Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002683.1 Hibiscus syriacus cultivar Beakdansim tig00005547_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: 68812
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:9598 original size:26 final size:26
Alignment explanation
Indices: 9530--9609 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
9520 ATTTAGCGCA
* *
9530 TATGGTGGGCACGACCTTATGTGTAA
1 TATGGTGGGAACGACCTTATGTGTAT
* *
9556 TATGAT-GGACACAACCTTATGTGTAT
1 TATGGTGGGA-ACGACCTTATGTGTAT
*
9582 TATGGTGGGAATGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
9608 TA
1 TA
9610 GCACTTCGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.04
26 40 0.89
27 3 0.07
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (26 bp):
TATGGTGGGAACGACCTTATGTGTAT
Found at i:10465 original size:89 final size:89
Alignment explanation
Indices: 10281--10459 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
10271 CTTAAATCGA
10281 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
1 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
10346 TTTTTGAATGAATAACTTCTAGTG
66 TTTTTGAATGAATAACTTCTAGTG
10370 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATC-A-ATATGGTTAATTGTAA
1 AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
10433 TTTTTGAATGAATAACTTCTAGTG
66 TTTTTGAATGAATAACTTCTAGTG
10457 AAT
1 AAT
10460 GTTAGTAAAT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 43 0.48
88 1 0.01
89 46 0.51
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (89 bp):
AATTAGTTTGATTAAAAAAATAAAAATTGATATTACTCGATAAATCAATATATGGTTAATTGTAA
TTTTTGAATGAATAACTTCTAGTG
Found at i:11284 original size:21 final size:22
Alignment explanation
Indices: 11250--11291 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
11240 TTAATATTGA
11250 AAAAATTGAAAGTTTAGGTACC
1 AAAAATTGAAAGTTTAGGTACC
*
11272 AAAAA-TGATAGTTTAGGTAC
1 AAAAATTGAAAGTTTAGGTAC
11292 TAAATGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (22 bp):
AAAAATTGAAAGTTTAGGTACC
Found at i:20924 original size:6 final size:6
Alignment explanation
Indices: 20893--20927 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
20883 GAGTAGAGTC
* *
20893 GTGGCG GCGGCG GCGGCG GTGGCG GTGGCG GTGGC
1 GTGGCG GTGGCG GTGGCG GTGGCG GTGGCG GTGGC
20928 ATGAATGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.66, T:0.11
Consensus pattern (6 bp):
GTGGCG
Found at i:21910 original size:17 final size:17
Alignment explanation
Indices: 21888--21929 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
21878 CGTAGGACTT
*
21888 TCAGAGGGATTAGCGGA
1 TCAGAGGAATTAGCGGA
21905 TCAGAGGAATTAGCGGA
1 TCAGAGGAATTAGCGGA
21922 TCAGAGGA
1 TCAGAGGA
21930 TGATATAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.38, T:0.17
Consensus pattern (17 bp):
TCAGAGGAATTAGCGGA
Found at i:24741 original size:29 final size:29
Alignment explanation
Indices: 24696--24765 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
24686 AGAGGAAGTG
* **
24696 CATGGCGACCTATAAGGTCGCCCGGATTA
1 CATGGCGACCTACAAGGTCGCCCGGAGGA
*
24725 CATGGCGACCTACAAGGTCGCCCGGAGGG
1 CATGGCGACCTACAAGGTCGCCCGGAGGA
24754 CATGGCGACCTA
1 CATGGCGACCTA
24766 TGCTTGGGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.16
Consensus pattern (29 bp):
CATGGCGACCTACAAGGTCGCCCGGAGGA
Found at i:25648 original size:21 final size:22
Alignment explanation
Indices: 25624--25664 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
25614 ATTAAAATGA
25624 ACTAAAAGTG-ATAGTTTAGAT
1 ACTAAAAGTGTATAGTTTAGAT
* *
25645 ACTAAATGTGTGTAGTTTAG
1 ACTAAAAGTGTATAGTTTAG
25665 CTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (22 bp):
ACTAAAAGTGTATAGTTTAGAT
Found at i:25856 original size:35 final size:33
Alignment explanation
Indices: 25800--25865 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
25790 TTTATGTTAT
*
25800 AAACTATAAAAAAATTCTTAAGTGATTAATACG
1 AAACTATAAAAAAATTCTTAAGTGATCAATACG
25833 AAACGTATATAAAAAATAT-TTAAGTGATCAATA
1 AAAC-TATA-AAAAAAT-TCTTAAGTGATCAATA
25866 AGAGTATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 4 0.14
35 20 0.69
