Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006502.1 Hibiscus syriacus cultivar Beakdansim tig00015825_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: 68800
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:2967 original size:22 final size:22
Alignment explanation
Indices: 2937--2987 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2927 TTAGGCACCC
*
2937 AAAACAATTGTCATTTTAATAA
1 AAAACAATTGTAATTTTAATAA
* * *
2959 AAAATAATTTTAATTTTATTAA
1 AAAACAATTGTAATTTTAATAA
2981 AACAACA
1 AA-AACA
2988 CTTTTAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAACAATTGTAATTTTAATAA
Found at i:3334 original size:12 final size:13
Alignment explanation
Indices: 3304--3332 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3294 GAATAATGAG
3304 AAAAA-TAAATTA
1 AAAAATTAAATTA
3316 AAAAATTAAATTA
1 AAAAATTAAATTA
3329 AAAA
1 AAAA
3333 TTTACCAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAATTA
Found at i:4910 original size:13 final size:13
Alignment explanation
Indices: 4892--4917 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4882 CAGAGTTTAA
4892 CGTTGACTTTGAC
1 CGTTGACTTTGAC
4905 CGTTGACTTTGAC
1 CGTTGACTTTGAC
4918 TAAAAAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
CGTTGACTTTGAC
Found at i:15601 original size:22 final size:22
Alignment explanation
Indices: 15558--15603 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
15548 ATATCTTCAT
**
15558 CCTTTAGCTTTCTCTTGGAAGA
1 CCTTTAGCTTTCTCTTCAAAGA
15580 CCTTTAGCTTTCTCTTCAAAGA
1 CCTTTAGCTTTCTCTTCAAAGA
15602 CC
1 CC
15604 CTCTCTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (22 bp):
CCTTTAGCTTTCTCTTCAAAGA
Found at i:16641 original size:23 final size:22
Alignment explanation
Indices: 16600--16651 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
16590 CTTTGATCCT
*
16600 TTTTTATTTATTTTTACTCATTC
1 TTTTTATTTATTTTCACTC-TTC
*
16623 TTTTTATTTCA-TTTCACTCTTT
1 TTTTTATTT-ATTTTCACTCTTC
16645 TTTTTAT
1 TTTTTAT
16652 CTTTTCCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 16 0.62
24 1 0.04
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTATTTATTTTCACTCTTC
Found at i:28288 original size:2 final size:2
Alignment explanation
Indices: 28281--28319 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
28271 TACAACAACC
28281 AT 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 AT A
28320 GTAACTGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31821 original size:3 final size:3
Alignment explanation
Indices: 31813--31848 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
31803 ATGTTCTATA
*
31813 TAT TAT TAT TAT TTT TAT T-T TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31849 GAAATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:31837 original size:17 final size:17
Alignment explanation
Indices: 31815--31848 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31805 GTTCTATATA
*
31815 TTATTATTATTTTTATT
1 TTATTATTATTATTATT
31832 TTATTATTATTATTATT
1 TTATTATTATTATTATT
31849 GAAATAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTATTATTATTATT
Found at i:31878 original size:3 final size:3
Alignment explanation
Indices: 31870--31895 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31860 AAATGTTCTA
