Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002512.1 Hibiscus syriacus cultivar Beakdansim tig00005112_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: 93130
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:5752 original size:20 final size:19
Alignment explanation
Indices: 5723--5761 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
5713 GAATAATCTT
5723 AAAATAAAAAAT-TCTAAAA
1 AAAAT-AAAAATGTCTAAAA
5742 AAAAGTAAAAATGTCTAAAA
1 AAAA-TAAAAATGTCTAAAA
5762 TTTTAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATGTCTAAAA
Found at i:9376 original size:29 final size:29
Alignment explanation
Indices: 9330--9390 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
9320 CGCTGTTCAT
* *
9330 AAAGCAATACTAATTTGTTGGC-CAAGAA
1 AAAGCAATACTAACTTGTTGGCGAAAGAA
*
9358 AAAGCAAATACTACCTTGTTGGCGAAAGAA
1 AAAGC-AATACTAACTTGTTGGCGAAAGAA
9388 AAA
1 AAA
9391 AAAGCAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.18
29 15 0.54
30 8 0.29
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (29 bp):
AAAGCAATACTAACTTGTTGGCGAAAGAA
Found at i:9671 original size:24 final size:24
Alignment explanation
Indices: 9631--9676 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
9621 GTTTACAACA
*
9631 ATAAATATTGATCAATTAATTTTC
1 ATAAATATCGATCAATTAATTTTC
*
9655 ATAAATATCGATTAATTAATTT
1 ATAAATATCGATCAATTAATTT
9677 AATTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAAATATCGATCAATTAATTTTC
Found at i:24084 original size:23 final size:23
Alignment explanation
Indices: 24058--24144 Score: 111
Period size: 23 Copynumber: 3.8 Consensus size: 23
24048 CAGCTCGTAT
24058 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
*
24081 AATTGCATCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * * *
24104 AATTGTACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
* *
24127 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
24145 TATAATAATG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:24400 original size:30 final size:30
Alignment explanation
Indices: 24356--24425 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
24346 ACATAATTTG
* * *
24356 TATCACGTAAACATATTATTTTCATACCTT
1 TATCACATAAACATATCATTTCCATACCTT
*
24386 TATCACATAGACATATCATTTCCATACCTT
1 TATCACATAAACATATCATTTCCATACCTT
24416 TATCACATAA
1 TATCACATAA
24426 CTCATATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
TATCACATAAACATATCATTTCCATACCTT
Found at i:24471 original size:13 final size:13
Alignment explanation
Indices: 24455--24480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24445 ATATTCATGT
24455 CACATAATACATA
1 CACATAATACATA
24468 CACATAATACATA
1 CACATAATACATA
24481 TGGTATGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (13 bp):
CACATAATACATA
Found at i:28266 original size:21 final size:21
Alignment explanation
Indices: 28189--28267 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 21
28179 TTGGTGCAGA
*
28189 GGGAATCGATACCCCC--TAG
1 GGGAACCGATACCCCCTTTAG
* *
28208 GGGAACCGATTCCCCCTCTGAAG
1 GGGAACCGATACCCCCT-T-TAG
*
28231 GGGAACCGATTCCCCCTTTAG
1 GGGAACCGATACCCCCTTTAG
* *
28252 GCGAATCGATACCCCC
1 GGGAACCGATACCCCC
28268 ACGAGTTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 14 0.29
21 15 0.31
22 1 0.02
23 19 0.39
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.18
Consensus pattern (21 bp):
GGGAACCGATACCCCCTTTAG
Found at i:32236 original size:61 final size:61
Alignment explanation
Indices: 32159--32539 Score: 310
