Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007518.1 Hibiscus syriacus cultivar Beakdansim tig00020944_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: 80488
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:823 original size:24 final size:24
Alignment explanation
Indices: 789--842 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
779 CTGAAACATC
* *
789 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
813 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
837 ATCAAA
1 ATCAAA
843 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:1845 original size:14 final size:16
Alignment explanation
Indices: 1825--1898 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1815 ATGAAATCGC
1825 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1840 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1857 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1876 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1892 -TTGCGAT
1 ATTGCGAT
1899 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1862 original size:19 final size:19
Alignment explanation
Indices: 1821--1888 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1811 GCGAATGAAA
1821 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1837 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1854 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1873 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1889 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2020 original size:14 final size:14
Alignment explanation
Indices: 2003--2039 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1993 ACATAATTAA
2003 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2017 ACAAATCATCTTTT
1 ACAAATCAACATTT
2031 ACAAATCAA
1 ACAAATCAA
2040 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3919 original size:19 final size:19
Alignment explanation
Indices: 3895--3949 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
3885 GAAACTTAAA
3895 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3914 ATCGCAACGCGAAATGGCT
1 ATCGCAACGCGAAATGACT
*
3933 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
3950 AAATCAACGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:4055 original size:14 final size:14
Alignment explanation
Indices: 4036--4093 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
4026 TTTCATTTCG
4036 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
4050 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
4066 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
4082 CGTTGCGATTTT
1 CGTTGCGATTTT
4094 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:4104 original size:33 final size:33
Alignment explanation
Indices: 4019--4109 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
4009 ACAAATCGCA
*
4019 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
4052 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
4084 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
4110 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:4117 original size:19 final size:20
Alignment explanation
Indices: 4095--4137 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4085 TGCGATTTTT
4095 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
4114 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
4134 ATTT
1 ATTT
4138 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:4128 original size:20 final size:20
Alignment explanation
Indices: 4103--4148 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
4093 TTATTTCGCA
4103 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
4123 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
4143 TTGCGA
1 TTGCGA
4149 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:4656 original size:18 final size:18
Alignment explanation
Indices: 4630--4674 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4620 GTCGATCAGA
*
4630 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4648 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4666 TGATGGCTC
1 TGATGGCTC
4675 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:6316 original size:22 final size:22
Alignment explanation
Indices: 6289--6332 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6279 GATGGAGATA
6289 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
6311 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
6333 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:6543 original size:20 final size:20
Alignment explanation
Indices: 6518--6611 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
