Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005991.1 Hibiscus syriacus cultivar Beakdansim tig00014096_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: 153408
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:10560 original size:31 final size:31
Alignment explanation
Indices: 10525--10585 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
10515 TAAAGTCCCA
10525 AACATTTAGTCTGTTTGCAAAATGGCCCCCC
1 AACATTTAGTCTGTTTGCAAAATGGCCCCCC
* *
10556 AACATTTAGTCTGTTTGCAATATGGTCCCC
1 AACATTTAGTCTGTTTGCAAAATGGCCCCC
10586 GTCCATGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (31 bp):
AACATTTAGTCTGTTTGCAAAATGGCCCCCC
Found at i:20304 original size:21 final size:22
Alignment explanation
Indices: 20280--20330 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 22
20270 TTTTTATATG
20280 CCCTTTTTTATATATCAA-GGA
1 CCCTTTTTTATATATCAAGGGA
*
20301 CCCTTTTTTATATATCAAGGGG
1 CCCTTTTTTATATATCAAGGGA
20323 CCCTTTTT
1 CCCTTTTT
20331 ATGCATCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (22 bp):
CCCTTTTTTATATATCAAGGGA
Found at i:24265 original size:12 final size:12
Alignment explanation
Indices: 24250--24292 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
24240 TTATAATATT
24250 TTATAATTGATA
1 TTATAATTGATA
*
24262 TTATAAATTTATTA
1 TTAT-AATTGA-TA
*
24276 TTATAATTGATG
1 TTATAATTGATA
24288 TTATA
1 TTATA
24293 GCTATATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 10 0.38
13 10 0.38
14 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TTATAATTGATA
Found at i:24279 original size:26 final size:25
Alignment explanation
Indices: 24245--24326 Score: 83
Period size: 26 Copynumber: 3.2 Consensus size: 25
24235 ATTAATTATA
24245 ATATTTTATAATTGATATTATAAAT
1 ATATTTTATAATTGATATTATAAAT
* * **
24270 TTATTATTATAATTGATGTTATAGCT
1 ATATT-TTATAATTGATATTATAAAT
* * *
24296 ATATTCTTATTATTAATATTATAAGT
1 ATATT-TTATAATTGATATTATAAAT
24322 ATATT
1 ATATT
24327 AATTAGCACA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 4 0.09
26 41 0.91
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (25 bp):
ATATTTTATAATTGATATTATAAAT
Found at i:45787 original size:2 final size:2
Alignment explanation
Indices: 45780--45818 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45770 TTTAAAGCGA
45780 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
45819 CAATAATCAA
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:46072 original size:20 final size:20
Alignment explanation
Indices: 46047--46119 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
46037 TAGTTGAAAA
*
46047 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
46067 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
46088 TCGCGTTGC-ACTTTTCCATT
1 TCGCGTTGCGA-TTTTCCATT
46108 TCGCGTTGCGAT
1 TCGCGTTGCGAT
46120 AGTTGAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 26 0.65
21 14 0.35
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:46134 original size:21 final size:21
Alignment explanation
Indices: 46026--46136 Score: 93
Period size: 21 Copynumber: 5.4 Consensus size: 21
46016 GCGTTGCATT
*
