
196 TTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCTGTAAACATCAAAGTGTTTAGTTAAGAC
*
29164 ATTTCAACCCTATTCAAAC
261 ATTTCAACACTATTCAAAC
* * * * * * * *
29183 TTTCATCAATTAATGTAAAAACTTGGATAATTTAACCTCCTTACTTCATAAATATCAAAGTGTTT
1 TTCCAACCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAATTCATAAACATCAAAGTGTTT
* * * *
29248 AGTTAAGACATTTCAACGTTATTCAAACTTTC-ATGCATTATTGTTAA-AATTTTCATAGGTTAA
66 AGTTAAGACATTTCAACGTTATTCAAACTTTCAAT-CATTAATG-TAACAACTTTGATAAGTTAA
* * ** * *
29311 CCTCTTTTGTCCGTAAATGTCAAAGTGTTTAGTTAAGACATTTCAA-TACTATTCAAACTTCTAT
129 CATCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAAGACATTTCAACGA-TATTCAAACTTCCAT
* * *
29375 CCATTAATGTAACAA-TTGGATAATTTAACCTCCTCAGTCTGTAAACA
193 CCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCTGTAAACA
29422 ACTTGTAGAA
Statistics
Matches: 437, Mismatches: 76, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
278 30 0.07
279 399 0.91
280 8 0.02
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (279 bp):
TTCCAACCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAATTCATAAACATCAAAGTGTTT
AGTTAAGACATTTCAACGTTATTCAAACTTTCAATCATTAATGTAACAACTTTGATAAGTTAACA
TCTTTAGTCCGTAAACATCAAAGTGTTTAGTTAAGACATTTCAACGATATTCAAACTTCCATCCA
TTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCTGTAAACATCAAAGTGTTTAGTTAAGAC
ATTTCAACACTATTCAAAC
Found at i:30957 original size:2 final size:2
Alignment explanation
Indices: 30950--31056 Score: 177
Period size: 2 Copynumber: 55.5 Consensus size: 2
30940 GATACAGATA
*
30950 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AA 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
30991 AT AT AT AT AT AT A- AT AT AT AT AT AT AT A- 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
31031 AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31057 CACATTTATT
Statistics
Matches: 99, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
1 4 0.04
2 95 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31069 original size:21 final size:20
Alignment explanation
Indices: 30950--31056 Score: 161
Period size: 19 Copynumber: 5.5 Consensus size: 20
30940 GATACAGATA
30950 ATATATATATAT-ATATATT
1 ATATATATATATAATATATT
30969 ATATATATATA-AATATA-T
1 ATATATATATATAATATATT
*
30987 ATATATATATAT-ATATAAT
1 ATATATATATATAATATATT
31006 ATATATATATATAATATATAT
1 ATATATATATATAATATAT-T
31027 ATATATATATATAATATA-T
1 ATATATATATATAATATATT
31046 ATATATATATA
1 ATATATATATA
31057 CACATTTATT
Statistics
Matches: 82, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
18 17 0.21
19 41 0.50
20 5 0.06
21 19 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATATATATAATATATT
Found at i:31138 original size:21 final size:21
Alignment explanation
Indices: 31113--31157 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
31103 TAACTAAATG
31113 ATAAA-AAAACATATATATATA
1 ATAAATAAAACATATATA-ATA
*
31134 ATAAATAAAACATATTTAATA
1 ATAAATAAAACATATATAATA
31155 ATA
1 ATA
31158 CTGTAAGTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAATAAAACATATATAATA
Found at i:32653 original size:3 final size:3
Alignment explanation
Indices: 32645--32671 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
32635 TATTTTTCGG
32645 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
32672 ACCTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45044 original size:24 final size:24
Alignment explanation
Indices: 44996--45047 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44986 TCCTGGCATA
* *
44996 TCTTGATAAGACCAGGAATATATT
1 TCTTGATAAGACCAGGAAAAGATT
* *
45020 TCTTGATAAGACTATGAAAAGATT
1 TCTTGATAAGACCAGGAAAAGATT
45044 TCTT
1 TCTT
45048 TGAAATCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (24 bp):
TCTTGATAAGACCAGGAAAAGATT
Found at i:47344 original size:19 final size:19
Alignment explanation
Indices: 47320--47356 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
47310 GGCCATTTTC
47320 TTGAGGTTTGGGTCATTTG
1 TTGAGGTTTGGGTCATTTG
47339 TTGAGGTTTGGGTCATTT
1 TTGAGGTTTGGGTCATTT
47357 TCTTGAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.05, G:0.35, T:0.49
Consensus pattern (19 bp):
TTGAGGTTTGGGTCATTTG
Found at i:49907 original size:14 final size:15
Alignment explanation
Indices: 49888--49929 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
49878 GTAAAACGTA
**
49888 TATATAAATTTAAT-
1 TATATAAAGGTAATG
49902 TATATAAAGGTAATG
1 TATATAAAGGTAATG
49917 TATAT-AAGGTAAT
1 TATATAAAGGTAAT
49930 ATAAGGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (15 bp):
TATATAAAGGTAATG
Done.