Period size: 61 Copynumber: 6.2 Consensus size: 61
32149 CATATTCGCA
* * * *
32159 TTGCAATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTACGATTTTCCAAATTTG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
* *
32220 TTGCGATAGTCGAAGTTCGCGTTGTGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
* * * ** * *
32281 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTTCCAAATT--CG
** * * * *
32344 TTGCGATTTTCCAAATT--CGTTGCGATAGTCGAAGTTCGAGGTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
* * * * ** * *
32403 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGTGATAGTCGAAGTTCACG
1 TTGCGATAGTCGAAGTTCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTTCCAAATT--CG
* * * * *
32466 TTGCGATTTATTCAAAATT--CGTTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
32529 TTGCGATAGTC
1 TTGCGATAGTC
32540 CAAAATTGCA
Statistics
Matches: 250, Mismatches: 52, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
59 23 0.09
61 150 0.60
63 62 0.25
64 1 0.00
65 14 0.06
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
Found at i:32365 original size:122 final size:124
Alignment explanation
Indices: 32239--32539 Score: 491
Period size: 122 Copynumber: 2.4 Consensus size: 124
32229 TCGAAGTTCG
*
32239 CGTTGTGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
1 CGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
*
32304 GCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGA-TT-TTCCAAATT
66 GCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCAAAATT
*
32361 CGTTGCGATAGTCGAAGTTCG-AGGTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 CGTTGCGATAGTCGAAGTTCGCA-TTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
32425 TGCGATTTATTCCAAATTCGTTGTGATAGTCGAAGTTCACGTTGCGATTTATTCAAAATT
65 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCAAAATT
* * *
32485 CGTTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 CGTTGCGATAGTCGAAGTTCGCATTGCGA-TT-TTCCAAATTCGTTGCGATAGTC
32540 CAAAATTGCA
Statistics
Matches: 165, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
121 1 0.01
122 106 0.64
123 2 0.01
124 32 0.19
125 2 0.01
126 22 0.13
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (124 bp):
CGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCAAAATT
Found at i:32543 original size:42 final size:42
Alignment explanation
Indices: 32239--32539 Score: 470
Period size: 42 Copynumber: 7.3 Consensus size: 42
32229 TCGAAGTTCG
* *
32239 CGTTGTGATAGTCGAAGTTCGCATTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32279 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
*
32321 CGTTGCGATAGTCGAAGTTCACGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
32361 CGTTGCGATAGTCGAAGTTCGAGGTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32401 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* * *
32443 CGTTGTGATAGTCGAAGTTCACGTTGCGATTTATTCAAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
* *
32485 CGTTGCGATAGTCCAAATTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
32527 CGTTGCGATAGTC
1 CGTTGCGATAGTC
32540 CAAAATTGCA
Statistics
Matches: 241, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
40 100 0.41
41 6 0.02
42 135 0.56
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:33325 original size:42 final size:42
Alignment explanation
Indices: 33266--33528 Score: 449
Period size: 42 Copynumber: 6.3 Consensus size: 42
33256 TGCGATTTTG