46026 TCGCGTTGCAATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
46047 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
46067 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
46088 TCGCGTTGC-ACT-TTTCCATT
1 TCGCGTTGCGA-TAGTTGAAAA
46108 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
46129 TCGCGTTG
1 TCGCGTTG
46137 TCGTTGCGAT
Statistics
Matches: 65, Mismatches: 21, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
20 29 0.45
21 36 0.55
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:46136 original size:41 final size:41
Alignment explanation
Indices: 46022--46136 Score: 196
Period size: 41 Copynumber: 2.8 Consensus size: 41
46012 ATTCGCGTTG
* *
46022 CATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
46063 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGC-ACTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGA-TTTTC
46104 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTG
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTG
46137 TCGTTGCGAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
40 1 0.01
41 70 0.99
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:46945 original size:21 final size:21
Alignment explanation
Indices: 46921--47010 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 21
46911 ACTATCACAA
* *
46921 CGAATTTGTAAAATCGCGACG
1 CGAATTTGAAAAATCGCAACG
* *
46942 CGAA-ATGAAAAATCGTAACG
1 CGAATTTGAAAAATCGCAACG
* **
46962 CGAATTTCAACTATCGCAACG
1 CGAATTTGAAAAATCGCAACG
* *
46983 CGAA-ATGGAAAATCGCAACG
1 CGAATTTGAAAAATCGCAACG
47003 CGAATTTG
1 CGAATTTG
47011 CGATAGTGGA
Statistics
Matches: 52, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 31 0.60
21 21 0.40
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (21 bp):
CGAATTTGAAAAATCGCAACG
Found at i:46966 original size:41 final size:42
Alignment explanation
Indices: 46921--47011 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 42
46911 ACTATCACAA
* * *
46921 CGAATTTGTAA-AATCGCGACGCGAAATGAAAAATCGTAACG
1 CGAATTTGCAACAATCGCAACGCGAAATGAAAAATCGCAACG
* *
46962 CGAATTT-CAACTATCGCAACGCGAAATGGAAAATCGCAACG
1 CGAATTTGCAACAATCGCAACGCGAAATGAAAAATCGCAACG
47003 CGAATTTGC
1 CGAATTTGC
47012 GATAGTGGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 2 0.05
41 40 0.93
42 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (42 bp):
CGAATTTGCAACAATCGCAACGCGAAATGAAAAATCGCAACG
Found at i:47870 original size:33 final size:33
Alignment explanation
Indices: 47833--47897 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
47823 TTTAGACAAC
*
47833 GTTTTATCGAAAATATTAAACATTTTAAGTAAA
1 GTTTTACCGAAAATATTAAACATTTTAAGTAAA
* * *
47866 GTTTTACCGAAAATTTTAAATATTTTAGGTAA
1 GTTTTACCGAAAATATTAAACATTTTAAGTAA
47898 CGTCCAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (33 bp):
GTTTTACCGAAAATATTAAACATTTTAAGTAAA
Found at i:49665 original size:24 final size:24
Alignment explanation
Indices: 49638--49686 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
49628 ATTGCAGAGC
*
49638 GCTCTCTTCTGATGATGATGAAAA
1 GCTCTCTTCTGATGACGATGAAAA
**
49662 GCTCTCTTCTTCTGACGATGAAAA
