Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003588.1 Hibiscus syriacus cultivar Beakdansim tig00007567_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: 101522
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:18136 original size:31 final size:31
Alignment explanation
Indices: 18101--18165 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
18091 AGTCTCTCAA
*
18101 TCACTTCATTTTCTTAATATTTGACAATTAT
1 TCACTTCATTTTCTTAATAATTGACAATTAT
18132 TCACTTCATTTTCTTAATAATTGACAATTAT
1 TCACTTCATTTTCTTAATAATTGACAATTAT
18163 TCA
1 TCA
18166 TTCGAGTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (31 bp):
TCACTTCATTTTCTTAATAATTGACAATTAT
Found at i:24656 original size:24 final size:24
Alignment explanation
Indices: 24629--24696 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
24619 TACATTTAAT
24629 TATTATTATATATTATATATATGA
1 TATTATTATATATTATATATATGA
*
24653 TATTA-TAT-TATTATATAT-TTA
1 TATTATTATATATTATATATATGA
24674 -ATTATTAATAATATTATATATAT
1 TATTATT-AT-ATATTATATATAT
24697 ATTTAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 12 0.32
23 3 0.08
24 15 0.39
25 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (24 bp):
TATTATTATATATTATATATATGA
Found at i:24688 original size:32 final size:32
Alignment explanation
Indices: 24627--24692 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
24617 GATACATTTA
*
24627 ATTATTATTATATATTATATATATGATATTAT
1 ATTATTATTATATATTATATATATAATATTAT
*
24659 ATTATTATATATTTAATTAT-TA-ATAATATTAT
1 ATTATTAT-TATAT-ATTATATATATAATATTAT
24691 AT
1 AT
24693 ATATATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 19 0.63
33 6 0.20
34 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
ATTATTATTATATATTATATATATAATATTAT
Found at i:25116 original size:14 final size:14
Alignment explanation
Indices: 25097--25126 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25087 TTTATCTGAA
*
25097 TAAATAAAATTTAT
1 TAAATAAAATTAAT
25111 TAAATAAAATTAAT
1 TAAATAAAATTAAT
25125 TA
1 TA
25127 TATACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATAAAATTAAT
Found at i:29966 original size:28 final size:28
Alignment explanation
Indices: 29930--29988 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
29920 TGAGTACAAT
*
29930 GAACCTTTTATTAAACATGTCACTGTTA
1 GAACATTTTATTAAACATGTCACTGTTA
29958 GAACATTTTATTAAACATGTCACTGTTA
1 GAACATTTTATTAAACATGTCACTGTTA
29986 GAA
1 GAA
29989 AGTTTGCCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (28 bp):
GAACATTTTATTAAACATGTCACTGTTA
Found at i:35919 original size:24 final size:25
Alignment explanation
Indices: 35883--35930 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
35873 TGTTGAAAAC
35883 ACCATGCGACTTCAA-TTTTCCAGT
1 ACCATGCGACTTCAATTTTTCCAGT
* *
35907 ACCATGTGTCTTCAATTTTTCCAG
1 ACCATGCGACTTCAATTTTTCCAG
35931 ACAACATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (25 bp):
ACCATGCGACTTCAATTTTTCCAGT
Found at i:36710 original size:16 final size:16
Alignment explanation
Indices: 36685--36717 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
36675 AATCCGATTC
*
36685 ATCATTCTAAAATGAA
1 ATCATACTAAAATGAA
36701 ATCATACTAAAATGAA
1 ATCATACTAAAATGAA
36717 A
1 A
36718 CATGTTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (16 bp):
ATCATACTAAAATGAA
Found at i:37143 original size:3 final size:3
Alignment explanation
Indices: 37135--37178 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
37125 TTTGTTTTAT
*
37135 TTA TTA TTA TTA TT- TTG TT- TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37179 ATTAATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:37159 original size:16 final size:16
Alignment explanation
Indices: 37132--37186 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
37122 TCATTTGTTT
37132 TATT-TATTATTATTA
1 TATTATATTATTATTA
* * *
37147 TTTTGTTTTATTATTA
1 TATTATATTATTATTA
37163 TATTATATTATTATTA
