Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005196.1 Hibiscus syriacus cultivar Beakdansim tig00011741_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: 99750
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:249 original size:20 final size:21
Alignment explanation
Indices: 224--262 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
214 TGGCCGACGA
224 ACCAAAACCTCGG-TGGACAC
1 ACCAAAACCTCGGCTGGACAC
244 ACCAAAACCTCGGCTGGAC
1 ACCAAAACCTCGGCTGGAC
263 GCATCAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.36, G:0.21, T:0.10
Consensus pattern (21 bp):
ACCAAAACCTCGGCTGGACAC
Found at i:821 original size:17 final size:17
Alignment explanation
Indices: 795--829 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
785 TAGAGGAGAG
*
795 GGGGGGGGGGGGAGGGA
1 GGGGGAGGGGGGAGGGA
812 GGGGGAGGGGGGAGGGA
1 GGGGGAGGGGGGAGGGA
829 G
1 G
830 AGAGGGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (17 bp):
GGGGGAGGGGGGAGGGA
Found at i:3245 original size:2 final size:2
Alignment explanation
Indices: 3238--3264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3228 GCATCCTACT
3238 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3265 TGCCTTCCTT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13263 original size:37 final size:37
Alignment explanation
Indices: 13221--13295 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
13211 GGTTTGAATG
13221 TTTCATATCAAATGGTTAAGAGTTATTTTTGAACAAA
1 TTTCATATCAAATGGTTAAGAGTTATTTTTGAACAAA
13258 TTTCATATCAAATGGTTAAGAGTTATTTTTGAACAAA
1 TTTCATATCAAATGGTTAAGAGTTATTTTTGAACAAA
13295 T
1 T
13296 GTTGCTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTCATATCAAATGGTTAAGAGTTATTTTTGAACAAA
Found at i:15564 original size:37 final size:37
Alignment explanation
Indices: 15514--15631 Score: 209
Period size: 37 Copynumber: 3.2 Consensus size: 37
15504 CTCACCAATG
*
15514 TCCTTCAATGGGATTCTCCAAATTTAAATGCAGCAGC
1 TCCTTCAATGGGATTCTCCTAATTTAAATGCAGCAGC
*
15551 TCCTTCAACGGGATTCTCCTAATTTAAATGCAGCAGC
1 TCCTTCAATGGGATTCTCCTAATTTAAATGCAGCAGC
15588 TCCTTCAATGGGATTCTCCTAATTTAAATGCAGCAGC
1 TCCTTCAATGGGATTCTCCTAATTTAAATGCAGCAGC
*
15625 TGCTTCA
1 TCCTTCA
15632 TCCCTCCTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 77 1.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (37 bp):
TCCTTCAATGGGATTCTCCTAATTTAAATGCAGCAGC
Found at i:15870 original size:18 final size:18
Alignment explanation
Indices: 15830--15873 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
15820 TATCGCAGTG
**
15830 AATTTTTTTAAAGGAGTT
1 AATTTTTTTAAAGGAGGA
*
15848 GATTTTTTTAAAGGAGGA
1 AATTTTTTTAAAGGAGGA
15866 AATTTTTT
1 AATTTTTT
15874 AAAATAGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (18 bp):
AATTTTTTTAAAGGAGGA
Found at i:15871 original size:17 final size:17
Alignment explanation
Indices: 15826--15876 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
15816 CGGATATCGC
15826 AGTGAATTTTTTTAAAGG
1 AGTGAA-TTTTTTAAAGG
*
15844 AGTTGATTTTTTTAAAGG
1 AG-TGAATTTTTTAAAGG
15862 AG-GAAATTTTTTAAA
1 AGTG-AATTTTTTAAA
15877 ATAGAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 10 0.34
18 15 0.52
19 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (17 bp):
AGTGAATTTTTTAAAGG
Found at i:18338 original size:4 final size:4
Alignment explanation
Indices: 18329--18355 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18319 TTTTATAATA
18329 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
18356 ATAAAACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:21427 original size:91 final size:92
Alignment explanation
Indices: 21244--21419 Score: 230
Period size: 91 Copynumber: 1.9 Consensus size: 92
21234 GTGATAAGAG
* * * * ***
21244 TCCTTGTAGATAAGAGTCTTAGGAAACAAGAAACCTAATAGTTTAAGGACTCTAGTTTATTTAAC
