Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001909.1 Hibiscus syriacus cultivar Beakdansim tig00003865_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: 101852
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:6510 original size:22 final size:20
Alignment explanation
Indices: 6470--6517 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
6460 AATAAAAATG
6470 AGAAAAAGAAAAAGAAGAAA
1 AGAAAAAGAAAAAGAAGAAA
6490 AGAAGAAAGGAAAAATG-AGAAA
1 AGAA-AAA-GAAAAA-GAAGAAA
6512 A-AAAAA
1 AGAAAAA
6518 ATGAGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.28
21 5 0.20
22 12 0.48
23 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AGAAAAAGAAAAAGAAGAAA
Found at i:6513 original size:9 final size:9
Alignment explanation
Indices: 6499--6585 Score: 64
Period size: 9 Copynumber: 10.4 Consensus size: 9
6489 AAGAAGAAAG
6499 GAAAAATGA
1 GAAAAATGA
6508 G-AAAA--A
1 GAAAAATGA
6514 -AAAAATGA
1 GAAAAATGA
*
6522 GGAAAATGA
1 GAAAAATGA
*
6531 AAAATAATGA
1 GAAA-AATGA
*
6541 AAAAAAT--
1 GAAAAATGA
6548 GAAAAATGA
1 GAAAAATGA
6557 -AAAAA-GA
1 GAAAAATGA
6564 GAAAAATGA
1 GAAAAATGA
* *
6573 AAAAAAAGA
1 GAAAAATGA
6582 GAAA
1 GAAA
6586 TAAAAGAGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
6 5 0.08
7 8 0.13
8 15 0.24
9 25 0.40
10 9 0.15
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (9 bp):
GAAAAATGA
Found at i:6552 original size:6 final size:7
Alignment explanation
Indices: 6463--6576 Score: 58
Period size: 7 Copynumber: 15.7 Consensus size: 7
6453 AAAAAATAAT
6463 AAAAATG
1 AAAAATG
*
6470 AGAAAAAG
1 A-AAAATG
6478 AAAAA-G
1 AAAAATG
*
6484 AAGAAAAG
1 AA-AAATG
*
6492 AAGAAAGG
1 AA-AAATG
6500 AAAAATG
1 AAAAATG
*
6507 AGAAAA-A
1 A-AAAATG
6514 AAAAATG
1 AAAAATG
6521 AGGAAAATG
1 A--AAAATG
6530 AAAAAT-
1 AAAAATG
*
6536 AATGAA--
1 AA-AAATG
6542 AAAAATG
1 AAAAATG
6549 AAAAATG
1 AAAAATG
*
6556 AAAAAAGAG
1 -AAAAA-TG
6565 AAAAATG
1 AAAAATG
6572 AAAAA
1 AAAAA
6577 AAAGAGAAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
5 2 0.02
6 11 0.13
7 35 0.41
8 30 0.35
9 8 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (7 bp):
AAAAATG
Found at i:6586 original size:16 final size:16
Alignment explanation
Indices: 6470--6590 Score: 78
Period size: 16 Copynumber: 7.8 Consensus size: 16
6460 AATAAAAATG
*
6470 AGAAAAA-GAAAAAGA
1 AGAAAAATGAAAAAAA
*
6485 AG-AAAA-G-AAGAAA
1 AGAAAAATGAAAAAAA
* *
6498 GGAAAAATG-AGAAAA
1 AGAAAAATGAAAAAAA
6513 A-AAAAATGAGGAAAATGAA
1 AGAAAAATGA--AAAA--AA
*
6532 A-AATAATGAAAAAAA
1 AGAAAAATGAAAAAAA
* *
6547 TGAAAAATGAAAAAAG
1 AGAAAAATGAAAAAAA
6563 AGAAAAATGAAAAAAA
1 AGAAAAATGAAAAAAA
*
6579 AGAGAAAT-AAAA
1 AGAAAAATGAAAA
6591 GAGGGTTCAA
Statistics
Matches: 84, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
13 5 0.06
14 16 0.19
15 13 0.15
16 33 0.39
17 7 0.08
19 10 0.12
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.07
Consensus pattern (16 bp):
AGAAAAATGAAAAAAA
Found at i:7893 original size:99 final size:100
Alignment explanation
Indices: 7696--8146 Score: 736
Period size: 99 Copynumber: 4.5 Consensus size: 100
7686 AGTGAAGCAA
7696 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTG-A--AATAGGGAGC-GACAAGTTCGTTGAA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
7757 GATTGAGTCCTACTCTCTGAATGAATAGGGAGCGG
66 GATTGAGTCCTACTCTCTGAATGAATAGGGAGCGG
7792 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC-AGTTCGTTTGA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG-TTGA
*
7856 AGATTGAGTCCTA-TAC-CTGAATGAATAGGGAGTGG
65 AGATTGAGTCCTACT-CTCTGAATGAATAGGGAGCGG
*
7891 ACAAGTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
7956 GATTGAGTCCCTACTCTCTGAATGAATAGGGAGCGG
66 GATTGAGT-CCTACTCTCTGAATGAATAGGGAGCGG
*
7992 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTCGTTGAA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
*
8057 GATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
66 GATTGAGTCC--TACTCTCTGAATGAATAGGGAGCGG
* * * *
8094 ACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAACAGGGAGCGGAC
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
