Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001671.1 Hibiscus syriacus cultivar Beakdansim tig00003344_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: 55037
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:228 original size:29 final size:28
Alignment explanation
Indices: 186--273 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 28
176 GAGTGACATG
186 TTGGGAATTAATTCAAAATGGGTGCTATT
1 TTGGGAATTAATTCAAAA-GGGTGCTATT
215 TTGGGAATTAATTCGAAAAGGGTGCTATT
1 TTGGGAATTAATTC-AAAAGGGTGCTATT
*** *
244 CCAGGAATTTAATTAAAAAGGGTGCTATT
1 TTGGGAA-TTAATTCAAAAGGGTGCTATT
273 T
1 T
274 CTGTAAAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 42 0.81
30 10 0.19
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (28 bp):
TTGGGAATTAATTCAAAAGGGTGCTATT
Found at i:5288 original size:28 final size:27
Alignment explanation
Indices: 5268--5330 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
5258 TTAATAATAT
*
5268 ATTTTATAAATTTATATATTATCTTAAA
1 ATTTTATAAATTTATATATTA-CATAAA
* *
5296 ATTTTATAAATTTATTCTTATAACATAAA
1 ATTTTATAAATTTA-T-ATATTACATAAA
5325 ATTTTA
1 ATTTTA
5331 CATTCACCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 14 0.47
29 12 0.40
30 4 0.13
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTTATAAATTTATATATTACATAAA
Found at i:9235 original size:20 final size:20
Alignment explanation
Indices: 9210--9255 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
9200 ATTTATTTTA
*
9210 AATCATCAAATTTCAGCATC
1 AATCATCAAATTTCAACATC
9230 AATCATCAAATTTCAACATC
1 AATCATCAAATTTCAACATC
9250 AATCAT
1 AATCAT
9256 AAAAAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.30
Consensus pattern (20 bp):
AATCATCAAATTTCAACATC
Found at i:15827 original size:21 final size:21
Alignment explanation
Indices: 15801--15848 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
15791 CGACCCGAAA
15801 TAATAACAAAATATTTTTATT
1 TAATAACAAAATATTTTTATT
*
15822 TAATAATAAAATATTTTTATT
1 TAATAACAAAATATTTTTATT
*
15843 CAATAA
1 TAATAA
15849 AAATAGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATAACAAAATATTTTTATT
Found at i:15853 original size:24 final size:23
Alignment explanation
Indices: 15799--15853 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
15789 CCCGACCCGA
*
15799 AATAATAACAAAATATTTTTATT
1 AATAATAATAAAATATTTTTATT
15822 --TAATAATAAAATATTTTTATT
1 AATAATAATAAAATATTTTTATT
*
15843 CAATAAAAATA
1 -AATAATAATA
15854 GTGATTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 20 0.74
24 7 0.26
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAATAATAAAATATTTTTATT
Found at i:16342 original size:22 final size:22
Alignment explanation
Indices: 16292--16345 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
16282 TTTATGTATT
*
16292 CTCAATTATTTGATAATGAACG
1 CTCAATTACTTGATAATGAACG
* *
16314 TTTAATTACTTGATAATGAACG
1 CTCAATTACTTGATAATGAACG
16336 CTCAATTACT
1 CTCAATTACT
16346 CTTGTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (22 bp):
CTCAATTACTTGATAATGAACG
Found at i:30531 original size:15 final size:15
Alignment explanation
Indices: 30511--30539 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30501 TTCTATGGCT
30511 TCGCCGCCGCCGCCA
1 TCGCCGCCGCCGCCA
30526 TCGCCGCCGCCGCC
1 TCGCCGCCGCCGCC
30540 GCCTATGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.62, G:0.28, T:0.07
Consensus pattern (15 bp):
TCGCCGCCGCCGCCA
Found at i:32410 original size:20 final size:21
Alignment explanation
Indices: 32385--32424 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
32375 CTTCACACAG
32385 TAGTATCAATACCAT-AGACT
1 TAGTATCAATACCATCAGACT
*
32405 TAGTATCGATACCATCAGAC
1 TAGTATCAATACCATCAGAC
32425 CCAACAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (21 bp):
TAGTATCAATACCATCAGACT
Found at i:37847 original size:20 final size:19
Alignment explanation
Indices: 37795--37853 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
37785 ACCTTTTATC
* *
37795 AATAGAAAATACAAAGAAA
1 AATAAAAAATATAAAGAAA
37814 AATAAAAAACTATAAAGAAA
1 AATAAAAAA-TATAAAGAAA
37834 AA-AATTAAAATATAAGAGAA
1 AATAA--AAAATATAA-AGAA
37854 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 10 0.29
20 16 0.47
21 8 0.24
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (19 bp):
AATAAAAAATATAAAGAAA
Found at i:40625 original size:9 final size:9
Alignment explanation
Indices: 40613--40661 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
40603 ATTTTATTCA
40613 TTTTTTATT
1 TTTTTTATT
*
40622 TTTTTAATAT
1 TTTTTTAT-T
*
40632 TTTTTAATAT
1 TTTTTTAT-T
*
40642 TTTTTTAAT
1 TTTTTTATT
40651 TTTTTTATT
1 TTTTTTATT
40660 TT
1 TT
40662 CCCTTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 18 0.51
10 17 0.49