1 TCCTTATAGATAAGAGTCTTAAGAAACAAGAAACCTAATAGCTTAAGAACTCTAGTTTACGGAAC
* *
21309 ACGCAACCTATTTAAAGGTTACGTTTT
66 ACACAACCTACTTAAAGGTTACGTTTT
* *
21336 TCCTTATAGAT-A-AGTCTTAAGAAACAAGAAACCTAAGTAGCTTAAGAATTCTCGTTTACGGAA
1 TCCTTATAGATAAGAGTCTTAAGAAACAAGAAACCTAA-TAGCTTAAGAACTCTAGTTTACGGAA
21399 CACACAACCTACTTAAAGGTT
65 CACACAACCTACTTAAAGGTT
21420 GTGTTTTTAC
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
90 23 0.32
91 39 0.54
92 10 0.14
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (92 bp):
TCCTTATAGATAAGAGTCTTAAGAAACAAGAAACCTAATAGCTTAAGAACTCTAGTTTACGGAAC
ACACAACCTACTTAAAGGTTACGTTTT
Found at i:23956 original size:20 final size:19
Alignment explanation
Indices: 23931--23979 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
23921 TACATCAAGA
23931 AAAAAAAAATAAGAAACATG
1 AAAAAAAAATAAGAAACA-G
* *
23951 AAAAAAAAATCAGAACCAG
1 AAAAAAAAATAAGAAACAG
23970 AAAAAAAAAT
1 AAAAAAAAAT
23980 TCAAGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (19 bp):
AAAAAAAAATAAGAAACAG
Found at i:25417 original size:75 final size:75
Alignment explanation
Indices: 25337--25558 Score: 381
Period size: 75 Copynumber: 3.0 Consensus size: 75
25327 AAGCTGCTTG
* * *
25337 TAAGTTCTTTAACTTGCTGTTCCAGCTTTTCCTTAGCTTCTTGGAATTCCCCAGTTTCCTTGGCA
1 TAAGTTCTTTAACTTGCTGTTCCAGCTTTTCCTTGGCTTCTTGGAATGCACCAGTTTCCTTGGCA
25402 GCCTGCATCT
66 GCCTGCATCT
*
25412 TAAGTTCTTTAACTTGCTGTTCCAGCTTTTCCTTGGCTTCTTGGAATGCACCAGTGTCCTTGGCA
1 TAAGTTCTTTAACTTGCTGTTCCAGCTTTTCCTTGGCTTCTTGGAATGCACCAGTTTCCTTGGCA
25477 GCCTGCATCT
66 GCCTGCATCT
* * *
25487 TAAGTTGTTTAACTTCCTGTTCCAGCTTTTCCTTGGCTTCTTGGAGTGCACCAGTTTCCTTGGCA
1 TAAGTTCTTTAACTTGCTGTTCCAGCTTTTCCTTGGCTTCTTGGAATGCACCAGTTTCCTTGGCA
25552 GCCTGCA
66 GCCTGCA
25559 GACAGACAGG
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 139 1.00
ACGTcount: A:0.14, C:0.27, G:0.19, T:0.40
Consensus pattern (75 bp):
TAAGTTCTTTAACTTGCTGTTCCAGCTTTTCCTTGGCTTCTTGGAATGCACCAGTTTCCTTGGCA
GCCTGCATCT
Found at i:26421 original size:21 final size:21
Alignment explanation
Indices: 26396--26456 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
26386 GGAAATTAAC
26396 TTTGAAAAATATTTTTTAAAG
1 TTTGAAAAATATTTTTTAAAG
* *
26417 TTTGATAAATA---TTT---C
1 TTTGAAAAATATTTTTTAAAG
26432 TTTGAAAAATATTTTTTAAAG
1 TTTGAAAAATATTTTTTAAAG
26453 TTTG
1 TTTG
26457 GTAGATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 10 0.33
18 6 0.20
21 14 0.47
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTTGAAAAATATTTTTTAAAG
Found at i:26442 original size:36 final size:36
Alignment explanation
Indices: 26395--26474 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
26385 AGGAAATTAA
26395 CTTTGAAAAATATTTTTTAAAGTTTGATAAATATTT
1 CTTTGAAAAATATTTTTTAAAGTTTGATAAATATTT
* *
26431 CTTTGAAAAATATTTTTTAAAGTTTGGTAGATATTT
1 CTTTGAAAAATATTTTTTAAAGTTTGATAAATATTT
*
26467 -GTTGAAAA
1 CTTTGAAAA
26475 TATGAATGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 7 0.17
36 34 0.83
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (36 bp):
CTTTGAAAAATATTTTTTAAAGTTTGATAAATATTT
Found at i:31004 original size:21 final size:21
Alignment explanation
Indices: 30980--31040 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
30970 GGCAACCAAC
30980 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
31001 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
31016 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
31037 TTTG
1 TTTG
31041 GTAGATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
17 4 0.13
19 4 0.13
21 13 0.43
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:31026 original size:36 final size:36
Alignment explanation
Indices: 30979--31058 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 36
30969 TGGCAACCAA
30979 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