8147 CTATTTATTG
Statistics
Matches: 332, Mismatches: 11, Indels: 18
0.92 0.03 0.05
Matches are distributed among these distances:
96 35 0.11
97 1 0.00
99 100 0.30
100 34 0.10
101 90 0.27
102 72 0.22
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (100 bp):
ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
GATTGAGTCCTACTCTCTGAATGAATAGGGAGCGG
Found at i:8003 original size:200 final size:200
Alignment explanation
Indices: 7696--8146 Score: 752
Period size: 200 Copynumber: 2.3 Consensus size: 200
7686 AGTGAAGCAA
7696 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTG-A-AATAGGGAGC-GACAAGTTCGTTGAAG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGAATAGGGAGCGGACAAGTTCGTTGAAG
7758 ATTGAGTCCTACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTC
66 ATTGAGTCCTACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTC
* *
7823 TCTGAATGAATAGGGAGCGGAC-AGTTCGTTTGAAGATTGAGTCCTATA-C-CTGAATGAATAGG
131 TCTGAATGAATAGAGAGCGGACAAGTTCG-TTGAAGATTGAGTCCTATACCTCTGAAGGAATAGG
*
7885 GAGTGG
195 GAGCGG
*
7891 ACAAGTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAA
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA-GAATAGGGAGCGGACAAGTTCGTTGAA
7956 GATTGAGTCCCTACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATAC
65 GATTGAGT-CCTACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATAC
8021 TCTCTGAATGAATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATA
129 TCTCTGAATGAATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATAC-CTCTGAAGGAATA
8086 GGGAGCGG
193 GGGAGCGG
* * *
8094 ACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAACAGGGAGCGGAC
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTG-AAGAATAGGGAGCGGAC
8147 CTATTTATTG
Statistics
Matches: 238, Mismatches: 8, Indels: 12
0.92 0.03 0.05
Matches are distributed among these distances:
195 34 0.14
196 1 0.00
198 10 0.04
199 23 0.10
200 98 0.41
201 6 0.03
202 1 0.00
203 63 0.26
204 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (200 bp):
ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGAATAGGGAGCGGACAAGTTCGTTGAAG
ATTGAGTCCTACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACTC
TCTGAATGAATAGAGAGCGGACAAGTTCGTTGAAGATTGAGTCCTATACCTCTGAAGGAATAGGG
AGCGG
Found at i:8162 original size:51 final size:51
Alignment explanation
Indices: 7696--8146 Score: 735
Period size: 51 Copynumber: 9.0 Consensus size: 51
7686 AGTGAAGCAA
7696 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTG-A--AATAGGGAGC-G
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
7743 ACAAGTTCGTTGAAGATTGAGTCC--TACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
7792 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
7843 AC-AGTTCGTTTGAAGATTGAGTCCTATA--C-CTGAATGAATAGGGAGTGG
1 ACAAGTTCG-TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
7891 ACAAGTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
7942 ACAAGTTCGTTGAAGATTGAGTCC-CTACTCTCTGAATGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
7992 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
*
8043 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
* * * *
8094 ACTAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAACAGGGAGCGG
1 ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
8145 AC
1 AC
8147 CTATTTATTG
Statistics
Matches: 379, Mismatches: 13, Indels: 20
0.92 0.03 0.05
Matches are distributed among these distances:
45 9 0.02
46 1 0.00
47 24 0.06
48 48 0.13
49 32 0.08
50 56 0.15
51 209 0.55
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (51 bp):
ACAAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGG
Found at i:8198 original size:55 final size:51
Alignment explanation
Indices: 7699--8253 Score: 531
Period size: 51 Copynumber: 10.9 Consensus size: 51
7689 GAAGCAAACA
* * *
7699 AGTTCGTTGAAGATTGAGTCCTATACTCTCTG-A--AATAGGGAGC-GACA
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * * *
7746 AGTTCGTTGAAGATTGAGTCC--TACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * *
7795 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC-
