Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003595.1 Hibiscus syriacus cultivar Beakdansim tig00007594_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: 116349
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:20649 original size:2 final size:2
Alignment explanation
Indices: 20642--20668 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20632 AATAAAAGTG
20642 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20669 CAAAATAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32343 original size:42 final size:42
Alignment explanation
Indices: 32285--32364 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
32275 AAAAACGTCA
* *
32285 CAAAAGGTGTGATATATAACGGCGTTTTTTATACAAACTGCG
1 CAAAAGGTCTGATATATAACGGCATTTTTTATACAAACTGCG
* * *
32327 CAAAAGGTCTGGTATATAGCGGCATTTTTTGTACAAAC
1 CAAAAGGTCTGATATATAACGGCATTTTTTATACAAAC
32365 GCAGGTATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (42 bp):
CAAAAGGTCTGATATATAACGGCATTTTTTATACAAACTGCG
Found at i:39538 original size:22 final size:22
Alignment explanation
Indices: 39513--39564 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
39503 TGTTCACGTT
*
39513 TTCAAAAGCTGTTATTTTCCTA
1 TTCAAAAGCTATTATTTTCCTA
*
39535 TTCAAAAGCTATTATTTTTCTA
1 TTCAAAAGCTATTATTTTCCTA
*
39557 TTCGAAAG
1 TTCAAAAG
39565 TAGAAAACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (22 bp):
TTCAAAAGCTATTATTTTCCTA
Found at i:40270 original size:82 final size:82
Alignment explanation
Indices: 40158--40363 Score: 229
Period size: 82 Copynumber: 2.5 Consensus size: 82
40148 GATAAATACC
* * * *
40158 GCTAAATTACTACTCTATAACATCATTTGTTGAACAAATACCACTATAAACAACCCTATTAC-GA
1 GCTAAATTACTACTCTATTACAGCGTTTGTTGAA-AAACACCACTATAAACAACCCTATT-CTGA
*
40222 CGTTTGT-ATAAAAACACT
64 CGTTTGTGATAAAAACACG
* ** *
40240 GCTAAATTACTACTCTATTAC-GACGTTTGTTGAAAAACGCCACTATAAACAACTTTATTCTGGC
1 GCTAAATTACTACTCTATTACAG-CGTTTGTTGAAAAACACCACTATAAACAACCCTATTCTGAC
* * *
40304 GTTTGTGCTATAAACGCG
65 GTTTGTGATAAAAACACG
* *
40322 GCTAAATTACCACTCTATTGCAGCGTTTGTTGGAAAAACACC
1 GCTAAATTACTACTCTATTACAGCGTTTGTT-GAAAAACACC
40364 GCTAAAATAT
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
80 1 0.01
81 29 0.28
82 64 0.62
83 10 0.10
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (82 bp):
GCTAAATTACTACTCTATTACAGCGTTTGTTGAAAAACACCACTATAAACAACCCTATTCTGACG
TTTGTGATAAAAACACG
Found at i:41733 original size:21 final size:23
Alignment explanation
Indices: 41699--41741 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
41689 ATATATTATC
41699 TTTGTTTTTATTGTCTT-AATTA
1 TTTGTTTTTATTGTCTTGAATTA
*
41721 TTTG-TTTTCTTGTCTTGAATT
1 TTTGTTTTTATTGTCTTGAATT
41742 TCATCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (23 bp):
TTTGTTTTTATTGTCTTGAATTA
Found at i:42778 original size:16 final size:17
Alignment explanation
Indices: 42746--42778 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42736 GTGAGGTTTC
*
42746 TTGTTTTATTTTCTTTT
1 TTGTTTAATTTTCTTTT
42763 TTGTTTAATTTT-TTTT
1 TTGTTTAATTTTCTTTT
42779 CTTTGAGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (17 bp):
