Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006376.1 Hibiscus syriacus cultivar Beakdansim tig00015339_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: 98066
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:229 original size:54 final size:54
Alignment explanation
Indices: 147--321 Score: 271
Period size: 54 Copynumber: 3.2 Consensus size: 54
137 TCTGAATGAC
147 TTTGTTTCGGAGAAGTTGGTGACGGTTCTGGCAAAACAGATAACTGGAGCAGAT
1 TTTGTTTCGGAGAAGTTGGTGACGGTTCTGGCAAAACAGATAACTGGAGCAGAT
*
201 TTTGTTTCGGAGAAGTTGGTGACGGTTCTGGCAAAACAGATAATTGGAGCAGAT
1 TTTGTTTCGGAGAAGTTGGTGACGGTTCTGGCAAAACAGATAACTGGAGCAGAT
* * * * *
255 TTTGTTTCGGAGAACTTGGTGATGGTTCTGGCAAAACAGAT-TCGTGGACCCGAT
1 TTTGTTTCGGAGAAGTTGGTGACGGTTCTGGCAAAACAGATAAC-TGGAGCAGAT
*
309 TTTGTTTGGGAGA
1 TTTGTTTCGGAGA
322 TTCTGTATCC
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
54 112 1.00
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (54 bp):
TTTGTTTCGGAGAAGTTGGTGACGGTTCTGGCAAAACAGATAACTGGAGCAGAT
Found at i:11123 original size:25 final size:25
Alignment explanation
Indices: 11057--11125 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
11047 AAATCCTGCG
***
11057 TTTTTTAAACGGGGACAAATACCGA
1 TTTTTTAAACGGGGACGGGTACCGA
* *
11082 TTTTTTAAACGGTGACGGGTATCGA
1 TTTTTTAAACGGGGACGGGTACCGA
11107 TTTTTTAAACGGGGACGGG
1 TTTTTTAAACGGGGACGGG
11126 GGACCAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (25 bp):
TTTTTTAAACGGGGACGGGTACCGA
Found at i:15367 original size:93 final size:93
Alignment explanation
Indices: 15176--15350 Score: 235
Period size: 93 Copynumber: 1.9 Consensus size: 93
15166 CATGAAACTG
15176 AAAGAAAATTTCTTTGGTGGTTCGACAGAGAAATATGCCGGTGTGTTATATGGTCTTGGTGTTGA
1 AAAGAAAATTTCTTTGGTGGTTCGACAGAGAAATATGCCGGTGTGTTATATGGTCTTGGTGTTGA
* * *
15241 GAATGGACAGAGTGCTCCGTAATGATTC
66 GAATGGACAGAATACTCAGTAATGATTC
* * * * * *
15269 AAAGAAAATTTCTTTAGTTGG-TGGACTGAGAAATATGCTGGTTTGTTATATGGTTTTGGTTGTT
1 AAAGAAAATTTCTTT-GGTGGTTCGACAGAGAAATATGCCGGTGTGTTATATGGTCTTGG-TGTT
*
15333 GAGAATTGACAGAATACT
64 GAGAATGGACAGAATACT
15351 TATTAAATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
93 48 0.68
94 23 0.32
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.35
Consensus pattern (93 bp):
AAAGAAAATTTCTTTGGTGGTTCGACAGAGAAATATGCCGGTGTGTTATATGGTCTTGGTGTTGA
GAATGGACAGAATACTCAGTAATGATTC
Found at i:23790 original size:22 final size:22
Alignment explanation
Indices: 23751--23792 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
23741 ACAACAATGA
* *
23751 TATTTGTATATTTTATTTTAAC
1 TATTTGTATATATGATTTTAAC
*
23773 TATTTGTTTATATGATTTTA
1 TATTTGTATATATGATTTTA
23793 TTTTTCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (22 bp):
TATTTGTATATATGATTTTAAC
Found at i:26505 original size:12 final size:12
Alignment explanation
Indices: 26488--26514 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
26478 TATAATGGTT
26488 TTTCTTTGCTCA
1 TTTCTTTGCTCA
26500 TTTCTTTGCTCA
1 TTTCTTTGCTCA
26512 TTT
1 TTT
26515 TTCTCTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTCTTTGCTCA
Found at i:26575 original size:23 final size:23
Alignment explanation
Indices: 26541--26645 Score: 119
Period size: 23 Copynumber: 4.7 Consensus size: 23
26531 TCTCAAATTA
26541 ATGGAAGAAGAAGAAATGAGTTT
1 ATGGAAGAAGAAGAAATGAGTTT
* *
