Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003329.1 Hibiscus syriacus cultivar Beakdansim tig00007010_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: 132996
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6709 original size:26 final size:26
Alignment explanation
Indices: 6641--6711 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
6631 AATATTTTTA
* *
6641 TGAATAGTGAACAATGAACAGTACCG
1 TGAACAGTGAACAATGTACAGTACCG
* *
6667 TGAACAGCGAACAATGTACATTACCG
1 TGAACAGTGAACAATGTACAGTACCG
6693 TGAACAGTGAACAATGTAC
1 TGAACAGTGAACAATGTAC
6712 CGATGCACTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (26 bp):
TGAACAGTGAACAATGTACAGTACCG
Found at i:6802 original size:21 final size:21
Alignment explanation
Indices: 6776--6815 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6766 AAAATTGTGT
*
6776 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTACTACAGTGC
6797 ATCGATGCACTACTACAGT
1 ATCGATGCACTACTACAGT
6816 AATTTCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTACTACAGTGC
Found at i:7324 original size:44 final size:44
Alignment explanation
Indices: 7213--7374 Score: 270
Period size: 44 Copynumber: 3.6 Consensus size: 44
7203 CTCTTACCAT
* * *
7213 TTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
7257 TTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 -TT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
7303 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
1 TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
*
7347 TTATTCTATAAGCTCGTAAGCTTATTTT
1 TTATTCCATAAGCTCGTAAGCTTATTTT
7375 CATACTTACC
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
44 69 0.62
45 4 0.04
46 39 0.35
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.40
Consensus pattern (44 bp):
TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCA
Found at i:7544 original size:40 final size:40
Alignment explanation
Indices: 7478--7676 Score: 335
Period size: 40 Copynumber: 5.0 Consensus size: 40
7468 ACCGTAGTGC
* ** *
7478 TACACATAAGGTCGTTCCCATTATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
7518 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
7558 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
7598 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
7638 TACACAAAAGGTCGTGCCCACCATATACACCAAAGTGTA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
7677 CTATAAACCT
Statistics
Matches: 153, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 153 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:9090 original size:4 final size:4
Alignment explanation
Indices: 9081--9107 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9071 TTCAACTATG
9081 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
9108 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:19133 original size:15 final size:15
Alignment explanation
Indices: 19113--19141 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19103 TAATGAATAT
19113 TGGTTATTTGATTTG
1 TGGTTATTTGATTTG
19128 TGGTTATTTGATTT
1 TGGTTATTTGATTT
19142 TGTTTGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (15 bp):
TGGTTATTTGATTTG
Found at i:20969 original size:32 final size:32
Alignment explanation
Indices: 20890--20959 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
20880 AGGTCCTCAA
*
20890 CTACTCTCCAACTAGTTTCAACTCCCATTTAG
1 CTACTCTCCAACTAGTTTCAACTCCCATTCAG
* * *
20922 CTATTCTCCAACTAGTTTCAACTCTCGTTCAG
1 CTACTCTCCAACTAGTTTCAACTCCCATTCAG
20954 CTACTC
1 CTACTC
20960 CCGAGCTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (32 bp):
CTACTCTCCAACTAGTTTCAACTCCCATTCAG