33266 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
33308 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
33350 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
33392 GACTATCGCAACGAACTTCGAATAAATCGTAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
33434 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
33476 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
33516 GACTATCGCAACG
1 GACTATCGCAACG
33529 CGAACTTAAC
Statistics
Matches: 210, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 32 0.15
41 1 0.00
42 177 0.84
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:33562 original size:61 final size:60
Alignment explanation
Indices: 33333--33571 Score: 168
Period size: 61 Copynumber: 3.9 Consensus size: 60
33323 CTTGGAATAA
* * *
33333 ATCGCAATGCGAACTTCGACTATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCAACAATCGCAAGCGAA-TT-G--TAAATCGCAACGCGAACTTCGACT
* * * * * * *
33396 ATCGCAA--CGAACTTCGAATAAATCGTAACGCGAACTTGGACTATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTC-AA-CAATCGCAA-GCGAA-TTGTA-AATCGCAACGCGAACTTCGACT
* * *
33457 AAATCGCAACGCGAACTTCGACTATCGCAA-CGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCAACAATCGCAAGCGAA-TT-GTAAATCGCAACGCGAACTTCGACT
*
33520 ATCGCAACGCGAACTT-AACAATCGCAATGCGAATATGTAAATCGCAATGCGA
1 ATCGCAACGCGAACTTCAACAATCGCAA-GCGAAT-TGTAAATCGCAACGCGA
33572 TAGTCGAAGT
Statistics
Matches: 137, Mismatches: 24, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
60 9 0.07
61 61 0.45
62 9 0.07
63 42 0.31
64 2 0.01
65 14 0.10
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (60 bp):
ATCGCAACGCGAACTTCAACAATCGCAAGCGAATTGTAAATCGCAACGCGAACTTCGACT
Found at i:37070 original size:45 final size:47
Alignment explanation
Indices: 37013--37102 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 47
37003 GAATAAATAC
37013 ATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAATAAGT
1 ATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAAGT
*
37058 ATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
1 ATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
37103 CAAAGCATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 26 0.62
46 9 0.21
47 7 0.17
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (47 bp):
ATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAAGT
Found at i:46760 original size:10 final size:10
Alignment explanation
Indices: 46745--46787 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
46735 CTTGAAGAAT
46745 AAATGAAAAA
1 AAATGAAAAA
46755 AAATGAATGAAAA
1 AAATG-A--AAAA
46768 AAATG-AAAA
1 AAATGAAAAA
46777 AAATGAAAAA
1 AAATGAAAAA
46787 A
1 A
46788 TAAAAATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.31
10 10 0.34
11 1 0.03
13 9 0.31
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:46769 original size:13 final size:14
Alignment explanation
Indices: 46746--46774 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
46736 TTGAAGAATA
46746 AATGAAAAAAAATG
1 AATGAAAAAAAATG
46760 AATG-AAAAAAATG
1 AATGAAAAAAAATG
46773 AA
1 AA
46775 AAAAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATGAAAAAAAATG
Found at i:46778 original size:8 final size:9
Alignment explanation
Indices: 46760--46900 Score: 72
Period size: 8 Copynumber: 16.1 Consensus size: 9
46750 AAAAAAAATG
46760 AATGAAAAA
1 AATGAAAAA
46769 AATGAAAAA
1 AATGAAAAA
46778 AATG-AAAA
1 AATGAAAAA
46786 AAT-AAAAA
1 AATGAAAAA
** **
46794 TGGTGAAAGC
1 -AATGAAAAA
