Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002173.1 Hibiscus syriacus cultivar Beakdansim tig00004429_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: 62442
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:4417 original size:22 final size:22
Alignment explanation
Indices: 4388--4445 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
4378 ATTATGAAGG
4388 GTCTTCTCGTCCTTGACGAATTA
1 GTCTTCTCGTCCTTGACGAA-TA
*
4411 -TCTTCTCGT-CTTGATGAATA
1 GTCTTCTCGTCCTTGACGAATA
4431 GTCTTCTCGTCCTTG
1 GTCTTCTCGTCCTTG
4446 GTACGACTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.06
21 17 0.53
22 13 0.41
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (22 bp):
GTCTTCTCGTCCTTGACGAATA
Found at i:5034 original size:22 final size:22
Alignment explanation
Indices: 5006--5048 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4996 CTTTCGAAGA
*
5006 AAAACGGGTAGAGGTTCAGTAT
1 AAAACGGGCAGAGGTTCAGTAT
*
5028 AAAACGGGCAGAGTTTCAGTA
1 AAAACGGGCAGAGGTTCAGTA
5049 ACACTAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.30, T:0.21
Consensus pattern (22 bp):
AAAACGGGCAGAGGTTCAGTAT
Found at i:10772 original size:14 final size:14
Alignment explanation
Indices: 10755--10812 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
10745 ATGTGTGTTT
10755 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
*
10769 GTTTATGTT--AT-
1 GTTTATGTTCGTTC
*
10780 -TTTATTTTCGTTC
1 GTTTATGTTCGTTC
10793 GTTTATGTTCGTTC
1 GTTTATGTTCGTTC
*
10807 ATTTAT
1 GTTTAT
10813 TTTTACCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
10 7 0.20
12 2 0.06
14 26 0.74
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.62
Consensus pattern (14 bp):
GTTTATGTTCGTTC
Found at i:10783 original size:24 final size:24
Alignment explanation
Indices: 10756--10801 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
10746 TGTGTGTTTG
10756 TTTATGTTCGTTCGTTTATGTTAT
1 TTTATGTTCGTTCGTTTATGTTAT
*
10780 TTTATTTTCGTTCGTTTATGTT
1 TTTATGTTCGTTCGTTTATGTT
10802 CGTTCATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.09, G:0.15, T:0.65
Consensus pattern (24 bp):
TTTATGTTCGTTCGTTTATGTTAT
Found at i:10810 original size:24 final size:24
Alignment explanation
Indices: 10762--10810 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
10752 TTTGTTTATG
* *
10762 TTCGTTCGTTTATGTTATTTTATT
1 TTCGTTCGTTTATGTTAGTTCATT
*
10786 TTCGTTCGTTTATGTTCGTTCATT
1 TTCGTTCGTTTATGTTAGTTCATT
10810 T
1 T
10811 ATTTTTACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.63
Consensus pattern (24 bp):
TTCGTTCGTTTATGTTAGTTCATT
Found at i:11952 original size:22 final size:22
Alignment explanation
Indices: 11926--11970 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11916 TTGAGTAAAC
*
11926 TTATATAAAAT-TTATAAAAATT
1 TTATAGAAAATATT-TAAAAATT
*
11948 TTATAGAAAGTATTTAAAAATT
1 TTATAGAAAATATTTAAAAATT
11970 T
1 T
11971 ACTATATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TTATAGAAAATATTTAAAAATT
Found at i:12560 original size:23 final size:23
Alignment explanation
Indices: 12529--12608 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
12519 TGTTTATTTA
* *
12529 TGTTCGTTTATGTTCATTTATTG
1 TGTTTGTTTACGTTCATTTATTG
12552 TGTTTGTTTACGTTCATTTATTG
1 TGTTTGTTTACGTTCATTTATTG
* *
12575 TGTTCT-TTTACGTTAATTCATTTG
1 TGTT-TGTTTACGTTCATTTA-TTG
12599 TGTTTGTTTA
1 TGTTTGTTTA
12609 TCATTTAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 38 0.76
24 12 0.24
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
TGTTTGTTTACGTTCATTTATTG
Found at i:12660 original size:31 final size:31
Alignment explanation
Indices: 12623--12696 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
12613 TTAAATGAAC
*
12623 GAACACGAACAAACTACATTTATTAACGAAT
1 GAACACGAACAAACTACATTCATTAACGAAT
12654 GAACACGAACAAACTACATTCATTAACGAAT
