Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005812.1 Hibiscus syriacus cultivar Beakdansim tig00013622_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: 52575
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:366 original size:56 final size:55
Alignment explanation
Indices: 294--410 Score: 150
Period size: 56 Copynumber: 2.1 Consensus size: 55
284 GATGCATAAA
* *
294 ATGCATTCATTGTTTCA-AAATAGCCTGAGTGCATCGATGCATGGCT-GGTGCATCG
1 ATGCATTCATTGTTTCATAAA-ACCCTGAGTGCATCGATGCATAG-TAGGTGCATCG
*
349 ATGCATTCGA-TGTTTTCATAAAACCCTGAGTGCATCGATGCATAGTATGTGCATCG
1 ATGCATTC-ATTG-TTTCATAAAACCCTGAGTGCATCGATGCATAGTAGGTGCATCG
405 ATGCAT
1 ATGCAT
411 GAAATGCATT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
55 11 0.20
56 41 0.75
57 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (55 bp):
ATGCATTCATTGTTTCATAAAACCCTGAGTGCATCGATGCATAGTAGGTGCATCG
Found at i:5929 original size:13 final size:14
Alignment explanation
Indices: 5911--5951 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
5901 TAAAAAAACT
*
5911 AATAAAATGAAA-A
1 AATAAAATAAAATA
5924 AATAAAATAAAATA
1 AATAAAATAAAATA
5938 AAT-AAAT-AAATA
1 AATAAAATAAAATA
5950 AA
1 AA
5952 CTAGTCGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 7 0.27
13 15 0.58
14 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
AATAAAATAAAATA
Found at i:5932 original size:18 final size:17
Alignment explanation
Indices: 5911--5951 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
5901 TAAAAAAACT
5911 AATAAAATGAAA-AAATAA
1 AATAAAAT-AAATAAAT-A
5929 AATAAAATAAATAAATA
1 AATAAAATAAATAAATA
5946 AATAAA
1 AATAAA
5952 CTAGTCGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
AATAAAATAAATAAATA
Found at i:17344 original size:182 final size:180
Alignment explanation
Indices: 17037--17511 Score: 716
Period size: 182 Copynumber: 2.7 Consensus size: 180
17027 GATACAAATA
* *
17037 AAAAATGTATCGATCCATATCAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-AAAACCGGTCTCGAAATGACA
* *
17102 AAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATACTTTAATATAAGCATCGACACTTT
65 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTT-ATATAAGTATCGACACTTT
* *
17167 TGGAATTTAAAAGAG-AAGCAGTAATAGCGCCTATAAAGTTTCGATACTTTAT
129 TGGAATTTAAAAG-GCAAGCAGTAATAGAGCCTATAAAGTGTCGATACTTTAT
* *
17219 AAAAATGTATCGATCCATAAAAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-AAAACCGGTCTCGAAATGACA
17284 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
65 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTA-TATAAGTATCGACACTTT
17349 TGGAATTTAAAAGGCAAGCAGTAATAGAGCCTATAAAGTGTCGATACTTTAT
129 TGGAATTTAAAAGGCAAGCAGTAATAGAGCCTATAAAGTGTCGATACTTTAT
* * * *
17401 AAAAATGTATCGA-CACTTAACAATATAATAGGT---AA-A--AAAAATCGGTCTCGAAATGACT
1 AAAAATGTATCGATC-CATAACAATATAACAGGTAAAAATATGAAAAACCGGTCTCGAAATGACA
*
17459 AAACCGGTAAAGCGTTACCGGATATGTTGAAAGTGTCGATACTTTA-ATAAGTA
65 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTATATAAGTA
17512 CGCGTAATAA
Statistics
Matches: 274, Mismatches: 16, Indels: 15
0.90 0.05 0.05
Matches are distributed among these distances:
173 7 0.03
175 63 0.23
176 1 0.00
178 1 0.00
179 2 0.01
181 3 0.01
182 197 0.72
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (180 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAACCGGTCTCGAAATGACAA
AACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTATATAAGTATCGACACTTTTG
GAATTTAAAAGGCAAGCAGTAATAGAGCCTATAAAGTGTCGATACTTTAT
Found at i:17961 original size:21 final size:19
Alignment explanation
Indices: 17913--17951 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
17903 TTGATACTTT
17913 TAGAAAATGATATTATAGG
1 TAGAAAATGATATTATAGG
17932 TAGAAAATGATATTATAGG
1 TAGAAAATGATATTATAGG
17951 T
1 T
17952 TGTAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (19 bp):
TAGAAAATGATATTATAGG
Found at i:19606 original size:199 final size:199
Alignment explanation
Indices: 19202--19929 Score: 1052
Period size: 199 Copynumber: 3.7 Consensus size: 199
19192 ACAGGTAAAA
* * *
19202 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATAGAAACAGATTATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * *
19267 ATAGGTAAATTTCCAATGTAATCGGTAGATATATACCAGTTTAATTAGAAAACAGGTAAACATAA
66 ATAGGTAAATTTCCAATGTAATCGGTAGAAATATACC-GGTTAATTAGAAAACAAGTAAACATAA
* ** *
19332 TGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCTAGAATGAACACCAAACGGGGTGTA
130 TGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTGCA
19397 CGCAT
195 CGCAT
* * *
19402 AAAGTGTCGATACATTTATTAAAAGTTTCGATCCCAAAAACATCGAAATAGAAAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* **
19467 ATAGGTAAATTTCTAATGTAAGT-GGTAGAAATATACCGGTTAATTAGAAAACAAGTTTACATAA
66 ATAGGTAAATTTCCAATGTAA-TCGGTAGAAATATACCGGTTAATTAGAAAACAAGTAAACATAA
*
19531 TGTAGT-GACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGGTGC
130 TGTA-TCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTGC
*
19595 ACGCGT
194 ACGCAT
*
19601 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACATATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * *
19666 ATAGGTAAATTTCCAATGTAATCGGTAGATATATACCGGTTTAATTAGAAAACAGGTAAGCATAA
66 ATAGGTAAATTTCCAATGTAATCGGTAGAAATATACCGG-TTAATTAGAAAACAAGTAAACATAA
* *
19731 TGTATCGACA-TATTTTAAA-TTATGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTGGGTG
130 TGTATCGACACT-TTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGGGGTG
*
19794 CACACAT
193 CACGCAT
* * * * * *
19801 CAAGTATCGATACATTAATTAAAAATAGCGATCCC-AAAACATCGAAATAGATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * * *
19865 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
66 ATAGGTAAATTTCCAATGTAATCGGTAGAAATATACCGGTTAATTAGAAAACAAGTAAACATAAT
19930 CGACACTTTT
Statistics
Matches: 476, Mismatches: 45, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
198 24 0.05
199 276 0.58
200 175 0.37
201 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (199 bp):
AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
ATAGGTAAATTTCCAATGTAATCGGTAGAAATATACCGGTTAATTAGAAAACAAGTAAACATAAT
GTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTGCAC
GCAT
Found at i:19984 original size:172 final size:174
Alignment explanation
Indices: 19763--20102 Score: 447
Period size: 172 Copynumber: 2.0 Consensus size: 174
19753 TGTCGATACT
*
19763 TTTTGTCCAGAATGAATGCCCAAACTGGGTGCACACATCAAGTATCGATACATTAATTAAAA-AT
1 TTTTGTCCAGAATGAATGCCCAAACTGGGTGCACACATAAAGTATCGATACATT--TTAAAATAT
* * * * **
19827 AGCGATCCC-AAAACATCGAAATAGATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGT
64 AGCAATCCCAAAAACATCAAAACAGATAATTACAATGTAATAGGTAAATTAACAATGTAACCGGT
* *
19891 AGAAATATACCGG-TTAATTAGAAAATAGGTATACATAATCGACAC
129 ACAAATATACCGGTTTAATGAGAAAATAGGTATACATAATCGACAC
* * *
19936 TTTTGTCTAGAATGAATG-CCAAA-TGGGGTGCACTCATAAAGTATCGATACATTTTAAAATGTA
1 TTTTGTCCAGAATGAATGCCCAAACT-GGGTGCACACATAAAGTATCGATACATTTTAAAATATA
* * *
19999 TCAATCCCAAAAACATCAAAACCGATAATTACAATGTAATAGGTAAATTAACAATGTAACTGGTA
65 GCAATCCCAAAAACATCAAAACAGATAATTACAATGTAATAGGTAAATTAACAATGTAACCGGTA
* * * *
20064 CATATTTACCGGTTTTATGAGAAAATAGGTCTACATAAT
130 CAAATATACCGGTTTAATGAGAAAATAGGTATACATAAT
20103 GTATCAACAC
Statistics
Matches: 144, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
170 6 0.04
171 9 0.06
172 89 0.62
173 40 0.28
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (174 bp):
TTTTGTCCAGAATGAATGCCCAAACTGGGTGCACACATAAAGTATCGATACATTTTAAAATATAG
CAATCCCAAAAACATCAAAACAGATAATTACAATGTAATAGGTAAATTAACAATGTAACCGGTAC
AAATATACCGGTTTAATGAGAAAATAGGTATACATAATCGACAC
Found at i:24673 original size:200 final size:198
Alignment explanation
Indices: 24320--24757 Score: 585
Period size: 200 Copynumber: 2.2 Consensus size: 198
24310 CAAGTAAACA
*
24320 AAAGTGTCC-ATACATTTTATAAAAGTATCGACCCCAAAAACATTAAAACCAATAATTATAATAT
1 AAAGTG-CCGATACATTTT-TAAAAGTATCGATCCCAAAAACATTAAAACCAATAATTATAATAT
* *
24384 AATCGGTAAATTAACAATGTAACCGATATAAATATACCAGTTTTAAGAGAGAACATGTCAACATA
64 AATAGGTAAATTAACAATGTAACCGATATAAATATACCAGTTTTAAGAGAGAACAGGTCAACATA
* * *
24449 ATGTATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAATGAGGTG
129 ATGTATCGACACTTGTGAAATTTGTGTCGATACTT-TTGTCCAAAATGAATGCCC-AACGAGGTG
*
24514 CACGCAT
192 CACACAT
** * *
24521 AAAGTGCCGATACATTTATTAAAAGTATCGATCCCAAAAACA-TCGAACCGATAATTATAATGTA
1 AAAGTGCCGATACATTT-TTAAAAGTATCGATCCCAAAAACATTAAAACCAATAATTATAATATA
* * * * * *
24585 ATAGGTAAATTTACAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCAACATAA
65 ATAGGTAAATTAACAATGTAACCGATATAAATATACCAGTTTTAAGAGAGAACAGGTCAACATAA
* * * *
24650 TGTATCGACACTTTTTAAATTTGTGTGGATACTTTTTTCCAAAATGAATGCCCAACGAGGTGCAC
130 TGTATCGACACTTGTGAAATTTGTGTCGATACTTTTGTCCAAAATGAATGCCCAACGAGGTGCAC
24715 ACAT
195 ACAT
* * *
24719 AAAGTGTCGATACA-TTTTAAATTGTATCGATCTCAAAAA
1 AAAGTGCCGATACATTTTTAAA-AGTATCGATCCCAAAAA
24758 TCTTCTAAAT
Statistics
Matches: 210, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
196 5 0.02
197 17 0.08
198 27 0.13
199 17 0.08
200 107 0.51
201 36 0.17
202 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (198 bp):
AAAGTGCCGATACATTTTTAAAAGTATCGATCCCAAAAACATTAAAACCAATAATTATAATATAA
TAGGTAAATTAACAATGTAACCGATATAAATATACCAGTTTTAAGAGAGAACAGGTCAACATAAT
GTATCGACACTTGTGAAATTTGTGTCGATACTTTTGTCCAAAATGAATGCCCAACGAGGTGCACA
CAT
Found at i:25256 original size:64 final size:64
Alignment explanation
Indices: 25137--25277 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 64
25127 TATAGAATGG
* * * *
25137 TTGTAAATTTATTTATTGCTATGAATTTTTGTATTATGTTTGACTTGAATATCCCCTACAATCA
1 TTGTAAATTTTTTTATTACTATGAATTTTTATATTATGTTTGACTTCAATATCCCCTACAATCA
* * * * *
25201 TTGTAAGTTTTTTTATTACTATGAATTTTTATATTATTTTTG-CTCTCAATTTCCCCTAGAATCG
1 TTGTAAATTTTTTTATTACTATGAATTTTTATATTATGTTTGACT-TCAATATCCCCTACAATCA
25265 TTGTAAATTTTTT
1 TTGTAAATTTTTT
25278 CAGTGGCTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
63 2 0.03