1 TATTATATTATTATTA
37179 -ATTA-ATTA
1 TATTATATTA
37187 ATTAATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 4 0.12
15 7 0.21
16 23 0.68
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTATATTATTATTA
Found at i:37171 original size:23 final size:23
Alignment explanation
Indices: 37125--37168 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
37115 TTTTATTTCA
37125 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTATTTATTATTATTAT
37148 TTTGTTTTA-TTATTA-TATTAT
1 TTTGTTTTATTTATTATTATTAT
37169 ATTATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTGTTTTATTTATTATTATTAT
Found at i:38660 original size:26 final size:29
Alignment explanation
Indices: 38617--38678 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
38607 CAAACTTTAC
*
38617 ATTTTAATACTATGATTTAATTTTAT-TT
1 ATTTTAATACTATGATTTAATTATATGTT
*
38645 ATTTTAA-AC-ATTATTTAATTATATGTT
1 ATTTTAATACTATGATTTAATTATATGTT
38672 ACTTTTA
1 A-TTTTA
38679 TATATTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 13 0.43
27 5 0.17
28 12 0.40
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
ATTTTAATACTATGATTTAATTATATGTT
Found at i:39876 original size:20 final size:20
Alignment explanation
Indices: 39851--39891 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39841 TCATATGCTC
39851 TATGTCTTCGTGAGAATTTA
1 TATGTCTTCGTGAGAATTTA
39871 TATGTCTTCGTGAGAATTTA
1 TATGTCTTCGTGAGAATTTA
39891 T
1 T
39892 TCTCTGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (20 bp):
TATGTCTTCGTGAGAATTTA
Found at i:41275 original size:12 final size:12
Alignment explanation
Indices: 41258--41285 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41248 ACATTCACAT
41258 ATTTACATTTGC
1 ATTTACATTTGC
41270 ATTTACATTTGC
1 ATTTACATTTGC
41282 ATTT
1 ATTT
41286 TTTACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:41295 original size:27 final size:27
Alignment explanation
Indices: 41259--41318 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
41249 CATTCACATA
41259 TTTACATTTGCATTTAC-ATTTGCATTT
1 TTTACATTTGCATTTACAATTT-CATTT
* *
41286 TTTACGTTTGTATTTACAATTTCA-TT
1 TTTACATTTGCATTTACAATTTCATTT
41312 TTTACAT
1 TTTACAT
41319 AATTACATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 17 0.59
28 4 0.14
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (27 bp):
TTTACATTTGCATTTACAATTTCATTT
Found at i:43265 original size:6 final size:6
Alignment explanation
Indices: 43255--43289 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
43245 AAAAAAGGAA
*
43255 AAAAAG GAAAAG AAAAAG AAAAAG AAAAAGG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAA
43290 TTGAATCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:43270 original size:12 final size:12
Alignment explanation
Indices: 43255--43289 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
43245 AAAAAAGGAA
43255 AAAAAGGAAAAG
1 AAAAAGGAAAAG
*
43267 AAAAAGAAAAAG
1 AAAAAGGAAAAG
43279 AAAAAGGAAAA
1 AAAAAGGAAAA
43290 TTGAATCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAAAG
Found at i:46630 original size:76 final size:76
Alignment explanation
Indices: 46550--46832 Score: 356
Period size: 76 Copynumber: 3.7 Consensus size: 76
46540 AACAAGAAGC
* *
46550 AAATGTTGGGGCATGCTAAAAACCCTTTTCAATCAGAATCATGAATGTTGATGTATCCTGAATGT
1 AAATGATGGGGCATGCTAAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAATGT
*
46615 TTATATCAGCA
66 TCATATCAGCA
* * * * *
46626 AAATGCTGGGGCATGCTAAAAACCCCTTTCAATCAGAATGAGGAATGTTGATATATCCTGAATGT
1 AAATGATGGGGCATGCTAAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAATGT
46691 TCATATCAGCA
66 TCATATCAGCA
** * ** *
46702 AAATGATGGGGCATGCTGAAAGCCCCTTTT-AATCAGAATGAAGAATGTTGATGTATTTTGAACG
1 AAATGATGGGGCATGCT-AAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAATG
* *
46766 TTCGTATCAG-T
65 TTCATATCAGCA
* * *
46777 AATTGATGGGGCATGAT-AAAAGCCTATTTCAATCAGAATCAAGAATGTTGATGTAT