46804 AA--AAAAA
1 AATGAAAAA
46811 AA-GAAGAAA
1 AATGAA-AAA
46820 AGA-GAATAAA
1 A-ATGAA-AAA
*
46830 AAAGAAAAGA
1 AATGAAAA-A
46840 GAAT-AAAAA
1 -AATGAAAAA
46849 AATG-AAAA
1 AATGAAAAA
46857 AATG-AAAA
1 AATGAAAAA
46865 AA-GAAGAAA
1 AATGAA-AAA
*
46874 AATG-TAAA
1 AATGAAAAA
46882 AATGAAAAA
1 AATGAAAAA
46891 GAA-GAAAAA
1 -AATGAAAAA
46900 A
1 A
46901 GAAAAAGAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
7 6 0.06
8 39 0.37
9 36 0.34
10 22 0.21
11 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.09
Consensus pattern (9 bp):
AATGAAAAA
Found at i:46785 original size:17 final size:17
Alignment explanation
Indices: 46760--46906 Score: 80
Period size: 17 Copynumber: 8.5 Consensus size: 17
46750 AAAAAAAATG
46760 AATGAAAAAAATGAAAAA
1 AATGAAAAAAATG-AAAA
46778 AATG-AAAAAAT-AAAA
1 AATGAAAAAAATGAAAA
*
46793 ATGGTGAAAGCAAAA--AAAA
1 A--ATGAAA--AAAATGAAAA
*
46812 AGAAGAAAAGAGAAT-AAAA
1 A-ATGAAAA-A-AATGAAAA
*
46831 AA-GAAAAGAGAATAAAAA
1 AATGAAAA-A-AATGAAAA
46849 AATG-AAAAAATGAAAA
1 AATGAAAAAAATGAAAA
*
46865 AA-GAAGAAAAATGTAAA
1 AATGAA-AAAAATGAAAA
46882 AATGAAAAAGAA-GAAAA
1 AATGAAAAA-AATGAAAA
46899 AA-GAAAAA
1 AATGAAAAA
46907 GAAATAAAAG
Statistics
Matches: 109, Mismatches: 6, Indels: 30
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.06
16 17 0.16
17 43 0.39
18 28 0.26
19 11 0.10
20 4 0.04
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.09
Consensus pattern (17 bp):
AATGAAAAAAATGAAAA
Found at i:46792 original size:22 final size:23
Alignment explanation
Indices: 46745--46795 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
46735 CTTGAAGAAT
*
46745 AAATGAAAAAAAATGAATGAAAA
1 AAATGAAAAAAAATGAATAAAAA
*
46768 AAATG-AAAAAAATGAAAAAATAA
1 AAATGAAAAAAAATGAATAAA-AA
46791 AAATG
1 AAATG
46796 GTGAAAGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.14
Consensus pattern (23 bp):
AAATGAAAAAAAATGAATAAAAA
Found at i:46792 original size:25 final size:25
Alignment explanation
Indices: 46763--46906 Score: 84
Period size: 25 Copynumber: 5.6 Consensus size: 25
46753 AAAAATGAAT
46763 GAAAAAAATGAAAAAAATGAAAAAA
1 GAAAAAAATGAAAAAAATGAAAAAA
* ** *
46788 TAAAAATGGTGAAAGCAAA--AAAAAA
1 GAAAAA-AATGAAA-AAAATGAAAAAA
*
46813 GAAGAAAAGA-GAATAAAAAAGAAAAGAGAA
1 GAA-AAAA-ATGAA-AAAAATG-AAA-A-AA
*
46843 TAAAAAAATG-AAAAAATGAAAAAA
1 GAAAAAAATGAAAAAAATGAAAAAA
*
46867 GAAGAAAAATG-TAAAAATG-AAAAA
1 GAA-AAAAATGAAAAAAATGAAAAAA
*
46891 GAAGAAAAAAGAAAAA
1 GAA-AAAAATGAAAAA
46907 GAAATAAAAG
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
24 19 0.21
25 37 0.40
26 12 0.13
27 9 0.10
28 5 0.05
29 6 0.07
30 4 0.04
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (25 bp):
GAAAAAAATGAAAAAAATGAAAAAA
Found at i:46837 original size:27 final size:26
Alignment explanation
Indices: 46807--46899 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 26
46797 TGAAAGCAAA
46807 AAAAAAGAAGAAAAGAGAATAAAAAAG
1 AAAAAAGAAGAAAA-AGAATAAAAAAG
* *
46834 AAAAGAGAATAAAAA-AATGAAAAAATG
1 AAAAAAGAAGAAAAAGAAT-AAAAAA-G
*
46861 AAAAAAGAAGAAAAATG--TAAAAATG
1 AAAAAAGAAGAAAAA-GAATAAAAAAG
46886 -AAAAAGAAGAAAAA
1 AAAAAAGAAGAAAAA
46900 AGAAAAAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
24 14 0.25
25 4 0.07
26 12 0.21
27 27 0.47
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (26 bp):
AAAAAAGAAGAAAAAGAATAAAAAAG
Found at i:46906 original size:8 final size:8
Alignment explanation
Indices: 46806--46906 Score: 62
Period size: 9 Copynumber: 11.6 Consensus size: 8
