Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004725.1 Hibiscus syriacus cultivar Beakdansim tig00010656_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: 80101
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4054 original size:139 final size:139
Alignment explanation
Indices: 3862--4135 Score: 453
Period size: 139 Copynumber: 2.0 Consensus size: 139
3852 TTTTGAAAAG
* * * *
3862 AAAAGAAAAGGAGAGTATTTGTGCAAATTTGACAGTCAGCTTCAGCATTGTACGCCACTTTAGAT
1 AAAAAAAAAGGAGAG-ATGTGTACAAATTTGACAGTCAGCTTCAGCATTGTACGCCACTTTAGAC
3927 TACCATAAATAAAGACAAACACATGCTCTAGTAGGCATGAAGAGAA-AAGATTCTTTTCTAACCT
65 TACCATAAATAAAGACAAACACATGCTCTAGTAGGCATGAAGAGAAGAAGATTC-TTTCTAACCT
3991 TTATTTTTTCAA
129 TT-TTTTTTCAA
*
4003 AAAAAAAAAGGAGAG-TGTGTACAAATTTGACCGTCAGCTTCAGCATTGTACGCCACTTTAGACT
1 AAAAAAAAAGGAGAGATGTGTACAAATTTGACAGTCAGCTTCAGCATTGTACGCCACTTTAGACT
*
4067 ACCATAAATAAAGACAAACACATGCTCTAGTAGGCATGAAGAGAAGAAGCTTCTTTCTAACCTTT
66 ACCATAAATAAAGACAAACACATGCTCTAGTAGGCATGAAGAGAAGAAGATTCTTTCTAACCTTT
4132 TTTT
131 TTTT
4136 CATGATTTTT
Statistics
Matches: 126, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
138 4 0.03
139 102 0.81
140 6 0.05
141 14 0.11
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (139 bp):
AAAAAAAAAGGAGAGATGTGTACAAATTTGACAGTCAGCTTCAGCATTGTACGCCACTTTAGACT
ACCATAAATAAAGACAAACACATGCTCTAGTAGGCATGAAGAGAAGAAGATTCTTTCTAACCTTT
TTTTTTCAA
Found at i:6486 original size:24 final size:25
Alignment explanation
Indices: 6458--6510 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
6448 AAGGTAATTG
**
6458 TTTAACTTCATTTATTTAATT-TTT
1 TTTAACTTCATAAATTTAATTATTT
* *
6482 TTTAATTTCATAAATTTACTTATTT
1 TTTAACTTCATAAATTTAATTATTT
6507 TTTA
1 TTTA
6511 TTTGTTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTAACTTCATAAATTTAATTATTT
Found at i:7785 original size:12 final size:12
Alignment explanation
Indices: 7770--7794 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7760 TTTGATTTTA
7770 TTAATTTTATTT
1 TTAATTTTATTT
7782 TTAATTTTATTT
1 TTAATTTTATTT
7794 T
1 T
7795 AAAATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTAATTTTATTT
Found at i:14496 original size:79 final size:79
Alignment explanation
Indices: 14360--14755 Score: 731
Period size: 79 Copynumber: 5.0 Consensus size: 79
14350 AACATGAACA
*
14360 TGGACAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
14425 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
* *
14439 TGTAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTTTA-AAAGATCCAAGTTCACAT
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCA-TTGAGAAAGATCCAAGTTCACAT
14503 GAAGGTGCAGGAATT
65 GAAGGTGCAGGAATT
14518 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
14583 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
* *
14597 TGGAAAACTTATTGCCACTCAGGTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
14662 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
14676 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
1 TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
14741 AAGGTGCAGGAATT
66 AAGGTGCAGGAATT
14755 T
1 T
14756 CACAGGTAAT
Statistics
Matches: 306, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
78 3 0.01
79 300 0.98
80 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (79 bp):
TGGAAAACTTATTGCTACTCAGCTAACTAGATCTTTAACCATTGAGAAAGATCCAAGTTCACATG
AAGGTGCAGGAATT
Found at i:17581 original size:30 final size:29
Alignment explanation
Indices: 17514--17591 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
17504 AACATATAGA
*
17514 TACCATATTGAACATTTTAGAAATATAAG
1 TACCATATTAAACATTTTAGAAATATAAG
*
17543 TACCATATTAAACATTTTAGAAATCTAAG
1 TACCATATTAAACATTTTAGAAATATAAG
* *
17572 TCCCCATATTAAACAATTTA
