Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000477.1 Hibiscus syriacus cultivar Beakdansim tig00000889_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: 80591
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4174 original size:31 final size:31
Alignment explanation
Indices: 4139--4217 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
4129 TTCTCTGTCC
4139 CATTTTGACCCTTAAAATATACTCATTTTCT
1 CATTTTGACCCTTAAAATATACTCATTTTCT
4170 CATTTTGACCCTTAAAATATACTCATTTTCT
1 CATTTTGACCCTTAAAATATACTCATTTTCT
4201 CATTTTGACCCTTAAAA
1 CATTTTGACCCTTAAAA
4218 CAATATGGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (31 bp):
CATTTTGACCCTTAAAATATACTCATTTTCT
Found at i:9483 original size:14 final size:14
Alignment explanation
Indices: 9446--9485 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
9436 ATTGCATCAT
*
9446 CCTAAACTCTAAAG
1 CCTAAACTCTAAAC
*
9460 CTTAAACTCTAAAC
1 CCTAAACTCTAAAC
*
9474 CCTAAGCTCTAA
1 CCTAAACTCTAA
9486 TTTAAAACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.30, G:0.05, T:0.25
Consensus pattern (14 bp):
CCTAAACTCTAAAC
Found at i:10019 original size:22 final size:22
Alignment explanation
Indices: 9982--10050 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
9972 TTAAATTTAT
*
9982 AATATTATATATATTAACTTAAA
1 AATATT-TTTATATTAACTTAAA
*
10005 AATATTTTTATATTAACTTATTA
1 AATATTTTTATATTAACTTA-AA
*
10028 AATATATATTATTATTAACTTAA
1 AATAT-TTTTA-TATTAACTTAA
10051 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
22 13 0.33
23 12 0.31
24 4 0.10
25 10 0.26
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATTTTTATATTAACTTAAA
Found at i:10034 original size:25 final size:24
Alignment explanation
Indices: 9982--10064 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 24
9972 TTAAATTTAT
*
9982 AATATTATATATATTAACTTA--AA
1 AATATT-TTTATATTAACTTATTAA
10005 AATATTTTTATATTAACTTATT-A
1 AATATTTTTATATTAACTTATTAA
*
10028 AATATATATTATTATTAACTTAATTTAAA
1 AATAT-TTTTA-TATTAACTT-A-TT-AA
10057 AATATTTT
1 AATATTTT
10065 ATTTTTATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
22 13 0.27
23 12 0.24
24 4 0.08
25 9 0.18
26 1 0.02
27 2 0.04
28 2 0.04
29 6 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATTTTTATATTAACTTATTAA
Found at i:11423 original size:40 final size:40
Alignment explanation
Indices: 11379--11467 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
11369 AACTAATATT
11379 CTATAGTCGAGGCATTTAGAGTAGTCAACAAAGCAATACC
1 CTATAGTCGAGGCATTTAGAGTAGTCAACAAAGCAATACC
11419 CTATAGTCGAGGCATTTAGAGTAGTCAACAAAGCAATACC
1 CTATAGTCGAGGCATTTAGAGTAGTCAACAAAGCAATACC
*
11459 TTATAGTCG
1 CTATAGTCG
11468 GGAGATCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (40 bp):
CTATAGTCGAGGCATTTAGAGTAGTCAACAAAGCAATACC
Found at i:11931 original size:12 final size:12
Alignment explanation
Indices: 11914--11962 Score: 98
Period size: 12 Copynumber: 4.1 Consensus size: 12
11904 AATAAAGCCT
11914 TCGTCATCTTCA
1 TCGTCATCTTCA
11926 TCGTCATCTTCA
1 TCGTCATCTTCA
11938 TCGTCATCTTCA
1 TCGTCATCTTCA
11950 TCGTCATCTTCA
1 TCGTCATCTTCA
11962 T
1 T
11963 TGTCTACGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.16, C:0.33, G:0.08, T:0.43
Consensus pattern (12 bp):
TCGTCATCTTCA
Found at i:11932 original size:6 final size:6
Alignment explanation
Indices: 11914--11962 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
11904 AATAAAGCCT
* * * *
11914 TCGTCA TCTTCA TCGTCA TCTTCA TCGTCA TCTTCA TCGTCA TCTTCA
1 TCGTCA TCGTCA TCGTCA TCGTCA TCGTCA TCGTCA TCGTCA TCGTCA
11962 T
1 T
11963 TGTCTACGAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.16, C:0.33, G:0.08, T:0.43
Consensus pattern (6 bp):
TCGTCA
Found at i:18064 original size:9 final size:9
Alignment explanation
Indices: 18050--18078 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
18040 GAAATCGGTT
18050 AATTAACCG
1 AATTAACCG
18059 AATTAACCG
1 AATTAACCG
18068 AATTAACCG
1 AATTAACCG
18077 AA
1 AA
18079 ATAAAATTTT
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:18422 original size:185 final size:186
Alignment explanation
Indices: 18089--18479 Score: 671
Period size: 185 Copynumber: 2.1 Consensus size: 186
18079 ATAAAATTTT
* *
18089 AAAT-TTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAATCCAATTAATA
1 AAATATTT-AATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATA
18153 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
*
18218 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
* *
