Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003698.1 Hibiscus syriacus cultivar Beakdansim tig00007907_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: 163610
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:8274 original size:181 final size:187
Alignment explanation
Indices: 7902--8354 Score: 542
Period size: 181 Copynumber: 2.4 Consensus size: 187
7892 ATGGGTCTTG
* * * * * *
7902 ACTCTAAAGCATATGTACATGAACATAAATGGAAGTTCTTGAGTGCTGATAATTAAATAGAAGAC
1 ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
* *
7967 CCTTTTGTCTCCACTGTTGCAAATGGAGAGGTCCATATTCATGTCATAGTATATGCATATGTATG
66 CCTTTTG--T---C--TTGCAAATAGAGAGGTCCATATGCATGTCATAGTATATGCATATGTA-G
* * * *
8032 CATGTATCATGTATGTCTGAAATTATAAATGCATGCATGCTTCTCAACATGGGTCTTGAGATAAA
123 CATGCATCAGGTATGTCTGAAATTAT-AA-GCATGCATGCTCCCCAACATGGGTCTTGAGATAAA
8097 CC
186 CC
* *
8099 ACTCTTAAGCATATATACATGCACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGGC
1 ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
* *
8164 CCTTATGTCTTGCAAATAGAGAGGTCCATATGCATG-CAT-GTATATGTACTATG-A-CATGCAT
66 CCTTTTGTCTTGCAAATAGAGAGGTCCATATGCATGTCATAGTATATGCA-TATGTAGCATGCAT
* *
8225 -AGGTATGTCTGTAATTAT-A-CATGCATGCTCCCCAATATGGGTCTTGAGATAAACC
130 CAGGTATGTCTGAAATTATAAGCATGCATGCTCCCCAACATGGGTCTTGAGATAAACC
* * * * * *
8280 ACTCTTGAGCATATATTCATGTACATGAAGGGAAGTTATAGAGTTTTGATGATTAAATAGAAGAC
1 ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
8345 CCTTTTGTCT
66 CCTTTTGTCT
8355 CCACTCTTGC
Statistics
Matches: 229, Mismatches: 26, Indels: 18
0.84 0.10 0.07
Matches are distributed among these distances:
181 100 0.44
183 1 0.00
185 16 0.07
186 6 0.03
188 9 0.04
189 7 0.03
190 25 0.11
192 1 0.00
195 1 0.00
197 63 0.28
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (187 bp):
ACTCTTAAGCATATATACATGAACATAAAGGGAAGTTATTGAGTGTTGATGATTAAATAGAAGAC
CCTTTTGTCTTGCAAATAGAGAGGTCCATATGCATGTCATAGTATATGCATATGTAGCATGCATC
AGGTATGTCTGAAATTATAAGCATGCATGCTCCCCAACATGGGTCTTGAGATAAACC
Found at i:10214 original size:2 final size:2
Alignment explanation
Indices: 10203--10240 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
10193 TTGATGAATT
10203 TA TA -A TA TA TA 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 TA TA TA TA TA TA T
10241 CCAAGTTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11045 original size:3 final size:3
Alignment explanation
Indices: 11037--11069 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
11027 AACCTATTAT
11037 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11070 TCAATTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15087 original size:4 final size:4
Alignment explanation
Indices: 15078--15103 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
15068 TATCTGAGGT
15078 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
15104 CTGAGGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:30721 original size:16 final size:16
Alignment explanation
Indices: 30702--30757 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
30692 ATTAAATATT
30702 AATTAAATTTTAACTA
1 AATTAAATTTTAACTA
* *
30718 AATT-AATTTCGAAAT-
1 AATTAAATTT-TAACTA
*
30733 AATTGAATTTTAACTA
1 AATTAAATTTTAACTA
30749 AATTAAATT
1 AATTAAATT
30758 CGAATAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (16 bp):
AATTAAATTTTAACTA
Found at i:30742 original size:31 final size:30
Alignment explanation