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * * * *
7845 AGTTCGTTTGAAGATTGAGTCCTATA--C-CTGAATGAATAGGGAGTGGACA
1 AGTTC-ATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * * * *
7894 AGTTCGTTGAAGATTGAGTCATATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * * * *
7945 AGTTCGTTGAAGATTGAGTCC-CTACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * *
7995 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGAGAGCGGACA
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* *
8046 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACT
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * * * *
8097 AGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAACAGGGAGCGGACCT
1 AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGA-CT
* * * *
8149 A-TTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGACC
1 AGTTCATTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
* * * * *
8203 CGTTTTATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGC
1 AG-TTCATTGAAGATTG----AGTCCTATACTCTCTGAAGGAATAGAGAGC
8254 ATACACGTTT
Statistics
Matches: 456, Mismatches: 29, Indels: 37
0.87 0.06 0.07
Matches are distributed among these distances:
45 9 0.02
46 1 0.00
47 21 0.05
48 48 0.11
49 31 0.07
50 55 0.12
51 217 0.48
52 4 0.01
53 2 0.00
54 3 0.01
55 29 0.06
56 36 0.08
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
AGTTCATTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACT
Found at i:8234 original size:56 final size:56
Alignment explanation
Indices: 8010--8298 Score: 187
Period size: 51 Copynumber: 5.4 Consensus size: 56
8000 GTTGAAGATT
* * * ** **
8010 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
8061 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * *
8112 GAGTCCTATACTCCCTGAAAGAACAGGGAGCGGA-CC-TATTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAACAGAGAGCGGACCCGT-TTTATTGAAGATTGTTC
* *
8167 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** * *
8223 AAGTCTTATACTCTCTGAATGAATAGAGAGCATACACG-TTTA-TGAAGATTGTTT
1 GAGTCTTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
8277 GAGTCTTATACT-TCCTGAAGGA
1 GAGTCTTATACTCT-CTGAAGGA
8299 TTAGGGAGCA
Statistics
Matches: 200, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
51 88 0.44
53 1 0.00
54 30 0.15
55 32 0.16
56 47 0.23
57 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAACAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:18788 original size:15 final size:15
Alignment explanation
Indices: 18766--18803 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
18756 GATTTAGGTG
18766 AAAAAATAAATTTAT
1 AAAAAATAAATTTAT
*
18781 ATAAAATAAATTTAT
1 AAAAAATAAATTTAT
18796 AAAAAATA
1 AAAAAATA
18804 TTCAACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAAATAAATTTAT
Found at i:22135 original size:21 final size:21
Alignment explanation
Indices: 22093--22135 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
22083 TTTTTGGGCT
* * *
22093 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
22114 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
22135 A
1 A
22136 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:22187 original size:20 final size:20
Alignment explanation
Indices: 22162--22199 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22152 GAATGCTAGA
*
22162 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
22182 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
22200 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:22998 original size:22 final size:22
Alignment explanation
Indices: 22955--22998 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22945 ATCATTATAT
*
22955 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCAATTATACG
* *
22977 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
22999 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.27
Consensus pattern (22 bp):
GGCACTACGGTGCAATTATACG
Found at i:29082 original size:21 final size:21
Alignment explanation