Found at i:21566 original size:155 final size:154
Alignment explanation
Indices: 21284--21576 Score: 468
Period size: 155 Copynumber: 1.9 Consensus size: 154
21274 TATGACCTGA
* * *
21284 TATAACTAAACCTAGCATATGATGCATATAGTAAGTTATAGTAAGTTAAGTATATGACATGAAAT
1 TATAACTAAACCTAGCATATGATGCATATAGTAAGTTATAGTAAGTGAAGAAAATGACATGAAAT
*
21349 CGCATCATGAAACATAAGGCATGAAATCATCAAACTTATTAGAATATAAGGTAAATGTATGGCAT
66 CGCATCATGAAACATAAGGCATGAAATCATCAAACTTATTAGAATATAAGGTAAATGCATGGCAT
21414 AGTAAAGTTAAGTATTTGACATGT
131 AGTAAAGTTAAGTATTTGACATGT
*
21438 TATAACTAAACCTAGCATATGATGCATATAGTAAGTTA-AGTATA-TGACATGAAAATG-CTTGA
1 TATAACTAAACCTAGCATATGATGCATATAGTAAGTTATAGTA-AGTGA-A-GAAAATGACATGA
21500 AAT-GCATGTCATGAAACATAAGGCATGAAATCATCAAACTTATTAGAATATAAGGTAAATGCAT
63 AATCGCA--TCATGAAACATAAGGCATGAAATCATCAAACTTATTAGAATATAAGGTAAATGCAT
21564 GGCATAGTAAAGT
126 GGCATAGTAAAGT
21577 ATGATGATCA
Statistics
Matches: 129, Mismatches: 5, Indels: 9
0.90 0.03 0.06
Matches are distributed among these distances:
153 9 0.07
154 47 0.36
155 73 0.57
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (154 bp):
TATAACTAAACCTAGCATATGATGCATATAGTAAGTTATAGTAAGTGAAGAAAATGACATGAAAT
CGCATCATGAAACATAAGGCATGAAATCATCAAACTTATTAGAATATAAGGTAAATGCATGGCAT
AGTAAAGTTAAGTATTTGACATGT
Found at i:22738 original size:65 final size:65
Alignment explanation
Indices: 22634--22764 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
22624 TGAAAGGGGA
*
22634 AAAACATTTTTGAAAGGTGAGCTAGGCTCAATGTGTCCCAACATTACCATAAAATCACAATAGGT
1 AAAACATTTTCGAAAGGTGAGCTAGGCTCAATGTGTCCCAACATTACCATAAAATCACAATAGGT
*
22699 AAAACATTTTCGAAAGGTGAGCTAGGCTCAGTGTGTCCCAACATTACCATAAAATCACAATAGGT
1 AAAACATTTTCGAAAGGTGAGCTAGGCTCAATGTGTCCCAACATTACCATAAAATCACAATAGGT
22764 A
1 A
22765 CATTAAACAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (65 bp):
AAAACATTTTCGAAAGGTGAGCTAGGCTCAATGTGTCCCAACATTACCATAAAATCACAATAGGT
Found at i:23855 original size:7 final size:7
Alignment explanation
Indices: 23842--23885 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
23832 ATCAAAGGAA
23842 GTCAACG
1 GTCAACG
*
23849 ATCAACG
1 GTCAACG
23856 GTCAA-G
1 GTCAACG
23862 GTCAACG
1 GTCAACG
23869 GTCAACG
1 GTCAACG
23876 GTCAACG
1 GTCAACG
23883 GTC
1 GTC
23886 GGGTCAGGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:23867 original size:20 final size:21
Alignment explanation
Indices: 23842--23885 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
23832 ATCAAAGGAA
23842 GTCAACGATCAACGGTCAA-G
1 GTCAACGATCAACGGTCAACG
*
23862 GTCAACGGTCAACGGTCAACG
1 GTCAACGATCAACGGTCAACG
23883 GTC
1 GTC
23886 GGGTCAGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
GTCAACGATCAACGGTCAACG
Found at i:23900 original size:14 final size:14
Alignment explanation
Indices: 23883--23913 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23873 ACGGTCAACG
23883 GTCGGGTCAGGTCT
1 GTCGGGTCAGGTCT
*
23897 GTCGGGTCGGGTCT
1 GTCGGGTCAGGTCT
23911 GTC
1 GTC
23914 AGTCAAACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.23, G:0.45, T:0.29
Consensus pattern (14 bp):
GTCGGGTCAGGTCT
Found at i:34749 original size:65 final size:62
Alignment explanation
Indices: 34630--34866 Score: 201
Period size: 65 Copynumber: 3.7 Consensus size: 62
34620 TTTTTCAGAG
* * * * * *
34630 TGATGCACCGATGCACTAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCAC--ATCCATGCACCGATGCACTAAGGATT--TTTGAAACATCGAATGCAT
34694 T
62 T
* * *
34695 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAAAACATCAAATGCATT
1 TGATGCATCGATGCACAT-CCATGCACCGATGCACTAAGGATTTT-TG-AAACATCGAATGCATT
* ** * *