46796 GTGAAAGCAA
46806 AAAAAAAG
1 AAAAAAAG
46814 AAGAAAAGAG
1 AA-AAAA-AG
46824 AATAAAAAAG
1 -A-AAAAAAG
*
46834 AAAAGAGAAT
1 AAAA-A-AAG
46844 AAAAAAATG
1 AAAAAAA-G
*
46853 AAAAAATG
1 AAAAAAAG
46861 -AAAAAAG
1 AAAAAAAG
46868 AAGAAAAATG
1 AA-AAAAA-G
* *
46878 TAAAAATG
1 AAAAAAAG
46886 AAAAAGAAG
1 AAAAA-AAG
46895 -AAAAAAG
1 AAAAAAAG
46902 AAAAA
1 AAAAA
46907 GAAATAAAAG
Statistics
Matches: 73, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
7 9 0.12
8 22 0.30
9 24 0.33
10 12 0.16
11 5 0.07
12 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (8 bp):
AAAAAAAG
Found at i:46911 original size:27 final size:27
Alignment explanation
Indices: 46827--46915 Score: 67
Period size: 31 Copynumber: 3.1 Consensus size: 27
46817 AAAAGAGAAT
* *
46827 AAAA-AAGAAAAGAGAATAAAAAAATGAA
1 AAAAGAAGAAAAAAGAA-AAAGAAATG-A
46855 AAAATGAA-AAAAGAAGAAAAATGTAAAAATGA
1 AAAA-GAAGAAAA-AAGAAAAA-G---AAATGA
46887 AAAAGAAGAAAAAAGAAAAAGAAAT-A
1 AAAAGAAGAAAAAAGAAAAAGAAATGA
46913 AAA
1 AAA
46916 GGAGGGTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
26 4 0.08
27 4 0.08
28 4 0.08
29 7 0.14
30 7 0.14
31 11 0.22
32 9 0.18
33 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.08
Consensus pattern (27 bp):
AAAAGAAGAAAAAAGAAAAAGAAATGA
Found at i:48407 original size:55 final size:54
Alignment explanation
Indices: 48274--48736 Score: 480
Period size: 55 Copynumber: 8.6 Consensus size: 54
48264 GTTGAAGATT
*
48274 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTT-GTTGAAGATTGTTC
* *
48325 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTT-GTTGAAGATTGTTC
*
48380 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA----TC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACG-TTGTTGAAGATTGTTC
* * * *
48431 GAGTCTTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACACGTTGT-TGAAGATTGTTC
* * * * *
48486 GAGTTCTATACTCCCTTAACGG-ATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACACG-TTGTTGAAGATTGTTC
* * * * *
48541 GAGTTCTATACTCTCTGAAGAAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTGT-TGAAGATTGTTC
* * * *
48596 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTTAGGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTGTT--GAAGATTGTTC
* * * *
48652 GAGTCTTATACTCCCTGAATGAATAGGGAGCAGACACGCTTGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACG-TTGTTGAAGATTGTTC
* * *
48707 GAGTCTTATACTC-CTTAAAAGAATAGGGAG
1 GAGTCCTATACTCTC-TGAAGGAATAGGGAG
48737 TAGACCCGTT
Statistics
Matches: 367, Mismatches: 27, Indels: 32
0.86 0.06 0.08
Matches are distributed among these distances:
50 3 0.01
51 88 0.24
52 2 0.01
54 8 0.02
55 215 0.59
56 47 0.13
57 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (54 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTGTTGAAGATTGTTC
Found at i:48409 original size:106 final size:108
Alignment explanation
Indices: 48274--48758 Score: 506
Period size: 106 Copynumber: 4.5 Consensus size: 108
48264 GTTGAAGATT
* **
48274 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA-TT-GAGTCCTATACT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATTTCGAGTCCTATACT
* * *
48337 CTCTGAAGGAATAGGGAGCGGACAAGTTCGT-TGAAGATTGTTT
66 CCCTGAAGGAATAGGGAGCGGACACGTT-GTATGAAGATTGTTC
*
48380 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGA--TCGAGTCTTATACT
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATTTCGAGTCCTATACT
* *
48443 CCCTGAACGG-ATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
