Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000241.1 Hibiscus syriacus cultivar Beakdansim tig00000415_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: 68541
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2311 original size:40 final size:41
Alignment explanation
Indices: 2250--2327 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
2240 ATCATCATAA
* *
2250 TTAGCTATTTTTAATTGTTTGGAGAAGTT-TAATAGGAGTT
1 TTAGCTATTTTTAATTCTTTGGAAAAGTTATAATAGGAGTT
* *
2290 TTAGCTATTTTTTATTCTTTGGAAAAGTTATAGTAGGA
1 TTAGCTATTTTTAATTCTTTGGAAAAGTTATAATAGGA
2328 ATATTTGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 26 0.79
41 7 0.21
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (41 bp):
TTAGCTATTTTTAATTCTTTGGAAAAGTTATAATAGGAGTT
Found at i:27140 original size:46 final size:45
Alignment explanation
Indices: 27029--27142 Score: 117
Period size: 46 Copynumber: 2.5 Consensus size: 45
27019 TATGTTGTAT
*
27029 TAATTATGTACTTTAAAAATATCATTTATTTAATGTGTTATAAGAC
1 TAATTATGTAC-TTAATAATATCATTTATTTAATGTGTTATAAGAC
* *
27075 TAATTATGTAATTAGATAATATCATTATATTATTAT-TGTT-TACA-AC
1 TAATTATGTACTTA-ATAATATCATT-TATT-TAATGTGTTATA-AGAC
*
27121 TAATTTTGTACTTGAATAATAT
1 TAATTATGTACTT-AATAATAT
27143 TATTGTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
45 3 0.05
46 42 0.72
47 10 0.17
48 3 0.05
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (45 bp):
TAATTATGTACTTAATAATATCATTTATTTAATGTGTTATAAGAC
Found at i:27171 original size:41 final size:42
Alignment explanation
Indices: 27123--27206 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
27113 TTTACAACTA
* * *
27123 ATTTTGTACTTGAATAATATTATTGTTTT-GTGTGGTGTATT
1 ATTTTGTACTTAAACAATATTATTGTTTTAGTATGGTGTATT
* *
27164 ATTTTGTATTTAAACAATATTATTGTTTTAGTATTGTGTATT
1 ATTTTGTACTTAAACAATATTATTGTTTTAGTATGGTGTATT
27206 A
1 A
27207 CTAATTGAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 26 0.70
42 11 0.30
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.56
Consensus pattern (42 bp):
ATTTTGTACTTAAACAATATTATTGTTTTAGTATGGTGTATT
Found at i:27529 original size:2 final size:2
Alignment explanation
Indices: 27522--27565 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
27512 AAATATTTTA
27522 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
27564 AT
1 AT
27566 TTTGTAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32984 original size:3 final size:3
Alignment explanation
Indices: 32976--33035 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
32966 TTCCTAAATA
*
32976 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33024 AAT AAT AAT AAT
1 AAT AAT AAT AAT
33036 CAAACTAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:33739 original size:21 final size:21
Alignment explanation
Indices: 33715--33760 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
33705 CGTGTATAGT
33715 TTATATAGATTGA-AATATATA
1 TTATATA-ATTGAGAATATATA
* *
33736 TTATATATTTTAGAATATATA
1 TTATATAATTGAGAATATATA
33757 TTAT
1 TTAT
33761 TTATATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TTATATAATTGAGAATATATA
Found at i:34142 original size:25 final size:25
Alignment explanation
Indices: 34113--34173 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
34103 ATCATTGGCT
34113 GCGCACACTTCAAAGCCATCATAAA
1 GCGCACACTTCAAAGCCATCATAAA
34138 GCGCACACTTCAAAGCCATCATAAA
1 GCGCACACTTCAAAGCCATCATAAA
*
34163 GCACCACACTT
1 GC-GCACACTT
34174 AGTAGGGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.38, C:0.34, G:0.11, T:0.16
Consensus pattern (25 bp):
GCGCACACTTCAAAGCCATCATAAA
Found at i:38487 original size:64 final size:64
Alignment explanation
Indices: 38418--38622 Score: 198
Period size: 64 Copynumber: 3.2 Consensus size: 64
38408 GCATTGATAA
** * *
38418 TGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGTAATTCATGCATCAATGCATAAGTA
1 TGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTCATGCATCAATGCATAAGGA
38481 G
64 G
* ** *
38482 TGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGCATCGATGCATAAGGAG
1 TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCAATGCATAAGGAG
** ** * ** * * * * *
38546 TGCATCGATGCATCCCAGCAATAATATTACATCGAATACCTTTTATGCACCGATGCATCAGTAG
1 TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCAATGCATAAGGAG
38610 TGCATCGATGCAT
1 TGCATCGATGCAT
38623 ACCTTCATTA
Statistics
Matches: 118, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
64 112 0.95
65 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGCATCAATGCATAAGGAG
Found at i:39274 original size:31 final size:31
Alignment explanation
Indices: 39236--39418 Score: 286
Period size: 31 Copynumber: 6.0 Consensus size: 31
39226 AGGGTCGAGG
39236 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
39267 GTTTACCTATGTTATTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
39298 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
39329 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
39360 GTTTACCTATGTTCTTCGGGAC--AT--ACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
39387 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
39418 G
1 G
39419 GTCATTCGGG
Statistics
Matches: 142, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
27 22 0.15
28 1 0.01
29 4 0.03
31 115 0.81
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:43059 original size:64 final size:64
Alignment explanation
Indices: 42991--43195 Score: 216
Period size: 64 Copynumber: 3.2 Consensus size: 64
42981 GCATTGATAA
** *
42991 TGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGTAATTCATGCATCGATGCATAAGTA
1 TGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGTAATTCATGCATCGATGCATAAGGA
43054 G
64 G
* **
43055 TGCATCGATGCATCCCATTAATAATGAAACATCGAATGTAATTGGTGCATCGATGCATAAGGAG
1 TGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATTCATGCATCGATGCATAAGGAG
** ** **** * * * *
43119 TGCATCGATGCATCCCAGCAATAATATTACATCGAATACCTTTTATGCACCGATGCATCAGTAG
1 TGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATTCATGCATCGATGCATAAGGAG
43183 TGCATCGATGCAT
1 TGCATCGATGCAT
43196 ACCTTCATTA
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
64 113 0.95
65 6 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATTCATGCATCGATGCATAAGGAG
Found at i:43842 original size:31 final size:31
Alignment explanation
Indices: 43804--43990 Score: 322
Period size: 31 Copynumber: 6.0 Consensus size: 31
43794 ATGGTCGAGG
43804 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
43835 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
43866 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
43897 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
43928 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
43959 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
43990 G
1 G
43991 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:54888 original size:2 final size:2
Alignment explanation
Indices: 54883--54950 Score: 50
Period size: 2 Copynumber: 34.0 Consensus size: 2
54873 TTTTTAAAAG
* * *
54883 TA TA TA TA TA TA TA TA TA TA TA TA GTT TT TA AA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
54925 TA TA GTT TT TA AA TA TA TA T- TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA
54951 GTTTTGAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
1 2 0.04
2 50 0.93
3 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:54912 original size:35 final size:30
Alignment explanation
Indices: 54858--54928 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 30
54848 ATTTTTGAAG
*
54858 TATATATGTTATATATTTTTAAAAGTATATAT
1 TATATATATTATATATTTTT-AAA-TATATAT
54890 ATATATATATATATATAGTTTTTAAATATATAT
1 -TATATATAT-TATATA-TTTTTAAATATATAT
54923 TATATA
1 TATATA
54929 GTTTTTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 6 0.17
33 15 0.43
34 9 0.26
35 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (30 bp):