1 GCTCTCTTCTGATGACGATGAAAA
49686 G
1 G
49687 AACTATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (24 bp):
GCTCTCTTCTGATGACGATGAAAA
Found at i:52185 original size:26 final size:27
Alignment explanation
Indices: 52138--52199 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
52128 TCTAATCATT
*
52138 TTAATTTTTTTAATAAATTTAAATTA-
1 TTAATTTTTATAATAAATTTAAATTAG
*
52164 TTAATTTTTATGATCAAA-TTAAATTAG
1 TTAATTTTTATAAT-AAATTTAAATTAG
*
52191 TTATTTTTT
1 TTAATTTTT
52200 TTATTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (27 bp):
TTAATTTTTATAATAAATTTAAATTAG
Found at i:62857 original size:32 final size:32
Alignment explanation
Indices: 62821--62889 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
62811 ATACAAGCAG
*
62821 TAGTAATATCCTATCTAATCACCTAATTAAAT
1 TAGTAATATCCTAACTAATCACCTAATTAAAT
* *
62853 TAGTAATATTCTAACTAATCTCCTAATTAAAT
1 TAGTAATATCCTAACTAATCACCTAATTAAAT
*
62885 AAGTA
1 TAGTA
62890 GTAGAATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (32 bp):
TAGTAATATCCTAACTAATCACCTAATTAAAT
Found at i:63202 original size:30 final size:30
Alignment explanation
Indices: 63167--63228 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
63157 TAAAAAAAAT
* * *
63167 TTCGAGGACTAAATTGGAATTTTAATTAAA
1 TTCGAGGACCAAAATGAAATTTTAATTAAA
*
63197 TTCGAGGACCAAAATGAAATTTTAGTTAAA
1 TTCGAGGACCAAAATGAAATTTTAATTAAA
63227 TT
1 TT
63229 TTTACCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (30 bp):
TTCGAGGACCAAAATGAAATTTTAATTAAA
Found at i:65033 original size:2 final size:2
Alignment explanation
Indices: 65026--65061 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
65016 CGGTTTTCTG
65026 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
65062 GTTTATCGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68430 original size:26 final size:26
Alignment explanation
Indices: 68400--68449 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
68390 ACTGAAAAGT
68400 GTATGTAGAACATGCTGAATTAGTGG
1 GTATGTAGAACATGCTGAATTAGTGG
68426 GTATGTAGAACATGCTGAATTAGT
1 GTATGTAGAACATGCTGAATTAGT
68450 TACTCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (26 bp):
GTATGTAGAACATGCTGAATTAGTGG
Found at i:77996 original size:161 final size:160
Alignment explanation
Indices: 77805--78125 Score: 617
Period size: 162 Copynumber: 2.0 Consensus size: 160
77795 TTTCCCAATT
77805 TATCCAGCTTAACAAAGGCCCAGCTGGAAT-ATTTTAAGAGGTGGAGAACCAAGTGGCCCATTAT
1 TATCCAGCTTAACAAAGGCCCAGCTGGAATAATTTTAAGAGGTGGAGAACCAAGTGGCCCATTAT
77869 CTGATGATTGGGCTATAGACCCATCAGCCGAAAAATTTGAAAATCTGCATCCCAAACCCGCGTAT
66 CTGATGATTGGGCTATAGACCCATCAGCCGAAAAATTTGAAAATCTGCATCCCAAACCCGCGTAT
77934 TCACCATAATTGTTATTCCCAAGATCCTGAC
131 TCACCATAATTG-TATTCCCAAGATCCTGAC
77965 TATCCAGCTTAACAAGAGGCCCAGCTGGAATAATTTTAAGAGGTGGAGAACCAAGTGGCCCATTA
1 TATCCAGCTTAACAA-AGGCCCAGCTGGAATAATTTTAAGAGGTGGAGAACCAAGTGGCCCATTA
78030 TCTGATGATTGGGCTATAGACCCATCAGCCGAAAAATTTGAAAATCTGCATCCCAAACCCGCGTA
65 TCTGATGATTGGGCTATAGACCCATCAGCCGAAAAATTTGAAAATCTGCATCCCAAACCCGCGTA
78095 TTCACCATAATTGTATTCCCAAGATCCTGAC
130 TTCACCATAATTGTATTCCCAAGATCCTGAC
78126 ACGCTGACTT
Statistics