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATT
Found at i:40626 original size:10 final size:10
Alignment explanation
Indices: 40613--40658 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
40603 ATTTTATTCA
40613 TTTTTTAT-T
1 TTTTTTATAT
*
40622 TTTTTAATAT
1 TTTTTTATAT
*
40632 TTTTTAATAT
1 TTTTTTATAT
40642 TTTTTTA-AT
1 TTTTTTATAT
40651 TTTTTTAT
1 TTTTTTAT
40659 TTTCCCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:40632 original size:11 final size:11
Alignment explanation
Indices: 40618--40656 Score: 64
Period size: 10 Copynumber: 3.7 Consensus size: 11
40608 ATTCATTTTT
40618 TATTTTTTTAA
1 TATTTTTTTAA
40629 TA-TTTTTTAA
1 TATTTTTTTAA
40639 TATTTTTTTAA
1 TATTTTTTTAA
40650 T-TTTTTT
1 TATTTTTT
40657 ATTTTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 16 0.59
11 11 0.41
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TATTTTTTTAA
Found at i:40644 original size:21 final size:20
Alignment explanation
Indices: 40618--40657 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
40608 ATTCATTTTT
40618 TATTTTTTTAATATTTTTTAA
1 TATTTTTTTAAT-TTTTTTAA
40639 TATTTTTTTAATTTTTTTA
1 TATTTTTTTAATTTTTTTA
40658 TTTTCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TATTTTTTTAATTTTTTTAA
Found at i:44616 original size:106 final size:106
Alignment explanation
Indices: 44431--45278 Score: 1346
Period size: 106 Copynumber: 8.0 Consensus size: 106
44421 AAGAAAATTA
*
44431 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTT
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
* * * * *
44495 CCACTTCTAGAGCCAATTTCAACTTCACAGTGAATGATAGTG
66 CAATTTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTG
* *
44537 GACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
*
44602 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
*
44643 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTT-T
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
44707 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
66 -CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
* * *
44749 GACTCCAGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCT
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
*
44814 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
* *
44855 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
*
44920 CAATATCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
* *
44961 GACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCT
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
*
45026 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
* *
45067 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
*
45132 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAAGAT-TTG
66 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
* * * * *
45172 GACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATAAACAATTTC-
1 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
** * *
45236 CGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTG
66 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTG
45277 GA
1 GA
45279 TTCGGAACAA
Statistics
Matches: 693, Mismatches: 44, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
103 1 0.00
104 30 0.04
105 69 0.10
106 584 0.84
107 9 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT
CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTG
Found at i:46214 original size:4 final size:4
Alignment explanation
Indices: 46205--46254 Score: 65
Period size: 4 Copynumber: 13.8 Consensus size: 4
46195 TATATTGTTG
46205 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTA -TTA -TTA -TTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
46248 TTTA TTT
1 TTTA TTT
46255 TTGTAGGCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 15 0.34
4 29 0.66
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:47472 original size:9 final size:10
Alignment explanation
Indices: 47445--47470 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47435 TTTTATTCAT
47445 TTTTTTTATA
1 TTTTTTTATA
47455 TTTTTTTATA
1 TTTTTTTATA
47465 TTTTTT
1 TTTTTT
47471 ATTTTCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:48275 original size:40 final size:41
Alignment explanation
Indices: 48214--48294 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 41
48204 AATGGAGGAG
* *
48214 ATGCATATCTTCCTAACGTCTTCTAAAAGACGCCAGATGATA
1 ATGCATA-CTTCCGAACGTCTTCCAAAAGACGCCAGATGATA
48256 ATGCATA-TTCCGAACGTCTTCCAAAAGACGCCAGATGAT
1 ATGCATACTTCCGAACGTCTTCCAAAAGACGCCAGATGAT
48295 TATGTTGACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 30 0.81
42 7 0.19
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (41 bp):
ATGCATACTTCCGAACGTCTTCCAAAAGACGCCAGATGATA
