Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000586.1 Hibiscus syriacus cultivar Beakdansim tig00001142_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: 115265
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4948 original size:24 final size:25
Alignment explanation
Indices: 4914--4966 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
4904 CTACACCATC
*
4914 TTAATTGAAAATAATTAAA-A-TATT
1 TTAATTAAAAATAA-TAAATATTATT
*
4938 TTAATTAAAAATTATAAATATTATT
1 TTAATTAAAAATAATAAATATTATT
4963 TTAA
1 TTAA
4967 GAGTGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.16
24 13 0.52
25 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAATTAAAAATAATAAATATTATT
Found at i:9104 original size:60 final size:60
Alignment explanation
Indices: 9031--9146 Score: 205
Period size: 60 Copynumber: 1.9 Consensus size: 60
9021 GAGGGCGTAT
* *
9031 TATACCCCTAAATACCCAACCCTTCATGTCCCCATCTCCCTATAAATATCCCATCCACGC
1 TATACCCCTAAATACCCAACCCTTCACGTCCCCATCTCCCTATAAATACCCCATCCACGC
*
9091 TATACCCCTAAATATCCAACCCTTCACGTCCCCATCTCCCTATAAATACCCCATCC
1 TATACCCCTAAATACCCAACCCTTCACGTCCCCATCTCCCTATAAATACCCCATCC
9147 TCAATCACTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.28, C:0.44, G:0.03, T:0.25
Consensus pattern (60 bp):
TATACCCCTAAATACCCAACCCTTCACGTCCCCATCTCCCTATAAATACCCCATCCACGC
Found at i:9207 original size:12 final size:10
Alignment explanation
Indices: 9166--9206 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
9156 TTTATCACAC
9166 CAAATTCTCT
1 CAAATTCTCT
9176 CAAATTCTCT
1 CAAATTCTCT
9186 -AAATTTCTCT
1 CAAA-TTCTCT
*
9196 CAAATACTCT
1 CAAATTCTCT
9206 C
1 C
9207 TTTTAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:9523 original size:111 final size:111
Alignment explanation
Indices: 9329--9550 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
9319 TGAAAATCAT
* *
9329 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
9394 TATTTAGTTGATTGATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
9440 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
9505 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
9551 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:11468 original size:21 final size:21
Alignment explanation
Indices: 11444--11483 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11434 ACCTGCTCAG
11444 GACGACGACGATGACGATGGT
1 GACGACGACGATGACGATGGT
11465 GACGACGACGATGACGATG
1 GACGACGACGATGACGATG
11484 ACAGCGAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.38, T:0.12
Consensus pattern (21 bp):
GACGACGACGATGACGATGGT
Found at i:27041 original size:15 final size:15
Alignment explanation
Indices: 27021--27051 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27011 CCATTGCAAG
27021 GTGGGATGAAACTGA
1 GTGGGATGAAACTGA
27036 GTGGGATGAAACTGA
1 GTGGGATGAAACTGA
27051 G
1 G
27052 GGTTTAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.19
Consensus pattern (15 bp):
GTGGGATGAAACTGA
Found at i:47420 original size:19 final size:20
Alignment explanation
Indices: 47388--47424 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47378 ATACATGAAT
*
47388 AAAA-AATATAAAAACAAAG
1 AAAATAATATAAAAAAAAAG
47407 AAAATAATATAAAAAAAA
1 AAAATAATATAAAAAAAA
47425 GCAAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (20 bp):
AAAATAATATAAAAAAAAAG
Found at i:47425 original size:19 final size:20
Alignment explanation
Indices: 47388--47431 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
47378 ATACATGAAT
47388 AAAA-AATATAAAAACAAAG
1 AAAATAATATAAAAACAAAG
47407 AAAATAATATAAAAA-AAAG
1 AAAATAATATAAAAACAAAG
*
47426 CAAATA
1 AAAATA
47432 TGAGTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAATAATATAAAAACAAAG
Found at i:47709 original size:31 final size:31
Alignment explanation
Indices: 47670--47772 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 31
47660 AATCGATTTG
47670 GGGA-CCAAATTAAATGTTTTTTAAAACAGA
1 GGGAGCCAAATTAAATGTTTTTTAAAACAGA
* * **** *
47700 GGGAGCCAAAATGAA-G-TTTACCCAACCGA
1 GGGAGCCAAATTAAATGTTTTTTAAAACAGA
47729 TTTGGG-GACCAAATTAAATGTTTTTTAAAACAGA
1 ---GGGAG-CCAAATTAAATGTTTTTTAAAACAGA
47763 GGGAGCCAAA
1 GGGAGCCAAA
47773 ATGAAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 15
0.64 0.17 0.19
Matches are distributed among these distances:
29 8 0.16
30 5 0.10
31 17 0.33
32 12 0.24
33 1 0.02
34 8 0.16
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (31 bp):