Matches: 159, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 15 0.09
161 33 0.21
162 111 0.70
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (160 bp):
TATCCAGCTTAACAAAGGCCCAGCTGGAATAATTTTAAGAGGTGGAGAACCAAGTGGCCCATTAT
CTGATGATTGGGCTATAGACCCATCAGCCGAAAAATTTGAAAATCTGCATCCCAAACCCGCGTAT
TCACCATAATTGTATTCCCAAGATCCTGAC
Found at i:79339 original size:17 final size:17
Alignment explanation
Indices: 79317--79349 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
79307 TCCCTTAACT
79317 TCGTCGAGACACTCGTC
1 TCGTCGAGACACTCGTC
79334 TCGTCGAGACACTCGT
1 TCGTCGAGACACTCGT
79350 TACTGAGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.33, G:0.24, T:0.24
Consensus pattern (17 bp):
TCGTCGAGACACTCGTC
Found at i:88093 original size:77 final size:77
Alignment explanation
Indices: 87966--88121 Score: 285
Period size: 77 Copynumber: 2.0 Consensus size: 77
87956 TAGCATTTGA
*
87966 CACGACTCTTGTGATGCAAACACAAGCCACCAATCTAGAGCATTCATACTAGACTATTCGATGCA
1 CACGACGCTTGTGATGCAAACACAAGCCACCAATCTAGAGCATTCATACTAGACTATTCGATGCA
88031 GACAAACAAACC
66 GACAAACAAACC
* *
88043 CACGACGCTTGTGATGCAAACACAATCCACCAATCTAGAGCATTCATACTAGATTATTCGATGCA
1 CACGACGCTTGTGATGCAAACACAAGCCACCAATCTAGAGCATTCATACTAGACTATTCGATGCA
88108 GACAAACAAACC
66 GACAAACAAACC
88120 CA
1 CA
88122 AATAAAAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (77 bp):
CACGACGCTTGTGATGCAAACACAAGCCACCAATCTAGAGCATTCATACTAGACTATTCGATGCA
GACAAACAAACC
Found at i:90236 original size:19 final size:20
Alignment explanation
Indices: 90208--90245 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
90198 TTTTTGTTTA
*
90208 AAAAATAATAATA-AATAAT
1 AAAAACAATAATATAATAAT
90227 AAAAACAATAATATAATAA
1 AAAAACAATAATATAATAA
90246 ATATAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAACAATAATATAATAAT
Found at i:90367 original size:127 final size:127
Alignment explanation
Indices: 90221--90472 Score: 459
Period size: 127 Copynumber: 2.0 Consensus size: 127
90211 AATAATAATA
90221 AATAATAAAAACAATAATATAATAAATATAATCTTTAATTTTAATTCTAAAAATTTAACCATTAA
1 AATAATAAAAACAATAATATAATAAATATAATCTTTAATTTTAATTCTAAAAATTTAACCATTAA
*
90286 TATTTTAATATTACATTAATTTAAACTTGATCTACTTTTGAAGCGCCTTAATGTTTAAAAAT
66 TATTTTAATATTACATTAATTTAAACTTGATCTACTTTTGAAGCGCCTTAATATTTAAAAAT
*
90348 AATAATAAAAACAATAATATAATAAATTTAATCTTTAATTTTAATTCTAAAAATTTAACCATTAA
1 AATAATAAAAACAATAATATAATAAATATAATCTTTAATTTTAATTCTAAAAATTTAACCATTAA
* * *
90413 TATTTTAATATTATATTAATTTAAACTTGATTTACTTTTGAAGCGCTTTAATATTTAAAA
66 TATTTTAATATTACATTAATTTAAACTTGATCTACTTTTGAAGCGCCTTAATATTTAAAA
90473 GAATGGTTTT
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 120 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (127 bp):
AATAATAAAAACAATAATATAATAAATATAATCTTTAATTTTAATTCTAAAAATTTAACCATTAA
TATTTTAATATTACATTAATTTAAACTTGATCTACTTTTGAAGCGCCTTAATATTTAAAAAT
Found at i:90392 original size:27 final size:28
Alignment explanation
Indices: 90362--90423 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
90352 ATAAAAACAA
* *
90362 TAATATAATAAATTTAATC-TTTA-ATTT
1 TAATATAA-AAATTTAACCATTAATATTT
*
90389 TAATTCTAAAAATTTAACCATTAATATTT