Indices: 30701--30766 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
30691 AATTAAATAT
*
30701 TAATTAAATTTTAACTAAATTAATTTCGAAA
1 TAATTAAATTTTAACTAAATTAAATTCG-AA
*
30732 TAATTGAATTTTAACTAAATTAAATTCGAA
1 TAATTAAATTTTAACTAAATTAAATTCGAA
30762 TAATT
1 TAATT
30767 TATTAACCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (30 bp):
TAATTAAATTTTAACTAAATTAAATTCGAA
Found at i:31778 original size:22 final size:22
Alignment explanation
Indices: 31730--31771 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31720 TTCTCTACTG
*
31730 ATATTTTAAAAATAATGATTTA
1 ATATTTTAAAAATAATAATTTA
31752 ATATTTTAAAAATAATAATT
1 ATATTTTAAAAATAATAATT
31772 ATATATTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTTAAAAATAATAATTTA
Found at i:31808 original size:57 final size:57
Alignment explanation
Indices: 31720--31833 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
31710 AATTCATCTC
31720 TTCTCTACTGATATTTTAAAAATAATGATTTAATATTTTAAAAATAATAATTATATA
1 TTCTCTACTGATATTTTAAAAATAATGATTTAATATTTTAAAAATAATAATTATATA
*
31777 TTCTCTACTGATATTTTAAAAATAATGATTTAATATTTTAGAAATAATAATTATATA
1 TTCTCTACTGATATTTTAAAAATAATGATTTAATATTTTAAAAATAATAATTATATA
31834 ATTGACATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (57 bp):
TTCTCTACTGATATTTTAAAAATAATGATTTAATATTTTAAAAATAATAATTATATA
Found at i:46343 original size:32 final size:31
Alignment explanation
Indices: 46270--46345 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
46260 CTAATGTGAC
* *
46270 TCTTAGGTAGGCTCTACGACCCTGAGATCTT
1 TCTTAGGTAGGCCCTACGACCCTAAGATCTT
** * * *
46301 TCTCGGGTAGGCCCTACGGCCCTAATATGTGT
1 TCTTAGGTAGGCCCTACGACCCTAAGATCT-T
46333 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
46346 TCGTGGCCCT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGACCCTAAGATCTT
Found at i:46939 original size:20 final size:21
Alignment explanation
Indices: 46898--46941 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
46888 CTGAAAATCT
*
46898 ATTTTATTTTGAATACTGATAA
1 ATTTTATTTTG-ATACTCATAA
46920 ATTTTATTTTG-TACTCATAA
1 ATTTTATTTTGATACTCATAA
46940 AT
1 AT
46942 GATTTTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTTATTTTGATACTCATAA
Found at i:48508 original size:22 final size:22
Alignment explanation
Indices: 48483--48524 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
48473 CATTTTACGA
48483 TTTTTTAAACATTTTTATATGT
1 TTTTTTAAACATTTTTATATGT
* **
48505 TTTTTTCAATTTTTTTATAT
1 TTTTTTAAACATTTTTATAT
48525 AAACCACTAA
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:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTAAACATTTTTATATGT
Found at i:51570 original size:2 final size:2
Alignment explanation
Indices: 51563--51621 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
51553 GGATTTTTAG
51563 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
51605 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
51622 ATGATTCATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51939 original size:2 final size:2
Alignment explanation
Indices: 51932--51975 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
51922 CCACACGCTT
* *
51932 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TT TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51973 TA T
1 TA T
51976 TTACATGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:57383 original size:3 final size:3
Alignment explanation