Indices: 29040--29082 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29030 TTTTTGGGCT
* *
29040 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
29061 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
29082 A
1 A
29083 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:29894 original size:149 final size:149
Alignment explanation
Indices: 29624--29927 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
29614 GGGTAGAGGG
* *
29624 TCTACGCGGTTCCTTGGGACATATGTATATTCTTTGGAACATGTGTGAGGTTTTGAAAGACACAT
1 TCTACGCGGTTCCTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
29689 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
29754 TAGGGCACTACGGTGCAAT
131 TAGGGCACTACGGTGCAAT
*
29773 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCCTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
29838 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
*
29903 TATGGCACTACGGTGCAAT
131 TAGGGCACTACGGTGCAAT
29922 TCTACG
1 TCTACG
29928 GGGCACTTCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCCTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TAGGGCACTACGGTGCAAT
Found at i:29950 original size:23 final size:23
Alignment explanation
Indices: 29906--29950 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29896 ATCATTATAT
*
29906 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
29929 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
29951 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:33952 original size:3 final size:3
Alignment explanation
Indices: 33938--33971 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
33928 TCTGTAGAAA
*
33938 TCT TCG TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
33972 TATGTGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.32, G:0.03, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:37358 original size:2 final size:2
Alignment explanation
Indices: 37349--37406 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
37339 CTTTTTTTAC
37349 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37390 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
37407 CAACTTTCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40807 original size:19 final size:18
Alignment explanation
Indices: 40778--40815 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
40768 TTCAAGGATC
40778 ATTTTATAACAATTTTAT
1 ATTTTATAACAATTTTAT
*
40796 ATTTTAATAACACTTTTAT
1 ATTTT-ATAACAATTTTAT
40815 A
1 A
40816 ATAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATAACAATTTTAT
Found at i:44125 original size:17 final size:19
Alignment explanation
Indices: 44091--44126 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
44081 TTTTTTTATA
44091 TAAATAAATAACAATAATT
1 TAAATAAATAACAATAATT
44110 TAAA-AAATAA-AATAATT
1 TAAATAAATAACAATAATT
44127 AATATCTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 6 0.35
19 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAATAAATAACAATAATT
Found at i:47121 original size:26 final size:26
Alignment explanation
Indices: 47087--47137 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
47077 ATAATTAAAT
*
47087 TATATTTAAA-TTTAAATTATAATATA
1 TATAGTTAAAGTTTAAA-TATAATATA
*
47113 TATAGTTAAAGTTTACATATAATAT
1 TATAGTTAAAGTTTAAATATAATAT
47138 GATCTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TATAGTTAAAGTTTAAATATAATATA
Found at i:50176 original size:20 final size:20
Alignment explanation
Indices: 50146--50187 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
50136 ATTTAGTAAC
50146 AAAATTTATTT-ATAAATTA
1 AAAATTTATTTGATAAATTA
*
50165 AAAATATTATTTGATATATTA
1 AAAAT-TTATTTGATAAATTA
50186 AA
1 AA
50188 CAATCAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATTTATTTGATAAATTA
Found at i:51841 original size:21 final size:21
Alignment explanation
Indices: 51799--51841 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
51789 TTTTCGGGTT
* * *
51799 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
51820 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
51841 A
1 A
51842 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:52576 original size:149 final size:149