31015 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
31051 -GTTGAAAA
1 CTTTGAAAA
31059 TAGGAATAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:37736 original size:31 final size:31
Alignment explanation
Indices: 37700--37758 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
37690 AACTTAAAAG
37700 AGTTTTGA-AATACTGAAATTTAAATAATTTT
1 AGTTTT-ATAATACTGAAATTTAAATAATTTT
37731 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTATAATACTGAAATTTAAATAAT
37759 CCATACAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTATAATACTGAAATTTAAATAATTTT
Found at i:37807 original size:22 final size:22
Alignment explanation
Indices: 37782--38187 Score: 509
Period size: 22 Copynumber: 18.5 Consensus size: 22
37772 ATAATAAATT
37782 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
37804 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
37826 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
37848 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
37870 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
*
37892 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
37914 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
37936 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
37958 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
37980 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
***
38002 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
38024 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATTCATA
*
38046 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* ***
38068 TTTTAAAACAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
38090 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
38112 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
38134 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
38156 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
38178 TTTTAAAATA
1 TTTTAAAATA
38188 GATTTTAAAA
Statistics
Matches: 333, Mismatches: 42, Indels: 18
0.85 0.11 0.05
Matches are distributed among these distances:
21 8 0.02
22 318 0.95
23 7 0.02
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:37852 original size:66 final size:66
Alignment explanation
Indices: 37782--38187 Score: 562
Period size: 66 Copynumber: 6.2 Consensus size: 66
37772 ATAATAAATT
* ***
37782 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
37847 A
66 A
** *
37848 TTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATCAATCCA
1 TTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCCA
37912 TA
65 TA
***
37914 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
37979 A
66 A
* *** * *
37980 TTTTAAAATAAATCAATTCATATTTTAAAATAAATTTTTTCATATTTTAAAATAAATCAATACAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
38045 A
66 A
* *** *
38046 TTTTAAAATAAATCAATCCATATTTTAAAACAAATTTTTTCATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
38111 A
66 A
*** * *
38112 TTTTAAAATAAATTTTTCCATATTTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCTAT
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
38177 A
66 A
38178 TTTTAAAATA
1 TTTTAAAATA
38188 GATTTTAAAA
Statistics
Matches: 303, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
65 4 0.01
66 295 0.97
67 4 0.01
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (66 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
A
Found at i:38194 original size:12 final size:12
Alignment explanation
Indices: 38177--38207 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
38167 ATCAATCTAT
38177 ATTTTAAAATAG
1 ATTTTAAAATAG
38189 ATTTTAAAATAG
1 ATTTTAAAATAG
38201 ATTTTAA
1 ATTTTAA
38208 TGATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAG
Found at i:41171 original size:2 final size:2
Alignment explanation
Indices: 41166--41190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41156 AGGATTTTTA
