Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004848.1 Hibiscus syriacus cultivar Beakdansim tig00010929_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: 81473
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7308 original size:42 final size:42
Alignment explanation
Indices: 7257--7610 Score: 460
Period size: 42 Copynumber: 8.5 Consensus size: 42
7247 ATGTTAACCA
*
7257 TATTGCGGCGTTTGAGCTATAAAAGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
* *
7299 TATTACGGCGTTTGAGCTATAAACGCCGTTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
* * * ** *
7341 TATTGTGGCGTTTTATCTATAAACGGTGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
7383 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
* * *
7425 TATTACGACGTTTGAGCTATAAACGCCGCTATATTACAATTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
** * * *
7467 TATTATGGTGTTTGATC-ATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
* * *
7508 TATTACGGCGTTTGTAGCT-CAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTG-AGCTATAAACGCCGCTATATTACAACTC
* * * *
7550 TATTGCGACATTTTAGCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
*
7592 TATTGCGGCGTTTTAGCTA
1 TATTGCGGCGTTTGAGCTA
7611 CTTGCGGCGT
Statistics
Matches: 272, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
41 38 0.14
42 234 0.86
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (42 bp):
TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
Found at i:7617 original size:18 final size:18
Alignment explanation
Indices: 7594--7629 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7584 TACTACTCTA
7594 TTGCGGCGTTTTAGCTAC
1 TTGCGGCGTTTTAGCTAC
7612 TTGCGGCGTTTTAGCTAC
1 TTGCGGCGTTTTAGCTAC
7630 AAACGCCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.28, T:0.39
Consensus pattern (18 bp):
TTGCGGCGTTTTAGCTAC
Found at i:9183 original size:41 final size:41
Alignment explanation
Indices: 9134--9352 Score: 139
Period size: 41 Copynumber: 5.3 Consensus size: 41
9124 CAGACAAACA
* * *
9134 TATTGCGGCGTTTGTAGGAAAATCGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTATAGCAAAA-CGCCGCTAAATTACTACTC
* * * *
9176 T-TTGCGGCATTTTTAGCACAAACGCCACTATAA--ACAACTC
1 TATTGCGGCGTTTATAGCA-AAACGCCGCTA-AATTACTACTC
**
9216 TATTGCGGCGTTTATATAAAAACGCCGCTAAATTACTACTC
1 TATTGCGGCGTTTATAGCAAAACGCCGCTAAATTACTACTC
* * * * *
9257 TATTGCGGTGTTTTTTTAG-AAAACGCCACTATAA--ACAACTA
1 TATTGCGGCG--TTTATAGCAAAACGCCGCTA-AATTACTACTC
* * * *
9298 TATTCCGGCGTTT-GAGCTATAAACGCCGCTAACTTAAC-ACCC
1 TATTGCGGCGTTTATAGC-A-AAACGCCGCTAAATT-ACTACTC
9340 TATTGCGGCGTTT
1 TATTGCGGCGTTT
9353 GTTTAAAAAA
Statistics
Matches: 137, Mismatches: 26, Indels: 28
0.72 0.14 0.15
Matches are distributed among these distances:
38 2 0.01
39 5 0.04
40 18 0.13
41 72 0.53
42 31 0.23
43 9 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (41 bp):
TATTGCGGCGTTTATAGCAAAACGCCGCTAAATTACTACTC
Found at i:9221 original size:82 final size:82
Alignment explanation
Indices: 9104--9347 Score: 248
Period size: 82 Copynumber: 3.0 Consensus size: 82
9094 TTTTGTGGCG
* * * *
9104 TTTTTATAAAAGCGCCACTACAGACAAAC-ATATTGCGGCGTTTGTAGGAAAATCGCCGCTAAAT
1 TTTTTAGAAAA-CGCCACTATAAAC-AACTATATTGCGGCGTTTGTA-GAAAAACGCCGCTAAAT
*
9168 TATTACTCT-TTGC-G-GCA
63 TACTACTCTATTGCGGTGCA
* * *
9185 TTTTTAGCACAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAATT
1 TTTTTAG-A-AAACGCCACTATAAACAACTATATTGCGGCGTTTGTAGAAAAACGCCGCTAAATT
**
9250 ACTACTCTATTGCGGTGTT
64 ACTACTCTATTGCGGTGCA
* * *
9269 TTTTTAGAAAACGCCACTATAAACAACTATATTCCGGCGTTTG-AGCTATAAACGCCGCTAACTT
1 TTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTGTAG--AAAAACGCCGCTAAATT
*
9333 AAC-ACCCTATTGCGG
64 -ACTACTCTATTGCGG
9348 CGTTTGTTTA
Statistics
Matches: 137, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
81 33 0.24
82 63 0.46
83 31 0.23
