Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006846.1 Hibiscus syriacus cultivar Beakdansim tig00017405_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: 66394
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:673 original size:17 final size:19
Alignment explanation
Indices: 637--673 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
627 TTTAATTAAC
*
637 TTCCATTGTTTCTCTTCAA
1 TTCCATTGTTTCTATTCAA
656 TTCCATT-TTTC-ATTCAA
1 TTCCATTGTTTCTATTCAA
673 T
1 T
674 CAAAATTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (19 bp):
TTCCATTGTTTCTATTCAA
Found at i:2215 original size:20 final size:18
Alignment explanation
Indices: 2190--2236 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
2180 AATTAAGGCC
2190 TTTAATTTATATATTTTACA
1 TTTAATTTAT-TATTTTA-A
2210 TTTAATCTTATTATTTTAA
1 TTTAAT-TTATTATTTTAA
*
2229 TTTTATTT
1 TTTAATTT
2237 GCTTCAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 13 0.52
21 4 0.16
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTAATTTATTATTTTAA
Found at i:6944 original size:10 final size:10
Alignment explanation
Indices: 6929--6953 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6919 TGCTCGAAGT
6929 AAGAAGAAAG
1 AAGAAGAAAG
6939 AAGAAGAAAG
1 AAGAAGAAAG
6949 AAGAA
1 AAGAA
6954 AAAAAAGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAG
Found at i:7457 original size:18 final size:16
Alignment explanation
Indices: 7421--7479 Score: 77
Period size: 16 Copynumber: 3.6 Consensus size: 16
7411 TCATTTATCA
7421 GAAAAA-AATAAAAAA-
1 GAAAAAGAA-AAAAAAT
7436 GAAAAAGAAAAAAGAGAT
1 GAAAAAGAAAAAA-A-AT
7454 GAAAAAGAAAAAAAAT
1 GAAAAAGAAAAAAAAT
7470 GAAAAAGAAA
1 GAAAAAGAAA
7480 TTCAATCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.25
16 15 0.38
17 2 0.05
18 13 0.32
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (16 bp):
GAAAAAGAAAAAAAAT
Found at i:9193 original size:54 final size:54
Alignment explanation
Indices: 9105--9256 Score: 196
Period size: 54 Copynumber: 2.8 Consensus size: 54
9095 AATCTGTGTA
* ** * * *
9105 AAACCACAGGAAATGATGAATGTATTGTCAAATGTTTTACGAGCATTTGGGTAG
1 AAACCACAGGAAAGGATGAATGCGTTGTCAAATGTTTTACGAACATCTGGGCAG
* * * *
9159 AAGCCACATGAAAGGATTAATGCGTTGTCAAATGTTTTACGAACATCTGTGCAG
1 AAACCACAGGAAAGGATGAATGCGTTGTCAAATGTTTTACGAACATCTGGGCAG
* *
9213 AAACCACAGGAAGGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 AAACCACAGGAAAGGATGAATGCGTTGTCAAATGTTTTACGAAC
9257 CAGTGATTAT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (54 bp):
AAACCACAGGAAAGGATGAATGCGTTGTCAAATGTTTTACGAACATCTGGGCAG
Found at i:10764 original size:3 final size:3
Alignment explanation
Indices: 10756--10804 Score: 64
Period size: 3 Copynumber: 16.3 Consensus size: 3
10746 CTGAACAAAA
**
10756 ATT ATT ATT ACA ATT ATT ATT ATT ATT ATT ATT A-T ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
10801 ATT A
1 ATT A
10805 CAATCCCGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:12190 original size:11 final size:11
Alignment explanation
Indices: 12174--12198 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12164 TAGTACTTTA
12174 ATTATTATTTC
1 ATTATTATTTC
12185 ATTATTATTTC
1 ATTATTATTTC
12196 ATT
1 ATT
12199 TTTCATATAA
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATTTC
Found at i:13275 original size:190 final size:191
Alignment explanation
Indices: 12900--13275 Score: 630
Period size: 191 Copynumber: 2.0 Consensus size: 191
12890 TCCTATTTAT
* * *
12900 TTAATGGTTCTTGATGATTTTTAATGAATATTTGTGATTTTTAAAGAGCTAATGTTGTTATAAAA
1 TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
* *
12965 TCATATTTGAAATTAGATTAAAGAAATTAAAGTTTACTAAGCAAAATGAATCAGTCTAGGTTATT
66 TCATATTTGAAATTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTATT
*
13030 TTCTAGAAATTCGGATTACCTTTGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAACA
131 TTCTAGAAATTCGGATTACCTATGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAACA
13091 TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGA-TTTTAAAGAGCTAATGCTATTATAAAA
1 TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
13155 TCATATTTGAAATTTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTAT
66 TCATATTTGAAA-TTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTAT
** * * *
13220 TTTCTAGAAATTTTGATTACCTATGATTTGTTG-TGATGATGTTTTGGATATGTTTT