36 1 0.03
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.30
Consensus pattern (33 bp):
AAACTATAAAAAAATTCTTAAGTGATCAATACG
Found at i:28146 original size:11 final size:11
Alignment explanation
Indices: 28132--28156 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28122 AAAAACTCAT
28132 AAAAAAGAAAA
1 AAAAAAGAAAA
28143 AAAAAAGAAAA
1 AAAAAAGAAAA
28154 AAA
1 AAA
28157 TCCCTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:31244 original size:149 final size:149
Alignment explanation
Indices: 30974--31277 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
30964 CGAAGTGCCC
*
30974 CGTAGAATTGCACCTTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
31039 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATATGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
31104 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
31123 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
31188 CATATACATATACTATGGATCAAGTATATGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATATGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
31253 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
31272 CGTAGA
1 CGTAGA
31278 CCCTCTACCC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATATGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:31870 original size:66 final size:66
Alignment explanation
Indices: 31759--31909 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 66
31749 TTTTTCTCAT
* *
31759 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGA
1 GGGGGTATCGGTT--CCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCAT-TACGA
31824 TGA-
63 TGAG
* * *
31827 GGGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTTGA
1 GGGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATTACGATGA
31892 G
66 G
31893 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
31910 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
65 6 0.08
66 59 0.77
68 12 0.16
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATTACGATGA
G
Found at i:38266 original size:149 final size:149
Alignment explanation
Indices: 37996--38299 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
37986 CGAAGTGCCC
* *
37996 CGTAGAATTGCACCTTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
38061 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
38126 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
38145 CGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
38210 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
38275 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
38294 CGTAGA
1 CGTAGA
38300 CCCTCTACCC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:38893 original size:67 final size:67
Alignment explanation
Indices: 38781--38932 Score: 234
Period size: 67 Copynumber: 2.3 Consensus size: 67
38771 TTTTTCTCAT
* *
38781 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCAT-TACGA
38846 TGA-
64 TGAG
* * *
38849 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATTACGATG
38914 AG
66 AG
38916 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
38933 TTGAATGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
66 6 0.08
67 60 0.77
68 12 0.15
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATTACGATG
AG
Found at i:40884 original size:19 final size:18
Alignment explanation
Indices: 40856--40894 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
40846 TCGAGAGATC
40856 TAATATATTAACAATTAT
1 TAATATATTAACAATTAT
*
40874 TAATAATATTAACATTTAT
1 TAAT-ATATTAACAATTAT
40893 TA
1 TA
40895 TTTGACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATATTAACAATTAT
Found at i:41972 original size:98 final size:98
Alignment explanation
Indices: 41803--41994 Score: 285
Period size: 98 Copynumber: 2.0 Consensus size: 98
41793 ATTTTTTATT
* * * * * *
41803 TAAAAATTAGATCATGGGAAATATTTTTAAGCTCAAATTGGATCAAGTGACGAGTGAAGTGATGT
1 TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGAGTGAAATGATGT
* *
41868 AATACTCGGATCATGTTTGAGTGACCCAAGAAC
66 AATACTCAGATCAGGTTTGAGTGACCCAAGAAC
*