TTGTTTAATTTTCTTTT
Found at i:43045 original size:18 final size:20
Alignment explanation
Indices: 43006--43045 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42996 AGGCGAGTAC
*
43006 AAACTCTGTTTCAAATACCA
1 AAACTCTGTTGCAAATACCA
43026 AAACTCT-TTGCAAA-ACCA
1 AAACTCTGTTGCAAATACCA
43044 AA
1 AA
43046 TTTCACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (20 bp):
AAACTCTGTTGCAAATACCA
Found at i:45844 original size:23 final size:22
Alignment explanation
Indices: 45814--45858 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
45804 TAAATATTAA
*
45814 AATTAATTATTAAGTAATAAAT
1 AATTAATTATTAAATAATAAAT
*
45836 AATTAAATTCTTAAATAATAAAT
1 AATT-AATTATTAAATAATAAAT
45859 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTAATTATTAAATAATAAAT
Found at i:45901 original size:26 final size:26
Alignment explanation
Indices: 45849--45909 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
45839 TAAATTCTTA
* *
45849 AATAATAAATTATTTTTAATGATATT
1 AATAATAAATTATTTGTAATGAAATT
45875 AATAATAAATTATTATGTAAT-AAATT
1 AATAATAAATTATT-TGTAATGAAATT
*
45901 -ATATTAAAT
1 AATAATAAAT
45910 ATAGAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.26
26 18 0.58
27 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
AATAATAAATTATTTGTAATGAAATT
Found at i:45922 original size:64 final size:63
Alignment explanation
Indices: 45807--45930 Score: 146
Period size: 64 Copynumber: 2.0 Consensus size: 63
45797 TTATAAATAA
* * *
45807 ATATTAAAATTAATTATTAAGTAATAAATAATTAAATTCTTAAATAATAAATTATTTTTAATG
1 ATATTAAAATAAATTATTAAGTAATAAATAATTAAATTCATAAATAATAAATTATATTTAATG
* *
45870 ATATTAATAATAAATTATTATGTAATAAATTATATTAAA-T-ATAGAAT-TTAAATTATATTTA
1 ATATTAA-AATAAATTATTAAGTAATAAA-TA-ATTAAATTCATA-AATAATAAATTATATTTA
45931 CTTTTAAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
63 7 0.13
64 33 0.63
65 6 0.12
66 6 0.12
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (63 bp):
ATATTAAAATAAATTATTAAGTAATAAATAATTAAATTCATAAATAATAAATTATATTTAATG
Found at i:57717 original size:21 final size:21
Alignment explanation
Indices: 57648--57707 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
57638 ACTACCATGA
57648 TCTCGGATCGAGAGACTCTAG
1 TCTCGGATCGAGAGACTCTAG
57669 TCTCGGATCGAGAGACTCTAG
1 TCTCGGATCGAGAGACTCTAG
*
57690 TCTCGGATCAAGAGACTC
1 TCTCGGATCGAGAGACTC
57708 CTCTCTCGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (21 bp):
TCTCGGATCGAGAGACTCTAG
Found at i:61942 original size:83 final size:83
Alignment explanation
Indices: 61840--62119 Score: 325
Period size: 83 Copynumber: 3.4 Consensus size: 83
61830 TGGTGTTTTC
*
61840 TTGAAAAAAGGCCACTATAGATGAACCCTATTGTAATGTTTGTATAAAAACACCGCTAAAGTACT
1 TTGAAAAAATGCCACTATAGATGAACCCTATTGTAATGTTTGTATAAAAACACCGCTAAAGTACT
*
61905 ACTTTGTTGCGGCGTTTG
66 ACTCTGTTGCGGCGTTTG
* * * *
61923 TTGAAAAAATGTCACTATAGATGAACCCTATTACGTCAT-TTT-TATACAAACACCGCTAGAGTA
1 TTGAAAAAATGCCACTATAGATGAACCCTATT--GTAATGTTTGTATAAAAACACCGCTAAAGTA
***
61986 CTACTCTGTCATGGCGTTTG
64 CTACTCTGTTGCGGCGTTTG
* * * *** * * *