130 TTTCTAGAAATTCGGATTACCTATGAGTTGTTGTTGATGATATTTTGGAGATGTTTT
13276 TCATTTTGGT
Statistics
Matches: 173, Mismatches: 11, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
190 58 0.34
191 115 0.66
ACGTcount: A:0.34, C:0.06, G:0.16, T:0.43
Consensus pattern (191 bp):
TTAATGGTTCTTGATGATTTGTAATGAATATTTGTGATTTTTAAAGAGCTAATGCTATTATAAAA
TCATATTTGAAATTAGATTAAAGAAATTAAAATTTACTAAGCAAAATAAATCAGTCTAGGTTATT
TTCTAGAAATTCGGATTACCTATGAGTTGTTGTTGATGATATTTTGGAGATGTTTTAAACA
Found at i:23521 original size:10 final size:11
Alignment explanation
Indices: 23501--23542 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
23491 GTTCGAATGA
23501 AAAAGAAAAAG
1 AAAAGAAAAAG
23512 AAAA-AAAAAG
1 AAAAGAAAAAG
* *
23522 ACATGAAAAAG
1 AAAAGAAAAAG
23533 AAATAGAAAA
1 AAA-AGAAAA
23543 CAAAACAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 12 0.48
12 5 0.20
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:28883 original size:15 final size:14
Alignment explanation
Indices: 28849--28886 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
28839 AAAGTTAATG
28849 GGGTTGACTCATAT
1 GGGTTGACTCATAT
*
28863 GAGTTGACTCAATAT
1 GGGTTGACTC-ATAT
28878 GGGTTGACT
1 GGGTTGACT
28887 TGGTTTAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (14 bp):
GGGTTGACTCATAT
Found at i:34466 original size:3 final size:3
Alignment explanation
Indices: 34458--34522 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
34448 AATATATATT
*
34458 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34506 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
34523 TGGGTAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35122 original size:113 final size:113
Alignment explanation
Indices: 34839--35256 Score: 685
Period size: 113 Copynumber: 3.7 Consensus size: 113
34829 GATAGAATTA
* *
34839 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
34904 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 CTTTCTCTGGAAAAGATGATCCATCAA-ATGATGAATTCAGGTAAAAGG
*
34953 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
35018 CTTTCTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
*
35066 TTGAACAAATTCTTCTCATTATGAACTT-TCTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * *
35130 ACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
65 ACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
35179 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
35244 CCTTCTCTGGAAA
66 CTTTCTCTGGAAA
35257 TGTAAATCGA
Statistics
Matches: 284, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
112 1 0.00
113 195 0.69
114 88 0.31
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGG
Found at i:36091 original size:83 final size:83
Alignment explanation
Indices: 35952--36427 Score: 882
Period size: 83 Copynumber: 5.7 Consensus size: 83
35942 GTAGTTCCTA
*
35952 CCAAACAAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
36017 ATTCAAAT-ATTGGTTCTG
66 ATTC-AATGATTGGTTCTG
36035 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
36100 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
36118 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
36183 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
36201 CTAAACCAGATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
36266 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
36284 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGAACACATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
36349 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
36367 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
36428 TCATTTAATT
Statistics
Matches: 382, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
82 3 0.01
83 379 0.99
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:37584 original size:10 final size:10
Alignment explanation
Indices: 37565--37624 Score: 77
Period size: 10 Copynumber: 5.9 Consensus size: 10
37555 TTGACCCCCC
37565 TTTTTC-TTT
1 TTTTTCTTTT
*
37574 TTTCTCTTTT
1 TTTTTCTTTT
37584 TTTTTCTTTTT
1 TTTTTC-TTTT
*
37595 TTTTTCTTTC
1 TTTTTCTTTT
37605 TTTTTCTTTCT
1 TTTTTCTTT-T
37616 TTTTTCTTT
1 TTTTTCTTT
37625 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
9 5 0.11
10 20 0.45
11 19 0.43
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:37597 original size:21 final size:20
