Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168177.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_415, 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: 27874
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Found at i:868 original size:4 final size:4
Alignment explanation
Indices: 851--899 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
841 ATATAATCCA
* * * *
851 ATAT ACAT ACAT ATAT ATAT ATAT ATAT ATAT TTAT ATAT TTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
899 A
1 A
900 AAAGTGTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:876 original size:10 final size:10
Alignment explanation
Indices: 851--899 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
841 ATATAATCCA
* *
851 ATATACATAC
1 ATATATATAT
861 ATATATATAT
1 ATATATATAT
871 ATATATATAT
1 ATATATATAT
*
881 ATTTATATAT
1 ATATATATAT
*
891 TTATATATA
1 ATATATATA
900 AAAGTGTGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATATATAT
Found at i:1703 original size:21 final size:24
Alignment explanation
Indices: 1663--1710 Score: 75
Period size: 21 Copynumber: 2.1 Consensus size: 24
1653 GATCAATTAA
1663 AATTAAAGTTCATACAAAATTATT
1 AATTAAAGTTCATACAAAATTATT
1687 AATTAAA-TT-AT-CAAAATTATT
1 AATTAAAGTTCATACAAAATTATT
1708 AAT
1 AAT
1711 AGTACATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.54
22 2 0.08
23 2 0.08
24 7 0.29
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTAAAGTTCATACAAAATTATT
Found at i:1712 original size:111 final size:113
Alignment explanation
Indices: 1595--1820 Score: 420
Period size: 111 Copynumber: 2.0 Consensus size: 113
1585 TTTATCTTCT
1595 TTAATAGTACATATCATGAGTTCTTAAATATATTTATATTATTTATTTATTTAATTTAGATCAAT
1 TTAATAGTACATATCATGAGTTCTTAAATATATTTATATTATTTATTTATTTAATTTAGATCAAT
1660 TAAAATTAAAGTTCATACAAAATTATTAATTAAATTAT-CAAA-ATTA
66 TAAAATTAAAGTTCATACAAAATTATTAATTAAATTATCCAAATATTA
*
1706 TTAATAGTACATATCATGAGTTCTTAAATATATTTATATTATTTATTTATTTATTTTAGATCAAT
1 TTAATAGTACATATCATGAGTTCTTAAATATATTTATATTATTTATTTATTTAATTTAGATCAAT
*
1771 TAGAATTAAAGTTCATACAAAATTATTAATTAAATTATCCAAATATTA
66 TAAAATTAAAGTTCATACAAAATTATTAATTAAATTATCCAAATATTA
1819 TT
1 TT
1821 GAGAAAGAGT
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
111 101 0.91
112 4 0.04
113 6 0.05
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (113 bp):
TTAATAGTACATATCATGAGTTCTTAAATATATTTATATTATTTATTTATTTAATTTAGATCAAT
TAAAATTAAAGTTCATACAAAATTATTAATTAAATTATCCAAATATTA
Found at i:3679 original size:22 final size:22
Alignment explanation
Indices: 3654--3764 Score: 93
Period size: 22 Copynumber: 5.0 Consensus size: 22
3644 AATTTAGGCG
* *
3654 AAATTAGTAATAACTTTATACT
1 AAATTAATAATAACTTTATAGT
* *
3676 AAATTAATGATAA-TTGTATAAT
1 AAATTAATAATAACTT-TATAGT
* *
3698 AAATT-ATGGATAACTTAATAGT
1 AAATTAAT-AATAACTTTATAGT
* *
3720 AAAATAATAATAACTTAATAGT
1 AAATTAATAATAACTTTATAGT
*
3742 AAATAAATAATAA-TTTAGTAGT
1 AAATTAATAATAACTTTA-TAGT
3764 A
1 A
3765 CATAATTAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.09
22 63 0.85
23 4 0.05
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
AAATTAATAATAACTTTATAGT
Found at i:3815 original size:22 final size:22
Alignment explanation
Indices: 3789--3836 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3779 ATAGTGTATG
*
3789 ATAACATAATAATAAAT-ACATA
1 ATAACATAATAAGAAATAACA-A
3811 ATAACATAATAAGAAATAACAA
1 ATAACATAATAAGAAATAACAA