1 GAACACGAACAAACTACATTCATTAACGAAT
12685 GAACACGAACAA
1 GAACACGAACAA
12697 TAATTTTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.50, C:0.22, G:0.11, T:0.18
Consensus pattern (31 bp):
GAACACGAACAAACTACATTCATTAACGAAT
Found at i:13842 original size:25 final size:26
Alignment explanation
Indices: 13795--13900 Score: 78
Period size: 25 Copynumber: 4.1 Consensus size: 26
13785 TATCTTAGTG
* * *
13795 TATAAATACTTAAATTCATAATATTT
1 TATAAATACTTAACTTTAAAATATTT
13821 TATAAATA-TTAACTTTAAAATATTT
1 TATAAATACTTAACTTTAAAATATTT
* *
13846 T-T-TATA-TTAACTTATTAAATTATTT
1 TATAAATACTTAAC-T-TTAAAATATTT
* *
13871 TATTATTAACTTAA-TTTAAAAATATTT
1 TATAAAT-ACTTAACTTT-AAAATATTT
13898 TAT
1 TAT
13901 TTTTTTATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
23 8 0.12
24 2 0.03
25 26 0.40
26 11 0.17
27 13 0.20
28 1 0.02
29 4 0.06
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (26 bp):
TATAAATACTTAACTTTAAAATATTT
Found at i:13856 original size:23 final size:23
Alignment explanation
Indices: 13826--13883 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
13816 TATTTTATAA
*
13826 ATATTAACTT-TAAAATATTTTTT
1 ATATTAACTTATAAAAT-TATTTT
*
13849 ATATTAACTTATTAAATTATTTT
1 ATATTAACTTATAAAATTATTTT
13872 ATTATTAACTTA
1 A-TATTAACTTA
13884 ATTTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTAACTTATAAAATTATTTT
Found at i:13871 original size:24 final size:24
Alignment explanation
Indices: 13826--13898 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 24
13816 TATTTTATAA
13826 ATATTAAC-T-TTAAAATATTTTTT
1 ATATTAACTTATTAAAATA-TTTTT
*
13849 ATATTAACTTATTAAATTA-TTTT
1 ATATTAACTTATTAAAATATTTTT
13872 ATTATTAACTTAATTTAAAAATATTTT
1 A-TATTAACTT-A-TT-AAAATATTTT
13899 ATTTTTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
23 13 0.32
24 10 0.24
25 8 0.20
26 2 0.05
27 5 0.12
28 3 0.07
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTAACTTATTAAAATATTTTT
Found at i:14099 original size:31 final size:31
Alignment explanation
Indices: 14064--14125 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
14054 TCACATTTTT
*
14064 ATTAAATAAAAACGAAAATGATAATATCTTA
1 ATTAAATAAAAACGAAAATAATAATATCTTA
* * *
14095 ATTAAATAAAAATGAAAGTAATTATATCTTA
1 ATTAAATAAAAACGAAAATAATAATATCTTA
14126 TGTTTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (31 bp):
ATTAAATAAAAACGAAAATAATAATATCTTA
Found at i:15257 original size:35 final size:37
Alignment explanation
Indices: 15186--15258 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
15176 GTTGAAAAAT
* *
15186 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
15223 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
15258 A
1 A
15259 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:15940 original size:37 final size:37
Alignment explanation
Indices: 15867--15941 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
15857 ACTATAAGAT
* *
15867 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
15904 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
15941 A
1 A
15942 AGATTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:19391 original size:59 final size:59
Alignment explanation
Indices: 19306--19425 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
19296 CAAACATCAG
19306 TCCAGAAGGCAATCGACCTACCATTCCCCAATTGGATCTTGGAATTTGTTCTCAAACAC
1 TCCAGAAGGCAATCGACCTACCATTCCCCAATTGGATCTTGGAATTTGTTCTCAAACAC
19365 TCCAGAAGGCAATCGACCTACCATTCCCCAATTGGATCTTGGAATTTGTTCTCAAACAC
1 TCCAGAAGGCAATCGACCTACCATTCCCCAATTGGATCTTGGAATTTGTTCTCAAACAC
19424 TC
1 TC
19426 TCCCATTGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (59 bp):
TCCAGAAGGCAATCGACCTACCATTCCCCAATTGGATCTTGGAATTTGTTCTCAAACAC
Found at i:26251 original size:26 final size:26
Alignment explanation
