Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001533.1 Hibiscus syriacus cultivar Beakdansim tig00003008_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: 84423
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5619 original size:21 final size:20
Alignment explanation
Indices: 5593--5632 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5583 GCATCAAGGT
*
5593 TTTTGTTGAAGCCATGAAATC
1 TTTTGTCGAAGCCAT-AAATC
*
5614 TTTTGTCGAGGCCATAAAT
1 TTTTGTCGAAGCCATAAAT
5633 TCCTGTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (20 bp):
TTTTGTCGAAGCCATAAATC
Found at i:13689 original size:28 final size:28
Alignment explanation
Indices: 13629--13702 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
13619 AAATAACCCC
* * *
13629 CATCATTTTTACTTTTTTATCTTATTTT
1 CATCTTTTTTACTTTTTCATCTTATTTG
*
13657 TATCTTTTTTACTTTTTCA-CTTAGTTTG
1 CATCTTTTTTACTTTTTCATCTTA-TTTG
*
13685 CATCTCTTCTT-CTTTTTC
1 CATCT-TTTTTACTTTTTC
13703 CTTCCTTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 4 0.11
28 30 0.79
29 4 0.11
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.65
Consensus pattern (28 bp):
CATCTTTTTTACTTTTTCATCTTATTTG
Found at i:16694 original size:22 final size:21
Alignment explanation
Indices: 16665--16705 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
16655 AAGATGCACA
16665 AGGAACCACTGCCACCTCTCC
1 AGGAACCACTGCCACCTCTCC
16686 AGGAGACCACTGCCACCTCT
1 AGGA-ACCACTGCCACCTCT
16706 GCTCCCCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.24, C:0.44, G:0.17, T:0.15
Consensus pattern (21 bp):
AGGAACCACTGCCACCTCTCC
Found at i:18744 original size:2 final size:2
Alignment explanation
Indices: 18733--18946 Score: 114
Period size: 2 Copynumber: 114.0 Consensus size: 2
18723 ATAATAACAT
18733 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
18772 TGA -A AA TA TA -A TA TA TGA -A GTT TA TA -A TA TA AA TA TA -A
1 T-A TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA
*
18810 TA -A TA TA TA TA CTA TA TA CTA TA TA -A AA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
18850 -A TA -A TA TA TA TCA AA TA TA TA CCA TA TA -A TA TA TA AA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
*
18891 -A TA TA TA T- TA TA AA T- TA -A TA TA TA CTA -A GTA 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
18930 TA -A TA -A TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
18947 CTTGTTGAGT
Statistics
Matches: 166, Mismatches: 14, Indels: 64
0.68 0.06 0.26
Matches are distributed among these distances:
1 23 0.14
2 132 0.80
3 11 0.07
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
TA
Found at i:18763 original size:41 final size:41
Alignment explanation
Indices: 18718--18946 Score: 172
Period size: 41 Copynumber: 5.5 Consensus size: 41
18708 ATATAATATA
*
18718 ATATAATAATAACATTATAATATATATATATATATATATAT
1 ATATAATAATAATATTATAATATATATATATATATATATAT
* * *
18759 ATATAAT-ATAATATGAAAATATA-ATATATGA-AGTTTATAAT
1 ATATAATAATAATATTATAATATATATATAT-ATA-TATAT-AT
* * *
18800 ATAAATATAATAATATATATACTATATACTATATA-AAATATA-
1 ATATA-ATAATAATAT-TATAATATATA-TATATATATATATAT
*
18842 ATATAATAATAATATATATCAA-ATATATACCATATA-ATATAT
1 ATATAATAATAATAT-TAT-AATATATATA-TATATATATATAT
*
18884 AAAT-ATAATATATATTATAA-AT-TAATATATACTAAGTATATAT
1 ATATAATAATA-ATATTATAATATAT-ATATATA-T-A-TATATAT
18927 ATATAATAATAATATATATA
1 ATATAATAATAATAT-TATA
18947 CTTGTTGAGT
Statistics
Matches: 152, Mismatches: 16, Indels: 37
0.74 0.08 0.18
Matches are distributed among these distances:
39 11 0.07
40 28 0.18
41 50 0.33
42 15 0.10
43 21 0.14
44 19 0.12
45 3 0.02
46 5 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (41 bp):
ATATAATAATAATATTATAATATATATATATATATATATAT
Found at i:18769 original size:32 final size:32
Alignment explanation
Indices: 18733--18946 Score: 158
Period size: 34 Copynumber: 6.4 Consensus size: 32
18723 ATAATAACAT
18733 TATAATATATATATATATATATATATATATAA
1 TATAATATATATATATATATATATATATATAA
* *
18765 TATAATATGAAAATATAATATATGAAGTTTATAATATAAA
1 TATAATAT--ATATAT-ATATAT--A-TATAT-ATAT-AA
*
18805 TATAATA-ATATATATACTATATACTATATAAAA
1 TATAATATATATATATA-TATATA-TATATATAA
*
18838 TATAATATA-ATAATAATATATATCAAATATATACCA
1 TATAATATATAT-AT-ATATATAT-ATATATATA--A
*
18874 TATAATATATAAATATA-ATATATAT-TATAA
1 TATAATATATATATATATATATATATATATAA
18904 -AT--TA-ATATATACTA-AGTATATATATATAA
1 TATAATATATATATA-TATA-TATATATATATAA
18933 TAATAATATATATA
1 T-ATAATATATATA
18947 CTTGTTGAGT
