Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003782.1 Hibiscus syriacus cultivar Beakdansim tig00008097_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: 101927
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2477 original size:25 final size:26
Alignment explanation
Indices: 2444--2495 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2434 CTGATTTCTG
*
2444 AATACTGC-TATTCGACACCTGATTT
1 AATACTGCTTATCCGACACCTGATTT
* *
2469 AATATTGCTTATCCGACATCTGATTT
1 AATACTGCTTATCCGACACCTGATTT
2495 A
1 A
2496 TCGTATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (26 bp):
AATACTGCTTATCCGACACCTGATTT
Found at i:5180 original size:39 final size:39
Alignment explanation
Indices: 5137--5254 Score: 166
Period size: 39 Copynumber: 3.0 Consensus size: 39
5127 TTATCGCTTT
*
5137 CCGCAGGCTCCTCGGCTTTGTGCTCAGGTTAAGTCCTTA
1 CCGCAGGCTCCTCGGCTTTGTGCACAGGTTAAGTCCTTA
*
5176 CCGCAGGCTCCTCGGCTTTGTGCACAAGG-TATGTCCTTA
1 CCGCAGGCTCCTCGGCTTTGTGCAC-AGGTTAAGTCCTTA
* * * *
5215 CTGCAGGCTTCTCTGCTTTGTGCACAGGTTAAGCCCTTA
1 CCGCAGGCTCCTCGGCTTTGTGCACAGGTTAAGTCCTTA
5254 C
1 C
5255 TTGGTGTACA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 3 0.04
39 64 0.91
40 3 0.04
ACGTcount: A:0.14, C:0.31, G:0.25, T:0.31
Consensus pattern (39 bp):
CCGCAGGCTCCTCGGCTTTGTGCACAGGTTAAGTCCTTA
Found at i:11713 original size:20 final size:20
Alignment explanation
Indices: 11688--11742 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
11678 TTTACACTTA
11688 GGGAACCGATTCCCCATGAG
1 GGGAACCGATTCCCCATGAG
11708 GGGAACCGATTCCCCATGAG
1 GGGAACCGATTCCCCATGAG
*
11728 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
11743 CCACGCTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGAACCGATTCCCCATGAG
Found at i:18629 original size:23 final size:23
Alignment explanation
Indices: 18603--18648 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
18593 TAAGAATTGT
18603 CCTAGGAGGTAGGAACGAATTCC
1 CCTAGGAGGTAGGAACGAATTCC
18626 CCTAGGAGGTAGGAACGAATTCC
1 CCTAGGAGGTAGGAACGAATTCC
18649 TATAGTTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.17
Consensus pattern (23 bp):
CCTAGGAGGTAGGAACGAATTCC
Found at i:37479 original size:99 final size:99
Alignment explanation
Indices: 37308--37606 Score: 598
Period size: 99 Copynumber: 3.0 Consensus size: 99
37298 ATACAAAATC
37308 AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
1 AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
37373 TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
66 TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
37407 AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
1 AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
37472 TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
66 TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
37506 AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
1 AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
37571 TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
66 TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
37605 AG
1 AG
37607 GTAAGGTAGT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 200 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (99 bp):
AGATTCTAAAATTTTCTCTAAACACGCACACTAACATAAGCATTCTAAAACTCATTAAAATTAGC
TGACCCTATTCCCATATGTAATGGGGTGAGGGGG
Found at i:40549 original size:30 final size:30
Alignment explanation
Indices: 40513--40571 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
40503 AATATTTGGC
* *
40513 CACTTTCATTTTTATTTTATCAAGATGTGT
1 CACTTTCATTTTTAATTAATCAAGATGTGT
* *
40543 CACTTTCGTTTTTAATTAATGAAGATGTG
1 CACTTTCATTTTTAATTAATCAAGATGTG
40572 GTCATTGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (30 bp):
CACTTTCATTTTTAATTAATCAAGATGTGT
Found at i:40866 original size:15 final size:16
Alignment explanation
Indices: 40827--40882 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
40817 AATAAGAGTT
* *
40827 TAAA-AATAATGGAAG
1 TAAATAATAATGAAAA
40842 TAATATAATAAT-AAAA
1 TAA-ATAATAATGAAAA