1 TAA-TATAAAAATTTAACCATTAATATTT
90418 TAATAT
1 TAATAT
90424 TATATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
27 12 0.43
28 9 0.32
29 7 0.25
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
TAATATAAAAATTTAACCATTAATATTT
Found at i:93535 original size:18 final size:18
Alignment explanation
Indices: 93512--93565 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
93502 AAGTTGGCGC
93512 TGGAGATGGAGATGGTGT
1 TGGAGATGGAGATGGTGT
* *
93530 TGGAGACGGAG-TCGGGGT
1 TGGAGATGGAGAT-GGTGT
*
93548 TGGCGATGGAGATGGTGT
1 TGGAGATGGAGATGGTGT
93566 CGGTGTTGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.19, C:0.06, G:0.52, T:0.24
Consensus pattern (18 bp):
TGGAGATGGAGATGGTGT
Found at i:93577 original size:12 final size:12
Alignment explanation
Indices: 93560--93595 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
93550 GCGATGGAGA
93560 TGGTGTCGGTGT
1 TGGTGTCGGTGT
* *
93572 TGGTGTTGGCGT
1 TGGTGTCGGTGT
93584 TGGTGTCGGTGT
1 TGGTGTCGGTGT
93596 GGGGGTAGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.08, G:0.50, T:0.42
Consensus pattern (12 bp):
TGGTGTCGGTGT
Found at i:100403 original size:5 final size:5
Alignment explanation
Indices: 100393--100418 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
100383 ATATTACAGA
100393 GTTTT GTTTT GTTTT GTTTT GTTTT G
1 GTTTT GTTTT GTTTT GTTTT GTTTT G
100419 ATGAGACAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (5 bp):
GTTTT
Found at i:107709 original size:14 final size:14
Alignment explanation
Indices: 107690--107726 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
107680 TTGAGGCATT
107690 GATATGGACAATTG
1 GATATGGACAATTG
*
107704 GATATGAACAATTG
1 GATATGGACAATTG
*
107718 GACATGGAC
1 GATATGGAC
107727 TAGACTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (14 bp):
GATATGGACAATTG
Found at i:111449 original size:23 final size:24
Alignment explanation
Indices: 111405--111460 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
111395 TCTTTAGTAT
** *
111405 TTTTATATTTAATCTTTTAAAT-A
1 TTTTATATTTAAAATTTAAAATAA
111428 TTTTATATTTAAAATTTAAAATAA
1 TTTTATATTTAAAATTTAAAATAA
111452 TTTT-TATTT
1 TTTTATATTT
111461 TTTTAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTATATTTAAAATTTAAAATAA
Found at i:116943 original size:367 final size:367
Alignment explanation
Indices: 116265--116996 Score: 1455
Period size: 367 Copynumber: 2.0 Consensus size: 367
116255 ATTAGAGTGT
*
116265 CATGTCATTAATCACTCCATAAATTCAGTAAATACTGTTGTGATCAATGAAGCCATGCCAAACTC
1 CATGCCATTAATCACTCCATAAATTCAGTAAATACTGTTGTGATCAATGAAGCCATGCCAAACTC
116330 GTTTCTTTTAATGATCTAAACAATTGTTTGGTTGTACTTGGAACCAAATATATGAATCTTTGGCA
66 GTTTCTTTTAATGATCTAAACAATTGTTTGGTTGTACTTGGAACCAAATATATGAATCTTTGGCA
116395 CTATCAAGGAGTAACTAGTTAATTTCTAAGAAGTGATTTGACCAGGGGAAACGCTACTTAGGTAT
131 CTATCAAGGAGTAACTAGTTAATTTCTAAGAAGTGATTTGACCAGGGGAAACGCTACTTAGGTAT
116460 ATCAAAAGCAGCTATCAACTTCACCTGTAGGAAACTTTTATGAGACACATGAGTTACAAGGCGCA
196 ATCAAAAGCAGCTATCAACTTCACCTGTAGGAAACTTTTATGAGACACATGAGTTACAAGGCGCA
116525 AAATGCCACATTTGTAACAGTTGTAACCTTCTACTCTGAATATTTGGCTGACTGCCATTTTCCTC
