Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001849.1 Hibiscus syriacus cultivar Beakdansim tig00003745_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: 27775
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1705 original size:19 final size:19
Alignment explanation
Indices: 1681--1744 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
1671 AGTTTTACTT
* **
1681 TCGCAACACGAAACTTAAA
1 TCGCAACGCGAAACCAAAA
1700 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1719 TCGCAACGCG-AATGAAAA
1 TCGCAACGCGAAACCAAAA
1737 TCGCAACG
1 TCGCAACG
1745 ACAAATCGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 14 0.35
19 26 0.65
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1754 original size:31 final size:31
Alignment explanation
Indices: 1715--1806 Score: 148
Period size: 31 Copynumber: 2.9 Consensus size: 31
1705 ACGCGAAACC
1715 AAAATCGCAACGCGAATGAAAATCGCAACGA
1 AAAATCGCAACGCGAATGAAAATCGCAACGA
* *
1746 CAAATCGCAATGCGAATGAAAATCGCAACGA
1 AAAATCGCAACGCGAATGAAAATCGCAACGA
1777 AAGAATCGCAACGCGAAATGAAAATCGCAA
1 AA-AATCGCAACGCG-AATGAAAATCGCAA
1807 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 30 0.55
32 11 0.20
33 14 0.25
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (31 bp):
AAAATCGCAACGCGAATGAAAATCGCAACGA
Found at i:1804 original size:19 final size:19
Alignment explanation
Indices: 1697--1811 Score: 94
Period size: 19 Copynumber: 6.7 Consensus size: 19
1687 CACGAAACTT
**
1697 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAATGA
1716 AAATCGCAACGCG-AATGA
1 AAATCGCAACGCGAAATGA
*
1734 AAATCGCAA--CG--A--C
1 AAATCGCAACGCGAAATGA
*
1747 AAATCGCAATGCG-AATGA
1 AAATCGCAACGCGAAATGA
1765 AAATCGCAA--CGAAA-G-
1 AAATCGCAACGCGAAATGA
1780 -AATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
*
1798 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1812 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 5, Indels: 22
0.75 0.05 0.21
Matches are distributed among these distances:
13 9 0.11
14 8 0.10
15 3 0.04
16 11 0.14
17 3 0.04
18 21 0.26
19 25 0.31
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.10
Consensus pattern (19 bp):
AAATCGCAACGCGAAATGA
Found at i:1894 original size:20 final size:19
Alignment explanation
Indices: 1807--1902 Score: 121
Period size: 19 Copynumber: 5.3 Consensus size: 19
1797 AAAATCGCAA
1807 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1826 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1840 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1859 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1878 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1898 TGCGA
1 TGCGA
1903 AAGTAAACTA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 11 0.16
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 39 0.58
20 13 0.19
ACGTcount: A:0.08, C:0.16, G:0.30, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2066 original size:93 final size:93
Alignment explanation
Indices: 1950--2230 Score: 532
Period size: 93 Copynumber: 3.1 Consensus size: 93
1940 ATGGATTGCA
1950 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2014 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2042 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2107 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2135 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2200 TAGCAGAATTGGCAG-AACCGAA-TAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2226 TTACT
1 TTACT
2231 AAGCAATCTA
Statistics
Matches: 187, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
91 8 0.04
92 11 0.06
93 168 0.90
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3944 original size:14 final size:14
Alignment explanation
Indices: 3925--4014 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3915 TTGAAATGAA
3925 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3939 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
3958 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3972 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3991 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4005 AATCGCAACG
1 AATCGCAACG
4015 CGAAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3962 original size:33 final size:33
Alignment explanation
Indices: 3917--4030 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3907 TCTTTTGGTT
3917 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3950 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3983 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4016 GAAAT-AAAATCGCAA
1 GAAATGAAAATCGCAA
