Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005463.1 Hibiscus syriacus cultivar Beakdansim tig00012511_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: 55979
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3312 original size:13 final size:13
Alignment explanation
Indices: 3275--3314 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
3265 GATATTAAAA
3275 AAAATAAATA-TT
1 AAAATAAATATTT
*
3287 AAAATAATTTATTT
1 AAAATAA-ATATTT
3301 AAAATAAATATTT
1 AAAATAAATATTT
3314 A
1 A
3315 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:4721 original size:3 final size:3
Alignment explanation
Indices: 4713--4763 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
4703 TTATTTTATT
* *
4713 TAA TAA TAA TAA TAA TAC TAA TAT 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
4761 TAA
1 TAA
4764 AACAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5054 original size:76 final size:76
Alignment explanation
Indices: 4928--6299 Score: 2338
Period size: 76 Copynumber: 18.0 Consensus size: 76
4918 GGTCTTATGA
* *
4928 ATGACCCCG-AGGGTTTAAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGA-CCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
4992 AAGGACTTACAG
65 AAGGACTTACAG
**
5004 ATGACCTTAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5069 AGGACTTACAG
66 AGGACTTACAG
** * *
5080 ATGACCTTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5145 AGGACTTACAG
66 AGGACTTACAG
* *
5156 ATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5221 AGGACTTACAG
66 AGGACTTACAG
*
5232 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5297 AGGACTTACAG
66 AGGACTTACAG
*
5308 ATGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
5372 AAGGACTTACAG
65 AAGGACTTACAG
*
5384 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5449 AGGACTTACAG
66 AGGACTTACAG
* * *
5460 ATGACCCGAAGGTTTTGAAAATATCAAAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5525 AGGACTTACAG
66 AGGACTTACAG
* *
5536 ATGACCCGAAGGTTTTGAAAATATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5601 AGGACTTACAG
66 AGGACTTACAG
* *
5612 ATGACCCGAAGGTTTTGAAAATATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5677 AGGACTTACAG
66 AGGACTTACAG
*
5688 ATGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
5752 AAGGACTTACAG
65 AAGGACTTACAG
* *
5764 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTAA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5829 AGGACTTACAG
66 AGGACTTACAG
* * *
5840 ATGACCTGAAGGTTTTGAAAATATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5905 AGGACTTACAG
66 AGGACTTACAG
* *
5916 ATGACCCGAAGGTTTTGAAAATATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
5981 AGGACTTACAG
66 AGGACTTACAG
*
5992 ATGACCCTG-AGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTG
6056 AAGGACTTACAG
65 AAGGACTTACAG
*
6068 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6133 AGGACTTACAG
66 AGGACTTACAG
* * *
6144 ATGACCCGAAGGTTTTGAAAATATCAAAAAGATCCCGAAGGCTTTTTGGAAATAATCATGCACTG
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAA-CATCATGCACTG
6209 AAGGACTTACAG
65 AAGGACTTACAG
* * * *
6221 GTGACCCGAAGGTTTTGAAAATATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGT
1 ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
6286 AGGACTTACAG
66 AGGACTTACAG
6297 ATG
1 ATG
6300 TGAGAAATAG
Statistics
Matches: 1253, Mismatches: 35, Indels: 16
0.96 0.03 0.01
Matches are distributed among these distances:
75 5 0.00
76 1171 0.93
77 77 0.06
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGACCCGAAGGCTTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:6998 original size:22 final size:22
Alignment explanation
Indices: 6973--7052 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
6963 CATAAAGCTT
*
6973 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* * *
6995 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAGAATCTA
* * **
7017 TCATCTCTGAAGTGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
7039 TTATCTTTAAAAAG
1 TCATCTTTAAAAAG
7053 TGTAGATATA
Statistics