Statistics
Matches: 147, Mismatches: 10, Indels: 48
0.72 0.05 0.23
Matches are distributed among these distances:
26 6 0.04
27 5 0.03
28 7 0.05
29 7 0.05
30 1 0.01
31 2 0.01
32 12 0.08
33 16 0.11
34 32 0.22
35 17 0.12
36 15 0.10
37 10 0.07
38 4 0.03
39 4 0.03
40 9 0.06
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (32 bp):
TATAATATATATATATATATATATATATATAA
Found at i:18770 original size:43 final size:41
Alignment explanation
Indices: 18690--18946 Score: 142
Period size: 39 Copynumber: 6.4 Consensus size: 41
18680 TAAATTGAAT
* *
18690 TAAATTA-AATAAATATGTATATA-ATATAATAT-A-ATAA
1 TAAATTATAATATATATATATATATATATAATATAATATAA
18727 TAACATTATAATATATATATATATATATATATATATAATATAA
1 TAA-ATTATAATATATATATATATATATATA-ATATAATATAA
* * *
18770 T--ATGAAAATATA-ATATATGA-AGTTTATAATATAAATATAA
1 TAAATTATAATATATATATAT-ATA-TATATAATAT-AATATAA
18810 T-AA-TAT-ATATACTATATACTATATA-A-AATATAATATAA
1 TAAATTATAATATA-TATATA-TATATATATAATATAATATAA
* * *
18848 T-AATAAT-ATATATCAAATATATACCATATAATAT-ATA-AA
1 TAAATTATAATATAT-ATATATATA-TATATAATATAATATAA
* *
18887 TATAATATATATTATAAAT-TA-ATATATACTAAGTAT-ATATATA
1 TA-AAT-TATAATATATATATATATATATA-TAA-TATAATATA-A
*
18930 T-AATAATAATATATATA
1 TAAATTATAATATATATA
18947 CTTGTTGAGT
Statistics
Matches: 173, Mismatches: 19, Indels: 52
0.71 0.08 0.21
Matches are distributed among these distances:
37 3 0.02
38 19 0.11
39 53 0.31
40 49 0.28
41 31 0.18
42 7 0.04
43 11 0.06
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (41 bp):
TAAATTATAATATATATATATATATATATAATATAATATAA
Found at i:18948 original size:32 final size:30
Alignment explanation
Indices: 18708--18946 Score: 161
Period size: 27 Copynumber: 8.1 Consensus size: 30
18698 ATAAATATGT
* *
18708 ATATAATATA-ATATAATAATAACATTATA-
1 ATATAATATATATAT-ATAATAATAATATAT
18737 ATATATATATATATATATATATATATAATATA-
1 ATATA-ATATATATATATA-ATA-ATAATATAT
* * *
18769 ATATGAAAATATAATATATGAAGTTTATAATATAA
1 ATAT-AATATAT-ATATAT-AA--TAATAATATAT
*
18804 ATATAATA-ATATATATACT-AT-ATACTAT
1 ATATAATATATATATATAATAATAATA-TAT
18832 ATA-AA-ATATA-ATATAATAATAATATAT
1 ATATAATATATATATATAATAATAATATAT
*
18859 ATCA-AATATATACCATATAAT-AT-ATA-A-
1 AT-ATAATATATA-TATATAATAATAATATAT
*
18886 ATATAATATATAT-TATAA-ATTAATATAT
1 ATATAATATATATATATAATAATAATATAT
*
18914 ACTA-AGTATATATATATAATAATAATATAT
1 A-TATAATATATATATATAATAATAATATAT
18944 ATA
1 ATA
18947 CTTGTTGAGT
Statistics
Matches: 172, Mismatches: 12, Indels: 52
0.73 0.05 0.22
Matches are distributed among these distances:
25 6 0.03
26 11 0.06
27 26 0.15
28 23 0.13
29 23 0.13
30 20 0.12
31 15 0.09
32 21 0.12
33 10 0.06
34 12 0.07
35 5 0.03
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATAATATATATATATAATAATAATATAT
Found at i:22389 original size:21 final size:21
Alignment explanation
Indices: 22363--22402 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22353 CAGAACCCCA
*
22363 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
22384 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
22403 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:26296 original size:22 final size:21
Alignment explanation
Indices: 26254--26293 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
26244 GAGTTTGTTT
*
26254 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
26275 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
26294 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:28591 original size:2 final size:2
Alignment explanation
Indices: 28579--28733 Score: 129
Period size: 2 Copynumber: 82.0 Consensus size: 2
28569 TCAACAATAC
* *
28579 TA TA TA CTA TA TA AA TA TA -A TA TA TA -A TA TA TA CTA AA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* * *
28621 TA TA CA T- TA TA -A TA TA TA AA TA TA AA TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28659 TA -A TA -A TA -A TA TA TA TA TA -A TA TA TA TA T- TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
28695 TA TA TA AA TA TA -A TA TA TA TA TA TA TA CTA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA
28734 AAAAACAAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
1 13 0.10
2 103 0.83
3 8 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:28618 original size:11 final size:10
Alignment explanation
Indices: 28586--28735 Score: 106
Period size: 11 Copynumber: 13.8 Consensus size: 10
28576 TACTATATAC
28586 TATATAAATA
1 TATATAAATA
28596 TAATATATAATA
1 T-ATATA-AATA