GGGAGCCAAATTAAATGTTTTTTAAAACAGA
Found at i:47762 original size:63 final size:63
Alignment explanation
Indices: 47663--47848 Score: 354
Period size: 63 Copynumber: 3.0 Consensus size: 63
47653 GGAATTAAAT
47663 CGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCCAAC
1 CGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCCAAC
47726 CGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCCAAC
1 CGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCCAAC
* *
47789 CGATTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 CGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
47849 CTTTTAGCAA
Statistics
Matches: 121, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 121 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (63 bp):
CGATTTGGGGACCAAATTAAATGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCCAAC
Found at i:48868 original size:43 final size:41
Alignment explanation
Indices: 48812--48893 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
48802 TAAATAAAAT
48812 TAATACTAATATATATATGTAAATATTATAAAAGTGTGGAG
1 TAATACTAATATATATATGTAAATATTATAAAAGTGTGGAG
*
48853 TAATACTAATATATATATGTAAGTATTATAAAAGTGTGGAG
1 TAATACTAATATATATATGTAAATATTATAAAAGTGTGGAG
48894 ACGAAATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (41 bp):
TAATACTAATATATATATGTAAATATTATAAAAGTGTGGAG
Found at i:53461 original size:21 final size:21
Alignment explanation
Indices: 53444--53502 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 21
53434 ATAATTTGCA
53444 CCGAAGTG-CCACATATTTGTC
1 CCGAA-TGACCACATATTTGTC
53465 CCGAATGACCACATAGATTTGTC
1 CCGAATGACCACAT--ATTTGTC
*
53488 CCGAAGGACCACATA
1 CCGAATGACCACATA
53503 GAATCCTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 2 0.06
21 12 0.35
23 20 0.59
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (21 bp):
CCGAATGACCACATATTTGTC
Found at i:53488 original size:23 final size:23
Alignment explanation
Indices: 53458--53504 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
53448 AGTGCCACAT
*
53458 ATTTGTCCCGAATGACCACATAG
1 ATTTGTCCCGAAGGACCACATAG
53481 ATTTGTCCCGAAGGACCACATAG
1 ATTTGTCCCGAAGGACCACATAG
53504 A
1 A
53505 ATCCTCGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (23 bp):
ATTTGTCCCGAAGGACCACATAG
Found at i:54460 original size:21 final size:20
Alignment explanation
Indices: 54414--54464 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
54404 ATTTAATTAT
54414 AGTATCGATACCTTCACACC
1 AGTATCGATACCTTCACACC
*
54434 AATATCGATACTTCTTCA-ACC
1 AGTATCGATAC--CTTCACACC
54455 AGTATCGATA
1 AGTATCGATA
54465 ATGTTCATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.29
Consensus pattern (20 bp):
AGTATCGATACCTTCACACC
Found at i:55795 original size:26 final size:27
Alignment explanation
Indices: 55766--55822 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
55756 TTATAATCAT
55766 TTAAAAATAATTTTGAAAATA-AAAA-A
1 TTAAAAATAATTTT-AAAATATAAAATA
**
55792 TT-AATTTAATTTTAAAATATAAAATA
1 TTAAAAATAATTTTAAAATATAAAATA
55818 TTAAA
1 TTAAA
55823 CTCATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 6 0.23
25 13 0.50
26 5 0.19
27 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TTAAAAATAATTTTAAAATATAAAATA
Found at i:55815 original size:25 final size:26
Alignment explanation
Indices: 55773--55821 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
55763 CATTTAAAAA
55773 TAATTTTGAAAATAAAAA-ATTAATT
1 TAATTTTGAAAATAAAAATATTAATT
55798 TAATTTT-AAAATATAAAATATTAA
1 TAATTTTGAAAATA-AAAATATTAA
55822 ACTCATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 11 0.50
26 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TAATTTTGAAAATAAAAATATTAATT
Found at i:55829 original size:26 final size:25
Alignment explanation
Indices: 55773--55830 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
55763 CATTTAAAAA
**
55773 TAATTTTGAAAATAAAAAATTAATT
1 TAATTTTGAAAATAAAAAATTAAAC
55798 TAATTTT-AAAATATAAAATATTAAAC
1 TAATTTTGAAAATA-AAAA-ATTAAAC
*
55824 TCATTTT
1 TAATTTT
55831 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 11 0.39
26 11 0.39
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTTTGAAAATAAAAAATTAAAC
Found at i:66297 original size:24 final size:25
Alignment explanation
Indices: 66261--66312 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
66251 TTCAATTGCA
*
66261 TAAAAAATAATTTGATTCATAAATT
1 TAAAAAATAATTTGAATCATAAATT
* * *
