Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002056.1 Hibiscus syriacus cultivar Beakdansim tig00004190_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: 133708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7969 original size:14 final size:13
Alignment explanation
Indices: 7933--7959 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7923 ACAAATTGTC
7933 GACTCAAAAAACT
1 GACTCAAAAAACT
7946 GACTCAAAAAACT
1 GACTCAAAAAACT
7959 G
1 G
7960 TAGTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (13 bp):
GACTCAAAAAACT
Found at i:8261 original size:30 final size:30
Alignment explanation
Indices: 8226--8293 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
8216 ACCCTAACCC
8226 GACGGGGAAAAACCGTTTATACTAAACGGG
1 GACGGGGAAAAACCGTTTATACTAAACGGG
**
8256 GACGGGGAAAAACCGTTTATGTTAAACGGG
1 GACGGGGAAAAACCGTTTATACTAAACGGG
*
8286 GATGGGGA
1 GACGGGGA
8294 CGGGGACGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.34, C:0.13, G:0.35, T:0.18
Consensus pattern (30 bp):
GACGGGGAAAAACCGTTTATACTAAACGGG
Found at i:8461 original size:17 final size:17
Alignment explanation
Indices: 8401--8464 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
8391 TATTTTAATA
* *
8401 AATTTAAAT-TAAATTA
1 AATTTAAATATATATTT
*
8417 AATTATAAATATATATAT
1 AATT-TAAATATATATTT
8435 AATATT---TATATATTT
1 AAT-TTAAATATATATTT
8450 AATTTAAATATATAT
1 AATTTAAATATATAT
8465 ACCTGGCCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
14 2 0.05
15 11 0.29
16 4 0.11
17 12 0.32
18 8 0.21
19 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAAATATATATTT
Found at i:17883 original size:21 final size:21
Alignment explanation
Indices: 17844--17883 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17834 ATCTAATTCC
*
17844 AGTATCAATACTCCTTGAATG
1 AGTATCAATACTACTTGAATG
17865 AGTATCAATAC-ACTATGAA
1 AGTATCAATACTACT-TGAA
17884 AGTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (21 bp):
AGTATCAATACTACTTGAATG
Found at i:20426 original size:21 final size:21
Alignment explanation
Indices: 20400--20441 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20390 GATCTGCAGC
20400 TTAGTAATACGAATTAATCAT
1 TTAGTAATACGAATTAATCAT
20421 TTAGTAATACGAATTAATCAT
1 TTAGTAATACGAATTAATCAT
20442 AGAAGATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAGTAATACGAATTAATCAT
Found at i:33672 original size:59 final size:59
Alignment explanation
Indices: 33600--33714 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 59
33590 AATGAGGGTT
* * *
33600 ATGGTTTGGGGATG-GATTTGATACGTTCAAAAGTTT-GGAGACTAATTTAAAATGAAAGC
1 ATGGTTTGAGGATGAAATTTGA-ACGTTCAAAAGTTTAGG-GACTAAATTAAAATGAAAGC
* * *
33659 ATGGTTTGAGGATGAAATTTGAATGTTTAAAAGTTTAGGGCCTAAATTAAAATGAA
1 ATGGTTTGAGGATGAAATTTGAACGTTCAAAAGTTTAGGGACTAAATTAAAATGAA
33715 GACTTAGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 40 0.83
60 8 0.17
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (59 bp):
ATGGTTTGAGGATGAAATTTGAACGTTCAAAAGTTTAGGGACTAAATTAAAATGAAAGC
Found at i:40649 original size:60 final size:59
Alignment explanation
Indices: 40568--40683 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 59
40558 AGTCAGGTGA
* *
40568 TCATTTTATAACTTTTAATAGTCGGAA-GACTCAATAAAATAACGTTCTATAGTCGGATGG
1 TCATTTTATAACTTTTAATAGTC--AAGGACTCAACAAAATAACGTCCTATAGTCGGATGG
* *
40628 TCATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAATAATGTCCTATAGTCGG
1 TCATTTTATAACTTTTAATAGTCAA-GGACTCAACAAAATAACGTCCTATAGTCGG
40684 GGACGACCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 2 0.04
60 48 0.96
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (59 bp):
TCATTTTATAACTTTTAATAGTCAAGGACTCAACAAAATAACGTCCTATAGTCGGATGG
Found at i:46932 original size:37 final size:36
Alignment explanation
Indices: 46857--46932 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
46847 TTTTTATATT
*
46857 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
46893 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
46930 TTT
1 TTT
46933 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:47095 original size:18 final size:19
Alignment explanation