Alignment explanation
Indices: 52391--52686 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
52381 GGTCTACGTA
52391 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
1 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
*
52456 CATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGCAC
66 CATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
52521 TACGGTGCAATTCTACGCG
131 TACGGTGCAATTCTACGCG
52540 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
1 GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
52605 CATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
66 CATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
52670 TACGGTGCAATTCTACG
131 TACGGTGCAATTCTACG
52687 GGGCACTTCG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
GTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATC
CATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCAC
TACGGTGCAATTCTACGCG
Found at i:52709 original size:23 final size:23
Alignment explanation
Indices: 52665--52709 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
52655 ATCATTATAT
*
52665 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
52688 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
52710 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:53478 original size:22 final size:22
Alignment explanation
Indices: 53461--53527 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
53451 CTCGTATAAA
53461 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
53483 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
53505 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
53527 T
1 T
53528 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:53788 original size:30 final size:31
Alignment explanation
Indices: 53747--53805 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
53737 TAGACATAGT
*
53747 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
53777 ATTTACATACCTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
53806 GAACTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:53862 original size:29 final size:29
Alignment explanation
Indices: 53820--53891 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
53810 TTTTCTGCAT
**
53820 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
53849 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
53878 ATTCATGTCATGTA
1 ATTCATGTCATGTA
53892 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:54312 original size:68 final size:68
Alignment explanation
Indices: 54194--54346 Score: 202
Period size: 68 Copynumber: 2.2 Consensus size: 68
54184 TTTTTCTCAT
* * * * *
54194 GGGGGAATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTTATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TAC-A
54259 -TGA-
64 TTGAG
* * *
54262 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCATT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATT
54327 GAG
66 GAG
54330 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
54347 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 1 0.01
67 5 0.07
68 69 0.92
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACATT
GAG
Found at i:54357 original size:68 final size:67
Alignment explanation
Indices: 54194--54368 Score: 185
Period size: 68 Copynumber: 2.6 Consensus size: 67
54184 TTTTTCTCAT
* * * * *
54194 GGGGGAATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTTATATACGA
1 GGGGGTATCGGT-TCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
54259 TGA
65 TGA
* * *
54262 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
54325 TTGA
65 -TGA
* *
54329 GGGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 -GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
54369 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
66 7 0.08
67 5 0.05
68 80 0.87
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:58438 original size:108 final size:109
Alignment explanation
Indices: 58261--58460 Score: 271
Period size: 108 Copynumber: 1.8 Consensus size: 109