66286 TAAAAGAT-ATTTTAATCATACATT
1 TAAAAAATAATTTGAATCATAAATT
66310 TAA
1 TAA
66313 GGAAGTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
TAAAAAATAATTTGAATCATAAATT
Found at i:74464 original size:29 final size:29
Alignment explanation
Indices: 74422--74510 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
74412 CTACAGTGGT
74422 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
74451 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
74480 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
74509 CT
1 CT
74511 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:74555 original size:18 final size:18
Alignment explanation
Indices: 74532--74568 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
74522 AGAATAGGGC
74532 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
74550 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
74568 C
1 C
74569 GTGGGAATGC
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:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:74597 original size:43 final size:44
Alignment explanation
Indices: 74550--74640 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 44
74540 CAACATGGGA
74550 CATGCAATCAACATGGGACGTGGGAATGCAT-GGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
74593 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
74637 CATG
1 CATG
74641 GGGTGGGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 31 0.66
44 16 0.34
ACGTcount: A:0.27, C:0.14, G:0.42, T:0.16
Consensus pattern (44 bp):
CATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATG
Found at i:74652 original size:15 final size:15
Alignment explanation
Indices: 74612--74791 Score: 128
Period size: 15 Copynumber: 11.1 Consensus size: 15
74602 AACATGGGAC
74612 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
74628 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
74643 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
74658 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
74675 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
74693 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
74708 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
74725 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
74741 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
74761 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
*
74776 GTGGGAATACATGGG
1 GTGGGAATGCATGGG
74791 G
1 G
74792 GAGGGGATGG
Statistics
Matches: 130, Mismatches: 19, Indels: 31
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.01
15 51 0.39
16 27 0.21
17 30 0.23
18 3 0.02
19 15 0.12
20 3 0.02
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:74672 original size:65 final size:66
Alignment explanation
Indices: 74599--74725 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
74589 GATGCATGCA
74599 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
74663 G
66 G
*
74664 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
74726 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:74776 original size:51 final size:51
Alignment explanation
Indices: 74677--74818 Score: 245
Period size: 51 Copynumber: 2.8 Consensus size: 51
74667 AACATGGGAT
*
74677 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
74725 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
*
74776 GTGGGAATACATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
74819 CTGTGCATGG
Statistics
Matches: 89, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
48 23 0.26
51 66 0.74
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:75278 original size:21 final size:21
Alignment explanation
Indices: 75230--75278 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
75220 ACTAAAATCT
*
75230 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
75252 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
75273 AGTTAT
1 AGTTAT
75279 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:75288 original size:28 final size:28
Alignment explanation
Indices: 75255--75315 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
75245 TAGTATAAAT
*
75255 TATTAGTTTGTAAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
*
75283 TATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
75311 TATTA
1 TATTA
75316 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
TATTAGTTTATAAGTTTAAGTTATATTA
Found at i:75374 original size:41 final size:45