26564 ATGAAAGAAGAAGAAA-AATGTTT
1 ATGGAAGAAGAAGAAATGA-GTTT
* * *
26587 TTGGAAGAAAAAGAAATGGGTTT
1 ATGGAAGAAGAAGAAATGAGTTT
*
26610 ATGGAAG-A-AA-AAATGTGTTT
1 ATGGAAGAAGAAGAAATGAGTTT
26630 ATGGAAGAAGAAGAAA
1 ATGGAAGAAGAAGAAA
26646 GACACGCTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
20 16 0.24
21 3 0.04
22 4 0.06
23 45 0.66
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (23 bp):
ATGGAAGAAGAAGAAATGAGTTT
Found at i:26593 original size:20 final size:20
Alignment explanation
Indices: 26570--26641 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
26560 GTTTATGAAA
26570 GAAGAAGAAAAATGTTTTTG
1 GAAGAAGAAAAATGTTTTTG
* *
26590 GAAGAAAAAGAAATGGGTTTATG
1 GAAGAAGAA-AAAT--GTTTTTG
26613 GAAG-A-AAAAATGTGTTTATG
1 GAAGAAGAAAAATGT-TTT-TG
26633 GAAGAAGAA
1 GAAGAAGAA
26642 GAAAGACACG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 18 0.43
21 7 0.17
22 3 0.07
23 10 0.24
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.24
Consensus pattern (20 bp):
GAAGAAGAAAAATGTTTTTG
Found at i:26610 original size:46 final size:43
Alignment explanation
Indices: 26541--26645 Score: 133
Period size: 46 Copynumber: 2.4 Consensus size: 43
26531 TCTCAAATTA
26541 ATGGAAGAAGAAGAAATGAGTTTATGAAAGAAGAAGAAAAATGT-TTT
1 ATGGAAGAAGAAGAAATGAGTTTATG---GAAG-A-AAAAATGTGTTT
* *
26588 -TGGAAGAAAAAGAAATGGGTTTATGGAAGAAAAAATGTGTTT
1 ATGGAAGAAGAAGAAATGAGTTTATGGAAGAAAAAATGTGTTT
26630 ATGGAAGAAGAAGAAA
1 ATGGAAGAAGAAGAAA
26646 GACACGCTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
41 8 0.15
42 4 0.08
43 18 0.34
46 23 0.43
ACGTcount: A:0.50, C:0.00, G:0.28, T:0.22
Consensus pattern (43 bp):
ATGGAAGAAGAAGAAATGAGTTTATGGAAGAAAAAATGTGTTT
Found at i:28025 original size:18 final size:19
Alignment explanation
Indices: 28002--28038 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
27992 CCAGTAATCC
28002 TATTCTC-TGGTAATCTTT
1 TATTCTCATGGTAATCTTT
28020 TATTCTCATTGGTAATCTT
1 TATTCTCA-TGGTAATCTT
28039 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.54
Consensus pattern (19 bp):
TATTCTCATGGTAATCTTT
Found at i:41695 original size:44 final size:44
Alignment explanation
Indices: 41622--41708 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
41612 AATATTATGT
*
41622 TTTGTTTCTATTTTGACAACGAATCATTAATTTTAATTGTTGAC
1 TTTGTTTCTATTTTGACAACAAATCATTAATTTTAATTGTTGAC
**
41666 TTTGTTTCTATTTTGATCATA-AAAT-ATTAATTTTGGTTGTTGA
1 TTTGTTTCTATTTTGA-CA-ACAAATCATTAATTTTAATTGTTGA
41709 ATTAATAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 32 0.84
45 5 0.13
46 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (44 bp):
TTTGTTTCTATTTTGACAACAAATCATTAATTTTAATTGTTGAC
Found at i:43094 original size:22 final size:22
Alignment explanation
Indices: 43053--43094 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43043 TTTGTTTTAG
*
43053 TCTACTTTTATAATACGATTGT
1 TCTACTTTTATAACACGATTGT
* *
43075 TCTACTTTTATGACATGATT
1 TCTACTTTTATAACACGATT
43095 TTGTTTATCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (22 bp):
TCTACTTTTATAACACGATTGT
Found at i:43394 original size:18 final size:18
Alignment explanation
Indices: 43371--43408 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
43361 ACTGAGATCG
43371 TTTGATACGTAAATTCTA
1 TTTGATACGTAAATTCTA
*
43389 TTTGATAGGTAAATTCTA
1 TTTGATACGTAAATTCTA
43407 TT
1 TT