62006 TTG-AGAAATGCGACTATGGATGAA-CCTATTGCGGTGTTTGTATTAAAACACCACTAAAGCACT
1 TTGAAAAAATGCCACTATAGATGAACCCTATTGTAATGTTTGTATAAAAACACCGCTAAAGTACT
*
62069 ACTCTGTTGCGGCGTTTA
66 ACTCTGTTGCGGCGTTTG
* *
62087 TTGAAAAAATGCCACTATAAATGAACCATATTG
1 TTGAAAAAATGCCACTATAGATGAACCCTATTG
62120 CGGCATTTTT
Statistics
Matches: 161, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
79 2 0.01
80 3 0.02
81 41 0.25
82 34 0.21
83 74 0.46
84 3 0.02
85 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (83 bp):
TTGAAAAAATGCCACTATAGATGAACCCTATTGTAATGTTTGTATAAAAACACCGCTAAAGTACT
ACTCTGTTGCGGCGTTTG
Found at i:62056 original size:164 final size:165
Alignment explanation
Indices: 61853--62152 Score: 449
Period size: 164 Copynumber: 1.8 Consensus size: 165
61843 AAAAAAGGCC
* * * *
61853 ACTATAGATGAACCCTATTGTAATGTTTGTATAAAAACACCGCTAAAGTACTACTTTGTTGCGGC
1 ACTATAGATGAACCCTATTGCAATGTTTGTATAAAAACACCACTAAAGCACTACTCTGTTGCGGC
* * * * * *
61918 GTTTGTTGAAAAAATGTCACTATAGATGAACCCTATTACGTCATTTTTATACAAACACCGCTAGA
66 GTTTATTGAAAAAATGCCACTATAAATGAACCATATTACGGCATTTTTATACAAACACCGCTAAA
61983 GTACTACTCTGTCATGGCGTTTGTTGAGAAATGCG
131 GTACTACTCTGTCATGGCGTTTGTTGAGAAATGCG
* ** *
62018 ACTATGGATGAA-CCTATTGCGGTGTTTGTATTAAAACACCACTAAAGCACTACTCTGTTGCGGC
1 ACTATAGATGAACCCTATTGCAATGTTTGTATAAAAACACCACTAAAGCACTACTCTGTTGCGGC
* *
62082 GTTTATTGAAAAAATGCCACTATAAATGAACCATATTGCGGCATTTTTATACAAACGCCGCTAAA
66 GTTTATTGAAAAAATGCCACTATAAATGAACCATATTACGGCATTTTTATACAAACACCGCTAAA
62147 GTACTA
131 GTACTA
62153 ATATGTCGTG
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
164 108 0.91
165 11 0.09
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (165 bp):
ACTATAGATGAACCCTATTGCAATGTTTGTATAAAAACACCACTAAAGCACTACTCTGTTGCGGC
GTTTATTGAAAAAATGCCACTATAAATGAACCATATTACGGCATTTTTATACAAACACCGCTAAA
GTACTACTCTGTCATGGCGTTTGTTGAGAAATGCG
Found at i:62073 original size:81 final size:82
Alignment explanation
Indices: 61840--62152 Score: 312
Period size: 83 Copynumber: 3.8 Consensus size: 82
61830 TGGTGTTTTC
* *** *
61840 TTGAAAAAAGGCCACTATAGATGAACCCTATTGTAATGTTTGTATAAAAACACCGCTAAAGTACT
1 TTGAAAAAATG-CACTATAGATGAACCCTATTGCGGTGTTTGTATTAAAACACCGCTAAAGTACT
*
61905 ACTTTGTTGCGGCGTTTG
65 ACTCTGTTGCGGCGTTTG
* * * *
61923 TTGAAAAAATGTCACTATAGATGAACCCTATTAC-GTCATTTTTA-TACAAACACCGCTAGAGTA
1 TTGAAAAAATG-CACTATAGATGAACCCTATTGCGGT-GTTTGTATTA-AAACACCGCTAAAGTA
***
61986 CTACTCTGTCATGGCGTTTG
63 CTACTCTGTTGCGGCGTTTG
* * * *
62006 TTG-AGAAATGCGACTATGGATGAA-CCTATTGCGGTGTTTGTATTAAAACACCACTAAAGCACT
1 TTGAAAAAATGC-ACTATAGATGAACCCTATTGCGGTGTTTGTATTAAAACACCGCTAAAGTACT
*
62069 ACTCTGTTGCGGCGTTTA
65 ACTCTGTTGCGGCGTTTG
* * ** * *
62087 TTGAAAAAATGCCACTATAAATGAACCATATTGCGGCATTTTTA-TACAAACGCCGCTAAAGTAC
1 TTGAAAAAATG-CACTATAGATGAACCCTATTGCGGTGTTTGTATTA-AAACACCGCTAAAGTAC
62151 TA
64 TA
62153 ATATGTCGTG
Statistics
Matches: 186, Mismatches: 35, Indels: 18
0.78 0.15 0.08
Matches are distributed among these distances:
81 45 0.24
82 41 0.22
83 100 0.54
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (82 bp):
TTGAAAAAATGCACTATAGATGAACCCTATTGCGGTGTTTGTATTAAAACACCGCTAAAGTACTA
