Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004158.1 Hibiscus syriacus cultivar Beakdansim tig00009096_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: 93257
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:4126 original size:13 final size:13
Alignment explanation
Indices: 4063--4128 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
4053 TTTCATATGT
*
4063 TCATGTACTCATA
1 TCATGTTCTCATA
**
4076 TCAT-TTCTTGTGA
1 TCATGTTCTCAT-A
4089 TCATGTATCTCATA
1 TCATGT-TCTCATA
*
4103 TCA--CT-TCATA
1 TCATGTTCTCATA
4113 TCATGTTCTCATA
1 TCATGTTCTCATA
4126 TCA
1 TCA
4129 CAGGTCATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
10 8 0.20
11 1 0.03
12 5 0.12
13 17 0.43
14 5 0.12
15 4 0.10
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (13 bp):
TCATGTTCTCATA
Found at i:4566 original size:64 final size:62
Alignment explanation
Indices: 4461--4617 Score: 147
Period size: 64 Copynumber: 2.5 Consensus size: 62
4451 TGAAGGTATA
* * * * * * *
4461 CATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATG-TAGTATTATTGATGTGATG
1 CATCGATGCACTCCT-ATGCATCGATGCACAAAAGGCATTCGATGTTAGTATT-TTAAAGAG-TG
* ** **
4525 CATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTTTATTTTAAAGAGTG
1 CATCGATGCACTCC-TATGCATCGATGCACAAAAGGCATTCGATGTTAGTATTTTAAAGAGTG
4588 CATCGATGCACTACC-ATGCATCGATGCACA
1 CATCGATGCACT-CCTATGCATCGATGCACA
4618 TTCATACAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
62 14 0.18
63 14 0.18
64 43 0.56
65 6 0.08
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (62 bp):
CATCGATGCACTCCTATGCATCGATGCACAAAAGGCATTCGATGTTAGTATTTTAAAGAGTG
Found at i:10716 original size:21 final size:22
Alignment explanation
Indices: 10681--10725 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
10671 TTAAACTATT
*
10681 TTTAAAAAATAAAATTAGTTAA
1 TTTAAAAAATAAAATGAGTTAA
10703 TTTAAAAAAT-AAATGAGTTAA
1 TTTAAAAAATAAAATGAGTTAA
10724 TT
1 TT
10726 GTTTAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
TTTAAAAAATAAAATGAGTTAA
Found at i:14041 original size:2 final size:2
Alignment explanation
Indices: 14034--14082 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
14024 GATCATGTCC
14034 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
14076 TA TA TA T
1 TA TA TA T
14083 TGATGGTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14395 original size:41 final size:42
Alignment explanation
Indices: 14320--14418 Score: 125
Period size: 41 Copynumber: 2.4 Consensus size: 42
14310 AGAAAGGTTA
*
14320 AACA-ATAGCGGCATTTATAGTAAAAACGCCGCAATATA-GT
1 AACATATAGCGGCGTTTATAGTAAAAACGCCGCAATATATGT
*
14360 AGACATATAGCGGCGTTT-TAGCT-AAAACGCCGCAATATATTT
1 A-ACATATAGCGGCGTTTATAG-TAAAAACGCCGCAATATATGT
*
14402 AACATTTAGCGGCGTTT
1 AACATATAGCGGCGTTT
14419 GTGAAAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
40 1 0.02
41 37 0.71
42 14 0.27
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (42 bp):
AACATATAGCGGCGTTTATAGTAAAAACGCCGCAATATATGT
Found at i:14462 original size:43 final size:43
Alignment explanation
Indices: 14410--14547 Score: 206
Period size: 43 Copynumber: 3.2 Consensus size: 43
14400 TTAACATTTA
* *
14410 GCGGCGTTTG-TGAAAAAAACGCCGCTAAATCTCAACACCTATT
1 GCGGCGTTTGTTG-GAAAAACGCCGCTAAATATCAACACCTATT
14453 GCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATT
1 GCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATT
* ** *
14496 GCGGTGTTTGTTGGTCAAACGCCACTAAATATCAACACCTATT
1 GCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATT
14539 GCGGCGTTT
1 GCGGCGTTT
14548 TTTGTTACCA
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 85 0.98
44 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (43 bp):
GCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTATT
Found at i:17362 original size:2 final size:2
Alignment explanation
Indices: 17355--17391 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17345 GTCCAACCCG
17355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17392 ATCATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26937 original size:23 final size:22
Alignment explanation
Indices: 26865--26942 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
26855 ACAAGAATGT
26865 TAGCACGTTTTCTCTGCTCTTG
1 TAGCACGTTTTCTCTGCTCTTG
**
26887 TAGCACGTTTTCTCTGCTCCCG
1 TAGCACGTTTTCTCTGCTCTTG
*
26909 TAGCACGCTTCTT-TCTACTCTTG
1 TAGCACG-TT-TTCTCTGCTCTTG
26932 TAGCACGTTTT
1 TAGCACGTTTT
26943 GTTGCAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.04
22 29 0.59
23 16 0.33
24 2 0.04
ACGTcount: A:0.12, C:0.29, G:0.17, T:0.42
