Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002946.1 Hibiscus syriacus cultivar Beakdansim tig00006078_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: 73163
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:18900 original size:30 final size:30
Alignment explanation
Indices: 18830--18888 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
18820 CAATTTAAGA
18830 CAAAATGTTTTTGGACTTGAATTGAATTTG
1 CAAAATGTTTTTGGACTTGAATTGAATTTG
*
18860 CAAAATGTTTTTGGATTTGAATTGAATTT
1 CAAAATGTTTTTGGACTTGAATTGAATTT
18889 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.46
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTG
Found at i:18997 original size:21 final size:21
Alignment explanation
Indices: 18971--19013 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
18961 AGGGTGTCAA
* *
18971 AGTGCATCCATGTATCCCTGC
1 AGTGCATCCATGCATCCATGC
18992 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCATCCATGC
19013 A
1 A
19014 TCTGCACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCATGC
Found at i:19049 original size:42 final size:44
Alignment explanation
Indices: 19001--19104 Score: 113
Period size: 46 Copynumber: 2.4 Consensus size: 44
18991 CAGTGCATCC
19001 ATGCATCCATGCATC-TGC-ACTAATGCATCGATGCATCAGGCA
1 ATGCATCCATGCATCATGCAACTAATGCATCGATGCATCAGGCA
** * * ** *
19043 ATGCATCCAAACATCGAATGCAATTAGTGCATCGATGCATCCTGCC
1 ATGCATCCATGCATC--ATGCAACTAATGCATCGATGCATCAGGCA
19089 ATGCATCCATGCATCA
1 ATGCATCCATGCATCA
19105 AGGCTGCAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
42 13 0.27
44 1 0.02
45 3 0.06
46 32 0.65
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (44 bp):
ATGCATCCATGCATCATGCAACTAATGCATCGATGCATCAGGCA
Found at i:20411 original size:19 final size:20
Alignment explanation
Indices: 20387--20434 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
20377 AATGATTTTC
*
20387 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
20406 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
20426 TTTTGAAAA
1 TTTTGAAAA
20435 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:21774 original size:30 final size:30
Alignment explanation
Indices: 21703--21762 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
21693 ACAATTTAAG
*
21703 GCAAAATATTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
21733 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
21763 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:25010 original size:16 final size:18
Alignment explanation
Indices: 24989--25032 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
24979 AACATTCTCA
24989 GTAATCTT-ATT-CACTG
1 GTAATCTTAATTCCACTG
25005 GTAATCTTACATTCCCACTG
1 GTAATCTTA-ATT-CCACTG
25025 GTAATCTT
1 GTAATCTT
25033 CCATTCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
18 3 0.12
20 13 0.54
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTAATTCCACTG
Found at i:25025 original size:20 final size:20
Alignment explanation
Indices: 25000--25039 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
24990 TAATCTTATT
25000 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
*
25020 CACTGGTAATCTTCCATTCC
1 CACTGGTAATCTTACATTCC
25040 ATGAACTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.35
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:26921 original size:11 final size:12
Alignment explanation
Indices: 26888--26921 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
26878 AAGTTTGTTT
26888 TTTAATATATAA
1 TTTAATATATAA
26900 TTTATATATATAA
1 TTTA-ATATATAA
26913 TTTAA-ATAT
1 TTTAATATAT
26922 TTATGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 5 0.24
13 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAATATATAA
Found at i:27629 original size:2 final size:2
Alignment explanation
Indices: 27622--27664 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
27612 CAAAAATAAT
27622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
27664 T
1 T
27665 GACAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31111 original size:16 final size:18
Alignment explanation
Indices: 31090--31133 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
31080 AACATTCTCA
31090 GTAATCTT-ATT-CACTG
1 GTAATCTTAATTCCACTG
31106 GTAATCTTACATTCCCACTG
1 GTAATCTTA-ATT-CCACTG
31126 GTAATCTT
1 GTAATCTT
31134 CCATTCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
18 3 0.12
20 13 0.54
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTAATTCCACTG
Found at i:31126 original size:20 final size:20