CTCTGTTGCGGCGTTTG
Found at i:63639 original size:93 final size:94
Alignment explanation
Indices: 63503--63686 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 94
63493 ATATTTTAAA
* *
63503 ACATTAAAATATTTCATATAAGAAAAAAAATCATAAATAGTCATAATAAAATAGTAATAAAAGTA
1 ACATAAAAATACTTCATATAAGAAAAAAAATCATAAATAGTCATAATAAAATAGTAATAAAAGT-
* *
63568 T-TTTTACAAAAATATGTGGAACTCCACAC
65 TGTTATACAAAAACATGTGGAACTCCACAC
63597 ACATAAAAATACTTCATATAAG-AAAAAAATCATAAATAGTCATAATAAAATAGTAATAAAAGTT
1 ACATAAAAATACTTCATATAAGAAAAAAAATCATAAATAGTCATAATAAAATAGTAATAAAAGTT
63661 GTTATACAAAAACATGTGGAACTCCA
66 GTTATACAAAAACATGTGGAACTCCA
63687 AAAGCACGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
92 1 0.01
93 64 0.75
94 20 0.24
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.27
Consensus pattern (94 bp):
ACATAAAAATACTTCATATAAGAAAAAAAATCATAAATAGTCATAATAAAATAGTAATAAAAGTT
GTTATACAAAAACATGTGGAACTCCACAC
Found at i:64601 original size:18 final size:18
Alignment explanation
Indices: 64580--64616 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
64570 TATACATAGA
*
64580 AGCATGACGTGGGTAACG
1 AGCATGACATGGGTAACG
64598 AGCATGACATGGGTAACG
1 AGCATGACATGGGTAACG
64616 A
1 A
64617 ACAACCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (18 bp):
AGCATGACATGGGTAACG
Found at i:64691 original size:18 final size:17
Alignment explanation
Indices: 64668--64705 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
64658 CTTGCATATA
64668 AAACTTCTCAAATTAGTC
1 AAACTTCTCAAATT-GTC
*
64686 AAACTTTTCAAATTGTC
1 AAACTTCTCAAATTGTC
64703 AAA
1 AAA
64706 TTGGTCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (17 bp):
AAACTTCTCAAATTGTC
Found at i:74251 original size:60 final size:61
Alignment explanation
Indices: 74120--74258 Score: 164
Period size: 60 Copynumber: 2.3 Consensus size: 61
74110 ATACGTACAT
*
74120 TTTG-GAATGAAATTAGAATGTTTAAAAAGTTTGGCGACTAATTTAAAATGAAGATCATAG
1 TTTGAGAATGAAATTAGAATGTTTAAAAAGTCTGGCGACTAATTTAAAATGAAGATCATAG
* * *
74180 TTTGAGCATGAAATT-GAAATG-TTCAAAAGTCTGAG-GACTAATTTAGAATGATAG-TCATAG
1 TTTGAGAATGAAATTAG-AATGTTTAAAAAGTCTG-GCGACTAATTTAAAATGA-AGATCATAG
74240 TTT-ATGAATGAAATTAGAA
1 TTTGA-GAATGAAATTAGAA
74259 CAATTCAAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
59 1 0.01
60 50 0.74
61 17 0.25
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (61 bp):
TTTGAGAATGAAATTAGAATGTTTAAAAAGTCTGGCGACTAATTTAAAATGAAGATCATAG
Found at i:74269 original size:60 final size:60
Alignment explanation
Indices: 74155--74288 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 60
74145 AAAGTTTGGC
* * *
74155 GACTAATTTAAAATGAAGATCATAGTTTGAGCATGAAATTGAAATGTTCAAAAGTCTGAG-
1 GACTAATTTAGAATGAAGATCATAGTTTGAGAATGAAATTGAAATATTCAAAAGT-TGAGA
*
74215 GACTAATTTAGAATGATAG-TCATAGTTT-ATGAATGAAATTAGAACA-ATTC-AAAGTTTAGA
1 GACTAATTTAGAATGA-AGATCATAGTTTGA-GAATGAAATT-GAA-ATATTCAAAAGTTGAGA
*
74275 GATTAATTTAGAAT
1 GACTAATTTAGAAT
74289 AGGGTAAACT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
59 4 0.06
60 51 0.80
61 8 0.12
