Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003988.1 Hibiscus syriacus cultivar Beakdansim tig00008678_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: 67653
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:4991 original size:21 final size:20
Alignment explanation
Indices: 4930--4993 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
4920 AACTCCAATT
*
4930 TCGCAACATGAA-TAGTAAAA
1 TCGCAACACGAATTAG-AAAA
*
4950 TCGCAACACGAATTGGAAAA
1 TCGCAACACGAATTAGAAAA
**
4970 TCGCAATGCGAATTTAGAAAA
1 TCGCAACACGAA-TTAGAAAA
4991 TCG
1 TCG
4994 TAAAATCGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAACACGAATTAGAAAA
Found at i:5380 original size:21 final size:20
Alignment explanation
Indices: 5348--5414 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
5338 TATAGATTCG
5348 TTGCGATTTTACTATTCACA
1 TTGCGATTTTACTATTCACA
5368 TTGCGATTTTTACTATTCACA
1 TTGCGA-TTTTACTATTCACA
* * *
5389 TTGCGGTTTTATTATTCACG
1 TTGCGATTTTACTATTCACA
5409 TTGCGA
1 TTGCGA
5415 AATTAGAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 23 0.55
21 19 0.45
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTACTATTCACA
Found at i:5430 original size:20 final size:21
Alignment explanation
Indices: 5407--5455 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
5397 TTATTATTCA
*
5407 CGTTGCGAAATTAGAGT-TCG
1 CGTTGCGAAATTAGACTATCG
*
5427 CGTTGCG-AATTTGACTATCG
1 CGTTGCGAAATTAGACTATCG
5447 CGTTGCGAA
1 CGTTGCGAA
5456 TTTGACTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.28
20 17 0.68
21 1 0.04
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (21 bp):
CGTTGCGAAATTAGACTATCG
Found at i:5451 original size:40 final size:40
Alignment explanation
Indices: 5407--5575 Score: 116
Period size: 40 Copynumber: 4.2 Consensus size: 40
5397 TTATTATTCA
*
5407 CGTTGCGAAATTAGAGTTCGCGTTGCGAATTTGACTATCG
1 CGTTGCGAAATTAGAGTTCGCGTTACGAATTTGACTATCG
* * * * *
5447 CGTTGCG-AATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCG
1 CGTTGCGAAATTAGAGTTC-GCGTTACGAATTTGAC-TA-TCG
* * * * *
5487 CGTTGCG-ATTTACAGATTCACGTTACGAAATTGGA--AACAG
1 CGTTGCGAAATTAGAG-TTCGCGTTACG-AATTTGACTATC-G
* * *
5527 GGTTGCGAAATTGGAGTTCGCGTTACGAATTTGACTTTCG
1 CGTTGCGAAATTAGAGTTCGCGTTACGAATTTGACTATCG
5567 CGTTGCGAA
1 CGTTGCGAA
5576 TTTATTGGTC
Statistics
Matches: 96, Mismatches: 22, Indels: 22
0.69 0.16 0.16
Matches are distributed among these distances:
38 2 0.02
39 21 0.22
40 60 0.62
41 9 0.09
42 3 0.03
43 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
CGTTGCGAAATTAGAGTTCGCGTTACGAATTTGACTATCG
Found at i:5474 original size:20 final size:20
Alignment explanation
Indices: 5424--5462 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5414 AAATTAGAGT
5424 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
5444 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
5463 TCTGTGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:5491 original size:20 final size:20
Alignment explanation
Indices: 5468--5510 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
5458 TGACTTCTGT
*
5468 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCAC
*
5488 GTTGCGATTTACAGATTCAC
1 GTTGCGATTTACAAATTCAC
5508 GTT
1 GTT
5511 ACGAAATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCAC
Found at i:6379 original size:32 final size:32
Alignment explanation
Indices: 6343--6415 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
6333 AAATGAAAGA
*
6343 ACAAAACTAAAAATTGATTATATAAACGAACT
1 ACAAAACTAAAAATTAATTATATAAACGAACT
* *
6375 ACAAAACTAAAAATTAATTGTATAAATGAACT
1 ACAAAACTAAAAATTAATTATATAAACGAACT
*
6407 A-TAAACTAA
1 ACAAAACTAA
6416 TGCTAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 7 0.19
32 30 0.81
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (32 bp):
