Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009619.1 Hibiscus syriacus cultivar Beakdansim tig00117008_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: 55102
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3089 original size:8 final size:8
Alignment explanation
Indices: 3076--3116 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
3066 CTCATTTTCA
3076 GAGAATTT
1 GAGAATTT
3084 GAGAATTT
1 GAGAATTT
*
3092 -AGAGTTT
1 GAGAATTT
*
3099 GGGAATTT
1 GAGAATTT
3107 GAGAATTT
1 GAGAATTT
3115 GA
1 GA
3117 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:3409 original size:126 final size:126
Alignment explanation
Indices: 3184--3788 Score: 1192
Period size: 126 Copynumber: 4.8 Consensus size: 126
3174 CTATAATCGG
3184 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
3249 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATTAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3310 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3375 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3436 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3501 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3562 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3627 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
3688 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
3753 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
3789 ATAACTTAAA
Statistics
Matches: 477, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 477 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:4237 original size:33 final size:34
Alignment explanation
Indices: 4176--4275 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
4166 AAATTTAATG
*
4176 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
4210 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
4243 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
4276 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:4883 original size:21 final size:21
Alignment explanation
Indices: 4795--4888 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
4785 TATGGTATAA
*
4795 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
4816 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
4837 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
4858 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
4879 AACCCTGCGG
1 AACCCTGCGG
4889 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:4918 original size:21 final size:21
Alignment explanation
Indices: 4892--4939 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4882 CCTGCGGAGA
*
4892 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
4913 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
4934 GGGCAT
1 TGGCAT
4940 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:6701 original size:33 final size:30
Alignment explanation
Indices: 6659--6745 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 30
6649 TTAATAATTC
6659 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTATATAAATA-TA--TTAA
* *
6693 TAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAATAATAATTATATAAATATATTAA
* *
6723 TATAAAAATAATAACTATTTAAA
1 TA-AAAAATAATAATTATATAAA
6746 AAAATACTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
30 6 0.13
31 16 0.35
32 2 0.04
33 18 0.39
34 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAAAAATAATAATTATATAAATATATTAA
Found at i:6723 original size:30 final size:32
Alignment explanation
Indices: 6659--6736 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
6649 TTAATAATTC
*
6659 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
6693 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
6723 TATAAAAATAATAA
1 TA-AAAAATAATAA
6737 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 6 0.15
31 10 0.25
32 2 0.05
33 18 0.45
34 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:6766 original size:33 final size:34
Alignment explanation