41901 TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGGGTGAAATGATGT
1 TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGAGTGAAATGATGT
* *
41966 AATACTCATATCAGGTTTGAGTGAGCCAA
66 AATACTCAGATCAGGTTTGAGTGACCCAA
41995 TAACCTGATC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
98 83 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (98 bp):
TAAAAATTAGACCATGAGAAATATTCTTAAACTCAAATTAGATCAAGTGACGAGTGAAATGATGT
AATACTCAGATCAGGTTTGAGTGACCCAAGAAC
Found at i:48239 original size:29 final size:29
Alignment explanation
Indices: 48206--48298 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
48196 ATTGGTCCCT
48206 AAACTTTTGAATATTTTAAATTCATCCTC
1 AAACTTTTGAATATTTTAAATTCATCCTC
* * *
48235 AAAC-TATGATACTCATTCTAAATT-AGTCCTT
1 AAACTTTTGA-A-T-ATTTTAAATTCA-TCCTC
** * *
48266 AAACTTTTGAGCATTTCAATTTCATCCTC
1 AAACTTTTGAATATTTTAAATTCATCCTC
48295 AAAC
1 AAAC
48299 AATGACCCGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
28 4 0.08
29 20 0.42
30 3 0.06
31 17 0.35
32 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.40
Consensus pattern (29 bp):
AAACTTTTGAATATTTTAAATTCATCCTC
Found at i:48250 original size:59 final size:60
Alignment explanation
Indices: 48187--48303 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
48177 AACTATGGCC
* * * * *
48187 CTCA-TCTATATTGGTCCCTAAACTTTTGAATATTTTAAATTCATCCTCAAACTATGATA
1 CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAAATTCATCCTCAAACAATGATA
* * *
48246 CTCATTCTAAATTAGTCCTTAAACTTTTGAGCATTTCAATTTCATCCTCAAACAATGA
1 CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAAATTCATCCTCAAACAATGA
48304 CCCGTATTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 4 0.08
60 45 0.92
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.39
Consensus pattern (60 bp):
CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAAATTCATCCTCAAACAATGATA
Found at i:48313 original size:60 final size:60
Alignment explanation
Indices: 48187--48318 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
48177 AACTATGGCC
* * * * * *
48187 CTCA-TCTATATTGGTCCCTAAACTTTTGAATATTTTAAATTCATCCTCAAACTATGATA
1 CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAAATTCATCCTCAAACAATGACA
* * * *
48246 CTCATTCTAAATTAGTCCTTAAACTTTTGAGCATTTCAATTTCATCCTCAAACAATGACC
1 CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAAATTCATCCTCAAACAATGACA
48306 CGT-ATTCTAAATT
1 C-TCATTCTAAATT
48319 GGCCCCCAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 4 0.07
60 56 0.92
61 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (60 bp):
CTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAAATTCATCCTCAAACAATGACA
Found at i:54862 original size:3 final size:3
Alignment explanation
Indices: 54856--54882 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54846 TATTAATAAT
54856 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
54883 CTAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55733 original size:23 final size:24
Alignment explanation
Indices: 55690--55737 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
55680 AGTATTTTGT
55690 ATTGTCCTTTTATTTTTTTATATC
1 ATTGTCCTTTTATTTTTTTATATC
55714 ATTGTCCTTTTA-TTTTTTATATC
1 ATTGTCCTTTTATTTTTTTATATC
55737 A
1 A
55738 CATATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTGTCCTTTTATTTTTTTATATC
Found at i:58898 original size:12 final size:13
Alignment explanation
Indices: 58881--58926 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
58871 TTTCCCTTTG
58881 ATTTGTTTA-TTT
1 ATTTGTTTATTTT
58893 ATTTGTTTATTTT
1 ATTTGTTTATTTT
58906 ATTTTTGTTT-TTTT
1 A--TTTGTTTATTTT
58920 A-TTGTTT
1 ATTTGTTT
58927 TTACTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.19
12 9 0.29
13 4 0.13
14 5 0.16
15 7 0.23
ACGTcount: A:0.13, C:0.00, G:0.09, T:0.78
Consensus pattern (13 bp):
ATTTGTTTATTTT
Found at i:58937 original size:27 final size:27
Alignment explanation
Indices: 58882--58937 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
58872 TTCCCTTTGA
*
58882 TTTGTTTATTTATTTGTTTATTTTATT
1 TTTGTTTATTTATTTGTTTACTTTATT
* *
58909 TTTGTTTTTTTATTGTTTTTACTTT-TT