34760 TGATGCATCGATGCACCAGT-CATGCATCGATGCACTCTGGCTATTTTTGGAACATCGAATGCAC
1 TGATGCATCGATGCA-CA-TCCATGCACCGATGCACTAAGG--ATTTTTGAAACATCGAATGCAT
34824 T
62 T
*
34825 TGATGCATCGATGCAC-TCTTAGTGCACCGATGCACTAAGGAT
1 TGATGCATCGATGCACATC-CA-TGCACCGATGCACTAAGGAT
34867 CCAACGGTCA
Statistics
Matches: 141, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
62 2 0.01
63 6 0.04
64 21 0.15
65 102 0.72
66 4 0.03
67 6 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (62 bp):
TGATGCATCGATGCACATCCATGCACCGATGCACTAAGGATTTTTGAAACATCGAATGCATT
Found at i:34840 original size:17 final size:19
Alignment explanation
Indices: 34812--34860 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
34802 ATTTTTGGAA
34812 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
34830 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
34849 CACCGATGCACT
1 CATCGATGCACT
34861 AAGGATCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:36795 original size:21 final size:21
Alignment explanation
Indices: 36770--36809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36760 AAGACTCTAT
36770 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
36791 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
36810 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:38954 original size:20 final size:20
Alignment explanation
Indices: 38929--38969 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
38919 TTTGATCATG
38929 ATATTTCAATATG-CATATAT
1 ATATTTC-ATATGACATATAT
38949 ATATTTCATATGACATATAT
1 ATATTTCATATGACATATAT
38969 A
1 A
38970 ACCAAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATTTCATATGACATATAT
Found at i:38966 original size:18 final size:20
Alignment explanation
Indices: 38929--38969 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
38919 TTTGATCATG
*
38929 ATATTTCAATATGCATATAT
1 ATATTTCAATATGCACATAT
38949 ATATTTC-ATATG-ACATAT
1 ATATTTCAATATGCACATAT
38967 ATA
1 ATA
38970 ACCAAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCACATAT
Found at i:45836 original size:20 final size:20
Alignment explanation
Indices: 45796--45836 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
45786 TTTGATCATG
*
45796 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
45816 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
45836 A
1 A
45837 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:46078 original size:15 final size:15
Alignment explanation
Indices: 46055--46149 Score: 127
Period size: 15 Copynumber: 6.3 Consensus size: 15
46045 CTGTAAGACC
46055 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
* *
46070 ACTATGTCCCGAAAG
1 ACTACGTCCCGAAGG
46085 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
* * *
46100 ACTACATTCTGAAGG
1 ACTACGTCCCGAAGG
46115 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
* *
46130 ACTACGTCCTGAACG
1 ACTACGTCCCGAAGG
46145 ACTAC
1 ACTAC
46150 AATACCCTCG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 68 1.00
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:51341 original size:21 final size:21
Alignment explanation
Indices: 51299--51342 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
51289 ACTCCGGGAG
* *
51299 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
51320 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
51341 CT
1 CT
51343 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:52609 original size:64 final size:66
Alignment explanation
Indices: 52452--52611 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 66
52442 AATTAAATTG
*
52452 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATACACCGATGCACTAAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTAAGGATTTTATGA
52516 A
66 A
* * * * ** *
52517 AACATTGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTAAGGAT-TTTATG
52580 -A
65 AA
*
52581 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
52612 TCTTAGTGCT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 30 0.36
65 48 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATACACCGATGCACTAAGGATTTTATGA
A
Found at i:55587 original size:18 final size:18
Alignment explanation
Indices: 55564--55601 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
55554 CTTTAGCCCA
55564 AAAAATGATA-TTTTAGTT
1 AAAAATG-TACTTTTAGTT
55582 AAAAATGTACTTTTTAGTT
1 AAAAATGTAC-TTTTAGTT
55601 A
1 A
55602 TATGTAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 7 0.39
19 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (18 bp):
AAAAATGTACTTTTAGTT
Found at i:63257 original size:139 final size:138
Alignment explanation
Indices: 63006--63386 Score: 383
Period size: 139 Copynumber: 2.7 Consensus size: 138
62996 GTATTAAACT
* * * * * * * * * *
63006 TAAAATGTAGACTCTAATATTAA-CCTAATCAAATTTTTATAAGTTATTGAATCGAATAATTAAA
1 TAAAATGAAGACTCTAGTATTAATCCTAACCAAA-TTTAACAAATTATCGGATCAAATAATTAAT
* * * *
63070 ATGGAACCTCGAGCATAAAAGCAAGAACCAAATTAAAAAGCCATCTAAATTAATGGACT-AACGT
65 ATGGAACCTCGAGCATAAAAGCGAGGACCAAATTAAAAAGCCA-CTAAATTAAAGGACTAAACAT
63134 GAAATTAAACC
129 GAAATT-AACC
** * * * * *
63145 TAAGGTGAAGACTCTATTATTAAAT-GTAACCCATTTTAACAATTTATCGGATCAAATAATTAAT
1 TAAAATGAAGACTCTAGTATT-AATCCTAACCAAATTTAACAAATTATCGGATCAAATAATTAAT
* * * *
63209 ATGGAACCTCGGGCATAAAAGTGAGGACCAAATTAAAATATCTC-CTAAATTAAAGGACTAAATA
65 ATGGAACCTCGAGCATAAAAGCGAGGACCAAATTAAAA-AGC-CACTAAATTAAAGGACTAAACA
*
63273 TGAAATTAATC
128 TGAAATTAACC
* * * * *
63284 TAAAATGAAGGCTTTAGTATTAATCCTAACCAAATTTAACAAATTGTTGGATCAGATAATTAATA
1 TAAAATGAAGACTCTAGTATTAATCCTAACCAAATTTAACAAATTATCGGATCAAATAATTAATA
* *
63349 TGGAACCTCAACCATAAAAGCGAGGACCAAATTAAAAA
66 TGGAACCTCGAGCATAAAAGCGAGGACCAAATTAAAAA
63387 TTACTTAGGT
Statistics
Matches: 196, Mismatches: 40, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
138 4 0.02
139 173 0.88
140 18 0.09
141 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (138 bp):
TAAAATGAAGACTCTAGTATTAATCCTAACCAAATTTAACAAATTATCGGATCAAATAATTAATA
TGGAACCTCGAGCATAAAAGCGAGGACCAAATTAAAAAGCCACTAAATTAAAGGACTAAACATGA
AATTAACC
Found at i:78332 original size:2 final size:2
Alignment explanation
Indices: 78327--78361 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
78317 TCTCTCCTTC
78327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78362 TGCAGTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79761 original size:39 final size:39
Alignment explanation
Indices: 79707--79785 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
79697 CACCTTGAGA
79707 TAAATAACTTTTATCTTTGAACGTGTCTATTAGAGCCTG
1 TAAATAACTTTTATCTTTGAACGTGTCTATTAGAGCCTG
* *
79746 TAAATAATTTTTATCTTTGAATGTGTCTATTAGAGCCTG
1 TAAATAACTTTTATCTTTGAACGTGTCTATTAGAGCCTG
79785 T
1 T
79786 GGAATACAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (39 bp):
TAAATAACTTTTATCTTTGAACGTGTCTATTAGAGCCTG
Found at i:88444 original size:15 final size:15
Alignment explanation
Indices: 88424--88479 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
88414 AACATTTTAG
88424 TAGACCAGATAATAA
1 TAGACCAGATAATAA
88439 TAGACCAGATAA-AA
1 TAGACCAGATAATAA
* *
88453 GTAGACCATATAATAG
1 -TAGACCAGATAATAA
88469 TAGACCAGATA
1 TAGACCAGATA
88480 GCAGAAGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 2 0.06
15 33 0.92
16 1 0.03
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (15 bp):