Indices: 57375--57401 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
57365 TATATCAGAT
57375 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
57402 AGAATGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:61139 original size:30 final size:26
Alignment explanation
Indices: 61093--61146 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 26
61083 TGTTCTTCTC
*
61093 CGTTGTTGTTCGTATCTCTCTCTGTCCT
1 CGTTGTTGTTCCTATCT-T-TCTGTCCT
61121 CGTTGGTTGCTTCCTATCTTTCTGTC
1 CGTT-GTTG-TTCCTATCTTTCTGTC
61147 TCTCCTCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 10 0.43
29 5 0.22
30 8 0.35
ACGTcount: A:0.04, C:0.28, G:0.19, T:0.50
Consensus pattern (26 bp):
CGTTGTTGTTCCTATCTTTCTGTCCT
Found at i:63610 original size:2 final size:2
Alignment explanation
Indices: 63603--63629 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63593 GATTACATGT
63603 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
63630 GAAATGCTTA
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:63815 original size:12 final size:12
Alignment explanation
Indices: 63791--63939 Score: 67
Period size: 12 Copynumber: 11.6 Consensus size: 12
63781 TCTCAAATCC
*
63791 ATATTTTT-TTA
1 ATATTTTTAATA
63802 ATATTTTTAATA
1 ATATTTTTAATA
63814 ATATTTTATTTAA-A
1 ATA--TT-TTTAATA
*
63828 TATATTTTT-TTA
1 -ATATTTTTAATA
63840 ATATTTTTAATA
1 ATATTTTTAATA
*
63852 ATATTTTATTTTAAAAA
1 ATA---T-TTTT-AATA
**
63869 ATCCATATTTTTTTA
1 AT--AT-TTTTAATA
63884 ATATTTTTAATA
1 ATATTTTTAATA
63896 ATATTTTATTTAA-A
1 ATA--TT-TTTAATA
63910 TATATTTTT--TA
1 -ATATTTTTAATA
63921 ATATTTTTAATA
1 ATATTTTTAATA
63933 ATATTTT
1 ATATTTT
63940 ATTTTAAAAA
Statistics
Matches: 108, Mismatches: 9, Indels: 41
0.68 0.06 0.26
Matches are distributed among these distances:
10 8 0.07
11 17 0.16
12 35 0.32
13 6 0.06
14 6 0.06
15 20 0.19
16 10 0.09
17 5 0.05
19 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTTTTAATA
Found at i:63936 original size:81 final size:82
Alignment explanation
Indices: 63785--63951 Score: 327
Period size: 82 Copynumber: 2.0 Consensus size: 82
63775 GACACGTCTC
63785 AAATCCATATTTTTTTAATATTTTTAATAATATTTTATTTAAATATATTTTTTTAATATTTTTAA
1 AAATCCATATTTTTTTAATATTTTTAATAATATTTTATTTAAATATATTTTTTTAATATTTTTAA
63850 TAATATTTTATTTTAAA
66 TAATATTTTATTTTAAA
63867 AAATCCATATTTTTTTAATATTTTTAATAATATTTTATTTAAATATA-TTTTTTAATATTTTTAA
1 AAATCCATATTTTTTTAATATTTTTAATAATATTTTATTTAAATATATTTTTTTAATATTTTTAA
63931 TAATATTTTATTTTAAA
66 TAATATTTTATTTTAAA
63948 AAAT
1 AAAT
63952 ATATACGTAA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 38 0.45
82 47 0.55
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (82 bp):
AAATCCATATTTTTTTAATATTTTTAATAATATTTTATTTAAATATATTTTTTTAATATTTTTAA
TAATATTTTATTTTAAA
Found at i:63947 original size:38 final size:38
Alignment explanation
Indices: 63791--63943 Score: 245
Period size: 38 Copynumber: 3.9 Consensus size: 38
63781 TCTCAAATCC
63791 ATATTTTTTTAATATTTTTAATAATATTTTATTTAAAT
1 ATATTTTTTTAATATTTTTAATAATATTTTATTTAAAT
63829 ATATTTTTTTAATATTTTTAATAATATTTTATTTTAAAAAAT
1 ATATTTTTTTAATATTTTTAATAATATTTTA-TTT---AAAT
63871 CCATATTTTTTTAATATTTTTAATAATATTTTATTTAAAT
1 --ATATTTTTTTAATATTTTTAATAATATTTTATTTAAAT
63911 ATA-TTTTTTAATATTTTTAATAATATTTTATTT
1 ATATTTTTTTAATATTTTTAATAATATTTTATTT
63944 TAAAAAATAT
Statistics
Matches: 109, Mismatches: 0, Indels: 13
0.89 0.00 0.11
Matches are distributed among these distances:
37 30 0.28
38 34 0.31
39 3 0.03
40 4 0.04
42 4 0.04
43 3 0.03
44 31 0.28
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (38 bp):
ATATTTTTTTAATATTTTTAATAATATTTTATTTAAAT
Found at i:64216 original size:18 final size:19
Alignment explanation
Indices: 64181--64218 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
64171 CACGGAATGT
64181 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
64201 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
64219 GATTACTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:68571 original size:2 final size:2
Alignment explanation
Indices: 68564--68630 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
68554 AGCAGAAAAC
68564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68606 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 T
68631 TAGAAAAATC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74532 original size:82 final size:80
Alignment explanation
Indices: 74371--74533 Score: 201
Period size: 82 Copynumber: 2.0 Consensus size: 80
74361 AAAAATTATG
*
74371 ATTAAAATATATAATTAAACATAATATTTTTGTATTATTATAATATATTATATTAAACTAGATTA
1 ATTAAAATATATAATTAAACATAATATTTTTGTATTATTATAATATATTATATTAAACTAGATAA
*
74436 ATTATGACATAATAT
66 ATTATAACATAATAT
*
74451 ATTAATATATTATAATTAAACATAATATTTTTCGCT-TTATTATAATATAATTAAATATATAAA-
1 ATTAAAATA-TATAATTAAACATAATATTTTT-G-TATTATTATAATAT-ATT--ATAT-TAAAC
74514 TA-A-AAATTA-AACATAATAT
59 TAGATAAATTATAACATAATAT
74533 A
1 A
74534 ATATATTAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
80 8 0.11
81 22 0.30
82 23 0.32
83 9 0.12
84 1 0.01
85 6 0.08
86 4 0.05
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (80 bp):
ATTAAAATATATAATTAAACATAATATTTTTGTATTATTATAATATATTATATTAAACTAGATAA
ATTATAACATAATAT
Found at i:74541 original size:19 final size:20
Alignment explanation
Indices: 74491--74543 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
74481 TTCGCTTTAT
*
74491 TATAATATAATTAAATATATA
1 TATAATAT-ATTAAACATATA
* *
74512 AATAA-AAATTAAACATA-A
1 TATAATATATTAAACATATA
74530 TATAATATATTAAA
1 TATAATATATTAAA
74544 GTAGATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 5 0.19
19 16 0.62
20 1 0.04
21 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAATATATTAAACATATA
Found at i:85387 original size:102 final size:102
Alignment explanation
Indices: 85274--85479 Score: 403
Period size: 102 Copynumber: 2.0 Consensus size: 102
85264 AGTGTTCTCA
85274 AATTTTTAGTCTAATTATAATATAAGTCATTGTAAGTTTAAATATTAGACAAATTAGAAGTTATC
1 AATTTTTAGTCTAATTATAATATAAGTCATTGTAAGTTTAAATATTAGACAAATTAGAAGTTATC
*
85339 TTTTGAGTTTTGAGTGAATATAAGATAATATTTGTAC
66 TTTTGAGTTTTGAGTGAATATAAAATAATATTTGTAC
85376 AATTTTTAGTCTAATTATAATATAAGTCATTGTAAGTTTAAATATTAGACAAATTAGAAGTTATC
1 AATTTTTAGTCTAATTATAATATAAGTCATTGTAAGTTTAAATATTAGACAAATTAGAAGTTATC
85441 TTTTGAGTTTTGAGTGAATATAAAATAATATTTGTAC
66 TTTTGAGTTTTGAGTGAATATAAAATAATATTTGTAC
85478 AA
1 AA
85480 AAAACTTTCA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (102 bp):
AATTTTTAGTCTAATTATAATATAAGTCATTGTAAGTTTAAATATTAGACAAATTAGAAGTTATC
TTTTGAGTTTTGAGTGAATATAAAATAATATTTGTAC
Found at i:85471 original size:51 final size:51
Alignment explanation
Indices: 85314--85472 Score: 119
Period size: 51 Copynumber: 3.1 Consensus size: 51
85304 TGTAAGTTTA
*
85314 AATATTAGACAAATTAGAAGTTATCTTTTGAGTTTTGAGTGAATATAAGAT
1 AATATTAGACAAATTAGAAGTTATCTTTTGAGTTTTGAGTGAATATAAAAT