1 T-ACCATATTAAACATTTTA
17592 TTAAAGTACA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 28 0.64
30 16 0.36
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (29 bp):
TACCATATTAAACATTTTAGAAATATAAG
Found at i:21466 original size:26 final size:26
Alignment explanation
Indices: 21430--21482 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
21420 CTAGTCAAGT
* *
21430 CGAGTAATGAGCAACGAGTCGAGCAA
1 CGAGCAATGAGCAACAAGTCGAGCAA
21456 CGAGCAATGAGCAACAAGTCGAGCAA
1 CGAGCAATGAGCAACAAGTCGAGCAA
21482 C
1 C
21483 AAATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.28, T:0.09
Consensus pattern (26 bp):
CGAGCAATGAGCAACAAGTCGAGCAA
Found at i:21510 original size:31 final size:32
Alignment explanation
Indices: 21461--21567 Score: 119
Period size: 32 Copynumber: 3.2 Consensus size: 32
21451 AGCAACGAGC
* *
21461 AATGAGCAACAAGTCGAGCAACAAATTTTTTT
1 AATGAGCAACGAGTCGAGCAACAATTTTTTTT
21493 AATGAGC-ACGAGTCGAGCAA-AATTTTATTGACCTT
1 AATGAGCAACGAGTCGAGCAACAATTTT-TT----TT
* *
21528 AACGAGCAACGAGTCAAGCAACAATTTTTTTT
1 AATGAGCAACGAGTCGAGCAACAATTTTTTTT
21560 AATGAGCA
1 AATGAGCA
21568 TGAATCGAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
30 5 0.08
31 14 0.22
32 16 0.25
35 8 0.13
36 14 0.22
37 6 0.10
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (32 bp):
AATGAGCAACGAGTCGAGCAACAATTTTTTTT
Found at i:26296 original size:11 final size:12
Alignment explanation
Indices: 26274--26305 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
26264 AAGGGGTAGC
26274 AGCAAGAGAAAG
1 AGCAAGAGAAAG
26286 AGCAA-AGAAAG
1 AGCAAGAGAAAG
26297 AG-AAGAGAA
1 AGCAAGAGAA
26306 CGCAGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 12 0.63
12 5 0.26
ACGTcount: A:0.62, C:0.06, G:0.31, T:0.00
Consensus pattern (12 bp):
AGCAAGAGAAAG
Found at i:26431 original size:2 final size:2
Alignment explanation
Indices: 26426--26451 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26416 AGGAGAGATC
26426 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
26452 TAGTTGTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27754 original size:21 final size:21
Alignment explanation
Indices: 27728--27782 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
27718 CGAAGGGTGG
27728 GTATCGATACTGATTCAAACA
1 GTATCGATACTGATTCAAACA
*
27749 GTATCGATACTGATTCAAATA
1 GTATCGATACTGATTCAAACA
27770 GTATCGATACTGA
1 GTATCGATACTGA
27783 AGGCTCAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
GTATCGATACTGATTCAAACA
Found at i:35457 original size:2 final size:2
Alignment explanation
Indices: 35450--35486 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35440 TCAATCTACA
35450 AT AT AT AT 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 AT AT AT AT A
35487 ATTTAGGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37074 original size:35 final size:33
Alignment explanation
Indices: 37025--37091 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 33
37015 TTTTAACCTA
*
37025 CAAGCTCTTACATTTATAGTTCACATGAATGTG
1 CAAGCTCTTACATTTACAGTTCACATGAATGTG
* *
37058 CAAGCTCATATACATTTACGGTTCATATGAATGT
1 CAAGCTC-T-TACATTTACAGTTCACATGAATGT
37092 ACAAAGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.24
34 1 0.03
35 21 0.72
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
CAAGCTCTTACATTTACAGTTCACATGAATGTG
Found at i:37912 original size:12 final size:12
Alignment explanation
Indices: 37897--37951 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
37887 ATTATTTAAA
37897 CGGGTATTGGGC
1 CGGGTATTGGGC
*
37909 CGGGTATTGGGT
1 CGGGTATTGGGC
37921 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
37933 CGAGAATCGGGC
1 CGGGTATTGGGC
37945 CGGGTAT
1 CGGGTAT