84 10 0.07
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (82 bp):
TTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTGTAGAAAAACGCCGCTAAATTAC
TACTCTATTGCGGTGCA
Found at i:10566 original size:33 final size:31
Alignment explanation
Indices: 10505--10611 Score: 139
Period size: 33 Copynumber: 3.4 Consensus size: 31
10495 GTCTGCATAT
10505 GCCATGCACATCCCCAACACCCAACACAGGTC
1 GCCATGCAC-TCCCCAACACCCAACACAGGTC
10537 GCCATGCACGTCCCCAACACCCCAACACAGGTC
1 GCCATGCAC-TCCCCAACA-CCCAACACAGGTC
* *
10570 GCCATGCACT-CCCAGCGA-CCTACA-AGGTC
1 GCCATGCACTCCCCAAC-ACCCAACACAGGTC
10599 GCCATGCACTCCC
1 GCCATGCACTCCC
10612 AGCGACCTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
29 15 0.22
30 7 0.10
31 5 0.07
32 20 0.29
33 22 0.32
ACGTcount: A:0.26, C:0.47, G:0.16, T:0.11
Consensus pattern (31 bp):
GCCATGCACTCCCCAACACCCAACACAGGTC
Found at i:10607 original size:29 final size:29
Alignment explanation
Indices: 10565--10647 Score: 112
Period size: 29 Copynumber: 2.9 Consensus size: 29
10555 ACCCCAACAC
10565 AGGTCGCCATGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
***
10594 AGGTCGCCATGCACTCCCAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* * *
10623 AGGTCGCCAAGCAGTCCCGGCGACC
1 AGGTCGCCATGCACTCCCAGCGACC
10648 AAGCTGGCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.20, C:0.40, G:0.25, T:0.14
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:10679 original size:26 final size:26
Alignment explanation
Indices: 10650--10701 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
10640 CGGCGACCAA
10650 GCTGGCGACCAAACTTAACCCTGCTC
1 GCTGGCGACCAAACTTAACCCTGCTC
* *
10676 GCTGGTGACTAAACTTAACCCTGCTC
1 GCTGGCGACCAAACTTAACCCTGCTC
10702 TCTCGTGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (26 bp):
GCTGGCGACCAAACTTAACCCTGCTC
Found at i:10749 original size:23 final size:23
Alignment explanation
Indices: 10716--10759 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
10706 GTGCATGCGT
*
10716 TGCATCTATAGCTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
10739 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
10760 GTAGCCAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:11732 original size:17 final size:17
Alignment explanation
Indices: 11710--11772 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
11700 GCGATATAAT
11710 TTTTGTTTAAAAAAATA
1 TTTTGTTTAAAAAAATA
*
11727 TTTTGTTTAAAAATATTTA
1 TTTTGTTTAAAAA-A-ATA
* *
11746 GTGTTGTTT-TAAAAATA
1 -TTTTGTTTAAAAAAATA
11763 TTTTGTTTAA
1 TTTTGTTTAA
11773 TTTATATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
16 7 0.19
17 15 0.42
18 2 0.06
19 5 0.14
20 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (17 bp):
TTTTGTTTAAAAAAATA
Found at i:11776 original size:20 final size:21
Alignment explanation
Indices: 11732--11776 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
11722 AAATATTTTG
**
11732 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
11753 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
11773 TTTA
1 TTTA
11777 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:12104 original size:27 final size:28
Alignment explanation
Indices: 12033--12101 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
12023 ACTAAATCTT
*
12033 ATTATTATTAAATCATTAAATATCAAATC
1 ATTATTATT-AATAATTAAATATCAAATC
* * *
12062 ATTA-GATTAATAATTAATTATTAAATC
1 ATTATTATTAATAATTAAATATCAAATC
*
12089 ATTATTAGTAATA
1 ATTATTATTAATA
12102 TTAGTAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 20 0.61
28 9 0.27
29 4 0.12
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (28 bp):
ATTATTATTAATAATTAAATATCAAATC
Found at i:14901 original size:23 final size:23
Alignment explanation
Indices: 14875--14935 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
14865 CTCATATAAA
*