28608 TATACTAAATA
1 TATA-TAAATA
*
28619 TATATACAT-
1 TATATAAATA
*
28628 TATAATATATA
1 TAT-ATAAATA
*
28639 AATATAAATA
1 TATATAAATA
28649 TA-ATATAATA
1 TATATA-AATA
28659 TAATAATAATATA
1 T-AT-ATAA-ATA
28672 TATATAATATA
1 TATATAA-ATA
*
28683 TATATTATATAA
1 TATA-TAAAT-A
28695 TATATAAATA
1 TATATAAATA
*
28705 TAATATATATA
1 T-ATATAAATA
*
28716 TATATACTATA
1 TATATA-AATA
28727 TCATATAAA
1 T-ATATAAA
28736 AAACAAAAAG
Statistics
Matches: 116, Mismatches: 9, Indels: 29
0.75 0.06 0.19
Matches are distributed among these distances:
9 6 0.05
10 29 0.25
11 52 0.45
12 22 0.19
13 7 0.06
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATATAAATA
Found at i:28624 original size:40 final size:39
Alignment explanation
Indices: 28574--28721 Score: 158
Period size: 33 Copynumber: 4.0 Consensus size: 39
28564 ATGTTTCAAC
*
28574 AATACTATATACTATATAAATATAATATATAATATATACTA
1 AATA-TATATAATATATAAATATAATATATAATATATA-TA
28615 AATATATATACAT-TATAATATATAA-ATATAA-ATATA-A
1 AATATATATA-ATATATAA-ATATAATATATAATATATATA
*
28652 TATA-ATATAATA-AT-AATAT-ATATATAATATATAT-
1 AATATATATAATATATAAATATAATATATAATATATATA
28686 -AT-TATATAATATATAAATATAATATAT-ATATATATA
1 AATATATATAATATATAAATATAATATATAATATATATA
28722 CTATATCATA
Statistics
Matches: 94, Mismatches: 2, Indels: 27
0.76 0.02 0.22
Matches are distributed among these distances:
32 1 0.01
33 20 0.21
34 8 0.09
35 17 0.18
36 11 0.12
37 4 0.04
39 5 0.05
40 17 0.18
41 11 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (39 bp):
AATATATATAATATATAAATATAATATATAATATATATA
Found at i:28733 original size:62 final size:56
Alignment explanation
Indices: 28579--28726 Score: 193
Period size: 53 Copynumber: 2.7 Consensus size: 56
28569 TCAACAATAC
* *
28579 TATATACTATATAAATATAATATATA-ATATATACTA-AATATATATACATTATAA
1 TATATAATATATAAATATAATATATATATATATACTATAATATATATAAATTATAA
28633 TATATAA-ATATAAATATAATATA-ATATA-ATA--ATAATATATATATAATATATATA
1 TATATAATATATAAATATAATATATATATATATACTATAATATATATA-AAT-TATA-A
28687 TTATATAATATATAAATATAATATATATATATATACTATA
1 -TATATAATATATAAATATAATATATATATATATACTATA
28727 TCATATAAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
50 1 0.01
51 10 0.12
52 6 0.07
53 23 0.28
54 7 0.09
55 7 0.09
56 16 0.20
57 5 0.06
58 3 0.04
60 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (56 bp):
TATATAATATATAAATATAATATATATATATATACTATAATATATATAAATTATAA
Found at i:28734 original size:27 final size:28
Alignment explanation
Indices: 28579--28727 Score: 175
Period size: 27 Copynumber: 5.4 Consensus size: 28
28569 TCAACAATAC
28579 TATATACTATATAAATATAATATATA-A
1 TATATACTATATAAATATAATATATATA
* *
28606 TATATACTAAATATATATACAT-TATA-A
1 TATATACTATATAAATATA-ATATATATA
*
28633 TATATA-AATATAAATATAATATA-ATA
1 TATATACTATATAAATATAATATATATA
* *
28659 TA-ATAATAATATATATATAATATATATA
1 TATATACT-ATATAAATATAATATATATA
*
28687 TTATATAATATATAAATATAATATATATA
1 -TATATACTATATAAATATAATATATATA
28716 TATATACTATAT
1 TATATACTATAT
28728 CATATAAAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
25 6 0.06
26 14 0.13
27 43 0.41
28 16 0.15
29 21 0.20
30 5 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
TATATACTATATAAATATAATATATATA
Found at i:36662 original size:11 final size:11
Alignment explanation
Indices: 36646--36670 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36636 AAGTAGATAA
36646 AAAAATTAAAT
1 AAAAATTAAAT
36657 AAAAATTAAAT
1 AAAAATTAAAT
36668 AAA
1 AAA
36671 TAAAAGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:37851 original size:17 final size:17
Alignment explanation
Indices: 37829--37882 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
37819 TTCTCCTTGA
37829 TTTTTGCTTGGTTGGTT
1 TTTTTGCTTGGTTGGTT
* *
37846 TTTTTGCTT-GCTCG-T
1 TTTTTGCTTGGTTGGTT
* *
37861 ATTTTACTTGGTTGGTT
1 TTTTTGCTTGGTTGGTT
37878 TTTTT
1 TTTTT
37883 ATGGTTTTCG
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 14 0.50
ACGTcount: A:0.04, C:0.09, G:0.22, T:0.65
Consensus pattern (17 bp):
TTTTTGCTTGGTTGGTT
Found at i:38483 original size:2 final size:2
Alignment explanation
Indices: 38457--38591 Score: 70
Period size: 2 Copynumber: 73.5 Consensus size: 2
38447 TTAGATCTAA
* *
38457 AT AT A- AT AT A- AT AA AT AT A- AT AT AT AT AT A- AT AT GA- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* *
38495 AT AT A- AT AT AT GA- ACT TT AT A- AT AT AA AT AT A- AT AT AT AT
1 AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