Indices: 47072--47108 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
47062 ACAGTAATTC
47072 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
47090 TATTCCTACTGGTAATCTT
1 TATTCC-ACTGGTAATCTT
47109 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:47114 original size:20 final size:20
Alignment explanation
Indices: 47078--47115 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47068 ATTCTATTCC
**
47078 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
47098 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
47116 GTGAACCAAA
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:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:55971 original size:13 final size:12
Alignment explanation
Indices: 55940--55972 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
55930 TATCTAAACT
55940 TTTAAAAATTTA
1 TTTAAAAATTTA
55952 TTTAAAAATTTA
1 TTTAAAAATTTA
55964 TTTAAAAAT
1 TTTAAAAAT
55973 CTTTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAAAATTTA
Found at i:55991 original size:20 final size:20
Alignment explanation
Indices: 55952--56011 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
55942 TAAAAATTTA
*
55952 TTTAAAAATTTATTTAAAAATC
1 TTTAAAAA--TATATAAAAATC
55974 TTTAAAAATATATAAAAA-C
1 TTTAAAAATATATAAAAATC
* * *
55993 TTTGAAACTATATTAAAAT
1 TTTAAAAATATATAAAAAT
56012 TAGAAAATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 16 0.48
20 9 0.27
22 8 0.24
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
TTTAAAAATATATAAAAATC
Found at i:57536 original size:353 final size:353
Alignment explanation
Indices: 56890--57595 Score: 1394
Period size: 353 Copynumber: 2.0 Consensus size: 353
56880 GGGGTGATAA
56890 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
56955 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
66 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
57020 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
131 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
57085 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
196 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
57150 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
261 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
57215 CAAGCCCACTATTATTCATTGCTAAGGT
326 CAAGCCCACTATTATTCATTGCTAAGGT
57243 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
1 TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
57308 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
66 CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
*
57373 TCATAGAATAATGGTTGGTGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
131 TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
57438 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
196 AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
*
57503 GTGCATAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
261 GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
57568 CAAGCCCACTATTATTCATTGCTAAGGT
326 CAAGCCCACTATTATTCATTGCTAAGGT
57596 GAGTAACATA
Statistics
Matches: 351, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
353 351 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (353 bp):
TGGATCATTGGTTTTACTTTGGATCTTAGTCCCATGAAAACCCTTGTCAAAACTTCTTAGTTGTA
CCAATTTTGCTAATACTAATTGATATAATCCAGTGGCTTAAATCTTCATGTGTTGATTTTACAAA
TCATAGAATAATGGTTGGCGTGGTGCTAAAATAATAATTTTCATGGAAACAGGGGCAAGGATGTT
AGGACTGAGAACATGCATCAAGGTTTCATTCGTGTTTCAATCTACATTTTATAGTACTGAAGGGA
GTGCAGAATATATAATTTGCAAACGTGTTCCTGCCCAACTTGGACAAGGTCATTGTATTTGACTA
CAAGCCCACTATTATTCATTGCTAAGGT
Found at i:60688 original size:14 final size:13
Alignment explanation
Indices: 60667--60708 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
60657 TTGCAATAAT
60667 GTATATTATAAAA
1 GTATATTATAAAA
60680 GTAATATTAATCAAAA
1 GT-ATATT-AT-AAAA
60696 GTATATTATAAAA
1 GTATATTATAAAA
60709 ATAAAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.23
14 7 0.27
15 7 0.27
16 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (13 bp):
GTATATTATAAAA
Found at i:61446 original size:105 final size:105