Alignment explanation
Indices: 31101--31140 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31091 TAATCTTATT
31101 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
*
31121 CACTGGTAATCTTCCATTCC
1 CACTGGTAATCTTACATTCC
31141 ATGAACTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.35
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:31745 original size:14 final size:14
Alignment explanation
Indices: 31726--31767 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31716 ATGTACATGT
31726 AAAATAAT-AATAAA
1 AAAATAATGAA-AAA
*
31740 AAAATAATGAAAAT
1 AAAATAATGAAAAA
31754 AAAATAA-GAAAAA
1 AAAATAATGAAAAA
31767 A
1 A
31768 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.24
14 17 0.68
15 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAATAATGAAAAA
Found at i:31926 original size:23 final size:23
Alignment explanation
Indices: 31896--31970 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
31886 AAGAGGGAGG
31896 AAAAAATATAATAATAATAGAAA
1 AAAAAATATAATAATAATAGAAA
*
31919 AAAAAATA-AATAAATAAT-G-TA
1 AAAAAATATAAT-AATAATAGAAA
* *
31940 AATAAATATAATAATAA-AGAAGT
1 AAAAAATATAATAATAATAGAA-A
31963 AAAAAATA
1 AAAAAATA
31971 GGGTAAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
21 14 0.33
22 7 0.17
23 21 0.50
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAAAATATAATAATAATAGAAA
Found at i:33213 original size:3 final size:3
Alignment explanation
Indices: 33205--33231 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
33195 ATACTTTGTA
33205 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
33232 GTCAGACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:33797 original size:105 final size:105
Alignment explanation
Indices: 33615--34382 Score: 1419
Period size: 105 Copynumber: 7.3 Consensus size: 105
33605 TGAGAATTGG
** * * *
33615 ATATCCTTCGTCATGAAGTTGAAATTGGTTCTAAAATTGAGAAATGTTTGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
*
33680 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
** *
33720 ATATCCTTCGTTGTGAAGCAGCAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
33785 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
33825 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
33890 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
33930 ATATCCTTCGTTGTGAAGTTGAAATCGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
33995 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
34035 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
34100 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
34140 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
34205 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
34245 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGT
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
*
34310 CCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCA
66 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
34350 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
34383 GGTAAAACCT
Statistics
Matches: 645, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 645 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAACCAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
Found at i:41797 original size:21 final size:22
Alignment explanation
Indices: 41772--41820 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
41762 TCTTTATTTG
*
41772 ATCTTCTAATATTTTTATCTTT
1 ATCTTCTAATATTTTTAGCTTT
* *
41794 -TCTTC-CATCTTTTTAGCTTT
1 ATCTTCTAATATTTTTAGCTTT
41814 ATCTTCT
1 ATCTTCT
41821 TCATCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
ATCTTCTAATATTTTTAGCTTT
Found at i:45767 original size:14 final size:14
Alignment explanation
Indices: 45748--45789 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
45738 ATGTACATGT
45748 AAAATAAT-AATAAA
1 AAAATAATGAA-AAA
*
45762 AAAATAATGAAAAT
1 AAAATAATGAAAAA
45776 AAAATAA-GAAAAA
1 AAAATAATGAAAAA
45789 A
1 A
45790 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.24
14 17 0.68
15 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAATAATGAAAAA
Found at i:45945 original size:22 final size:22
Alignment explanation
Indices: 45920--45993 Score: 82
Period size: 21 Copynumber: 3.4 Consensus size: 22
45910 AAGAGGGAGG
45920 AAAAAATATAATAATAATAGAA
1 AAAAAATATAATAATAATAGAA
*
45942 AAAAAATA-AATAAATAAT-GTA
1 AAAAAATATAAT-AATAATAGAA
*
45963 AATAAATATAATAATAA-AGAA
1 AAAAAATATAATAATAATAGAA
45984 GTAAAAAATA
1 --AAAAAATA