Consensus pattern (22 bp):
TAGCACGTTTTCTCTGCTCTTG
Found at i:38818 original size:21 final size:20
Alignment explanation
Indices: 38732--38889 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
38722 AAATGACCAA
**
38732 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
38751 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
38771 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
38791 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
38812 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
38833 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
38853 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
38874 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
38890 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:38880 original size:20 final size:20
Alignment explanation
Indices: 38856--39125 Score: 299
Period size: 20 Copynumber: 13.5 Consensus size: 20
38846 CGATTTTCCA
** *
38856 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
38876 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
38896 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
38916 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
38936 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
38956 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
38976 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
38996 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
39016 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
39036 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
39056 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
39076 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
39096 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
39116 AAATCACAAC
1 AAATCGCAAC
39126 ACTGAAATTT
Statistics
Matches: 222, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 221 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:39847 original size:24 final size:24
Alignment explanation
Indices: 39808--39854 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
39798 AAATTTGGTC
39808 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
39832 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
39855 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:42366 original size:19 final size:19
Alignment explanation
Indices: 42297--42466 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
42287 GCAACGAGAG
42297 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42316 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
42330 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
42350 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42369 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
42383 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
42402 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
42421 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
42435 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
42454 AATCGCATTGCGA
1 AATCGCAATGCGA
42467 TTCTCCCGTT
Statistics
Matches: 127, Mismatches: 8, Indels: 32
0.76 0.05 0.19
Matches are distributed among these distances:
14 32 0.25
15 2 0.02
16 5 0.04
17 5 0.04
18 2 0.02
19 65 0.51
20 16 0.13
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:42420 original size:52 final size:52
Alignment explanation
Indices: 42297--42466 Score: 279
Period size: 52 Copynumber: 3.2 Consensus size: 52
42287 GCAACGAGAG
* *
42297 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
42350 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
42402 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
42454 AATCGCATTGCGA
1 AATCGCAATGCGA
42467 TTCTCCCGTT
Statistics
Matches: 112, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
52 71 0.63
53 40 0.36
54 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:42458 original size:33 final size:33
Alignment explanation
Indices: 42283--42460 Score: 161
Period size: 33 Copynumber: 5.2 Consensus size: 33
42273 CGGAAATTAC
*
42283 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
42316 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
42350 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
42383 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
* *
42421 AATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
42454 AATCGCA
1 AATCGCA
42461 TTGCGATTCT
Statistics
Matches: 126, Mismatches: 7, Indels: 24
0.80 0.04 0.15
Matches are distributed among these distances:
32 1 0.01