1 TTTGTTTATTTATT-TGTTTACTTTATT
58936 TT
1 TT
58938 CCTTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (27 bp):
TTTGTTTATTTATTTGTTTACTTTATT
Found at i:62983 original size:95 final size:95
Alignment explanation
Indices: 62819--62997 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 95
62809 ATATTATTTA
* * * * *
62819 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATGGATAAT
1 TATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGACTTTATGGATAAG
*
62884 ATTCAGCTAGCCTAATAAAGGTGATTATAC
66 ATTCAGCTAACCTAATAAAGGTGATTATAC
*
62914 TATACAATAAAACTTGAGCTGTCCCTCTA-AGGCAATTAGTTAAATGCCCCGACTTTATGGATAA
1 TATACAATAAAACTTGAGCTGTCCCTCTAGA-GCAATTAGTTAAACGCCCCGACTTTATGGATAA
*
62978 GATTCAGCTAACCTGATAAA
65 GATTCAGCTAACCTAATAAA
62998 AGTATTTGCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
94 1 0.01
95 74 0.99
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (95 bp):
TATACAATAAAACTTGAGCTGTCCCTCTAGAGCAATTAGTTAAACGCCCCGACTTTATGGATAAG
ATTCAGCTAACCTAATAAAGGTGATTATAC
Found at i:64527 original size:73 final size:73
Alignment explanation
Indices: 64373--64532 Score: 205
Period size: 73 Copynumber: 2.2 Consensus size: 73
64363 TAATTTACTC
* * * *
64373 AAAAC-AAAGTTTGTCTCTTTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAA
1 AAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAA
*
64437 TTTCTCGT
66 TTTCCCGT
* * * *
64445 AAAAAAAAATTTTGTCTCTCTTGAGATATTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAG
1 AAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAA
*
64510 TTTCCCTT
66 TTTCCCGT
*
64518 GAAACAAAATCTTTG
1 AAAACAAAAT-TTTG
64533 AATATGTTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 4 0.05
73 66 0.89
74 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (73 bp):
AAAACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAA
TTTCCCGT
Found at i:64588 original size:65 final size:65
Alignment explanation
Indices: 64465--64869 Score: 287
Period size: 65 Copynumber: 6.1 Consensus size: 65
64455 TTTGTCTCTC
* ** *
64465 TTGAGATA-TTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATC
1 TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAATC
64529 T
65 T
* **
64530 TTGAATATGTTTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATAT
1 TTGAATAT-TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAA-A-
64594 TGTCTCT
63 ----TCT
* * *
64601 CTTGAGACA-TTTTCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 -TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAAT
64662 CT
64 CT
* * * *
64664 TTGAATCTGTTTTC-CTTGAAACAAATTTCGTCTCCCTGGAGACAG-TTCCTTTTAAAACAAATT
1 TTGAATAT-TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCC-CTTAAAACAAA--
*
64727 TTGTCTCT
62 ----ATCT
* * * *
64735 CTTGAGACA-TTTTCTCTT---AGAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAAT
1 -TTGA-ATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAAT
64796 C-
64 CT
* * * * * **
64797 TTGAATCTATTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAATTTTTCTTGAAACACAAAAT
1 TTGAATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-AAA-ACAAAAT
64862 CT
64 CT
64864 TTGAAT
1 TTGAAT
64870 TTATTTCCAT
Statistics
Matches: 265, Mismatches: 41, Indels: 66
0.71 0.11 0.18
Matches are distributed among these distances:
60 1 0.00
61 12 0.05
62 7 0.03
63 10 0.04
64 36 0.14
65 75 0.28
66 14 0.05
67 6 0.02
68 1 0.00
69 64 0.24
70 6 0.02
71 16 0.06
72 14 0.05
73 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.40
Consensus pattern (65 bp):
TTGAATATTTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACAAAATCT
Found at i:64599 original size:36 final size:34
Alignment explanation
Indices: 64374--64659 Score: 212
Period size: 36 Copynumber: 8.2 Consensus size: 34
64364 AATTTACTCA
* *
64374 AAACAAAGTTTGTCTCTTTTGAGACAATTTCTCTT
1 AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* * *
64409 AAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTAA
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTC-T-T
* * *
64447 AAAAAAATTTTGTCTCTCTTGAGATATTTTCTCTT
1 AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