40858 TAAATAATAATGAGAAAA
1 TAAATAATAAT--GAAAA
40876 TAAATAA
1 TAAATAA
40883 AGCAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 11 0.32
16 6 0.18
17 6 0.18
18 11 0.32
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (16 bp):
TAAATAATAATGAAAA
Found at i:49625 original size:9 final size:8
Alignment explanation
Indices: 49610--49652 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 8
49600 AAAAATTAAT
49610 TAAAATAA
1 TAAAATAA
49618 T--AATAA
1 TAAAATAA
49624 TAAAATAA
1 TAAAATAA
49632 TAGAAATAA
1 TA-AAATAA
49641 TAGAAATAA
1 TA-AAATAA
49650 TAA
1 TAA
49653 TACTAATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.19
8 9 0.28
9 17 0.53
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (8 bp):
TAAAATAA
Found at i:49878 original size:12 final size:12
Alignment explanation
Indices: 49861--49886 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
49851 ATTTACTCCA
49861 AGTTAGTAAATT
1 AGTTAGTAAATT
49873 AGTTAGTAAATT
1 AGTTAGTAAATT
49885 AG
1 AG
49887 GATTCACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (12 bp):
AGTTAGTAAATT
Found at i:51560 original size:20 final size:20
Alignment explanation
Indices: 51535--51580 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
51525 AAACGAATGA
51535 TGTGCAATACTGCCATGGAC
1 TGTGCAATACTGCCATGGAC
51555 TGTGCAATACTGCCATGGAC
1 TGTGCAATACTGCCATGGAC
51575 TGTGCA
1 TGTGCA
51581 CCAAACACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (20 bp):
TGTGCAATACTGCCATGGAC
Found at i:54119 original size:30 final size:30
Alignment explanation
Indices: 54083--54141 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
54073 AATATTTGGC
* *
54083 CACTTTCATTTTTATTTTATCAAGATGTGT
1 CACTTTCATTTTTAATTAATCAAGATGTGT
* *
54113 CACTTTCGTTTTTAATTAATGAAGATGTG
1 CACTTTCATTTTTAATTAATCAAGATGTG
54142 GTCATTGAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (30 bp):
CACTTTCATTTTTAATTAATCAAGATGTGT
Found at i:54445 original size:18 final size:16
Alignment explanation
Indices: 54415--54452 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
54405 TGGAAGTAAT
54415 ATAATAATAAAAATAA
1 ATAATAATAAAAATAA
54431 ATAATAATGAGAAAATAA
1 ATAATAAT-A-AAAATAA
54449 ATAA
1 ATAA
54453 AGCAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
ATAATAATAAAAATAA
Found at i:63151 original size:9 final size:9
Alignment explanation
Indices: 63145--63177 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
63135 TTAAAATAAT
63145 AATAATA-A
1 AATAATAGA
63153 AATAATAGA
1 AATAATAGA
63162 AATAATAGA
1 AATAATAGA
63171 AATAATA
1 AATAATA
63178 TACTAATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (9 bp):
AATAATAGA
Found at i:63403 original size:12 final size:12
Alignment explanation
Indices: 63386--63411 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
63376 ATTTACTCCA
63386 AGTTAGTAAATT
1 AGTTAGTAAATT
63398 AGTTAGTAAATT
1 AGTTAGTAAATT
63410 AG
1 AG
63412 GATTCACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (12 bp):
AGTTAGTAAATT
Found at i:67974 original size:31 final size:32
Alignment explanation
Indices: 67933--67997 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
67923 ATACCAAACT
*
67933 TTGAACCAAGCATAAT-CGGTGCCAAACTTTG
1 TTGAAACAAGCATAATGCGGTGCCAAACTTTG
*
67964 TTGAAACAAGCATACTCGGCGGTGCCAAACTTTG
1 TTGAAACAAGCATAAT--GCGGTGCCAAACTTTG
67998 ATTTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
34 15 0.52
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (32 bp):
TTGAAACAAGCATAATGCGGTGCCAAACTTTG
Found at i:72483 original size:31 final size:32
Alignment explanation
Indices: 72442--72506 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
72432 ATACCAAACT
*
72442 TTGAACCAAGCATAAT-CGGTGCCAAACTTTG
1 TTGAAACAAGCATAATACGGTGCCAAACTTTG
*
72473 TTGAAACAAGCATACTCGACGGTGCCAAACTTTG
1 TTGAAACAAGCATAAT--ACGGTGCCAAACTTTG
72507 ATTTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
34 15 0.52
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (32 bp):
TTGAAACAAGCATAATACGGTGCCAAACTTTG