45994 GGGTAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 19 0.44
22 17 0.40
23 7 0.16
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
AAAAAATATAATAATAATAGAA
Found at i:46043 original size:21 final size:21
Alignment explanation
Indices: 46018--46082 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
46008 ATGTGTACAT
46018 ATATACATATATATAAATATA
1 ATATACATATATATAAATATA
* *
46039 ATATAACACATAAATGAAATAATA
1 ATAT-ACATATATAT-AAAT-ATA
*
46063 CTATAC-TA-ATAATAAATATA
1 ATATACATATAT-ATAAATATA
46083 TACGAATGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
20 3 0.09
21 9 0.26
22 11 0.31
23 6 0.17
24 6 0.17
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATACATATATATAAATATA
Found at i:47243 original size:3 final size:3
Alignment explanation
Indices: 47235--47261 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
47225 ATACTTTGTA
47235 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
47262 GTCAGACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49116 original size:11 final size:12
Alignment explanation
Indices: 49083--49116 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
49073 AAGTTTGTTT
49083 TTTAATATATAA
1 TTTAATATATAA
49095 TTTATATATATAA
1 TTTA-ATATATAA
49108 TTTAA-ATAT
1 TTTAATATAT
49117 TTATGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 5 0.24
13 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAATATATAA
Found at i:55927 original size:21 final size:21
Alignment explanation
Indices: 55901--55952 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
55891 GGACCTATAA
* *
55901 TCCCGAGGGATGTCATATGTG
1 TCCCGAAGGATGTAATATGTG
*
55922 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTAATATGTG
*
55943 TCCCGTAGGA
1 TCCCGAAGGA
55953 CCTATCATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (21 bp):
TCCCGAAGGATGTAATATGTG
Found at i:56166 original size:46 final size:46
Alignment explanation
Indices: 56109--56213 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
56099 ATGTGTAACC
56109 ATGT-ATTTCATATCATATCACATGTATCACGTATTACACATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACACATTCAT
* * *
56154 ATGTCATTTCATATCATATCACATGTATTACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACACATTCAT
*
56200 ATATCATTTCATAT
1 ATGTCATTTCATAT
56214 ACTCACATAG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 4 0.07
46 51 0.93
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACACATTCAT
Found at i:56667 original size:35 final size:36
Alignment explanation
Indices: 56621--56690 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 36
56611 TTCATTTAGT
*
56621 GGGAATCGATACCCCCCAGGGG-GAATCTGTTCCCG
1 GGGAATCGATACCCCCCAGGGGAAAATCTGTTCCCG
56656 GGGAATCGATACCCCCCAGGGGAAAATCTGTTCCC
1 GGGAATCGATACCCCCCAGGGGAAAATCTGTTCCC
56691 CCTGCACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 22 0.67
36 11 0.33
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.17
Consensus pattern (36 bp):
GGGAATCGATACCCCCCAGGGGAAAATCTGTTCCCG
Found at i:61446 original size:12 final size:12
Alignment explanation
Indices: 61421--61461 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
61411 AAACTTTTTA
*
61421 AGATAGACAGAC
1 AGATAGATAGAC
*
61433 AGACAGATAGAC
1 AGATAGATAGAC
*
61445 AGATAGATAGAT
1 AGATAGATAGAC
61457 AGATA
1 AGATA
61462 TTGCTCCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (12 bp):
AGATAGATAGAC
Found at i:61461 original size:8 final size:8
Alignment explanation
Indices: 61421--61459 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
61411 AAACTTTTTA
61421 AGATAGAC
1 AGATAGAC
*
61429 AGACAGAC
1 AGATAGAC
61437 AGATAGAC
1 AGATAGAC
*
61445 AGATAGAT
1 AGATAGAC
61453 AGATAGA
1 AGATAGA
61460 TATTGCTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.10, G:0.26, T:0.13
Consensus pattern (8 bp):
AGATAGAC
Found at i:66372 original size:56 final size:56
Alignment explanation
Indices: 66300--66406 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
66290 ATATATATTG
66300 ATAGTTTGGAATGAAATTAAAATATTCAAAAGTTTG-GGATCAATTTAAAAGGGTC
1 ATAGTTTGGAATGAAATTAAAATATTCAAAAGTTTGAGGATCAATTTAAAAGGGTC
* ** * * * *
66355 ATAGTTTAGGGATGAAATTGGATTGTTTAAAAGTTTGAGGATTAATTTAAAA
1 ATAGTTT-GGAATGAAATTAAAATATTCAAAAGTTTGAGGATCAATTTAAAA
66407 TGAAAATCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 7 0.16
56 23 0.53
57 13 0.30
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (56 bp):
ATAGTTTGGAATGAAATTAAAATATTCAAAAGTTTGAGGATCAATTTAAAAGGGTC
Done.