3833 ATAA
1 ATAA
3837 TTTAACAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (22 bp):
ATAACATAATAAGAAATAACAA
Found at i:3921 original size:22 final size:22
Alignment explanation
Indices: 3887--4003 Score: 119
Period size: 22 Copynumber: 5.3 Consensus size: 22
3877 CACATATGAG
3887 TAAATTAAA-GATAACTTAATAA
1 TAAA-TAAATGATAACTTAATAA
* * *
3909 AAAATAAATGATAACTTAGTAG
1 TAAATAAATGATAACTTAATAA
* * * *
3931 TTAATTATTGATAACTTAGTAA
1 TAAATAAATGATAACTTAATAA
* * *
3953 TAATTCAATGATAACTTAATAG
1 TAAATAAATGATAACTTAATAA
*
3975 TAAATTAATGATAACTTAATAA
1 TAAATAAATGATAACTTAATAA
3997 TAAATAA
1 TAAATAA
4004 GATTCAGTTT
Statistics
Matches: 76, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
21 4 0.05
22 72 0.95
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (22 bp):
TAAATAAATGATAACTTAATAA
Found at i:3937 original size:44 final size:44
Alignment explanation
Indices: 3885--4003 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 44
3875 AACACATATG
* * *
3885 AGTAAATTAAAGATAACTTAATAAAAAATAAATGATAACTTAGT
1 AGTAAATTAATGATAACTTAATAATAAATAAATGATAACTTAAT
* * * * *
3929 AGTTAATTATTGATAACTTAGTAATAATTCAATGATAACTTAAT
1 AGTAAATTAATGATAACTTAATAATAAATAAATGATAACTTAAT
3973 AGTAAATTAATGATAACTTAATAATAAATAA
1 AGTAAATTAATGATAACTTAATAATAAATAA
4004 GATTCAGTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 62 1.00
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.34
Consensus pattern (44 bp):
AGTAAATTAATGATAACTTAATAATAAATAAATGATAACTTAAT
Found at i:4368 original size:47 final size:45
Alignment explanation
Indices: 4317--4415 Score: 105
Period size: 46 Copynumber: 2.2 Consensus size: 45
4307 ATAAATAGCT
* *
4317 TAGTAATAAATCAA-TGATAATTTAATAGTAAAT-AATTTATAAC-TAA
1 TAGTAATAAAT-AATTGA-AAATTAAAAGTAAATCAA--TATAACTTAA
*
4363 GTAGTAATTAATAATTGAAAATTAAAAGTAAATCAATATAACTTAA
1 -TAGTAATAAATAATTGAAAATTAAAAGTAAATCAATATAACTTAA
4409 TAGTAAT
1 TAGTAAT
4416 CATCAGTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
45 13 0.28
46 18 0.39
47 15 0.33
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (45 bp):
TAGTAATAAATAATTGAAAATTAAAAGTAAATCAATATAACTTAA
Found at i:4565 original size:22 final size:22
Alignment explanation
Indices: 4540--4598 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
4530 AACTTAATAA
*
4540 TAAATCAATTATAACATAGTTG
1 TAAATCAATAATAACATAGTTG
4562 TAAATGC-ATAATAACATAGTTG
1 TAAAT-CAATAATAACATAGTTG
* *
4584 TAAATTAATGATAAC
1 TAAATCAATAATAAC
4599 TTCATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (22 bp):
TAAATCAATAATAACATAGTTG
Found at i:4886 original size:44 final size:44
Alignment explanation
Indices: 4838--5149 Score: 172
Period size: 44 Copynumber: 7.0 Consensus size: 44
4828 TATAATAGTA
*
4838 TAATAGTAAATCATTAATAATTTAGTAGTAAATTATTGATAACT
1 TAATAGTAAATCATTAATAATTTAGTAGTAAATCATTGATAACT
* ** * *
4882 TAATAGTAAATCAATAATAACATAATAGTAAAACATTGATAACT
1 TAATAGTAAATCATTAATAATTTAGTAGTAAATCATTGATAACT
* * * * *
4926 TAATTGTAAATCAGTGATAATTTAGTTA-TAAATCAATGATAATTTAGTT
1 TAATAGTAAATCATTAATAATTTAG-TAGTAAATCATTGAT-A---A-CT
* * * *
4975 GTAAATTAGTTAATTATTAATAACTTTA-TAGTAAATCATTAACAACAT
1 -T-AA-TAGTAAATCATTAATAA-TTTAGTAGTAAATCATTGATAAC-T
* * * * * **
5023 T-ATAATAAATTATTAATAACTTAATAGTAAATTATCAAT-AC-
1 TAATAGTAAATCATTAATAATTTAGTAGTAAATCATTGATAACT
* * * *
5064 TAAGTAATAAATCATTTATAACTTAGCAGTAAATCATCT-ATAACT
1 TAA-TAGTAAATCATTAATAATTTAGTAGTAAATCAT-TGATAACT