1 AAATGATGGGGCATGCTAAAAACCCT-TTTCAATCAGAATCAAGAATGTTGATGTAT
46833 TTTGACCGTT
Statistics
Matches: 181, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
73 5 0.03
74 3 0.02
75 40 0.22
76 124 0.69
77 9 0.05
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (76 bp):
AAATGATGGGGCATGCTAAAAACCCTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAATGT
TCATATCAGCA
Found at i:46856 original size:75 final size:75
Alignment explanation
Indices: 46547--46868 Score: 347
Period size: 76 Copynumber: 4.3 Consensus size: 75
46537 ATTAACAAGA
* * * *
46547 AGCAAATGTTGGGGCATGCTAAAAACCCTTTTCAATCAGAATCATGAATGTTGATGTATCCTGAA
1 AGCAAATGATGGGGCATGCTAAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
* *
46612 TGTTTATATC
66 CGTTCATATC
* * * * *
46622 AGCAAAATGCTGGGGCATGCTAAAAACCCCTTTCAATCAGAATGAGGAATGTTGATATATCCTGA
1 AGC-AAATGATGGGGCATGCTAAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
*
46687 ATGTTCATATC
65 ACGTTCATATC
* * * **
46698 AGCAAAATGATGGGGCATGCTGAAAGCCCCTTTTAATCAGAATGAAGAATGTTGATGTATTTTGA
1 AGC-AAATGATGGGGCATGCTAAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
*
46763 ACGTTCGTATC
65 ACGTTCATATC
* * * ** ** *
46774 AGTAATTGATGGGGCATGATAAAAGCCTATTTCAATCAGAATCAAGAATGTTGATGTATTTTGAC
1 AGCAAATGATGGGGCATGCTAAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
* *
46839 CGTTCGTATT
66 CGTTCATATC
* * *
46849 AGCAATTGTTGGGGCGTGCT
1 AGCAAATGATGGGGCATGCT
46869 GAAGGCCTAT
Statistics
Matches: 216, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
75 82 0.38
76 134 0.62
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (75 bp):
AGCAAATGATGGGGCATGCTAAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
CGTTCATATC
Found at i:48857 original size:112 final size:113
Alignment explanation
Indices: 48605--48885 Score: 469
Period size: 112 Copynumber: 2.5 Consensus size: 113
48595 TAGCAAATAT
* * *
48605 TCAAATCCATCAC--AATGAATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGA
*
48668 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGC
* *
48716 TCAAATCCATCACTTGATGGGTCAACATTTCCAGAGAAAGATCATAATGAGAAGAACTCATATGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGA
48781 AGAAGGAAGAAG-AGTTCATAATGAGAAGAGCTTATTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGC
* *
48828 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGGAAGTTCATAATGAGAAGAACT
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT
48886 TGTTTGACTT
Statistics
Matches: 158, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
111 13 0.08
112 88 0.56
113 57 0.36
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGC
Found at i:49041 original size:13 final size:13
Alignment explanation
Indices: 49023--49053 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
49013 GTTTATAATG
49023 AGAAGAAGGAAGA
1 AGAAGAAGGAAGA
49036 AGAAGAAGGAAGA
1 AGAAGAAGGAAGA
49049 AGAAG
1 AGAAG
49054 TTCATAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (13 bp):
AGAAGAAGGAAGA
Found at i:49283 original size:113 final size:113
Alignment explanation
Indices: 49037--49267 Score: 408
Period size: 113 Copynumber: 2.0 Consensus size: 113
49027 GAAGGAAGAA
* * *
49037 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACTTTTCGCTTGAATTCATCATTC
1 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTC
*
49102 GATGGATCATCATTGCCAGGTTGAGTTCATAATGAGAAGAACTCATCT
66 GATGGATCATCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCT
*
49150 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATTATTC
1 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTC
*
49215 GATGGATCATCATTGCTAGGTCGAGTTCATAATGAGAAGAACTCATCT
66 GATGGATCATCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCT
49263 GAAGA
1 GAAGA
49268 GAGAAGAGCT
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (113 bp):
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATTCATCATTC
GATGGATCATCATTGCCAGGTCGAGTTCATAATGAGAAGAACTCATCT
Found at i:49488 original size:122 final size:122
Alignment explanation
Indices: 49268--49492 Score: 344
Period size: 122 Copynumber: 1.8 Consensus size: 122
49258 CATCTGAAGA
* * * * **
49268 GAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAACATCAATTTT
1 GAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAAAAGAAGATAAACCAACATCAACATT
*
49333 TTCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAATAAGAAGTTCACAAT
66 TTCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCACAAT
*
49390 GAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAAAAGAAGATAAACCAACATCAACATT
1 GAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAAAAGAAGATAAACCAACATCAACATT
* *
49455 TTCAGA-AGTGTTTATAATGAGAAGAACTCATCTGAAGA
66 TTCAGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGA
49493 ATAAGGAGCA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
121 1 0.01
122 91 0.99
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (122 bp):
GAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAAAAGAAGATAAACCAACATCAACATT
TTCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCACAAT
Found at i:49756 original size:3 final size:3
Alignment explanation
Indices: 49748--49788 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
49738 TTTGTTTTAT
49748 TTA TTA TTA TTA TT- TT- TTA TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49789 ATTAATTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 8 0.23
3 27 0.77
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49762 original size:13 final size:13
Alignment explanation
Indices: 49744--49792 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
49734 TTCATTTGTT
49744 TTATTTATTATTA
1 TTATTTATTATTA
*
49757 TTATTTTTTATTA
1 TTATTTATTATTA
49770 TTATATTA-TATTA
1 TTAT-TTATTATTA
*
49783 TTATTAATTA
1 TTATTTATTA
49793 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:49768 original size:16 final size:16
Alignment explanation
Indices: 49747--49792 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
49737 ATTTGTTTTA
49747 TTTATTATTATTATT-T
1 TTTATTATTA-TATTAT
49763 TTTATTATTATATTAT
1 TTTATTATTATATTAT
*
49779 ATTATTATTA-ATTA
1 TTTATTATTATATTA
49793 ATTAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTATTATATTAT
Found at i:51146 original size:26 final size:29
Alignment explanation
Indices: 51103--51164 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
51093 CAAACTTTAC
*
51103 ATTTTAATACTATGATTTAATTTTAT-TT
1 ATTTTAATACTATGATTTAATTATATGTT
*
51131 ATTTTAA-AC-ATTATTTAATTATATGTT
1 ATTTTAATACTATGATTTAATTATATGTT
51158 ACTTTTA
1 A-TTTTA
51165 TATATTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 13 0.43
27 5 0.17
28 12 0.40
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
ATTTTAATACTATGATTTAATTATATGTT
Found at i:51435 original size:17 final size:18
Alignment explanation
Indices: 51413--51447 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
51403 AAATATAAAA
51413 ATAAATAT-TTTTTATAT
1 ATAAATATATTTTTATAT
*
51430 ATAAATCTATTTTTATAT
1 ATAAATATATTTTTATAT
51448 TGTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAAATATATTTTTATAT
Found at i:51463 original size:28 final size:28
Alignment explanation
Indices: 51417--51486 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
51407 ATAAAAATAA
51417 ATATTTTTTATA-TATAAATCTATTT-TT
1 ATATTTTTTATATTA-AAATCTATTTATT
*
51444 ATATTGTTTTATATTAAAATTTATTTATT
1 ATATT-TTTTATATTAAAATCTATTTATT
51473 -TA-TTTTTATATTAA
1 ATATTTTTTATATTAA
51487 GAAAGGAGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 11 0.28
27 6 0.15
28 18 0.46
29 4 0.10
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
ATATTTTTTATATTAAAATCTATTTATT
Found at i:53644 original size:12 final size:11
Alignment explanation
Indices: 53613--53646 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