Indices: 6694--6766 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
6684 TTATTTTAAT
* * *
6694 AAAA-AATAATATTTACATAAATATATTAATATA
1 AAAATAATAATATTTACATAAAAATACTAACATA
6727 AAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAATAATAA-TATTTACATAAAAATACTAACATA
6760 AAAATAA
1 AAAATAA
6767 ATTTCTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 23 0.66
34 6 0.17
35 6 0.17
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
AAAATAATAATATTTACATAAAAATACTAACATA
Found at i:16932 original size:85 final size:84
Alignment explanation
Indices: 16756--17104 Score: 358
Period size: 85 Copynumber: 4.2 Consensus size: 84
16746 TTGCTGACTG
* * ** ** *
16756 ATAACCCTTCTCGCATTGAGTTATGCTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAAC
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * * *
16821 TCGAAGGAC-TTTGATGACAT
64 TCGAAGGTCTTTTGTTGGCAA
* * *
16841 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTACCTTTGAGCTGAGTGTAATCAAACTT
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
16906 GAAGGTCTTTTTGTTGGCAG
66 GAAGGTC-TTTTGTTGGCAA
* * *
16926 ACAACCCTTCTCGCCTTGAGTTATACTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
16991 GAAGGTCTTTTGTTAGAAA
66 GAAGGTCTTTTGTTGGCAA
** * * *
17010 ATAACCCTTCTTTCCTTGAGCTATGTTGCAAATGGTGTGCCTTTGAGCTGAGTG-----GAACTC
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
17070 GAAGGTC---T-TTGGCAA
66 GAAGGTCTTTTGTTGGCAA
* *
17085 ATAGCCCTTCTTGCCTTGAG
1 ATAACCCTTCTCGCCTTGAG
17105 CTTTGAATTG
Statistics
Matches: 227, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
75 23 0.10
76 1 0.00
79 13 0.06
83 30 0.13
84 56 0.25
85 104 0.46
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (84 bp):
ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAA
Found at i:17055 original size:169 final size:170
Alignment explanation
Indices: 16758--17063 Score: 429
Period size: 169 Copynumber: 1.8 Consensus size: 170
16748 GCTGACTGAT
*
16758 AACCCTTCTCGCATTGAGTTATGCTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
1 AACCCTTCTCGCATTGAGTTATACTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
* *
16823 GAAGGACTTTGATGACATATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTACCTTTGAG
66 GAAGGACTTTGATGACAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTACCTTTGAG
16888 CTGAGTGTAATCAAACTTGAAGGTCTTTTTGTTGGCAGAC
131 CTGAGTGTAATCAAACTTGAAGGTCTTTTTGTTGGCAGAC
* ** ** *
16928 AACCCTTCTCGCCTTGAGTTATACTGTAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 AACCCTTCTCGCATTGAGTTATACTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
* * ** * * *
16991 GAAGGTCTTTTGTTAGA-AAATAACCCTTCTTTCCTTGAGCTATGTTGCAAATGGTGTGCCTTTG
66 GAAGGAC-TTTGAT-GACAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTACCTTTG
17055 AGCTGAGTG
129 AGCTGAGTG
17064 GAACTCGAAG
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
168 33 0.28
169 55 0.47
170 30 0.25
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (170 bp):
AACCCTTCTCGCATTGAGTTATACTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
GAAGGACTTTGATGACAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTACCTTTGAG
CTGAGTGTAATCAAACTTGAAGGTCTTTTTGTTGGCAGAC
Found at i:17426 original size:112 final size:112
Alignment explanation
Indices: 17285--17539 Score: 316
Period size: 112 Copynumber: 2.3 Consensus size: 112
17275 TGTTACTTAT
* *
17285 GGCACGATATC-CTTCGTCGTGAAGTTGAAATCGTGGATGACCTATTCATTGTAAAGTTGAGCCT
1 GGCACGAT-TCACTTCGTCGTGAAGTTGAAATCATGGATGACCCATTCATTGTAAAGTTGAGCCT
* * *
17349 TGAATTGGATGTCTTTAATCGTGAAGTTGAAATCAAATGTTGTTGGTGA
65 TGAATTGGATATCCTTAATCGTGAAGTTGAAATCAAATGTTGCT-GTGA
* * * * ** *
17398 -GCATGATTCACTTCGTCGTGAAGTTGAAACCATGGATGGCCCATTCGTTGTGTAGTTGAGTCTT
1 GGCACGATTCACTTCGTCGTGAAGTTGAAATCATGGATGACCCATTCATTGTAAAGTTGAGCCTT
** * *
17462 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGTTGCTGTTA
66 GAATTGGATATCCTTAATCGTGAAGTTGAAATCAAATGTTGCTGTGA
* *
17509 GGCACGATTCCCTTCGTCGTGAAGTCGAAAT