14875 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
14898 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
14921 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
14936 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:15069 original size:18 final size:18
Alignment explanation
Indices: 15046--15081 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15036 GAATACATAT
15046 ATGTCCCAAAGGACCACA
1 ATGTCCCAAAGGACCACA
*
15064 ATGTCCCGAAGGACCACA
1 ATGTCCCAAAGGACCACA
15082 TATCATTCCT
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:0.36, C:0.33, G:0.19, T:0.11
Consensus pattern (18 bp):
ATGTCCCAAAGGACCACA
Found at i:15156 original size:121 final size:121
Alignment explanation
Indices: 14942--15305 Score: 656
Period size: 121 Copynumber: 3.0 Consensus size: 121
14932 GCCATATAAT
** * *
14942 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGT
*
15007 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCAAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
15063 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATTATATACATATGCTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGT
* *
15128 GTCTCACCAGACTTCCCACATGTTCCAAAGAATACATATATGTCCCGAATGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
15184 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGT
15249 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
15305 A
1 A
15306 TAGACCCTCG
Statistics
Matches: 232, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 232 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (121 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:15190 original size:18 final size:18
Alignment explanation
Indices: 15167--15202 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15157 GAATACATAT
*
15167 ATGTCCCGAATGACCACA
1 ATGTCCCGAAGGACCACA
15185 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
15203 TATCATTCCT
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:0.33, C:0.33, G:0.19, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:15280 original size:62 final size:63
Alignment explanation
Indices: 14972--15288 Score: 158
Period size: 62 Copynumber: 5.2 Consensus size: 63
14962 ATCATTCCTT
* *
14972 AAGAAT-CATATACATATACTAGGGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * * * *
15034 AAGAATACATAT--ATGTCCCAAAGGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATAT-CCTAGGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
15089 CCTT
61 CC-A
* * *
15093 AAGAAT-TATATACATATGCTAGGGATCAAGTATGTGTCTCACCAGACTTCCCACATGTTCCA
1 AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * ** * * * *
15155 AAGAATACATAT--ATGTCCCGAATGACCACA--A--TGTC-C-CGAAGGAC--CACATATCATT
1 AAGAATACATATACATAT-CCTAGGGATCA-AGTATGTGTCTCAC-CA-GACTTCACACAT-GTT
*
15210 CCTT
61 CC-A
*
15214 AAGAAT-CATATACATATGCTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
15276 AAGAATACATATA
1 AAGAATACATATA
15289 TGTCCCGAAG
Statistics
Matches: 177, Mismatches: 43, Indels: 69
0.61 0.15 0.24
Matches are distributed among these distances:
57 13 0.07
58 23 0.13
59 38 0.21
60 8 0.05
61 8 0.05
62 45 0.25
63 29 0.16
64 13 0.07
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (63 bp):
AAGAATACATATACATATCCTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
Found at i:16624 original size:63 final size:61
Alignment explanation
Indices: 16518--16675 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 61
16508 TAATGGAGGC
* * *
16518 ATGCATCGATGCACTCTTGATGCATCGATGCACTGAGGGCATTCGATGTT-CATTT-TATTAGAA
1 ATGCATCGATGCACTCTT-ATGCATCGATGCACTGACGACATTCGATGTTGCATTTAAATT---A
* * *
16581 ATGCATCGATGCACTCCTTATGTATCGATGCACTGACGACATTCGATTTTGTATTTAAATTA
1 ATGCATCGATGCACT-CTTATGCATCGATGCACTGACGACATTCGATGTTGCATTTAAATTA
*
16643 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCAC-TCTTATGCATCGATGCAC