18275 AAATATTTAATATATTATATATGACATATGGACTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTTAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
*
18340 TTTAAGATTCAATAAC-TTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* *
18404 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
*
18460 AAATATTTAAT-TTTTATATA
1 AAATATTTAATATATTATATA
18480 AATTAGAAAA
Statistics
Matches: 195, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
184 8 0.04
185 112 0.57
186 72 0.37
187 3 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (186 bp):
AAATATTTAATATATTATATATAACATATGGACTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTAAA
Found at i:20307 original size:21 final size:20
Alignment explanation
Indices: 20283--20330 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
20273 AATAAATTAC
* *
20283 ATTATTAATAATATAATAAT
1 ATTATTAATAATAAAAAAAT
**
20303 AATTAAAAATAATAAAAAAAT
1 -ATTATTAATAATAAAAAAAT
20324 ATTATTA
1 ATTATTA
20331 TAACAATATA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATTAATAATAAAAAAAT
Found at i:29744 original size:72 final size:71
Alignment explanation
Indices: 29662--29806 Score: 227
Period size: 71 Copynumber: 2.0 Consensus size: 71
29652 GAAGGTGAAT
* * *
29662 AAGAAGAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGGCATTT
1 AAGAAGAACGAAAGGAAGCACCAACACTTTCGATTC-AAGTGAACGGAAGGAAGCATCAGCACTT
29727 TCGATTC
65 TCGATTC
** *
29734 AAGAAGAACGAAAGGAAGCACCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCGTCAGCACTTT
1 AAGAAGAACGAAAGGAAGCACCAACACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
29799 CGATTC
66 CGATTC
29805 AA
1 AA
29807 TTGTTCATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
71 34 0.51
72 33 0.49
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCACCAACACTTTCGATTCAAGTGAACGGAAGGAAGCATCAGCACTTT
CGATTC
Found at i:29785 original size:35 final size:35
Alignment explanation
Indices: 29667--29806 Score: 181
Period size: 36 Copynumber: 3.9 Consensus size: 35
29657 TGAATAAGAA
*
29667 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTC-AAGT
* * * *
29703 GAACGGAAGGAAGCATCGGCATTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAG-T
* *
29739 GAACGAAAGGAAGCACCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
29774 GAACGGAAGGAAGCGTCAGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCAGCACTTTCGATTCAA
29807 TTGTTCATTT
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 32 0.36
36 58 0.64
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:30463 original size:30 final size:30
Alignment explanation
Indices: 30429--30500 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
30419 GGATACTAAC
* * * *
30429 TTATTACATTTATTATATTCTTAACTTAAA
1 TTATTAAATATATTATAGTATTAACTTAAA
* *
30459 TTATTAAATATATTCTAGTATTATCTTAAA
1 TTATTAAATATATTATAGTATTAACTTAAA
*
30489 TTAGTAAATATA
1 TTATTAAATATA
30501 ATTTATCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (30 bp):
TTATTAAATATATTATAGTATTAACTTAAA
Found at i:37219 original size:105 final size:104
Alignment explanation
Indices: 37140--37384 Score: 285
Period size: 105 Copynumber: 2.3 Consensus size: 104
37130 GCAATGAGGG
* *
37140 AGCAAGGCATTAAGCCTGATGTTGTCACATATAATATATTGGTTGATGCTTATTGCAAGGAGCGA
1 AGCAAGGCATTAAGCCTAATGTTGTCACATATAATATATTGGTCGATGCTTATTGCAAGGAGCGA
* *
37205 ACGGTTTCCAAAGCTAAAGATATTATTGACACCATGAGAA
66 ACGATTTCCAAAGCTAAAGATATTAATGACA-CATGAGAA
* * * *
37245 AGCAAGGGATTGAGCCTAATGTTGTCACGTATAATATATTGGTCGATGCTTATTGCAAGGAGGGA
1 AGCAAGGCATTAAGCCTAATGTTGTCACATATAATATATTGGTCGATGCTTATTGCAAGGAGCGA
* * * * * *
37310 ATGATTTCCAAAGGTGAAGGTATT-GTCAACACAATGAGAA
66 ACGATTTCCAAAGCTAAAGATATTAAT-GACAC-ATGAGAA
* * ** *
37350 ACCAAAGCATCGAGCCTAATGTAGTCACATATAAT
1 AGCAAGGCATTAAGCCTAATGTTGTCACATATAAT
37385 GCATTGATGA
Statistics
Matches: 119, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
104 2 0.02
105 117 0.98
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (104 bp):
AGCAAGGCATTAAGCCTAATGTTGTCACATATAATATATTGGTCGATGCTTATTGCAAGGAGCGA
ACGATTTCCAAAGCTAAAGATATTAATGACACATGAGAA
Found at i:50253 original size:58 final size:58
Alignment explanation
Indices: 50163--50281 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
50153 TTGATTTCTG
50163 TTCAAGGTATTTTTTTATTACTCTAGGGTGCTTACAAGTGATAGTATACGTTTAAATA
1 TTCAAGGTATTTTTTTATTACTCTAGGGTGCTTACAAGTGATAGTATACGTTTAAATA
50221 TTCAAGGTATTTTTTTATTACTCTAGGGTGCTTACAAGTGATAGTATACGTTTAAATA
1 TTCAAGGTATTTTTTTATTACTCTAGGGTGCTTACAAGTGATAGTATACGTTTAAATA