66 CCCTGAA-GGAATAGGGAGCGGACACGTTGTATGAAGATTGTTC
* * * * *
48486 GAGTTCTATACTCCCTTAACGG-ATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTCTAT
1 GAGTCCTATACTCTCTGAA-GGAATAGGGAGCGGACACGTTTATTGAAGA-T-TTCGAGTCCTAT
* * * * *
48550 ACTCTCTGAAGAAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
63 ACTCCCTGAAGGAATAGGGAGCGGACACGTTGTATGAAGATTGTTC
* * * *
48596 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TTAGGAAGATTGTTCGAGTCTTA
1 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATT--GAAGA-T-TTCGAGTCCTA
* *
48660 TACTCCCTGAATGAATAGGGAGCAGACACGCTTGT-TGAAGATTGTTC
62 TACTCCCTGAAGGAATAGGGAGCGGACACG-TTGTATGAAGATTGTTC
* * * ** *
48707 GAGTCTTATACTC-CTTAAAAGAATAGGGAGTAGACCCG-TTATTTGAAGATTT
1 GAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACACGTTTA-TTGAAGATTT
48759 TTCAAGTCTC
Statistics
Matches: 326, Mismatches: 37, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
105 2 0.01
106 132 0.40
107 4 0.01
108 2 0.01
109 6 0.02
110 93 0.29
111 82 0.25
112 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (108 bp):
GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTATTGAAGATTTCGAGTCCTATACT
CCCTGAAGGAATAGGGAGCGGACACGTTGTATGAAGATTGTTC
Found at i:54794 original size:29 final size:29
Alignment explanation
Indices: 54712--54794 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
54702 CGGTTAATCG
* *
54712 TTGGGCTCCTAATTTT-TATATTTATAAT
1 TTGGGATCTTAATTTTCTATATTTATAAT
* *
54740 TTGGGTTCTCAA-TTTCTATATTTATAA-
1 TTGGGATCTTAATTTTCTATATTTATAAT
54767 TTGGGATCATTAATTTTCTATATTTATA
1 TTGGGATC-TTAATTTTCTATATTTATA
54795 GACTTCCTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 10 0.21
28 23 0.49
29 14 0.30
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.53
Consensus pattern (29 bp):
TTGGGATCTTAATTTTCTATATTTATAAT
Found at i:63858 original size:23 final size:23
Alignment explanation
Indices: 63832--63892 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
63822 CTCATATAAA
*
63832 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
63855 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
63878 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
63893 TATAATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:64079 original size:103 final size:103
Alignment explanation
Indices: 63908--64125 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
63898 TAATGTCCAT
* *
63908 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
63973 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
64011 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
64076 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
64114 AAGGACCACATA
1 AAGGACCACATA
64126 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:68931 original size:23 final size:23
Alignment explanation
Indices: 68913--68965 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
68903 AATGCACCAA
68913 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
* * *
68936 AGTGCCGCGTAGAATTCCACCGT
1 AGTGCCACATAGAATTGCACCGT
68959 AGTGCCA
1 AGTGCCA
68966 TATAATAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGT
Found at i:69152 original size:103 final size:103
Alignment explanation
Indices: 68981--69198 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
68971 TAATGTCCAT
* *
68981 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
69046 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