64 64 0.97
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (64 bp):
TTGTAAATTTTTTTATTACTATGAATTTTTATATTATGTTTGACTTCAATATCCCCTACAATCA
Found at i:25756 original size:43 final size:43
Alignment explanation
Indices: 25596--25757 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
25586 CAGACCAAGA
* * * * **
25596 AAAATGTTTGGTTGTGTATTTTGTTTTATATGTGTGAAGACCAGGT
1 AAAATGTTT-GATATGTATTTTGTTTGATA--TGTGAAGACTAAAT
* *
25642 AAAATGTTTGGTTATGTATTTTGTTTGATATGTGAAGACTAAGT
1 AAAATGTTT-GATATGTATTTTGTTTGATATGTGAAGACTAAAT
* * * *
25686 AAAATATTTGATCTTTATCTTGTTTGATATGTGAAGTAC-AAAT
1 AAAATGTTTGATATGTATTTTGTTTGATATGTGAAG-ACTAAAT
*
25729 AAAATGTTTGATATGTATTTTGATTGATA
1 AAAATGTTTGATATGTATTTTGTTTGATA
25758 GTGTTTTGTT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
43 50 0.50
44 22 0.22
46 28 0.28
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (43 bp):
AAAATGTTTGATATGTATTTTGTTTGATATGTGAAGACTAAAT
Found at i:25999 original size:157 final size:157
Alignment explanation
Indices: 25682--26048 Score: 578
Period size: 157 Copynumber: 2.3 Consensus size: 157
25672 TGTGAAGACT
* *
25682 AAGTAAAATATTTGATCTTTATCTTGTTTGATATGTGAAGTACAAATAAAATGTTTGATATGTAT
1 AAGTAAAATATTTGATATTTATCTTGTTTGATATGTGAAGTACAAATAAAATATTTGATATGTAT
*
25747 TTTGATTGATAGTGTTTTGTTGATGACATGAGTGAAAACAAGTTAAAAGATTAGAAACAATAGCG
66 TTTGATTGATAGTGTTTTGTTGATGACATGAGTGAAAACAAGTTAAAAGATTAAAAACAATAGCG
*
25812 GATCAAGACACCTGAAATTAACGAAAA
131 GATCAAGACACCTAAAATTAACGAAAA
* * *
25839 AAGTAAAATATTTTATATTTATCTTGTTTGCTATGTAAAGTACAAATAAAATATTTGATATGTAT
1 AAGTAAAATATTTGATATTTATCTTGTTTGATATGTGAAGTACAAATAAAATATTTGATATGTAT
* * *
25904 TTT-ATTAGATAGTGTTTTGTTTATGGCATGAGTGAAAAACAAGTTAAAAGATTAAAAACAGTAG
66 TTTGATT-GATAGTGTTTTGTTGATGACATGAGTG-AAAACAAGTTAAAAGATTAAAAACAATAG
* *
25968 TGGATCAA-AGCACCTAAAATTAAC-AACA
129 CGGATCAAGA-CACCTAAAATTAACGAAAA
25996 AAGTAAAATATTTGATATTTATCTTGTTTGATATGTGAAGTACAAATAAAATA
1 AAGTAAAATATTTGATATTTATCTTGTTTGATATGTGAAGTACAAATAAAATA
26049 GTAGTGAATC
Statistics
Matches: 192, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
156 3 0.02
157 142 0.74
158 47 0.24
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.35
Consensus pattern (157 bp):
AAGTAAAATATTTGATATTTATCTTGTTTGATATGTGAAGTACAAATAAAATATTTGATATGTAT
TTTGATTGATAGTGTTTTGTTGATGACATGAGTGAAAACAAGTTAAAAGATTAAAAACAATAGCG
GATCAAGACACCTAAAATTAACGAAAA
Found at i:26239 original size:21 final size:21
Alignment explanation
Indices: 26213--26282 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
26203 CTACATTTGC
*
26213 ACATTTGCATAACCTAAATCA
1 ACATTTGCATAACATAAATCA
26234 ACATTTGCATAACATAAATCA
1 ACATTTGCATAACATAAATCA
*
26255 ACATTTTCATAACATAAATCA
1 ACATTTGCATAACATAAATCA
26276 ACATTTG
1 ACATTTG
26283 TACATTCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.31
Consensus pattern (21 bp):
ACATTTGCATAACATAAATCA
Found at i:26436 original size:18 final size:18
Alignment explanation
Indices: 26413--26447 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26403 ATTTACCTGC
26413 ACAAAAGCTAATGCCTAT
1 ACAAAAGCTAATGCCTAT
* *
26431 ACAAAAGTTATTGCCTA
1 ACAAAAGCTAATGCCTA
26448 CATAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (18 bp):
ACAAAAGCTAATGCCTAT
Found at i:28637 original size:11 final size:11
Alignment explanation