Alignment explanation
Indices: 75277--75386 Score: 129
Period size: 48 Copynumber: 2.4 Consensus size: 45
75267 AGTTTAAGTT
75277 ATATTATATTAGTTTATTAGTTTAAGTTATATTATATTATATAAAAA
1 ATATTA-ATTAGTTTATTAGTTTAAGTTATATTATA-TATATAAAAA
*
75324 ATTAGTTAATTAGTTTCTTAGTTTAAG-T-TATTA-A-ATATAAAAA
1 A-TA-TTAATTAGTTTATTAGTTTAAGTTATATTATATATATAAAAA
* *
75367 ATATTAATTAATTTGTTAGT
1 ATATTAATTAGTTTATTAGT
75387 GTCTTTAAAC
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
41 15 0.26
42 2 0.03
43 10 0.17
45 1 0.02
46 5 0.09
47 2 0.03
48 20 0.34
49 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (45 bp):
ATATTAATTAGTTTATTAGTTTAAGTTATATTATATATATAAAAA
Found at i:75864 original size:20 final size:21
Alignment explanation
Indices: 75820--75864 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
75810 AAATATTGTG
**
75820 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
75841 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
75861 TTTA
1 TTTA
75865 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:76146 original size:26 final size:25
Alignment explanation
Indices: 76117--76175 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
76107 AAATCATATT
*
76117 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
76143 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
76169 ATTATTA
1 ATTATTA
76176 GGTTATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:76921 original size:47 final size:47
Alignment explanation
Indices: 76818--76908 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
76808 CAACAAACAA
76818 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
* *
76866 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
76909 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
Found at i:76977 original size:41 final size:40
Alignment explanation
Indices: 76839--76977 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 40
76829 CTATTTAACT
* * *
76839 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATT
1 AACATAAACTAATTAAAT-ATTTTTTAACTAT-A-TAACTATA
*
76881 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATATTTTTTAACTATATAACTAT-A
* * *
76925 AACATATACTAATTAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATATTTTTTAA-CTATATA-ACTATA
*
76966 AACTTAAACTAA
1 AACATAAACTAA
76978 CAATCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
41 30 0.38
42 8 0.10
43 15 0.19
44 12 0.15
45 15 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (40 bp):
AACATAAACTAATTAAATATTTTTTAACTATATAACTATA
Found at i:77140 original size:4 final size:4
Alignment explanation
Indices: 77131--77169 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
77121 TCCTTTCTCC
**
77131 CTTT CTTT CTTT CTTT CCTTT CTCC CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CT
77170 CGGCTGCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:77149 original size:25 final size:25
Alignment explanation
Indices: 77120--77169 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
77110 TTCTTCTTAC
77120 TTCCTTTCTCCCTTTCTTTCTTTCT
1 TTCCTTTCTCCCTTTCTTTCTTTCT
77145 TTCCTTTCTCCCTTTCTTTCTTTCT
1 TTCCTTTCTCCCTTTCTTTCTTTCT
77170 CGGCTGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (25 bp):
TTCCTTTCTCCCTTTCTTTCTTTCT
Found at i:77259 original size:25 final size:25
Alignment explanation
Indices: 77231--77282 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
77221 TTTCTTTTAT
*
77231 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
77256 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
77281 AA
1 AA
77283 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:77430 original size:23 final size:23
Alignment explanation
Indices: 77403--77449 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
77393 GAATCTATAT
77403 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
77426 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
77449 G
1 G
77450 AATGGACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.26
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:77454 original size:13 final size:13
Alignment explanation
Indices: 77436--77467 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
77426 GGCTGCATGT
*
77436 GAATGGATGATGG
1 GAATGGACGATGG
77449 GAATGGACGATGG
1 GAATGGACGATGG
77462 GAATGG
1 GAATGG
77468 CGCCGGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (13 bp):
