Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002212.1 Hibiscus syriacus cultivar Beakdansim tig00004506_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: 72732
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2763 original size:40 final size:40
Alignment explanation
Indices: 2697--2846 Score: 237
Period size: 40 Copynumber: 3.8 Consensus size: 40
2687 ACCGTAGTGC
* **
2697 TACACATAAGGTCGTGCCCACTATATACAATGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
2737 TACACATAAGGTCATGCACACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
2777 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2817 TACACATAAGGTCGTGCCCACCATATACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
2847 TTAGTGTCCT
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 99 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2860 original size:40 final size:40
Alignment explanation
Indices: 2697--2865 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
2687 ACCGTAGTGC
* *
2697 TACACATAAGGTCGTGCCCACTATATACA-ATGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCT-AAGTGTAT
* * *
2737 TACACATAAGGTCATGCACACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
* *
2777 TACACATAAGGTCGTGCCCACCATATATACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
* *
2817 TACACATAAGGTCGTGCCCACCATATACA-CTTAGTGTCCT
1 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGT-AT
2857 TACACATAA
1 TACACATAA
2866 TAGTGTAATA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 6 0.05
40 108 0.95
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
Found at i:3764 original size:29 final size:30
Alignment explanation
Indices: 3727--3784 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3717 AACCCATCAA
*
3727 TTTTCC-AAAATTACTAAATTGATCCCCAAC
1 TTTTCCAAAAATTAC-AAAATGATCCCCAAC
*
3757 TTTT-CAAAAATTACAAAATGGTCCCCAA
1 TTTTCCAAAAATTACAAAATGATCCCCAA
3785 AATTTTCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (30 bp):
TTTTCCAAAAATTACAAAATGATCCCCAAC
Found at i:3791 original size:30 final size:30
Alignment explanation
Indices: 3725--3791 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
3715 ACAACCCATC
* *
3725 AATTTTCCAAAATTACTAAATTGATCCCCA
1 AATTTTCAAAAATTACTAAAATGATCCCCA
* *
3755 ACTTTTCAAAAATTAC-AAAATGGTCCCCAA
1 AATTTTCAAAAATTACTAAAATGATCCCC-A
3785 AATTTTC
1 AATTTTC
3792 TAAGGCTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.33
Consensus pattern (30 bp):
AATTTTCAAAAATTACTAAAATGATCCCCA
Found at i:11814 original size:6 final size:6
Alignment explanation
Indices: 11805--11851 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
11795 GAAGATGAAA
*
11805 GAAAGT GAAAGT GAAAGT GAAAGT GAAAAG- GTAAAGT AAAAGT GAAA
1 GAAAGT GAAAGT GAAAGT GAAAGT G-AAAGT G-AAAGT GAAAGT GAAA
11852 AGAAGATAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 32 0.89
7 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
GAAAGT
Found at i:11840 original size:19 final size:20
Alignment explanation
Indices: 11805--11853 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11795 GAAGATGAAA
11805 GAAAGTG-AAA-GTGAAAGT
1 GAAAGTGAAAAGGTGAAAGT
11823 GAAAGTGAAAAGGT-AAAGT
1 GAAAGTGAAAAGGTGAAAGT
*
11842 AAAAGTGAAAAG
1 GAAAGTGAAAAG
11854 AAGATAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 7 0.25
19 19 0.68
20 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.31, T:0.14
Consensus pattern (20 bp):
GAAAGTGAAAAGGTGAAAGT
Found at i:32096 original size:2 final size:2
Alignment explanation
Indices: 32089--32130 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
32079 AATTAAAAAT
* *
32089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32131 ACTATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32268 original size:18 final size:19
Alignment explanation
Indices: 32225--32268 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
32215 TTTGGTTCAC
* *
32225 GGAATGTAAGATTACCAGTG
1 GGAATATAAGATTACCAG-A
32245 GGAATATAAGATTACCA-A
1 GGAATATAAGATTACCAGA
32263 GGAATA
1 GGAATA
32269 AGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCAGA
Found at i:34039 original size:18 final size:18
Alignment explanation
Indices: 34016--34051 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
34006 AGGTTTGATT
*
34016 TCACATGAATTGATAGTC
1 TCACATGAATTCATAGTC
34034 TCACATGAATTCATAGTC
1 TCACATGAATTCATAGTC
34052 GAAACTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
TCACATGAATTCATAGTC