Indices: 28621--28664 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
28611 ACAAATGGTC
28621 TAATATGTTAT
1 TAATATGTTAT
28632 TAATAT-TT-T
1 TAATATGTTAT
* *
28641 TAATATATTGT
1 TAATATGTTAT
28652 TAATATGTTAT
1 TAATATGTTAT
28663 TA
1 TA
28665 TTAATATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 7 0.24
10 4 0.14
11 18 0.62
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
TAATATGTTAT
Found at i:28679 original size:9 final size:9
Alignment explanation
Indices: 28665--28739 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
28655 TATGTTATTA
28665 TTAATATGG
1 TTAATATGG
28674 TTAATATGG
1 TTAATATGG
* *
28683 TAAAGGATGG
1 TTAA-TATGG
*
28693 TTTAATATGA
1 -TTAATATGG
*
28703 TTAATATTG
1 TTAATATGG
*
28712 -TAATGAAGG
1 TTAAT-ATGG
28721 CTTTAATATGG
1 --TTAATATGG
28732 TTAATATG
1 TTAATATG
28740 TTATGGAATG
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
8 4 0.08
9 29 0.58
10 7 0.14
11 6 0.12
12 4 0.08
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.41
Consensus pattern (9 bp):
TTAATATGG
Found at i:28707 original size:29 final size:27
Alignment explanation
Indices: 28665--28762 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 27
28655 TATGTTATTA
*
28665 TTAATATGGTTAATATGGTAAAGGATGGT
1 TTAATATGATTAATAT-GT-AAGGATGGT
* *
28694 TTAATATGATTAATATTGTAATGAAGGCT
1 TTAATATGATTAATA-TGTAAGGATGG-T
* *
28723 TTAATATGGTTAATATGTTATGGAATGGT
1 TTAATATGATTAATATG-TAAGG-ATGGT
28752 TTAATAT-ATTA
1 TTAATATGATTA
28763 TTAATATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 11 0.19
29 42 0.74
30 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.20, T:0.43
Consensus pattern (27 bp):
TTAATATGATTAATATGTAAGGATGGT
Found at i:28768 original size:11 final size:11
Alignment explanation
Indices: 28752--28848 Score: 60
Period size: 11 Copynumber: 8.9 Consensus size: 11
28742 ATGGAATGGT
28752 TTAATATATTA
1 TTAATATATTA
28763 TTAATAT-TT-
1 TTAATATATTA
* *
28772 TTAATATACTG
1 TTAATATATTA
* *
28783 GTAATATGTTA
1 TTAATATATTA
*
28794 TTAATATGTTA
1 TTAATATATTA
28805 TTAATGA-ATGGT-
1 TTAAT-ATAT--TA
*
28817 TTAATATGTTA
1 TTAATATATTA
*
28828 TTAATAT-TTT
1 TTAATATATTA
28838 TTAAATATATT
1 TT-AATATATT
28849 TATTTTTTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
9 7 0.10
10 8 0.12
11 43 0.63
12 9 0.13
13 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.54
Consensus pattern (11 bp):
TTAATATATTA
Found at i:28822 original size:34 final size:32
Alignment explanation
Indices: 28689--28838 Score: 133
Period size: 29 Copynumber: 4.8 Consensus size: 32
28679 ATGGTAAAGG
*
28689 ATGGTTTAATATG--ATTAATA-TTGTAATGA
1 ATGGTTTAATATGTTATTAATATTTTTAATGA
* *
28718 A-GGCTTTAATATG--GTTAATA-TGTT-ATGGA
1 ATGG-TTTAATATGTTATTAATATTTTTAAT-GA
*
28747 ATGGTTTAATATATTATTAATATTTTTAAT-A
1 ATGGTTTAATATGTTATTAATATTTTTAATGA
28778 TACTGG--TAATATGTTATTAATATGTTATTAATGA
1 -A-TGGTTTAATATGTTATTAATAT-TT-TTAATGA
28812 ATGGTTTAATATGTTATTAATATTTTT
1 ATGGTTTAATATGTTATTAATATTTTT
28839 TAAATATATT
Statistics
Matches: 100, Mismatches: 7, Indels: 25
0.76 0.05 0.19
Matches are distributed among these distances:
28 4 0.04
29 29 0.29
30 2 0.02
31 23 0.23
32 11 0.11
33 13 0.13
34 18 0.18
ACGTcount: A:0.35, C:0.01, G:0.15, T:0.49
Consensus pattern (32 bp):
