Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001106.1 Hibiscus syriacus cultivar Beakdansim tig00002188_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: 71661
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3492 original size:29 final size:30
Alignment explanation
Indices: 3455--3512 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
3445 CTAAAAAAAA
* *
3455 TTCAAGGACTAAATTG-AATTTTAATTAAG
1 TTCAAGGACCAAAGTGAAATTTTAATTAAG
* *
3484 TTCAGGGACCAAAGTGAAATTTTGATTAA
1 TTCAAGGACCAAAGTGAAATTTTAATTAA
3513 ATTTGGATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (30 bp):
TTCAAGGACCAAAGTGAAATTTTAATTAAG
Found at i:4841 original size:39 final size:39
Alignment explanation
Indices: 4787--4870 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
4777 GACCTTACTA
* ** *
4787 CTTACCGCAAGCTCCTTGGCTTTCTACTCAGGGTAAGTC
1 CTTACTGCAAGCTCCTCAGCTTTCTACTAAGGGTAAGTC
* *
4826 CTTACTGCAAGCTCCTCAGCTTTGTGCTAAGGGTAAGTC
1 CTTACTGCAAGCTCCTCAGCTTTCTACTAAGGGTAAGTC
4865 CTTACT
1 CTTACT
4871 ACAGGATCCT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.19, C:0.29, G:0.20, T:0.32
Consensus pattern (39 bp):
CTTACTGCAAGCTCCTCAGCTTTCTACTAAGGGTAAGTC
Found at i:4881 original size:39 final size:39
Alignment explanation
Indices: 4815--4949 Score: 155
Period size: 39 Copynumber: 3.5 Consensus size: 39
4805 GCTTTCTACT
* *
4815 CAGGGTAAGTCCTTACTGCAAGCTCCTCAGCTTTGTGCTA
1 CAGGGTAAGTCCTTACTACAAGCTCCTCTGCTTTGTGC-A
* *
4855 -AGGGTAAGTCCTTACTACAGGATCCTCTGCTTTGTGCA
1 CAGGGTAAGTCCTTACTACAAGCTCCTCTGCTTTGTGCA
* * * * *
4893 CATGATAAGACCTTACCACATGCTCCTCTGCTTTGTGCA
1 CAGGGTAAGTCCTTACTACAAGCTCCTCTGCTTTGTGCA
* *
4932 CAAGGTAAGCCCTTACTA
1 CAGGGTAAGTCCTTACTA
4950 GGTGTACAAG
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
38 1 0.01
39 79 0.99
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (39 bp):
CAGGGTAAGTCCTTACTACAAGCTCCTCTGCTTTGTGCA
Found at i:5330 original size:2 final size:2
Alignment explanation
Indices: 5325--5359 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5315 TGTGTGTGTG
5325 TA TA TA TA 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 TA TA TA TA T
5360 GTTTATCGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5885 original size:21 final size:20
Alignment explanation
Indices: 5861--5900 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5851 TAGCATCAAG
*
5861 TTAAAATTAAGTATGAAATTT
1 TTAAAATTAA-TATCAAATTT
5882 TTAAAATTAATATCAAATT
1 TTAAAATTAATATCAAATT
5901 ATATAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
TTAAAATTAATATCAAATTT
Found at i:5907 original size:21 final size:20
Alignment explanation
Indices: 5862--5913 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5852 AGCATCAAGT
* *
5862 TAAAATTAAGTATGAAATTTT
1 TAAAATTAA-TATCAAATTTA
5883 TAAAATTAATATCAAATTATA
1 TAAAATTAATATCAAATT-TA
*
5904 TAAAACTAAT
1 TAAAATTAAT
5914 TCTAATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAAATTAATATCAAATTTA
Found at i:6686 original size:6 final size:6
Alignment explanation
Indices: 6675--6701 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6665 TTATCATTTT
6675 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
6702 TAATAAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:7170 original size:8 final size:8
Alignment explanation
Indices: 7132--7188 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
7122 AACAATTCAA
7132 AATAATTT
1 AATAATTT
7140 AATAAATTT
1 AAT-AATTT
7149 AA-AATATT
1 AATAAT-TT
*
7157 TA-AATTT
1 AATAATTT
7164 AATAATTT
1 AATAATTT
*
7172 AATAATTC
1 AATAATTT
*
7180 AATAGTTT
1 AATAATTT
7188 A
1 A
7189 TTAACAATCA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
7 6 0.15
8 28 0.68
9 7 0.17
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (8 bp):
AATAATTT
Found at i:9586 original size:11 final size:11
Alignment explanation
Indices: 9561--9593 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
9551 TGTTTTTTCT
9561 TTAGTT-CAT-
1 TTAGTTGCATA
9570 TTAGTTGCATA
1 TTAGTTGCATA
9581 TTAGTTGCATA
1 TTAGTTGCATA
9592 TT
1 TT
9594 TCATGAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.27
10 3 0.14
11 13 0.59
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (11 bp):
TTAGTTGCATA
Found at i:23592 original size:11 final size:11
Alignment explanation
Indices: 23576--23631 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
