Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009147.1 Hibiscus syriacus cultivar Beakdansim tig00112662_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: 40549
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1328 original size:19 final size:19
Alignment explanation
Indices: 1306--1629 Score: 387
Period size: 19 Copynumber: 18.4 Consensus size: 19
1296 CGGAAAATAC
*
1306 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1325 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1339 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1359 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1373 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1392 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1411 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1425 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1444 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1463 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1477 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1496 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1515 AATCGCAATACG-AATG-A
1 AATCGCAATGCGAAATGAA
1532 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1551 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1570 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1584 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1622 AATCGCAA
1 AATCGCAA
1630 CGAGATAATC
Statistics
Matches: 265, Mismatches: 12, Indels: 56
0.80 0.04 0.17
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 24 0.09
18 11 0.04
19 151 0.57
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1393 original size:33 final size:34
Alignment explanation
Indices: 1306--1629 Score: 303
Period size: 33 Copynumber: 9.2 Consensus size: 34
1296 CGGAAAATAC
* *
1306 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1339 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
1373 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1411 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1444 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
1477 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
1515 AATCGCAATACG-AATG-AAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1551 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
1583 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
1622 AATCGCAA
1 AATCGCAA
1630 CGAGATAATC
Statistics
Matches: 253, Mismatches: 12, Indels: 47
0.81 0.04 0.15
Matches are distributed among these distances:
32 2 0.01
33 111 0.44
34 32 0.13
35 9 0.04
36 36 0.14
37 12 0.05
38 49 0.19
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:1667 original size:52 final size:52
Alignment explanation
Indices: 1334--1651 Score: 557
Period size: 52 Copynumber: 6.0 Consensus size: 52
1324 AAATCCCAAC
1334 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1387 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1439 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1491 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGA-ATGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACGAGA-G-AATCGCAATGCGAA
*
1546 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1598 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1650 AT
1 AT
1652 TATAAACGCA
Statistics
Matches: 256, Mismatches: 4, Indels: 11
0.94 0.01 0.04
Matches are distributed among these distances:
52 183 0.71
53 23 0.09
54 7 0.03
55 43 0.17
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1667 original size:159 final size:159
Alignment explanation
Indices: 1334--1651 Score: 563
Period size: 159 Copynumber: 2.0 Consensus size: 159
1324 AAATCCCAAC
*
1334 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG-A-GAGAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAATGA-AATCGCAATGCGAAATGAAAAT
*
1395 CGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
64 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1460 GAAAATCGCAACGAGAGAATCGCAATGCGAA
129 GAAAATCGCAACGAGAGAATCGCAATGCGAA
1491 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAATGAAATCGCAATGCGAAATGAAAATCG
1 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAATGAAATCGCAATGCGAAATGAAAATCG
1556 CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
66 CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
*
1621 AAATCGCAACGAGATAATCGCAATGCGAA
131 AAATCGCAACGAGAGAATCGCAATGCGAA
1650 AT
1 AT
1652 TATAAACGCA
Statistics
Matches: 154, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
159 119 0.77
160 2 0.01
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (159 bp):
ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAATGAAATCGCAATGCGAAATGAAAATCG
CAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
AAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1767 original size:19 final size:19
Alignment explanation
Indices: 1658--1759 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1648 AAATTATAAA
1658 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1677 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1697 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1713 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1730 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1749 CGCATTGCGAT
1 CGCATTGCGAT
1760 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1885 original size:14 final size:14
Alignment explanation
Indices: 1866--1902 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1856 CATCAATTAC
1866 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1880 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1894 ACAAATCAA
1 ACAAATCAA
1903 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:1930 original size:37 final size:37
Alignment explanation
Indices: 1883--1953 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1873 AACTTTTACA
*
1883 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
1920 AATCAACTTTTACAAATCAATTAAACAATCAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAA
1954 ACAATCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
Found at i:3802 original size:19 final size:19
Alignment explanation
Indices: 3762--3896 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
3752 TAGTTTACTT
* *
3762 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3782 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3801 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3820 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
3834 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3853 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3867 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3886 TCGCAATGCGA