* * * *
5109 TAAT-GATAAATC-GTGATAATTTAGTAGTAAATTAGTGATAA
1 TAATAG-TAAATCATTAATAATTTAGTAGTAAATCATTGATAA
5150 GATAGTAGTA
Statistics
Matches: 205, Mismatches: 43, Indels: 41
0.71 0.15 0.14
Matches are distributed among these distances:
41 1 0.00
42 2 0.01
43 56 0.27
44 103 0.50
45 7 0.03
47 1 0.00
48 3 0.01
49 1 0.00
50 1 0.00
51 5 0.02
52 21 0.10
53 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (44 bp):
TAATAGTAAATCATTAATAATTTAGTAGTAAATCATTGATAACT
Found at i:4935 original size:66 final size:66
Alignment explanation
Indices: 4837--4967 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
4827 GTATAATAGT
* * * * *
4837 ATAATAGTAAATCATTAATAATTTAGTAGTAAATTATTGATAACTTA-ATAGTAAATCAATAATA
1 ATAATAGTAAAACATTAATAACTTAATAGTAAATCAGTGATAACTTAGATA-TAAATCAATAATA
4901 AC
65 AC
* * * * *
4903 ATAATAGTAAAACATTGATAACTTAATTGTAAATCAGTGATAATTTAGTTATAAATCAATGATAA
1 ATAATAGTAAAACATTAATAACTTAATAGTAAATCAGTGATAACTTAGATATAAATCAATAATAA
4968 TTTAGTTGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 52 0.96
67 2 0.04
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (66 bp):
ATAATAGTAAAACATTAATAACTTAATAGTAAATCAGTGATAACTTAGATATAAATCAATAATAA
C
Found at i:4943 original size:22 final size:22
Alignment explanation
Indices: 4610--4967 Score: 140
Period size: 22 Copynumber: 16.3 Consensus size: 22
4600 TCATAAAAAA
*
4610 TGATAACTTAATAGTTAATCAT
1 TGATAACTTAATAGTAAATCAT
* * * *
4632 TGATAATTTAGTGGTAAATCAA
1 TGATAACTTAATAGTAAATCAT
* * * *
4654 TGAAAACTTAGTAGTAAATTAG
1 TGATAACTTAATAGTAAATCAT
* *
4676 TGATAGCATAATAGTAAAT--T
1 TGATAACTTAATAGTAAATCAT
* ** * * *
4696 TAGTTTAGTTTAAAAGTAATTAAAT
1 T-G-ATAACTTAATAGTAAAT-CAT
* *
4721 T-ATAAATTTAGTAGTAAATCAT
1 TGAT-AACTTAATAGTAAATCAT
** ** * *
4743 AAATAACTTAGCAATAAATCAA
1 TGATAACTTAATAGTAAATCAT
* *
4765 TGATAATTTAATAGCT-AATCAC
1 TGATAACTTAATAG-TAAATCAT
* * *
4787 T-AAAACTCAATAGTAAATCAA
1 TGATAACTTAATAGTAAATCAT
* * *
4808 TGATAAC-AAATTAGCAAAT-GT
1 TGATAACTTAA-TAGTAAATCAT
* *
4829 ATAAT-AGTATAATAGTAAATCAT
1 -TGATAACT-TAATAGTAAATCAT
* * * *
4852 TAATAATTTAGTAGTAAATTAT
1 TGATAACTTAATAGTAAATCAT
*
4874 TGATAACTTAATAGTAAATCAA
1 TGATAACTTAATAGTAAATCAT
* * *
4896 TAATAACATAATAGTAAAACAT
1 TGATAACTTAATAGTAAATCAT
* *
4918 TGATAACTTAATTGTAAATCAG
1 TGATAACTTAATAGTAAATCAT
* * *
4940 TGATAATTTAGTTA-TAAATCAA
1 TGATAACTTA-ATAGTAAATCAT
4962 TGATAA
1 TGATAA
4968 TTTAGTTGTA
Statistics
Matches: 246, Mismatches: 73, Indels: 34
0.70 0.21 0.10
Matches are distributed among these distances:
20 2 0.01
21 19 0.08
22 203 0.83
23 20 0.08
25 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (22 bp):
TGATAACTTAATAGTAAATCAT
Found at i:5015 original size:22 final size:22
Alignment explanation
Indices: 4981--5109 Score: 86
Period size: 22 Copynumber: 5.9 Consensus size: 22
4971 AGTTGTAAAT
* *
4981 TAGTTAATTATTAATAACTTTA
1 TAGTAAATCATTAATAACTTTA
* *
5003 TAGTAAATCATTAACAACATTA
1 TAGTAAATCATTAATAACTTTA
* * *
5025 TAATAAATTATTAATAACTTAA
1 TAGTAAATCATTAATAACTTTA
* * *
5047 TAGTAAATTATCAAT-AC-TAA
1 TAGTAAATCATTAATAACTTTA
* *
5067 GTAATAAATCATTTATAAC-TTA
1 -TAGTAAATCATTAATAACTTTA
*
5089 GCAGTAAATCATCT-ATAACTT
1 -TAGTAAATCAT-TAATAACTT
5110 AATGATAAAT
Statistics
Matches: 85, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
20 3 0.04
21 13 0.15
22 67 0.79
23 2 0.02
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (22 bp):