38535 A- AT AT AT A- AT AT AT ACT AT AT A- AT A- AT A- AT A- AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
38571 A- AT AT AT ACT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT A
38592 ATAATAATGT
Statistics
Matches: 104, Mismatches: 7, Indels: 44
0.67 0.05 0.28
Matches are distributed among these distances:
1 17 0.16
2 81 0.78
3 6 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:38503 original size:29 final size:26
Alignment explanation
Indices: 38457--38594 Score: 105
Period size: 27 Copynumber: 5.3 Consensus size: 26
38447 TTAGATCTAA
38457 ATATAATAT--AATA-AATATAATATAT
1 ATATAATATAAAATATAATAT-ATA-AT
38482 ATATAATATGAAAATATAATATATGAACT
1 ATATAATAT-AAAATATAATATAT-AA-T
*
38511 TTATAATAT-AAATATAATATAT-AT
1 ATATAATATAAAATATAATATATAAT
* *
38535 A-AT-ATATAATATATACTATATAAT
1 ATATAATATAAAATATAATATATAAT
38559 A-ATAATAATAATAATAT-ATACTATATAT
1 ATATAAT-ATAA-AATATAATA-TATA-AT
38587 ATATAATA
1 ATATAATA
38595 ATAATGTATC
Statistics
Matches: 93, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
22 4 0.04
23 13 0.14
24 6 0.06
25 12 0.13
26 6 0.06
27 21 0.23
28 11 0.12
29 20 0.22
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (26 bp):
ATATAATATAAAATATAATATATAAT
Found at i:38562 original size:3 final size:3
Alignment explanation
Indices: 38524--38599 Score: 57
Period size: 3 Copynumber: 23.7 Consensus size: 3
38514 TAATATAAAT
*
38524 ATA AT- ATA TATA ATA TATA ATA TATA CTA TATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA -ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA
*
38572 ATA TATA CT- ATA TATA TATA ATA ATA AT
1 ATA -ATA ATA ATA -ATA -ATA ATA ATA AT
38600 GTATCATATA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
2 3 0.05
3 37 0.61
4 21 0.34
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:38578 original size:38 final size:37
Alignment explanation
Indices: 38458--38594 Score: 82
Period size: 35 Copynumber: 3.8 Consensus size: 37
38448 TAGATCTAAA
38458 TATAATATA-ATA-AATAT-AATATAT-ATATA-ATA
1 TATAATATATATATAATATAAATATATAATATATATA
* *
38490 TGAAAATATAATATATGAACTTTATAATATA-AATATA-ATA
1 T-ATAATAT-ATATAT-AA-TATA-AATATATAATATATATA
*
38530 TAT-ATA-ATATATAATATATACTATATAATA-ATA-A
1 TATAATATATATATAATATA-AATATATAATATATATA
* *
38564 TAATAATA-ATATATACTATATATATATAATA
1 T-ATAATATATATATAATATAAATATATAATA
38595 ATAATGTATC
Statistics
Matches: 84, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
32 1 0.01
33 6 0.07
34 13 0.15
35 21 0.25
36 20 0.24
37 2 0.02
38 5 0.06
39 1 0.01
40 15 0.18
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (37 bp):
TATAATATATATATAATATAAATATATAATATATATA
Found at i:38594 original size:65 final size:65
Alignment explanation
Indices: 38454--38592 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 65
38444 AATTTAGATC
*
38454 TAAATATAATATAATAAATATAATATATATATAATATGAAAATATAATATATGAACTTTATAATA
1 TAAATATAATATAATAAATATAATATATATATAATATGAAAATATAATATATGAACTATATAATA
38519 TAAATATAATATATATAATATATAATATATACTAT-ATAAT-AATAATAATAATAATAT-ATACT
1 TAAATATAATATA-ATAA-ATATAATATATA-TATAAT-ATGAA-AAT-ATAAT-ATATGA-ACT
38581 ATATATATA
58 ATATA-ATA
38590 TAA
1 TAA
38593 TAATAATGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
65 13 0.20
66 4 0.06
67 16 0.25
68 8 0.12
69 6 0.09
70 11 0.17
71 6 0.09
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (65 bp):
TAAATATAATATAATAAATATAATATATATATAATATGAAAATATAATATATGAACTATATAATA
Found at i:38595 original size:29 final size:29
Alignment explanation
Indices: 38513--38599 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 29
38503 TATGAACTTT
*
38513 ATAATATA-AATATA-ATATAT-ATAATA
1 ATAATATATACTATATATATATAATAATA
38539 TATAATATATACTATATA-ATAATAATAATA
1 -ATAATATATACTATATATAT-ATAATAATA
38569 ATAATATATACTATATATATATAATAATA
1 ATAATATATACTATATATATATAATAATA
38598 AT
1 AT
38600 GTATCATATA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
27 8 0.15
28 7 0.13
29 31 0.57
30 8 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAATATATACTATATATATATAATAATA
Found at i:38596 original size:38 final size:34
Alignment explanation
Indices: 38459--38599 Score: 143
Period size: 36 Copynumber: 4.1 Consensus size: 34
38449 AGATCTAAAT
38459 ATAATATAATAA-ATATAATATATATATA-ATATGA
1 ATAATATAATAATATATAATATATATATATA-AT-A
* *
38493 A-AATATAAT-ATATGA-ACTTTATA-ATATAA-A
1 ATAATATAATAATAT-ATAATATATATATATAATA
38523 TATAATATATATAATATATAATATATACTATATAATA
1 -ATAATATA-ATAATATATAATATATA-TATATAATA
