Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000735.1 Hibiscus syriacus cultivar Beakdansim tig00001425_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: 60423
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:694 original size:29 final size:29
Alignment explanation
Indices: 652--710 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
642 ATTTTCAGCT
652 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
681 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
710 A
1 A
711 TTAATTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:3696 original size:16 final size:16
Alignment explanation
Indices: 3675--3705 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3665 CTTACAAGAA
3675 GGACAAGACCAACATC
1 GGACAAGACCAACATC
3691 GGACAAGACCAACAT
1 GGACAAGACCAACAT
3706 ATATGACACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.06
Consensus pattern (16 bp):
GGACAAGACCAACATC
Found at i:10219 original size:142 final size:143
Alignment explanation
Indices: 10015--10278 Score: 440
Period size: 142 Copynumber: 1.9 Consensus size: 143
10005 TAGATTACCC
10015 TAATTTATTAACCGCGAGTATTAAAATAAAAACTAGATATAATTTAATAAATTAAAATTTGAATA
1 TAATTTATTAACCGCGAGTATTAAAATAAAAACTAGATATAATTTAATAAATTAAAATTTGAATA
* *
10080 ACAAAGCGAAATAAAAATAAAAATTTAATTTTTAAACATGAAATTTACCCTTAATTAGCCTACTA
66 ACAAAACGAAATAAAAATAAAAATTTAATTATTAAACATGAAATTTACCCTTAATTAGCCTACTA
10145 TTAGGCTATGGTT
131 TTAGGCTATGGTT
* *
10158 TAATTTATTAATCGCGAGTATTAAAAT-AAAATTAGATATAATTTAATAAATTAAAATTTGAATA
1 TAATTTATTAACCGCGAGTATTAAAATAAAAACTAGATATAATTTAATAAATTAAAATTTGAATA
** * * *
10222 TTAAAACGAAATAAAAATAATATTTTAATTATTAAACATGAAATTTACCTTTAATTA
66 ACAAAACGAAATAAAAATAAAAATTTAATTATTAAACATGAAATTTACCCTTAATTA
10279 AAATAGTTAA
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
142 86 0.77
143 26 0.23
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (143 bp):
TAATTTATTAACCGCGAGTATTAAAATAAAAACTAGATATAATTTAATAAATTAAAATTTGAATA
ACAAAACGAAATAAAAATAAAAATTTAATTATTAAACATGAAATTTACCCTTAATTAGCCTACTA
TTAGGCTATGGTT
Found at i:10866 original size:16 final size:17
Alignment explanation
Indices: 10837--10870 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
10827 CCATTTATTT
10837 TTATTTTATATTTTAAA
1 TTATTTTATATTTTAAA
10854 TTATTTT-TATTTTAAA
1 TTATTTTATATTTTAAA
10870 T
1 T
10871 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTTATATTTTAAA
Found at i:17053 original size:21 final size:22
Alignment explanation
Indices: 17007--17067 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
16997 CCCCTCATGA
**
17007 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TCAAAG
17030 GGGAACCGATTCCCCC-CAAAG
1 GGGAACCGATTCCCCCTCAAAG
* *
17051 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
17068 AGGATTCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.52
23 16 0.48
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTCAAAG
Found at i:19014 original size:24 final size:23
Alignment explanation
Indices: 18964--19037 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
18954 GCTTCAACTT
* *
18964 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
18987 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
19011 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
19034 TTTG
1 TTTG
19038 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.05
22 2 0.05
23 12 0.27
24 12 0.27
25 12 0.27
26 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:23539 original size:17 final size:17
Alignment explanation
Indices: 23517--23549 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
23507 TACAAAATTG
23517 AAAAAATGGAATTAAAC
1 AAAAAATGGAATTAAAC
*
23534 AAAAAATTGAATTAAA
1 AAAAAATGGAATTAAA
23550 AGAAGTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAAAATGGAATTAAAC
Found at i:24790 original size:2 final size:2
Alignment explanation
Indices: 24783--24855 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
24773 GGCTTCTATC
24783 AT AT AT 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 AT AT AT
24825 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 A
24856 ATCCTATCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31421 original size:29 final size:29
Alignment explanation
Indices: 31385--31497 Score: 201
Period size: 29 Copynumber: 3.9 Consensus size: 29
31375 CAACATAGGT
*
31385 CGCCATGCACGCCCGGCGTCCT-TATAGGT
1 CGCCATGCACGCCCGGCGTCCTATA-AGGA
31414 CGCCATGCACGCCCGGCGTCCTATAAGGA
1 CGCCATGCACGCCCGGCGTCCTATAAGGA
31443 CGCCATGCACGCCCGGCGTCCTATAAGGA
1 CGCCATGCACGCCCGGCGTCCTATAAGGA
31472 CGCCATGCACGCCCGGCGTCCTATAA
1 CGCCATGCACGCCCGGCGTCCTATAA
31498 TTATTTGCTT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
29 80 0.98
30 2 0.02
ACGTcount: A:0.19, C:0.39, G:0.27, T:0.16
Consensus pattern (29 bp):
CGCCATGCACGCCCGGCGTCCTATAAGGA
Found at i:31549 original size:40 final size:40
Alignment explanation
Indices: 31494--31573 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
31484 CCGGCGTCCT
31494 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
31534 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
31574 CTTTGGGGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.10, C:0.17, G:0.38, T:0.35
Consensus pattern (40 bp):