6508 GATTATGTAT
6518 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6538 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
6558 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
6579 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6599 TATCGCATTGCGA
1 TATCGCGTTGCGA
6612 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6612 original size:20 final size:20
Alignment explanation
Indices: 6498--6612 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
6488 CGCTTTGAAA
*
6498 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
6519 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
6539 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
6559 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
6580 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
6600 ATCGCATTGCGAT
1 ATCGCATTGCGAT
6613 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:6630 original size:21 final size:21
Alignment explanation
Indices: 6601--6693 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
6591 ATAGTCAGTA
6601 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6622 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6642 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6663 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6683 TCGCATTGCGA
1 TCGCATTGCGA
6694 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:6631 original size:41 final size:41
Alignment explanation
Indices: 6540--6674 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
6530 AAAGTCAGTA
* * * ** *
6540 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
6580 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
6622 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
6663 TCGCGTTGCGAT
1 TCGCGTTGCGAT
6675 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:6675 original size:41 final size:41
Alignment explanation
Indices: 6601--6693 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
6591 ATAGTCAGTA
6601 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
6642 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
6683 TCGCATTGCGA
1 TCGCATTGCGA
6694 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:7157 original size:2 final size:2
Alignment explanation
Indices: 7152--7180 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7142 AATAATGATA
7152 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 A
7181 AATTTAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7506 original size:49 final size:48
Alignment explanation
Indices: 7449--7542 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 48
7439 ATTGAATGCA
* * * *
7449 AAAATAATTTAAGGACCATATTAAGTTTTTTTTTAAAGTACAAGGGCCT
1 AAAATAATTTAAGGACCACATTAAG-ATTTTTTAAAAGCACAAGGGCCT
7498 AAAATAATTTAAGGACCACATTAAGATTTTTTAAAAGCACAAGGG
1 AAAATAATTTAAGGACCACATTAAGATTTTTTAAAAGCACAAGGG
7543 TCTCTTGTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 17 0.41
49 24 0.59
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (48 bp):
AAAATAATTTAAGGACCACATTAAGATTTTTTAAAAGCACAAGGGCCT
Found at i:13144 original size:29 final size:29
Alignment explanation
Indices: 13111--13176 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
13101 ATTTTACTCC
13111 TATGTAAAATATGGTTATT-AATGATAATT
1 TATGTAAAATATGGTT-TTCAATGATAATT
** * *
13140 TATGTGCACTATGGTTTTCAGTGATAATT
1 TATGTAAAATATGGTTTTCAATGATAATT
*
13169 TATATAAA
1 TATGTAAA
13177 CTTTATTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (29 bp):
TATGTAAAATATGGTTTTCAATGATAATT
Found at i:14199 original size:52 final size:52
Alignment explanation
Indices: 14121--14223 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
14111 TTATAATATT
14121 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
14173 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
14224 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:18792 original size:52 final size:52
Alignment explanation
Indices: 18714--18816 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
18704 TTATAATATT
*
18714 CTTGTAATTAGTTGTAATCCCCTAACTATAGGCTAGTCTCCTATTTTTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTATAGGCTAGTCTCCTATTTCTATGC
* *
18766 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTATAGGCTAGTCTCCTATTTCTATG
18817 TGTCCAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTATAGGCTAGTCTCCTATTTCTATGC
Found at i:19120 original size:21 final size:21
Alignment explanation
Indices: 19072--19121 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
19062 GTTTCCAGAT
*
19072 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