ACAAAACTAAAAATTAATTATATAAACGAACT
Found at i:10144 original size:19 final size:19
Alignment explanation
Indices: 10085--10148 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
10075 TTGCAAGGTA
*
10085 ATTTTTTTAACTTTTT--TT
1 ATTTTTTTAA-TTTTTAAAT
*
10103 ATTTGTTTTATTTGTTTATAAT
1 ATTT-TTTTAATT-TTTA-AAT
10125 ATTTTTTTAATTTTTAAAT
1 ATTTTTTTAATTTTTAAAT
10144 ATTTT
1 ATTTT
10149 AGATGGCGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 6 0.16
19 16 0.42
20 4 0.11
21 7 0.18
22 5 0.13
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (19 bp):
ATTTTTTTAATTTTTAAAT
Found at i:11929 original size:20 final size:22
Alignment explanation
Indices: 11888--11930 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
11878 TCATGATGAA
11888 ATATGGAATATAAAGATGGTTT
1 ATATGGAATATAAAGATGGTTT
*
11910 ATATGG-ATAT-AAGTTGGTTT
1 ATATGGAATATAAAGATGGTTT
11930 A
1 A
11931 AGTAATGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (22 bp):
ATATGGAATATAAAGATGGTTT
Found at i:13820 original size:23 final size:23
Alignment explanation
Indices: 13790--13849 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
13780 CATTTTATAT
13790 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
13813 GGCACTTCGGTGTAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
13836 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
13850 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:17227 original size:21 final size:20
Alignment explanation
Indices: 17199--17237 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17189 CACTGTAAGA
*
17199 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
17219 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
17238 GGCCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:21845 original size:21 final size:22
Alignment explanation
Indices: 21819--21870 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
21809 TGTCCAAATT
*
21819 ACTGTAGCAAGGTATCGGTA-C
1 ACTGTAGCAAGGTATCGATACC
*
21840 ACTGTAGCAGGGTATCGATACC
1 ACTGTAGCAAGGTATCGATACC
*
21862 CCTGTAGCA
1 ACTGTAGCA
21871 TTCTGAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (22 bp):
ACTGTAGCAAGGTATCGATACC
Found at i:23886 original size:26 final size:26
Alignment explanation
Indices: 23846--23904 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
23836 ATTTTATATT
23846 AGATGAATAAATTTATAAAATTCTATA
1 AGAT-AATAAATTTATAAAATTCTATA
*
23873 AGATAATAAATTTATAAAATTTTATA
1 AGATAATAAATTTATAAAATTCTATA
*
23899 AAATAA
1 AGATAA
23905 AACTAGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (26 bp):
AGATAATAAATTTATAAAATTCTATA
Found at i:27524 original size:12 final size:12
Alignment explanation
Indices: 27490--27527 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
27480 TGAGATATTG
27490 TTTTGAGTAAGA
1 TTTTGAGTAAGA
*
27502 TATTGGAGTAAGA
1 T-TTTGAGTAAGA
27515 TTTTGAGTAAGA
1 TTTTGAGTAAGA
27527 T
1 T
27528 ATAGATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.39
Consensus pattern (12 bp):
TTTTGAGTAAGA
Found at i:33658 original size:18 final size:18
Alignment explanation
Indices: 33635--33684 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
33625 ATGGGTGACC
33635 TAATTAAAGC-TATGTAAT
1 TAATTAAA-CATATGTAAT
*
33653 TAATTAAACATATGTCAT
1 TAATTAAACATATGTAAT
* *
33671 TAACTAAATATATG
1 TAATTAAACATATG
33685 ATTGAGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (18 bp):
TAATTAAACATATGTAAT
Found at i:34564 original size:15 final size:16
Alignment explanation
Indices: 34527--34564 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
34517 GATTTAAAAT
34527 ATATATAAATATTTAAA
1 ATAT-TAAATATTTAAA
34544 AT-TTAAA-ATTTAAA
1 ATATTAAATATTTAAA
34558 ATATTAA
1 ATATTAA
34565 TTTAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 8 0.40