58251 TATTCATGTA
* * *
58261 ATAATTTTTTAAAAAAATTTCACACTTTAAAGTTATTATTGATATAGTCATGGATAATGATTAAG
1 ATAATTTTTTAAAAAAATTTCACACTTTAAAGTTATTATCGATATAGTCATGGATAATAACTAAG
*** *
58326 AATCTATTGGAGTTGATCAAAAAATTTCGGTAAATATATATATG
66 AATCTATCAAAGTTGATAAAAAAATTTCGGTAAATATATATATG
** *
58370 ATAATTTTTTTTAAAAATTT-ACACTTT-ATGATTATTATCGATATAGTCATGGATAATAACT-A
1 ATAATTTTTTAAAAAAATTTCACACTTTAAAG-TTATTATCGATATAGTCATGGATAATAACTAA
58432 GAAATCTATCAAAGTTGATAAAAAAATTT
65 G-AATCTATCAAAGTTGATAAAAAAATTT
58461 GACAGTGAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
107 4 0.05
108 57 0.72
109 18 0.23
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (109 bp):
ATAATTTTTTAAAAAAATTTCACACTTTAAAGTTATTATCGATATAGTCATGGATAATAACTAAG
AATCTATCAAAGTTGATAAAAAAATTTCGGTAAATATATATATG
Found at i:63541 original size:234 final size:234
Alignment explanation
Indices: 63116--63559 Score: 678
Period size: 234 Copynumber: 1.9 Consensus size: 234
63106 CTCAGTCTTC
* * * * *
63116 AAATGTATGGTTGCAGAGTGATTCAGTAGGTGCATGGACTGTAATTCCCCTTCTTTTTCTTAAAG
1 AAATATATGGCTGCAGAGTGATTCAGAAGATGCATGGACTGTAATTCCCCATCTTTTTCTTAAAG
* *
63181 AAAAAAATGTCATGCTTTAATGTAGTTAATTTTTTTAGTCTTGAGAACCGTAGCCTCCATCTTAC
66 AAAAAAATGTCATGCTTTAATGGAGTTAATTTTGTTAGTCTTGAGAACCGTAGCCTCCATCTTAC
* * *
63246 GTTGAAGTCATTTTAGCTTACATTCCCTGACTTAGTATACTGTACATGCTGCATAGAACCATTTT
131 GCTGAAGTCATTTTAGCTTACATTCCCTGACTTAGCATACTGGACATGCTGCATAGAACCATTTT
*
63311 AATGATTCGAGTTACTGGTCACGTATTGGCTCTGCCTTT
196 AATGATTCGAATTACTGGTCACGTATTGGCTCTGCCTTT
63350 AAATATATGGCTGCAGAGTGATTCAGAAGATGCATGGACTGTAATTCCCCATCTTTTT-TTAAAA
1 AAATATATGGCTGCAGAGTGATTCAGAAGATGCATGGACTGTAATTCCCCATCTTTTTCTT-AAA
* * *
63414 GAAAAAAATGTCATGCTTTAATGGAGTTAA-TTTGTTAGTGTTGATAGCCGTAGCCTCCATCTTA
65 GAAAAAAATGTCATGCTTTAATGGAGTTAATTTTGTTAGTCTTGAGAACCGTAGCCTCCATCTTA
* * * *
63478 TGCTGAAGTCATTTTAGAC-TACATTCCCTGGCTTTAGCATATTGGACATGCTGCATGGAACCAT
130 CGCTGAAGTCATTTTAG-CTTACATTCCCTGAC-TTAGCATACTGGACATGCTGCATAGAACCAT
63542 TTTAATGATTCGAATTAC
193 TTTAATGATTCGAATTAC
63560 AATAGATATG
Statistics
Matches: 189, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
233 59 0.31
234 130 0.69
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (234 bp):
AAATATATGGCTGCAGAGTGATTCAGAAGATGCATGGACTGTAATTCCCCATCTTTTTCTTAAAG
AAAAAAATGTCATGCTTTAATGGAGTTAATTTTGTTAGTCTTGAGAACCGTAGCCTCCATCTTAC
GCTGAAGTCATTTTAGCTTACATTCCCTGACTTAGCATACTGGACATGCTGCATAGAACCATTTT
AATGATTCGAATTACTGGTCACGTATTGGCTCTGCCTTT
Found at i:65722 original size:16 final size:16
Alignment explanation
Indices: 65690--65733 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
65680 AAATTAACCG
65690 AAAACCGAT--CC-AA
1 AAAACCGATAACCGAA
65703 AAAACCGATAACCGAA
1 AAAACCGATAACCGAA
65719 AAAACCCGA-AACCGA
1 AAAA-CCGATAACCGA
65734 TTTAGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
15 2 0.07
16 12 0.44
17 4 0.15
ACGTcount: A:0.55, C:0.30, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAACCGATAACCGAA
Found at i:68896 original size:6 final size:6
Alignment explanation
Indices: 68873--68921 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
68863 GTATTACTCC
68873 CTCCCT CTCTCC- CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT
1 CTCCCT CTC-CCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT CTCCCT
68921 C
1 C
68922 CTATGAGCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 2 0.05
6 37 0.90
7 2 0.05
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:68937 original size:7 final size:7
Alignment explanation
Indices: 68925--68969 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
68915 CTCCCTCCTA
68925 TGAGCTT
1 TGAGCTT
68932 TGAGCTT
1 TGAGCTT
68939 TGAGCTT
1 TGAGCTT
68946 TGAGCTT
1 TGAGCTT
68953 TGAGCTT
1 TGAGCTT
68960 TGAGCTT
1 TGAGCTT
68967 TGA
1 TGA
68970 AGTTGACTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (7 bp):
TGAGCTT
Found at i:69486 original size:27 final size:26
Alignment explanation
Indices: 69428--69488 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
69418 TTTAAAATGT
* *
69428 AAATAAAATAAATACACATTTATATT