4031 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
32 10 0.13
33 69 0.87
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3963 original size:19 final size:19
Alignment explanation
Indices: 3939--4035 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 19
3929 GCAACGAGAG
*
3939 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
3958 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3972 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3991 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
4005 AATCGCAACGCGAAAT-AA
1 AATCGCAACGCGAAATGAA
*
4023 AATCGCAATGCGA
1 AATCGCAACGCGA
4036 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 15 0.24
19 18 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:4120 original size:20 final size:20
Alignment explanation
Indices: 4054--4149 Score: 122
Period size: 21 Copynumber: 4.8 Consensus size: 20
4044 TCGCGTTGCG
4054 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
4074 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
4093 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
4114 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
4134 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
4150 CTCTTCTGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.25
20 22 0.34
21 26 0.41
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:4137 original size:41 final size:40
Alignment explanation
Indices: 4055--4150 Score: 138
Period size: 41 Copynumber: 2.4 Consensus size: 40
4045 CGCGTTGCGA
***
4055 TTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTTCGCGTTGCGATTTTCAT
*
4095 TTCTCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATT-TCGCGTTGCGATTTTCAT
*
4136 TTATCTCGTTGCGAC
1 TTCTCTCGTTGCGAC
4151 TCTTCTGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 19 0.38
41 31 0.62
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (40 bp):
TTCTCTCGTTGCGACAGTCATTTCGCGTTGCGATTTTCAT
Found at i:4270 original size:33 final size:33
Alignment explanation
Indices: 4228--4299 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
4218 AAATACTAAC
*
4228 ATGAAAATCGCAACGAGAGAATAGCAACGCGAA
1 ATGAAAATCGCAACGACAGAATAGCAACGCGAA
* *
4261 ATGAAAATCGCAACGACAGAATCGTAACGCGAA
1 ATGAAAATCGCAACGACAGAATAGCAACGCGAA
4294 ATGAAA
1 ATGAAA
4300 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGACAGAATAGCAACGCGAA
Found at i:4531 original size:22 final size:22
Alignment explanation
Indices: 4479--4533 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4469 TGGTTGTGAG
**
4479 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
4501 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
4523 GGATTTCTTCG
1 GGATTTCTTCG
4534 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:4705 original size:20 final size:20
Alignment explanation
Indices: 4680--4873 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
4670 CTTTAAATAT
4680 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4700 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
4722 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4741 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
4761 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
4781 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4801 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4821 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4841 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4861 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4874 TTGGAAAATC
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:4867 original size:60 final size:60
Alignment explanation
Indices: 4680--4873 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
4670 CTTTAAATAT
**
4680 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
4741 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
4801 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
4861 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4874 TTGGAAAATC
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:5659 original size:2 final size:2
Alignment explanation
Indices: 5652--5689 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5642 TTTATTTTTC
5652 AT AT AT AT AT AT 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 AT AT AT AT AT AT
5690 TAATACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7663 original size:10 final size:10
Alignment explanation
Indices: 7648--7690 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
7638 TTCATCACAC
7648 CAAATCCTCT
1 CAAATCCTCT
7658 CAAATCCTCT
1 CAAATCCTCT
* *
7668 CAACTTCTCT
1 CAAATCCTCT
*
7678 TAAATCCTCT
