Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004897.1 Hibiscus syriacus cultivar Beakdansim tig00011020_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: 57076
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2506 original size:181 final size:184
Alignment explanation
Indices: 1880--2539 Score: 1182
Period size: 181 Copynumber: 3.7 Consensus size: 184
1870 TTTTAAATGG
* *
1880 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
1945 TAA-AAC-GTATATTTATACC-GTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2006 GATGTGTAAAATGTCGACAC-TTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2059 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2124 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTTTTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
2189 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2243 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
2308 TAAGACCGG--TA-TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
2370 GATGTGTAAAATGTCGACACTTTTTTAAATCGTA-CGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
2423 TA-GGACAT-AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
2486 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATT-TATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
2540 ATGTTGAAAG
Statistics
Matches: 465, Mismatches: 8, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
178 64 0.14
179 72 0.15
180 33 0.07
181 127 0.27
182 12 0.03
183 51 0.11
184 106 0.23
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:3892 original size:3 final size:3
Alignment explanation
Indices: 3884--3964 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
3874 ACTTGTTTGG
* * * **
3884 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
3932 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
3965 TTTATCGTCA
Statistics
Matches: 61, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.25, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:3907 original size:18 final size:18
Alignment explanation
Indices: 3884--3985 Score: 78
Period size: 18 Copynumber: 5.7 Consensus size: 18
3874 ACTTGTTTGG
3884 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
3902 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
3920 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
3938 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* * *
3956 ATCGTCATCTTTATCGTC
1 ATCATCATCTTCATCATC
* *
3974 AGCTTCATCTTC
1 ATCATCATCTTC
3986 TGCGACCGAT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:3951 original size:42 final size:42
Alignment explanation
Indices: 3892--3982 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
3882 GGATCATCAT
*
3892 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * * *
3934 CTTCATCGTCATCATCATCATCATCGTCATCTTTATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
3976 CTTCATC
1 CTTCATC
3983 TTCTGCGACC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.34, G:0.08, T:0.36
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:6506 original size:199 final size:199
Alignment explanation
Indices: 5443--7358 Score: 3506
Period size: 199 Copynumber: 9.7 Consensus size: 199
5433 TTTAAATTAG
* *
5443 TATCGACACAAA--ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
5506 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
5569 CGACACGTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
5634 AAAA
196 AAAA
*
5638 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
5703 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
5767 CGACACTTTTTATATATGGATCGACAC-TTATGGGTGCACCTTGTTTTT-ATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
5830 AAAA
196 AAAA
*
5834 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