* *** * * * * * * * * **
85365 AATATTTGTAC-AATTTTTAGTCTA-ATTAT-A-ATATAAGTCATTGTAAGTTT
1 AATATTAG-ACAAATTAGAAGT-TATCTTTTGAGTTTTGAGTGAATATAA-AAT
85415 AAATATTAGACAAATTAGAAGTTATCTTTTGAGTTTTGAGTGAATATAAAAT
1 -AATATTAGACAAATTAGAAGTTATCTTTTGAGTTTTGAGTGAATATAAAAT
85467 AATATT
1 AATATT
85473 TGTACAAAAA
Statistics
Matches: 72, Mismatches: 28, Indels: 16
0.62 0.24 0.14
Matches are distributed among these distances:
49 10 0.14
50 6 0.08
51 40 0.56
52 6 0.08
53 10 0.14
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (51 bp):
AATATTAGACAAATTAGAAGTTATCTTTTGAGTTTTGAGTGAATATAAAAT
Found at i:94495 original size:20 final size:22
Alignment explanation
Indices: 94463--94511 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
94453 TATCTAAATT
*
94463 AATT-TTTTATTTAG-GTGTCA
1 AATTATTTTATTTAGTCTGTCA
94483 AATTATTTT-TTTAGTCTGTCA
1 AATTATTTTATTTAGTCTGTCA
*
94504 AAGTATTT
1 AATTATTT
94512 AATGTTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (22 bp):
AATTATTTTATTTAGTCTGTCA
Found at i:100049 original size:9 final size:10
Alignment explanation
Indices: 100029--100054 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
100019 AGAAGAGAAT
100029 AAAATTTAAA
1 AAAATTTAAA
100039 AAAATTTAAA
1 AAAATTTAAA
100049 AAAATT
1 AAAATT
100055 ACTATTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:102136 original size:2 final size:2
Alignment explanation
Indices: 102129--102160 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
102119 CTATTTAATA
102129 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
102161 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:102212 original size:2 final size:2
Alignment explanation
Indices: 102160--102192 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
102150 TCTCTCTCTC
102160 TA TA TA 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 TA TA TA T
102193 TTAAGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103924 original size:31 final size:31
Alignment explanation
Indices: 103889--103948 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
103879 ACCCGACTCG
103889 ACCCGA-CTCGTTTACCCGAACCGTTGACCCA
1 ACCCGACCT-GTTTACCCGAACCGTTGACCCA
*
103920 ACCCGACCTGTTTACCCGACCCGTTGACC
1 ACCCGACCTGTTTACCCGAACCGTTGACC
103949 GTTGACTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.20, C:0.43, G:0.17, T:0.20
Consensus pattern (31 bp):
ACCCGACCTGTTTACCCGAACCGTTGACCCA
Found at i:106475 original size:24 final size:24
Alignment explanation
Indices: 106448--106538 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
106438 TCAAATTTGA
* * *
106448 ATTCTGTTATGATACCTAACCTGG
1 ATTCTGATATGATACATGACCTGG
* * *
106472 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGG
*
106495 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
* *
106519 ATTCTGATATAATACTTGAC
1 ATTCTGATATGATACATGAC
106539 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:106499 original size:23 final size:24
Alignment explanation
Indices: 106469--106526 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
106459 ATACCTAACC
*
106469 TGGATTCTGATCTGATA-TTGACA
1 TGGATTCTGATCTGATACATGACA
*
106492 TGGATTCTGATCTGATACATGACC
1 TGGATTCTGATCTGATACATGACA
106516 TGGATTCTGAT
1 TGGATTCTGAT
106527 ATAATACTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 17 0.53
24 15 0.47
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (24 bp):
TGGATTCTGATCTGATACATGACA