ATGGTTTAATATGTTATTAATATTTTTAATGA
Found at i:29001 original size:95 final size:96
Alignment explanation
Indices: 28877--29161 Score: 466
Period size: 95 Copynumber: 3.0 Consensus size: 96
28867 TGTATTAGTT
* *
28877 TATTAG-TTATTAGTTTAGAACTTTACTGTTAGGTTATGAAATAAAGTTAAAGTGTTTATTTCTT
1 TATTAGTTTATTAGTTTAGGACTTTACTGTTAGGTTATGAAACAAAGTTAAAGTGTTTATTTCTT
28941 TTTTTGTTCAAGTTAAAGTCTTCATTAGAC-
66 TTTTTGTTCAAGTTAAAGTCTTCATTAGACG
* *
28971 TATTAGTTTATTATTTTAGGACTTTACTGTTAGGTTATGAAACAAGGTTAAAGTGTTTATTTCTT
1 TATTAGTTTATTAGTTTAGGACTTTACTGTTAGGTTATGAAACAAAGTTAAAGTGTTTATTTCTT
29036 TTTTTGTTCAAGTTAAAGTCTTCATTAGACTG
66 TTTTTGTTCAAGTTAAAGTCTTCATTAGAC-G
*
29068 TATTAGTTTATTAGTTTAGGACTTTACTTGTTAGGTTATGAAACAAAGTTAAAAGTGTTTATTAC
1 TATTAGTTTATTAGTTTAGGACTTTAC-TGTTAGGTTATGAAACAAAGTT-AAAGTGTTTATTTC
* *
29133 TTTCTTAGTTCAAGTTAAAGTCTTCATTA
64 TTTTTTTGTTCAAGTTAAAGTCTTCATTA
29162 CTTTACTACT
Statistics
Matches: 177, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
94 6 0.03
95 84 0.47
97 26 0.15
98 21 0.12
99 40 0.23
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.47
Consensus pattern (96 bp):
TATTAGTTTATTAGTTTAGGACTTTACTGTTAGGTTATGAAACAAAGTTAAAGTGTTTATTTCTT
TTTTTGTTCAAGTTAAAGTCTTCATTAGACG
Found at i:37632 original size:11 final size:11
Alignment explanation
Indices: 37618--37653 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
37608 AAATTTTGAC
37618 TTTTTAGTTTT
1 TTTTTAGTTTT
37629 TTTTTAGTTTT
1 TTTTTAGTTTT
37640 TTTTT-GTTTT
1 TTTTTAGTTTT
37650 TTTT
1 TTTT
37654 GCCTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (11 bp):
TTTTTAGTTTT
Found at i:37632 original size:18 final size:18
Alignment explanation
Indices: 37611--37670 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
37601 TTTTTTGAAA
*
37611 TTTTGACTTTTTAGTTTTT
1 TTTTGACTTTTTTG-TTTT
**
37630 TTTTAGTTTTTTTTTGTTTT
1 TTTT-G-ACTTTTTTGTTTT
*
37650 TTTTGCCTTTTTTGTTTT
1 TTTTGACTTTTTTGTTTT
37668 TTT
1 TTT
37671 GAAAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 14 0.41
19 5 0.15
20 9 0.26
21 6 0.18
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.80
Consensus pattern (18 bp):
TTTTGACTTTTTTGTTTT
Found at i:41043 original size:19 final size:20
Alignment explanation
Indices: 41021--41064 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
41011 TTTTTTGAAA
41021 TTTTGACCTTTTTT-TTGTTT
1 TTTTG-CCTTTTTTGTTGTTT
41041 TTTTGCCTTTTTTGTT-TTT
1 TTTTGCCTTTTTTGTTGTTT
41060 TTTTG
1 TTTTG
41065 GAAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.02, C:0.09, G:0.11, T:0.77
Consensus pattern (20 bp):
TTTTGCCTTTTTTGTTGTTT
Found at i:41650 original size:9 final size:9
Alignment explanation
Indices: 41636--41661 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41626 TAGGGGTTGA
41636 GTTCTAAAG
1 GTTCTAAAG
41645 GTTCTAAAG
1 GTTCTAAAG
41654 GTTCTAAA
1 GTTCTAAA
41662 TAACTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (9 bp):
GTTCTAAAG
Found at i:48304 original size:21 final size:20
Alignment explanation
Indices: 48279--48317 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
48269 AATCAAAGTC
*
48279 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
48300 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
48318 TCATGTCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Done.