50279 TTC
1 TTC
50282 TGTAATTATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.44
Consensus pattern (58 bp):
TTCAAGGTATTTTTTTATTACTCTAGGGTGCTTACAAGTGATAGTATACGTTTAAATA
Found at i:50708 original size:18 final size:19
Alignment explanation
Indices: 50685--50720 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
50675 TTTTAAAAAG
50685 AAACATAAAA-TTTGAAAT
1 AAACATAAAACTTTGAAAT
50703 AAACATAAAACTTTGAAA
1 AAACATAAAACTTTGAAA
50721 ACCTTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (19 bp):
AAACATAAAACTTTGAAAT
Found at i:56802 original size:4 final size:4
Alignment explanation
Indices: 56793--56817 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56783 GGCTACCAAC
56793 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
56818 TTCAACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:58384 original size:34 final size:32
Alignment explanation
Indices: 58331--58400 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
58321 ACCTTACAAC
*
58331 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
58363 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
58397 TCCC
1 TCCC
58401 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:58710 original size:21 final size:21
Alignment explanation
Indices: 58684--58725 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
58674 CCAGAATGGG
*
58684 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
58705 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
58726 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:58787 original size:21 final size:21
Alignment explanation
Indices: 58761--58804 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
58751 CTGTTGAACA
58761 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
58782 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
58803 GG
1 GG
58805 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:58856 original size:21 final size:21
Alignment explanation
Indices: 58830--58910 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
58820 GCTTTAGACA
*
58830 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCT-G
*
58852 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
58869 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
58888 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
58909 GG
1 GG
58911 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 20 0.40
22 12 0.24
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:58874 original size:15 final size:15
Alignment explanation
Indices: 58854--58883 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58844 CCCCCTGGGG
58854 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
58869 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
58884 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:58899 original size:36 final size:37
Alignment explanation
Indices: 58832--58904 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
58822 TTTAGACAGG
*
58832 GGGGAATCGGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
* *
58869 GGGGTATCTGTACCCCCT-GGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
58905 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (37 bp):
GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
Found at i:61911 original size:34 final size:32
Alignment explanation
Indices: 61858--61927 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
61848 ACCTTACAAC
*
61858 TCCCTAGTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* * *
61890 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
61924 TCCC
1 TCCC
61928 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:62237 original size:21 final size:21
Alignment explanation
Indices: 62211--62252 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
62201 CCAGAATGGG
*
62211 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
62232 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
62253 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:62314 original size:21 final size:21
Alignment explanation
Indices: 62288--62331 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
62278 CTGTTGAACA
62288 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
62309 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
62330 GG
1 GG
62332 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:62384 original size:21 final size:21
Alignment explanation
Indices: 62358--62438 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