37952 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:37956 original size:2 final size:2
Alignment explanation
Indices: 37949--38040 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
37939 TCGGGCCGGG
* * * *
37949 TA TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
37990 TA T- TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38027 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
38041 AATAATTATT
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
1 6 0.09
2 61 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38080 original size:13 final size:13
Alignment explanation
Indices: 38062--38098 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
38052 TTTAATATTT
38062 ATCGGGTCGGGTA
1 ATCGGGTCGGGTA
38075 ATCGGGTCGGGTA
1 ATCGGGTCGGGTA
*
38088 ATCGGGGCGGG
1 ATCGGGTCGGG
38099 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.16, G:0.51, T:0.19
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:42435 original size:12 final size:11
Alignment explanation
Indices: 42411--42523 Score: 66
Period size: 12 Copynumber: 9.4 Consensus size: 11
42401 TTCAAAGAGG
42411 TTTTAT-TTAA
1 TTTTATATTAA
42421 TTTTATATTATA
1 TTTTATATTA-A
*
42433 TTTTATTTTAA
1 TTTTATATTAA
42444 TTTTAATATTAA
1 TTTT-ATATTAA
* *
42456 TTTTTTAAATAAA
1 --TTTTATATTAA
**
42469 TTAAATATTAATA
1 TTTTATATT-A-A
42482 TTTTAATATTATA
1 TTTT-ATATTA-A
*
42495 TTATAGATATTAA
1 TT-T-TATATTAA
42508 TTTTAATATTAA
1 TTTT-ATATTAA
42520 TTTT
1 TTTT
42524 TTAAATAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
10 6 0.08
11 13 0.16
12 29 0.36
13 16 0.20
14 16 0.20
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:42497 original size:26 final size:27
Alignment explanation
Indices: 42425--42519 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 27
42415 ATTTAATTTT
* *
42425 ATATT-ATATTTT-AT-TTTAATTTTA
1 ATATTAATATTTTAATATTAAATTATA
*
42449 ATATTAATTTTTTAA-A-TAAATTA-A
1 ATATTAATATTTTAATATTAAATTATA
*
42473 ATATTAATATTTTAATATTATATTATA
1 ATATTAATATTTTAATATTAAATTATA
42500 GATATT-A-ATTTTAATATTAA
1 -ATATTAATATTTTAATATTAA
42520 TTTTTTAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
24 20 0.34
25 12 0.21
26 19 0.33
27 2 0.03
28 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (27 bp):
ATATTAATATTTTAATATTAAATTATA
Found at i:42519 original size:64 final size:64
Alignment explanation
Indices: 42420--42577 Score: 259
Period size: 64 Copynumber: 2.5 Consensus size: 64
42410 GTTTTATTTA
* *
42420 ATTTT-ATATTATATT-T-TATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
42481 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
1 ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
*
42545 TTTTTAATATTATATTATAGATATTTAATTTTA
1 ATTTTAATATTATATTATAGATA-TTAATTTTA
42578 TATCATATAA
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
61 5 0.06
62 10 0.11
63 1 0.01
64 65 0.72
65 9 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (64 bp):
ATTTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAAT
Found at i:42527 original size:40 final size:37
Alignment explanation
Indices: 42472--42560 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 37
42462 AAATAAATTA
*
42472 AATATTAATATTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAATATTTTAA-A-TAAATTA-A-ATATTAATTTTT
*
42512 AATATTAATTTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAATATTTTAAATAAATTAAATATTAA-TTTTT
42550 AATATT-ATATT
1 AATATTAATATT
42561 ATAGATATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 7 0.16
37 5 0.11
38 16 0.36
39 1 0.02
40 15 0.34
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
AATATTAATATTTTAAATAAATTAAATATTAATTTTT
Found at i:42632 original size:20 final size:19
Alignment explanation
