Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004289.1 Hibiscus syriacus cultivar Beakdansim tig00009405_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: 74730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2109 original size:4 final size:4
Alignment explanation
Indices: 2100--2378 Score: 470
Period size: 4 Copynumber: 70.0 Consensus size: 4
2090 GAAACTCACC
*
2100 ATGT ATGT ATGT ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2148 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2195 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2243 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
2291 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
2339 ATGC ATGC ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2379 GTGTGTGTGT
Statistics
Matches: 264, Mismatches: 10, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
3 3 0.01
4 261 0.99
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:2383 original size:2 final size:2
Alignment explanation
Indices: 2376--2410 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2366 CATGTATGTA
*
2376 TG TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2411 TGCAGGGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:9610 original size:18 final size:17
Alignment explanation
Indices: 9538--9612 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 17
9528 ATAAAAATAA
* *
9538 TATTAAATTTGTATATAT
1 TATTAAA-TTATATATTT
*
9556 TATTAAACTATA-ATTT
1 TATTAAATTATATATTT
*
9572 T-TTACATT-TAT-TTT
1 TATTAAATTATATATTT
9586 TA-T-AATTATATATATT
1 TATTAAATTATATAT-TT
9602 TATTAAATTAT
1 TATTAAATTAT
9613 TTTTTAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
13 3 0.07
14 10 0.23
15 6 0.14
16 8 0.18
17 4 0.09
18 13 0.30
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (17 bp):
TATTAAATTATATATTT
Found at i:11121 original size:114 final size:114
Alignment explanation
Indices: 10887--11128 Score: 317
Period size: 114 Copynumber: 2.1 Consensus size: 114
10877 CCAAATTATT
* *
10887 ATTTTTTCAAAATCATGCCTAACATTACGTTTTGGTTTTATTTTGGTCACCGACCGTTAAAAAAT
1 ATTTTTTCAAAATCATACCTAACATTACGTTTTAGTTTTATTTTGGTCACCGACCGTTAAAAAAT
* *
10952 AGCAATGACACTGACATGTCATCATATGATAATATCACATCATCATTGA
66 AGCAATGACACTAACATGTCATCATAAGATAATATCACATCATCATTGA
** * *
11001 ATTTTTTTTAAATCATACCTAACATTACGTTTTAGTTTTATTTTGGTCACCTACTGTTAAAAAGA
1 ATTTTTTCAAAATCATACCTAACATTACGTTTTAGTTTTATTTTGGTCACCGACCGTTAAAAA-A
** * * *
11066 TAGCAATGGTGA-TAACGTGTCA-CTATAAGATAGTGTCACATCATCATTGA
65 TAGCAAT-GACACTAACATGTCATC-ATAAGATAATATCACATCATCATTGA
*
11116 ATTTTTTGAAAAT
1 ATTTTTTCAAAAT
11129 ATCACTTTAA
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
114 58 0.53
115 50 0.45
116 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (114 bp):
ATTTTTTCAAAATCATACCTAACATTACGTTTTAGTTTTATTTTGGTCACCGACCGTTAAAAAAT
AGCAATGACACTAACATGTCATCATAAGATAATATCACATCATCATTGA
Found at i:11476 original size:6 final size:6
Alignment explanation
Indices: 11465--12374 Score: 1598
Period size: 6 Copynumber: 154.7 Consensus size: 6
11455 CCTCACATAT
11465 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11513 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TA-TTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11560 TA-TTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11607 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11655 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11703 TATTTA TA-TT- TATTTA TATTTA TA-TTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11748 TATTTA TA-TTA TATTTA TATTTA TA-TTA TATTTA TATTTA TA-TT-
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11792 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT-
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11839 TATTTA TA-TT- TATTTA TATTTA TA-TTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11884 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
11932 TATTTA TATTTA TATATTA TATTTA TA-TTA TATTTA TATTTA TA-TTA
1 TATTTA TATTTA TAT-TTA TATTTA TATTTA TATTTA TATTTA TATTTA
11979 TATTTA TATTTA TATTTA TTATTT- TATTTA TATTTATA TATTTA TATTTA
1 TATTTA TATTTA TATTTA -TATTTA TATTTA TA-TT-TA TATTTA TATTTA
12029 TATTTA TATTTA TATTTA TATTTA TA-TT- TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
12075 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
12123 TATTTA TATTTA TATTTTA TTATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TA-TTTA -TATTTA TATTTA TATTTA TATTTA TATTTA
12173 TA-TTA TATTTA TATTTA TATTTA TA-TT- TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
12218 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TA-TTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