1 AAATAAAATAAACACACATTTATATG
69454 AGAATAAAATAAACACACATTTATACTG
1 A-AATAAAATAAACACACATTTATA-TG
69482 AAATAAA
1 AAATAAA
69489 TATGTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (26 bp):
AAATAAAATAAACACACATTTATATG
Found at i:75296 original size:22 final size:22
Alignment explanation
Indices: 75271--75321 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
75261 TTGAATAGTA
75271 TGCCATCCATCTACGCTACGCT
1 TGCCATCCATCTACGCTACGCT
75293 TGCCATCCATCTACGCTACGCT
1 TGCCATCCATCTACGCTACGCT
75315 TGCCATC
1 TGCCATC
75322 TGCCAGGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.41, G:0.14, T:0.27
Consensus pattern (22 bp):
TGCCATCCATCTACGCTACGCT
Found at i:82620 original size:15 final size:15
Alignment explanation
Indices: 82602--82633 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
82592 TTTATTATTA
82602 TTTATTAATTATTTT
1 TTTATTAATTATTTT
82617 TTTATTAATTATTTT
1 TTTATTAATTATTTT
82632 TT
1 TT
82634 ATTTTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTAATTATTTT
Found at i:82635 original size:22 final size:22
Alignment explanation
Indices: 82581--82645 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
82571 AAATAGGTTT
* * *
82581 TTATTAATGATTTTATTATTAT
1 TTATTAATTATTTTTTTATTAA
82603 TTATTAATTATTTTTTTATTAA
1 TTATTAATTATTTTTTTATTAA
**
82625 TTATTTTTTATTTTTTTATTA
1 TTATTAATTATTTTTTTATTA
82646 CAAATAGTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTATTAATTATTTTTTTATTAA
Found at i:85250 original size:22 final size:23
Alignment explanation
Indices: 85219--85262 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
85209 TATATTATCA
*
85219 ATAAAATATAT-AAAATAAATAC
1 ATAAAATATATGAAAAAAAATAC
*
85241 ATAAATTATATGAAAAAAAATA
1 ATAAAATATATGAAAAAAAATA
85263 AAATTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
ATAAAATATATGAAAAAAAATAC
Found at i:85957 original size:2 final size:2
Alignment explanation
Indices: 85950--85991 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
85940 AAAGCTCACT
85950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85992 AACGTTGATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88231 original size:22 final size:22
Alignment explanation
Indices: 88204--88245 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
88194 TTAGTATTTA
88204 AAATGCTAATTCTGAAGAAGGT
1 AAATGCTAATTCTGAAGAAGGT
*
88226 AAATGCTATTTCTGAAGAAG
1 AAATGCTAATTCTGAAGAAG
88246 ATAGGATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (22 bp):
AAATGCTAATTCTGAAGAAGGT
Found at i:90103 original size:15 final size:15
Alignment explanation
Indices: 90083--90122 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
90073 CTTGGACTTG
90083 GAAGAGGAAAGGACT
1 GAAGAGGAAAGGACT
90098 GAAGAGGAAAGGACT
1 GAAGAGGAAAGGACT
90113 GAAG-GGAAAG
1 GAAGAGGAAAG
90123 CGGTGGTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.47, C:0.05, G:0.42, T:0.05
Consensus pattern (15 bp):
GAAGAGGAAAGGACT
Found at i:90943 original size:21 final size:21
Alignment explanation
Indices: 90919--91009 Score: 83
Period size: 21 Copynumber: 4.3 Consensus size: 21
90909 AAAAGTTAAG
* *
90919 ACCTTTCGCTGAAAAGACTTA
1 ACCTTTTGATGAAAAGACTTA
* * *
90940 ACCTTTTGATTAAAAGACATG
1 ACCTTTTGATGAAAAGACTTA
* *
90961 TCCTTTTGATGAAAAGTCTTA
1 ACCTTTTGATGAAAAGACTTA
* * *
90982 ACCTTTTCATGAAATGATTTA
1 ACCTTTTGATGAAAAGACTTA
*
91003 ATCTTTT
1 ACCTTTT
91010 CATGGAGAGA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (21 bp):
ACCTTTTGATGAAAAGACTTA
Found at i:90954 original size:42 final size:43
Alignment explanation
Indices: 90902--90988 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
90892 AAAGAGTAAA
** *
90902 TTGACTTAAAAGTTAAGACCTTTCGCTGAAAAGACTTAACCTT
1 TTGACTTAAAAGACAAGACCTTTCGATGAAAAGACTTAACCTT
* * * *
90945 TTGA-TTAAAAGACATGTCCTTTTGATGAAAAGTCTTAACCTT
1 TTGACTTAAAAGACAAGACCTTTCGATGAAAAGACTTAACCTT
90987 TT
1 TT
90989 CATGAAATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 33 0.89
43 4 0.11
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (43 bp):
TTGACTTAAAAGACAAGACCTTTCGATGAAAAGACTTAACCTT
Done.