Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004974.1 Hibiscus syriacus cultivar Beakdansim tig00011169_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: 66039
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1889 original size:17 final size:17
Alignment explanation
Indices: 1869--1903 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1859 ACTTTTTTTG
* *
1869 TTTTTGTTAGTTTTATT
1 TTTTTGTAAATTTTATT
1886 TTTTTGTAAATTTTATT
1 TTTTTGTAAATTTTATT
1903 T
1 T
1904 ATGATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTTGTAAATTTTATT
Found at i:4627 original size:2 final size:2
Alignment explanation
Indices: 4620--4645 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4610 TTTCTTATCC
4620 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
4646 CCCTTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5892 original size:32 final size:33
Alignment explanation
Indices: 5856--5929 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 33
5846 GTATCTTTAA
*
5856 AGATTCAATAGTAAATATTGGGGCATATTT-GG
1 AGATTCAACAGTAAATATTGGGGCATATTTAGG
* *
5888 AGATTCAACATTGAATATTGGGGCATATTTAGG
1 AGATTCAACAGTAAATATTGGGGCATATTTAGG
5921 -GATTCAACA
1 AGATTCAACA
5930 TCCTGATGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 36 0.95
33 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (33 bp):
AGATTCAACAGTAAATATTGGGGCATATTTAGG
Found at i:5930 original size:32 final size:32
Alignment explanation
Indices: 5869--5930 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
5859 TTCAATAGTA
5869 AATATTGGGGCATATTTGGAGATTCAACATTG
1 AATATTGGGGCATATTTGGAGATTCAACATTG
5901 AATATTGGGGCATATTTAGG-GATTCAACAT
1 AATATTGGGGCATATTT-GGAGATTCAACAT
5931 CCTGATGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (32 bp):
AATATTGGGGCATATTTGGAGATTCAACATTG
Found at i:6270 original size:65 final size:66
Alignment explanation
Indices: 6187--6312 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
6177 TGAGCTTCTG
*
6187 TCAACAAATAACTTTCC-AATTTCATTAAGAGTCAACTTCAACTTCACAGCGAAGGATATTTTTA
1 TCAACAAACAACTTTCCAAATTTCATTAAGAGTCAACTTCAACTTCACAGCGAAGGATATTTTTA
6251 C
66 C
* * *
6252 TCAACAAACAATTTTCCAAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT
1 TCAACAAACAACTTTCCAAATTTCATTAAGAGTCAACTTCAACTTCACAGCGAAGGATATT
6313 GAACTCGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
65 15 0.27
66 41 0.73
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.32
Consensus pattern (66 bp):
TCAACAAACAACTTTCCAAATTTCATTAAGAGTCAACTTCAACTTCACAGCGAAGGATATTTTTA
C
Found at i:6578 original size:43 final size:43
Alignment explanation
Indices: 6524--6733 Score: 233
Period size: 43 Copynumber: 4.9 Consensus size: 43
6514 ACGAATGGGC
* *
6524 CATCCATGATTTCAACTCCATGACGGAGGATATCGTACCAACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
6567 GATCCACGATTTCAACTCCACGACGGAGGATATCATGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * * *
6610 CATCTACTATTTAAACTCCACGACAGAGGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
6653 GATCCACGATTTCAACTCCACGATGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
6696 CAACCACGGTTTCAACTTCACGACGAAGAGA-ATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAG-GATATCGTAC
6734 ACACAAGCAG
Statistics
Matches: 135, Mismatches: 31, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
43 133 0.99
44 2 0.01
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:6718 original size:86 final size:86
Alignment explanation
Indices: 6531--6719 Score: 279
Period size: 86 Copynumber: 2.2 Consensus size: 86
6521 GGCCATCCAT
* *
6531 GATTTCAACTCCATGACGGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
1 GATTTCAACTCCACGACAGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
* *
6596 ATATCATGCCCACACATCTAC
66 ATATCATGCCCACACAACCAC
* * * *