69084 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTTACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
69149 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
69187 AAGGACCACATA
1 AAGGACCACATA
69199 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:70761 original size:21 final size:21
Alignment explanation
Indices: 70737--70781 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
70727 TTTTGTTCGT
* *
70737 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
70758 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
70779 TTG
1 TTG
70782 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:76755 original size:742 final size:741
Alignment explanation
Indices: 75318--76800 Score: 2754
Period size: 742 Copynumber: 2.0 Consensus size: 741
75308 GTCCTAGCTA
*
75318 ACAACTTATAATTATCTTGTGCAGGAGCTATCCACTTTGTTGGGTTGTTGAGTTGTAGGTCAGTT
1 ACAACTTATAATTATCTTGTGAAGGAGCTATCCACTTTGTTGGGTTGTTGAGTTGTAGGTCAGTT
*
75383 TTTCCTTTCCCACTAAACAGGTAATGAGCTGCTCCAATGTGTCATTTGTTTTAATTATCACATGT
66 CTTCCTTTCCCACTAAACAGGTAATGAGCTGCTCCAATGTGTCATTTGTTTTAATTATCACATGT
*
75448 TTCTCACGTGTCTTCTTTTCTGCCTTCCCATCCCCAATTTTCTCAATTGATTTAGTCCAAATCCC
131 TTCTCACGTGTCTTATTTTCTGCCTTCCCATCCCCAATTTTCTCAATTGATTTAGTCCAAATCCC
*
75513 TAATCCTTTCTAGATTATTCCTAATTCTCCTCCCTTTCGTCTGACCTCTTCTTCTCCAACCGCGA
196 TAACCCTTTCTAGATTATTCCTAATTCTCCTCCCTTTCGTCTGACCTCTTCTTCTCCAACCGCGA
*
75578 CATATTTTTATTCAAATTTAAAAATTTACATGTCAACTATATAACTTATTTCAATAATTCATTTG
261 CATATTTTTATTCAAATTTAAAAATTTACACGTCAACTATATAACTTATTTCAATAATTCATTTG
75643 TTAAAATATTAATAATATAAAAAATAATATGTCTTGTTTAAATTCAAAGACATTATCTTTGCGTG
326 TTAAAATATTAATAATATAAAAAATAATATGTCTTGTTTAAATTCAAAGACATTATCTTTGCGTG
*
75708 TAGGGACAGAGCCAGAATTAAATATTGGCAAGGATCGAAATATTAGATTATTTAAGAAAAATATA
391 CAGGGACAGAGCCAGAATTAAATATTGGCAAGGATCGAAATATTAGATTATTTAAGAAAAATATA
75773 AAGACTTATTAGACATTTAAACTCGAAATTCAGCATGAACCAAGCGACCTTAGTGATTAAGGGAT
456 AAGACTTATTAGACATTTAAACTCGAAATTCAGCATGAACCAAGCGACCTTAGTGATTAAGGGAT
*
75838 TGTTGTTATCCTCGAGGTCCCGAGTTCAAGCATGTATATAGGGGTATGAGCCTTCATTGTCAAAT
521 TGTTGTTATCCTCGAGATCCCGAGTTCAAGCATGTATATAGGGGTATGAGCCTTCATTGTCAAAT
75903 AGCTGAAAGTCTTTGTATAGATATTACCTTGTATTCACCCTAAATTAAAAAAAATCAAAACTCAA
586 AGCTGAAAGTCTTTGTATAGATATTACCTTGTATTCACCCTAAATTAAAAAAAATCAAAACTCAA
75968 AAGACTTCTAATTTGTCTAATATTTAAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTT
651 AAGACTTCTAATTTGTCTAATATTTAAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTT
76033 GAGAACATAGACTTATCATTCTTTAG
716 GAGAACATAGACTTATCATTCTTTAG
* *
76059 ACAACTTATAATTGTCTTGTGAAGGTGCTATCCACTTTGTTGGGTTGTTGAGTTGTAGGT-ATGT
1 ACAACTTATAATTATCTTGTGAAGGAGCTATCCACTTTGTTGGGTTGTTGAGTTGTAGGTCA-GT
*
76123 TCTTCCTTTCCCACTAAACAGGTAATGGGCTGCTCCAATGTGTCATTTGTTTTAATTATCACATG
65 TCTTCCTTTCCCACTAAACAGGTAATGAGCTGCTCCAATGTGTCATTTGTTTTAATTATCACATG
* *
76188 TTTCTCACGTGTCTTATTTTTTGCCTTCCCATCCCCAATTTTCTCAATTGATTTGGTCCAAATCC
130 TTTCTCACGTGTCTTATTTTCTGCCTTCCCATCCCCAATTTTCTCAATTGATTTAGTCCAAATCC
*
76253 CTAACCCTTTCTCGATTATTCCTAATTCTCCTCCCTTTCGTCTGACCTCTTCTTCTCCAACCGCG
195 CTAACCCTTTCTAGATTATTCCTAATTCTCCTCCCTTTCGTCTGACCTCTTCTTCTCCAACCGCG
76318 ACATATTTTTATTCAAATTTAAAAATTTACACGTCAACTATATAACTTATTTCAATAATTCATTT
260 ACATATTTTTATTCAAATTTAAAAATTTACACGTCAACTATATAACTTATTTCAATAATTCATTT
*
76383 TTTAAAATATTAATAATATAAAAAAATAATATGTCTTGTTTAAATTCAAAGACATTATCTTTGCG
325 GTTAAAATATTAATAATAT-AAAAAATAATATGTCTTGTTTAAATTCAAAGACATTATCTTTGCG
*
76448 TGCAGGGACGGAGCCAGAATTAAATATTGGCAAGGA-CTGAAATATTAGATTATTTAAGAAAAAT