33 77 0.61
34 17 0.13
35 2 0.02
36 4 0.03
37 2 0.02
38 10 0.08
39 13 0.10
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:42515 original size:19 final size:19
Alignment explanation
Indices: 42475--42572 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
42465 GATTCTCCCG
42475 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
42495 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42514 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
42528 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42547 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42566 TTGCGAT
1 TTGCGAT
42573 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:42569 original size:52 final size:53
Alignment explanation
Indices: 42456--42572 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
42446 GAAATTAAAA
42456 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
42509 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
42561 TCGCATTGCGAT
1 TCGCATTGCGAT
42573 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:42698 original size:14 final size:14
Alignment explanation
Indices: 42679--42715 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
42669 CATCAATTAC
42679 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
42693 ACAAATCATCTTTT
1 ACAAATCAACTTTT
42707 ACAAATCAA
1 ACAAATCAA
42716 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:43167 original size:93 final size:93
Alignment explanation
Indices: 43055--43254 Score: 391
Period size: 93 Copynumber: 2.2 Consensus size: 93
43045 TCGTATATAT
43055 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
43120 TACACAGTTTAGCAGAATTGGCAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
43148 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
1 CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
43213 TACACAGTTTAGCAGAATTGGCAGCAAC
66 TACACAGTTTAGCAGAATTGGCAGCAAC
*
43241 CGAATAAATTTACT
1 CGAACAAATTTACT
43255 AAGCAATCTA
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 106 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
CGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAA
TACACAGTTTAGCAGAATTGGCAGCAAC
Found at i:44979 original size:14 final size:14
Alignment explanation
Indices: 44960--45049 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
44950 TTGAAATGAA
44960 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
44974 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
44993 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
45007 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
45026 AATCGCAACGAGAG
1 AATCGCAACGAGAG
45040 AATCGCAACG
1 AATCGCAACG
45050 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:44992 original size:33 final size:33
Alignment explanation
Indices: 44952--45066 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
44942 TCTTTTGGTT
44952 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
44985 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
45018 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
45051 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
45067 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:44998 original size:19 final size:19
Alignment explanation
Indices: 44974--45071 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
44964 GCAACGAGAG
44974 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
44993 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
45007 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
45026 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
45040 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
45059 AATCGCAATGCGA
1 AATCGCAACGCGA
45072 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:45115 original size:33 final size:33
Alignment explanation
Indices: 45067--45180 Score: 201
Period size: 33 Copynumber: 3.5 Consensus size: 33
45057 AAAATCGCAA
**
45067 TGCGATTTTGGTTTCGCGTTGCGATTCTCTAGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
45100 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
*
45133 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
45166 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
45181 TCTCGTTGCG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTAGT
Found at i:45168 original size:14 final size:14
Alignment explanation
Indices: 45083--45172 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
45073 TTTGGTTTCG
45083 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