6617 TATTTAAACTCCACGACAGAGGATATCGTACCAACGGATCCACGATTTCAACTCCACGATGGAGG
1 GATTTCAACTCCACGACAGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
*
6682 ATATCGTGCCCACACAACCAC
66 ATATCATGCCCACACAACCAC
* *
6703 GGTTTCAACTTCACGAC
1 GATTTCAACTCCACGAC
6720 GAAGAGAATC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 90 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.21
Consensus pattern (86 bp):
GATTTCAACTCCACGACAGAGGATATCGTACCAACAGATCCACGATTTCAACTCCACGACGGAGG
ATATCATGCCCACACAACCAC
Found at i:6983 original size:84 final size:83
Alignment explanation
Indices: 6811--7345 Score: 685
Period size: 84 Copynumber: 6.4 Consensus size: 83
6801 GGGTATCTGG
* * * * *
6811 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
*
6876 AGAAGGGCTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * *
6894 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGG
1 -CAAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTACAGCATAACTCAAGG
*
6959 TTAGAAGGGTTATCTGTCAA
64 CTAGAAGGGTTATCTGTCAA
* *
6979 CAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGCT
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
7044 AGAAGGGTTATCTGTCAA
66 AGAAGGGTTATCTGTCAA
* * * * * *
7062 AAAACACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
* ** *
7127 ATAAGGGTTATCTACCGA
66 AGAAGGGTTATCTGTCAA
* * * * * *
7145 CAAAAGTCCTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCAATTGCAGCATAACTCAAAGC
1 C-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGC
*
7210 TAGAAGGATTATCTGTCAA
65 TAGAAGGGTTATCTGTCAA
* * *
7229 CAAAGACC-TCGAGTTTGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCAATG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAGCATAACTCAAGG
* *
7293 CGAGAAGGGTTATCTGTCAT
64 CTAGAAGGGTTATCTGTCAA
* * *
7313 CAAAGACCTTCGAGTTTGATTTCATTCAGCTCA
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
7346 GGGGCATATC
Statistics
Matches: 392, Mismatches: 54, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
82 33 0.08
83 125 0.32
84 169 0.43
85 65 0.17
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (83 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAACTCAAGGCT
AGAAGGGTTATCTGTCAA
Found at i:7182 original size:167 final size:165
Alignment explanation
Indices: 6795--7345 Score: 694
Period size: 167 Copynumber: 3.3 Consensus size: 165
6785 TTCTAACTCA
* *
6795 AAGAAGGGGTATCTG--GCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
1 AAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
* * * * *
6858 GCAGCATAGCTTAAGTCAAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTACACTCA
66 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
6923 GCTTCGAGGGCACATCATTTACAACATAACTCAAGGT
130 GC-TCAAAGGCACATCATTTACAGCATAGCTCAAGGC
* *
6960 TAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATT
1 AAGAAGGGTTATCTGTC-ACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATT
** * * *
7025 TATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAACACCTTCGAGTTCGATTTCACTCA
65 TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCA
*
7090 GCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGC
130 GCTCAAAGGCACATCATTTACAGCATAGCTCAAGGC
* ** * * * *
7126 AATAAGGGTTATCTACCGACAAAAGTCCTTCGAGTTTGATTACACTCAGCTCAAAGGCATATCAA
1 AAGAAGGGTTATCTGTC-AC-AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAT
* * *
7191 TTGCAGCATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACC-TCGAGTTTGATTACACTC
64 TTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTC
*
7255 AGCTCAAAGGCACATCAAATTTACAGCATAGCTCAATGC
129 AGCTCAAAGGCACATC--ATTTACAGCATAGCTCAAGGC
* * * *
7294 GAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTTGATTTCATTCAGCTCA
1 AAGAAGGGTTATCTGTCA-CAAAGACCTTCGAGTTCGATTACACTCAGCTCA
7346 GGGGCATATC
Statistics