5899 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
5964 CGACAC-TTTT-TATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
6027 AAAA
196 AAAA
6031 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6096 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT-GGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
6160 CGACAC-TTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
6223 AAAA
196 AAAA
6227 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6292 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
6357 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAA
6421 AAAAA
195 AAAAA
6426 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6491 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
6556 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTAATTCATTATGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-GAA
6620 AAAAA
195 AAAAA
6625 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6690 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6755 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-GAA
6820 AAAAA
195 AAAAA
6825 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
6890 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
6955 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
7020 AAAA
196 AAAA
7024 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
7089 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
7154 CGACAC-TTTTATATATGGATCGACAC-TTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
7216 AAAA
196 AAAA
7220 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
7285 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
7350 CGACACTTT
131 CGACACTTT
7359 ATTGATGCAC
Statistics
Matches: 1683, Mismatches: 24, Indels: 26
0.97 0.01 0.02
Matches are distributed among these distances:
195 27 0.02
196 436 0.26
197 336 0.20
198 168 0.10
199 503 0.30
200 213 0.13
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAA
Found at i:7534 original size:19 final size:19
Alignment explanation
Indices: 7507--7551 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
7497 ATTCACATAA
*
7507 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
7526 AAAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
7545 AAAATTA
1 AAAATTA
7552 ACTCGACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:9149 original size:15 final size:14
Alignment explanation
Indices: 9104--9151 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
9094 TGGGCCTCTC
*
9104 CTTCCTCCTCATTT
1 CTTCCTCCTCTTTT
9118 CTTCCAT-CTCTTCTT
1 CTTCC-TCCTCTT-TT
9133 CTTCCTCCCTCTTTT
1 CTTCCT-CCTCTTTT
9148 CTTC
1 CTTC
9152 TTCATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.34
15 14 0.48
16 5 0.17
ACGTcount: A:0.04, C:0.44, G:0.00, T:0.52
Consensus pattern (14 bp):
CTTCCTCCTCTTTT
Found at i:9373 original size:33 final size:33
Alignment explanation
Indices: 9336--9401 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
9326 CATCTTAATA
*
9336 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
9369 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
9402 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:11535 original size:24 final size:24
Alignment explanation
Indices: 11498--11550 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
11488 CCGTTCTATC
11498 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
11522 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
11546 TATTT
1 TATTT
11551 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:11739 original size:20 final size:19
Alignment explanation
Indices: 11695--11739 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
11685 TCCGGTATCA
*
11695 TTTACCGTTTTTATCATTT
1 TTTACCGGTTTTATCATTT
**
11714 GATACCGGTTTTATCATATT
1 TTTACCGGTTTTATCAT-TT
11734 TTTACC
1 TTTACC