*
38560 ATAATAATAATAATATATACTATATATATATAATA
1 ATAAT-ATAATAATATATAATATATATATATAATA
38595 ATAAT
1 ATAAT
38600 GTATCATATA
Statistics
Matches: 90, Mismatches: 5, Indels: 23
0.76 0.04 0.19
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 11 0.12
33 20 0.22
34 12 0.13
35 14 0.16
36 27 0.30
37 4 0.04
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (34 bp):
ATAATATAATAATATATAATATATATATATAATA
Found at i:38609 original size:26 final size:27
Alignment explanation
Indices: 38471--38599 Score: 110
Period size: 29 Copynumber: 4.7 Consensus size: 27
38461 AATATAATAA
*
38471 ATATAATATAT-AT-ATAATATGA-A-A
1 ATATAATATATAATAATAATAT-ATACT
* *
38495 ATATAATATATGAACTTTATAATATA-AAT
1 ATATAATATAT-AA--TAATAATATATACT
38524 ATA-ATATATATAATATATAATATATACT
1 ATATA-ATATATAATA-ATAATATATACT
38552 ATATAATAATAATAATAATAATATATACT
1 ATATAAT-AT-ATAATAATAATATATACT
38581 ATAT-ATATATAATAATAAT
1 ATATAATATATAATAATAAT
38600 GTATCATATA
Statistics
Matches: 90, Mismatches: 3, Indels: 22
0.78 0.03 0.19
Matches are distributed among these distances:
24 11 0.12
26 13 0.14
27 10 0.11
28 15 0.17
29 35 0.39
30 6 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATAATATATAATAATAATATATACT
Found at i:39409 original size:37 final size:38
Alignment explanation
Indices: 39321--39409 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
39311 TTCACCCTAA
* *
39321 ACCCGAACCCGACCCGAATATCACACTTAAAAAAATCCC
1 ACCCG-ACCCGAACCGAATATCACACGTAAAAAAATCCC
* * * *
39360 ACCCGACTCGAACTGAATATCACACGTAAAAAACT-CG
1 ACCCGACCCGAACCGAATATCACACGTAAAAAAATCCC
*
39397 ACCTGACCCGAAC
1 ACCCGACCCGAAC
39410 AAAATAAAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
37 12 0.29
38 25 0.60
39 5 0.12
ACGTcount: A:0.39, C:0.36, G:0.11, T:0.13
Consensus pattern (38 bp):
ACCCGACCCGAACCGAATATCACACGTAAAAAAATCCC
Found at i:39645 original size:27 final size:28
Alignment explanation
Indices: 39587--39649 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
39577 AACCCGAACA
*
39587 CGACCCGAATATCACACTTAAAAAAACT
1 CGACCCGAATATCACACTTAAAAAAACC
*
39615 CGACCCGAATATTACACTT-AAAAAACC
1 CGACCCGAATATCACACTTAAAAAAACC
39642 CGACCCGA
1 CGACCCGA
39650 CTCGAACAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 15 0.45
28 18 0.55
ACGTcount: A:0.43, C:0.32, G:0.10, T:0.16
Consensus pattern (28 bp):
CGACCCGAATATCACACTTAAAAAAACC
Found at i:39869 original size:39 final size:40
Alignment explanation
Indices: 39810--39904 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 40
39800 TTTTCACCCT
39810 AAACTCGAACCCGACCCGACCCGAATATCACACGTAAAAA
1 AAACTCGAACCCGACCCGACCCGAATATCACACGTAAAAA
* * *
39850 AAACTCG-ACCCGACTCGACCCGAATATCACTC-T-TAAA
1 AAACTCGAACCCGACCCGACCCGAATATCACACGTAAAAA
*
39887 AAACCCG-ACCCGACCCGA
1 AAACTCGAACCCGACCCGA
39905 ACAAAATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 19 0.38
38 1 0.02
39 23 0.46
40 7 0.14
ACGTcount: A:0.38, C:0.38, G:0.13, T:0.12
Consensus pattern (40 bp):
AAACTCGAACCCGACCCGACCCGAATATCACACGTAAAAA
Found at i:39962 original size:36 final size:36
Alignment explanation
Indices: 39922--40008 Score: 165
Period size: 36 Copynumber: 2.4 Consensus size: 36
39912 AAAGTTTCAT
39922 CCGACCCGACCCGAATATATGAATTAGAAATCCAAC
1 CCGACCCGACCCGAATATATGAATTAGAAATCCAAC
*
39958 CCGACCCGATCCGAATATATGAATTAGAAATCCAAC
1 CCGACCCGACCCGAATATATGAATTAGAAATCCAAC
39994 CCGACCCGACCCGAA
1 CCGACCCGACCCGAA
40009 ATAATAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.37, C:0.33, G:0.15, T:0.15
Consensus pattern (36 bp):
CCGACCCGACCCGAATATATGAATTAGAAATCCAAC
Found at i:42880 original size:14 final size:14
Alignment explanation
Indices: 42861--42887 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42851 GGTGTTATCG
42861 TTTTCTTTTTGTTC
1 TTTTCTTTTTGTTC
42875 TTTTCTTTTTGTT
1 TTTTCTTTTTGTT
42888 AATTAATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTGTTC
Found at i:43080 original size:13 final size:13
Alignment explanation
Indices: 43062--43097 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
43052 AAAAAAGGGT
43062 AAATTAATTTCAA
1 AAATTAATTTCAA
43075 AAATTAATTTCAA
1 AAATTAATTTCAA
43088 AAATTAATTT
1 AAATTAATTT
43098 ATCCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATTAATTTCAA
Found at i:43353 original size:14 final size:15
Alignment explanation
Indices: 43322--43360 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
43312 GATTGGAGGA
*
43322 TAATTT-TTTAATTT
1 TAATTTATTTAATTC