Alignment explanation
Indices: 60917--61799 Score: 1444
Period size: 105 Copynumber: 8.4 Consensus size: 105
60907 GGAGAGTTCC
* * * * * *
60917 GAGTCCAATATCCTCCGATGTGAAGTTGAAATTGGTTCTGGAACTGGA-AAATTATTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTTGAGAAA-TGTTTATTGACA
*
60981 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
61023 GAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGCTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTATTGACAA
*
61088 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
61129 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTACTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTATTGACAA
*
61194 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
61235 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGATTCTGAATTTGAGAAGTTGCTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA-ATGTTTATTGACAA
61300 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
61341 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAATTTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAAC
61406 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
61446 GAGTCCAATATCCTCCGTTGTGAAGTGGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAAC
61511 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
61551 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAAC
*
61616 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
61656 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAAC
*
61721 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
61761 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
61800 AGGTAAATCC
Statistics
Matches: 743, Mismatches: 32, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
105 404 0.54
106 339 0.46
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:62628 original size:50 final size:50
Alignment explanation
Indices: 62566--62661 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
62556 TTTTTTCCTC
* * *
62566 TTTTTCTTTTTTTAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGT
1 TTTTTCTTTTTTTAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
* *
62616 TTTTTTTTTTTTTAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTCTTTTTTTAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
62662 GCGTAGTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (50 bp):
TTTTTCTTTTTTTAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGT
Found at i:72069 original size:10 final size:10
Alignment explanation
Indices: 72044--72108 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
72034 GAGATTAGTA
*
72044 AAATAGAAAT
1 AAATAAAAAT
*
72054 AGATAAAAAT
1 AAATAAAAAT
72064 AAATAAAAAT
1 AAATAAAAAT
**
72074 AAATGGTAAAT
1 AAAT-AAAAAT
72085 GAAA-AAAACAT
1 -AAATAAAA-AT
*
72096 AAAAAAAAAT
1 AAATAAAAAT
72106 AAA
1 AAA
72109 AAAGGTTAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
10 31 0.70
11 10 0.23
12 3 0.07
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:73253 original size:2 final size:2
Alignment explanation
Indices: 73241--73277 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
73231 CTATTATAAG
* *
73241 TA TA TA CA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73278 TAAAATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:74695 original size:14 final size:13
Alignment explanation
Indices: 74674--74715 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
74664 TTGCAATAAT
74674 GTATATTATAAAA
1 GTATATTATAAAA
74687 GTAATATTAATCAAAA
1 GT-ATATT-AT-AAAA
74703 GTATATTATAAAA
1 GTATATTATAAAA
74716 ATAAAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.23
14 7 0.27
15 7 0.27
16 6 0.23
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (13 bp):
GTATATTATAAAA
Found at i:80003 original size:17 final size:18
Alignment explanation
Indices: 79968--80003 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
79958 GTAATAAGAA
*
79968 AAAATATTACTTTTAAAT
1 AAAATATTACTTATAAAT
79986 AAAATATTA-TTATAAAT
1 AAAATATTACTTATAAAT
80003 A
1 A
80004 TAATTTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATTACTTATAAAT
Found at i:81132 original size:20 final size:20
Alignment explanation
Indices: 81107--81146 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
81097 TTTGATTCAC
*
81107 GGAATGAAATATTATCAGTG
1 GGAATGAAAGATTATCAGTG
*
81127 GGAATGTAAGATTATCAGTG
1 GGAATGAAAGATTATCAGTG
81147 AATAGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (20 bp):
GGAATGAAAGATTATCAGTG
Found at i:86123 original size:23 final size:25
Alignment explanation
Indices: 86097--86165 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 25
86087 TATTTAAACT
86097 TTTTAATAATTTATAAATTT-TGA-
1 TTTTAATAATTTATAAATTTATGAC
* ** * *
86120 TTTTTATAGCTTATAAGTTTATTAC
1 TTTTAATAATTTATAAATTTATGAC
*
86145 TTTTAAT-ATTTTTAAATTTAT
1 TTTTAATAATTTATAAATTTAT
86166 TTAGTTTTTG
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
23 16 0.47
24 12 0.35
25 6 0.18
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTTAATAATTTATAAATTTATGAC
Found at i:86235 original size:17 final size:19
Alignment explanation
Indices: 86192--86235 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
86182 TTATCTGTGT
86192 TAATTTCTTGAATATTTAAA
1 TAATTT-TTGAATATTTAAA
86212 T-ATTTTT-AAT-TTTAAA
1 TAATTTTTGAATATTTAAA
86228 TAATTTTT
1 TAATTTTT
86236 TATTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 9 0.39
18 2 0.09
19 4 0.17
20 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTTTTGAATATTTAAA
Found at i:89741 original size:2 final size:2
Alignment explanation
Indices: 89729--89758 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
89719 GGAATCACGC
89729 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
89759 AACCAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:92680 original size:107 final size:107
Alignment explanation
Indices: 92492--92704 Score: 417
Period size: 107 Copynumber: 2.0 Consensus size: 107
92482 GTCCATTCTA
92492 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
1 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
*
92557 AAATCAGAAAATAGTTTAATAATCCCCTTCAAATGAGAGAAG
66 AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAAG
92599 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
1 CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
92664 AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAA
66 AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAA
92705 ATATGAGAAA
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (107 bp):
CTGATACAGAATTTGTACTTAAAATACGCTGTATCTACAGTTTTAGGCATGTTAGGGACATGGTT
AAATCAGAAAACAGTTTAATAATCCCCTTCAAATGAGAGAAG
Found at i:95401 original size:34 final size:34
Alignment explanation
Indices: 95358--95424 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
95348 TTTGCAGTTG
95358 GAAATAATTTAATTAGTGAACTTTTTATATATAC
1 GAAATAATTTAATTAGTGAACTTTTTATATATAC
*
95392 GAAATAATTTAATTAGTGAATTTTTTATATATA
1 GAAATAATTTAATTAGTGAACTTTTTATATATA
95425 AATATAGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (34 bp):
GAAATAATTTAATTAGTGAACTTTTTATATATAC
Found at i:99148 original size:25 final size:24
Alignment explanation
Indices: 99115--99161 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
99105 TTTAAATGAT
*
99115 TTAATATTTTATTA-ATTATTTTTA
1 TTAATATTTAATTACA-TATTTTTA
99139 TTAATAATTTAATTACATATTTT
1 TTAAT-ATTTAATTACATATTTT
99162 AAATATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATATTTAATTACATATTTTTA
Found at i:99162 original size:13 final size:12
Alignment explanation
Indices: 99115--99163 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
99105 TTTAAATGAT
99115 TTAATATTTT-A
1 TTAATATTTTAA
*
99126 TTAATTATTTTTA
1 TTAA-TATTTTAA
*
99139 TTAATAATTTAA
1 TTAATATTTTAA
99151 TTACATATTTTAA
1 TTA-ATATTTTAA
99164 ATATTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 4 0.12
12 15 0.47
13 13 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAATATTTTAA
Found at i:110063 original size:18 final size:18
Alignment explanation
Indices: 110040--110075 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
110030 TTTCGGTTTG
*
110040 AAAAAAATCGGTTTTTAA
1 AAAAAAACCGGTTTTTAA
110058 AAAAAAACCGGTTTTTAA