389 TGCAGGGACAGAGCCAGAATTAAATATTGGCAAGGATC-GAAATATTAGATTATTTAAGAAAAAT
* *
76512 ATAAAGACTTATTAGACATTTAAACTCGAAATTCAGCATGAACCAAGCGACCTTATTGATTAGGG
453 ATAAAGACTTATTAGACATTTAAACTCGAAATTCAGCATGAACCAAGCGACCTTAGTGATTAAGG
*
76577 GATTGTTGTTATCCTCGAGATCCCGAGTTCAAGCATGTATGTAGGGGTATGAGCCTTCATTGTCA
518 GATTGTTGTTATCCTCGAGATCCCGAGTTCAAGCATGTATATAGGGGTATGAGCCTTCATTGTCA
*
76642 AATAGCTGAAAGTCTTTGTATAGATATTACTTTGTATTCACCCTAAATTAAAAAAAATCAAAACT
583 AATAGCTGAAAGTCTTTGTATAGATATTACCTTGTATTCACCCTAAATTAAAAAAAATCAAAACT
76707 CAAAAGACTTCTAATTTGTCTAATATTTAAACTTACAATGACTTAAATTGTAATTAGACCAAAAA
648 CAAAAGACTTCTAATTTGTCTAATATTTAAACTTACAATGACTTAAATTGTAATTAGACCAAAAA
76772 TTTGAGAACATAGACTTATCATTCTTTAG
713 TTTGAGAACATAGACTTATCATTCTTTAG
76801 TTCTACCCCT
Statistics
Matches: 720, Mismatches: 19, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
740 1 0.00
741 330 0.46
742 389 0.54
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (741 bp):
ACAACTTATAATTATCTTGTGAAGGAGCTATCCACTTTGTTGGGTTGTTGAGTTGTAGGTCAGTT
CTTCCTTTCCCACTAAACAGGTAATGAGCTGCTCCAATGTGTCATTTGTTTTAATTATCACATGT
TTCTCACGTGTCTTATTTTCTGCCTTCCCATCCCCAATTTTCTCAATTGATTTAGTCCAAATCCC
TAACCCTTTCTAGATTATTCCTAATTCTCCTCCCTTTCGTCTGACCTCTTCTTCTCCAACCGCGA
CATATTTTTATTCAAATTTAAAAATTTACACGTCAACTATATAACTTATTTCAATAATTCATTTG
TTAAAATATTAATAATATAAAAAATAATATGTCTTGTTTAAATTCAAAGACATTATCTTTGCGTG
CAGGGACAGAGCCAGAATTAAATATTGGCAAGGATCGAAATATTAGATTATTTAAGAAAAATATA
AAGACTTATTAGACATTTAAACTCGAAATTCAGCATGAACCAAGCGACCTTAGTGATTAAGGGAT
TGTTGTTATCCTCGAGATCCCGAGTTCAAGCATGTATATAGGGGTATGAGCCTTCATTGTCAAAT
AGCTGAAAGTCTTTGTATAGATATTACCTTGTATTCACCCTAAATTAAAAAAAATCAAAACTCAA
AAGACTTCTAATTTGTCTAATATTTAAACTTACAATGACTTAAATTGTAATTAGACCAAAAATTT
GAGAACATAGACTTATCATTCTTTAG
Found at i:76984 original size:2 final size:2
Alignment explanation
Indices: 76979--77005 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
76969 GTAGGAGTTT
76979 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
77006 TATGATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:78445 original size:2 final size:2
Alignment explanation
Indices: 78438--78463 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78428 TGCCAAAAAG
78438 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
78464 TAATAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81316 original size:18 final size:17
Alignment explanation
Indices: 81285--81318 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
81275 TTTTCATTGA
81285 TTAATAAATCATTTTTG
1 TTAATAAATCATTTTTG
*
81302 TTAATTAAATTATTTTT
1 TTAA-TAAATCATTTTT
81319 TATGGAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAATAAATCATTTTTG
Found at i:86408 original size:18 final size:19
Alignment explanation
Indices: 86385--86428 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
86375 ATATGTATAT
86385 AGAGAAAGAAAAAGAT-AG
1 AGAGAAAGAAAAAGATAAG
*
86403 AGAGAAAGAAAAAGGTAAG
1 AGAGAAAGAAAAAGATAAG
86422 AGAGAAA
1 AGAGAAA
86429 ATAGGTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (19 bp):
AGAGAAAGAAAAAGATAAG
Found at i:86429 original size:15 final size:16
Alignment explanation
Indices: 86409--86438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
86399 ATAGAGAGAA
86409 AGAAAA-AGGTAAGAG
1 AGAAAATAGGTAAGAG
86424 AGAAAATAGGTAAGA
1 AGAAAATAGGTAAGA
86439 AACTGCTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.30, T:0.10
Consensus pattern (16 bp):
AGAAAATAGGTAAGAG
Done.