TATATATATTATATATTTTTAAATATATAT
Found at i:54929 original size:22 final size:22
Alignment explanation
Indices: 54892--55036 Score: 172
Period size: 22 Copynumber: 6.6 Consensus size: 22
54882 GTATATATAT
54892 ATATATATATATATAGTTTTTAA
1 ATATATAT-TATATAGTTTTTAA
54915 ATATATATTATATAGTTTTTAA
1 ATATATATTATATAGTTTTTAA
*
54937 ATATATATTATATAGTTTTGAA
1 ATATATATTATATAGTTTTTAA
*
54959 ATCTATATGTTATATA-TTTTT-A
1 A--TATATATTATATAGTTTTTAA
54981 A-ATATA-TATATAGTTTTTTAA
1 ATATATATTATATAG-TTTTTAA
* *
55002 ATATATATTATATAATTTTAAA
1 ATATATATTATATAGTTTTTAA
* *
55024 ATATGTATCATAT
1 ATATATATTATAT
55037 TATATATATA
Statistics
Matches: 107, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.06
19 4 0.04
20 5 0.05
21 2 0.02
22 60 0.56
23 18 0.17
24 12 0.11
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATATATTATATAGTTTTTAA
Found at i:54956 original size:102 final size:95
Alignment explanation
Indices: 54797--54992 Score: 284
Period size: 102 Copynumber: 2.0 Consensus size: 95
54787 ATAGTTTGAA
* *
54797 ATATATTATATATTTTAAAATATATATATAGATTTTAAAAATATATTATATATTTTTGAAGTATA
1 ATATATTATATATTTTAAAATATATATATAGATTTTAAAAATATATTATATAGTTTTGAAATATA
54862 TATGTTATATATTTTTAAAAGTATATATATAT
66 TATGTTATATATTTTT-AAA-TATATATATAT
* *
54894 ATATATATATATAGTTTTTAAATATATATTATATAGTTTTTAAATATATATTATATAGTTTTGAA
1 ATATAT-TATATA--TTTTAAA-ATATA-TATATAGATTTTAAAAATATATTATATAGTTTTGAA
*
54959 ATCTATATGTTATATATTTTTAAATATATATATA
61 ATATATATGTTATATATTTTTAAATATATATATA
54993 GTTTTTTAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
97 6 0.07
98 6 0.07
100 17 0.19
101 8 0.09
102 52 0.58
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.52
Consensus pattern (95 bp):
ATATATTATATATTTTAAAATATATATATAGATTTTAAAAATATATTATATAGTTTTGAAATATA
TATGTTATATATTTTTAAATATATATATAT
Found at i:56112 original size:20 final size:20
Alignment explanation
Indices: 56087--56130 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
56077 TGTAGATCCG
56087 GTATAAATGGTAAGTTCGAT
1 GTATAAATGGTAAGTTCGAT
*
56107 GTATAAATGGTAAGTTTGAT
1 GTATAAATGGTAAGTTCGAT
56127 GTAT
1 GTAT
56131 CTGATCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (20 bp):
GTATAAATGGTAAGTTCGAT
Found at i:56467 original size:20 final size:21
Alignment explanation
Indices: 56437--56477 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
56427 AAACATTAAA
*
56437 CTTCAACATTTTTTTCTTTTT
1 CTTCAACATTTTTTCCTTTTT
56458 CTTC-ACATTTTTTCCTTTTT
1 CTTCAACATTTTTTCCTTTTT
56478 TGCTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (21 bp):
CTTCAACATTTTTTCCTTTTT
Found at i:56478 original size:21 final size:22
Alignment explanation
Indices: 56437--56483 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
56427 AAACATTAAA
*
56437 CTTCAACATTTTTTTCTTTTT-
1 CTTCAACATTTTTTCCTTTTTG
56458 CTTC-ACATTTTTTCCTTTTTTG
1 CTTCAACATTTTTTCC-TTTTTG
56480 CTTC
1 CTTC
56484 TTTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.11, C:0.23, G:0.02, T:0.64
Consensus pattern (22 bp):
CTTCAACATTTTTTCCTTTTTG
Found at i:57699 original size:77 final size:77
Alignment explanation
Indices: 57605--57754 Score: 216
Period size: 77 Copynumber: 1.9 Consensus size: 77
57595 TTATTTAAAA
*
57605 TTTATTAAATTCTTATTTAATTAATT-CAAATTAAATATCCATT-AAAGACTTATAAT-ATGAAT
1 TTTATTAAACTCTTATTTAATT-ATTCCAAATTAAATATCCATTAAAAGACTTATAATCA-GAAT
57667 TACACTCTTTAATG
64 TACACTCTTTAATG
* *
57681 TTTACTTAAACTCTTATTTAATTATTCCAAATTAAATATCCATTAAAAGAGTTGTAATCAGAATT
1 TTTA-TTAAACTCTTATTTAATTATTCCAAATTAAATATCCATTAAAAGACTTATAATCAGAATT
*
57746 ACATTCTTT
65 ACACTCTTT
57755 TAGTACTATA
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
76 7 0.11
77 34 0.52
78 24 0.36
79 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (77 bp):
TTTATTAAACTCTTATTTAATTATTCCAAATTAAATATCCATTAAAAGACTTATAATCAGAATTA
CACTCTTTAATG
Found at i:58881 original size:10 final size:10
Alignment explanation