TAGTAAATCATTAATAACTTTA
Found at i:5041 original size:11 final size:11
Alignment explanation
Indices: 4986--5062 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
4976 TAAATTAGTT
4986 AATTATTAATA
1 AATTATTAATA
* *
4997 ACTT-TATAGTA
1 AATTAT-TAATA
* *
5008 AATCATTAACA
1 AATTATTAATA
5019 ACATTA-TAATA
1 A-ATTATTAATA
5030 AATTATTAATA
1 AATTATTAATA
* * *
5041 ACTTAATAGTA
1 AATTATTAATA
*
5052 AATTATCAATA
1 AATTATTAATA
5063 CTAAGTAATA
Statistics
Matches: 47, Mismatches: 15, Indels: 8
0.67 0.21 0.11
Matches are distributed among these distances:
10 5 0.11
11 38 0.81
12 4 0.09
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.39
Consensus pattern (11 bp):
AATTATTAATA
Found at i:5448 original size:22 final size:22
Alignment explanation
Indices: 5401--5483 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
5391 TATACCATAA
* *
5401 ATAACTTAGTAGTAATTCAA-TA
1 ATAACTTAGTAGTAAAT-AATTG
*
5423 ATAATTTAGTAGTAAATAATTG
1 ATAACTTAGTAGTAAATAATTG
* *
5445 ATAACTTAATAGCTAACT-ATTG
1 ATAACTTAGTAG-TAAATAATTG
* *
5467 AAAACTTAGTAATAAAT
1 ATAACTTAGTAGTAAAT
5484 CAATGTAATT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
21 6 0.12
22 39 0.80
23 4 0.08
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (22 bp):
ATAACTTAGTAGTAAATAATTG
Found at i:5674 original size:66 final size:66
Alignment explanation
Indices: 5604--5777 Score: 179
Period size: 66 Copynumber: 2.6 Consensus size: 66
5594 AATTTTGGAG
* * * *
5604 TAAATTATCGATAACTTCA-TAGTAAATTAGTTATAACTTTATAATAAATTATCAATAACTTAGT
1 TAAATTATCAATAACTT-AGTAGTAAATCAGTTATAACTTAATAATAAATCATCAATAACTTAGT
5668 AC
65 AC
* * * * *
5670 TAAATTATCAATAACTTAGTAGTAAATCATTTATAACTTAATAGTAAATCATTAATAATTTAATA
1 TAAATTATCAATAACTTAGTAGTAAATCAGTTATAACTTAATAATAAATCATCAATAACTTAGTA
*
5735 A
66 C
** * * * * *
5736 TAAACCATTAATAACGTAGTAATAAATCAGTAATGACTTAAT
1 TAAATTATCAATAACTTAGTAGTAAATCAGTTATAACTTAAT
5778 TGTCAATTGA
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
65 1 0.01
66 88 0.99
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (66 bp):
TAAATTATCAATAACTTAGTAGTAAATCAGTTATAACTTAATAATAAATCATCAATAACTTAGTA
C
Found at i:5732 original size:22 final size:22
Alignment explanation
Indices: 5614--5777 Score: 132
Period size: 22 Copynumber: 7.5 Consensus size: 22
5604 TAAATTATCG
* *
5614 ATAACTTCATAGTAAATTAGTT-
1 ATAACTTAATAGTAAATCA-TTA
* * * *
5636 ATAACTTTATAATAAATTATCA
1 ATAACTTAATAGTAAATCATTA
* * * *
5658 ATAACTTAGTACTAAATTATCA
1 ATAACTTAATAGTAAATCATTA
* *
5680 ATAACTTAGTAGTAAATCATTT
1 ATAACTTAATAGTAAATCATTA
5702 ATAACTTAATAGTAAATCATTA
1 ATAACTTAATAGTAAATCATTA
* * *
5724 ATAATTTAATAATAAACCATTA
1 ATAACTTAATAGTAAATCATTA
* * * *
5746 ATAACGTAGTAATAAATCAGTA
1 ATAACTTAATAGTAAATCATTA
*
5768 ATGACTTAAT
1 ATAACTTAAT
5778 TGTCAATTGA
Statistics
Matches: 118, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
21 1 0.01
22 117 0.99
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (22 bp):
ATAACTTAATAGTAAATCATTA
Found at i:5975 original size:22 final size:22
Alignment explanation
Indices: 5941--6017 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
5931 AGATCAGTGA
*
5941 TAATAATAAATCAATGATAACT
1 TAATAGTAAATCAATGATAACT
* ** *
5963 TATTAGTAAATCAATTTTAGCT
1 TAATAGTAAATCAATGATAACT
* * *
5985 TAGTACTAAAGTCTA-GATAACT
1 TAATAGTAAA-TCAATGATAACT
6007 TAATAGTAAAT
1 TAATAGTAAAT
6018 TATTCATATT
Statistics