TAGACCAGATAATAA
Found at i:88457 original size:30 final size:30
Alignment explanation
Indices: 88422--88479 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
88412 AGAACATTTT
88422 AGTAGACCAGATAATAATAGACCAGATAAA
1 AGTAGACCAGATAATAATAGACCAGATAAA
* *
88452 AGTAGACCATATAATAGTAGACCAGATA
1 AGTAGACCAGATAATAATAGACCAGATA
88480 GCAGAAGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (30 bp):
AGTAGACCAGATAATAATAGACCAGATAAA
Found at i:90915 original size:34 final size:33
Alignment explanation
Indices: 90851--91053 Score: 97
Period size: 34 Copynumber: 6.1 Consensus size: 33
90841 CTCCAACCAG
*
90851 ATATATTTTAATATCTAAAT-TTAAATAGATAATA
1 ATATATTTTAATTTC-AAATATTAAA-AGATAATA
*
90885 ATATCTTTTAATTTCAAATATTCAAAAGAT-ATA
1 ATATATTTTAATTTCAAATATT-AAAAGATAATA
*
90918 A-ACTATTTTTAATATTCAAA-CTT--AAG-TAGAT-
1 ATA-TA-TTTTAAT-TTCAAATATTAAAAGATA-ATA
*
90949 AT-TATTTTAATTTAAAATATTTAAAAAGGAT-ATA
1 ATATATTTTAATTTCAAATA-TT-AAAA-GATAATA
* *
90983 ATTATCTTTTAATATTCAAA-GTTAAATAGATAATAA
1 A-TATATTTTAAT-TTCAAATATTAAA-AGATAAT-A
* * * *
91019 ATAATTTTTTAATTTGAGATATTAAAA-AGAATA
1 AT-ATATTTTAATTTCAAATATTAAAAGATAATA
91052 AT
1 AT
91054 TATCCTTCTA
Statistics
Matches: 131, Mismatches: 14, Indels: 49
0.68 0.07 0.25
Matches are distributed among these distances:
28 5 0.04
29 7 0.05
30 5 0.04
31 4 0.03
32 3 0.02
33 16 0.12
34 40 0.31
35 22 0.17
36 24 0.18
37 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (33 bp):
ATATATTTTAATTTCAAATATTAAAAGATAATA
Found at i:91000 original size:65 final size:63
Alignment explanation
Indices: 90890--91014 Score: 171
Period size: 65 Copynumber: 2.0 Consensus size: 63
90880 TAATAATATC
* * *
90890 TTTTAATTTCAAATATTCAAAAGATATAAACTATTTTTAATATTCAAACTTAAGTAGATATTA
1 TTTTAATTTAAAATATTAAAAAGATATAAACTATTTTTAATATTCAAACTTAAATAGATATTA
* *
90953 TTTTAATTTAAAATATTTAAAAAGGATAT-AATTATCTTTTAATATTCAAAGTTAAATAGATA
1 TTTTAATTTAAAATA-TTAAAAA-GATATAAACTAT-TTTTAATATTCAAACTTAAATAGATA
91015 ATAAATAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 14 0.26
64 11 0.20
65 29 0.54
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (63 bp):
TTTTAATTTAAAATATTAAAAAGATATAAACTATTTTTAATATTCAAACTTAAATAGATATTA
Found at i:91077 original size:69 final size:71
Alignment explanation
Indices: 90953--91083 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 71
90943 GTAGATATTA
*
90953 TTTTAATTTAAAATATTTAAAAAGGATATAATTATCTTTTAATATTCAAAGTTAAATAGATAATA
1 TTTTAATTTAAAATATTTAAAAAGGATATAATTATCTTCTAATATTCAAAGTTAAATA-ATAATA
91018 AATAATT
65 AATAATT
* * *
91025 TTTTAATTTGAGATA-TTAAAAA-GA-ATAATTATCCTTCTAATGTTCAAA-TTAAATAATAA
1 TTTTAATTTAAAATATTTAAAAAGGATATAATTAT-CTTCTAATATTCAAAGTTAAATAATAA
91084 CTTTTAACTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
68 4 0.07
69 15 0.28
70 15 0.28
71 7 0.13
72 13 0.24
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (71 bp):
TTTTAATTTAAAATATTTAAAAAGGATATAATTATCTTCTAATATTCAAAGTTAAATAATAATAA
ATAATT
Found at i:98424 original size:12 final size:12
Alignment explanation
Indices: 98407--98440 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
98397 GAAAATAAAG
98407 AAAACTTAATGT
1 AAAACTTAATGT
*
98419 AAAACTTGATGT
1 AAAACTTAATGT
98431 AAAAC-TAATG
1 AAAACTTAATG
98441 GCCTTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:99539 original size:28 final size:26
Alignment explanation
Indices: 99470--99539 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
99460 AGCCATATAA
*
99470 CTTT-TTTTTTCATTGCACAATCTCT
1 CTTTCTTTTTTCTTTGCACAATCTCT
* *
99495 CTTTCTTTATTTCCTTTGCACAATTTTT
1 CTTTCTTT-TTT-CTTTGCACAATCTCT
99523 GCTTCTCTTTTTTCTTT