43336 TAATTTATTTAA-TC
1 TAATTTATTTAATTC
43350 TAATTTATTTA
1 TAATTTATTTA
43361 TTTTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTATTTAATTC
Found at i:43416 original size:20 final size:20
Alignment explanation
Indices: 43391--43431 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43381 ACGTGTCACT
43391 ACTTTTATTAAAGGAAAACA
1 ACTTTTATTAAAGGAAAACA
43411 ACTTTTATTAAAGGAAAACA
1 ACTTTTATTAAAGGAAAACA
43431 A
1 A
43432 TTGGAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (20 bp):
ACTTTTATTAAAGGAAAACA
Found at i:43502 original size:38 final size:37
Alignment explanation
Indices: 43434--43505 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
43424 GAAAACAATT
* * *
43434 GGAGAAAATAAAATGCTACTATGTGGCTTCGAACAAA
1 GGAGAAAATAAAATGCCACTACGCGGCTTCGAACAAA
*
43471 GGAGAAAATAAAATGCCACTCCGCGGCCTTCGAAC
1 GGAGAAAATAAAATGCCACTACGCGG-CTTCGAAC
43506 CAATGGCCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 22 0.73
38 8 0.27
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (37 bp):
GGAGAAAATAAAATGCCACTACGCGGCTTCGAACAAA
Found at i:46420 original size:15 final size:15
Alignment explanation
Indices: 46392--46424 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
46382 AACAAATCTC
46392 CCTAAAACTATAAAGT
1 CCTAAAACTATAAA-T
46408 CCTAAAA-TATAAAT
1 CCTAAAACTATAAAT
46422 CCT
1 CCT
46425 TCAAAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.27
Consensus pattern (15 bp):
CCTAAAACTATAAAT
Found at i:47228 original size:169 final size:170
Alignment explanation
Indices: 46948--47286 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 170
46938 TTATTCAAGC
*
46948 CTAGACTTACTAGGGAGTATGAGAACATATAAATCATTAAAACAAATCTAATAATTGATTAAAAA
1 CTAGACTTACTAAGGAGTATGAGAACATATAAATCATTAAAACAAATCTAATAATTGATTAAAAA
47013 TGAGTTTAAGATTTTTATTGAATTAAATAAATTAAAATTTAAAAGAAAATGTATCTAATTAGATA
66 TGAGTTTAAGATTTTTATTGAATTAAATAAATTAAAATTTAAAAGAAAATGTATCTAATTAGATA
47078 ATGATATATGTTATTATTTGATTAAAAAACTAAATTTATT
131 ATGATATATGTTATTATTTGATTAAAAAACTAAATTTATT
47118 CTAGACTTACTAAGGAGTATGAGAACATATAAATCATTAAAA-AAATCTAATAATTGATTAAAAA
1 CTAGACTTACTAAGGAGTATGAGAACATATAAATCATTAAAACAAATCTAATAATTGATTAAAAA
47182 TGAGTTTAAGATTTTTATTGAATTAAATAAATTAAAATTTAAAAGAAAATGTATCTAATTAGATA
66 TGAGTTTAAGATTTTTATTGAATTAAATAAATTAAAATTTAAAAGAAAATGTATCTAATTAGATA
47247 ATGATATATGTTATTATTTGATTAAAAAACTAAATTTATT
131 ATGATATATGTTATTATTTGATTAAAAAACTAAATTTATT
47287 GAATTAAACT
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
169 127 0.76
170 41 0.24
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (170 bp):
CTAGACTTACTAAGGAGTATGAGAACATATAAATCATTAAAACAAATCTAATAATTGATTAAAAA
TGAGTTTAAGATTTTTATTGAATTAAATAAATTAAAATTTAAAAGAAAATGTATCTAATTAGATA
ATGATATATGTTATTATTTGATTAAAAAACTAAATTTATT
Found at i:50303 original size:20 final size:20
Alignment explanation
Indices: 50278--50315 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
50268 GTTACACGAG
50278 TAGGAGTAGCCGAGTAGGAT
1 TAGGAGTAGCCGAGTAGGAT
50298 TAGGAGTAGCCGAGTAGG
1 TAGGAGTAGCCGAGTAGG
50316 CAGAAGACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.42, T:0.18
Consensus pattern (20 bp):
TAGGAGTAGCCGAGTAGGAT
Found at i:50890 original size:14 final size:14
Alignment explanation
Indices: 50871--50897 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
50861 TTTGAGTAAA
50871 AAAATTAAAAATAG
1 AAAATTAAAAATAG
50885 AAAATTAAAAATA
1 AAAATTAAAAATA
50898 TTTTAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAATTAAAAATAG
Found at i:50893 original size:23 final size:23
Alignment explanation
Indices: 50867--50913 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
50857 AATATTTGAG
50867 TAAAAA-AATTAAAAATAGAAAAT
1 TAAAAATAATTAAAAATA-AAAAT
* *
50890 TAAAAATATTTTAAAATAAAAAT
1 TAAAAATAATTAAAAATAAAAAT
50913 T
1 T
50914 TATACAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAAATAATTAAAAATAAAAAT
Found at i:52022 original size:24 final size:25
Alignment explanation
Indices: 51980--52043 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
51970 AATACATGGG
* *
51980 CCCAAACCAAAACCGAAACCCA-GA
1 CCCAAAACAAAACCCAAACCCAGGA
*
52004 CCCAAAACAAGACCCAAACCCAGGA
1 CCCAAAACAAAACCCAAACCCAGGA
52029 -CCAAAACCAAAACCC
1 CCCAAAA-CAAAACCC
52044 TAGCCTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 25 0.74
25 9 0.26
ACGTcount: A:0.50, C:0.42, G:0.08, T:0.00
Consensus pattern (25 bp):
CCCAAAACAAAACCCAAACCCAGGA
Found at i:52030 original size:13 final size:12