261 AAATGCCACATTTGTAACAGTTGTAACCTTCTACTCTGAATATTTGGCTGACTGCCATTTTCCTC
116590 CATTTAATGTGGAACTGATCTTAATTATATCGTAATTGAAGC
326 CATTTAATGTGGAACTGATCTTAATTATATCGTAATTGAAGC
116632 CATGCCATTAATCACTCCATAAATTCAGTAAATACTGTTGTGATCAATGAAGCCATGCCAAACTC
1 CATGCCATTAATCACTCCATAAATTCAGTAAATACTGTTGTGATCAATGAAGCCATGCCAAACTC
116697 GTTTCTTTTAATGATCTAAACAATTGTTTGGTTGTACTTGGAACCAAATATATGAATCTTTGGCA
66 GTTTCTTTTAATGATCTAAACAATTGTTTGGTTGTACTTGGAACCAAATATATGAATCTTTGGCA
116762 CTATCAAGGAGTAACTAGTTAATTTCTAAGAAGTGATTTGACCAGGGGAAACGCTACTTAGGTAT
131 CTATCAAGGAGTAACTAGTTAATTTCTAAGAAGTGATTTGACCAGGGGAAACGCTACTTAGGTAT
116827 ATCAAAAGCAGCTATCAACTTCACCTGTAGGAAACTTTTATGAGACACATGAGTTACAAGGCGCA
196 ATCAAAAGCAGCTATCAACTTCACCTGTAGGAAACTTTTATGAGACACATGAGTTACAAGGCGCA
116892 AAATGCCACATTTGTAACAGTTGTAACCTTCTACTCTGAATATTTGGCTGACTGCCATTTTCCTC
261 AAATGCCACATTTGTAACAGTTGTAACCTTCTACTCTGAATATTTGGCTGACTGCCATTTTCCTC
116957 CATTTAATGTGGAACTGATCTTAATTATATCGTAATTGAA
326 CATTTAATGTGGAACTGATCTTAATTATATCGTAATTGAA
116997 ATTATGGTCG
Statistics
Matches: 364, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
367 364 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (367 bp):
CATGCCATTAATCACTCCATAAATTCAGTAAATACTGTTGTGATCAATGAAGCCATGCCAAACTC
GTTTCTTTTAATGATCTAAACAATTGTTTGGTTGTACTTGGAACCAAATATATGAATCTTTGGCA
CTATCAAGGAGTAACTAGTTAATTTCTAAGAAGTGATTTGACCAGGGGAAACGCTACTTAGGTAT
ATCAAAAGCAGCTATCAACTTCACCTGTAGGAAACTTTTATGAGACACATGAGTTACAAGGCGCA
AAATGCCACATTTGTAACAGTTGTAACCTTCTACTCTGAATATTTGGCTGACTGCCATTTTCCTC
CATTTAATGTGGAACTGATCTTAATTATATCGTAATTGAAGC
Found at i:123523 original size:59 final size:60
Alignment explanation
Indices: 123459--123587 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 60
123449 ACTCCCGTTC
** * *
123459 TAAATTAGTCTTTAAACTTGTGAACATTCTAATTGCATCCTC-AACTATGATCCTTTTTT
1 TAAATTAGTCTCCAAACTTGTGAACATTCCAATTGCATCCTCAAACTATGATCATTTTTT
* * * * *
123518 TAAATTATTCTCCAGACTTTTGAATATTCCAATTTCATCCTCAAACTATGATCATTTTTT
1 TAAATTAGTCTCCAAACTTGTGAACATTCCAATTGCATCCTCAAACTATGATCATTTTTT
123578 TAAATTAGTC
1 TAAATTAGTC
123588 ATCAGACTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
59 34 0.58
60 25 0.42
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (60 bp):
TAAATTAGTCTCCAAACTTGTGAACATTCCAATTGCATCCTCAAACTATGATCATTTTTT
Found at i:123594 original size:60 final size:58
Alignment explanation
Indices: 123459--123604 Score: 184
Period size: 60 Copynumber: 2.4 Consensus size: 58
123449 ACTCCCGTTC
* * * * * *
123459 TAAATTAGTCTTTAAACTTGTGAACATTCTAATTGCATCCTCAACTATGATCCTTTTTT
1 TAAATTAGTC-TCAGACTTTTGAATATTCCAATTGCATCCTCAACTATGATCATTTTTT
* *
123518 TAAATTATTCTCCAGACTTTTGAATATTCCAATTTCATCCTCAAACTATGATCATTTTTT
1 TAAATTAGTCT-CAGACTTTTGAATATTCCAATTGCATCCTC-AACTATGATCATTTTTT
123578 TAAATTAGTCATCAGACTTTTGAATAT
1 TAAATTAGTC-TCAGACTTTTGAATAT
123605 ATTTTAATTC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.01
59 33 0.44
60 40 0.53
61 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.44
Consensus pattern (58 bp):
TAAATTAGTCTCAGACTTTTGAATATTCCAATTGCATCCTCAACTATGATCATTTTTT
Found at i:143087 original size:29 final size:29