16676 CTTCAACAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
62 30 0.36
63 43 0.52
64 7 0.08
65 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (61 bp):
ATGCATCGATGCACTCTTATGCATCGATGCACTGACGACATTCGATGTTGCATTTAAATTA
Found at i:16667 original size:19 final size:20
Alignment explanation
Indices: 16643--16680 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
16633 ATTTAAATTA
16643 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
16662 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
16681 ACAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:18187 original size:10 final size:10
Alignment explanation
Indices: 18172--18203 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
18162 AGTAATGATA
18172 TATGTATTTC
1 TATGTATTTC
18182 TATGTATTTC
1 TATGTATTTC
18192 TATGTATTTC
1 TATGTATTTC
18202 TA
1 TA
18204 AGATTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.59
Consensus pattern (10 bp):
TATGTATTTC
Found at i:18273 original size:60 final size:60
Alignment explanation
Indices: 18205--18853 Score: 509
Period size: 60 Copynumber: 11.2 Consensus size: 60
18195 GTATTTCTAA
18205 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
18265 GATTTAGTAATGATTAGTAATAATGAAAATATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
18325 GATTTAGTAATGATTAGTAATAATGAAATTTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAA-TTATTATTAATATTTAATGATTTGATAGTAAT
* *
18386 GA-TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * ** ** * ** * *
18444 GATTTAGTAATGATTTGATAGTAATG-CTTTACGACTTGAACAATGAACAATG-TTTGGTTCAAT
1 GATTTAGTAATGATTAG-TAATAATGAAATTATTA-TT-AA-TAT--TTAATGATTT-GAT--AG
18507 TAACCAT
57 T-A--AT
* * * * * * * * *
18514 -ATTTTCGTTA-CATAACTAGTAATGAAATTA-TAATAATGATTTAGT-A-ATGAT--TAAT
1 GA-TTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-ATTTAATGATTTGATAGTAAT
* * * * * ** * *
18569 AATAATA-AAATTATTATTAAT-ATTTAA-TAAT-TTGATA-TTAATGATTT---AGTAAT
1 GAT-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
18622 GA-TTAG---T-A--A-TAAT-A--AAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
18671 GATTTAGTAATCATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
18731 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
18791 GA-TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
18839 GATTTAGTAATGATT
1 GATTTAGTAATGATT
18854 TGATAGTAAT
Statistics
Matches: 478, Mismatches: 59, Indels: 109
0.74 0.09 0.17
Matches are distributed among these distances:
43 2 0.00
44 3 0.01
45 10 0.02
46 11 0.02
48 33 0.07
49 13 0.03
50 4 0.01
51 2 0.00
52 12 0.03
53 10 0.02
54 7 0.01
55 10 0.02
56 10 0.02
57 5 0.01
58 34 0.07
59 19 0.04
60 210 0.44
61 33 0.07
62 4 0.01
63 3 0.01
64 5 0.01
65 6 0.01
66 4 0.01
67 4 0.01
68 10 0.02
69 6 0.01
70 8 0.02
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:18282 original size:21 final size:20
Alignment explanation
Indices: 18206--18346 Score: 69
Period size: 21 Copynumber: 7.0 Consensus size: 20
18196 TATTTCTAAG
18206 ATTTAGTAATGATTAGTAAT
1 ATTTAGTAATGATTAGTAAT
* * * *
18226 A-AT-GAAATTATTATTAAT
1 ATTTAGTAATGATTAGTAAT
* *
18244 ATTTAATGATTTGA-TAGTAAT
1 ATTTAGT-A-ATGATTAGTAAT
18265 GATTTAGTAATGATTAGTAAT
1 -ATTTAGTAATGATTAGTAAT
* * * *
18286 AATGA-AAAT-ATTATTAAT
1 ATTTAGTAATGATTAGTAAT
* * *
18304 ATTTAATGATTTGA-TATTAAT
1 ATTTAGT-A-ATGATTAGTAAT
18325 GATTTAGTAATGATTAGTAAT
1 -ATTTAGTAATGATTAGTAAT
18346 A
1 A
18347 ATGAAATTTA
Statistics
Matches: 86, Mismatches: 23, Indels: 24
0.65 0.17 0.18
Matches are distributed among these distances:
18 24 0.28
19 5 0.06
20 12 0.14
21 30 0.35
22 15 0.17
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.45
Consensus pattern (20 bp):
ATTTAGTAATGATTAGTAAT
Found at i:18392 original size:10 final size:10