Indices: 58857--58910 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
58847 AGTGTACCTA
*
58857 AAAATATAAAG
1 AAAA-ATAAAT
58868 AAAAATAAAT
1 AAAAATAAAT
58878 AAAAAAGTAAAT
1 -AAAAA-TAAAT
*
58890 -AAAGTAAAT
1 AAAAATAAAT
58899 AAAAATAAAT
1 AAAAATAAAT
58909 AA
1 AA
58911 TAAAATGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 5 0.14
10 18 0.49
11 9 0.24
12 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:58888 original size:22 final size:21
Alignment explanation
Indices: 58855--58905 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
58845 CTAGTGTACC
58855 TAAAAATATAAAGAAAAATAAA
1 TAAAAATATAAA-AAAAATAAA
* *
58877 TAAAAA-AGTAAATAAAGTAAA
1 TAAAAATA-TAAAAAAAATAAA
58898 TAAAAATA
1 TAAAAATA
58906 AATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (21 bp):
TAAAAATATAAAAAAAATAAA
Found at i:58893 original size:9 final size:9
Alignment explanation
Indices: 58870--58901 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
58860 ATATAAAGAA
58870 AAATAAA-T
1 AAATAAAGT
58878 AAA-AAAGT
1 AAATAAAGT
58886 AAATAAAGT
1 AAATAAAGT
58895 AAATAAA
1 AAATAAA
58902 AATAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 3 0.14
8 7 0.32
9 12 0.55
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (9 bp):
AAATAAAGT
Found at i:62782 original size:13 final size:13
Alignment explanation
Indices: 62764--62797 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
62754 AGCATTGTGG
62764 AAAGAAAATAATA
1 AAAGAAAATAATA
*
62777 AAAGAAAATAATG
1 AAAGAAAATAATA
62790 AAAGAAAA
1 AAAGAAAA
62798 GTGGAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (13 bp):
AAAGAAAATAATA
Found at i:62937 original size:3 final size:3
Alignment explanation
Indices: 62929--62960 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
62919 TTCATAAATA
62929 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
62961 TAAACTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:66239 original size:65 final size:65
Alignment explanation
Indices: 66161--66285 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 65
66151 GCACCAATCT
* *
66161 ATGCATCGATGCACCATGAATTAAAATTG-AA-CATCGAATGCATTTCATGCATCGATGCACATA
1 ATGCACCGATGCACCAAGAATT-AAA-TGAAATCATCGAATGCATTTCATGCATCGATGCACATA
66224 CC
64 CC
* * ** *
66226 ATGCACCGATGCACTAAGGATTTTATGAAATCATCGAATGCATTTGATGCATCGATGCAC
1 ATGCACCGATGCACCAAGAATTAAATGAAATCATCGAATGCATTTCATGCATCGATGCAC
66286 CAGCCATGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
63 2 0.04
64 3 0.06
65 46 0.90
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (65 bp):
ATGCACCGATGCACCAAGAATTAAATGAAATCATCGAATGCATTTCATGCATCGATGCACATACC
Found at i:66293 original size:65 final size:65
Alignment explanation
Indices: 66190--66349 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
66180 ATTAAAATTG
* * *
66190 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCACCGATGCACTAAGGAT-TTTATG
1 AACATCGAATGCATTTAATGCATCGATGCACCATACCATGCACCAATACACTAAGGATATTT-TG
66253 A
65 A
* * * ** *
66254 AATCATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCAATACACTCTGGCTATTTTG
1 AA-CATCGAATGCATTTAATGCATCGATGCACCATACCATGCACCAATACACTAAGGATATTTTG
66318 A
65 A
*
66319 AACATCGAATGCACTTAATGCATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
66350 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 29 0.35
65 49 0.59
66 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTAATGCATCGATGCACCATACCATGCACCAATACACTAAGGATATTTTGA
Found at i:66349 original size:17 final size:18
Alignment explanation
Indices: 66321--66365 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
66311 TATTTTGAAA
66321 CATCGAATGCA-CTTAATG
1 CATCG-ATGCACCTTAATG
*
66339 CATCGATGCACTCTTAGTG
1 CATCGATGCAC-CTTAATG
66358 CATCGATG
1 CATCGATG
66366 TACTAAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 5 0.21
18 5 0.21
19 14 0.58
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (18 bp):
CATCGATGCACCTTAATG
Done.