Alignment explanation
Indices: 37564--37627 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
37554 CTTGACCCCC
*
37564 CTTTTTC-TTTTTTCTCTTT
1 CTTTTTCTTTTTTTTTCTTT
*
37583 TTTTTTCTTTTTTTTTTCTTT
1 CTTTTTC-TTTTTTTTTCTTT
37604 CTTTTTCTTTCTTTTTTCTTT
1 CTTTTTCTTT-TTTTTTCTTT
37625 CTT
1 CTT
37628 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
19 6 0.15
20 3 0.08
21 30 0.77
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
CTTTTTCTTTTTTTTTCTTT
Found at i:37623 original size:11 final size:11
Alignment explanation
Indices: 37567--37627 Score: 88
Period size: 11 Copynumber: 5.5 Consensus size: 11
37557 GACCCCCCTT
37567 TTTCTTTTTTC
1 TTTCTTTTTTC
*
37578 TCTTTTTTTTTC
1 T-TTCTTTTTTC
*
37590 TTTTTTTTTTC
1 TTTCTTTTTTC
37601 TTTC-TTTTTC
1 TTTCTTTTTTC
37611 TTTCTTTTTTC
1 TTTCTTTTTTC
37622 TTTCTT
1 TTTCTT
37628 CAAGCATAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.22
11 26 0.57
12 10 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:37625 original size:25 final size:26
Alignment explanation
Indices: 37565--37628 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
37555 TTGACCCCCC
* *
37565 TTTTTCTTTTTTCTCTTTTTTTTTCT
1 TTTTTCTTTCTTCTCTTTTTCTTTCT
*
37591 TTTTTTTTTCTT-TCTTTTTCTTTCT
1 TTTTTCTTTCTTCTCTTTTTCTTTCT
37616 TTTTTCTTTCTTC
1 TTTTTCTTTCTTC
37629 AAGCATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (26 bp):
TTTTTCTTTCTTCTCTTTTTCTTTCT
Found at i:45955 original size:17 final size:17
Alignment explanation
Indices: 45933--45967 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
45923 AAAATAAAAC
*
45933 ATATAAATATTATGAAA
1 ATATAAAAATTATGAAA
*
45950 ATATAAAAATTTTGAAA
1 ATATAAAAATTATGAAA
45967 A
1 A
45968 GAAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATAAAAATTATGAAA
Found at i:48132 original size:3 final size:3
Alignment explanation
Indices: 48124--48182 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
48114 AATATATATT
*
48124 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48172 TAA TAA TAA TA
1 TAA TAA TAA TA
48183 TGGGTAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49971 original size:18 final size:18
Alignment explanation
Indices: 49934--49970 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49924 CTTAATAACC
49934 TTATTTATTATAGAAATT
1 TTATTTATTATAGAAATT
*
49952 TTATTTATTCTAG-AATT
1 TTATTTATTATAGAAATT
49969 TT
1 TT
49971 TTTCCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (18 bp):
TTATTTATTATAGAAATT
Found at i:52404 original size:23 final size:25
Alignment explanation
Indices: 52352--52413 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 25
52342 GAAAAATGTT
52352 TTAAATATATGTATGAATTTGAGTTTAG
1 TTAAATATATGTATGAATTT-AG--TAG
52380 TTAAATATATGTATGAATTT-G-AG
1 TTAAATATATGTATGAATTTAGTAG
52403 TTAAATATATG
1 TTAAATATATG
52414 GTTATTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.38
26 1 0.03
28 20 0.59
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
TTAAATATATGTATGAATTTAGTAG
Found at i:53947 original size:15 final size:15
Alignment explanation
Indices: 53927--53969 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
53917 CGAAAGGGGT
53927 AGTATCGATACCATA
1 AGTATCGATACCATA
*
53942 AGTATCGATACCATG
1 AGTATCGATACCATA
53957 AGTATCGATACCA
1 AGTATCGATACCA
53970 GAAGGCAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (15 bp):
AGTATCGATACCATA
Found at i:60528 original size:17 final size:17
Alignment explanation
Indices: 60505--60549 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
60495 TATACTCCAT
60505 AAAAAAAACAGCAGTTCG
1 AAAAAAAA-AGCAGTTCG
**
60523 AAAAAAAAAGTTGTTCG
1 AAAAAAAAAGCAGTTCG
60540 AAAAAAAAAG
1 AAAAAAAAAG
60550 AAAAAAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.62, C:0.09, G:0.16, T:0.13
Consensus pattern (17 bp):
AAAAAAAAAGCAGTTCG
Found at i:62521 original size:23 final size:23
Alignment explanation
Indices: 62495--62561 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
62485 ATTTTATATA
*
62495 GCACTTTGGTACATTTCTACGCG
1 GCACTTCGGTACATTTCTACGCG
* *
62518 GCACTTCGGTGA-AATTCTACGTG
1 GCACTTCGGT-ACATTTCTACGCG
* *
62541 GCACTTCGGTGCATTTTTACG
1 GCACTTCGGTACATTTCTACG
62562 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTACATTTCTACGCG
Done.