Matches: 332, Mismatches: 47, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
165 13 0.04
166 75 0.23
167 136 0.41
168 108 0.33
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (165 bp):
AAGAAGGGTTATCTGTCACAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCACATCATTTACAGCATAGCTCAAGGC
Found at i:7301 original size:251 final size:251
Alignment explanation
Indices: 6816--7345 Score: 749
Period size: 251 Copynumber: 2.1 Consensus size: 251
6806 TCTGGCAAAG
* * *
6816 ACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAG
1 ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
** * * * *
6881 GGCTATCTGTCAACCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
66 GGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCAAAGGCACATCAATTACA
* * *
6946 ACATAACTCAAGGTTAGAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
131 ACATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
* *
7011 AAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAAC
196 AAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAC
*
7067 ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAATAAG
1 ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
* * * * * *
7132 GGTTATCTACCGACAAAAGTCCTTCGAGTTTGATTACACTCAGC-TCAAAGGCATATCAATTGCA
66 GGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCAAAGGCACATCAATTACA
* * *
7196 GCATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACC-TCGAGTTTGATTACACTCAGCTC
131 ACATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
* * ** *
7260 AAAGGCACATCAAATTTACAGCATAGCTCAATGCGAGAAGGGTTATCTGTCATCAAAG
196 AAAGGCACATC--ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAC
* *
7318 ACCTTCGAGTTTGATTTCATTCAGCTCA
1 ACCTTCGAGTTCGATTTCACTCAGCTCA
7346 GGGGCATATC
Statistics
Matches: 246, Mismatches: 31, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
249 32 0.13
250 52 0.21
251 162 0.66
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (251 bp):
ACCTTCGAGTTCGATTTCACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAAG
GGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTTCAAAGGCACATCAATTACA
ACATAACTCAAAGCTAGAAGGATTATCTGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAAAAAC
Found at i:8626 original size:30 final size:30
Alignment explanation
Indices: 8592--8654 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
8582 GTCTTTCTAG
*
8592 TTTCTATTAATACTATTTTAATCCTTTAAT
1 TTTCTATTAATACTATTTTAATACTTTAAT
** * *
8622 TTTCTATTTGTGCTATTTTAGTACTTTAAT
1 TTTCTATTAATACTATTTTAATACTTTAAT
8652 TTT
1 TTT
8655 TTTCCTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTCTATTAATACTATTTTAATACTTTAAT
Found at i:8808 original size:18 final size:17
Alignment explanation
Indices: 8777--8811 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
8767 ATTTTCTTTC
8777 ATTTCTTTTATTTATTT
1 ATTTCTTTTATTTATTT
*
8794 ATTTACTTTTTTTTATTT
1 ATTT-CTTTTATTTATTT
8812 CGATCTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTCTTTTATTTATTT
Found at i:13144 original size:20 final size:20
Alignment explanation
Indices: 13107--13144 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13097 TTTATATAAT
*
13107 TTAATTTTATAATTAATATG
1 TTAATTTTATAATGAATATG
13127 TTAATTGTTA-AATGAATA
1 TTAATT-TTATAATGAATA
13145 ATATTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (20 bp):
TTAATTTTATAATGAATATG
Found at i:19624 original size:28 final size:28
Alignment explanation
Indices: 19593--19648 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
19583 CCAAAGAGCT
*
19593 ATAATCACCAAATTCAAATAGTTTGCCA
1 ATAATCACCAAATTCAAATAATTTGCCA
19621 ATAATCACCAAATTCAAATAATTTGCCA
1 ATAATCACCAAATTCAAATAATTTGCCA
19649 TTCTTATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (28 bp):
ATAATCACCAAATTCAAATAATTTGCCA
Found at i:25770 original size:27 final size:27