41166 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41191 ATTTAAACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42380 original size:131 final size:131
Alignment explanation
Indices: 42191--42531 Score: 443
Period size: 131 Copynumber: 2.6 Consensus size: 131
42181 ATTCTAGGAG
* *
42191 AGAAAGCGATAGTATCTAATTATTTTCAATCGAGAATAAATGATC-TCTCATGCCTTAAAGCAGT
1 AGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGA-CATCTCATGCCTTAAAGCAGT
* * * *
42255 CATTTATTACTCCAAACGAAATGAAGAGACATCATTATTTCGTCTTAAAATTCAACATTGATTC-
65 CATTTATTACTCCAAACGAAATGAAGAGACATCACTATTCCGACTTAAAAATCAACATTGATTCG
42319 AA
130 AA
* * * * *
42321 GTGAAAATGATAATATCTAATGATTTTCAATCGAGAATAAATGACATCTCTTGCTTTAAAGCAGT
1 -AGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACATCTCATGCCTTAAAGCAGT
* * ** * * *
42386 CATTTATTATTTCATTCGAAATGAAGAGATATCACTATTCCGACTTAAAAATCAATATTGCTTCG
65 CATTTATTACTCCAAACGAAATGAAGAGACATCACTATTCCGACTTAAAAATCAACATTGATTCG
42451 AA
130 AA
* * * * *
42453 AGAAAACAATAATATCTAATTATTTCCAATTGAGAATAAAAGACATCTCATGCCTTAAAGCAATC
1 AGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACATCTCATGCCTTAAAGCAGTC
42518 ATTTATTACTCCAA
66 ATTTATTACTCCAA
42532 CTGAAACGAA
Statistics
Matches: 177, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
130 1 0.01
131 174 0.98
132 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
AGAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGACATCTCATGCCTTAAAGCAGTC
ATTTATTACTCCAAACGAAATGAAGAGACATCACTATTCCGACTTAAAAATCAACATTGATTCGA
A
Found at i:46454 original size:19 final size:20
Alignment explanation
Indices: 46417--46461 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
46407 TTCATGAAAC
46417 CAACATAATTAAATAAAAAA
1 CAACATAATTAAATAAAAAA
*
46437 CAACA-AATTAAA-ACAAAA
1 CAACATAATTAAATAAAAAA
46455 CACACAT
1 CA-ACAT
46462 TTTTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.16
Consensus pattern (20 bp):
CAACATAATTAAATAAAAAA
Found at i:46454 original size:20 final size:20
Alignment explanation
Indices: 46417--46454 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46407 TTCATGAAAC
*
46417 CAACATAATTAAATAAAAAA
1 CAACATAATTAAACAAAAAA
46437 CAACA-AATTAAAACAAAA
1 CAACATAATT-AAACAAAA
46455 CACACATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (20 bp):
CAACATAATTAAACAAAAAA
Found at i:46887 original size:21 final size:22
Alignment explanation
Indices: 46844--46888 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
46834 TAAAACCAAA
* **
46844 ACCTGATGGGGTGTATCGGTAC
1 ACCTGATGAGGTGTATCAATAC
46866 ACCTG-TGAGGTGTATCAATAC
1 ACCTGATGAGGTGTATCAATAC
46887 AC
1 AC
46889 ATTCAAGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (22 bp):
ACCTGATGAGGTGTATCAATAC
Found at i:46930 original size:21 final size:23
Alignment explanation
Indices: 46876--46931 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
46866 ACCTGTGAGG
46876 TGTATCAATACACATTCAAGGAA
1 TGTATCAATACACATTCAAGGAA
* *
46899 CGTATCTATACACATTCAA-G-A
1 TGTATCAATACACATTCAAGGAA
*
46920 TGTATCGATACA
1 TGTATCAATACA
46932 TAGCAAGGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 1 0.03
23 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (23 bp):
TGTATCAATACACATTCAAGGAA
Found at i:51949 original size:23 final size:23
Alignment explanation
Indices: 51905--51957 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
51895 ACATCACACA
*
51905 TTATT-TCCATCATTAATCTTAT
1 TTATTATCCATCATTAATATTAT
*
51927 TCTATTATCCA-CATTATTATTAT
1 T-TATTATCCATCATTAATATTAT
51950 TTA-TATCC
1 TTATTATCC
51958 TTTAATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 3 0.11
23 15 0.56
24 4 0.15
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (23 bp):
TTATTATCCATCATTAATATTAT
Found at i:61838 original size:17 final size:17