43409 AGTTAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (18 bp):
TTTGATACGTAAATTCTA
Found at i:46530 original size:18 final size:19
Alignment explanation
Indices: 46495--46531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
46485 CACGGAATGT
46495 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
46515 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
46532 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:47271 original size:21 final size:20
Alignment explanation
Indices: 47245--47293 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
47235 TACTATGTTA
47245 TTTTAATTTTTTATATATATT
1 TTTTAATTTTTTATATATA-T
* *
47266 TTTTAATATTTTATTTATAT
1 TTTTAATTTTTTATATATAT
47286 TTTTAATT
1 TTTTAATT
47294 GAAAATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTAATTTTTTATATATAT
Found at i:57240 original size:3 final size:3
Alignment explanation
Indices: 57232--57282 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
57222 ATTAAACTTG
57232 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57280 TTA
1 TTA
57283 GTAGTAGTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58645 original size:25 final size:28
Alignment explanation
Indices: 58617--58678 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 28
58607 TTTGGTACTG
*
58617 CTTTTCTTATTTTTTGC-A-T-TTTTAT
1 CTTTTCTTATTTTTAGCTATTATTTTAT
58642 CTTTGT-TTATTTTTAGCTATTATTTTAT
1 CTTT-TCTTATTTTTAGCTATTATTTTAT
*
58670 GTTTTCTTA
1 CTTTTCTTA
58679 CACTTGGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 14 0.47
26 2 0.07
27 2 0.07
28 12 0.40
ACGTcount: A:0.15, C:0.10, G:0.06, T:0.69
Consensus pattern (28 bp):
CTTTTCTTATTTTTAGCTATTATTTTAT
Found at i:63813 original size:106 final size:106
Alignment explanation
Indices: 62437--63812 Score: 2061
Period size: 106 Copynumber: 13.0 Consensus size: 106
62427 GTATCGTGCC
* * * * * *
62437 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
62502 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* **
62543 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
62608 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
62649 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* *
62714 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
62755 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
62820 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
62861 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
62926 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
62967 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
63032 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
63073 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
63138 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
63179 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
63244 AATTTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
63285 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
63350 AATTTCAGAGCCAATTTCAACTTCATAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
63391 ACTCAAGACAACGCAAGTTCAACATCACGACGAAGGGACCACTGATTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
63456 AATTTCGGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
63497 AC-CCAAGACAACACAAGCTCAACTTCACGACAAAGGGGCGGCTGATTGTCAAT--A-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC
* * *
63556 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAATGATATTAG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
63596 ACTCGAGACAGCACAAGTTCAACTTCACAAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCAC-GACGAAGGGACCGCTGGTTGTCAATAAACAACTTCC
*
63661 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
63703 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
**
63768 GGTTTCAGAGCCAATTTCAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
63809 ACTC
1 ACTC
63813 GGAACAATGC
Statistics
Matches: 1165, Mismatches: 93, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
99 55 0.05
100 22 0.02
101 1 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 4 0.00
106 1012 0.87
107 61 0.05
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:66636 original size:29 final size:29
Alignment explanation
Indices: 66604--66672 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
66594 TCATATTAGT
* **
66604 CCTTAAATTTTTATTATGCTTCTTTTGAC
1 CCTTAAACTTTTATTACACTTCTTTTGAC
66633 CCTTAAACTTTTATTACACTTCTTTTGAC
1 CCTTAAACTTTTATTACACTTCTTTTGAC
*
66662 CCTCAAACTTT
1 CCTTAAACTTT
66673 ATTTTTGTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.04, T:0.49
Consensus pattern (29 bp):
CCTTAAACTTTTATTACACTTCTTTTGAC
Found at i:67616 original size:28 final size:28
Alignment explanation
Indices: 67595--67654 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
67585 TCGTTGAGCT
67595 AGTGTTTTAAGCATAATGTCGTGGAGTC
1 AGTGTTTTAAGCATAATGTCGTGGAGTC
*
67623 AGTGTTTTAAGCATTATGTCGTGGAGTC
1 AGTGTTTTAAGCATAATGTCGTGGAGTC
67651 AGTG
1 AGTG
67655 CTTGAAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.30, T:0.37
Consensus pattern (28 bp):
AGTGTTTTAAGCATAATGTCGTGGAGTC
Found at i:77554 original size:17 final size:16
Alignment explanation
Indices: 77534--77576 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
77524 GGCCGGATAT
*
77534 ATATATTTAA-ATTAA
1 ATATATATAATATTAA
77549 ATATATA-AATATTAA
1 ATATATATAATATTAA
77564 ATATATAT-ATATT
1 ATATATATAATATT
77577 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATATAATATTAA
Found at i:77570 original size:15 final size:15
Alignment explanation
Indices: 77544--77576 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
77534 ATATATTTAA
77544 ATTAAATATATAAAT
1 ATTAAATATATAAAT
*
77559 ATTAAATATATATAT
1 ATTAAATATATAAAT
77574 ATT
1 ATT
77577 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAAATATATAAAT
Found at i:77746 original size:34 final size:34
Alignment explanation
Indices: 77708--77774 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
77698 CCCATCCCCG
77708 TCCCCGTTTAACATAAACAGTTTTCCCCGTCCCA
1 TCCCCGTTTAACATAAACAGTTTTCCCCGTCCCA
* * *
77742 TCCCCGTTTAGCATAAACGGTTTTTCCCGTCCC
1 TCCCCGTTTAACATAAACAGTTTTCCCCGTCCC
77775 CGTTTAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.19, C:0.37, G:0.12, T:0.31
Consensus pattern (34 bp):
TCCCCGTTTAACATAAACAGTTTTCCCCGTCCCA
Found at i:77779 original size:29 final size:30
Alignment explanation
Indices: 77704--77781 Score: 86
Period size: 34 Copynumber: 2.5 Consensus size: 30
77694 GTCCCCCATC
77704 CCCGTCCCCGTTTAACATAAACAGTTTTCCCCGT
1 CCCGTCCCCGTTTAACATAAACAGTTTT---C-T
* * *
77738 CCCATCCCCGTTTAGCATAAACGGTTTT-T
1 CCCGTCCCCGTTTAACATAAACAGTTTTCT