Found at i:34870 original size:22 final size:23
Alignment explanation
Indices: 34839--34885 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
34829 TAATCGCGAG
34839 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* *
34861 TTTAGCAGATACGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
34884 TT
1 TT
34886 ATTTAGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:35731 original size:35 final size:35
Alignment explanation
Indices: 35692--35807 Score: 92
Period size: 35 Copynumber: 3.2 Consensus size: 35
35682 GGCCTTTCTG
35692 GCGCTTCTTGTGCATAAAGCGAGCGCTTTCGCTTA
1 GCGCTTCTTGTGCATAAAGCGAGCGCTTTCGCTTA
* * ** * * *
35727 GCGCTTC-GGCGTC-TAGGACCCTAGGCGCTTTAGGGCTCTG
1 GCGCTTCTTGTG-CATA--AAGCGA-GCGCTTT--CGCT-TA
35767 GCGCTTCTTGTGCATAAAGCGAGCGCTTTCGCTTA
1 GCGCTTCTTGTGCATAAAGCGAGCGCTTTCGCTTA
35802 GCGCTT
1 GCGCTT
35808 AGCGCTTCGG
Statistics
Matches: 58, Mismatches: 14, Indels: 18
0.64 0.16 0.20
Matches are distributed among these distances:
34 4 0.07
35 15 0.26
36 6 0.10
37 7 0.12
38 7 0.12
39 6 0.10
40 9 0.16
41 4 0.07
ACGTcount: A:0.14, C:0.28, G:0.29, T:0.29
Consensus pattern (35 bp):
GCGCTTCTTGTGCATAAAGCGAGCGCTTTCGCTTA
Found at i:39651 original size:3 final size:3
Alignment explanation
Indices: 39643--40194 Score: 1032
Period size: 3 Copynumber: 186.7 Consensus size: 3
39633 TTATCAACGT
39643 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39691 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39739 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
39784 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39832 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39878 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39926 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39973 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40019 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40066 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40114 TTA TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40160 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40195 TTGTGTTTGT
Statistics
Matches: 539, Mismatches: 0, Indels: 20
0.96 0.00 0.04
Matches are distributed among these distances:
2 18 0.03
3 518 0.96
4 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:43861 original size:21 final size:21
Alignment explanation
Indices: 43837--43881 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43827 TTCCATAGGA
* *
43837 TCTGGATTATTAATTTTTTAT
1 TCTGGAATATTAATATTTTAT
*
43858 TCTGGAATATTAATATTTTCT
1 TCTGGAATATTAATATTTTAT
43879 TCT
1 TCT
43882 ATTGAAGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (21 bp):
TCTGGAATATTAATATTTTAT
Found at i:46355 original size:21 final size:21
Alignment explanation
Indices: 46241--46361 Score: 152
Period size: 21 Copynumber: 5.8 Consensus size: 21
46231 AGGGTTCTAC
46241 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
46262 GTGATCCTTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
46283 GCGGTCTTTCGAGACATATAT
1 GTGGTCCTTCGGGACATATAT
* * *
46304 TTGGTCCTTTGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
46325 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
*
46346 GTAGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
46362 ATTCTACGAG
Statistics
Matches: 81, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:47296 original size:16 final size:16
Alignment explanation
Indices: 47271--47317 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
47261 TATATTAATA
*
47271 TTTTAAAATAATTTAT
1 TTTTATAATAATTTAT
47287 TTTTATAATAA--TAT
1 TTTTATAATAATTTAT
* *
47301 ATTTATAATTATTTAT
1 TTTTATAATAATTTAT
47317 T
1 T
47318 ATATTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
16 13 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATAATAATTTAT
Found at i:47317 original size:30 final size:29
Alignment explanation
Indices: 47261--47317 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
47251 CTGATTCAAA
*
47261 TATATTAATATTTTAAAATAATTTATTTT
1 TATAATAATATTTTAAAATAATTTATTTT
* *
47290 TATAATAATATATTTATAATTATTTATT
1 TATAATAATAT-TTTAAAATAATTTATT
47318 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TATAATAATATTTTAAAATAATTTATTTT
Found at i:47350 original size:33 final size:33
Alignment explanation
Indices: 47305--47373 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
47295 TAATATATTT
47305 ATAATTATTTATTATATTTTAAAT-GTT-AATA
1 ATAATTATTTATTATATTTTAAATAGTTAAATA