Alignment explanation
Indices: 25739--25806 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
25729 TCTATTTACA
25739 AAATCATATCTCTATAGGAATGATAAC
1 AAATCATATCTCTATAGGAATGATAAC
*
25766 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGATAAC
25793 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
25807 ATTCCTACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGATAAC
Found at i:32687 original size:20 final size:21
Alignment explanation
Indices: 32662--32700 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32652 GGCTGCTGGA
32662 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
32682 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
32701 GATCGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:32698 original size:10 final size:9
Alignment explanation
Indices: 32663--32779 Score: 90
Period size: 10 Copynumber: 12.2 Consensus size: 9
32653 GCTGCTGGAA
*
32663 ACCGGTTTA
1 ACCGGTTTG
*
32672 ACCGGTTTTCA
1 ACCGG-TTT-G
32683 ACCGGTTCTG
1 ACCGGTT-TG
32693 ACCGGTTTG
1 ACCGGTTTG
*
32702 ATCGGTTTTG
1 ACCGG-TTTG
32712 ACCGGTTTG
1 ACCGGTTTG
* *
32721 ATCGGTTTTA
1 ACCGG-TTTG
*
32731 ACCGGTTCG
1 ACCGGTTTG
*
32740 AACCAGTTTG
1 -ACCGGTTTG
*
32750 ACCGGTCTG
1 ACCGGTTTG
32759 AACCGGTTTG
1 -ACCGGTTTG
*
32769 ACCGGTCTG
1 ACCGGTTTG
32778 AC
1 AC
32780 TCGACCCGAC
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
9 38 0.44
10 42 0.48
11 7 0.08
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.32
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:32713 original size:19 final size:19
Alignment explanation
Indices: 32685--32737 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
32675 GGTTTTCAAC
*
32685 CGGTTCTGACCGGTTTGAT
1 CGGTTTTGACCGGTTTGAT
32704 CGGTTTTGACCGGTTTGAT
1 CGGTTTTGACCGGTTTGAT
*
32723 CGGTTTTAACCGGTT
1 CGGTTTTGACCGGTT
32738 CGAACCAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.30, T:0.40
Consensus pattern (19 bp):
CGGTTTTGACCGGTTTGAT
Found at i:32750 original size:48 final size:49
Alignment explanation
Indices: 32662--32774 Score: 142
Period size: 48 Copynumber: 2.3 Consensus size: 49
32652 GGCTGCTGGA
* * * *
32662 AACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGTTTGATCGGTTTTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTGACCAGTTTGACCGG-TCTG
*
32712 -ACCGGTTTGATCGGTTTT-AACCGGTTC-GAACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG-ACCAGTTTGACCGGTCTG
32759 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
32775 CTGACTCGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
47 4 0.07
48 35 0.64
49 16 0.29
ACGTcount: A:0.17, C:0.23, G:0.27, T:0.33
Consensus pattern (49 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCTGACCAGTTTGACCGGTCTG
Found at i:32753 original size:19 final size:20
Alignment explanation
Indices: 32731--32778 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
32721 ATCGGTTTTA
32731 ACCGGTTC-GAACCAGTTTG
1 ACCGGTTCTGAACCAGTTTG
*
32750 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAACCAGTTTG
32769 ACCGG-TCTGA
1 ACCGGTTCTGA
32779 CTCGACCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (20 bp):
ACCGGTTCTGAACCAGTTTG
Found at i:32803 original size:17 final size:17
Alignment explanation
Indices: 32783--32836 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 17
32773 GTCTGACTCG
32783 ACCCGACCGTTGACCCA
1 ACCCGACCGTTGACCCA
*
32800 ACCCGATCCGACTGTTGACCCG
1 ACCCGA--C--C-GTTGACCCA
32822 ACCCGACCGTTGACC
1 ACCCGACCGTTGACC
32837 GTTGACCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 13 0.42
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 14 0.45
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.15
Consensus pattern (17 bp):
ACCCGACCGTTGACCCA
Found at i:32816 original size:22 final size:22