GAATGGACGATGG
Found at i:77501 original size:29 final size:29
Alignment explanation
Indices: 77468--77576 Score: 166
Period size: 29 Copynumber: 3.8 Consensus size: 29
77458 ATGGGAATGG
*
77468 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
77497 CGCCGGGAGTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
77526 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
77555 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
77577 CTCTATTCCA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
29 72 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.32, T:0.16
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:77632 original size:43 final size:43
Alignment explanation
Indices: 77571--77734 Score: 187
Period size: 43 Copynumber: 3.9 Consensus size: 43
77561 GGCTGCATGG
77571 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
***
77614 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCG--
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
* * **
77655 C-A-CTC-GTATGGCTCGTA-TGCATGGGGACCTCGCATGGGGAGAA
1 CGACCTCTCTAT---TC-CACTGCATGGCCACCTCGCATGGGGAGAA
77698 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGG
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGG
77735 CTCGCACTCG
Statistics
Matches: 97, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 1 0.01
41 22 0.23
42 2 0.02
43 59 0.61
44 1 0.01
45 3 0.03
46 3 0.03
ACGTcount: A:0.18, C:0.35, G:0.24, T:0.23
Consensus pattern (43 bp):
CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
Found at i:77688 original size:41 final size:41
Alignment explanation
Indices: 77631--77762 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
77621 TCTATTCCAC
77631 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
77672 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
77714 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
77756 TGCATGG
1 TGCATGG
77763 GGAGAACCAT
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:77729 original size:84 final size:84
Alignment explanation
Indices: 77588--77765 Score: 338
Period size: 84 Copynumber: 2.1 Consensus size: 84
77578 TCTATTCCAC
**
77588 TGCATGGCCACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
77653 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
77672 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
1 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
77737 CGCACTCGTATGGCTCGTA
66 CGCACTCGTATGGCTCGTA
77756 TGCATGGGGA
1 TGCATGGGGA
77766 GAACCATTGG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (84 bp):
TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCT
CGCACTCGTATGGCTCGTA
Found at i:77787 original size:35 final size:35
Alignment explanation
Indices: 77741--77853 Score: 226
Period size: 35 Copynumber: 3.2 Consensus size: 35
77731 ATGGCTCGCA
77741 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
77776 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
77811 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
1 CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
77846 CTCGTATG
1 CTCGTATG
77854 TTCCCGTATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
CTCGTATGGCTCGTATGCATGGGGAGAACCATTGG
Found at i:81202 original size:22 final size:22
Alignment explanation
Indices: 81174--81217 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
81164 AGATCTTGAC
81174 CCATTTGATTAATAAGAAAACT
1 CCATTTGATTAATAAGAAAACT
81196 CCATTTGATTAATAAGAAAACT
1 CCATTTGATTAATAAGAAAACT
81218 TTCGGACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
CCATTTGATTAATAAGAAAACT
Found at i:87350 original size:42 final size:42
Alignment explanation
Indices: 87281--87394 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 42
87271 AGTTTCAGCC
* * * **
87281 GTTTCGGTTGGTGGAGATGCAGCAGGAGACTCTGCGGAAGGT
1 GTTTCGGTTGGCGGAGACGCAGGAGGAGACTCCACGGAAGGT
*
87323 GTTTCGGTTGGCGGAGACACAGGAGGAGACTCCACGGAAGGT
1 GTTTCGGTTGGCGGAGACGCAGGAGGAGACTCCACGGAAGGT
*
87365 GTTTTGGTTGGCGGAGACGCAGGAGGAGAC
1 GTTTCGGTTGGCGGAGACGCAGGAGGAGAC
87395 AACGTAGAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.43, T:0.20
Consensus pattern (42 bp):
GTTTCGGTTGGCGGAGACGCAGGAGGAGACTCCACGGAAGGT
Found at i:87405 original size:42 final size:41
Alignment explanation
Indices: 87281--87407 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 41
87271 AGTTTCAGCC
* ** * **