Alignment explanation
Indices: 61816--61853 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
61806 CAACGATCAC
61816 GGTCAACAGTCAGATCG
1 GGTCAACAGTCAGATCG
* *
61833 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCAGATCG
61850 GGTC
1 GGTC
61854 GGTCAGACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.37, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCAGATCG
Found at i:61885 original size:10 final size:10
Alignment explanation
Indices: 61872--61905 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
61862 CGGTTCGAAG
61872 CGGTCAAAAC
1 CGGTCAAAAC
61882 CGGTTCAAAAC
1 CGG-TCAAAAC
61893 CGGTC-AAAC
1 CGGTCAAAAC
61902 CGGT
1 CGGT
61906 TTTCAGCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.35
10 5 0.22
11 10 0.43
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (10 bp):
CGGTCAAAAC
Found at i:61885 original size:20 final size:20
Alignment explanation
Indices: 61853--61906 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
61843 CGGGTCGGGT
* * *
61853 CGGTCAGACCGGTTC-GAAG
1 CGGTCAAACCGGTTCAAAAC
61872 CGGTCAAAACCGGTTCAAAAC
1 CGGTC-AAACCGGTTCAAAAC
61893 CGGTCAAACCGGTT
1 CGGTCAAACCGGTT
61907 TTCAGCCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.17
20 18 0.60
21 7 0.23
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (20 bp):
CGGTCAAACCGGTTCAAAAC
Found at i:66800 original size:13 final size:13
Alignment explanation
Indices: 66779--66823 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
66769 AAATTCTAGG
*
66779 CATTTCCATCTAA
1 CATTGCCATCTAA
66792 CATTGCCATCTAA
1 CATTGCCATCTAA
66805 CATTGCCATCTAA
1 CATTGCCATCTAA
66818 CATTGC
1 CATTGC
66824 GATCCTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (13 bp):
CATTGCCATCTAA
Found at i:69099 original size:16 final size:16
Alignment explanation
Indices: 69078--69112 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
69068 AGGAAGTCAA
*
69078 CGGTCAACGGTCGGGT
1 CGGTCAACAGTCGGGT
69094 CGGTCAACAGTCGGGT
1 CGGTCAACAGTCGGGT
69110 CGG
1 CGG
69113 GTCAGGTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (16 bp):
CGGTCAACAGTCGGGT
Found at i:70617 original size:30 final size:31
Alignment explanation
Indices: 70558--70618 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
70548 TCAAACACTT
*
70558 GGTTCAAACATTGCATTCATAAATATTCAAA
1 GGTTCAAACATTGCATTCATAAACATTCAAA
*
70589 GGTTCAAA-ATTGCATTCATAAACGTTCAAA
1 GGTTCAAACATTGCATTCATAAACATTCAAA
70619 ATTAATAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 20 0.71
31 8 0.29
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (31 bp):
GGTTCAAACATTGCATTCATAAACATTCAAA
Found at i:71331 original size:20 final size:21
Alignment explanation
Indices: 71306--71347 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
71296 TCCCCCTCTT
*
71306 CCCCTTCTTCGTTC-CCCTTC
1 CCCCTTCTCCGTTCTCCCTTC
*
71326 CCCCTTCTCCTTTCTCCCTTC
1 CCCCTTCTCCGTTCTCCCTTC
71347 C
1 C
71348 ATAATCGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.00, C:0.57, G:0.02, T:0.40
Consensus pattern (21 bp):
CCCCTTCTCCGTTCTCCCTTC
Found at i:71699 original size:13 final size:12
Alignment explanation
Indices: 71670--71708 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
71660 TTTTTATAAA
71670 TAAATTAATTTT
1 TAAATTAATTTT
*
71682 TAAATTTATTTT
1 TAAATTAATTTT
*
71694 TAAAATAATATTT
1 TAAATTAAT-TTT
71707 TA
1 TA
71709 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TAAATTAATTTT
Found at i:71742 original size:12 final size:11
Alignment explanation
Indices: 71714--71740 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
71704 TTTTATTTTT
71714 AAAAATTTAAA
1 AAAAATTTAAA
71725 AAAAATTTAAA
1 AAAAATTTAAA
71736 AAAAA
1 AAAAA
71741 ATGACAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAATTTAAA
Found at i:72642 original size:19 final size:18