12265 TATTTA TATTTA TATTTA T-TTTA T-TTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
12311 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
12359 TATTTA TATTTA TATT
1 TATTTA TATTTA TATT
12375 AATTTTATTA
Statistics
Matches: 875, Mismatches: 0, Indels: 58
0.94 0.00 0.06
Matches are distributed among these distances:
4 10 0.01
5 90 0.10
6 746 0.85
7 23 0.03
8 6 0.01
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:13551 original size:11 final size:11
Alignment explanation
Indices: 13535--13560 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13525 TTTAAATTTT
13535 AAAAAAAAACA
1 AAAAAAAAACA
13546 AAAAAAAAACA
1 AAAAAAAAACA
13557 AAAA
1 AAAA
13561 TGTGATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:30710 original size:14 final size:14
Alignment explanation
Indices: 30691--30718 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30681 TTAAAAGTAG
30691 AATTTAAAATTATT
1 AATTTAAAATTATT
30705 AATTTAAAATTATT
1 AATTTAAAATTATT
30719 TATTAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAAATTATT
Found at i:32783 original size:20 final size:20
Alignment explanation
Indices: 32747--32784 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32737 ATCATATTCT
**
32747 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
32767 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
32785 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:35512 original size:24 final size:24
Alignment explanation
Indices: 35459--35512 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
35449 GCTTTAATAT
35459 AATTT-TTAAATAAATTAACCAAA
1 AATTTATTAAATAAATTAACCAAA
* *
35482 AA-ATATTAAA-ATATTAACCTAAA
1 AATTTATTAAATAAATTAACC-AAA
35505 AATTTATT
1 AATTTATT
35513 GAATGACCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 9 0.36
23 12 0.48
24 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTTATTAAATAAATTAACCAAA
Found at i:46588 original size:20 final size:19
Alignment explanation
Indices: 46550--46604 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
46540 GATACTATAT
46550 TGAT-AATTTAAAGATTTAA
1 TGATAAATTTAAA-ATTTAA
* *
46569 TTATAATGTTTAAAATTTAA
1 TGATAA-ATTTAAAATTTAA
46589 TGATAAATTTAAAATT
1 TGATAAATTTAAAATT
46605 AGCGTCCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 12 0.40
20 12 0.40
21 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (19 bp):
TGATAAATTTAAAATTTAA
Found at i:47204 original size:23 final size:24
Alignment explanation
Indices: 47169--47213 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
47159 ATTTATTTTC
47169 TTTTTATGAAAAAA-TAGAAAATTA
1 TTTTTATGAAAAAAGTA-AAAATTA
*
47193 TTTTT-TGCAAAAAGTAAAAAT
1 TTTTTATGAAAAAAGTAAAAAT
47214 AAATCTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (24 bp):
TTTTTATGAAAAAAGTAAAAATTA
Found at i:47204 original size:24 final size:23
Alignment explanation
Indices: 47169--47213 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
47159 ATTTATTTTC
47169 TTTTTATGAAAAAATAGAAAATTA
1 TTTTTATGAAAAAATA-AAAATTA
*
47193 TTTTT-TGCAAAAAGTAAAAAT
1 TTTTTATG-AAAAAATAAAAAT
47214 AAATCTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (23 bp):
TTTTTATGAAAAAATAAAAATTA
Found at i:48484 original size:14 final size:14
Alignment explanation
Indices: 48465--48510 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
48455 GACCTACCCC
48465 TCGGATGCACTCGG
1 TCGGATGCACTCGG
*
48479 TCGGATG----CGC
1 TCGGATGCACTCGG
48489 TCGGATGCACTCGG
1 TCGGATGCACTCGG
48503 TCGGATGC
1 TCGGATGC
48511 GCTCAGATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
10 9 0.35
14 17 0.65
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.22
Consensus pattern (14 bp):
TCGGATGCACTCGG
Found at i:48496 original size:24 final size:24
Alignment explanation
Indices: 48464--48549 Score: 120
Period size: 24 Copynumber: 3.6 Consensus size: 24
48454 CGACCTACCC
48464 CTCGGATGCACTCGGTCGGATGCG
1 CTCGGATGCACTCGGTCGGATGCG
48488 CTCGGATGCACTCGGTCGGATGCG
1 CTCGGATGCACTCGGTCGGATGCG
* * *
48512 CTCAGATACCCTCGGTCGGATG-G
1 CTCGGATGCACTCGGTCGGATGCG
*
48535 CCTCGGATGCTCTCG
1 -CTCGGATGCACTCG
48550 CATAGCTCGC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 1 0.02
24 54 0.98
ACGTcount: A:0.13, C:0.31, G:0.34, T:0.22
Consensus pattern (24 bp):
CTCGGATGCACTCGGTCGGATGCG
Found at i:48838 original size:2 final size:2
Alignment explanation
Indices: 48792--48820 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48782 ATATAATTGC
48792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48821 ATGTTGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49383 original size:42 final size:42
Alignment explanation