62348 GCTTTAGACA
*
62358 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCT-G
*
62380 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
62397 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
62416 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
62437 GG
1 GG
62439 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 20 0.40
22 12 0.24
ACGTcount: A:0.12, C:0.27, G:0.41, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:62402 original size:15 final size:15
Alignment explanation
Indices: 62382--62411 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
62372 CCCCCTGGGG
62382 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
62397 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
62412 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:62427 original size:36 final size:37
Alignment explanation
Indices: 62360--62432 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
62350 TTTAGACAGG
*
62360 GGGGAATCGGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
* *
62397 GGGGTATCTGTACCCCCT-GGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
62433 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (37 bp):
GGGGAATCGGTACCCCCTGGGGGGGGAATCTGTACCC
Found at i:66099 original size:37 final size:36
Alignment explanation
Indices: 66027--66100 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
66017 CTTGGAAAAT
* *
66027 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
*
66063 ATTTATATAATTTTTTTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
66100 A
1 A
66101 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 10 0.30
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:66102 original size:38 final size:37
Alignment explanation
Indices: 66022--66102 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
66012 AACAACTTGG
* *
66022 AAAATATTTATATATTTTCTTTAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAATTGAAAATCAT
*
66060 -AAAATTTATATAATTTTTTTTATAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTA-AAAATTGAAAATCAT
66097 AAAAAT
1 AAAAAT
66103 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 8 0.22
37 14 0.38
38 15 0.41
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (37 bp):
AAAAATTTATATATTTTCTTTAAAAATTGAAAATCAT
Found at i:66614 original size:33 final size:30
Alignment explanation
Indices: 66546--66632 Score: 111
Period size: 30 Copynumber: 2.7 Consensus size: 30
66536 TGTATAATTT
* *
66546 AAAAAATGTCAGAGACCTAACTGCACTAAAGA
1 AAAAAAT-T-AGATACCTAATTGCACTAAAGA
66578 AAAAAATTAGATACCTAATTGCACTAAAGAA
1 AAAAAATTAGATACCTAATTGCACTAAAG-A
66609 AAAAAAGCTTAGATACCTAATTGC
1 AAAAAA--TTAGATACCTAATTGC
66633 GCGGACTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
30 19 0.38
31 8 0.16
32 7 0.14
33 16 0.32
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.21
Consensus pattern (30 bp):
AAAAAATTAGATACCTAATTGCACTAAAGA
Found at i:73992 original size:24 final size:24
Alignment explanation
Indices: 73957--74018 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
73947 GTTGCATGGC
*
73957 TTGCCATAAGTCTCCCCGAAGGGG
1 TTGCCATGAGTCTCCCCGAAGGGG
* *
73981 TTTCCATGAGTCTCCCCGGAGGGG
1 TTGCCATGAGTCTCCCCGAAGGGG
*
74005 TTGCCATGTGTCTC
1 TTGCCATGAGTCTC
74019 TCGGGGGTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (24 bp):
TTGCCATGAGTCTCCCCGAAGGGG
Found at i:76971 original size:25 final size:24
Alignment explanation
Indices: 76911--76971 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
76901 TTTTATTTGT
* *
76911 ATCTTATCTTTAAAATATATTTTA
1 ATCTTATCTTAAAAATATATCTTA
*
76935 ATCTTTAACTTAAAAATTATATCTTA
1 ATC-TTATCTTAAAAA-TATATCTTA
*
76961 TTCTTATCTTA
1 ATCTTATCTTA
76972 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 3 0.10
25 17 0.57
26 10 0.33
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (24 bp):
ATCTTATCTTAAAAATATATCTTA
Found at i:77197 original size:32 final size:28
Alignment explanation
Indices: 77157--77239 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 28
77147 GTATATTAAT
*
77157 AAAATAATAATAAAAATATAATGTCATAA
1 AAAATAATAATAAAAATATAATGAC-TAA
*
77186 AAATTATTAATAA-AATAAATTAGAATGACTAA
1 AAA--A-TAATAATAA-AAA-TATAATGACTAA
77218 AAAATAATAATAAAAATATAAT
1 AAAATAATAATAAAAATATAAT
77240 TACATAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
28 5 0.11
29 12 0.27
30 3 0.07
31 3 0.07
32 15 0.33
33 7 0.16
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (28 bp):
AAAATAATAATAAAAATATAATGACTAA
Done.