23566 AATTTAATCA
* *
23576 TATTTTGTTAG
1 TATTTTATTAT
*
23587 TATTTTTTTAAT
1 TATTTTATT-AT
23599 TATTTTATTAT
1 TATTTTATTAT
23610 TATTTTATTTAAT
1 TATTTTA-TT-AT
23623 TATTTTATT
1 TATTTTATT
23632 TTTTTTGCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.44
12 13 0.33
13 9 0.23
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:23625 original size:24 final size:24
Alignment explanation
Indices: 23567--23631 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
23557 CTTTCTATAA
*
23567 ATTTAATCATATTTTGTTAGTATTTT
1 ATTTAAT--TATTTTATTAGTATTTT
*
23593 -TTTAATTATTTTATTATTATTTT
1 ATTTAATTATTTTATTAGTATTTT
23616 ATTTAATTATTTTATT
1 ATTTAATTATTTTATT
23632 TTTTTTGCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 15 0.42
24 15 0.42
25 6 0.17
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (24 bp):
ATTTAATTATTTTATTAGTATTTT
Found at i:23908 original size:13 final size:13
Alignment explanation
Indices: 23890--23949 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
23880 AACTGCAAAA
23890 AAATAAAATAATT
1 AAATAAAATAATT
23903 AAATAAAATAA-T
1 AAATAAAATAATT
*
23915 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
23928 -AATACAATAATT
1 AAATAAAATAATT
23940 AAATAAAATA
1 AAATAAAATA
23950 CTAACAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.10
12 13 0.32
13 23 0.57
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:23915 original size:21 final size:21
Alignment explanation
Indices: 23886--23929 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
23876 TTATAACTGC
*
23886 AAAAAAATAAAATAATTAAAT
1 AAAAAAATAAAAAAATTAAAT
*
23907 AAAATAATAAAAAAATTAAAT
1 AAAAAAATAAAAAAATTAAAT
23928 AA
1 AA
23930 TACAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAAATAAAAAAATTAAAT
Found at i:23922 original size:16 final size:16
Alignment explanation
Indices: 23886--23945 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
23876 TTATAACTGC
23886 AAAAAAATAAAATAAT
1 AAAAAAATAAAATAAT
*
23902 ---TAAATAAAATAAT
1 AAAAAAATAAAATAAT
*
23915 AAAAAAATTAAATAAT
1 AAAAAAATAAAATAAT
* * *
23931 ACAATAATTAAATAA
1 AAAAAAATAAAATAA
23946 AATACTAACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
13 12 0.33
16 24 0.67
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAAATAAAATAAT
Found at i:23943 original size:21 final size:21
Alignment explanation
Indices: 23886--23937 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
23876 TTATAACTGC
* *
23886 AAAAAAATAAAATAATTAAAT
1 AAAACAATAAAAAAATTAAAT
*
23907 AAAATAATAAAAAAATTAAAT
1 AAAACAATAAAAAAATTAAAT
*
23928 AATACAATAA
1 AAAACAATAA
23938 TTAAATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAACAATAAAAAAATTAAAT
Found at i:23948 original size:21 final size:20
Alignment explanation
Indices: 23895--23949 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 20
23885 CAAAAAAATA
23895 AAATAATTAAATAAAATAAT
1 AAATAATTAAATAAAATAAT
*
23915 -AA-AA--AAATTAAATAAT
1 AAATAATTAAATAAAATAAT
23931 ACAATAATTAAATAAAATA
1 A-AATAATTAAATAAAATA
23950 CTAACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 11 0.39
18 4 0.14
19 4 0.14
21 9 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAATTAAATAAAATAAT
Found at i:31900 original size:23 final size:23
Alignment explanation
Indices: 31849--31912 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
31839 AAAGATATAT
**
31849 CCTTTTGTTTTAAAGAGACATGC
1 CCTTTTGTTTTAAAGAGACACAC
*
31872 CCTTTTGTTTTAAAGAGATACAC
1 CCTTTTGTTTTAAAGAGACACAC
* * *
31895 CTTTTTCTTGTAAAGAGA
1 CCTTTTGTTTTAAAGAGA
31913 AATGTCCTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (23 bp):
CCTTTTGTTTTAAAGAGACACAC
Found at i:33045 original size:24 final size:24
Alignment explanation
Indices: 33018--33069 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
33008 AACGGATATA
*
33018 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
33042 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
33066 TCAA
1 TCAA
33070 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:33070 original size:24 final size:24
Alignment explanation
Indices: 33038--33150 Score: 149
Period size: 24 Copynumber: 4.7 Consensus size: 24
33028 AAACATAAAT
*
33038 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
33062 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
33086 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