Indices: 26222--26272 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
26212 TGCACTCCTA
* *
26222 CCTAGTTTCTTTAATTCACGGTTGCT
1 CCTACTTTCTTGAATTCACGGTTGCT
26248 CCTACTTTCTTGAATTCACGGTTGC
1 CCTACTTTCTTGAATTCACGGTTGC
26273 AGAGGAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.16, C:0.25, G:0.16, T:0.43
Consensus pattern (26 bp):
CCTACTTTCTTGAATTCACGGTTGCT
Found at i:29427 original size:29 final size:29
Alignment explanation
Indices: 29394--29452 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
29384 GTAAAAGTAT
*
29394 AACATATATTCAATTAACCCCCCAAAAAA
1 AACATATATTCAATTAACCCCACAAAAAA
29423 AACATATATTCAATTAACCCCACAAAAAA
1 AACATATATTCAATTAACCCCACAAAAAA
29452 A
1 A
29453 GTTTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.20
Consensus pattern (29 bp):
AACATATATTCAATTAACCCCACAAAAAA
Found at i:31234 original size:12 final size:12
Alignment explanation
Indices: 31217--31254 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
31207 CGAAGGCGAT
31217 GAGTTCGAAGAA
1 GAGTTCGAAGAA
31229 GAGTTCGAAGAA
1 GAGTTCGAAGAA
*
31241 GAGGTCGAAGAA
1 GAGTTCGAAGAA
31253 GA
1 GA
31255 CGTGAATCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.37, T:0.13
Consensus pattern (12 bp):
GAGTTCGAAGAA
Found at i:33339 original size:14 final size:14
Alignment explanation
Indices: 33322--33349 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33312 ATCATAACAA
33322 AATTATATAACTAT
1 AATTATATAACTAT
33336 AATTATATAACTAT
1 AATTATATAACTAT
33350 TCTTTCACTT
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:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:33423 original size:16 final size:16
Alignment explanation
Indices: 33402--33432 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33392 CTTCTAATTT
33402 TTTTTGAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
*
33418 TTTTTGAGTTGAAGT
1 TTTTTGAGTTCAAGT
33433 TTCAATATTA
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:0.19, C:0.06, G:0.23, T:0.52
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:33950 original size:19 final size:20
Alignment explanation
Indices: 33926--33968 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
33916 AAAAAAAGAT
33926 AAACGA-AAACAACAGCAAA
1 AAACGATAAACAACAGCAAA
**
33945 AAACGATAAACAATGGCAAA
1 AAACGATAAACAACAGCAAA
33965 AAAC
1 AAAC
33969 TGTAAGTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.65, C:0.19, G:0.12, T:0.05
Consensus pattern (20 bp):
AAACGATAAACAACAGCAAA
Found at i:41599 original size:2 final size:2
Alignment explanation
Indices: 41592--41664 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
41582 ATTAGGCTTA
41592 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
41634 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
41665 GGGGAATCTC
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:42685 original size:19 final size:19
Alignment explanation
Indices: 42657--42719 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
42647 AATTGTTGAA
*
42657 TATT-TAATATATACTCTT
1 TATTATAATATATAATCTT
*
42675 TATTATAATATAATATTC-T
1 TATTATAATAT-ATAATCTT
* *
42694 TATTTTAATATTATAATTTT
1 TATTATAATA-TATAATCTT
42714 TATTAT
1 TATTAT
42720 TTTAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 4 0.11
19 20 0.56
20 12 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATAATATATAATCTT
Found at i:44781 original size:15 final size:15
Alignment explanation
Indices: 44752--44796 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
44742 AAAAGCTCAA
44752 GCTATCAAG-TCTACT
1 GCTAT-AAGTTCTACT
*
44767 GGTATAAGTTCTACT
1 GCTATAAGTTCTACT
*
44782 GCTATATGTTCTACT
1 GCTATAAGTTCTACT
44797 ATCTGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (15 bp):
GCTATAAGTTCTACT
Found at i:50988 original size:45 final size:45
Alignment explanation