19093 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
19114 TCGCAATG
1 TCGCAATG
19122 TGAATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:19159 original size:21 final size:20
Alignment explanation
Indices: 19086--19166 Score: 58
Period size: 21 Copynumber: 4.0 Consensus size: 20
19076 AACGCGAACT
19086 TCGACTATCGCAATGCGA-A
1 TCGACTATCGCAATGCGATA
* *
19105 CTTGGACTATCGCAATGTGAATA
1 --TCGACTATCGCAATGCG-ATA
** *
19128 TATA-AATCGCAATGCGATA
1 TCGACTATCGCAATGCGATA
*
19147 GTCGACTATCGCATTGCGAT
1 -TCGACTATCGCAATGCGAT
19167 TTACATATTC
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.07
20 12 0.26
21 29 0.63
22 1 0.02
23 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (20 bp):
TCGACTATCGCAATGCGATA
Found at i:19204 original size:19 final size:20
Alignment explanation
Indices: 19180--19230 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
19170 CATATTCGCA
19180 TTGCGATAGTCCAAATT-CG
1 TTGCGATAGTCCAAATTCCG
* *
19199 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATTC-CG
19220 TTGCGATAGTC
1 TTGCGATAGTC
19231 GAAGTTTGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 15 0.54
21 13 0.46
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCCAAATTCCG
Found at i:19223 original size:21 final size:21
Alignment explanation
Indices: 19174--19247 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
19164 GATTTACATA
* * *
19174 TTCGCATTGCGATAGTCCAAA
1 TTCGCGTTGCGATAGTCGAAG
19195 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
19214 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
19235 TTTGCGTTGCGAT
1 TTCGCGTTGCGAT
19248 TTATTCCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.34
21 31 0.66
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.32
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:21311 original size:3 final size:3
Alignment explanation
Indices: 21303--21327 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21293 ATATGATAGC
21303 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
21328 TTAAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:23869 original size:5 final size:5
Alignment explanation
Indices: 23863--23893 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
23853 GATCTGATCT
*
23863 CCCCT CCCCA CCCCA CCCCA CCCCA CCCCA C
1 CCCCA CCCCA CCCCA CCCCA CCCCA CCCCA C
23894 GCAACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.81, G:0.00, T:0.03
Consensus pattern (5 bp):
CCCCA
Found at i:31761 original size:20 final size:18
Alignment explanation
Indices: 31732--31771 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
31722 AAACTTTAAC
31732 TTTTATATTTTCAAATAAT
1 TTTTATA-TTTCAAATAAT
31751 TTTTAATATTTCAAATAAT
1 TTTT-ATATTTCAAATAAT
31770 TT
1 TT
31772 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATATTTCAAATAAT
Found at i:36585 original size:12 final size:12
Alignment explanation
Indices: 36568--36597 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
36558 TATCTGCTTA
36568 TTGCCTTTGTGT
1 TTGCCTTTGTGT
36580 TTGCCTTTGTGT
1 TTGCCTTTGTGT
36592 TTGCCT
1 TTGCCT
36598 CTAAAAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.23, T:0.57
Consensus pattern (12 bp):
TTGCCTTTGTGT
Found at i:36619 original size:16 final size:16
Alignment explanation
Indices: 36595--36633 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
36585 TTTGTGTTTG
*
36595 CCTCTAAAAGGTGGAT
1 CCTCCAAAAGGTGGAT
36611 CCTCCAAAAGGTGGAT
1 CCTCCAAAAGGTGGAT
36627 CCTCCAA
1 CCTCCAA
36634 CATAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (16 bp):
CCTCCAAAAGGTGGAT
Found at i:44019 original size:21 final size:20
Alignment explanation
Indices: 43993--44033 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
43983 CAAGGGTTAG
*
43993 TCTAAATATACCAAATATTTT
1 TCTAAACATACCAAAT-TTTT
*
44014 TCTAAACCTACCAAATTTTT
1 TCTAAACATACCAAATTTTT
44034 ATTAAAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (20 bp):
TCTAAACATACCAAATTTTT
Found at i:44090 original size:41 final size:39
Alignment explanation
Indices: 44015--44133 Score: 175
Period size: 39 Copynumber: 3.0 Consensus size: 39
44005 AAATATTTTT
* *
44015 CTAAACCTACCAAATTTTTATTAAAACACTAAAAGATTA
1 CTAAACCTACCAATTTTTTATTAAAACACCAAAAGATTA
44054 CTAAACCTACCAATTTTTTTTATTAAAACACCAAAAGATTA
1 CTAAACCTACCAA--TTTTTTATTAAAACACCAAAAGATTA
* * *
44095 TTAAACCTATCAATTTTTTATTAAAACGCCAAAAGATTA
1 CTAAACCTACCAATTTTTTATTAAAACACCAAAAGATTA
44134 AAGTAATTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
39 38 0.52
41 35 0.48
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (39 bp):
CTAAACCTACCAATTTTTTATTAAAACACCAAAAGATTA
Found at i:47304 original size:16 final size:16