Alignment explanation
Indices: 51980--52036 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
51970 AATACATGGG
* *
51980 CCCAAACCAAAA
1 CCCAAACCCAGA
*
51992 CCGAAACCCAGA
1 CCCAAACCCAGA
* *
52004 CCCAAAACAAGA
1 CCCAAACCCAGA
52016 CCCAAACCCAGGA
1 CCCAAACCCA-GA
*
52029 CCAAAACC
1 CCCAAACC
52037 AAAACCCTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
12 26 0.74
13 9 0.26
ACGTcount: A:0.49, C:0.42, G:0.09, T:0.00
Consensus pattern (12 bp):
CCCAAACCCAGA
Found at i:55521 original size:18 final size:18
Alignment explanation
Indices: 55500--55546 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
55490 ACAATAAGTA
* *
55500 GTATTGATATCGTATATG
1 GTATCGATACCGTATATG
55518 GTATCGATACCGTATATG
1 GTATCGATACCGTATATG
55536 GTATCGATACC
1 GTATCGATACC
55547 ATTTTAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (18 bp):
GTATCGATACCGTATATG
Found at i:58244 original size:42 final size:42
Alignment explanation
Indices: 58197--58278 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
58187 CCGAGGTTGC
58197 AAGAACACTATCGGTACTGGATGAACAATATCGATACTAACA
1 AAGAACACTATCGGTACTGGATGAACAATATCGATACTAACA
* * * * * *
58239 AAGAACAGTATTGGTGCTGGATGTACATTATCGGTACTAA
1 AAGAACACTATCGGTACTGGATGAACAATATCGATACTAA
58279 GTGCACAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.26
Consensus pattern (42 bp):
AAGAACACTATCGGTACTGGATGAACAATATCGATACTAACA
Found at i:61999 original size:21 final size:21
Alignment explanation
Indices: 61975--62017 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
61965 TCATTTTCAT
61975 TTTTAAATTTTGAAATCATGA
1 TTTTAAATTTTGAAATCATGA
**
61996 TTTTATGTTTTGAAATCATGA
1 TTTTAAATTTTGAAATCATGA
62017 T
1 T
62018 ATCAAATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTTAAATTTTGAAATCATGA
Found at i:64066 original size:24 final size:22
Alignment explanation
Indices: 64016--64066 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
64006 AACCAAAAAG
64016 GTAGTATCGCTACCATCACTAA
1 GTAGTATCGCTACCATCACTAA
* *
64038 G-AGTATCGGTACTACTACACTAA
1 GTAGTATCGCTACCA-T-CACTAA
64061 GTAGTA
1 GTAGTA
64067 CCGATACCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 7 0.29
24 4 0.17
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (22 bp):
GTAGTATCGCTACCATCACTAA
Found at i:79616 original size:18 final size:16
Alignment explanation
Indices: 79583--79657 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 16
79573 ACCTAAAGAG
*
79583 GAAAAAATTAAGAAAAA
1 GAAAAAA-TAATAAAAA
79600 TGAAAAAATGAAT-AAAA
1 -GAAAAAAT-AATAAAAA
79617 GAAAAAATATATAAAAAA
1 GAAAAAATA-AT-AAAAA
79635 GAATAAGAA-AA-AAAAA
1 GAA-AA-AATAATAAAAA
79651 GAAAAAA
1 GAAAAAA
79658 AAGAAAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
14 2 0.04
15 3 0.06
16 18 0.36
17 5 0.10
18 17 0.34
19 3 0.06
20 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.12
Consensus pattern (16 bp):
GAAAAAATAATAAAAA
Found at i:79666 original size:16 final size:16
Alignment explanation
Indices: 79592--79666 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
79582 GGAAAAAATT
*
79592 AAGAAAAATG-AAAAA
1 AAGAAAAAAGAAAAAA
*
79607 ATGAATAAAAGAAAAAA
1 AAGAA-AAAAGAAAAAA
* *
79624 TATATAAAAAAGAATAAGA
1 -A-AGAAAAAAGAA-AAAA
79643 AA-AAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
79658 AAGAAAAAA
1 AAGAAAAAA
79667 AAGGAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
15 9 0.19
16 19 0.40
17 6 0.12
18 9 0.19
19 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:79668 original size:9 final size:9
Alignment explanation
Indices: 79613--79676 Score: 60
Period size: 9 Copynumber: 7.2 Consensus size: 9
79603 AAAAATGAAT
79613 AAAAGAAAA
1 AAAAGAAAA
* * *
79622 AATATATAA
1 AAAAGAAAA
*
79631 AAAAG-AAT
1 AAAAGAAAA
*
79639 AAGA-AAAA
1 AAAAGAAAA
79647 AAAAGAAAA
1 AAAAGAAAA
79656 AAAAGAAAA
1 AAAAGAAAA
79665 AAAAGGAAAA
1 AAAA-GAAAA
79675 AA
1 AA
79677 GAGGAAGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
8 9 0.21
9 26 0.62
10 7 0.17
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:79682 original size:10 final size:10
Alignment explanation
Indices: 79639--79676 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
79629 AAAAAAGAAT
79639 AAGAAAAAAA
1 AAGAAAAAAA
79649 AAG-AAAAAA
1 AAGAAAAAAA
79658 AAGAAAAAAA
1 AAGAAAAAAA
*
79668 AGGAAAAAA
1 AAGAAAAAA
79677 GAGGAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:79687 original size:19 final size:19
Alignment explanation