Alignment explanation
Indices: 32785--32827 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
32775 CTGACTCGAC
32785 CCGACCGTTGACCCAACCCGAT
1 CCGACCGTTGACCCAACCCGAT
* *
32807 CCGACTGTTGACCCGACCCGA
1 CCGACCGTTGACCCAACCCGA
32828 CCGTTGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.14
Consensus pattern (22 bp):
CCGACCGTTGACCCAACCCGAT
Found at i:40059 original size:17 final size:17
Alignment explanation
Indices: 40037--40092 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
40027 TTGACCGGTC
40037 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
40054 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
40071 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
40088 TGACC
1 TGACC
40093 GTTGACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:45137 original size:101 final size:101
Alignment explanation
Indices: 45007--45208 Score: 395
Period size: 101 Copynumber: 2.0 Consensus size: 101
44997 ACTAGCATCG
45007 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
1 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
45072 AGACCAATTTTAATCTATATAATGAATCAATCATAA
66 AGACCAATTTTAATCTATATAATGAATCAATCATAA
*
45108 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGGGAAA
1 GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
45173 AGACCAATTTTAATCTATATAATGAATCAATCATAA
66 AGACCAATTTTAATCTATATAATGAATCAATCATAA
45209 CCAAATTATT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (101 bp):
GGAAGAACATAATTTAAGTCGAGTGTTGTACAACTCTTCTTTCAATTAAGCAATGGAAAGAGAAA
AGACCAATTTTAATCTATATAATGAATCAATCATAA
Found at i:48940 original size:20 final size:20
Alignment explanation
Indices: 48917--48959 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
48907 ATGTTAGACT
48917 TTTTTTTCTCCATCTTTTAC
1 TTTTTTTCTCCATCTTTTAC
48937 TTTTTTTCTCCATCTTTTAC
1 TTTTTTTCTCCATCTTTTAC
48957 TTT
1 TTT
48960 GCATGCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTTCTCCATCTTTTAC
Found at i:50881 original size:36 final size:37
Alignment explanation
Indices: 50807--50882 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
50797 TCTAATCTAA
50807 CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
1 CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
**
50844 CATTGATTTTTGGTAAATTTTAACTT-AAAATGTTAT
1 CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
50880 CAT
1 CAT
50883 GTATAATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 13 0.35
37 24 0.65
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (37 bp):
CATTGATTTTCAGTAAATTTTAACTTAAAAATGTTAT
Found at i:52695 original size:24 final size:24
Alignment explanation
Indices: 52663--52711 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
52653 AGTTCCAATC
52663 ACCTCTACCACGTTTCTTTTGTTG
1 ACCTCTACCACGTTTCTTTTGTTG
**
52687 ACCTCTACCATTTTTCTTTTGTTG
1 ACCTCTACCACGTTTCTTTTGTTG
52711 A
1 A
52712 AAAGCTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.10, T:0.49
Consensus pattern (24 bp):
ACCTCTACCACGTTTCTTTTGTTG
Found at i:55926 original size:25 final size:25
Alignment explanation
Indices: 55893--55951 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
55883 GTATTTTATG
* *
55893 TTATTAGGG-CGAACTTTTAAAATT
1 TTATGAGGGACGAACTTATAAAATT
*
55917 TTATGGAGGGATGAACTTATAAAATT
1 TTAT-GAGGGACGAACTTATAAAATT
55943 TTATGAGGG
1 TTATGAGGG
55952 GTGAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 17 0.57
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (25 bp):
TTATGAGGGACGAACTTATAAAATT
Found at i:55956 original size:25 final size:26
Alignment explanation
Indices: 55903--55956 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
55893 TTATTAGGGC
*
55903 GAACTTTTAAAATTTTATGGAGGGAT
1 GAACTTATAAAATTTTATGGAGGGAT
*
55929 GAACTTATAAAATTTTAT-GAGGGGT
1 GAACTTATAAAATTTTATGGAGGGAT