Indices: 49322--49422 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
49312 TATCATTGAT
* **
49322 TGTTAT-GA-GTTGATATGACAGTTCACAATATTAACGTGGA
1 TGTTATCGATGTTGATGTGACAGTTCACAATATTAACGTAAA
* * * *
49362 TGTTATCGATGTTGATGTGACAGTTTATAATGTTAACTTAAA
1 TGTTATCGATGTTGATGTGACAGTTCACAATATTAACGTAAA
*
49404 TGTTATCGTTGTTGATGTG
1 TGTTATCGATGTTGATGTG
49423 GTAATTCACA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 6 0.12
41 2 0.04
42 43 0.84
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.42
Consensus pattern (42 bp):
TGTTATCGATGTTGATGTGACAGTTCACAATATTAACGTAAA
Found at i:52749 original size:2 final size:2
Alignment explanation
Indices: 52742--52777 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52732 TGTTCCATCA
52742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52778 TACAAACTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58860 original size:3 final size:3
Alignment explanation
Indices: 58827--58963 Score: 62
Period size: 3 Copynumber: 45.7 Consensus size: 3
58817 AGAGAAATCG
* * * * * * * *
58827 CCA CCA CCG CCA TCA TCA CCA GCA CCG CCA CCA CCA CCA CAA CCA ACT
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
* * * * * * *
58875 CCA TCA CCA CCA CCA TCA CCA GCG CCC CCA TCA TCC- CCA TCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA -CCA CCA CCA CCA
* * * * *
58920 CCA CCA CCA CCA TCC- CTA TCA TCA CCA CCA CCA TCA ACA CCA CC
1 CCA CCA CCA CCA -CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
58964 CCCAACTCAT
Statistics
Matches: 96, Mismatches: 34, Indels: 8
0.70 0.25 0.06
Matches are distributed among these distances:
2 3 0.03
3 90 0.94
4 3 0.03
ACGTcount: A:0.30, C:0.57, G:0.04, T:0.09
Consensus pattern (3 bp):
CCA
Found at i:58895 original size:36 final size:36
Alignment explanation
Indices: 58840--58931 Score: 94
Period size: 36 Copynumber: 2.6 Consensus size: 36
58830 CCACCGCCAT
* * *
58840 CATCACCAGCACCGCCACCACCACCACAACCAACTC
1 CATCACCACCACCACCACCACCACCACAACCAACCC
* * * * * * *
58876 CATCACCACCACCATCACCAGCGCCCCCATCATCCC
1 CATCACCACCACCACCACCACCACCACAACCAACCC
58912 CATCACCACCACCACCACCA
1 CATCACCACCACCACCACCA
58932 TCCCTATCAT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.30, C:0.58, G:0.04, T:0.08
Consensus pattern (36 bp):
CATCACCACCACCACCACCACCACCACAACCAACCC
Found at i:58933 original size:24 final size:24
Alignment explanation
Indices: 58827--58963 Score: 89
Period size: 24 Copynumber: 5.6 Consensus size: 24
58817 AGAGAAATCG
* * *
58827 CCACCACCGCCATCATCACCAGCA
1 CCACCACCACCACCATCACCACCA
* * *
58851 CCGCCACCACCACCA-CAACCAACT
1 CCACCACCACCACCATC-ACCACCA
* * *
58875 CCATCACCACCACCATCACCAGCG
1 CCACCACCACCACCATCACCACCA
* *
58899 CCCCCATCATCC-CCATCACCACCA
1 CCACCACCA-CCACCATCACCACCA
*
58923 CCACCACCATCCCTATCATCACCACCA
1 CCACCACCA--CC-ACCATCACCACCA
* *
58950 CCATCAACACCACC
1 CCACCACCACCACC
58964 CCCAACTCAT
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
23 1 0.01
24 60 0.70
25 7 0.08
27 18 0.21
ACGTcount: A:0.30, C:0.57, G:0.04, T:0.09
Consensus pattern (24 bp):
CCACCACCACCACCATCACCACCA
Found at i:58984 original size:21 final size:20
Alignment explanation
Indices: 58942--58989 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
58932 TCCCTATCAT
58942 CACCACC-AC-CATCAACAC
1 CACCACCAACTCATCAACAC
* *
58960 CACCCCCAACTCATCACACTC
1 CACCACCAACTCATCA-ACAC
58981 CACCACCAA
1 CACCACCAA
58990 AGTCGACAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 5 0.21
21 11 0.46
ACGTcount: A:0.35, C:0.56, G:0.00, T:0.08
Consensus pattern (20 bp):
CACCACCAACTCATCAACAC
Found at i:71445 original size:18 final size:18
Alignment explanation
Indices: 71422--71457 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
71412 TTAGAAGCAA
71422 ATTTTCAAATTTCCAAAG
1 ATTTTCAAATTTCCAAAG
71440 ATTTTCAAATTTCCAAAG
1 ATTTTCAAATTTCCAAAG
71458 CGCATGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
ATTTTCAAATTTCCAAAG
Found at i:71490 original size:4 final size:4
Alignment explanation
Indices: 71483--71513 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
71473 ATGTGTGTGC
71483 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCG
1 GCGT GCGT GCGT GCGT GCGT GCGT GCGT GCG
71514 ATAGGGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.52, T:0.23
Consensus pattern (4 bp):
GCGT
Found at i:73423 original size:6 final size:6
Alignment explanation
Indices: 73414--73455 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
73404 CCTCCTCCTC
73414 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
1 CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT CCCCTT
73456 TCTCCTTTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCCCTT
Done.