Indices: 42572--42633 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
42562 TAGATATTTA
*
42572 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
42591 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
42609 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
42629 ATTTT
1 ATTTT
42634 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:43106 original size:31 final size:31
Alignment explanation
Indices: 43047--43107 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
43037 GTAGTTGTAT
* * **
43047 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATATCAGTATTACAAAACTA
43078 AAATTATTTAAATATCAGTATTACAAAACT
1 AAATTATTTAAATATCAGTATTACAAAACT
43108 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATATCAGTATTACAAAACTA
Found at i:54007 original size:89 final size:90
Alignment explanation
Indices: 53910--54076 Score: 275
Period size: 90 Copynumber: 1.9 Consensus size: 90
53900 GTTAATAAAC
* * *
53910 AACATTGATTTTTAGTTTTCGATCGACTTTTACT-TAAA-AAAATTATTTTGATTCGTATTAGAG
1 AACATTGATTTTTAGTTTTCGATCGACTTCTA-TATAAAGAAAATCATTTTGATTCATATTAGAG
53973 CGTCGATGATTAAAGTACAAGTGTAT
65 CGTCGATGATTAAAGTACAAGTGTAT
*
53999 AACATTGATTTTTAGTTTTCGATCGACTTCTATATAAAGAAAATCATTTTGATTCATATTGGAGC
1 AACATTGATTTTTAGTTTTCGATCGACTTCTATATAAAGAAAATCATTTTGATTCATATTAGAGC
54064 GTCGATGATTAAA
66 GTCGATGATTAAA
54077 TTATATAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
88 1 0.01
89 35 0.49
90 36 0.50
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (90 bp):
AACATTGATTTTTAGTTTTCGATCGACTTCTATATAAAGAAAATCATTTTGATTCATATTAGAGC
GTCGATGATTAAAGTACAAGTGTAT
Found at i:71979 original size:18 final size:19
Alignment explanation
Indices: 71944--71983 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
71934 ATCATTTCGC
* *
71944 TTTTTTGTTTCTTGTAATT
1 TTTTTTGTATATTGTAATT
71963 TTTTTTGTATATT-TAATT
1 TTTTTTGTATATTGTAATT
71981 TTT
1 TTT
71984 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (19 bp):
TTTTTTGTATATTGTAATT
Found at i:75201 original size:24 final size:24
Alignment explanation
Indices: 75169--75215 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
75159 GGGTAGTTGG
75169 ATTAGCTCAATTGGTTAGAGCGTT
1 ATTAGCTCAATTGGTTAGAGCGTT
*
75193 ATTAGCTCAGTTGGTTAGAGCGT
1 ATTAGCTCAATTGGTTAGAGCGT
75216 CGTGCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (24 bp):
ATTAGCTCAATTGGTTAGAGCGTT
Found at i:76762 original size:20 final size:20
Alignment explanation
Indices: 76737--76814 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
76727 GTTGGTTCAC
* *
76737 GGAATGGAAGATTATCGGTG
1 GGAATGGAAGATTACCAGTG
* *
76757 GGAATGGAATATTACCAATG
1 GGAATGGAAGATTACCAGTG
76777 GGAATGGAAGATTACCAGTG
1 GGAATGGAAGATTACCAGTG
*
76797 GGAATGTAAGATTACCAG
1 GGAATGGAAGATTACCAG
76815 GGAATAGGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.36, C:0.09, G:0.32, T:0.23
Consensus pattern (20 bp):
GGAATGGAAGATTACCAGTG
Found at i:77539 original size:35 final size:35
Alignment explanation
Indices: 77492--77560 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
77482 ATAATGTTAG
77492 AAAATATATTAAGGCAAACTGGAAACAATTTGTAT
1 AAAATATATTAAGGCAAACTGGAAACAATTTGTAT
*
77527 AAAATATTTTAAGGCAAACTGGAAACAATTTGTA
1 AAAATATATTAAGGCAAACTGGAAACAATTTGTA
77561 CACATATTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.29
Consensus pattern (35 bp):
AAAATATATTAAGGCAAACTGGAAACAATTTGTAT
Found at i:77977 original size:12 final size:13
Alignment explanation
Indices: 77955--77984 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
77945 AGAGGAAGTT
77955 AATATAATAAATA
1 AATATAATAAATA
77968 AATA-AATAAATA
1 AATATAATAAATA
77980 AATAT
1 AATAT
77985 TATTGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATATAATAAATA
Done.