Alignment explanation
Indices: 18379--18405 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18369 AATGATTTGA
18379 TAGTAATGAT
1 TAGTAATGAT
18389 TAGTAATGAT
1 TAGTAATGAT
18399 TAGTAAT
1 TAGTAAT
18406 AATAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:18429 original size:21 final size:22
Alignment explanation
Indices: 18405--18454 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
18395 TGATTAGTAA
18405 TAATAATTT-ATTATTAAT-ATT
1 TAATAATTTGA-TATTAATGATT
*
18426 TAATGATTTGATATTAATGATT
1 TAATAATTTGATATTAATGATT
*
18448 TAGTAAT
1 TAATAAT
18455 GATTTGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (22 bp):
TAATAATTTGATATTAATGATT
Found at i:18442 original size:14 final size:14
Alignment explanation
Indices: 18426--18469 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
18416 TATTAATATT
*
18426 TAATGATTTGATAT
1 TAATGATTTGATAG
18440 TAATGA-TT--TAG
1 TAATGATTTGATAG
18451 TAATGATTTGATAG
1 TAATGATTTGATAG
18465 TAATG
1 TAATG
18470 CTTTACGACT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 8 0.31
12 2 0.08
13 2 0.08
14 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:18568 original size:21 final size:20
Alignment explanation
Indices: 18544--18632 Score: 58
Period size: 21 Copynumber: 4.4 Consensus size: 20
18534 AATGAAATTA
18544 TAATAATGATTTAGTAATGAT
1 TAATAAT-ATTTAGTAATGAT
* * *
18565 TAATAATA-ATA-AAATTAT
1 TAATAATATTTAGTAATGAT
* *
18583 TATTAATATTTAATAATTTGA-
1 TAATAATATTTAGTAA--TGAT
*
18604 TATTAATGATTTAGTAATGAT
1 TAATAAT-ATTTAGTAATGAT
*
18625 TAGTAATA
1 TAATAATA
18633 ATAAAATTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
18 12 0.23
19 4 0.08
20 7 0.13
21 20 0.38
22 10 0.19
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (20 bp):
TAATAATATTTAGTAATGAT
Found at i:18673 original size:49 final size:49
Alignment explanation
Indices: 18615--19161 Score: 376
Period size: 48 Copynumber: 10.3 Consensus size: 49
18605 ATTAATGATT
18615 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
18664 TAGTAATGATTTAGTAATCATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTA
1 TAGTAATGA-TTAG---T-A--A-TAAT-A--AAATTATTATTAATATTT-A--A--TG--ATT-
18729 ATGA
47 -TGA
*
18733 TTTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
*
18784 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
* * * * *
18832 TATTAATGATTTAGTAATGAT----TTGA-TAGTAATGATTT-ACGACTTGAACAA
1 TAGTAATGA-TTAGTAATAATAAAATT-ATTATTAAT-ATTTAATGATTTG----A
** * ** * * *
18882 TGAACAATGTTTAGTTCAATTAACCATATT-TTAGTTACATAACCAGTAATGAAATTATAATAAT
1 T-AGTAATGATTAG-T-AA-TAATAAAATTATTA-TTA-AT----A-T--T-TAATGAT--T--T
18946 GA
48 GA
*
18948 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
* *
18999 TATTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
*
19048 TAGTAATGATTAGTAATAA-AAATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
* *
19096 TATTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
*
19144 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
19162 GATTTGATAG
Statistics
Matches: 407, Mismatches: 34, Indels: 114
0.73 0.06 0.21
Matches are distributed among these distances:
46 14 0.03
47 5 0.01
48 116 0.29
49 111 0.27
50 10 0.02
51 12 0.03
52 2 0.00
53 7 0.02
54 1 0.00
55 7 0.02
56 4 0.01
57 9 0.02
58 4 0.01
59 2 0.00
60 35 0.09
61 2 0.00
62 2 0.00
63 7 0.02
64 12 0.03
65 7 0.02
66 5 0.01
67 13 0.03
68 2 0.00
69 3 0.01
70 6 0.01
71 9 0.02
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
Found at i:18837 original size:14 final size:14
Alignment explanation
Indices: 18821--18868 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
18811 TATTAATATT
*
18821 TAATGATTTGATAT
1 TAATGATTTGATAG
18835 TAATGA-TT--TAG
1 TAATGATTTGATAG
18846 TAATGATTTGATAG
1 TAATGATTTGATAG
18860 TAATGATTT
1 TAATGATTT