1 CAAATCCTCT
7688 CAA
1 CAA
7691 CTTAAGGTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:7682 original size:20 final size:20
Alignment explanation
Indices: 7654--7693 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7644 ACACCAAATC
7654 CTCTCAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
*
7674 CTCTTAAATCCTCTCAACTT
1 CTCTCAAATCCTCTCAACTT
7694 AAGGTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCTCAAATCCTCTCAACTT
Found at i:7716 original size:12 final size:12
Alignment explanation
Indices: 7699--7755 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
7689 AACTTAAGGT
7699 ATATTTTATTTA
1 ATATTTTATTTA
7711 ATATTTTA-TTA
1 ATATTTTATTTA
*
7722 GTA-TTTATTT-
1 ATATTTTATTTA
*
7732 A-ATTAT-TTTA
1 ATATTTTATTTA
7742 ATATTTTATTTA
1 ATATTTTATTTA
7754 AT
1 AT
7756 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
9 4 0.11
10 7 0.19
11 11 0.31
12 14 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
ATATTTTATTTA
Found at i:7728 original size:18 final size:17
Alignment explanation
Indices: 7700--7763 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 17
7690 ACTTAAGGTA
*
7700 TATTTTATTTAATATTT
1 TATTATATTTAATATTT
7717 TATTAGTA-TT--TATTT
1 TATTA-TATTTAATATTT
*
7732 AATTAT-TTTAATATTT
1 TATTATATTTAATATTT
*
7748 TATT-TAATTAAT-TTT
1 TATTATATTTAATATTT
7763 T
1 T
7764 TTTTTTTGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
14 3 0.08
15 14 0.37
16 13 0.34
17 6 0.16
18 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATATTTAATATTT
Found at i:7769 original size:21 final size:21
Alignment explanation
Indices: 7699--7762 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 21
7689 AACTTAAGGT
7699 ATATTTTATTTAA-TATTTTA
1 ATATTTTATTTAATTATTTTA
*
7719 TTAGTATTTATTTAATTATTTTA
1 ATA-T-TTTATTTAATTATTTTA
7742 ATATTTTATTTAATTAATTTT
1 ATATTTTATTTAATT-ATTTT
7763 TTTTTTTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 15 0.39
23 9 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
ATATTTTATTTAATTATTTTA
Found at i:14628 original size:191 final size:191
Alignment explanation
Indices: 14302--15376 Score: 1835
Period size: 191 Copynumber: 5.6 Consensus size: 191
14292 TAAGATAATT
* * *
14302 AAATATAACATCATGTCAAAATTTAATTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* *
14367 ACATAAAAAATAGGAACACAATATGTATATTTACCAATAACCAGTTAGTCTAGTGGGATGAGGCG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * *
14432 TTAGATCCCTTAAGAAATGTTAGAAGTTTGAATCATGGTGTTTACAAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
*
14493 AAATATAAAATCATGACAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
14558 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * *
14623 TTAGATCCCTTAAGAAATGTTAGAAGTTCGAATCCTGCTGTTTACGAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
14684 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* * * ****
14749 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACTAGTTAGTCTAGTGTGATAAAACA
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
14814 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
14875 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
*
14940 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAATCAGTTAGTCTAGTGGGATGAGGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* *
15005 TTAGATCCTTTAAGAAAGGTTAGAAGTTTGAATCCTGCTGTTTACGAATGGAGGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
15066 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* *
15131 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAATCAGTTAGTCTAGTGGGATAAGGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
* * * *
15196 TTAGATCCATTAAGAAAGGTTAGAAGTTCGAATCCTGGTGTTTACGAATAGAAGAAACTAG
131 TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
*
15257 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATCAGTAGAAATTAATATTTAAGC
1 AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
* * * * * *
15322 ACATAAAAAATAGGAACACAATATGGATATATACCAACAACTAGTTGGTCCAGTG
66 ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTG
15377 AAATGAGACA
Statistics
Matches: 840, Mismatches: 44, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
191 840 1.00
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (191 bp):
AAATATAAAATCATGCCAAAATTTAGTTGTTAATATTTAAAATTAGTAGAAATTAATATTTAAGC
ACATAAAAAATAGGAACACAATATGTATATCTACCAATAACCAGTTAGTCTAGTGGGATGAGGTG
TTAGATCCCTTAAGAAAGGTTAGAAGTTTGAATCCTGGTGTTTACGAATGGAGGAAACTAG
Found at i:17794 original size:22 final size:22
Alignment explanation
Indices: 17769--17862 Score: 70
Period size: 23 Copynumber: 4.2 Consensus size: 22
17759 TAAATTGCAA