62 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.33
Consensus pattern (60 bp):
GACTAATTTAGAATGAAGATCATAGTTTGAGAATGAAATTGAAATATTCAAAAGTTGAGA
Found at i:81034 original size:2 final size:2
Alignment explanation
Indices: 80993--81020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80983 TAATGTTAGC
80993 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
81021 TGGTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89083 original size:20 final size:20
Alignment explanation
Indices: 89058--89096 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89048 ATATCATCAA
*
89058 ATTCATCCATTATCGATACT
1 ATTCATCCAGTATCGATACT
*
89078 ATTCATCTAGTATCGATAC
1 ATTCATCCAGTATCGATAC
89097 CCTAACCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (20 bp):
ATTCATCCAGTATCGATACT
Found at i:100261 original size:29 final size:28
Alignment explanation
Indices: 100206--100277 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
100196 CATCGAAAAA
* *
100206 AAAAAGAAAAAAAAGAACAGCAGTATTTC
1 AAAAAGAAAGAAAA-AACAGAAGTATTTC
* *
100235 AAAAAGAAAGAAAAAATAGAAGTTATTTG
1 AAAAAGAAAGAAAAAACAGAAG-TATTTC
*
100264 GAAAA-AAAGAAAAA
1 AAAAAGAAAGAAAAA
100278 GAAAAAAGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.14
Consensus pattern (28 bp):
AAAAAGAAAGAAAAAACAGAAGTATTTC
Found at i:105981 original size:26 final size:26
Alignment explanation
Indices: 105923--105985 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
105913 TTTTAAATTG
105923 AGTCAAATCAAAAAGATCAATTATCA
1 AGTCAAATCAAAAAGATCAATTATCA
** * *
105949 AAACAAATCAAAAA-ATTAATTTTTCA
1 AGTCAAATCAAAAAGATCAA-TTATCA
105975 AGTCAAATCAA
1 AGTCAAATCAA
105986 TTTTTGTTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (26 bp):
AGTCAAATCAAAAAGATCAATTATCA
Found at i:110108 original size:18 final size:17
Alignment explanation
Indices: 110085--110133 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
110075 GTGACTTAAA
*
110085 AAACCCTAAACCTGACC
1 AAACCCTAAACCTAACC
* *
110102 TAAACCCTAAGCTCAAACC
1 -AAACCCTAAAC-CTAACC
110121 AAACCCTAAACCT
1 AAACCCTAAACCT
110134 TAATCTCGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 1 0.04
18 20 0.80
19 4 0.16
ACGTcount: A:0.43, C:0.39, G:0.04, T:0.14
Consensus pattern (17 bp):
AAACCCTAAACCTAACC
Found at i:112231 original size:17 final size:17
Alignment explanation
Indices: 112209--112243 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
112199 CTTCCCAAAG
112209 ACTTTGCACTAGAGATC
1 ACTTTGCACTAGAGATC
*
112226 ACTTTGCACTAGGGATC
1 ACTTTGCACTAGAGATC
112243 A
1 A
112244 AGCAACAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (17 bp):
ACTTTGCACTAGAGATC
Found at i:115851 original size:14 final size:14
Alignment explanation
Indices: 115832--115882 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
115822 AAGTTAATGG
*
115832 GTTGACTCATACGA
1 GTTGACTCAAACGA
*
115846 GTTGACTCAAATGA
1 GTTGACTCAAACGA
* *
115860 TTTGACTCAGATCGA
1 GTTGACTCA-AACGA
115875 GTTGACTC
1 GTTGACTC
115883 GGTGAATGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (14 bp):
GTTGACTCAAACGA
Done.