1 AAAAAAACCGGTTTTTAA
110076 TCCGGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (18 bp):
AAAAAAACCGGTTTTTAA
Found at i:110126 original size:19 final size:20
Alignment explanation
Indices: 110102--110165 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
110092 ATCATCCAAT
110102 TTTTTAAA-CCCATACCGGA
1 TTTTTAAACCCCATACCGGA
* *
110121 TTTTTAAACCCCATACTGAA
1 TTTTTAAACCCCATACCGGA
110141 TTTTTAAACCCCATACCGGA
1 TTTTTAAACCCCATACCGGA
110161 TTTTT
1 TTTTT
110166 TTCCGGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (20 bp):
TTTTTAAACCCCATACCGGA
Found at i:111467 original size:2 final size:2
Alignment explanation
Indices: 111455--111498 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
111445 ATTATAAGTG
*
111455 TA TA CA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
111497 TA
1 TA
111499 ATTATAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:111826 original size:14 final size:14
Alignment explanation
Indices: 111809--111842 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
111799 TCGAGGTCCT
111809 TACCAAGAGGGAGG
1 TACCAAGAGGGAGG
111823 TACCAAGAGGGAGG
1 TACCAAGAGGGAGG
111837 TACCAA
1 TACCAA
111843 CAGGTGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.35, T:0.09
Consensus pattern (14 bp):
TACCAAGAGGGAGG
Found at i:121207 original size:14 final size:14
Alignment explanation
Indices: 121188--121214 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
121178 GGTAAAACAT
121188 CCTTACTTTTCAGA
1 CCTTACTTTTCAGA
121202 CCTTACTTTTCAG
1 CCTTACTTTTCAG
121215 TGTATAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.30, G:0.07, T:0.44
Consensus pattern (14 bp):
CCTTACTTTTCAGA
Found at i:121455 original size:23 final size:24
Alignment explanation
Indices: 121417--121473 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
121407 ATTTTAATAA
*
121417 AATAATATTAATTATTAACATATTT
1 AATAATA-TATTTATTAACATATTT
* *
121442 AA-AATATATTTATTAATATTTTT
1 AATAATATATTTATTAACATATTT
121465 AATAATATA
1 AATAATATA
121474 ATATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.57
24 10 0.36
25 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
AATAATATATTTATTAACATATTT
Found at i:121465 original size:12 final size:12
Alignment explanation
Indices: 121417--121473 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
121407 ATTTTAATAA
*
121417 AATAATATTAATT
1 AATAATA-TATTT
* *
121430 ATTAACATATTT
1 AATAATATATTT
121442 AA-AATATATTT
1 AATAATATATTT
* *
121453 ATTAATATTTTT
1 AATAATATATTT
121465 AATAATATA
1 AATAATATA
121474 ATATAATATT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
11 9 0.26
12 20 0.59
13 5 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AATAATATATTT
Found at i:121530 original size:23 final size:20
Alignment explanation
Indices: 121471--121518 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
121461 TTTTAATAAT
121471 ATAATATA-ATATTATTACA
1 ATAATATACATATTATTACA
121490 ATAATATACATATTATTACA
1 ATAATATACATATTATTACA
121510 ATAATATAC
1 ATAATATAC
121519 TCAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATATACATATTATTACA
Found at i:121949 original size:22 final size:20
Alignment explanation
Indices: 121897--121950 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
121887 ATTATTATCA
*
121897 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
121917 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
121940 TATTTATTATA
1 TATTT-TTATA
121951 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:132193 original size:26 final size:26
Alignment explanation
Indices: 132115--132204 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
132105 TAATTATGAA
*
132115 AATATATTT-ATTAATAATTTTAATAAAT
1 AATATATTTAATT-AT-ATTGTAAT-AAT
* * * *
132143 AATAT-TATTAGTTTTAGTGTTATAAT
1 AATATAT-TTAATTATATTGTAATAAT
132169 AATATATTTAATTATATTGTAATAAT
1 AATATATTTAATTATATTGTAATAAT
132195 ACATGATATT
1 A-AT-ATATT
132205 ATATTCTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
26 24 0.50
27 9 0.19
28 13 0.27
29 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (26 bp):
AATATATTTAATTATATTGTAATAAT
Done.