17769 CGAAGTG-CCACATAAAATGTCC
1 CGAAGTGACCACAT-AAATGTCC
*
17791 CGAA-TGACCACATAGATGTCC
1 CGAAGTGACCACATAAATGTCC
* *
17812 CGAAG-GACCGCGTAGAATTGTCC
1 CGAAGTGACCACATA-AA-TGTCC
*
17835 CGAAG-GACCGCATAGAATTGTCC
1 CGAAGTGACCACATA-AA-TGTCC
*
17858 TGAAG
1 CGAAG
17863 AACCGCGCAG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
21 20 0.32
22 11 0.18
23 31 0.50
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (22 bp):
CGAAGTGACCACATAAATGTCC
Found at i:17811 original size:21 final size:21
Alignment explanation
Indices: 17776--17850 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
17766 CAACGAAGTG
* *
17776 CCACATAAAATGTCCCGAATGA
1 CCACAT-AGATGTCCCGAAGGA
17798 CCACATAGATGTCCCGAAGGA
1 CCACATAGATGTCCCGAAGGA
* *
17819 CCGCGTAGAATTGTCCCGAAGGA
1 CCACATAG-A-TGTCCCGAAGGA
*
17842 CCGCATAGA
1 CCACATAGA
17851 ATTGTCCTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 19 0.41
22 8 0.17
23 19 0.41
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
CCACATAGATGTCCCGAAGGA
Found at i:17836 original size:44 final size:46
Alignment explanation
Indices: 17786--17874 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
17776 CCACATAAAA
* * *
17786 TGTCCCGAATGACCACATAG-A-TGTCCCGAAGGACCGCGTAGAAT
1 TGTCCCGAAGGACCACATAGAATTGTCCCGAAGAACCGCGCAGAAT
* *
17830 TGTCCCGAAGGACCGCATAGAATTGTCCTGAAGAACCGCGCAGAA
1 TGTCCCGAAGGACCACATAGAATTGTCCCGAAGAACCGCGCAGAA
17875 CCCTCAACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 18 0.47
45 1 0.03
46 19 0.50
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (46 bp):
TGTCCCGAAGGACCACATAGAATTGTCCCGAAGAACCGCGCAGAAT
Found at i:17837 original size:23 final size:23
Alignment explanation
Indices: 17786--17868 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
17776 CCACATAAAA
* *
17786 TGTCCCGAATGACCACATAG-A-
1 TGTCCCGAAGGACCGCATAGAAT
*
17807 TGTCCCGAAGGACCGCGTAGAAT
1 TGTCCCGAAGGACCGCATAGAAT
17830 TGTCCCGAAGGACCGCATAGAAT
1 TGTCCCGAAGGACCGCATAGAAT
* *
17853 TGTCCTGAAGAACCGC
1 TGTCCCGAAGGACCGC
17869 GCAGAACCCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.31
22 1 0.02
23 36 0.67
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCGCATAGAAT
Found at i:20416 original size:23 final size:23
Alignment explanation
Indices: 20385--20428 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20375 TAAAAATAAT
20385 TCTGCCTTTATGACACATTTTTC
1 TCTGCCTTTATGACACATTTTTC
* *
20408 TCTGTCTTTATGACACGTTTT
1 TCTGCCTTTATGACACATTTT
20429 CGATCGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.23, G:0.11, T:0.50
Consensus pattern (23 bp):
TCTGCCTTTATGACACATTTTTC
Found at i:20864 original size:2 final size:2
Alignment explanation
Indices: 20852--20901 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
20842 TCTTTTTATT
20852 TA TA T- 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
20893 TA TA TA TA T
1 TA TA TA TA T
20902 TAATTAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21684 original size:2 final size:2
Alignment explanation
Indices: 21677--21703 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21667 TATGATAATG
21677 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 A
21704 CACACAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22859 original size:41 final size:41
Alignment explanation
Indices: 22798--22948 Score: 266
Period size: 41 Copynumber: 3.7 Consensus size: 41
22788 ATTTCGCGTT
*
22798 GCGATTTTCCATTTCGCGTTGCGGTAGTTGAAAATCGCAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
* *
22839 GCGGTTTTCCATTTCGCGTTGCGATAGTTGAAAATCGTAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
*
22880 GCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
22921 GCGATTTTCCATTTCGCGTTGCGATAGT
1 GCGATTTTCCATTTCGCGTTGCGATAGT
22949 CTACAGTTGT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
GCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCAAC
Found at i:22964 original size:22 final size:23
Alignment explanation
Indices: 22937--22990 Score: 92
Period size: 22 Copynumber: 2.4 Consensus size: 23
22927 TTCCATTTCG
22937 CGTTGCGATAGTCTACAG-TTGT
1 CGTTGCGATAGTCTACAGTTTGT
*
22959 TGTTGCGATAGTCTACAGTTTGT
1 CGTTGCGATAGTCTACAGTTTGT
22982 CGTTGCGAT
1 CGTTGCGAT
22991 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (23 bp):
CGTTGCGATAGTCTACAGTTTGT
Found at i:23630 original size:6 final size:6
Alignment explanation
Indices: 23604--23645 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
23594 TCTCGTCTTG
23604 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
23646 AATACGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.29
Consensus pattern (6 bp):
GGTCGT
Done.