ATAATTATTTGCTTGGGGTGGCCGCTGTTGGTGGCCGCTG
Found at i:31568 original size:13 final size:13
Alignment explanation
Indices: 31550--31606 Score: 78
Period size: 13 Copynumber: 4.1 Consensus size: 13
31540 ATTTGCTTGG
31550 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
31563 GGTGGCCGCTGCTTT
1 GGTGGCCGCTG--TT
31578 GGGGTGGCCGCTGTT
1 --GGTGGCCGCTGTT
31593 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
31606 G
1 G
31607 CTCGTCCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 25 0.62
15 4 0.10
17 11 0.28
ACGTcount: A:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (13 bp):
GGTGGCCGCTGTT
Found at i:31582 original size:30 final size:30
Alignment explanation
Indices: 31546--31603 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
31536 AATTATTTGC
31546 TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
1 TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
31576 TTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 TTGGGGTGGCCGCTGTTGGTGGCCGCTG
31604 TTGCTCGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.00, C:0.22, G:0.48, T:0.29
Consensus pattern (30 bp):
TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
Found at i:31889 original size:12 final size:12
Alignment explanation
Indices: 31872--31896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31862 CCGACGACAT
31872 GGTAGGTGGTAG
1 GGTAGGTGGTAG
31884 GGTAGGTGGTAG
1 GGTAGGTGGTAG
31896 G
1 G
31897 TCGCCATGGA
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:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:31972 original size:35 final size:35
Alignment explanation
Indices: 31933--32000 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
31923 TCCTGCATCG
*
31933 CGACCCAGCTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
31968 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
32001 GTTGCATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.25
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:32462 original size:21 final size:21
Alignment explanation
Indices: 32437--32480 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
32427 AATCTAGTTA
*
32437 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
32458 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
32479 AT
1 AT
32481 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:32514 original size:8 final size:8
Alignment explanation
Indices: 32501--32532 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
32491 ATATATAAAA
32501 AATTAGTT
1 AATTAGTT
32509 AATTAGTT
1 AATTAGTT
32517 AATTAGTT
1 AATTAGTT
32525 AATTAGTT
1 AATTAGTT
32533 TAAGTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
AATTAGTT
Found at i:33031 original size:19 final size:19
Alignment explanation
Indices: 32988--33035 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
32978 GAGATAATTT
*
32988 TTGTTTAAAAATTATATTG
1 TTGTTTAAAAATTATAGTG
33007 -TGTTTAAAATATT-TAGTG
1 TTGTTTAAAA-ATTATAGTG
33025 TTGTTTAAAAA
1 TTGTTTAAAAA
33036 AAATATTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (19 bp):
TTGTTTAAAAATTATAGTG
Found at i:33048 original size:18 final size:18
Alignment explanation
Indices: 32986--33048 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
32976 GCGAGATAAT
*
32986 TTTTGTTTAAAAATTATA
1 TTTTGTTTAAAAAATATA
* * *
33004 TTGTGTTTAAAATATTTA
1 TTTTGTTTAAAAAATATA
* *
33022 GTGTTGTTTAAAAAAAATA
1 -TTTTGTTTAAAAAATATA
33041 TTTTGTTT
1 TTTTGTTT
33049 TTTATATTGT
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTGTTTAAAAAATATA
Found at i:33286 original size:26 final size:25
Alignment explanation
Indices: 33257--33321 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
33247 AAATCATATT
*
33257 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
33283 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
33309 ATTATT-AATAATA
1 ATTATTAAATAATA
33322 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:36411 original size:15 final size:14
Alignment explanation
Indices: 36388--36418 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
36378 TACAACACTA
36388 AACTTTAATATAAT
1 AACTTTAATATAAT
36402 AACTTATAATATAAT
1 AACTT-TAATATAAT
36417 AA
1 AA
36419 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:36426 original size:16 final size:16
Alignment explanation
Indices: 36393--36439 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
36383 CACTAAACTT
*
36393 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
36408 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
36424 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
36440 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:36555 original size:32 final size:34
Alignment explanation
Indices: 36480--36561 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
36470 CCAAACCCTT
* *
36480 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
36513 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
36546 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
36562 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:36689 original size:46 final size:49
Alignment explanation
Indices: 36598--36689 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 49
36588 TCAACAAACA