31870 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
31896 ATTGCAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:32042 original size:23 final size:23
Alignment explanation
Indices: 32008--32122 Score: 133
Period size: 23 Copynumber: 5.0 Consensus size: 23
31998 TACTATATAC
* *
32008 CCTAGTGGTTGATACTTTGGTAT
1 CCTAGTGTTTGATACTTCGGTAT
* *
32031 CCTAATGTTTGATACTT-TGTAT
1 CCTAGTGTTTGATACTTCGGTAT
* *
32053 CCTAGTGATTGATACTTCGTTAT
1 CCTAGTGTTTGATACTTCGGTAT
*
32076 CTTAGTGTTTGATACTTCGGTAT
1 CCTAGTGTTTGATACTTCGGTAT
** *
32099 CCTAGTAATTGATACTTCAGTAT
1 CCTAGTGTTTGATACTTCGGTAT
32122 C
1 C
32123 TTATCGTGAC
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
22 19 0.25
23 58 0.75
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (23 bp):
CCTAGTGTTTGATACTTCGGTAT
Found at i:32085 original size:45 final size:45
Alignment explanation
Indices: 32008--32125 Score: 148
Period size: 45 Copynumber: 2.6 Consensus size: 45
31998 TACTATATAC
* * * *
32008 CCTAGTGGTTGATACTTTGGTATCCTAATGTTTGATACTT-TGTAT
1 CCTAGTGATTGATAC-TTCGTATCTTAATGTTTGATACTTCGGTAT
*
32053 CCTAGTGATTGATACTTCGTTATCTTAGTGTTTGATACTTCGGTAT
1 CCTAGTGATTGATACTTCG-TATCTTAATGTTTGATACTTCGGTAT
*
32099 CCTAGTAATTGATACTTCAGTATCTTA
1 CCTAGTGATTGATACTTC-GTATCTTA
32126 TCGTGACTCG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 3 0.05
45 32 0.50
46 28 0.44
47 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (45 bp):
CCTAGTGATTGATACTTCGTATCTTAATGTTTGATACTTCGGTAT
Found at i:33683 original size:26 final size:26
Alignment explanation
Indices: 33653--33704 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
33643 CTTTCCTGTT
33653 TGGCCCATCTCTCGCTGAATTTTCTG
1 TGGCCCATCTCTCGCTGAATTTTCTG
* * *
33679 TGGCCCATTTCTCGTTGAGTTTTCTG
1 TGGCCCATCTCTCGCTGAATTTTCTG
33705 AGGCTTGTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.10, C:0.27, G:0.21, T:0.42
Consensus pattern (26 bp):
TGGCCCATCTCTCGCTGAATTTTCTG
Found at i:43578 original size:15 final size:15
Alignment explanation
Indices: 43530--43579 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
43520 GCCAACCTTC
*
43530 ATTTATATGATATGAT
1 ATTTAT-TGATATGTT
* *
43546 ATTTTATTGAAATTTT
1 A-TTTATTGATATGTT
43562 ATTTATTGATATGTT
1 ATTTATTGATATGTT
43577 ATT
1 ATT
43580 AAACAATGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 15 0.54
16 8 0.29
17 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (15 bp):
ATTTATTGATATGTT
Found at i:43816 original size:19 final size:19
Alignment explanation
Indices: 43792--43829 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
43782 AGTTAATCTA
43792 GTGATTGGTACTT-CAATAC
1 GTGATTGGTA-TTACAATAC
43811 GTGATTGGTATTACAATAC
1 GTGATTGGTATTACAATAC
43830 CCTAGTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (19 bp):
GTGATTGGTATTACAATAC
Found at i:43856 original size:23 final size:23
Alignment explanation
Indices: 43830--43899 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
43820 ATTACAATAC
* *
43830 CCTAGTGATTAATACTTAGGTAT
1 CCTAATGATTGATACTTAGGTAT
* * * *
43853 CCTATTGTTTGGTACTTCGGTAT
1 CCTAATGATTGATACTTAGGTAT
* *
43876 CCTAATGATGGATACTTTGGTAT
1 CCTAATGATTGATACTTAGGTAT
43899 C
1 C
43900 TTATCGTGAC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (23 bp):
CCTAATGATTGATACTTAGGTAT