Found at i:48475 original size:21 final size:21
Alignment explanation
Indices: 48451--48502 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
48441 CGGATTTCAA
48451 TCCGATCCGGATCGGTTTTGT
1 TCCGATCCGGATCGGTTTTGT
48472 TCCGATCCGGATCGGTTTTGT
1 TCCGATCCGGATCGGTTTTGT
48493 TCCGATCCGG
1 TCCGATCCGG
48503 TTTTTTCCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.10, C:0.27, G:0.29, T:0.35
Consensus pattern (21 bp):
TCCGATCCGGATCGGTTTTGT
Found at i:48616 original size:15 final size:15
Alignment explanation
Indices: 48598--48653 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
48588 TAACCGGTTT
48598 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
48613 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
48630 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
48645 CGATTTTAA
1 CGGTTTTAA
48654 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:48626 original size:17 final size:17
Alignment explanation
Indices: 48601--48651 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
48591 CCGGTTTCGG
48601 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
48618 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
48633 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
48650 TT
1 TT
48652 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:48848 original size:21 final size:21
Alignment explanation
Indices: 48824--48876 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
48814 ACACTTAGGG
48824 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
48845 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
48866 TACCGATTCCC
1 AACCGATTCCC
48877 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:49093 original size:13 final size:13
Alignment explanation
Indices: 49072--49126 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
49062 AAGTTCGATA
*
49072 AATTCAAATACTT
1 AATTGAAATACTT
49085 AATTGAAATACTT
1 AATTGAAATACTT
* *
49098 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
49112 AATTGAAATACTT
1 AATTGAAATACTT
49125 AA
1 AA
49127 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:49208 original size:32 final size:33
Alignment explanation
Indices: 49112--49210 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
49102 AACTCAACAT
* * *
49112 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
49145 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
49178 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
49210 A
1 A
49211 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:49229 original size:21 final size:21
Alignment explanation
Indices: 49205--49244 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49195 ACTTCAAGTT
49205 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
49226 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
49245 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:52017 original size:15 final size:16
Alignment explanation
Indices: 51988--52020 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
51978 GGTAAGATTA
51988 CATCCATACATCCATG
1 CATCCATACATCCATG
52004 CATCCATA-ATCCATG
1 CATCCATACATCCATG
52019 CA
1 CA
52021 ATATGCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.24
Consensus pattern (16 bp):
CATCCATACATCCATG
Found at i:53046 original size:74 final size:72
Alignment explanation
Indices: 52873--53060 Score: 228
Period size: 68 Copynumber: 2.7 Consensus size: 72
52863 GTTAAAGAGC
*
52873 TTAACCGAACAAAAGCCAACACCATGCATAGAAATCCATACTTCCTACCCTAAATAAGTACATTA
1 TTAACCGAACAAAAGGCAACACCATGCATAGAAATCCATACTTCCTACCCTAAATAAGTACATTA
52938 ATTTAAA
66 ATTTAAA
* * *
52945 TT----GAACAAAA-GCAAACACCATGAATAGAAATCCGTACTTTCTACCCTAAAATAAGTACAT
1 TTAACCGAACAAAAGGC-AACACCATGCATAGAAATCCATACTTCCTACCCT-AAATAAGTACAT
* *
53005 TGATTTAAC
64 TAATTTAAA
*
53014 TTAAACCGAACAAAAGGCAGCACCATGCATAGAAAATCC--ACTTCCTA
1 TT-AACCGAACAAAAGGCAACACCATGCATAG-AAATCCATACTTCCTA
53061 TACTTTACCC
Statistics
Matches: 98, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
67 1 0.01
68 39 0.40
69 21 0.21
72 2 0.02
73 7 0.07
74 20 0.20
75 8 0.08
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (72 bp):
TTAACCGAACAAAAGGCAACACCATGCATAGAAATCCATACTTCCTACCCTAAATAAGTACATTA
ATTTAAA
Found at i:53408 original size:28 final size:28
Alignment explanation
Indices: 53376--53438 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
53366 CAAAGGCATC
*
53376 AGATCACCCAATCAAAAGGGTACCTAAT
1 AGATCAACCAATCAAAAGGGTACCTAAT
53404 AGATCAACCAATCAAAAGGGTACCTAAT
1 AGATCAACCAATCAAAAGGGTACCTAAT
53432 AGATCAA
1 AGATCAA
53439 AGATATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.17
Consensus pattern (28 bp):
AGATCAACCAATCAAAAGGGTACCTAAT
Done.