Matches: 41, Mismatches: 13, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
21 1 0.02
22 37 0.90
23 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATAGTAAATCAATGATAACT
Found at i:6048 original size:22 final size:22
Alignment explanation
Indices: 6006--6048 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5996 TCTAGATAAC
* * *
6006 TTAATAGTAAATTATTCATATT
1 TTAATAATAAATTAGTAATATT
6028 TTAATAATAAATTAGTAATAT
1 TTAATAATAAATTAGTAATAT
6049 AACTTAATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAATAATAAATTAGTAATATT
Found at i:7633 original size:20 final size:19
Alignment explanation
Indices: 7593--7629 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7583 TTTTATAGTC
7593 AAAAAAATTTTAAAAAAAG
1 AAAAAAATTTTAAAAAAAG
*
7612 AAAAATATTTTAAAAAAA
1 AAAAAAATTTTAAAAAAA
7630 AGAATGAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
AAAAAAATTTTAAAAAAAG
Found at i:7838 original size:19 final size:19
Alignment explanation
Indices: 7814--7856 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
7804 TTTTAATTTT
7814 ATTATTATAAAATATTAAA
1 ATTATTATAAAATATTAAA
** *
7833 ATTATTATAGTATATTATA
1 ATTATTATAAAATATTAAA
7852 ATTAT
1 ATTAT
7857 AATTTGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTATTATAAAATATTAAA
Found at i:11135 original size:40 final size:40
Alignment explanation
Indices: 11091--11166 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
11081 AAGAGTTCAA
* *
11091 CTCTCATCGTAATGCCAATCCACTGAGATCCAAATGAACC
1 CTCTCATCGTAATGACAATCCACTAAGATCCAAATGAACC
* * *
11131 CTCTCATTGTAATGATACTCCACTAAGATCCAAATG
1 CTCTCATCGTAATGACAATCCACTAAGATCCAAATG
11167 GACTCTGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (40 bp):
CTCTCATCGTAATGACAATCCACTAAGATCCAAATGAACC
Found at i:23905 original size:2 final size:2
Alignment explanation
Indices: 23898--23924 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23888 TTTTCAAAAG
23898 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 A
23925 AAGTGTGTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24263 original size:19 final size:19
Alignment explanation
Indices: 24239--24281 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
24229 CCAAGAAACC
24239 ATCTCAAAGTTCACAAAGG
1 ATCTCAAAGTTCACAAAGG
*
24258 ATCTCAAAGTTCTCAAAGG
1 ATCTCAAAGTTCACAAAGG
24277 ATCTC
1 ATCTC
24282 CGTTATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (19 bp):
ATCTCAAAGTTCACAAAGG
Found at i:25348 original size:44 final size:42
Alignment explanation
Indices: 25296--25402 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 42
25286 TTATATGTAA
* * *
25296 TAAAATTTTTTAATTATTTAATATTTTTAAAATTAATAAATAAT
1 TAAAATTTTTTAATTATTT-ATA-TGTCAAAATTAATAAACAAT
* * *
25340 TCAAATTTTATTAAATTATTTTTATGTCAAATTTAATAAACAAT
1 TAAAATTTT-TT-AATTATTTATATGTCAAAATTAATAAACAAT
25384 TAAAATTTATTT-ATTATTT
1 TAAAATTT-TTTAATTATTT
25403 CATAAATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
42 7 0.13
44 33 0.62
45 5 0.09
46 8 0.15
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (42 bp):
TAAAATTTTTTAATTATTTATATGTCAAAATTAATAAACAAT
Found at i:25563 original size:6 final size:6
Alignment explanation
Indices: 25552--25576 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25542 CACAAATTTT
25552 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
25577 TTTATTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Done.