Matches: 42, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:9927 original size:93 final size:93
Alignment explanation
Indices: 9766--9957 Score: 280
Period size: 93 Copynumber: 2.1 Consensus size: 93
9756 TCCTTATTTC
* *
9766 TACTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATC
1 TACTATGAGCAAAATTCATCTTCCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATC
9831 AGATAACTCAAAGAACACTTCCAAAAGA
66 AGATAACTCAAAGAACACTTCCAAAAGA
* * * * *
9859 TGCTATGAGC-ACATTCATCTTCCAAATTCAATGATTGGTTCTGTGG-TTTCATACCAAACCAGA
1 TACTATGAGCAAAATTCATCTTCCAAATCCAATGATTGATT-T-TGGAGTTCATACCAAACCAGA
*
9922 TCAGATAACTCAAAGAACACTTCCAGAAGA
64 TCAGATAACTCAAAGAACACTTCCAAAAGA
9952 TACTAT
1 TACTAT
9958 TGGGTCTTCT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
92 26 0.30
93 59 0.67
94 3 0.03
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.29
Consensus pattern (93 bp):
TACTATGAGCAAAATTCATCTTCCAAATCCAATGATTGATTTTGGAGTTCATACCAAACCAGATC
AGATAACTCAAAGAACACTTCCAAAAGA
Found at i:12066 original size:10 final size:10
Alignment explanation
Indices: 12051--12085 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
12041 TCAATTTTCC
12051 TTTTTTTCTT
1 TTTTTTTCTT
12061 TTTTTTTCTTT
1 TTTTTTTC-TT
12072 TTTTTTTCTT
1 TTTTTTTCTT
12082 TTTT
1 TTTT
12086 CTTTGCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:12067 original size:11 final size:11
Alignment explanation
Indices: 12051--12085 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
12041 TCAATTTTCC
12051 TTTTTTTC-TT
1 TTTTTTTCTTT
12061 TTTTTTTCTTT
1 TTTTTTTCTTT
12072 TTTTTTTCTTT
1 TTTTTTTCTTT
12083 TTT
1 TTT
12086 CTTTGCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:12071 original size:18 final size:18
Alignment explanation
Indices: 12045--12089 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
12035 CTTGATTCAA
*
12045 TTTTCCTTTTTTTCTTT-T
1 TTTTTCTTTTTTT-TTTCT
12063 TTTTTCTTTTTTTTTTCT
1 TTTTTCTTTTTTTTTTCT
12081 TTTTTCTTT
1 TTTTTCTTT
12090 GCTGGATGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTTCT
Found at i:16789 original size:30 final size:29
Alignment explanation
Indices: 16744--16810 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 29
16734 TGCAAATAAA
*
16744 ATGAAATATTAATAAGAAAATATATAAATATT
1 ATGAAA-ATTAATAAG--AATATATAAAAATT
*
16776 ATGAAAA-TAATAAGTATATATAAAAATT
1 ATGAAAATTAATAAGAATATATAAAAATT
*
16804 TTGAAAA
1 ATGAAAA
16811 GAAAGAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 18 0.56
30 7 0.22
31 1 0.03
32 6 0.19
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (29 bp):
ATGAAAATTAATAAGAATATATAAAAATT
Found at i:16800 original size:18 final size:19
Alignment explanation
Indices: 16759--16802 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
16749 ATATTAATAA
16759 GAAAATATATAAATATTAT
1 GAAAATATATAAATATTAT
*
16778 GAAAATA-ATAAGTATATAT
1 GAAAATATATAAATAT-TAT
*
16797 AAAAAT
1 GAAAAT
16803 TTTGAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
GAAAATATATAAATATTAT
Found at i:18944 original size:3 final size:3
Alignment explanation
Indices: 18938--18982 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
18928 TTTTTTTATT
* *
18938 TAA TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18983 AACAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18998 original size:17 final size:16
Alignment explanation
Indices: 18972--19005 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18962 TATTAATAAT
*
18972 AATAATAATAAAACAAA
1 AATAAAAATAAAA-AAA
18989 AATAAAAATAAAAAAA
1 AATAAAAATAAAAAAA
19005 A
1 A
19006 TTAATGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AATAAAAATAAAAAAA
Found at i:24416 original size:14 final size:15
Alignment explanation
Indices: 24381--24422 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
24371 GGTTTGGCTC
* *
24381 GGTTGGATCAGTTCA
1 GGTTGGGTCAATTCA
24396 GGTTGGGTCAATTCA
1 GGTTGGGTCAATTCA
*
24411 -GTTGGGCCAATT
1 GGTTGGGTCAATT
24423 TTAGTTCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (15 bp):
GGTTGGGTCAATTCA
Found at i:29222 original size:26 final size:25
Alignment explanation