Indices: 50939--51026 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
50929 GAACATCGAA
*
50939 TGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACA-AGCCATGCATCGATGCACTCAG
*
50984 TGCATTTGATGCATCGATGCACAAGCTATGCATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTC
51027 TGGCTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (45 bp):
TGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAG
Found at i:52447 original size:19 final size:20
Alignment explanation
Indices: 52423--52460 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
52413 TGCAATTAAG
52423 AAATGAAGAAGAA-AAGAGA
1 AAATGAAGAAGAATAAGAGA
*
52442 AAATGATGAAGAATAAGAG
1 AAATGAAGAAGAATAAGAG
52461 GGGAATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (20 bp):
AAATGAAGAAGAATAAGAGA
Found at i:55457 original size:17 final size:17
Alignment explanation
Indices: 55435--55472 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
55425 AACGGTCAAC
55435 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
55452 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
55469 GGTC
1 GGTC
55473 GGGTCAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:55462 original size:7 final size:7
Alignment explanation
Indices: 55404--55445 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
55394 AAAGAAAGTA
55404 AACGGTC
1 AACGGTC
*
55411 AACGGAC
1 AACGGTC
*
55418 AACGGAC
1 AACGGTC
55425 AACGGTC
1 AACGGTC
55432 AACGGTC
1 AACGGTC
55439 AACGGTC
1 AACGGTC
55446 GGGTCGGGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (7 bp):
AACGGTC
Found at i:55500 original size:14 final size:13
Alignment explanation
Indices: 55447--55500 Score: 62
Period size: 14 Copynumber: 4.3 Consensus size: 13
55437 TCAACGGTCG
55447 GGTCGGGTCA-AC
1 GGTCGGGTCAGAC
55459 GGTCGGGTC-G--
1 GGTCGGGTCAGAC
55469 GGTCGGGTCAGAC
1 GGTCGGGTCAGAC
55482 GGGTCGGGTCAGACC
1 -GGTCGGGTCAGA-C
55497 GGTC
1 GGTC
55501 AAACCGGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
12 9 0.25
14 16 0.44
15 1 0.03
ACGTcount: A:0.11, C:0.24, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCGGGTCAGAC
Found at i:55515 original size:19 final size:19
Alignment explanation
Indices: 55491--55566 Score: 116
Period size: 19 Copynumber: 3.9 Consensus size: 19
55481 CGGGTCGGGT
55491 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
55510 CAGACCGGTCAAACCGGTC
1 CAGACCGGTCAAACCGGTC
55529 CAGACCGGTCAAACCGGTTC
1 CAGACCGGTCAAACCGG-TC
* * *
55549 AAAACTGGTCAAACCGGT
1 CAGACCGGTCAAACCGGT
55567 TTTCCAGCAG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
19 37 0.70
20 16 0.30
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.13
Consensus pattern (19 bp):
CAGACCGGTCAAACCGGTC
Found at i:55518 original size:10 final size:10
Alignment explanation
Indices: 55491--55538 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
55481 CGGGTCGGGT
55491 CAGACCGGT-
1 CAGACCGGTC
*
55500 CAAACCGGTC
1 CAGACCGGTC
55510 CAGACCGGT-
1 CAGACCGGTC
*
55519 CAAACCGGTC
1 CAGACCGGTC
55529 CAGACCGGTC
1 CAGACCGGTC
55539 AAACCGGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.25, C:0.38, G:0.27, T:0.10
Consensus pattern (10 bp):
CAGACCGGTC
Found at i:55550 original size:10 final size:9
Alignment explanation
Indices: 55488--55566 Score: 86
Period size: 9 Copynumber: 8.3 Consensus size: 9
55478 AGACGGGTCG
*
55488 GGTCAGACC
1 GGTCAAACC
55497 GGTCAAACC
1 GGTCAAACC
*
55506 GGTCCAGACC
1 GGT-CAAACC
55516 GGTCAAACC
1 GGTCAAACC
*
55525 GGTCCAGACC
1 GGT-CAAACC
55535 GGTCAAACC
1 GGTCAAACC
*
55544 GGTTCAAAACT
1 GG-TC-AAACC
55555 GGTCAAACC
1 GGTCAAACC
55564 GGT
1 GGT
55567 TTTCCAGCAG
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 33 0.56
10 20 0.34
11 6 0.10
ACGTcount: A:0.28, C:0.32, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Done.