Found at i:44187 original size:59 final size:62
Alignment explanation
Indices: 44090--44207 Score: 188
Period size: 61 Copynumber: 1.9 Consensus size: 62
44080 AATAAATTAA
*
44090 TGTGTTATATTTATGCTTTTACATATTGATGAGATGATAC-ATTTTTAATGGTTGTTTAATT
1 TGTGTTATATTTAAGCTTTTACATATTGATGAGATGATACAATTTTTAATGGTTGTTTAATT
*
44151 TGTGTTATATTTAAGC-TTTGCATA-TGATGAGATGATACATATTTTTAATGGTTGTTT
1 TGTGTTATATTTAAGCTTTTACATATTGATGAGATGATACA-ATTTTTAATGGTTGTTT
44208 GTATTGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
59 14 0.26
60 7 0.13
61 32 0.60
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.51
Consensus pattern (62 bp):
TGTGTTATATTTAAGCTTTTACATATTGATGAGATGATACAATTTTTAATGGTTGTTTAATT
Found at i:44216 original size:59 final size:61
Alignment explanation
Indices: 44089--44224 Score: 181
Period size: 61 Copynumber: 2.2 Consensus size: 61
44079 GAATAAATTA
*
44089 ATGTGTTATATTTATGCTTTTACATATTGATGAGATGATACATTTTTAATGGTTGTTTAAT
1 ATGTGTTATATTTAAGCTTTTACATATTGATGAGATGATACATTTTTAATGGTTGTTTAAT
* * *
44150 TTGTGTTATATTTAAGC-TTTGCATA-TGATGAGATGATACATATTTTTAATGGTTGTTT-GT
1 ATGTGTTATATTTAAGCTTTTACATATTGATGAGATGATAC--ATTTTTAATGGTTGTTTAAT
44210 AT-TGTTATTATTTAA
1 ATGTGTTA-TATTTAA
44225 ATGTCTCACT
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 19 0.28
60 16 0.24
61 32 0.48
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.51
Consensus pattern (61 bp):
ATGTGTTATATTTAAGCTTTTACATATTGATGAGATGATACATTTTTAATGGTTGTTTAAT
Found at i:53895 original size:22 final size:23
Alignment explanation
Indices: 53861--53918 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 23
53851 ATTTATTTGT
* *
53861 TTTTATACTAATTTTTATATATT-
1 TTTTATA-AAATTTTTAAATATTA
53884 TTCTT-TAAAA-TTTTAAATATTA
1 TT-TTATAAAATTTTTAAATATTA
53906 TTTTATAAAATTT
1 TTTTATAAAATTT
53919 CAATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 12 0.41
22 9 0.31
23 6 0.21
24 2 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTATAAAATTTTTAAATATTA
Found at i:53897 original size:21 final size:22
Alignment explanation
Indices: 53873--53918 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
53863 TTATACTAAT
*
53873 TTTTATATATT-TTCTT-TAAAA
1 TTTTAAATATTATT-TTATAAAA
53894 TTTTAAATATTATTTTATAAAA
1 TTTTAAATATTATTTTATAAAA
53916 TTT
1 TTT
53919 CAATTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTAAATATTATTTTATAAAA
Found at i:55393 original size:14 final size:14
Alignment explanation
Indices: 55374--55404 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55364 TTTCGGAAAG
55374 GTTTTTAAAATATT
1 GTTTTTAAAATATT
*
55388 GTTTTTAATATATT
1 GTTTTTAAAATATT
55402 GTT
1 GTT
55405 GCAGGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (14 bp):
GTTTTTAAAATATT
Found at i:55618 original size:203 final size:204
Alignment explanation
Indices: 55263--55667 Score: 636
Period size: 203 Copynumber: 2.0 Consensus size: 204
55253 AGCATCCGAG
*
55263 AAGAATAGTAGAGAAAATTTTGAACGAAATTTTCTTCTAATCTATAATCTGTAAGTATTATTCGA
1 AAGAATAGTAGAGAAAATTTTGAACAAAATTTTCTTCTAATCTATAATCTGTAAGTATTATTCGA
* * * *
55328 ATAAAATTTTATTCGTATTAGAATAAAATATCTCTATTTCGGAAAGGTTTTTAAAATATTGTTTT
66 ATAAAATTTTACTCGTATTAGAATAAAATATCTCTATTTCGGAAAAGTTATTAAAATATTATTTT
* *
55393 TAATATATTGTTGCAGGTAAAAAATAAGTGATTAAGAAATTCGAGAAA-GTTTTTTAATAACATC