18869 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:18942 original size:395 final size:392
Alignment explanation
Indices: 18205--19112 Score: 1435
Period size: 395 Copynumber: 2.3 Consensus size: 392
18195 GTATTTCTAA
*
18205 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
*
18270 AGTAATGATTAGTAATAATGAAAATATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
66 AGTAAT-ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
*
18335 TGATTAGTAATAATGAAATTTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATGATT
130 TGATTAGTAATAATGAAAATTATTATTAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATGATT
18400 AGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAG
191 AGTAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAG
* * *
18465 TAATGCTTTACGACTTGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAAC
256 TAATGATTTACGACTTGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAAC
*
18530 TAGTAATGAAATTATAATAATGATTTAGTAATGATTAATAATAATAAAATTATTATTAATATTTA
321 CAGTAATGAAATTATAATAATGATTTAGTAATGATTAATAATAATAAAATTATTATTAATA-TT-
18595 ATAATTTGATATTAAT
384 -TAA--TG--ATT--T
18611 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
18676 AGTAATCATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
66 AGTAAT-ATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
18741 TGATTAGTAATAAT-AAAATTATTATTAATTTTT-A-A-TGAT-T-TGA-TAGTAATGATTAGTA
130 TGATTAGTAATAATGAAAATTATTATTAATTTTTAAGATTGATATATGATTAGTAATGATTAGTA
18799 ATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAAT
195 ATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAAT
18864 GATTTACGACTTGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGT
260 GATTTACGACTTGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGT
* *
18929 AATGAAATTATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA
325 AATGAAATTATAATAATGATTTAGTAATGATTAATAATAATAAAATTATTATTAATATTTAATGA
18994 TTT
390 TTT
* *
18997 GA--TATTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TT
1 GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
19059 AGT-A-A-TA--AA-AAT----TTATTATTAATATTTAATGATTTGATATTAATGA-TTAGTAAT
66 AGTAATATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
19113 AATAATTTAT
Statistics
Matches: 490, Mismatches: 12, Indels: 35
0.91 0.02 0.07
Matches are distributed among these distances:
371 8 0.02
372 34 0.07
376 3 0.01
377 2 0.00
379 2 0.00
380 1 0.00
382 1 0.00
383 5 0.01
384 56 0.11
386 3 0.01
388 3 0.01
390 2 0.00
392 3 0.01
394 2 0.00
395 196 0.40
396 3 0.01
398 1 0.00
400 4 0.01
402 1 0.00
404 1 0.00
405 18 0.04
406 141 0.29
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (392 bp):
GATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
AGTAATATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
GATTAGTAATAATGAAAATTATTATTAATTTTTAAGATTGATATATGATTAGTAATGATTAGTAA
TAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATG
ATTTACGACTTGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGTA
ATGAAATTATAATAATGATTTAGTAATGATTAATAATAATAAAATTATTATTAATATTTAATGAT
TT
Found at i:19103 original size:14 final size:14
Alignment explanation
Indices: 19084--19180 Score: 65
Period size: 14 Copynumber: 6.7 Consensus size: 14
19074 TTATTAATAT
19084 TTAATGATTTGATA
1 TTAATGATTTGATA
*
19098 TTAATGATTAGTAATA
1 TTAATGATT--TGATA
* * *
19114 ATAATTTATTATTAATA
1 TTAA-TGA-T-TTGATA
19131 TTTAATGATTTGATA
1 -TTAATGATTTGATA
19146 TTAATGA-TT--TA
1 TTAATGATTTGATA
*
19157 GTAATGATTTGATA
1 TTAATGATTTGATA
*
19171 GTAATGATTT
1 TTAATGATTT
19181 ACGACTTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
11 8 0.12
12 2 0.03
13 2 0.03
14 28 0.42
15 5 0.07
16 8 0.12
17 9 0.13
18 4 0.06
19 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (14 bp):
TTAATGATTTGATA
Found at i:19129 original size:312 final size:327
Alignment explanation