1 TCGCAACGCGA
3897 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3837 original size:14 final size:14
Alignment explanation
Indices: 3818--3874 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3808 GCGAAATGAA
*
3818 AATCGCAACGACAG
1 AATCGCAACGAAAG
3832 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
3849 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3865 AATCGCAACG
1 AATCGCAACG
3875 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3841 original size:33 final size:33
Alignment explanation
Indices: 3799--3891 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
3789 GCGAAACCAA
*
3799 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3832 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3865 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3892 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3888 original size:52 final size:54
Alignment explanation
Indices: 3762--3896 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
3752 TAGTTTACTT
*
3762 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
3820 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
3867 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
3897 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:3914 original size:19 final size:19
Alignment explanation
Indices: 3892--3968 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
3882 AAAATCGCAA
3892 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3911 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3925 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3944 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3964 TGCGA
1 TGCGA
3969 AGTAAACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 20 0.42
20 13 0.27
ACGTcount: A:0.09, C:0.16, G:0.30, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4300 original size:92 final size:93
Alignment explanation
Indices: 4011--4388 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
4001 TTGAATGGAT
4011 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4075 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4103 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4168 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4196 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
4260 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4288 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
4352 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
4380 AAATTTACT
1 AAATTTACT
4389 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 15 0.05
92 171 0.60
93 97 0.34
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:6112 original size:14 final size:14
Alignment explanation
Indices: 6093--6182 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
6083 TTGAAATGAA
6093 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6107 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
6124 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
6140 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
6159 AATCGCAACGAGAG
1 AATCGCAACGAGAG
6173 AATCGCAACG
1 AATCGCAACG
6183 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6130 original size:33 final size:33
Alignment explanation
Indices: 6085--6199 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
6075 TCTTTTGGTT
6085 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
6118 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6151 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
6184 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
6200 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:6131 original size:19 final size:18
Alignment explanation
Indices: 6092--6204 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
6082 GTTGAAATGA
6092 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
6107 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
6124 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
6140 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
6157 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
6173 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
6190 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
6205 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:6235 original size:14 final size:14
Alignment explanation
Indices: 6216--6270 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
6206 TTTGGTTTCG
6216 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6230 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
6249 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6263 CGTTGCGA
1 CGTTGCGA
6271 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6433 original size:33 final size:33
Alignment explanation
Indices: 6391--6461 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6381 AATACTAACT
*
6391 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
6424 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
6457 TGAAA
1 TGAAA
6462 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:6695 original size:22 final size:22
Alignment explanation
Indices: 6643--6697 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
6633 TGGTTGTGAG
**
6643 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
6665 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
6687 GGATTTCTTCG
1 GGATTTCTTCG
6698 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:6868 original size:20 final size:20
Alignment explanation
Indices: 6843--7036 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
6833 CTTTAAATAT
6843 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6863 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
6885 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6904 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
6924 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
6944 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
6964 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
6984 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
7004 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
7024 CGCGTTGCGATTT
1 CGCGTTGCGATTT
7037 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:7030 original size:60 final size:60
Alignment explanation
Indices: 6843--7036 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
6833 CTTTAAATAT
**
6843 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
6904 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
6964 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
7024 CGCGTTGCGATTT
1 CGCGTTGCGATTT