1 -CTT-TCTTTTTTCTTT
99540 TTCTTTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.11
26 3 0.08
27 3 0.08
28 16 0.43
29 6 0.16
30 5 0.14
ACGTcount: A:0.11, C:0.23, G:0.04, T:0.61
Consensus pattern (26 bp):
CTTTCTTTTTTCTTTGCACAATCTCT
Found at i:104450 original size:12 final size:12
Alignment explanation
Indices: 104433--104466 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
104423 GAAAATAAAG
104433 AAAACTTAATGT
1 AAAACTTAATGT
*
104445 AAAACTTGATGT
1 AAAACTTAATGT
104457 AAAAC-TAATG
1 AAAACTTAATG
104467 GCCCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:109156 original size:24 final size:24
Alignment explanation
Indices: 109124--109172 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
109114 CATAGCCAAC
109124 TCCTTTAACTACTTCTTTTTTCTT
1 TCCTTTAACTACTTCTTTTTTCTT
*
109148 TCCTTTAACTGCTTCTTTTTTCTT
1 TCCTTTAACTACTTCTTTTTTCTT
109172 T
1 T
109173 TTCTCCGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.63
Consensus pattern (24 bp):
TCCTTTAACTACTTCTTTTTTCTT
Found at i:112666 original size:17 final size:17
Alignment explanation
Indices: 112646--112678 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
112636 TTCCCTTCAG
112646 ATTATGATTCCAAAAAT
1 ATTATGATTCCAAAAAT
112663 ATTATGATTCCAAAAA
1 ATTATGATTCCAAAAA
112679 CCTTGTCTGC
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:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (17 bp):
ATTATGATTCCAAAAAT
Found at i:125459 original size:38 final size:38
Alignment explanation
Indices: 125412--125525 Score: 101
Period size: 38 Copynumber: 3.1 Consensus size: 38
125402 ATGTAAAATG
* *
125412 TATAGTTTTTAAAAAAATAGTTTTAAAAACATATAGTA
1 TATAATTTTTAAAAAAATAGTTTTAAAAACATATAATA
* * * *
125450 TATAATTTTT---AAGATAATTTTAAAAGCTTATAATA
1 TATAATTTTTAAAAAAATAGTTTTAAAAACATATAATA
* * * *
125485 TAGAA-TTTTAAAAAAAAATGTTTTGAAAATATATAATA
1 TATAATTTTTAAAAAAATA-GTTTTAAAAACATATAATA
125523 TAT
1 TAT
125526 TTTTTCAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
34 4 0.07
35 24 0.42
37 4 0.07
38 25 0.44
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (38 bp):
TATAATTTTTAAAAAAATAGTTTTAAAAACATATAATA
Found at i:131232 original size:33 final size:32
Alignment explanation
Indices: 131190--131263 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
131180 GTAATAACAA
* *
131190 AATTAAACAAAATAATTTAACAA-AAACTCCAAC
1 AATTTAACAAAATAAATTAA-AATAAA-TCCAAC
131223 AATTTAACAAAATAAATTAAAATAAATCCAAC
1 AATTTAACAAAATAAATTAAAATAAATCCAAC
*
131255 TATATTAAC
1 AAT-TTAAC
131264 GAATTAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 10 0.28
33 26 0.72
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (32 bp):
AATTTAACAAAATAAATTAAAATAAATCCAAC
Found at i:131468 original size:6 final size:6
Alignment explanation
Indices: 131459--131501 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
131449 ATCATCATCA
* *
131459 TCGTCC TCGTCC TCGTCC TCGTCC TCGTCA TTGTCC TCGTCC T
1 TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC T
131502 GAGTAGCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.02, C:0.44, G:0.16, T:0.37
Consensus pattern (6 bp):
TCGTCC
Found at i:131851 original size:27 final size:27
Alignment explanation
Indices: 131814--131877 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
131804 CAGGTAATGG
* * *
131814 TGGCGGCGGCGGCATCGGGTATGGGAA
1 TGGCGGTGGCGACATCGGGTAAGGGAA
* *
131841 TTGTGGTGGCGACATCGGGTAAGGGAA
1 TGGCGGTGGCGACATCGGGTAAGGGAA
131868 TGGCGGTGGC
1 TGGCGGTGGC
131878 TGCTGTGAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.19
Consensus pattern (27 bp):
TGGCGGTGGCGACATCGGGTAAGGGAA
Done.