Found at i:106663 original size:35 final size:35
Alignment explanation
Indices: 106616--106688 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
106606 TGGAGGAAGA
* *
106616 TTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTAAGGGCC
106651 TTACTTGCAGGCTCCTCGGCTTTGTGCTAAGGGCC
1 TTACTTGCAGGCTCCTCGGCTTTGTGCTAAGGGCC
106686 TTA
1 TTA
106689 TTGTTCGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.11, C:0.27, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTTTGTGCTAAGGGCC
Found at i:113131 original size:16 final size:16
Alignment explanation
Indices: 113107--113140 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
113097 TATCGCCGAC
*
113107 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
113123 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
113139 CG
1 CG
113141 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:113613 original size:36 final size:36
Alignment explanation
Indices: 113568--113639 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
113558 ACATCTACCA
* *
113568 AAATTTTACCAAACTTT-GAAAAACATTTTTCAAAG
1 AAATTTTACCAAACTTTAAAAAAACATTTTCCAAAG
113603 AAATATTTACCAAACTTTAAAAAAACATTTTCCAAAG
1 AAAT-TTTACCAAACTTTAAAAAAACATTTTCCAAAG
113640 TTGGTTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 4 0.12
36 13 0.39
37 16 0.48
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (36 bp):
AAATTTTACCAAACTTTAAAAAAACATTTTCCAAAG
Found at i:114570 original size:10 final size:9
Alignment explanation
Indices: 114553--114577 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
114543 TTTTCTAATA
114553 TATTTTTTT
1 TATTTTTTT
114562 TATTTTTTT
1 TATTTTTTT
114571 TATTTTT
1 TATTTTT
114578 ATAAATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:124339 original size:27 final size:21
Alignment explanation
Indices: 124262--124328 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
124252 TGAATTGTTC
* *
124262 ACCATAAGACTCGATCCAATG
1 ACCATAAGACTCGATCCCACG
124283 ACCATAAGACTCGATCCCACG
1 ACCATAAGACTCGATCCCACG
124304 ACCATAAGACTCGATCCCACG
1 ACCATAAGACTCGATCCCACG
124325 ACCA
1 ACCA
124329 CAATACTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.15
Consensus pattern (21 bp):
ACCATAAGACTCGATCCCACG
Found at i:125418 original size:66 final size:66
Alignment explanation
Indices: 125343--125475 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
125333 AAATCTAGTA
* * * *
125343 TTAGGTGTCTTTTTTTATATGATCTTCTAATTAAAAATTAATAGAATAAATACAATCTTGTAGAC
1 TTAGGTGTCTTTTTTTATATGATCTTCTAATAAAAAACTAATAGAAGAAACACAATCTTGTAGAC
125408 T
66 T
125409 TTAGGTGTCTTTTTTTATATGATCTTCTAATAAAAAACTAATAGAAGAAACACAATCTTGTAGAC
1 TTAGGTGTCTTTTTTTATATGATCTTCTAATAAAAAACTAATAGAAGAAACACAATCTTGTAGAC
125474 T
66 T
125475 T
1 T
125476 GAGAACATCC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (66 bp):
TTAGGTGTCTTTTTTTATATGATCTTCTAATAAAAAACTAATAGAAGAAACACAATCTTGTAGAC
T
Found at i:126940 original size:25 final size:24
Alignment explanation
Indices: 126912--126961 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
126902 TAACATTTAA
126912 TTAAACAAATCATTTTGATCCATAT
1 TTAAA-AAATCATTTTGATCCATAT
* * *
126937 TTAAATAGTTATTTTGATCCATAT
1 TTAAAAAATCATTTTGATCCATAT
126961 T
1 T
126962 GTTTTTGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.46
Consensus pattern (24 bp):
TTAAAAAATCATTTTGATCCATAT
Found at i:142026 original size:31 final size:31