87281 GTTTCGGTTGGTGGAGATGCAGCAGGAGACTCTGCGGAAGGT
1 GTTTCGGTTGGCGGAGACACAGGAGGAGAC-CAACGGAAGGT
*
87323 GTTTCGGTTGGCGGAGACACAGGAGGAGACTCCACGGAAGGT
1 GTTTCGGTTGGCGGAGACACAGGAGGAGAC-CAACGGAAGGT
* *
87365 GTTTTGGTTGGCGGAGACGCAGGAGGAGA-CAACGTAGAAGGT
1 GTTTCGGTTGGCGGAGACACAGGAGGAGACCAACG--GAAGGT
87407 G
1 G
87408 CCAGAGGTGG
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.05
42 70 0.95
ACGTcount: A:0.23, C:0.15, G:0.43, T:0.20
Consensus pattern (41 bp):
GTTTCGGTTGGCGGAGACACAGGAGGAGACCAACGGAAGGT
Found at i:94248 original size:18 final size:19
Alignment explanation
Indices: 94206--94249 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
94196 TTTGGTTTAC
*
94206 GGAATATAAGATTACCAATG
1 GGAATAAAAGATTACC-ATG
*
94226 AGAATAAAAGATTACC-TG
1 GGAATAAAAGATTACCATG
94244 GGAATA
1 GGAATA
94250 GGATTACTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCATG
Found at i:94417 original size:15 final size:15
Alignment explanation
Indices: 94399--94429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
94389 AAATTCTAAA
94399 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
94414 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
94429 T
1 T
94430 CTATATGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:96679 original size:84 final size:84
Alignment explanation
Indices: 96538--96699 Score: 315
Period size: 84 Copynumber: 1.9 Consensus size: 84
96528 TGACTAACAA
*
96538 TTAAAAAGAAAATTAACAAAAGCCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
1 TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
96603 AGCCAGAAAAACAGTTTAT
66 AGCCAGAAAAACAGTTTAT
96622 TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
1 TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
96687 AGCCAGAAAAACA
66 AGCCAGAAAAACA
96700 ATATATAAAC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (84 bp):
TTAAAAAGAAAATTAACAAAAACCCAAACATCCAACAAATTCAGATAAGAGATGTCAAAAGTAAA
AGCCAGAAAAACAGTTTAT
Found at i:97588 original size:24 final size:24
Alignment explanation
Indices: 97561--97608 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
97551 TTCTGTCTAT
97561 TTTTTCTTGGATGGATGCTATAAC
1 TTTTTCTTGGATGGATGCTATAAC
*
97585 TTTTTCTTGGATGGGTGCTATAAC
1 TTTTTCTTGGATGGATGCTATAAC
97609 CAGTTACTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.23, T:0.46
Consensus pattern (24 bp):
TTTTTCTTGGATGGATGCTATAAC
Found at i:100523 original size:25 final size:25
Alignment explanation
Indices: 100493--100559 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
100483 TATATATATA
*
100493 TATATATATAACATTTTATATTAAT
1 TATATATATAATATTTTATATTAAT
*
100518 TATATATATAATTTTTTATATTAAT
1 TATATATATAATATTTTATATTAAT
100543 TATATATATAATATTTT
1 TATATATATAATATTTT
100560 CTGGTTCGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATATATAATATTTTATATTAAT
Found at i:100801 original size:25 final size:25
Alignment explanation
Indices: 100773--100821 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
100763 AAAGATGACA
*
100773 TATTCTGTAAACAAGCAATAAAATG
1 TATTCCGTAAACAAGCAATAAAATG
*
100798 TATTCCGTAAACAATCAATAAAAT
1 TATTCCGTAAACAAGCAATAAAAT
100822 AACCGATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (25 bp):
TATTCCGTAAACAAGCAATAAAATG
Found at i:102041 original size:10 final size:11
Alignment explanation
Indices: 102011--102051 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
102001 TATTTAACAC
102011 AATATATAT-A
1 AATATATATAA
*
102021 TATATATATAA
1 AATATATATAA
102032 AATATA-ATAA
1 AATATATATAA
*
102042 AATTTATATA
1 AATATATATA
102052 TTTAAGTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATATATAA
Found at i:105190 original size:29 final size:29
Alignment explanation
Indices: 105144--105202 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
105134 GGCTTTAGGA
105144 TCAAAATACACTAAAAATTACTAAATTAT
1 TCAAAATACACTAAAAATTACTAAATTAT
*
105173 TCAAAATACACTATAAATTACTAAATTAT
1 TCAAAATACACTAAAAATTACTAAATTAT
105202 T
1 T
105203 TGAATTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (29 bp):
TCAAAATACACTAAAAATTACTAAATTAT
Found at i:105512 original size:14 final size:14
Alignment explanation
Indices: 105495--105523 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
105485 TGGGTTTAAT
105495 ATCTATTAAGAGCA
1 ATCTATTAAGAGCA
105509 ATCTATTAAGAGCA
1 ATCTATTAAGAGCA
105523 A
1 A
105524 AAAGTCTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
ATCTATTAAGAGCA
Done.