131 TAATATATTGTTGCAGGTAAAAAAGAAGTGAGTAAGAAATTCGA-AAAGGTTTTTTAATAACATC
*
55457 AAGTTGTCAA
195 AACTTGTCAA
*
55467 AAGAATAGTAGAGAAAATTTTGAACAAAATTTTCTT-TCAATCTATAATCTGTAAGTATTATTGG
1 AAGAATAGTAGAGAAAATTTTGAACAAAATTTTCTTCT-AATCTATAATCTGTAAGTATTATTCG
* *
55531 AAT-AAATTTTACTCGTATTCGAATAATATATCTCTATTTCGGAAAAGTTATTAAAATATTATTT
65 AATAAAATTTTACTCGTATTAGAATAAAATATCTCTATTTCGGAAAAGTTATTAAAATATTATTT
* * * *
55595 TTAATATGTTGTTGCATGTAAAAAAGAAGTGAGTAAGAAATTTGAAAAGGTTTTTTTATAACATC
130 TTAATATATTGTTGCAGGTAAAAAAGAAGTGAGTAAGAAATTCGAAAAGGTTTTTTAATAACATC
55660 AACTTGTC
195 AACTTGTC
55668 GGAAGAAACT
Statistics
Matches: 184, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
202 3 0.02
203 118 0.64
204 63 0.34
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (204 bp):
AAGAATAGTAGAGAAAATTTTGAACAAAATTTTCTTCTAATCTATAATCTGTAAGTATTATTCGA
ATAAAATTTTACTCGTATTAGAATAAAATATCTCTATTTCGGAAAAGTTATTAAAATATTATTTT
TAATATATTGTTGCAGGTAAAAAAGAAGTGAGTAAGAAATTCGAAAAGGTTTTTTAATAACATCA
ACTTGTCAA
Found at i:55887 original size:20 final size:23
Alignment explanation
Indices: 55860--55912 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
55850 TGTAGTAGGA
*
55860 AAATAATATTTATTATAATGACG
1 AAATAATATTCATTATAATGACG
55883 AAATAATATTCATTATAATGAC-
1 AAATAATATTCATTATAATGACG
*
55905 AAAAAATA
1 AAATAATA
55913 ACGGCAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (23 bp):
AAATAATATTCATTATAATGACG
Found at i:55971 original size:44 final size:45
Alignment explanation
Indices: 55921--56005 Score: 145
Period size: 44 Copynumber: 1.9 Consensus size: 45
55911 TAACGGCAAC
*
55921 ATTAATTATCTATTAATAACCCGAGTAGG-TGGTGGTTGGTGATT
1 ATTAATTATCCATTAATAACCCGAGTAGGTTGGTGGTTGGTGATT
*
55965 ATTAATTATCCATTAATAACCCTAGTAGGTTGGTGGTTGGT
1 ATTAATTATCCATTAATAACCCGAGTAGGTTGGTGGTTGGT
56006 TGTTGAACGA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 27 0.71
45 11 0.29
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.39
Consensus pattern (45 bp):
ATTAATTATCCATTAATAACCCGAGTAGGTTGGTGGTTGGTGATT
Found at i:56343 original size:38 final size:38
Alignment explanation
Indices: 56270--56354 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
56260 AGGTTGATGA
* *
56270 TTGGTGGTTATTAATTCTCCATTAATAATATGGGTATG
1 TTGGTGGTTATTAATTCTCCATTAATAATACGGGTAGG
**
56308 TTGGTGGTTATTAA-TCATCCATTAATGCCT-CGGGTAGG
1 TTGGTGGTTATTAATTC-TCCATTAAT-AATACGGGTAGG
56346 TTGGTGGTT
1 TTGGTGGTT
56355 GAACTGGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.05
38 38 0.93
39 1 0.02
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (38 bp):
TTGGTGGTTATTAATTCTCCATTAATAATACGGGTAGG
Found at i:58286 original size:14 final size:14
Alignment explanation
Indices: 58269--58302 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
58259 CATATCCCAT
58269 ATATTGTATCTGTC
1 ATATTGTATCTGTC
58283 ATATTGTATCTGTC
1 ATATTGTATCTGTC
58297 ATATTG
1 ATATTG
58303 GTAAGAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
ATATTGTATCTGTC
Found at i:60619 original size:20 final size:20
Alignment explanation
Indices: 60596--60680 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 20
60586 GCATTAAATA
60596 ATGCATTAAGGCATGAAAGG
1 ATGCATTAAGGCATGAAAGG
* *
60616 ATGCCATAATTAAAATGCATGAAATG
1 ATG-C---ATT--AAGGCATGAAAGG