53603 GTTTGACATC
*
53613 AAGTTTTCATT
1 AAGTTTTCTTT
53624 AAGTTTTCTTT
1 AAGTTTTCTTT
53635 AAGTTTTTCTTT
1 AAG-TTTTCTTT
53647 TGGTGTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (11 bp):
AAGTTTTCTTT
Found at i:56120 original size:102 final size:102
Alignment explanation
Indices: 55951--56152 Score: 298
Period size: 102 Copynumber: 2.0 Consensus size: 102
55941 CATAAAGACA
55951 AACCTAAAGGAATCAAAAGCGAAAAACCGAAGGAATTTGTCATAAGTCCTCCTTTTCCCGCTAGA
1 AACCTAAAGGAATCAAAAGCGAAAAACCGAAGGAATTTGTCATAAGTCCTCCTTTTCCCGCTAGA
* * *
56016 TTCGCTAAGTCCAAGAAGGAAGCAGAAGAGAAAGATC
66 TTCACTAAGTCCAAGAAAGAAGAAGAAGAGAAAGATC
* * * * * *
56053 AACCTAAAGGACTCAAAAGCGAAAAACTGAAGGAATTTTTCATATA-TCTTTCTTTTCCCTCTAG
1 AACCTAAAGGAATCAAAAGCGAAAAACCGAAGGAATTTGTCATA-AGTCCTCCTTTTCCCGCTAG
*
56117 ATTCACTAAGTCCAAGAAAGAAGAAGAATAGAAAGA
65 ATTCACTAAGTCCAAGAAAGAAGAAGAAGAGAAAGA
56153 AATTCTTGAG
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 88 0.99
103 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (102 bp):
AACCTAAAGGAATCAAAAGCGAAAAACCGAAGGAATTTGTCATAAGTCCTCCTTTTCCCGCTAGA
TTCACTAAGTCCAAGAAAGAAGAAGAAGAGAAAGATC
Found at i:61096 original size:11 final size:11
Alignment explanation
Indices: 61074--61103 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61064 AATCCCATGA
61074 AAAGAA-AAAT
1 AAAGAATAAAT
61084 AAAGAATAAAT
1 AAAGAATAAAT
61095 AAAGAATAA
1 AAAGAATAA
61104 GAATATCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (11 bp):
AAAGAATAAAT
Found at i:61253 original size:28 final size:26
Alignment explanation
Indices: 61232--61293 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
61222 AAAGAGCTAT
*
61232 TAAATCTCTTTTAATTAAAAAGATAA
1 TAAATCTCTTTTAATAAAAAAGATAA
61258 TAAATCTCTTTTAAT-AAAAA-A-AA
1 TAAATCTCTTTTAATAAAAAAGATAA
*
61281 TATATCTCTTTTA
1 TAAATCTCTTTTA
61294 TTTTTATCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 14 0.40
24 1 0.03
25 5 0.14
26 15 0.43
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAATCTCTTTTAATAAAAAAGATAA
Found at i:61287 original size:23 final size:26
Alignment explanation
Indices: 61232--61293 Score: 94
Period size: 23 Copynumber: 2.5 Consensus size: 26
61222 AAAGAGCTAT
61232 TAAATCTCTTTTAATTAAAAAGATAA
1 TAAATCTCTTTTAATTAAAAAGATAA
61258 TAAATCTCTTTTAA-TAAAAA-A-AA
1 TAAATCTCTTTTAATTAAAAAGATAA
*
61281 TATATCTCTTTTA
1 TAAATCTCTTTTA
61294 TTTTTATCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 14 0.40
24 1 0.03
25 6 0.17
26 14 0.40
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAATCTCTTTTAATTAAAAAGATAA
Found at i:62727 original size:16 final size:17
Alignment explanation
Indices: 62702--62734 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62692 TAGAGTTTAA
*
62702 TTTTATTTTGCTTTTGT
1 TTTTATTTTGATTTTGT
62719 TTTTA-TTTGATTTTGT
1 TTTTATTTTGATTTTGT
62735 AGGTACTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.03, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTTATTTTGATTTTGT
Found at i:98088 original size:21 final size:21
Alignment explanation
Indices: 98016--98088 Score: 53
Period size: 21 Copynumber: 3.4 Consensus size: 21
98006 CAGAGAGAAT
98016 CGATA-CCCCCAT-GAGGGAAC
1 CGATACCCCCCATAG-GGGAAC
* **
98036 CGATTCCCCCTTTGAAGGGGAAC
1 CGATACCCCCCAT--AGGGGAAC
*
98059 CGACT-CCCCCCATAGGGGAAT
1 CGA-TACCCCCCATAGGGGAAC
98080 CGATACCCC
1 CGATACCCC
98089 TGGGTTCTGG
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.12
21 19 0.46
23 15 0.37
24 2 0.05
ACGTcount: A:0.25, C:0.37, G:0.23, T:0.15
Consensus pattern (21 bp):
CGATACCCCCCATAGGGGAAC
Found at i:100312 original size:13 final size:13
Alignment explanation
Indices: 100294--100318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
100284 AATGAATTTT
100294 AAGATTTTCTAAA
1 AAGATTTTCTAAA
100307 AAGATTTTCTAA
1 AAGATTTTCTAA
100319 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Done.