55954 GAA
1 GAA
55957 AAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (26 bp):
GAACTTATAAAATTTTATGGAGGGAT
Found at i:61272 original size:11 final size:10
Alignment explanation
Indices: 61254--61278 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
61244 ATAAAAATAA
61254 TATTTTTTTT
1 TATTTTTTTT
61264 TATTTTTTTT
1 TATTTTTTTT
61274 TATTT
1 TATTT
61279 CGGATCAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TATTTTTTTT
Found at i:61861 original size:12 final size:12
Alignment explanation
Indices: 61844--61869 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61834 AAAACTGTTC
61844 TTTAGCGGCGTT
1 TTTAGCGGCGTT
61856 TTTAGCGGCGTT
1 TTTAGCGGCGTT
61868 TT
1 TT
61870 AAGAGTAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:62031 original size:40 final size:40
Alignment explanation
Indices: 61953--62041 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
61943 GCATTTATTT
* * *
61953 ACAAACGCCGCAATAGGGTTTATATAGTGGCGTGTTTTCG
1 ACAAACGCCGCAATAGGGTATATATAGTGGCATGTTTTCA
* *
61993 ACAAACGCCGCAATA-GGTCCATCTATAGTGGTAT-TTTTCA
1 ACAAACGCCGCAATAGGGT--ATATATAGTGGCATGTTTTCA
*
62033 ATAAACGCC
1 ACAAACGCC
62042 ACAACAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.07
40 28 0.68
41 10 0.24
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (40 bp):
ACAAACGCCGCAATAGGGTATATATAGTGGCATGTTTTCA
Found at i:62118 original size:82 final size:82
Alignment explanation
Indices: 61993--62332 Score: 339
Period size: 82 Copynumber: 4.2 Consensus size: 82
61983 CGTGTTTTCG
* * ** * * *
61993 ACAAACGCCGCAATAG-GTCCATCTATAGTGGTATTTTTCAATAAACGCCACAACAGATTAGTAT
1 ACAAACGCCGCAATAGAGTTCACCTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGAAC
* *
62057 TTTAGCGGAGTTTTAAT
66 TTTAGCGGCGTTTTTAT
** * * * *
62074 ACAAACGCCGCAATAG-GTGAACTCTATAGTGGCGTTTTTTAATAAATGTCGCAACAAATTAGAA
1 ACAAACGCCGCAATAGAGTTCAC-CTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGAA
*
62138 CTTTAGCGGTGTTTTTAT
65 CTTTAGCGGCGTTTTTAT
* * * * *
62156 AAAAATGCCGTAATAGAGTTCACCTATTGTGGCGTTTTTTAAATAAAC-CCGCAACAGATTAGAA
1 ACAAACGCCGCAATAGAGTTCACCTATAGTGGCG-TTTTTCAATAAACGCCGCAACAGATTAGAA
62220 CTTTAGCGGCG-TTTTAT
65 CTTTAGCGGCGTTTTTAT
* * * * ** * *
62237 ACAAATGTCGCAATAGTGTTTACCTATAGTGATGTTTTTCAATAAACGCCGCAAGATATTA-ATA
1 ACAAACGCCGCAATAGAGTTCACCTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGA-A
*
62301 TTTTAGCGGCGTTTTTAT
65 CTTTAGCGGCGTTTTTAT
*
62319 ACAAACGCCACAAT
1 ACAAACGCCGCAAT
62333 TTATCAATAA
Statistics
Matches: 213, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
80 13 0.06
81 73 0.34
82 112 0.53
83 15 0.07
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (82 bp):
ACAAACGCCGCAATAGAGTTCACCTATAGTGGCGTTTTTCAATAAACGCCGCAACAGATTAGAAC
TTTAGCGGCGTTTTTAT
Found at i:62231 original size:41 final size:41
Alignment explanation
Indices: 62026--62234 Score: 101
Period size: 41 Copynumber: 5.1 Consensus size: 41
62016 TATAGTGGTA
* * * * *
62026 TTTTTCAATAAACGCCACAACAGATTAGTATTTTAGCGGAG-
1 TTTTTAAATAAAC-CCGCAACAGATTAGAACTTTAGCGGCGT
* * * *
62067 -TTTTAATACAAACGCCGCAATAG-GT-GAACTCTATAGTGGCGT
1 TTTTTAA-ATAAAC-CCGCAACAGATTAGAACT-T-TAGCGGCGT
** * *
62109 TTTTT-AATAAATGTCGCAACAAATTAGAACTTTAGCGGTGT
1 TTTTTAAATAAA-CCCGCAACAGATTAGAACTTTAGCGGCGT
** * * * * *
62150 TTTTATAAA-AATGCCGTAATAGAGTT-CACCTATT-GTGGCGT
1 TTTT-TAAATAAACCCGCAACAGA-TTAGAACT-TTAGCGGCGT
62191 TTTTTAAATAAACCCGCAACAGATTAGAACTTTAGCGGCGT
1 TTTTTAAATAAACCCGCAACAGATTAGAACTTTAGCGGCGT
62232 TTT
1 TTT
62235 ATACAAATGT
Statistics
Matches: 120, Mismatches: 33, Indels: 30
0.66 0.18 0.16
Matches are distributed among these distances:
39 3 0.03
40 15 0.12
41 81 0.68
42 10 0.08
43 11 0.09
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (41 bp):
TTTTTAAATAAACCCGCAACAGATTAGAACTTTAGCGGCGT
Done.