45097 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
45116 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
45130 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
45149 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
45163 CGTTGCGATT
1 CGTTGCGATT
45173 TTCATTTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
14 28 0.48
16 6 0.10
17 6 0.10
19 18 0.31
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:45183 original size:21 final size:21
Alignment explanation
Indices: 45157--45253 Score: 151
Period size: 21 Copynumber: 4.7 Consensus size: 21
45147 CGCGTTGCGA
45157 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
45178 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
45199 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
45219 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
45240 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
45254 CTCTTCTACA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.25
21 51 0.75
ACGTcount: A:0.11, C:0.25, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:45235 original size:41 final size:42
Alignment explanation
Indices: 45157--45254 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 42
45147 CGCGTTGCGA
***
45157 TTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTTCTCTCGTTGCGATTTTCAT
45199 TTCTCTCGTTGCGACAGTCA-TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTTCTCTCGTTGCGATTTTCAT
*
45240 TTATCTCGTTGCGAC
1 TTCTCTCGTTGCGAC
45255 TCTTCTACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 35 0.67
42 17 0.33
ACGTcount: A:0.11, C:0.26, G:0.16, T:0.47
Consensus pattern (42 bp):
TTCTCTCGTTGCGACAGTCATTTCTCTCGTTGCGATTTTCAT
Found at i:45375 original size:33 final size:33
Alignment explanation
Indices: 45333--45403 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
45323 AATACTAACT
*
45333 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
45366 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
45399 TGAAA
1 TGAAA
45404 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:45635 original size:22 final size:22
Alignment explanation
Indices: 45583--45637 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
45573 TGGTTGTGAG
**
45583 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
45605 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
45627 GGATTTCTTCG
1 GGATTTCTTCG
45638 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:45809 original size:20 final size:20
Alignment explanation
Indices: 45784--45937 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
45774 CTTTAAATAT
45784 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
45804 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
45826 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
45845 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
45865 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
45885 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
45905 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
45925 CGCGTTGCGATTT
1 CGCGTTGCGATTT
45938 TGAAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:45911 original size:40 final size:40
Alignment explanation
Indices: 45783--45937 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
45773 GCTTTAAATA
*
45783 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
45824 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
45864 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
45904 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
45938 TGAAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:45954 original size:21 final size:21
Alignment explanation
Indices: 45924--46002 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
45914 ATTTTCATAT
*
45924 TCGCGTTGCGATTTTGAAAAA
1 TCGCATTGCGATTTTGAAAAA
* * * **
45945 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGAAAAA
* *
45966 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAAAAA
*
45987 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
46003 GAAACTGATT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGAAAAA
Found at i:45997 original size:42 final size:43
Alignment explanation
Indices: 45904--46002 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
45894 ATTTATGTGT
* *
45904 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
** *
45945 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTCAAAAA
*
45987 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
46003 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 8 0.17