16 1 0.05
17 2 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTAAATATTTAAA
Found at i:34622 original size:13 final size:13
Alignment explanation
Indices: 34606--34646 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
34596 ATTATTTATT
34606 AAATAAAAAAATA
1 AAATAAAAAAATA
34619 AAATAAAAAAATTA
1 AAATAAAAAAA-TA
*
34633 AAAAATAAAAAATA
1 AAATA-AAAAAATA
34647 TTTATTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 11 0.44
14 8 0.32
15 6 0.24
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAATAAAAAAATA
Found at i:35398 original size:18 final size:18
Alignment explanation
Indices: 35375--35428 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
35365 ACCAAGTTTC
35375 CAAAAAAATCAAATTTTA
1 CAAAAAAATCAAATTTTA
35393 CAAAAAAATCAAATTTTA
1 CAAAAAAATCAAATTTTA
35411 CAAAAAAATCAAATTTTA
1 CAAAAAAATCAAATTTTA
35429 TAAGCCTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (18 bp):
CAAAAAAATCAAATTTTA
Found at i:37058 original size:21 final size:21
Alignment explanation
Indices: 37034--37095 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
37024 GCAAATTCGC
37034 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
37055 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
37075 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
37096 ATCTACAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:37881 original size:19 final size:19
Alignment explanation
Indices: 37857--37925 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
37847 CAACGAATTT
37857 TCGCAACGAATTTAGAAAA
1 TCGCAACGAATTTAGAAAA
* **
37876 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTAGAAAA
*
37898 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTAGAAAA
*
37917 TAGCAACGA
1 TCGCAACGA
37926 CAACTATAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 21 0.54
20 2 0.05
21 2 0.05
22 14 0.36
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTAGAAAA
Found at i:37900 original size:22 final size:22
Alignment explanation
Indices: 37875--37946 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
37865 AATTTAGAAA
*
37875 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTATAGACT
* * **
37897 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTATAGACT
*
37916 ATAGCAACGACAACTATAGACT
1 ATCGCAACGACAACTATAGACT
37938 ATCGCAACG
1 ATCGCAACG
37947 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTATAGACT
Found at i:37902 original size:41 final size:41
Alignment explanation
Indices: 37857--37946 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
37847 CAACGAATTT
* *
37857 TCGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTAGAAAATAGCAACGACAACTATAGACTA
*
37898 TCGCAACGAATTTGGAAAATAGCAACGACAACTATAGACTA
1 TCGCAACGAATTTAGAAAATAGCAACGACAACTATAGACTA
37939 TCGCAACG
1 TCGCAACG
37947 CGAAATGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATTTAGAAAATAGCAACGACAACTATAGACTA
Found at i:37967 original size:20 final size:20
Alignment explanation
Indices: 37942--37989 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
37932 TAGACTATCG
*
37942 CAACGCGAAATGGAAAATCA
1 CAACGCGAAATGAAAAATCA
*
37962 CAACGCGAAATGAAAAATCG
1 CAACGCGAAATGAAAAATCA
37982 CAACGCGA
1 CAACGCGA
37990 TTTTCAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.23, G:0.21, T:0.08
Consensus pattern (20 bp):
CAACGCGAAATGAAAAATCA
Found at i:38018 original size:21 final size:21
Alignment explanation
Indices: 37938--38018 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 21
37928 ACTATAGACT
*
37938 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGAAATGCAACA
* *
37958 ATCACAACGCGAAATG-AAAA
1 ATCGCAACGCGAAATGCAACA
** * *
37978 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACA
*