Indices: 79639--79676 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
79629 AAAAAAGAAT
79639 AAGAAAAAAAAAGAAAAAA
1 AAGAAAAAAAAAGAAAAAA
*
79658 AAGAAAAAAAAGGAAAAAA
1 AAGAAAAAAAAAGAAAAAA
79677 GAGGAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAAGAAAAAA
Found at i:82487 original size:119 final size:120
Alignment explanation
Indices: 82198--82557 Score: 388
Period size: 119 Copynumber: 3.0 Consensus size: 120
82188 GATAAACCAG
* * *
82198 TCAA-CATTTCCATTGGAATGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCA
1 TCAATCATTTCCAATGGAATGGTTCATAATGAGAAGAACTCATCCGAGGAGGAAGAAAAAGTTCA
* * ** * *
82262 TAATGAGAAGAACTTGTTCAACC-TTTGCTTGATTCCATCACAAAAGGAGGTGGG
66 TAATGAGAAGAACTTGTTCGACCTTTTACTCAAATCCATCACAAAAGGAGGTGGA
* * * * * * *
82316 TCAAT-ACTTACAA-AGAAAGAGTTCATAATGAGAAGAACTCATCCAAGAAGGAAGAAGAAGTTC
1 TCAATCATTTCCAATGGAATG-GTTCATAATGAGAAGAACTCATCCGAGGAGGAAGAAAAAGTTC
* * * *
82379 ATAATGCGAAGACCGTGTTCGACCTTTTACTCAAATCCATCACAGAAGGAGGTGGA
65 ATAATGAGAAGAACTTGTTCGACCTTTTACTCAAATCCATCACAAAAGGAGGTGGA
* * * *
82435 TC-GTCATTTCCAATGGAATGGCTCATAATGAGAAGAACTCGTCCGAGGAGGAAGAATAAGTTCA
1 TCAATCATTTCCAATGGAATGGTTCATAATGAGAAGAACTCATCCGAGGAGGAAGAAAAAGTTCA
* ** * * * *
82499 TAATGAGAAGAAATTGTTCGACCTTTTTGTTTAAATTCATCACATAAGGAGTTGGA
66 TAATGAGAAGAACTTGTTCGACC-TTTTACTCAAATCCATCACAAAAGGAGGTGGA
82555 TCA
1 TCA
82558 CCATCATCAC
Statistics
Matches: 195, Mismatches: 40, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
117 4 0.02
118 68 0.35
119 91 0.47
120 32 0.16
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (120 bp):
TCAATCATTTCCAATGGAATGGTTCATAATGAGAAGAACTCATCCGAGGAGGAAGAAAAAGTTCA
TAATGAGAAGAACTTGTTCGACCTTTTACTCAAATCCATCACAAAAGGAGGTGGA
Found at i:82779 original size:20 final size:17
Alignment explanation
Indices: 82729--82771 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
82719 CAACATTTCC
82729 AATGAG-AG-AGTTCAT
1 AATGAGAAGAAGTTCAT
82744 AATGAGAAGAAGTTCAT
1 AATGAGAAGAAGTTCAT
82761 AATGAGAAGAA
1 AATGAGAAGAA
82772 CTTGTTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.23
16 2 0.08
17 18 0.69
ACGTcount: A:0.49, C:0.05, G:0.26, T:0.21
Consensus pattern (17 bp):
AATGAGAAGAAGTTCAT
Found at i:82815 original size:96 final size:96
Alignment explanation
Indices: 82651--82850 Score: 287
Period size: 96 Copynumber: 2.1 Consensus size: 96
82641 TCCGATGAGG
* * * *
82651 GAGAAAAAGTTCATAATGAGAATAACTTATTCAACCTTAGCCTGATTCCATCACAGAATGAGGTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTAGCCTGATTCCATCACAAAAGGAGGTG
82716 GATCAACATTTCCAAT-GAGAGAGTTCATAAT
66 GATCAACATTTCCAATGGA-AGAGTTCATAAT
* ** *
82747 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT-GGTTCGATTCTATCACAAAAGGAGGT
1 GAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTAGCCT-GATTCCATCACAAAAGGAGGT
*
82811 GGATCAATATTTCCAATGGAAGAGTTCATAAT
65 GGATCAACATTTCCAATGGAAGAGTTCATAAT
82843 GAGAAGAA
1 GAGAAGAA
82851 CTCACCCGAT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 2 0.02
96 89 0.96
97 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (96 bp):
GAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTAGCCTGATTCCATCACAAAAGGAGGTG
GATCAACATTTCCAATGGAAGAGTTCATAAT
Found at i:83015 original size:117 final size:118
Alignment explanation
Indices: 82747--83052 Score: 488
Period size: 117 Copynumber: 2.6 Consensus size: 118
82737 AGTTCATAAT
* * *
82747 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCTATCACAAAAGGAGGTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGATG
*
82812 GATCAATATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCACCCGATAAAG
66 GATCAATATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCAACCGATAAAG
* * *
82865 GAGAAAAAGTTCATAATGAGAAGAACTTATTCAACCTTAGCTCGATTCTATTACAAAAGGAGATG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGATG
* *
82930 GATCAATATTTCTAATGG-AGAGTTCATAATGAGAAGAACTCAACCGATAAGG
66 GATCAATATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCAACCGATAAAG
* * * *
82982 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCCATCACATAAGGAGTTG
1 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGATG
83047 GATCAA
66 GATCAA
83053 CATCAACACT
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
117 96 0.56
118 76 0.44
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (118 bp):
GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCTATCACAAAAGGAGATG
GATCAATATTTCCAATGGAAGAGTTCATAATGAGAAGAACTCAACCGATAAAG
Done.