64482 AAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTT
1 -AAACAAA-TTTGTCTCTCTTGAGACAGTTTCTCTT
* *
64518 GAAACAAA-----ATCT-TTGA-ATATGTTT-TCCTT
1 -AAACAAATTTGTCTCTCTTGAGACA-GTTTCT-CTT
* *
64547 GAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTT
1 -AAACAAATTT-GTCTCTCTTGAGACAGTTTCTCTT
*
64583 AAAACAAATATTGTCTCTCTTGAGACATTTTCTCTT
1 -AAACAAAT-TTGTCTCTCTTGAGACAGTTTCTCTT
* *
64619 AAA-AATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
64652 GAAACAAA
1 -AAACAAA
64660 ATCTTTGAAT
Statistics
Matches: 204, Mismatches: 29, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
33 24 0.12
34 6 0.03
35 7 0.03
36 107 0.52
37 37 0.18
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (34 bp):
AAACAAATTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:64658 original size:134 final size:134
Alignment explanation
Indices: 64401--64840 Score: 657
Period size: 134 Copynumber: 3.3 Consensus size: 134
64391 TTTGAGACAA
* * * * * * * *
64401 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATAATTTCTCGTAAAAAAAAATTTTGTCTCTCT
1 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCT-TTTAAAACAAATTTTGTCTCTCT
* *
64466 TGAGATATTTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTT
64 TGAGACATTTTCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTT
*
64531 TGAATATGT
126 TGAATCTGT
*
64540 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATATTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
64605 AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
66 AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
64670 CTGT
131 CTGT
* *
64674 TTTCCTTGAAACAAATTTCGTCTCCCTGGAGACAGTTCCTTTTAAAACAAATTTTGTCTCTCTTG
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
*
64739 AGACATTTTCTCTTAGAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATC-TTGAAT
66 AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
*
64803 CTAT
131 CTGT
* * *
64807 TTCCCTTGAAACAAGTTTTGTCTCCCTTGAGACA
1 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
64841 ATTTTTCTTG
Statistics
Matches: 280, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
133 39 0.14
134 170 0.61
135 2 0.01
137 34 0.12
138 31 0.11
139 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (134 bp):
TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTG
AGACATTTTCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
CTGT
Found at i:64764 original size:33 final size:32
Alignment explanation
Indices: 64722--64789 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
64712 CTTTTAAAAC
* *
64722 AAATTTTGTCTCTCTTGAGACATTTTCTCTTAG
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTT-G
64755 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
64787 AAA
1 AAA
64790 CAAAATCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (32 bp):
AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:64838 original size:64 final size:67
Alignment explanation
Indices: 64758--64887 Score: 176
Period size: 64 Copynumber: 2.0 Consensus size: 67
64748 CTCTTAGAAA
* * * *
64758 TTTTGTCTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATC-TTGAATCTATTTCCCTTGAAACA
1 TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAAATCTTTGAATCTATTTCCATTAAAACA
64820 AG
66 AG
** *
64822 TTTTGTCTCCCTTGAGACAATTTTTCTTGAAACACAAAATCTTTGAATTTATTTCCATTAAAACA
1 TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAAATCTTTGAATCTATTTCCATTAAAACA
64887 A
66 A
64888 AACTTTGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
64 25 0.45
65 2 0.04
66 8 0.14
67 21 0.38
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (67 bp):
TTTTGTCTCCCTTGAGACAATTTCCCTTGAAACACAAAATCTTTGAATCTATTTCCATTAAAACA
AG
Found at i:66692 original size:19 final size:19
Alignment explanation
Indices: 66670--66708 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
66660 TTGTTTTTAC
* *
66670 TTTTTTCCTTTTGATTTTT
1 TTTTTTCATTTTCATTTTT
*
66689 TTTTTTTATTTTCATTTTT
1 TTTTTTCATTTTCATTTTT
66708 T
1 T
66709 ACGTTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTTCATTTTCATTTTT
Done.