Alignment explanation
Indices: 47269--47323 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
47259 TTCAAGTTAT
*
47269 TTTCGGTTC-GATTGC
1 TTTCGGTTCGGATTAC
*
47284 TTTCGGTTCGGGTTAC
1 TTTCGGTTCGGATTAC
* *
47300 TTTCGATTTGGATTAC
1 TTTCGGTTCGGATTAC
47316 TTTCGGTT
1 TTTCGGTT
47324 TGGTTAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 9 0.27
16 24 0.73
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.49
Consensus pattern (16 bp):
TTTCGGTTCGGATTAC
Found at i:47357 original size:58 final size:59
Alignment explanation
Indices: 47284--47410 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 59
47274 GTTCGATTGC
* ** * **
47284 TTTCGGTTCGGGTTACTTTCGATTTGGA-TTACTTTCGGTTTGG-TTAAATTTGAGTCGG
1 TTTCGGTTCGGGTTACTTTC-AGTTCAAGTTACTTTCGGTTTGGCTAAAATTTGAGTCAA
** *
47342 TTTCGGTTCTTGTTACTTTCAGTTCAAGTTACTTTCGGTTTGGCTAAAATTTGGGTCAA
1 TTTCGGTTCGGGTTACTTTCAGTTCAAGTTACTTTCGGTTTGGCTAAAATTTGAGTCAA
47401 TTTCGGTTCG
1 TTTCGGTTCG
47411 ATTTTATTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
57 4 0.07
58 33 0.58
59 20 0.35
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.46
Consensus pattern (59 bp):
TTTCGGTTCGGGTTACTTTCAGTTCAAGTTACTTTCGGTTTGGCTAAAATTTGAGTCAA
Found at i:48678 original size:12 final size:12
Alignment explanation
Indices: 48663--48687 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48653 TTTTTTAATG
48663 TTAATTTTATAA
1 TTAATTTTATAA
48675 TTAATTTTATAA
1 TTAATTTTATAA
48687 T
1 T
48688 AGATATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTAATTTTATAA
Found at i:50973 original size:18 final size:19
Alignment explanation
Indices: 50940--50975 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
50930 TATTTGATAA
*
50940 AATATAAATTTTAAAAGAC
1 AATATAAATTTAAAAAGAC
50959 AATAT-AATTTAAAAAGA
1 AATATAAATTTAAAAAGA
50976 AAAAGAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (19 bp):
AATATAAATTTAAAAAGAC
Found at i:51558 original size:3 final size:3
Alignment explanation
Indices: 51544--51600 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
51534 AGCCTAAGAT
51544 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51590 TAA T-A TAA TAA
1 TAA TAA TAA TAA
51601 GGGTAAAGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52532 original size:18 final size:17
Alignment explanation
Indices: 52505--52543 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
52495 CGAGTTTGAG
52505 TTTTTCAAGGATTATATT
1 TTTTTCAAGGATTAT-TT
* *
52523 TTTTTGAAGGCTTATTT
1 TTTTTCAAGGATTATTT
52540 TTTT
1 TTTT
52544 ATTTTTAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.62
Consensus pattern (17 bp):
TTTTTCAAGGATTATTT
Found at i:56909 original size:52 final size:52
Alignment explanation
Indices: 56831--56930 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
56821 CGGCTCTGGG
* * *
56831 TATTTTTTGGCTCGGGATAAAATAAAAGAAAT-AGACCTCTATTTATGTTCTT
1 TATTTTTTGGCCCAGGACAAAATAAAAGAAATGAG-CCTCTATTTATGTTCTT
* *
56883 TATTTTTTGGCCCAGGACGAAATAAAATAAATGAGCCTCTATTTATGT
1 TATTTTTTGGCCCAGGACAAAATAAAAGAAATGAGCCTCTATTTATGT
56931 GATATTAACA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 40 0.95
53 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (52 bp):
TATTTTTTGGCCCAGGACAAAATAAAAGAAATGAGCCTCTATTTATGTTCTT
Found at i:61602 original size:20 final size:19
Alignment explanation
Indices: 61565--61608 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
61555 TTTTATTATA
61565 TATTTTCTTTTAAAAA-TT
1 TATTTTCTTTTAAAAATTT
*
61583 TATTTTCGTTTTCTAAAATTT
1 TATTTTC-TTTT-AAAAATTT
61604 TATTT
1 TATTT
61609 CGTCCCCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
20 4 0.18
21 7 0.32
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTCTTTTAAAAATTT
Found at i:64853 original size:21 final size:21
Alignment explanation
Indices: 64829--64873 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
64819 TCGTTGACTG
**
64829 TTACAGTGTTGACATGACAAT
1 TTACAGTACTGACATGACAAT
* *
64850 TTACGGTACTGACATGATAAT
1 TTACAGTACTGACATGACAAT
64871 TTA
1 TTA
64874 TGATGCTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (21 bp):
TTACAGTACTGACATGACAAT
Found at i:65326 original size:42 final size:42
Alignment explanation
Indices: 65264--65356 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
65254 GTAAGTTTTA
* * * *
65264 GATCGATCCCTTGAAGAAAATGATCGATCCCTAGATGTAAAG
1 GATCGATCCCTTCAACAAAATGATCGATCCATAGATGAAAAG
* * *
65306 GATCGATCCCTTCACCAAAATGATTGATCCATTGATGAAAAG
1 GATCGATCCCTTCAACAAAATGATCGATCCATAGATGAAAAG
*
65348 GATTGATCC
1 GATCGATCC
65357 ATTCCCTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (42 bp):