42 36 0.77
43 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCAAAAA
Found at i:52440 original size:51 final size:51
Alignment explanation
Indices: 52366--52469 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
52356 TAACGTTACA
52366 AACGTTAGCACTTTAGGTATTGGGCCGTCAATAGAGTTAGTTTTTTCCGTT
1 AACGTTAGCACTTTAGGTATTGGGCCGTCAATAGAGTTAGTTTTTTCCGTT
*
52417 AACGTTAGCACTTTAGGTGTTGGGCCGTCAATAGAGTTAGTTTTTTCCGTT
1 AACGTTAGCACTTTAGGTATTGGGCCGTCAATAGAGTTAGTTTTTTCCGTT
52468 AA
1 AA
52470 GTGACATGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (51 bp):
AACGTTAGCACTTTAGGTATTGGGCCGTCAATAGAGTTAGTTTTTTCCGTT
Found at i:55346 original size:31 final size:30
Alignment explanation
Indices: 55309--55408 Score: 121
Period size: 30 Copynumber: 3.3 Consensus size: 30
55299 AAAATTGGAT
*
55309 ACTTTAAGTATCTATTTTAACTAAAAAGATA
1 ACTTTAAATATCTATTTTAACTAAAAA-ATA
* * * *
55340 ATTTTAAATACCTATTTTGACCAAAAAATA
1 ACTTTAAATATCTATTTTAACTAAAAAATA
* *
55370 ACTTTAAATATTTATTTTAACTAAGAAAT-
1 ACTTTAAATATCTATTTTAACTAAAAAATA
55399 ACTTTAAATA
1 ACTTTAAATA
55409 CTTCAATAAG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 10 0.17
30 26 0.45
31 22 0.38
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (30 bp):
ACTTTAAATATCTATTTTAACTAAAAAATA
Found at i:57109 original size:114 final size:114
Alignment explanation
Indices: 56909--57134 Score: 398
Period size: 114 Copynumber: 2.0 Consensus size: 114
56899 GAGCGGGAAT
* * *
56909 GGATATAAGTTTAGTAGATAGTGGGCGGGTATGGATGTAAAAAATCATACTTATTGTGGGTAGAG
1 GGATATAAGTTTAGTAGATAGTGGACGGATATGGATGTAAAAAATCATACTTACTGTGGGTAGAG
56974 AGTGAGTAGGTGATGGATTTAGACCTTATCCGCTCTGCATCCGTCTGTC
66 AGTGAGTAGGTGATGGATTTAGACCTTATCCGCTCTGCATCCGTCTGTC
* * *
57023 GGATATAAGTTTAGTGGATAGTGGACGGATATGGATGTAAAAAGTCATACTTACTGTGGGTAGTG
1 GGATATAAGTTTAGTAGATAGTGGACGGATATGGATGTAAAAAATCATACTTACTGTGGGTAGAG
57088 AGTGAGTAGGTGATGGATTTAGACCTTATCCGCTCTGCATCCGTCTG
66 AGTGAGTAGGTGATGGATTTAGACCTTATCCGCTCTGCATCCGTCTG
57135 CCCCACATCT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.31
Consensus pattern (114 bp):
GGATATAAGTTTAGTAGATAGTGGACGGATATGGATGTAAAAAATCATACTTACTGTGGGTAGAG
AGTGAGTAGGTGATGGATTTAGACCTTATCCGCTCTGCATCCGTCTGTC
Found at i:59802 original size:16 final size:16
Alignment explanation
Indices: 59765--59795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59755 GAAAATAATA
*
59765 CAAATCGAAATCAACT
1 CAAACCGAAATCAACT
59781 CAAACCGAAATCAAC
1 CAAACCGAAATCAAC
59796 ATGAACCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.29, G:0.06, T:0.13
Consensus pattern (16 bp):
CAAACCGAAATCAACT
Found at i:63494 original size:3 final size:3
Alignment explanation
Indices: 63486--63511 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
63476 TTTTAATGTT
63486 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
63512 CGAGTGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:74213 original size:164 final size:164
Alignment explanation
Indices: 73941--74239 Score: 472
Period size: 164 Copynumber: 1.8 Consensus size: 164
73931 ACATGTTGAC
73941 TCTTCTTCTTCTTCTTCTTAAGTAGTTTGGTCCCACATGGTAAAACATGCTAAGTCAATTAGTTT
1 TCTTCTTCTTCTTCTTCTTAAGTAGTTTGGTCCCACATGGTAAAACATGCTAAGTCAATTAGTTT
* * *
74006 AACGTGCCATTTCAACATTCTATTACTGCAGTAATGGTTGTTAAATCAACTGATTTAACGTGTCA
66 AACGTGCCATTTCAACATTCTATTACTGCAATAATGATTGTTAAATCAACTGATTTAACATGTCA
74071 TGTCAGCATTCTGTTGCTGCAATAATCTTCTTGT
131 TGTCAGCATTCTGTTGCTGCAATAATCTTCTTGT
* * * *
74105 TCTTGTTCTTCTTCTTCTTAAGTAGTTTGGTTCTACATGGTCAAACATGCTAAGTCAATTAGTTT
1 TCTTCTTCTTCTTCTTCTTAAGTAGTTTGGTCCCACATGGTAAAACATGCTAAGTCAATTAGTTT
* * * * * * *
74170 AACGTGTCATTTCAGCATTCTGTTATTGCAATAATGATTGTTAAGTCAATTGGTTTAACATGTCA
66 AACGTGCCATTTCAACATTCTATTACTGCAATAATGATTGTTAAATCAACTGATTTAACATGTCA
74235 TGTCA
131 TGTCA
74240 ATATTTTGTT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
164 121 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (164 bp):
TCTTCTTCTTCTTCTTCTTAAGTAGTTTGGTCCCACATGGTAAAACATGCTAAGTCAATTAGTTT
AACGTGCCATTTCAACATTCTATTACTGCAATAATGATTGTTAAATCAACTGATTTAACATGTCA
TGTCAGCATTCTGTTGCTGCAATAATCTTCTTGT
Found at i:74250 original size:56 final size:56
Alignment explanation
Indices: 74155--74269 Score: 149
Period size: 56 Copynumber: 2.1 Consensus size: 56
74145 TCAAACATGC
* * * * *
74155 TAAGTCAATTAGTTTAACGTGTCATTTCAGCATTCTGTTATTGCAATAATGATTGT
1 TAAGTCAATTAGTTTAACATGTCATGTCAACATTCTGTTACTCCAATAATGATTGT
* * * *
74211 TAAGTCAATTGGTTTAACATGTCATGTCAATATTTTGTTACTCCAGTAATGATTGT
1 TAAGTCAATTAGTTTAACATGTCATGTCAACATTCTGTTACTCCAATAATGATTGT
74267 TAA