33110 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
33134 CATGTCAAGTATCAGAT
1 CAGGTCAAGTATCAGAT
33151 TATGATTCAA
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
23 5 0.06
24 74 0.91
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:37768 original size:24 final size:24
Alignment explanation
Indices: 37741--37792 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
37731 AACGGATATA
*
37741 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
37765 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
37789 TCAA
1 TCAA
37793 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:37793 original size:24 final size:24
Alignment explanation
Indices: 37757--37875 Score: 113
Period size: 24 Copynumber: 5.0 Consensus size: 24
37747 ATCAAAACAT
*
37757 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
37781 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
37805 -AATCCAAGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
*
37829 -AATCTATGTC-AGATATCAGAT-A-
1 AAATC-AGGTCAAG-TATCAGATCAG
* *
37851 AAATCCATGTCAAGTATCATATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
37876 GATTCAAATC
Statistics
Matches: 81, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
23 22 0.27
24 59 0.73
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:37849 original size:48 final size:47
Alignment explanation
Indices: 37764--37875 Score: 138
Period size: 47 Copynumber: 2.4 Consensus size: 47
37754 CATAAATCAG
*
37764 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGAT-AAAATCCAA
* * * *
37812 GTCAAGTATCAGATCAG-AATCTATGTC-AGATATCAGATAAAATCCAT
1 GTCAAGTATCATATCAGAAATC-AGGTCAAG-TAACAGATAAAATCCAA
37859 GTCAAGTATCATATCAG
1 GTCAAGTATCATATCAG
37876 GATTCAAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
47 29 0.52
48 27 0.48
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATAAAATCCAA
Found at i:40433 original size:13 final size:13
Alignment explanation
Indices: 40415--40469 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
40405 CGGTCAACGG
40415 GTCAACGGGTCGA
1 GTCAACGGGTCGA
*
40428 GTCAACGGGTCGG
1 GTCAACGGGTCGA
* *
40441 GTCAACAGGTCGG
1 GTCAACGGGTCGA
*
40454 GTAAACGGGTCGA
1 GTCAACGGGTCGA
40467 GTC
1 GTC
40470 GGGTCGGGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:53291 original size:45 final size:45
Alignment explanation
Indices: 53158--53481 Score: 452
Period size: 45 Copynumber: 7.2 Consensus size: 45
53148 ATTATTCATT
* *
53158 ATTTCCATTTATGGCATCCATTCATGCCTTCAATGCACCGTTATGC
1 ATTT-CATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
53204 ATTTCATTTATGGCATCC-TTCATGCCTTTAATACATCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
53248 ATTTCATTTATGGCATCCTTTCAGGCCTTTAATGCACCGTTATGG
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * * *
53293 ATTTCATTTATGGCATCCTTTTATGCCTTTAATGAAACATTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
53338 ATTTCATTTATGACATCCATTCATGCCTTTAATGCACCGTTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
53383 ATTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGG
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
53428 ATTTCATTTATGGAACCCTTTCATTCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
53473 ATTTCATTT
1 ATTTCATTT
53482 GTGTAATAAA
Statistics
Matches: 248, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
44 40 0.16
45 204 0.82
46 4 0.02
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:57023 original size:24 final size:24
Alignment explanation
Indices: 56977--57028 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
56967 CCTTGGCACT
* * *
56977 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAACTGTTGGAACA
* *
57001 TCAAGTGGCATAACTGTTGGAACG
1 TCAAGTGGCACAACTGTTGGAACA
57025 TCAA
1 TCAA
57029 ATGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAACTGTTGGAACA
Found at i:58339 original size:23 final size:24
Alignment explanation
Indices: 58301--58353 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
58291 CTTTCTTTTT
58301 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* * *
58325 TTTCTTCTTTT-GAGTTCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
58348 TTTCTT
1 TTTCTT
58354 TGCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.64
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:65962 original size:45 final size:45