Alignment explanation
Indices: 72575--72646 Score: 117
Period size: 18 Copynumber: 3.9 Consensus size: 18
72565 ACTGAATATT
*
72575 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
72593 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
72611 CGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
72629 TGTCCCATAAGGACCACT
1 TGTCCCA-AAGGACCACT
72647 GATATGTCCC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
18 40 0.80
19 10 0.20
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:72667 original size:21 final size:22
Alignment explanation
Indices: 72627--72671 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
72617 AAAGGACCAC
* *
72627 TATGTCCCATAAGGACCACTGA
1 TATGTCCCAGAAGAACCACTGA
72649 TATGTCCC-GAAGAACCACTGA
1 TATGTCCCAGAAGAACCACTGA
72670 TA
1 TA
72672 ATCCCTCGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (22 bp):
TATGTCCCAGAAGAACCACTGA
Found at i:77619 original size:19 final size:19
Alignment explanation
Indices: 77595--77641 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
77585 CTAAACTATA
77595 ACACATATGATCATGTTAT
1 ACACATATGATCATGTTAT
77614 ACACATATGATCATGTTAT
1 ACACATATGATCATGTTAT
*
77633 GCACATATG
1 ACACATATG
77642 CAAATAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (19 bp):
ACACATATGATCATGTTAT
Found at i:77870 original size:21 final size:20
Alignment explanation
Indices: 77793--77866 Score: 102
Period size: 18 Copynumber: 3.9 Consensus size: 20
77783 ACTGAATATT
*
77793 TGTCCCGAATGACCACTATA
1 TGTCCCGAAGGACCACTATA
77813 --TCCCGAAGGACCAC--TA
1 TGTCCCGAAGGACCACTATA
77829 TGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACT-ATA
77850 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
77867 GATAATCCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
16 2 0.04
18 27 0.56
21 19 0.40
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.19
Consensus pattern (20 bp):
TGTCCCGAAGGACCACTATA
Found at i:79437 original size:20 final size:22
Alignment explanation
Indices: 79409--79463 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
79399 TTCCCATTGA
*
79409 AGTGCATCGATACAT-TTT-AC
1 AGTGTATCGATACATCTTTAAC
*
79429 AGTGTATCGATGCATCCTTTAAC
1 AGTGTATCGATACAT-CTTTAAC
79452 ATGTGTATCGAT
1 A-GTGTATCGAT
79464 GCACTACCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 13 0.45
22 3 0.10
23 3 0.10
24 10 0.34
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (22 bp):
AGTGTATCGATACATCTTTAAC
Found at i:83008 original size:18 final size:18
Alignment explanation
Indices: 82985--83056 Score: 81
Period size: 18 Copynumber: 3.8 Consensus size: 18
82975 TGAATATTTG
*
82985 TCCCGAATGACCACTATA
1 TCCCGAAGGACCACTATA
* *
83003 TCCCGAAGGACTACTATG
1 TCCCGAAGGACCACTATA
83021 TCCCGAAGGACCACTGATA
1 TCCCGAAGGACCACT-ATA
*
83040 TGTACCGAAGGACCACT
1 --TCCCGAAGGACCACT
83057 GATAATCCCT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 29 0.64
19 2 0.04
21 14 0.31
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:83047 original size:21 final size:21
Alignment explanation
Indices: 83017--83060 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
83007 GAAGGACTAC
*
83017 TATGTCCCGAAGGACCACTGA
1 TATGTACCGAAGGACCACTGA
83038 TATGTACCGAAGGACCACTGA
1 TATGTACCGAAGGACCACTGA
83059 TA
1 TA
83061 ATCCCTCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (21 bp):
TATGTACCGAAGGACCACTGA
Found at i:97287 original size:2 final size:2
Alignment explanation
Indices: 97280--97363 Score: 154
Period size: 2 Copynumber: 43.0 Consensus size: 2
97270 AAAGTACGAA
97280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97322 A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
97362 AT
1 AT
97364 GGTTACAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 78 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.