Indices: 18607--19262 Score: 1054
Period size: 312 Copynumber: 2.0 Consensus size: 327
18597 AATTTGATAT
18607 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
1 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
*
18672 ATTTAGTAATCATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTA
66 ATTTAG--ATCA-TAGTAATAA-GAAATTATTATTAATATTT-ATGATATGA-ATT-ATGA-TTA
*
18737 GTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATA
123 GTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATA
18802 ATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGAT
188 ATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGAT
18867 TTACGACTTGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGTAAT
253 TTACGACTTGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGTAAT
18932 GAAATTATAA
318 GAAATTATAA
* *
18942 TAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
19007 A-TTAG-T-A-A-TAAT-A-AAATTATTATTAAT-TTT-T-A-ATG-ATT-TGA-TAGTAATGAT
66 ATTTAGATCATAGTAATAAGAAATTATTATTAATATTTATGATATGAATTATGATTAGTAATGAT
* *
19058 TAGTAATAA-AAATTTATTATTAATATTTAATGATTTGATATTAATGATTAGTAATAATAATTTA
131 TAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAATTTA
19122 TTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGATTTACGACT
196 TTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGATTTACGACT
* * *
19187 TGAACAATGAACAATGTTTGGTTCAATTAACCATATTTTCGTTACATAACTAGTAATGAAATTAT
261 TGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGTAATGAAATTAT
19252 AA
326 AA
19254 TAATGATTT
1 TAATGATTT
19263 GATACTAAAA
Statistics
Matches: 312, Mismatches: 9, Indels: 23
0.91 0.03 0.07
Matches are distributed among these distances:
312 190 0.61
313 19 0.06
315 3 0.01
317 3 0.01
319 2 0.01
320 1 0.00
321 1 0.00
323 3 0.01
324 14 0.04
326 1 0.00
327 4 0.01
328 1 0.00
330 1 0.00
331 1 0.00
334 4 0.01
335 64 0.21
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.44
Consensus pattern (327 bp):
TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATG
ATTTAGATCATAGTAATAAGAAATTATTATTAATATTTATGATATGAATTATGATTAGTAATGAT
TAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATAATTTA
TTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGATTTACGACT
TGAACAATGAACAATGTTTAGTTCAATTAACCATATTTTAGTTACATAACCAGTAATGAAATTAT
AA
Found at i:21416 original size:15 final size:14
Alignment explanation
Indices: 21393--21423 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
21383 TACAACATTA
21393 AACTTTAATATAAT
1 AACTTTAATATAAT
21407 AACTTATAATATAAT
1 AACTT-TAATATAAT
21422 AA
1 AA
21424 ACTAACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:21952 original size:29 final size:29
Alignment explanation
Indices: 21920--21984 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 29
21910 TTCTCACTTT
*
21920 CTTTCTTTCTCTGCTGCAATTTCTTCTCC
1 CTTTCTTTCTCTGCTGCAATCTCTTCTCC
21949 CTTTC--T-TCTGCTGCAATCTCTTCTCC
1 CTTTCTTTCTCTGCTGCAATCTCTTCTCC
21975 CTTTCTTTCT
1 CTTTCTTTCT
21985 TTTATGTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 24 0.75
27 1 0.03
28 1 0.03
29 6 0.19
ACGTcount: A:0.06, C:0.35, G:0.06, T:0.52
Consensus pattern (29 bp):
CTTTCTTTCTCTGCTGCAATCTCTTCTCC
Found at i:22327 original size:29 final size:29
Alignment explanation
Indices: 22280--22336 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
22270 AAACCCCACA
22280 AAGGTCGCCTGAAAGGCATGGCGACCTAC
1 AAGGTCGCCTGAAAGGCATGGCGACCTAC
* **
22309 AAGGTCGCCTGGATTGCATGGCGACCTA
1 AAGGTCGCCTGAAAGGCATGGCGACCTA
22337 TGGCCATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.26, G:0.32, T:0.18
Consensus pattern (29 bp):
AAGGTCGCCTGAAAGGCATGGCGACCTAC
Found at i:22636 original size:32 final size:32
Alignment explanation
Indices: 22594--22662 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
22584 GACCTTGTAG
* *