*
47336 ATAATATATTTTATTATATTTTTAATAGTTAAATA
1 ATAAT-TA-TTTATTATATTTTAAATAGTTAAATA
47371 ATA
1 ATA
47374 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 5 0.15
32 2 0.06
33 16 0.48
34 3 0.09
35 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (33 bp):
ATAATTATTTATTATATTTTAAATAGTTAAATA
Found at i:47875 original size:20 final size:20
Alignment explanation
Indices: 47825--47875 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
47815 CTTTTTACTC
47825 AAATCTTAAATCCTAAACCTA
1 AAAT-TTAAATCCTAAACCTA
** * *
47846 AACCTAAAATCCTAAATCTA
1 AAATTTAAATCCTAAACCTA
47866 AAATTTAAAT
1 AAATTTAAAT
47876 ATTAAAACCC
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATTTAAATCCTAAACCTA
Found at i:53074 original size:159 final size:159
Alignment explanation
Indices: 52785--53089 Score: 567
Period size: 159 Copynumber: 1.9 Consensus size: 159
52775 AACCTCAGAC
*
52785 ATACGGACAGCCAAAATATGTCATCCAGACCTTAAATGATATGCTTAGGTGCACCATTATAGACC
1 ATACGGACAGCCAAAATATGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
52850 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGAAATTTTCAGTCG
66 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGAAATTTTCAGTCG
52915 AGCATTTAGATGGCTCCGTAAGAGGCCTT
131 AGCATTTAGATGGCTCCGTAAGAGGCCTT
* *
52944 ATACGGACAGCCAAAATGTGTCATCCATACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
1 ATACGGACAGCCAAAATATGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
53009 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATA-ACAATTTTCAGTC
66 TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGA-AATTTTCAGTC
53073 GAGCATTTAGATGGCTC
130 GAGCATTTAGATGGCTC
53090 TACTTTATTA
Statistics
Matches: 142, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
158 1 0.01
159 141 0.99
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (159 bp):
ATACGGACAGCCAAAATATGTCATCCAGACCTTAAAGGATATGCTTAGGTGCACCATTATAGACC
TCGAGGGTAGTTGTGAGGACCACCTGCCATTGTTGGAGTTTACGTAAAATAGAAATTTTCAGTCG
AGCATTTAGATGGCTCCGTAAGAGGCCTT
Found at i:55567 original size:23 final size:23
Alignment explanation
Indices: 55541--55590 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
55531 GTCATGTTAT
55541 TTGTGGTTAATTGCCAAGTGCAA
1 TTGTGGTTAATTGCCAAGTGCAA
*
55564 TTGTGGTTAATTGCTAAGTGCAA
1 TTGTGGTTAATTGCCAAGTGCAA
55587 TTGT
1 TTGT
55591 TATTCAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (23 bp):
TTGTGGTTAATTGCCAAGTGCAA
Found at i:58229 original size:22 final size:22
Alignment explanation
Indices: 58201--58244 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
58191 ATATATATCC
* *
58201 TATAAAATAGTTGTTCGAATTT
1 TATAAAATAGTTATTCAAATTT
58223 TATAAAATAGTTATTCAAATTT
1 TATAAAATAGTTATTCAAATTT
58245 CAAACTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (22 bp):
TATAAAATAGTTATTCAAATTT
Found at i:58885 original size:6 final size:7
Alignment explanation
Indices: 58869--58905 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
58859 CTAGGCAAGA
58869 AAAAATG
1 AAAAATG
58876 AAAAAT-
1 AAAAATG
58882 AAAAATG
1 AAAAATG
58889 AAAAAT-
1 AAAAATG
58895 -AAAATG
1 AAAAATG
58901 AAAAA
1 AAAAA
58906 AACATCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.19
6 6 0.22
7 16 0.59
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:58892 original size:12 final size:11
Alignment explanation
Indices: 58868--58907 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
58858 GCTAGGCAAG
58868 AAAAAATGAAAA
1 AAAAAATG-AAA
58880 ATAAAAATGAAA
1 A-AAAAATGAAA
58892 AATAAAATGAAA
1 AA-AAAATGAAA
58904 AAAA
1 AAAA
58908 CATCATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.12
12 16 0.62
13 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (11 bp):
AAAAAATGAAA
Found at i:58906 original size:13 final size:13
Alignment explanation
Indices: 58869--58905 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
58859 CTAGGCAAGA
58869 AAAAATGAAAAAT
1 AAAAATGAAAAAT
58882 AAAAATGAAAAAT
1 AAAAATGAAAAAT
58895 -AAAATGAAAAA
1 AAAAATGAAAAA
58906 AACATCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (13 bp):
AAAAATGAAAAAT
Found at i:68358 original size:20 final size:20
Alignment explanation
Indices: 68333--68370 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
68323 ACCTTACAAC
68333 TGACACATTAAAAATCACAT
1 TGACACATTAAAAATCACAT
68353 TGACACATTAAAAATCAC
1 TGACACATTAAAAATCAC
68371 TACGAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (20 bp):
TGACACATTAAAAATCACAT
Done.