1 TAA
74270 TAGTGAGTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.43
Consensus pattern (56 bp):
TAAGTCAATTAGTTTAACATGTCATGTCAACATTCTGTTACTCCAATAATGATTGT
Found at i:75901 original size:18 final size:18
Alignment explanation
Indices: 75878--75912 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
75868 TAATGATATA
75878 TATATATATGTGCGTGTT
1 TATATATATGTGCGTGTT
*
75896 TATATATATGTGTGTGT
1 TATATATATGTGCGTGT
75913 GGTGTGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (18 bp):
TATATATATGTGCGTGTT
Found at i:76299 original size:43 final size:43
Alignment explanation
Indices: 76238--76324 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
76228 GTCCCCGACT
*
76238 ATTAAAAGTTGCAAAACGATCACTCGACTATTCATTGTGTTCC
1 ATTAAAAGTTGCAAAACGATCACTCGACTATTCATTGTATTCC
*
76281 ATTAAAAGTTGCAAAACGATCACTTGACTATTCATTGTATTCC
1 ATTAAAAGTTGCAAAACGATCACTCGACTATTCATTGTATTCC
76324 A
1 A
76325 AACTCATCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (43 bp):
ATTAAAAGTTGCAAAACGATCACTCGACTATTCATTGTATTCC
Found at i:77815 original size:85 final size:85
Alignment explanation
Indices: 77656--77815 Score: 268
Period size: 85 Copynumber: 1.9 Consensus size: 85
77646 TATGTTATAT
77656 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
* *
77721 ATCGTTTATAATAAAATAGG
66 AGCGCTTATAATAAAATAGG
* *
77741 TATTTAA-CGAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGG
1 TATTTAACCG-GAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGA
77805 TAGCGCTTATA
65 TAGCGCTTATA
77816 TTGACCTATT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 2 0.03
85 68 0.97
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (85 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATAATAAAATAGG
Found at i:79915 original size:201 final size:200
Alignment explanation
Indices: 79032--79972 Score: 1648
Period size: 200 Copynumber: 4.7 Consensus size: 200
79022 TTATATAACA
* * * * *
79032 ATTCTCCCATAAAACAGGTATACTTATACCGGTTAGATTAAAAAATTACCTAATACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* *
79097 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
79162 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
79227 GACCT
196 GACCT
*
79232 ATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
79297 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATAAATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
79362 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
*
79427 GACAT
196 GACCT
*
79432 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCAATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* *
79497 ATGGATTTCGATGTTTATGGGATCGACCCTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
* *
79562 TGTTTGCCATTCATTATGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
79627 GACCT
196 GACCT
* *
79632 ATTCTCTCATAAAACCGGTATACCTGTACAGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
79697 ATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
* *
79762 TGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAAGTGTCGATACATTATTT
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTAC-AAAAGTGTCGACACATTATTT
79827 AGACCT
195 AGACCT
* *
79833 ATTCTCTCATAAAACCGGTATACCTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * *
79898 TTGGGTTTCGTTGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
79963 TGTTTGCCAT
131 TGTTTGCCAT
79973 ATTGTAAATT
Statistics
Matches: 707, Mismatches: 33, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
200 547 0.77
201 160 0.23
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACCT
Found at i:80217 original size:18 final size:18
Alignment explanation
Indices: 80194--80254 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
80184 TCTCATTCAT
*
80194 AATTATATTCACATACAA
1 AATTATAATCACATACAA
*
80212 AATTATAAATCATATACAA
1 AATTAT-AATCACATACAA
**
80231 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
80250 AATTA
1 AATTA
80255 ACCCTACAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 6 0.15
19 33 0.85
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:80230 original size:19 final size:19
Alignment explanation
Indices: 80206--80254 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
80196 TTATATTCAC
80206 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
80225 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
80244 ATACAAAATTA
1 ATACAAAATTA
80255 ACCCTACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:80842 original size:4 final size:4
Alignment explanation
Indices: 80833--80860 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