Found at i:76715 original size:12 final size:12
Alignment explanation
Indices: 76698--76727 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
76688 ATGAGGTGGA
76698 GTGATTATGATT
1 GTGATTATGATT
76710 GTGATTATGATT
1 GTGATTATGATT
*
76722 ATGATT
1 GTGATT
76728 TGGTACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (12 bp):
GTGATTATGATT
Found at i:79859 original size:24 final size:27
Alignment explanation
Indices: 79812--79863 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 27
79802 AAATTTAAGA
79812 AAAAATATAAATATTTGAAATAAAAAT
1 AAAAATATAAATATTTGAAATAAAAAT
*
79839 AAAAATA-AAA-A-TTGAATTAAAAAT
1 AAAAATATAAATATTTGAAATAAAAAT
79863 A
1 A
79864 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 13 0.54
25 1 0.04
26 3 0.12
27 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (27 bp):
AAAAATATAAATATTTGAAATAAAAAT
Found at i:81955 original size:18 final size:18
Alignment explanation
Indices: 81932--81968 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
81922 AGGTCTTGAG
81932 TTTAAACTTGATATCGTT
1 TTTAAACTTGATATCGTT
81950 TTTAAACTTGATATCGTT
1 TTTAAACTTGATATCGTT
81968 T
1 T
81969 AAACAAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTAAACTTGATATCGTT
Found at i:81969 original size:16 final size:16
Alignment explanation
Indices: 81931--81972 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 16
81921 AAGGTCTTGA
81931 GTTTAAACTTGATATC
1 GTTTAAACTTGATATC
81947 GTTTTTAAACTTGATATC
1 G--TTTAAACTTGATATC
81965 GTTTAAAC
1 GTTTAAAC
81973 AAGGTCTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
18 16 0.67
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
GTTTAAACTTGATATC
Found at i:82739 original size:31 final size:31
Alignment explanation
Indices: 82701--82771 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
82691 CTTTTAAAAC
**
82701 TTGCAATATAATCCCCCAACATTTAGTTTGT
1 TTGCAATATAATCCCCCAACATTTAGTCCGT
** **
82732 TTGCAATATGGTCCCTTAACATTTAGTCCGT
1 TTGCAATATAATCCCCCAACATTTAGTCCGT
82763 TTGCAATAT
1 TTGCAATAT
82772 GGTCCCTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (31 bp):
TTGCAATATAATCCCCCAACATTTAGTCCGT
Found at i:82772 original size:31 final size:31
Alignment explanation
Indices: 82718--82778 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
82708 ATAATCCCCC
**
82718 AACATTTAGTTTGTTTGCAATATGGTCCCTT
1 AACATTTAGTCCGTTTGCAATATGGTCCCTT
82749 AACATTTAGTCCGTTTGCAATATGGTCCCT
1 AACATTTAGTCCGTTTGCAATATGGTCCCT
82779 GACGTAACTG
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:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (31 bp):
AACATTTAGTCCGTTTGCAATATGGTCCCTT
Found at i:84578 original size:18 final size:18
Alignment explanation
Indices: 84548--84591 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
84538 GAATTATAAT
84548 AAAATTA-AATTTAA-TC
1 AAAATTATAATTTAACTC
84564 ACAAATTATAATTTAACTC
1 A-AAATTATAATTTAACTC
84583 AAAA-TATAA
1 AAAATTATAA
84592 CATCTTAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 11 0.44
18 10 0.40
19 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTATAATTTAACTC
Found at i:87774 original size:13 final size:13
Alignment explanation
Indices: 87756--87784 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
87746 TGATATACAC
87756 CATTAATGATGTA
1 CATTAATGATGTA
87769 CATTAATGATGTA
1 CATTAATGATGTA
87782 CAT
1 CAT
87785 CGATATACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTAATGATGTA
Found at i:88846 original size:35 final size:35
Alignment explanation
Indices: 88768--88902 Score: 109
Period size: 35 Copynumber: 3.9 Consensus size: 35
88758 TTAAAAATCT
*
88768 TAAACCCTAAACCTAAA-CCTTAA-TCTAATTATTA
1 TAAACCCTAAACCTAAATCCTAAACTCTAA-TATTA
* * *
88802 AAAATCCTAAATCCTAAATCCTAAACTCTAA-ATTC
1 TAAACCCTAAA-CCTAAATCCTAAACTCTAATATTA
**
88837 TAAACCCTAAACTCTAAATCCTAAAC-CATAA-AACA
1 TAAACCCTAAAC-CTAAATCCTAAACTC-TAATATTA
* * *
88872 TAAACCATAAACCATAAAACCTAAACCCTAA
1 TAAACCCTAAACC-TAAATCCTAAACTCTAA
88903 ACCATAACAC
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