11740 TGTTATATCG
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:11886 original size:19 final size:19
Alignment explanation
Indices: 11862--11919 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
11852 ACTTTTAATT
11862 TTACCGGTTTATCATTTTG
1 TTACCGGTTTATCATTTTG
11881 TTACCGGTTTATCATATTT-
1 TTACCGGTTTATCAT-TTTG
* *
11900 TTACCTGGTATATCGTTTTG
1 TTACC-GGTTTATCATTTTG
11920 GATCGATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 23 0.68
20 11 0.32
ACGTcount: A:0.17, C:0.16, G:0.16, T:0.52
Consensus pattern (19 bp):
TTACCGGTTTATCATTTTG
Found at i:16114 original size:72 final size:72
Alignment explanation
Indices: 16019--16188 Score: 227
Period size: 72 Copynumber: 2.4 Consensus size: 72
16009 CAAGCTCTAG
* * *
16019 ATGATTGTG-CCAGCCATCATGATCACC-TGGACCATGGACATAAACATGAACATGCTCATAGTC
1 ATGATTGTGCCCA-CCATCATGATCACCAT-GACCATGGACACAAACATGAAAATGCTCATAGTA
16082 ATGACAACC
64 ATGACAACC
* * *
16091 ATGATTCTGCCCACCATCGTGATCACCATGACCATGGACACAAACATGAAAATGCTCATATTAAT
1 ATGATTGTGCCCACCATCATGATCACCATGACCATGGACACAAACATGAAAATGCTCATAGTAAT
* *
16156 GACCATC
66 GACAACC
*
16163 ATGATTGTGCCCATCATCATGATCAC
1 ATGATTGTGCCCACCATCATGATCAC
16189 AATCATCATC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 81 0.95
73 4 0.05
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (72 bp):
ATGATTGTGCCCACCATCATGATCACCATGACCATGGACACAAACATGAAAATGCTCATAGTAAT
GACAACC
Found at i:17789 original size:11 final size:11
Alignment explanation
Indices: 17766--17799 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
17756 TAAGTTTGAA
17766 TAAATATTATTT
1 TAAATA-TATTT
17778 TAAATATATTT
1 TAAATATATTT
17789 TAAATGATATT
1 TAAAT-ATATT
17800 ATATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TAAATATATTT
Found at i:18467 original size:16 final size:16
Alignment explanation
Indices: 18446--18476 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18436 GTTAAATTCG
*
18446 GGTTATTTTAGGTTCA
1 GGTTATTTTAAGTTCA
18462 GGTTATTTTAAGTTC
1 GGTTATTTTAAGTTC
18477 GAGTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (16 bp):
GGTTATTTTAAGTTCA
Found at i:18745 original size:3 final size:3
Alignment explanation
Indices: 18737--18767 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
18727 CTAAAACTCT
18737 TTC TTC TTC TTC TTC TTC TTCC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC
18768 CTCCTCCCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:18761 original size:13 final size:13
Alignment explanation
Indices: 18737--18772 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
18727 CTAAAACTCT
18737 TTCTTCTT-CTTC
1 TTCTTCTTCCTTC
18749 TTCTTCTTCCTTC
1 TTCTTCTTCCTTC
*
18762 TTCTTCCTCCT
1 TTCTTCTTCCT
18773 CCCGTGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (13 bp):
TTCTTCTTCCTTC
Found at i:26677 original size:42 final size:42
Alignment explanation
Indices: 26626--26890 Score: 229
Period size: 42 Copynumber: 6.2 Consensus size: 42
26616 GGAAAAAAAT
26626 GATTGAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAGTGA
1 GATT-AAAAAATTAGGGACTTCAATTATAAAGGTAAAAAGTGA
* * *
26669 GATTAAAAAATTAGGGACCTCAATTTTAAAGGTAAAGAGTGA
1 GATTAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAGTGA
* * * * *
26711 AATTGAAAAA-TAGGG-GTCTAAATTATATAA-GTAAAAA-TGG
1 GATTAAAAAATTAGGGACT-TCAATTATA-AAGGTAAAAAGTGA
* * * * *
26751 GATTGAAAAAAGTAAGAGCCTT-AATTATAAAGATTAAAAGTGA
1 GATT-AAAAAA-TTAGGGACTTCAATTATAAAGGTAAAAAGTGA
* *
26794 GATTAAAAAATTAGGGATCTT-AATTATAAAGGTAGAATGTGA
1 GATTAAAAAATTAGGGA-CTTCAATTATAAAGGTAAAAAGTGA
* * *
26836 GATTAAAAAATTA-GGATCATCAATTAAAAATGTAAAAAAAGTGA
1 GATTAAAAAATTAGGGA-CTTCAATTATAAAGGT--AAAAAGTGA
26880 GATTGAAAAAA
1 GATT-AAAAAA
26891 ATTAAAATAC
Statistics
Matches: 178, Mismatches: 31, Indels: 24
0.76 0.13 0.10
Matches are distributed among these distances:
40 5 0.03
41 35 0.20
42 106 0.60
43 14 0.08
44 12 0.07
45 6 0.03
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.26
Consensus pattern (42 bp):
GATTAAAAAATTAGGGACTTCAATTATAAAGGTAAAAAGTGA
Found at i:26782 original size:83 final size:84
Alignment explanation
Indices: 26631--26846 Score: 228
Period size: 83 Copynumber: 2.6 Consensus size: 84
26621 AAAATGATTG
* * * *
26631 AAAAAATTAGGGA-CTTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACCTCAATTT
1 AAAAAATTAGGGATC-TAAATTATAAAGGTAAAAAGTGAGATTAAAAAATAAGAGACCTCAATTA
26695 TAAAG-GTAAAGAGTGAAATT
65 TAAAGAGTAAA-AGTGAAATT
* * * *
26715 GAAAAA-TAGGGGTCTAAATTATATAA-GTAAAAA-TGGGATTGAAAAAAGTAAGAG-CCTTAAT
1 AAAAAATTAGGGATCTAAATTATA-AAGGTAAAAAGTGAGATT-AAAAAA-TAAGAGACCTCAAT
* *
26776 TATAAAGATTAAAAGTGAGATT
63 TATAAAGAGTAAAAGTGAAATT
* * *
26798 AAAAAATTAGGGATCTTAATTATAAAGGTAGAATGTGAGATTAAAAAAT
1 AAAAAATTAGGGATCTAAATTATAAAGGTAAAAAGTGAGATTAAAAAAT
26847 TAGGATCATC
Statistics
Matches: 108, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
82 6 0.06
83 54 0.50
84 42 0.39
85 6 0.06
ACGTcount: A:0.50, C:0.04, G:0.19, T:0.27
Consensus pattern (84 bp):
AAAAAATTAGGGATCTAAATTATAAAGGTAAAAAGTGAGATTAAAAAATAAGAGACCTCAATTAT
AAAGAGTAAAAGTGAAATT
Found at i:28486 original size:133 final size:133
Alignment explanation
Indices: 28325--28597 Score: 546
Period size: 133 Copynumber: 2.1 Consensus size: 133
28315 TGCTCTCTAC
28325 TACTTCTTGTATTTCTTCATGCTCATTTTTGCTTTAGTTTTGTTTTATTATTTTCTCTTCCCTTC
1 TACTTCTTGTATTTCTTCATGCTCATTTTTGCTTTAGTTTTGTTTTATTATTTTCTCTTCCCTTC
28390 AAAGTTCCGAGTCTCGGTCCTCTATAACTTCTCAAACAATGCTAAATAGATGTGCAGATGCTTTG
66 AAAGTTCCGAGTCTCGGTCCTCTATAACTTCTCAAACAATGCTAAATAGATGTGCAGATGCTTTG
28455 AAT
131 AAT
28458 TACTTCTTGTATTTCTTCATGCTCATTTTTGCTTTAGTTTTGTTTTATTATTTTCTCTTCCCTTC
1 TACTTCTTGTATTTCTTCATGCTCATTTTTGCTTTAGTTTTGTTTTATTATTTTCTCTTCCCTTC
28523 AAAGTTCCGAGTCTCGGTCCTCTATAACTTCTCAAACAATGCTAAATAGATGTGCAGATGCTTTG
66 AAAGTTCCGAGTCTCGGTCCTCTATAACTTCTCAAACAATGCTAAATAGATGTGCAGATGCTTTG
28588 AAT
131 AAT
28591 TACTTCT
1 TACTTCT
28598 CATATGTGCC
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 140 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (133 bp):
TACTTCTTGTATTTCTTCATGCTCATTTTTGCTTTAGTTTTGTTTTATTATTTTCTCTTCCCTTC
AAAGTTCCGAGTCTCGGTCCTCTATAACTTCTCAAACAATGCTAAATAGATGTGCAGATGCTTTG
AAT
Found at i:35974 original size:2 final size:2
Alignment explanation
Indices: 35967--36012 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35957 CCAAACCCCA
35967 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
36009 AT AT
1 AT AT
36013 TAAAAAGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37251 original size:40 final size:40
Alignment explanation
Indices: 37207--37369 Score: 290
Period size: 40 Copynumber: 4.1 Consensus size: 40
37197 AGTAGTATAC
*
37207 ATAAGAGTGTACATGAATTATAGTTTGAATAAATAAAATT
1 ATAAGAGTGTACATGAATTAAAGTTTGAATAAATAAAATT
* *
37247 ATAAGAGCGTACATGAATTAAAGTTTGATTAAATAAAATT
1 ATAAGAGTGTACATGAATTAAAGTTTGAATAAATAAAATT
*
37287 ATAAGAGTGCACATGAATTAAAGTTTGAATAAATAAAATT
1 ATAAGAGTGTACATGAATTAAAGTTTGAATAAATAAAATT
37327 ATAAGAGTGTACATGAATTAAAGTTTGAATAAATAAAATT
1 ATAAGAGTGTACATGAATTAAAGTTTGAATAAATAAAATT
37367 ATA
1 ATA
37370 TTTTATATTT
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 116 1.00
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.33
Consensus pattern (40 bp):
ATAAGAGTGTACATGAATTAAAGTTTGAATAAATAAAATT
Found at i:39008 original size:21 final size:21
Alignment explanation
Indices: 38953--39008 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
38943 AAAGTTGACG
*
38953 TTTTTATTGAATTTTATTCAC
1 TTTTTATTGATTTTTATTCAC
* **
38974 TTTTAATTCTTTTTTATTGCA-
1 TTTTTATTGATTTTTATT-CAC
38995 TTTTTATTGATTTT
1 TTTTTATTGATTTT
39009 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTTTATTGATTTTTATTCAC
Found at i:39084 original size:22 final size:21
Alignment explanation
Indices: 39058--39120 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
39048 GATTGTAATT
39058 AAAAGTATAAAAATGCAATAAA
1 AAAAGTATAAAAATG-AATAAA
* *
39080 AAAAGAATTAAAATTGAATAAA
1 AAAAGTA-TAAAAATGAATAAA
39102 ATTAAA-TATAAAAA-GAATA
1 A--AAAGTATAAAAATGAATA
39121 TAAAGTCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 5 0.15
22 18 0.53
23 8 0.24
24 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAAAGTATAAAAATGAATAAA
Found at i:39162 original size:26 final size:26
Alignment explanation
Indices: 39133--39182 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
39123 AAGTCAATTT
39133 TTTTTCAAAATATATAAA-ATTTATAA
1 TTTTTCAAAATATA-AAATATTTATAA
* *
39159 TTTTTTAAATTATAAAATATTTAT
1 TTTTTCAAAATATAAAATATTTAT
39183 TATCATCGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTTCAAAATATAAAATATTTATAA
Found at i:39250 original size:11 final size:11
Alignment explanation
Indices: 39220--39251 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
39210 TAAATACTAG
*
39220 TTATAAAACTT
1 TTATAAAATTT
39231 TTATAAAATTT
1 TTATAAAATTT
39242 TTATAAAATT
1 TTATAAAATT
39252 ATTCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATAAAATTT
Found at i:43350 original size:20 final size:20
Alignment explanation
Indices: 43325--43378 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
43315 TGTGGCAGGC
43325 AGACATCTAAAACTCATGTT
1 AGACATCTAAAACTCATGTT
43345 AGACATCTAAAACTCATGTT
1 AGACATCTAAAACTCATGTT
*
43365 AGATATCTAAAACT
1 AGACATCTAAAACT
43379 AATGCTCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.30
Consensus pattern (20 bp):
AGACATCTAAAACTCATGTT
Found at i:44579 original size:19 final size:19
Alignment explanation
Indices: 44546--44582 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44536 ATGACCAACA
*
44546 AAATCGCAATACGATCTCT
1 AAATCGCAACACGATCTCT
*
44565 AAATCGCAACGCGATCTC
1 AAATCGCAACACGATCTC
44583 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:47853 original size:18 final size:18
Alignment explanation
Indices: 47830--47864 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
47820 AGCAAAAGGC
*
47830 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
47848 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
47865 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:48060 original size:20 final size:20
Alignment explanation
Indices: 48035--48144 Score: 74
Period size: 20 Copynumber: 5.8 Consensus size: 20
48025 TTACACATTC
48035 ATTTGAATATCGCAACACGA
1 ATTTGAATATCGCAACACGA
*
48055 ATTTGACTATCGC-A-ACG-
1 ATTTGAATATCGCAACACGA
* * *
48072 --CT-AAAATCGCAACGCGA
1 ATTTGAATATCGCAACACGA
* *
48089 ATTTGACTATCGCAACGCGA
1 ATTTGAATATCGCAACACGA
* *
48109 ACTTGATTATCGCAACGA-GA
1 ATTTGAATATCGCAAC-ACGA
48129 ATTT-AACTATCGCAAC
1 ATTTGAA-TATCGCAAC
48145 GAGAAAATTG
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
14 6 0.09
15 2 0.03
16 2 0.03
18 3 0.04
19 3 0.04
20 53 0.77
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (20 bp):
ATTTGAATATCGCAACACGA
Found at i:48090 original size:34 final size:34
Alignment explanation
Indices: 48043--48183 Score: 138
Period size: 34 Copynumber: 4.0 Consensus size: 34
48033 TCATTTGAAT
* *
48043 ATCGCAACACGAATTTGACTATCGCAACGCTAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAAA
48077 ATCGCAACGCGAATTTGACTATCGCAACGCGAACTTGA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA----A
* * *
48115 TTATCGCAACGAGAATTTAACTATCGCAACGAGAAA
1 --ATCGCAACGCGAATTTGACTATCGCAACGCGAAA
* * * * *
48151 ATTGCAAAGCGTATTAGACTATCGCAACACGAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAA
48184 TTGACTTTCG
Statistics
Matches: 88, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
34 56 0.64