80823 AATGTCCTTT
80833 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
80861 TCAATCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:82097 original size:33 final size:33
Alignment explanation
Indices: 82060--82125 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
82050 CATCTTAATA
*
82060 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
82093 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
82126 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:82196 original size:21 final size:21
Alignment explanation
Indices: 82170--82222 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
82160 TCTCAGTGTA
*
82170 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
82191 TCTTCGACTCTATCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
82212 TCTTCGACTCT
1 TCTTCGACTCT
82223 TGATTGTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.32, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCGACTCTATCAAGTTTC
Found at i:84666 original size:177 final size:178
Alignment explanation
Indices: 84368--84835 Score: 665
Period size: 177 Copynumber: 2.6 Consensus size: 178
84358 CGTACTTACG
*
84368 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTC-A-ATATCCGGTAACGTTTTACCGGTTTTATCA-TTTGATACCGGTTT
* * * *
84433 TATCATATTTTTA-CTTGT-TATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
63 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTAT
* *
84496 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
127 AGGAGCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
84547 AAAGTATCGACACTTTCAATATCCGGTAACGTTTTACCGGTTTTATCATTTGATACCGGTTTTAT
1 AAAGTATCGACACTTTCAATATCCGGTAACGTTTTACCGGTTTTATCATTTGATACCGGTTTTAT
*
84612 CATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACTTTATAGGA
66 CATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAGGA
** *
84677 TTTAAAACTGATTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 GCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * *
84725 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAA--TATCCGGTAACGTTTTACCGGTTTTATCATTT-GATACCGGTTT
* * * *
84790 TGTCATAGTTTTACCTGTTATATCG-TTTGGATCGACACATTTTTAA
63 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTAA
84836 TTTGGATCGA
Statistics
Matches: 263, Mismatches: 20, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
176 27 0.10
177 100 0.38
178 37 0.14
179 17 0.06
180 50 0.19
181 32 0.12
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (178 bp):
AAAGTATCGACACTTTCAATATCCGGTAACGTTTTACCGGTTTTATCATTTGATACCGGTTTTAT
CATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAGGA
GCTAAAACTGATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:90470 original size:35 final size:35
Alignment explanation
Indices: 90423--90508 Score: 118
Period size: 35 Copynumber: 2.5 Consensus size: 35
90413 AAAACAGCCC
* * *
90423 TCAATTTCATTCTAAACCCCAAATTCTAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* *
90458 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
90493 TCAATTGAATTCTAAA
1 TCAATTTAATTCTAAA
90509 ATACTTCAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:90504 original size:21 final size:21
Alignment explanation
Indices: 90479--90519 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
90469 CTAAACCCTA
90479 AATTCCAAAATAATTCAATTG
1 AATTCCAAAATAATTCAATTG
* *
90500 AATTCTAAAATACTTCAATT
1 AATTCCAAAATAATTCAATT
90520 TAAGGTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTCCAAAATAATTCAATTG
Found at i:90562 original size:35 final size:35
Alignment explanation
Indices: 90516--90590 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
90506 AAAATACTTC
* * *
90516 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
*
90551 AATTTAGGGTTTAAAATGAAATTGAATTACTTTGG
1 AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
90586 AATTT
1 AATTT
90591 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAAAATGAAATTGAATTACTTTGG
Found at i:90594 original size:24 final size:24
Alignment explanation
Indices: 90567--90638 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
90557 GGGTTTAAAA
90567 TGAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
*
90591 TGAACA-TGAATTTACTATTTAGAA---
1 TGAA-ATTGAA-TTAC--TTTGGAATTT
*
90615 TAAAATTGAATTACTTTGGAATTT
1 TGAAATTGAATTACTTTGGAATTT
90639 GGGGTTTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
21 6 0.16
23 5 0.14
24 15 0.41
25 5 0.14
27 6 0.16
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (24 bp):
TGAAATTGAATTACTTTGGAATTT
Done.