60642 ATGCATTAAGGCATGAAAGG
1 ATGCATTAAGGCATGAAAGG
*
60662 ATGCATTAAGGCATTAAAG
1 ATGCATTAAGGCATGAAAG
60681 AATGTCATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 32 0.59
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 14 0.26
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
ATGCATTAAGGCATGAAAGG
Found at i:60626 original size:46 final size:46
Alignment explanation
Indices: 60569--60777 Score: 200
Period size: 46 Copynumber: 4.6 Consensus size: 46
60559 GCTCTAAATC
60569 GAAT-CCATAATTAAAATGCATTAAATAATGCATTAAGGCATGAAA
1 GAATGCCATAATTAAAATGCATTAAATAATGCATTAAGGCATGAAA
* * *
60614 GGATGCCATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAA
1 GAATGCCATAATTAAAATGCATTAAATAATGCATTAAGGCATGAAA
* * * *
60660 GGATG-C---ATT--AAGGCATTAAAGAATGTCATAATTAAAATGCATGAAA
1 GAATGCCATAATTAAAATGCATTAAATAATG-C---ATT--AAGGCATGAAA
* ** *
60706 GAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGTATGAAA
1 GAATGCCATAATTAAAATGCATTAAATAATGCATTAAGGCATGAAA
*
60752 GAATGACATAATTAAAATGCA-TAAAT
1 GAATGCCATAATTAAAATGCATTAAAT
60778 GGATGTGTTA
Statistics
Matches: 134, Mismatches: 17, Indels: 26
0.76 0.10 0.15
Matches are distributed among these distances:
40 12 0.09
41 1 0.01
42 3 0.02
44 3 0.02
45 7 0.05
46 87 0.65
47 1 0.01
48 3 0.02
50 3 0.02
51 1 0.01
52 13 0.10
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (46 bp):
GAATGCCATAATTAAAATGCATTAAATAATGCATTAAGGCATGAAA
Found at i:60718 original size:26 final size:25
Alignment explanation
Indices: 60569--60647 Score: 53
Period size: 26 Copynumber: 3.3 Consensus size: 25
60559 GCTCTAAATC
* *
60569 GAATCCATAATTAAAATGCATTAAA
1 GAATGCATAATTAAAATGCATGAAA
* *
60594 TAATGC---ATT--AAGGCATGAAA
1 GAATGCATAATTAAAATGCATGAAA
*
60614 GGATGCCATAATTAAAATGCATGAAA
1 GAATG-CATAATTAAAATGCATGAAA
60640 TG-ATGCAT
1 -GAATGCAT
60648 TAAGGCATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
20 12 0.30
21 1 0.03
22 3 0.08
24 3 0.08
25 7 0.17
26 13 0.32
27 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (25 bp):
GAATGCATAATTAAAATGCATGAAA
Found at i:60719 original size:26 final size:26
Alignment explanation
Indices: 60672--60737 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
60662 ATGCATTAAG
* *
60672 GCATTAAAGAATGTCATAATTAAAAT
1 GCATGAAAGAATGCCATAATTAAAAT
60698 GCATGAAAGAATGCCATAATTAAAAT
1 GCATGAAAGAATGCCATAATTAAAAT
*
60724 GCATGAAAGGATGC
1 GCATGAAAGAATGC
60738 ATTAAGGTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (26 bp):
GCATGAAAGAATGCCATAATTAAAAT
Found at i:66947 original size:20 final size:19
Alignment explanation
Indices: 66922--66974 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
66912 TGATTCAATC
*
66922 AGTATCGATACCAACGAGGA
1 AGTATCGATACCAAAG-GGA
66942 AGTATCGATACCAAAGGGA
1 AGTATCGATACCAAAGGGA
66961 AGATATCGATACCA
1 AG-TATCGATACCA
66975 TTTCAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:67132 original size:22 final size:23
Alignment explanation
Indices: 67088--67134 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
67078 GGGTGTTGGT
* *
67088 AAAATGATATTTAACTAATAATA
1 AAAATGATATTAAACTAAAAATA
*
67111 AAAATGA-ATTAAAGTAAAAATA
1 AAAATGATATTAAACTAAAAATA
67133 AA
1 AA
67135 GAAAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (23 bp):
AAAATGATATTAAACTAAAAATA
Done.