Alignment explanation
Indices: 141968--142088 Score: 149
Period size: 31 Copynumber: 4.0 Consensus size: 31
141958 GAGTCGAGGG
* *
141968 TTACCTATGTTCTTC-AGA-ACATGGACTGA
1 TTACCTATGTTCTTCGAGACATATGGACTGT
*
141997 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGAGACATATGGACTGT
* *
142028 TTACCTATGTTCTTCG-GAATATATGGATTGT
1 TTACCTATGTTCTTCGAG-ACATATGGACTGT
* *
142059 TTACCTAGGTTCTTCGAGACCTATGGACTG
1 TTACCTATGTTCTTCGAGACATATGGACTG
142089 GTCTTTCGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.19
30 3 0.04
31 60 0.76
32 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGAGACATATGGACTGT
Found at i:142807 original size:19 final size:20
Alignment explanation
Indices: 142773--142812 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
142763 TACTATTTGC
*
142773 ACAGTATCGATACTATTCAT
1 ACAGTATAGATACTATTCAT
142793 ACAGTATAG-TACTATTCAT
1 ACAGTATAGATACTATTCAT
142812 A
1 A
142813 AAAACAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (20 bp):
ACAGTATAGATACTATTCAT
Found at i:145898 original size:5 final size:5
Alignment explanation
Indices: 145888--145914 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
145878 TCAATTAATT
145888 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
145915 AGACAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:151504 original size:15 final size:16
Alignment explanation
Indices: 151472--151504 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
151462 AAAATCTTTC
151472 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
151488 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
151503 TT
1 TT
151505 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:152281 original size:16 final size:17
Alignment explanation
Indices: 152254--152288 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
152244 TATCGCCGAC
152254 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
152271 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
152287 CG
1 CG
152289 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:155032 original size:31 final size:30
Alignment explanation
Indices: 154997--155068 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 30
154987 TATGTGTCCT
*
154997 ATCATTACTTAGAACACA-TGATATATATCAC
1 ATCATTACTTAG-ACA-AGTAATATATATCAC
* * *
155028 ATCATCATTTTAGACAAGTAATATGTATCAC
1 ATCATTA-CTTAGACAAGTAATATATATCAC
155059 ATCATTACTT
1 ATCATTACTT
155069 TGAAATAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (30 bp):
ATCATTACTTAGACAAGTAATATATATCAC
Found at i:157854 original size:20 final size:19
Alignment explanation
Indices: 157820--157868 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
157810 AGTTCAACCT
*
157820 AATTTTTTGATTTTTTATTA
1 AATTTTTT-AGTTTTTATTA
*
157840 AATATTTTTAGTTTTTATTT
1 AAT-TTTTTAGTTTTTATTA
157860 AATTTTTTA
1 AATTTTTTA
157869 AATAATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 15 0.58
21 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
AATTTTTTAGTTTTTATTA
Found at i:160842 original size:27 final size:27
Alignment explanation
Indices: 160811--160863 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
160801 GACGTAGTGC
*
160811 AATAAAAGCATCTGAGCTTTAAAAGAA
1 AATAAAAGCATCCGAGCTTTAAAAGAA
160838 AATAAAAGCATCCGAGCTTTAAAAGA
1 AATAAAAGCATCCGAGCTTTAAAAGA
160864 CCAACTTCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (27 bp):
AATAAAAGCATCCGAGCTTTAAAAGAA
Done.