36 1 0.01
38 1 0.01
40 30 0.34
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAAA
Found at i:48145 original size:20 final size:20
Alignment explanation
Indices: 48077--48149 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
48067 CAACGCTAAA
*
48077 ATCGCAACGCGAATTTGACT
1 ATCGCAACGAGAATTTGACT
* * *
48097 ATCGCAACGCGAACTTGATT
1 ATCGCAACGAGAATTTGACT
*
48117 ATCGCAACGAGAATTTAACT
1 ATCGCAACGAGAATTTGACT
48137 ATCGCAACGAGAA
1 ATCGCAACGAGAA
48150 AATTGCAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGAATTTGACT
Found at i:48171 original size:74 final size:73
Alignment explanation
Indices: 48037--48187 Score: 196
Period size: 74 Copynumber: 2.1 Consensus size: 73
48027 ACACATTCAT
* ** * *
48037 TTGAATATCGCAACACGAATTTGACTATCGCAACGCTAAAATCGCAACGCGAATTTGACTATCGC
1 TTGAATATCGCAACACGAATTTAACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACTATCGC
*
48102 AACGCGAA
66 AACACGAA
* * *
48110 CTTGATTATCGCAACGA-GAATTTAACTATCGCAACGAGAAAATTGCAAAGCGTATTAGACTATC
1 -TTGAATATCGCAAC-ACGAATTTAACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACTATC
48174 GCAACACGAA
64 GCAACACGAA
48184 TTGA
1 TTGA
48188 CTTTCGCGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
73 4 0.06
74 62 0.93
75 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (73 bp):
TTGAATATCGCAACACGAATTTAACTATCGCAACGAGAAAATCGCAAAGCGAATTAGACTATCGC
AACACGAA
Found at i:48213 original size:20 final size:20
Alignment explanation
Indices: 48188--48226 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
48178 CACGAATTGA
*
48188 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
48208 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
48227 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:50108 original size:12 final size:12
Alignment explanation
Indices: 50085--50121 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
50075 TCTCTTCGTT
50085 TCTTTTTCCCTTC
1 TCTTTTT-CCTTC
50098 TCTTTTTCCTTC
1 TCTTTTTCCTTC
50110 TCTTTTTCCTTC
1 TCTTTTTCCTTC
50122 ACCCTCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (12 bp):
TCTTTTTCCTTC
Found at i:51412 original size:20 final size:22
Alignment explanation
Indices: 51374--51413 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
51364 TTTGAGTAGA
51374 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
51396 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
51414 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:52577 original size:19 final size:20
Alignment explanation
Indices: 52553--52600 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
52543 AAACAATTTC
*
52553 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* * *
52572 TTTTGACAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
52592 TTTTGAAAA
1 TTTTGAAAA
52601 GGATTTAGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:53392 original size:20 final size:20
Alignment explanation
Indices: 53369--53406 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53359 ATATGTACTT
*
53369 AATTTTAACAATTAGTATCA
1 AATTTAAACAATTAGTATCA
*
53389 AATTTAAACAATTGGTAT
1 AATTTAAACAATTAGTAT
53407 TGCATAAAGT
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:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
AATTTAAACAATTAGTATCA
Found at i:53777 original size:21 final size:18
Alignment explanation
Indices: 53734--53791 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
53724 CAACAATTGG
53734 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
*
53752 TAACAATTGATGTCATTTTGT
1 TAACAATTGATATC--TTT-T
53773 TAACAATTGATATCTTTT
1 TAACAATTGATATCTTTT
53791 T
1 T
53792 CATTAAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 15 0.43
19 3 0.09
20 3 0.09
21 14 0.40
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (18 bp):
TAACAATTGATATCTTTT
Done.