Alignment explanation
Indices: 65854--66135 Score: 442
Period size: 45 Copynumber: 6.3 Consensus size: 45
65844 TATTCATTAT
* **
65854 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAAATTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCAC-CGTTATGCA
65900 TTTCATTTATGAT-ATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATG-TCATCCTTTCATGCCTTTAATGCACCGTTATGCA
65945 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* **
65990 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
66035 TTTCATTTATG-GATCCTTTCATGCCTTTAATGCATCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
66079 TTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
66124 TTTCATTTATGT
1 TTTCATTTATGT
66136 AATGAAACAT
Statistics
Matches: 219, Mismatches: 14, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
44 42 0.19
45 143 0.65
46 34 0.16
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:66074 original size:134 final size:136
Alignment explanation
Indices: 65854--66130 Score: 468
Period size: 134 Copynumber: 2.1 Consensus size: 136
65844 TATTCATTAT
* * *
65854 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGATATCCTT
1 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGAGATCCTT
*
65919 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGT
66 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGT
65984 TATGCA
131 TATGCA
**
65990 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCAC-CGTTATGCATTTCATTTATG-GATCCTT
1 TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGAGATCCTT
* *
66053 TCATGCCTTTAATGCATCGTTATGCATTTTATTTATGACATCCTTTCATGCCTTTAATGCACCGT
66 TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGT
66118 TATGCA
131 TATGCA
66124 TTTCATT
1 TTTCATT
66131 TATGTAATGA
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 81 0.61
135 18 0.14
136 34 0.26
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (136 bp):
TTTCATTGATGGAATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGAGATCCTT
TCATGCCTTTAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTTTAATGCACCGT
TATGCA
Found at i:66100 original size:89 final size:87
Alignment explanation
Indices: 65854--66134 Score: 445
Period size: 89 Copynumber: 3.1 Consensus size: 87
65844 TATTCATTAT
*
65854 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACAAATTATGCATTTCATTTATGATATCCTT
1 TTTCATTTATGG-ATCCTTTCATGCCTTTAATGCAC--GTTATGCATTTCATTTATGA-ATCCTT
65919 TCATGCCTTTAATGCACCGTTATGCA
62 TCATGCCTTTAATGCACCGTTATGCA
* *
65945 TTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTGATGGAATCCTTT
1 TTTCATTTATG-GATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTAT-GAATCCTTT
66010 CATGCCTTTAATGCACCGTTATGCA
63 CATGCCTTTAATGCACCGTTATGCA
*
66035 TTTCATTTATGGATCCTTTCATGCCTTTAATGCATCGTTATGCATTTTATTTATGACATCCTTTC
1 TTTCATTTATGGATCCTTTCATGCCTTTAATGCA-CGTTATGCATTTCATTTATGA-ATCCTTTC
66100 ATGCCTTTAATGCACCGTTATGCA
64 ATGCCTTTAATGCACCGTTATGCA
66124 TTTCATTTATG
1 TTTCATTTATG
66135 TAATGAAACA
Statistics
Matches: 179, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
88 2 0.01
89 82 0.46
90 59 0.33
91 35 0.20
92 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (87 bp):
TTTCATTTATGGATCCTTTCATGCCTTTAATGCACGTTATGCATTTCATTTATGAATCCTTTCAT
GCCTTTAATGCACCGTTATGCA
Found at i:68642 original size:44 final size:44
Alignment explanation
Indices: 68527--68832 Score: 393
Period size: 44 Copynumber: 7.0 Consensus size: 44
68517 ATACCATGAG
* * * * *
68527 TGGCACCTTTCTGTCAATAATGTACCGCTATGCATTTTAATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
68571 TGTCACATTT-T-CCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** *
68613 TGGCATGTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
68657 TGTCACATTTCTGCCAAAAATGCACCATTATGCATTTTGATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
68701 TGGCACCTTTCTGCCAATAATGCACCGTTATACATTTTCATGTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * *
68745 TGGTACCTTTCTGCCAATAATGCACCGTTATACATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
**
68789 TGGCACATTTCTGGTAATAATGCACCGTTA-GCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
68832 T
1 T
68833 TTTAGAGCAT
Statistics
Matches: 231, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 33 0.14
43 15 0.06
44 183 0.79
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Done.