77767 CCCGTCCCCGTTTAA
1 CCCGTCCCCGTTTAA
77782 TTCGGTTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 14 0.36
34 25 0.64
ACGTcount: A:0.19, C:0.37, G:0.13, T:0.31
Consensus pattern (30 bp):
CCCGTCCCCGTTTAACATAAACAGTTTTCT
Found at i:78160 original size:15 final size:15
Alignment explanation
Indices: 78140--78179 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
78130 TCTCTTTCAA
* *
78140 TTATTTATTTTTATT
1 TTATTTAATTTTAGT
78155 TTATTTAATTTTAGT
1 TTATTTAATTTTAGT
*
78170 TTATTCAATT
1 TTATTTAATT
78180 AAATTCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (15 bp):
TTATTTAATTTTAGT
Found at i:78338 original size:21 final size:22
Alignment explanation
Indices: 78299--78339 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
78289 TATTATTTTA
*
78299 TTTATTTAAATTGAGAATTAGG
1 TTTATTTAAATTGACAATTAGG
*
78321 TTTATTT-ATTTGACAATTA
1 TTTATTTAAATTGACAATTA
78340 CCGATGCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTATTTAAATTGACAATTAGG
Found at i:81866 original size:24 final size:24
Alignment explanation
Indices: 81834--81889 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
81824 ATCCGACCGA
81834 TCGCCTCGGGAGGCGACTCTTTCC
1 TCGCCTCGGGAGGCGACTCTTTCC
81858 TCGCCTCGGGAGGCGACTCTTTCC
1 TCGCCTCGGGAGGCGACTCTTTCC
81882 TCGCCTCG
1 TCGCCTCG
81890 TGAAATCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.07, C:0.39, G:0.29, T:0.25
Consensus pattern (24 bp):
TCGCCTCGGGAGGCGACTCTTTCC
Found at i:87670 original size:59 final size:60
Alignment explanation
Indices: 87548--87677 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 60
87538 TTGGGGATCG
* *
87548 ATTTAAAATGATGGTCATAATTTGGGAATGAAATTGAAATATTCAAAAGTTTGAGGACTA
1 ATTTAAAATGATAGTCATAATTTGGGAATGAAATTGAAATATTCAAAAGTTTGAGGACCA
* * * * *
87608 ATTTAGAATGATATTCATAGTTTAGGG-ATG-AATTGGAATATTTAAAAGTTT-AGAGACCA
1 ATTTAAAATGATAGTCATAATTT-GGGAATGAAATTGAAATATTCAAAAGTTTGAG-GACCA
87667 ATTTAAAATGA
1 ATTTAAAATGA
87678 GAGTTGTACA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.03
59 33 0.55
60 22 0.37
61 3 0.05
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (60 bp):
ATTTAAAATGATAGTCATAATTTGGGAATGAAATTGAAATATTCAAAAGTTTGAGGACCA
Found at i:88350 original size:31 final size:30
Alignment explanation
Indices: 88276--88377 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 30
88266 AAATAATAAT
*
88276 ATATTTAGATAAA-TTAGATGATTATTTTATA
1 ATATTTA-ATAAATTTA-ATAATTATTTTATA
* *
88307 ATATTATGATAAATTTAATAATTATTTTATT
1 ATATT-TAATAAATTTAATAATTATTTTATA
* *
88338 ATAATTTAATAAATTTAATTATTATTTAATA
1 AT-ATTTAATAAATTTAATAATTATTTTATA
88369 A-A-TTAATAA
1 ATATTTAATAA
88378 GTACAATGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.11
29 1 0.02
31 46 0.75
32 7 0.11
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (30 bp):
ATATTTAATAAATTTAATAATTATTTTATA
Found at i:88358 original size:20 final size:20
Alignment explanation
Indices: 88318--88372 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
88308 TATTATGATA
*
88318 AATTTAATAATTATTTTATTAT
1 AATTTAATAA--ATTTAATTAT
88340 AATTTAATAAATTTAATTAT
1 AATTTAATAAATTTAATTAT
*
88360 TATTTAATAAATT
1 AATTTAATAAATT
88373 AATAAGTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 21 0.68
22 10 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTAATAAATTTAATTAT
Done.