22594 GCATGGCGACCTGTGTTGGGGTGTTGGGGA-GT
1 GCATGACGACCTGTGTT-GGGTGTTGGAGACGT
22626 GCATGACGACCTGTGTTGGGTGTTGGAGACGT
1 GCATGACGACCTGTGTTGGGTGTTGGAGACGT
22658 GCATG
1 GCATG
22663 GCACATGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 11 0.32
32 23 0.68
ACGTcount: A:0.13, C:0.14, G:0.45, T:0.28
Consensus pattern (32 bp):
GCATGACGACCTGTGTTGGGTGTTGGAGACGT
Found at i:48224 original size:7 final size:7
Alignment explanation
Indices: 48212--48236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48202 GTAAACCTAT
48212 TTTCATG
1 TTTCATG
48219 TTTCATG
1 TTTCATG
48226 TTTCATG
1 TTTCATG
48233 TTTC
1 TTTC
48237 CGCACATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.60
Consensus pattern (7 bp):
TTTCATG
Found at i:56852 original size:22 final size:23
Alignment explanation
Indices: 56810--56856 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
56800 ATCGAGCTCG
56810 AGGGTTAAGTTGAGTTTTTTTTA
1 AGGGTTAAGTTGAGTTTTTTTTA
* * *
56833 AGGGTTTATTTGATTTTTTTTTA
1 AGGGTTAAGTTGAGTTTTTTTTA
56856 A
1 A
56857 AATATTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (23 bp):
AGGGTTAAGTTGAGTTTTTTTTA
Found at i:57445 original size:29 final size:29
Alignment explanation
Indices: 57384--57469 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
57374 TGATTAATAT
* *
57384 TTTTATTTTTATTTTTTTAGTAATTTAAC
1 TTTTATTTTTATATTTTTAGTAATTTAAA
57413 TTTTATTTTTAGTATTTTTA-T-ATTTAGAA
1 TTTTATTTTTA-TATTTTTAGTAATTTA-AA
* *
57442 --TT-TTCTTATATTTTTA-TATTTTAAA
1 TTTTATTTTTATATTTTTAGTAATTTAAA
57467 TTT
1 TTT
57470 AAAATTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 11 0.23
26 9 0.19
27 3 0.06
28 5 0.10
29 13 0.27
30 7 0.15
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (29 bp):
TTTTATTTTTATATTTTTAGTAATTTAAA
Found at i:65446 original size:2 final size:2
Alignment explanation
Indices: 65439--65465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65429 ATGTTTATGC
65439 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
65466 GGGGGAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:67564 original size:4 final size:4
Alignment explanation
Indices: 67555--67585 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
67545 ATTGATATGA
67555 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
67586 ATGAGAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:67681 original size:18 final size:19
Alignment explanation
Indices: 67642--67684 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
67632 TTGGTTCACG
*
67642 GAATATAAGATTACCAGTGA
1 GAATAAAAGATTACCAG-GA
67662 GAATAAAAGATTACCA-GA
1 GAATAAAAGATTACCAGGA
67680 GAATA
1 GAATA
67685 GCATTATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (19 bp):
GAATAAAAGATTACCAGGA
Found at i:67873 original size:39 final size:38
Alignment explanation
Indices: 67830--67917 Score: 88
Period size: 39 Copynumber: 2.3 Consensus size: 38
67820 AACAACTTGG
* * *
67830 AAAATATTTATATATATATTTTAAAAAATTTAAATTCAT
1 AAAATATTTATAAATATATTTTAAAAAATTGAAAAT-AT
* * *
67869 AAAAT-TTATATAAATTTTTTTTACAAAATTGAAAATAT
1 AAAATATT-TATAAATATATTTTAAAAAATTGAAAATAT
67907 AAAATAGTTTA
1 AAAATA-TTTA
67918 ATGAAAGAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
38 9 0.22
39 29 0.73
40 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (38 bp):
AAAATATTTATAAATATATTTTAAAAAATTGAAAATAT
Found at i:70124 original size:32 final size:32
Alignment explanation
Indices: 70088--70166 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
70078 CAGTAAAGCT
70088 TATGATCACCACAAACAATTTAATTTAAGGCA
1 TATGATCACCACAAACAATTTAATTTAAGGCA
70120 TATGATCACCACAAACAATTTAATTTAAGGCA
1 TATGATCACCACAAACAATTTAATTTAAGGCA
*
70152 TATGACCACCACAAA
1 TATGATCACCACAAA
70167 GACGCATAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (32 bp):
TATGATCACCACAAACAATTTAATTTAAGGCA
Done.