7037 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:7053 original size:21 final size:20
Alignment explanation
Indices: 7029--7105 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
7019 ATATTCGCGT
7029 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
7050 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
7070 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
7092 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
7106 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:7116 original size:20 final size:20
Alignment explanation
Indices: 7091--7142 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
7081 AAGAATCGCG
*
7091 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
7111 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
7131 TTGCGATTCTGG
1 TTGCGATTCTGG
7143 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:7313 original size:3 final size:3
Alignment explanation
Indices: 7305--7363 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
7295 GGAATAAAAA
* * *
7305 TAT TAT TAT AAT AAT TA- TGT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
7351 TAC TAA TAT TAT T
1 TAT TAT TAT TAT T
7364 TACATAATAC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 3 0.06
3 44 0.94
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:7339 original size:26 final size:26
Alignment explanation
Indices: 7303--7371 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
7293 CAGGAATAAA
*
7303 AATATTATTATAATAATTATGTTATT
1 AATATTATTATAATAATTATGTTACT
* * * *
7329 ATTATTATTATTATTATTATTTTACT
1 AATATTATTATAATAATTATGTTACT
7355 AATATTATT-TACATAAT
1 AATATTATTATA-ATAAT
7372 ACATTTTGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
25 1 0.03
26 33 0.97
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
AATATTATTATAATAATTATGTTACT
Found at i:8691 original size:20 final size:20
Alignment explanation
Indices: 8668--8705 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8658 TCTTCTTTGA
* *
8668 TTTATTTATTTACTTATTTT
1 TTTATTTAATTAATTATTTT
8688 TTTATTTAATTAATTATT
1 TTTATTTAATTAATTATT
8706 ATTCGATATT
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:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTTAATTAATTATTTT
Found at i:18087 original size:9 final size:9
Alignment explanation
Indices: 18073--18101 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
18063 TTAATTCGAA
18073 AATTAACCG
1 AATTAACCG
18082 AATTAACCG
1 AATTAACCG
18091 AATTAACCG
1 AATTAACCG
18100 AA
1 AA
18102 ATTTATTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:20517 original size:63 final size:64
Alignment explanation
Indices: 20392--20541 Score: 166
Period size: 63 Copynumber: 2.4 Consensus size: 64
20382 TGAACATTGA
*
20392 ATGC-CAA-TAGTGCATCGATGCA-CCCGTTTAAAATACAAACATCGAATGTCATCAATGTATCG
1 ATGCACAAGTAGTGCATCGATGCACCCCG-TTAAAATACAAACATCGAAGGTCATCAATGTATCG
* * ***
20454 ATGCACAAGTAGTGCATCGATGCACCCCG-TAATATTA-AAACATCGAAGGTGATTTGTGTATCG
1 ATGCACAAGTAGTGCATCGATGCACCCCGTTAA-AATACAAACATCGAAGGTCATCAATGTATCG
***
20517 ATGCATGGGTAGTGCATCGATGCAC
1 ATGCACAAGTAGTGCATCGATGCAC
20542 TTCAAGGGGA
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
62 4 0.05
63 49 0.65
64 18 0.24
65 4 0.05
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (64 bp):
ATGCACAAGTAGTGCATCGATGCACCCCGTTAAAATACAAACATCGAAGGTCATCAATGTATCG
Found at i:21953 original size:23 final size:23
Alignment explanation
Indices: 21885--21945 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
21875 ACATTTTATA
21885 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
21908 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
21931 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
21946 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:26185 original size:25 final size:25
Alignment explanation
Indices: 26157--26207 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
26147 AACACACTTT
*
26157 ACTTGTGGTTTTGATGATTAAACTA
1 ACTTGTGGTTTAGATGATTAAACTA
26182 ACTTGTGGTTTAGATGATTAAACTA
1 ACTTGTGGTTTAGATGATTAAACTA
26207 A
1 A
26208 ACTATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (25 bp):
ACTTGTGGTTTAGATGATTAAACTA
Found at i:30744 original size:29 final size:25
Alignment explanation
Indices: 30687--30738 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
30677 ACTCTTAGAA
30687 AGTTAAATAGATAAGGATAACTACT
1 AGTTAAATAGATAAGGATAACTACT
30712 AGTTAAATAGATAAGGATAACTACT
1 AGTTAAATAGATAAGGATAACTACT
30737 AG
1 AG
30739 GTAGTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (25 bp):
AGTTAAATAGATAAGGATAACTACT
Found at i:35989 original size:57 final size:57
Alignment explanation
Indices: 35841--36068 Score: 368
Period size: 57 Copynumber: 4.0 Consensus size: 57
35831 CATAACCATA
* * * * *
35841 CAACCTCGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGCAAGTAAT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
35898 CAA-CCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCTGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
*
35954 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGAAACCTGCAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
36011 CAACACCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGTAAGTATT
1 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
36068 C
1 C
36069 TTCCTCCAAC
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
56 50 0.31
57 109 0.69
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.14
Consensus pattern (57 bp):
CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:36068 original size:114 final size:113
Alignment explanation
Indices: 35841--36068 Score: 375
Period size: 113 Copynumber: 2.0 Consensus size: 113
35831 CATAACCATA
* * *
35841 CAACCTCGTCACGAACAGTAAGGCCCTGAGCACAAAGCCAAGGAACCTGCAAGTAATCAACCCGT
1 CAACCCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGAAACCTGCAAGTAATCAACCCGT
*
35906 CACGAACAGTAAGGCTCTCAGCACAAAGCTGAGGAACCTGCAAGTATT
66 CACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
* * *
35954 CAACCCCGTCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGAAACCTGCAAGTATTCAACACCG
1 CAACCCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGAAACCTGCAAGTAATCAAC-CCG
*
36019 TCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGTAAGTATT
65 TCACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
36068 C
1 C
36069 TTCCTCCAAC
Statistics
Matches: 106, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
113 55 0.52
114 51 0.48
ACGTcount: A:0.35, C:0.30, G:0.21, T:0.14
Consensus pattern (113 bp):
CAACCCCGTCACGAACAGTAAGGCCCTCAGCACAAAGCCAAGAAACCTGCAAGTAATCAACCCGT
CACGAACAGTAAGGCTCTCAGCACAAAGCCGAGGAACCTGCAAGTATT
Done.