34 12 0.14
35 60 0.72
36 6 0.07
37 5 0.06
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (35 bp):
TAAACCCTAAACCTAAATCCTAAACTCTAATATTA
Found at i:88927 original size:7 final size:7
Alignment explanation
Indices: 88807--88928 Score: 102
Period size: 7 Copynumber: 17.4 Consensus size: 7
88797 TATTAAAAAT
*
88807 CCTAAAT
1 CCTAAAC
*
88814 CCTAAAT
1 CCTAAAC
88821 CCTAAAC
1 CCTAAAC
* *
88828 TCTAAAT
1 CCTAAAC
*
88835 TCTAAAC
1 CCTAAAC
88842 CCTAAAC
1 CCTAAAC
* *
88849 TCTAAAT
1 CCTAAAC
88856 CCTAAAC
1 CCTAAAC
* *
88863 CATAAAA
1 CCTAAAC
*
88870 CATAAAC
1 CCTAAAC
*
88877 CATAAAC
1 CCTAAAC
* *
88884 CATAAAA
1 CCTAAAC
88891 CCTAAAC
1 CCTAAAC
88898 CCTAAAC
1 CCTAAAC
*
88905 CAT-AAC
1 CCTAAAC
88911 ACCTAAAC
1 -CCTAAAC
88919 CCTAAAC
1 CCTAAAC
88926 CCT
1 CCT
88929 TAATCTGATT
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
6 3 0.03
7 90 0.94
8 3 0.03
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:90173 original size:11 final size:11
Alignment explanation
Indices: 90157--90244 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
90147 GGACTGGGTC
90157 AATCGAGCTTG
1 AATCGAGCTTG
**
90168 AATCGAGCTCAA
1 AATCGAGCT-TG
*
90180 AATCAAGCTTG
1 AATCGAGCTTG
**
90191 AATCGAGCTCAA
1 AATCGAGCT-TG
* *
90203 AATTGAGCTTC
1 AATCGAGCTTG
*
90214 AATCGAGCTCG
1 AATCGAGCTTG
* *
90225 AGTCGAGCTTT
1 AATCGAGCTTG
*
90236 ATTCGAGCT
1 AATCGAGCT
90245 GATGAATTTT
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
11 41 0.72
12 16 0.28
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (11 bp):
AATCGAGCTTG
Found at i:90183 original size:23 final size:23
Alignment explanation
Indices: 90157--90223 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
90147 GGACTGGGTC
90157 AATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
*
90180 AATCAAGCTTGAATCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
* *
90203 AATTGAGCTTCAATCGAGCTC
1 AATCGAGCTTGAATCGAGCTC
90224 GAGTCGAGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGCTCAA
Found at i:90495 original size:16 final size:16
Alignment explanation
Indices: 90476--90559 Score: 109
Period size: 16 Copynumber: 5.3 Consensus size: 16
90466 TTTATGTTTG
90476 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
90492 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
90508 TTTATGTTCGTGTTCGT
1 TTTATGTTCGTGTTC-A
* *
90525 TTTATGTTCTTGTTCG
1 TTTATGTTCGTGTTCA
90541 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
90555 TTTAT
1 TTTAT
90560 TAAATGAACG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 40 0.66
17 14 0.23
ACGTcount: A:0.10, C:0.11, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:90539 original size:33 final size:32
Alignment explanation
Indices: 90470--90559 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 32
90460 CCAACGTTTA
*
90470 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
* *
90502 TGTTCGTTTATGTTCGTGTTCGTTTTATGTTCT
1 TGTTCGTTTATGTTCGTGTTC-ATTTATGTTCG
90535 TGTTCGTTTATGTTCGT-TT-ATTTAT
1 TGTTCGTTTATGTTCGTGTTCATTTAT
90560 TAAATGAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.09
32 22 0.42
33 26 0.49
ACGTcount: A:0.09, C:0.10, G:0.20, T:0.61
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
Found at i:99512 original size:23 final size:24
Alignment explanation
Indices: 99460--99513 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
99450 GAGTCAAGGG
*
99460 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTATGTAGTCCTTCGGGACAAA
*
99484 -TATATGTAGTCCTTC-GGACAAA
1 TTCTATGTAGTCCTTCGGGACAAA
99506 TTCTATGT
1 TTCTATGT
99514 GGCACTTAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (24 bp):
TTCTATGTAGTCCTTCGGGACAAA
Found at i:101754 original size:3 final size:3
Alignment explanation
Indices: 101746--101783 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
101736 TCTCAAAAAT
101746 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
101784 TAACATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.