Indices: 29184--29235 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
29174 CACAAAAAGG
29184 AAAAGAGAAAAAGGAAAAAAAAAAAT
1 AAAAGAGAAAAA-GAAAAAAAAAAAT
* *
29210 AAAAGA-AAGAAAGAAGAAATAAAAT
1 AAAAGAGAA-AAAGAAAAAAAAAAAT
29235 A
1 A
29236 GATCCAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (25 bp):
AAAAGAGAAAAAGAAAAAAAAAAAT
Found at i:33766 original size:21 final size:22
Alignment explanation
Indices: 33717--33770 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
33707 ATGCAAATTT
33717 TTATTATAGTTAGTAATAAATCA
1 TTATTATA-TTAGTAATAAATCA
*
33740 AT-TTATATTA-TAAATAAAT-A
1 TTATTATATTAGT-AATAAATCA
33760 TTATTATATTA
1 TTATTATATTA
33771 AATTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 3 0.11
21 18 0.67
22 5 0.19
23 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
TTATTATATTAGTAATAAATCA
Found at i:36683 original size:22 final size:21
Alignment explanation
Indices: 36631--36688 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
36621 ATTTATATAA
*
36631 ATTAATTATTAATTAAAATTTT
1 ATTAATTTTTAA-TAAAATTTT
* *
36653 ATTTTATTTTTAATAGAATTATT
1 A-TTAATTTTTAATAAAATT-TT
*
36676 ATTAATTTATAAT
1 ATTAATTTTTAAT
36689 TCTTTTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTAATTTTTAATAAAATTTT
Found at i:38442 original size:20 final size:20
Alignment explanation
Indices: 38400--38443 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
38390 CAACAAGTGG
* *
38400 GTATCGATACCAAAGGTTTA
1 GTATCGATACCAAAGGGTCA
*
38420 GTATCGATACTAAAGGGTCA
1 GTATCGATACCAAAGGGTCA
38440 GTAT
1 GTAT
38444 TGGTACCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (20 bp):
GTATCGATACCAAAGGGTCA
Found at i:39414 original size:12 final size:13
Alignment explanation
Indices: 39397--39429 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
39387 AATTACTACT
39397 TTATTTTATT-CA
1 TTATTTTATTACA
39409 TTATTTTATTAGCA
1 TTATTTTATTA-CA
39423 TTATTTT
1 TTATTTT
39430 CACATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
14 9 0.47
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (13 bp):
TTATTTTATTACA
Found at i:46193 original size:16 final size:16
Alignment explanation
Indices: 46172--46206 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
46162 TGGTAAATGA
46172 TTTAAAAATTCATATT
1 TTTAAAAATTCATATT
**
46188 TTTAAAGGTTCATATT
1 TTTAAAAATTCATATT
46204 TTT
1 TTT
46207 TCTACTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (16 bp):
TTTAAAAATTCATATT
Found at i:48045 original size:29 final size:30
Alignment explanation
Indices: 47977--48045 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
47967 TGATTTGGTA
**
47977 GATGGACTTAATTGATTTTTTGATTGCATTT
1 GATGGACTTAATTGATTTTTTGAAAG-ATTT
48008 GATGG-CTTAATTGATTTTTTAGAAAG-TTT
1 GATGGACTTAATTGATTTTTT-GAAAGATTT
48037 GA-GGACTTA
1 GATGGACTTA
48046 TCTATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 9 0.26
30 15 0.44
31 8 0.24
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (30 bp):
GATGGACTTAATTGATTTTTTGAAAGATTT
Found at i:48377 original size:21 final size:20
Alignment explanation
Indices: 48343--48383 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
48333 ACATCTTTTT
48343 ATATTTTTCATATTTTCACAA
1 ATATTTTTCATATTTT-ACAA
**
48364 ATATTTTTTTTATTTTACAA
1 ATATTTTTCATATTTTACAA
48384 CTAAACACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTTTCATATTTTACAA
Found at i:49578 original size:19 final size:19
Alignment explanation
Indices: 49535--49581 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
49525 ATCTTTGTAC
49535 TTTAATTTTCTTTATTATT
1 TTTAATTTTCTTTATTATT
*
49554 TGTAATTTT-TATTATT-TT
1 TTTAATTTTCT-TTATTATT
49572 GTTTAATTTT
1 -TTTAATTTT
49582 AGTATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTAATTTTCTTTATTATT
Found at i:52574 original size:14 final size:15
Alignment explanation
Indices: 52545--52574 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52535 ATTGCACTCA
52545 GACAGTTCAGTACCC
1 GACAGTTCAGTACCC
52560 GACAGTTCA-TACCC
1 GACAGTTCAGTACCC
52574 G
1 G
52575 CTACCCATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
GACAGTTCAGTACCC
Done.