Alignment explanation
Indices: 143045--143153 Score: 182
Period size: 29 Copynumber: 3.8 Consensus size: 29
143035 AAGACCGGTG
143045 TGCATGGCGACCTATAAGGACGTCGGGCT
1 TGCATGGCGACCTATAAGGACGTCGGGCT
* *
143074 TGCATGGCGACCTATAAGGACGCCGGGCG
1 TGCATGGCGACCTATAAGGACGTCGGGCT
**
143103 TATATGGCGACCTATAAGGACGTCGGGCT
1 TGCATGGCGACCTATAAGGACGTCGGGCT
143132 TGCATGGCGACCTATAAGGACG
1 TGCATGGCGACCTATAAGGACG
143154 CCGGACGTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.23, C:0.24, G:0.34, T:0.19
Consensus pattern (29 bp):
TGCATGGCGACCTATAAGGACGTCGGGCT
Found at i:143138 original size:58 final size:58
Alignment explanation
Indices: 143048--143175 Score: 247
Period size: 58 Copynumber: 2.2 Consensus size: 58
143038 ACCGGTGTGC
*
143048 ATGGCGACCTATAAGGACGTCGGGCTTGCATGGCGACCTATAAGGACGCCGGGCGTAT
1 ATGGCGACCTATAAGGACGTCGGGCTTGCATGGCGACCTATAAGGACGCCGGACGTAT
143106 ATGGCGACCTATAAGGACGTCGGGCTTGCATGGCGACCTATAAGGACGCCGGACGTAT
1 ATGGCGACCTATAAGGACGTCGGGCTTGCATGGCGACCTATAAGGACGCCGGACGTAT
143164 ATGGCGACCTAT
1 ATGGCGACCTAT
143176 GGTGGTTCGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 69 1.00
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.20
Consensus pattern (58 bp):
ATGGCGACCTATAAGGACGTCGGGCTTGCATGGCGACCTATAAGGACGCCGGACGTAT
Found at i:143167 original size:29 final size:29
Alignment explanation
Indices: 143047--143175 Score: 177
Period size: 29 Copynumber: 4.4 Consensus size: 29
143037 GACCGGTGTG
* * *
143047 CATGGCGACCTATAAGGACGTCGGGCTTG
1 CATGGCGACCTATAAGGACGCCGGGCGTA
143076 CATGGCGACCTATAAGGACGCCGGGCGTA
1 CATGGCGACCTATAAGGACGCCGGGCGTA
* * * *
143105 TATGGCGACCTATAAGGACGTCGGGCTTG
1 CATGGCGACCTATAAGGACGCCGGGCGTA
*
143134 CATGGCGACCTATAAGGACGCCGGACGTA
1 CATGGCGACCTATAAGGACGCCGGGCGTA
*
143163 TATGGCGACCTAT
1 CATGGCGACCTAT
143176 GGTGGTTCGT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 87 1.00
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (29 bp):
CATGGCGACCTATAAGGACGCCGGGCGTA
Found at i:147071 original size:27 final size:27
Alignment explanation
Indices: 146967--147061 Score: 181
Period size: 27 Copynumber: 3.5 Consensus size: 27
146957 TCCCCTCATC
146967 TTTGTAATATCTTTTTTTGCTGTTAATT
1 TTTGTAATATC-TTTTTTGCTGTTAATT
146995 TTTGTAATATCTTTTTTGCTGTTAATT
1 TTTGTAATATCTTTTTTGCTGTTAATT
147022 TTTGTAATATCTTTTTTGCTGTTAATT
1 TTTGTAATATCTTTTTTGCTGTTAATT
147049 TTTGTAATATCTT
1 TTTGTAATATCTT
147062 CTTCAGTGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
27 56 0.84
28 11 0.16
ACGTcount: A:0.19, C:0.07, G:0.11, T:0.63
Consensus pattern (27 bp):
TTTGTAATATCTTTTTTGCTGTTAATT
Found at i:147081 original size:35 final size:35
Alignment explanation
Indices: 147035--147110 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
147025 GTAATATCTT
147035 TTTTGCTGTTAATTTTTGTAATATCTTCTTCAGTG
1 TTTTGCTGTTAATTTTTGTAATATCTTCTTCAGTG
147070 TTTTGCTGTTAATTTTTGTAATATCTTCTTCAGTG
1 TTTTGCTGTTAATTTTTGTAATATCTTCTTCAGTG
147105 TTTTGC
1 TTTTGC
147111 AAATTAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.58
Consensus pattern (35 bp):
TTTTGCTGTTAATTTTTGTAATATCTTCTTCAGTG
Done.