37999 ATCGCAACGAGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
38019 GCGAATTTGC
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
19 2 0.04
20 28 0.58
21 18 0.38
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACA
Found at i:46659 original size:20 final size:20
Alignment explanation
Indices: 46626--46663 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46616 TTTGGTTCAC
46626 GGAATATAAAATTACTAGTG
1 GGAATATAAAATTACTAGTG
* *
46646 GGAATGTAAGATTACTAG
1 GGAATATAAAATTACTAG
46664 GGAATAAGAT
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:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (20 bp):
GGAATATAAAATTACTAGTG
Found at i:46668 original size:18 final size:19
Alignment explanation
Indices: 46626--46669 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
46616 TTTGGTTCAC
46626 GGAATATAAAATTACTAGTG
1 GGAATATAAAATTACTAG-G
* *
46646 GGAATGTAAGATTACTA-G
1 GGAATATAAAATTACTAGG
46664 GGAATA
1 GGAATA
46670 AGATTGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (19 bp):
GGAATATAAAATTACTAGG
Found at i:48840 original size:23 final size:22
Alignment explanation
Indices: 48766--48839 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
48756 TACTTTTATA
* *
48766 TAAAAATATTTAA-TTATATTTA
1 TAAAAATACTTAATTTA-ATTTT
*
48788 TAAAAATACTT-ATTTAATATT
1 TAAAAATACTTAATTTAATTTT
* *
48809 TACAAATAAGTTAATTTAATTTT
1 TAAAAAT-ACTTAATTTAATTTT
48832 TAAAAATA
1 TAAAAATA
48840 AACACAGTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 10 0.24
22 17 0.40
23 15 0.36
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (22 bp):
TAAAAATACTTAATTTAATTTT
Found at i:60397 original size:3 final size:3
Alignment explanation
Indices: 60389--60433 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
60379 TCGTTTGTTC
60389 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
60434 GATTTGAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:64652 original size:15 final size:16
Alignment explanation
Indices: 64619--64665 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
64609 TCTAACGTTA
64619 ATGTTCGTGTTCATTT
1 ATGTTCGTGTTCATTT
64635 ATGTTCGTGTTC-TTT
1 ATGTTCGTGTTCATTT
64650 ATGTTCGT-TT-ATTT
1 ATGTTCGTGTTCATTT
64664 AT
1 AT
64666 TAAATGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.23
15 11 0.37
16 12 0.40
ACGTcount: A:0.13, C:0.11, G:0.17, T:0.60
Consensus pattern (16 bp):
ATGTTCGTGTTCATTT
Found at i:64748 original size:16 final size:16
Alignment explanation
Indices: 64727--64757 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64717 AAAAAAAAAT
64727 TGTTCGCTTATGTTCG
1 TGTTCGCTTATGTTCG
*
64743 TGTTCGTTTATGTTC
1 TGTTCGCTTATGTTC
64758 ATTTATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.16, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTTCGCTTATGTTCG
Found at i:65019 original size:3 final size:3
Alignment explanation
Indices: 65005--65073 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
64995 ACTCCAAACC
65005 ATT ATT -TT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65051 ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
65074 CCCAATGCTT
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 60 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:67026 original size:26 final size:27
Alignment explanation
Indices: 66977--67038 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
66967 GAACGGAAAC
66977 AAAATTTTATATTAAAAAACAATTTAT
1 AAAATTTTATATTAAAAAACAATTTAT
*
67004 AAAATTTTAT-TT-AAGAACAAATTTAT
1 AAAATTTTATATTAAAAAAC-AATTTAT
67030 AAAATTTTA
1 AAAATTTTA
67039 AAAGATATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 5 0.15
26 18 0.55
27 10 0.30
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (27 bp):
AAAATTTTATATTAAAAAACAATTTAT
Done.