GATCGATCCCTTCAACAAAATGATCGATCCATAGATGAAAAG
Found at i:65359 original size:21 final size:21
Alignment explanation
Indices: 65264--65356 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
65254 GTAAGTTTTA
* *
65264 GATCGATCCCTTGAAGAAAAT
1 GATCGATCCCTTGATGAAAAG
* *
65285 GATCGATCCCTAGATGTAAAG
1 GATCGATCCCTTGATGAAAAG
* ** *
65306 GATCGATCCCTTCACCAAAAT
1 GATCGATCCCTTGATGAAAAG
* *
65327 GATTGATCCATTGATGAAAAG
1 GATCGATCCCTTGATGAAAAG
*
65348 GATTGATCC
1 GATCGATCC
65357 ATTCCCTTAA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (21 bp):
GATCGATCCCTTGATGAAAAG
Found at i:69863 original size:23 final size:23
Alignment explanation
Indices: 69836--69879 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
69826 TCTTAGAGTG
69836 TTTAGTATG-TCTTTTATGCATGT
1 TTTAGTATGTTC-TTTATGCATGT
69859 TTTAGTATGTTCTTTATGCAT
1 TTTAGTATGTTCTTTATGCAT
69880 TTTGATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTAGTATGTTCTTTATGCATGT
Found at i:76403 original size:3 final size:3
Alignment explanation
Indices: 76397--76454 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
76387 GTTGTTGTTG
76397 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
76445 TTA TTA TTA T
1 TTA TTA TTA T
76455 CAACTCAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:78074 original size:35 final size:35
Alignment explanation
Indices: 78028--78103 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
78018 AAAACAATCC
* *
78028 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
78063 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
78098 TCAATT
1 TCAATT
78104 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:78636 original size:126 final size:126
Alignment explanation
Indices: 78483--78738 Score: 408
Period size: 128 Copynumber: 2.0 Consensus size: 126
78473 TTCAGTCTTT
* **
78483 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAGAA-TTAATAAATTAATCA-TTAATTAGG
1 ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
*
78546 ATCTGACATGTGTTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
66 ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
*
78607 ATTATTTATATGCTATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
1 ATTATTTATAT--AATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCA
* * *
78672 GGATCTGACATGTGTTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTA
64 GGATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
78735 ATTA
1 ATTA
78739 GAAGAAAATT
Statistics
Matches: 120, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
124 11 0.09
126 26 0.22
127 15 0.12
128 68 0.57
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (126 bp):
ATTATTTATATAATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGG
ATCTGACATGTGTTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTA
Found at i:78708 original size:23 final size:21
Alignment explanation
Indices: 78665--78711 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
78655 AATTAATCAT
78665 TTAACCAGGATCTGACATGTG
1 TTAACCAGGATCTGACATGTG
* *
78686 TTAACACATGATCATGATATGTG
1 TTAAC-CAGGATC-TGACATGTG
78709 TTA
1 TTA
78712 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATGTG
Found at i:78789 original size:21 final size:20
Alignment explanation
Indices: 78738--78781 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
78728 CCACCTAATT
78738 AGAAGAAAATTAAGTTACAA
1 AGAAGAAAATTAAGTTACAA
78758 AGAAGAAAATTAAGTTACAA
1 AGAAGAAAATTAAGTTACAA
78778 AGAA
1 AGAA
78782 ATAAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (20 bp):
AGAAGAAAATTAAGTTACAA
Found at i:79112 original size:28 final size:27
Alignment explanation
Indices: 79081--79143 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
79071 AGTTGATACA
*
79081 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
79109 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
79137 ATATTTT
1 ATATTTT
79144 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:79242 original size:16 final size:18
Alignment explanation
Indices: 79221--79254 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
79211 ATTTCTTATT
79221 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
79237 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
79255 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:79312 original size:15 final size:15
Alignment explanation
Indices: 79292--79323 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
79282 ATACATCTAA
79292 ATATAATATACTTTT
1 ATATAATATACTTTT
*
79307 ATATAATATATTTTT
1 ATATAATATACTTTT
79322 AT
1 AT
79324 TCTATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATAATATACTTTT
Done.