36598 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
*
36647 ATATAAC-TAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTT
1 ATATAACTTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT
36690 AACTATATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 12 0.29
46 11 0.27
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (49 bp):
ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
Found at i:36700 original size:47 final size:48
Alignment explanation
Indices: 36598--36702 Score: 128
Period size: 47 Copynumber: 2.2 Consensus size: 48
36588 TCAACAAACA
*
36598 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTCT
*
36647 ATATAACTAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTTT--CT
36694 ATATAACTA
1 ATATAACTA
36703 TCAAACATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
45 12 0.24
46 11 0.22
47 15 0.29
48 6 0.12
49 7 0.14
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTCT
Found at i:36758 original size:41 final size:40
Alignment explanation
Indices: 36670--36758 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
36660 TTAACAAAAC
* *
36670 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
36711 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
36752 AAACTAA
1 AAACTAA
36759 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:36823 original size:16 final size:18
Alignment explanation
Indices: 36794--36832 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
36784 ACTAATTAAC
*
36794 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
36812 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
36828 ATTTA
1 ATTTA
36833 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:37164 original size:50 final size:50
Alignment explanation
Indices: 37047--37154 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 50
37037 TAGGATCACA
*
37047 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
37096 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTAT-T
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
37145 TGGC-TGCATG
1 TGGCATGCATG
37155 TGCATGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
48 6 0.11
49 13 0.23
50 38 0.67
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.20
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
Found at i:37221 original size:29 final size:29
Alignment explanation
Indices: 37189--37283 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 29
37179 GGGACGCCGG
37189 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
37218 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
* ** *
37247 GGAGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
37276 GGCGACCT
1 GGCGACCT
37284 CTCTATTGGC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.24, C:0.32, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:37307 original size:32 final size:32
Alignment explanation
Indices: 37270--37341 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
37260 GTCGCCCAGA
*
37270 CTGCATGGCGACCTCTCTATTGGCTGACTCCT
1 CTGCATGGCGACCTCTCCATTGGCTGACTCCT
* * * *
37302 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGACTCCT
37334 CTGCATGG
1 CTGCATGG
37342 TGAGTATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.10, C:0.32, G:0.28, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGACTCCT
Found at i:37381 original size:39 final size:33
Alignment explanation
Indices: 37326--37438 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
37316 CTCCGTTGGC
37326 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
37359 TGGCTCGTCTGCATGGTGATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGC------ATGGTGAGTATATGGCTTGTA
37398 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
37431 TGGCTCGT
1 TGGCTCGT
37439 ATGTCACTCG
Statistics
Matches: 74, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
33 41 0.55
39 33 0.45
ACGTcount: A:0.14, C:0.15, G:0.35, T:0.36
Consensus pattern (33 bp):
TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
Found at i:42503 original size:60 final size:60
Alignment explanation
Indices: 42393--42551 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
42383 AATTTCAATT
* * * * * * *
42393 TAAATTGGTCCTTAAACTTTTCAATATTTTAATTTCATCCTCAAATTATGATTCTCATTC
1 TAAATTGGTCCTTAAACTTTTGAACATCTCAATTTCATCCCCAAACTATGATCCTCATTC
* * * *
42453 TTAATTTGTCCTTAAACTTTTGAACATGTCAATTTCATCCCCAAACTATGATCCTTATTC
1 TAAATTGGTCCTTAAACTTTTGAACATCTCAATTTCATCCCCAAACTATGATCCTCATTC
*
42513 TAAATTGGTCCTCAAACTTTTGAATC-TCTCAATTTCATC
1 TAAATTGGTCCTTAAACTTTTGAA-CATCTCAATTTCATC
42552 TTCAAATTTA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 83 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.43
Consensus pattern (60 bp):
TAAATTGGTCCTTAAACTTTTGAACATCTCAATTTCATCCCCAAACTATGATCCTCATTC
Found at i:51246 original size:20 final size:20
Alignment explanation
Indices: 51221--51264 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
51211 CTGCGTATCG
*
51221 TAAATTCGCTGCTACTTTTC
1 TAAATTCGCTACTACTTTTC
*
51241 TAAATTCGCTATTACTTTTC
1 TAAATTCGCTACTACTTTTC
51261 TAAA
1 TAAA
51265 AGCACGACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.45
Consensus pattern (20 bp):
TAAATTCGCTACTACTTTTC
Done.