1 GGCACGATTCACTTCGTCGTGAAGTTGAAAT
17540 TAACTATGAT
Statistics
Matches: 120, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
111 5 0.04
112 115 0.96
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (112 bp):
GGCACGATTCACTTCGTCGTGAAGTTGAAATCATGGATGACCCATTCATTGTAAAGTTGAGCCTT
GAATTGGATATCCTTAATCGTGAAGTTGAAATCAAATGTTGCTGTGA
Found at i:17704 original size:43 final size:44
Alignment explanation
Indices: 17657--17765 Score: 141
Period size: 43 Copynumber: 2.5 Consensus size: 44
17647 ATTCCCTTCG
* *
17657 TCGTGAAGTTGAAACCGTGGATGT-GTGGACACGATATCCTCCA
1 TCGTGGAGTTGAAATCGTGGATGTCGTGGACACGATATCCTCCA
* ** * *
17700 TCGTGGAGTTGAAATTGTGGAT-TCGTGGGTATGATATCCTCCG
1 TCGTGGAGTTGAAATCGTGGATGTCGTGGACACGATATCCTCCA
17743 TCGTGGAGTTGAAATCGTGGATG
1 TCGTGGAGTTGAAATCGTGGATG
17766 GCTCCTTCGT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (44 bp):
TCGTGGAGTTGAAATCGTGGATGTCGTGGACACGATATCCTCCA
Found at i:17925 original size:43 final size:43
Alignment explanation
Indices: 17878--17961 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
17868 CTGTGGTTGA
* * *
17878 GTGGGCACGATATTTTTCGTCGTGGAGTTGAAATCGTGGATCC
1 GTGGGCACGATATTCTCCGTCGTGGAGTTAAAATCGTGGATCC
*
17921 GTGGGTACGATATTCTCCGTCGTGGAGTTAAAATCGTGGAT
1 GTGGGCACGATATTCTCCGTCGTGGAGTTAAAATCGTGGAT
17962 GACCCCTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.32
Consensus pattern (43 bp):
GTGGGCACGATATTCTCCGTCGTGGAGTTAAAATCGTGGATCC
Found at i:18220 original size:64 final size:64
Alignment explanation
Indices: 18119--18258 Score: 201
Period size: 64 Copynumber: 2.2 Consensus size: 64
18109 ACTCTCGAGC
* * *
18119 AAATTGTATGTTGAGTTCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
1 AAATTGTTTGTTGAGTACAATATCCTTCGACGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
* * *
18183 AAATTGTTTGTTGAGTACAATATCCTTC-ACCGTGAAGTTGAAATTGACTCTTAATGAAATTGGA
1 AAATTGTTTGTTGAGTACAATATCCTTCGA-CGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
*
18247 AAGTTGTTTGTT
1 AAATTGTTTGTT
18259 AACAGAAGCT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 1 0.01
64 67 0.99
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (64 bp):
AAATTGTTTGTTGAGTACAATATCCTTCGACGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
Found at i:18586 original size:32 final size:32
Alignment explanation
Indices: 18517--18605 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
18507 TAGCATTAGT
* *
18517 ATGTTGAATCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
* **
18549 ATGTTGAATCTCCAAATATGCCTCAACATTTG
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
* ** *
18581 TTGTTGAATCTTTAAAGATGCCCCA
1 ATGTTGAATCTCCAAATATGCCCCA
18606 TTGTTCCTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCCCAACATTCA
Found at i:25004 original size:16 final size:17
Alignment explanation
Indices: 24983--25016 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
24973 TGAATTTTAC
24983 TTCAAA-ATTACTTTCT
1 TTCAAATATTACTTTCT
*
24999 TTCAAATTTTACTTTCT
1 TTCAAATATTACTTTCT
25016 T
1 T
25017 CGAACACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCAAATATTACTTTCT
Found at i:25092 original size:29 final size:29
Alignment explanation
Indices: 25059--25117 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
25049 CAATTTCCGC
*
25059 CTAGCCCAGACA-CAAGACCAATTCATCGA
1 CTAGCCCAGA-AGCAAAACCAATTCATCGA
25088 CTAGCCCAGAAGCAAAACCAATTCATCGA
1 CTAGCCCAGAAGCAAAACCAATTCATCGA
25117 C
1 C
25118 AATTTCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.39, C:0.34, G:0.14, T:0.14
Consensus pattern (29 bp):
CTAGCCCAGAAGCAAAACCAATTCATCGA
Found at i:31196 original size:85 final size:84
Alignment explanation
Indices: 31020--31368 Score: 349
Period size: 85 Copynumber: 4.2 Consensus size: 84
31010 TTGCTGACTG
* * ** ** *
31020 ATAACCCTTCTCGCATTGAGTTATGCTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAAC
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * * *
31085 TCGAAGGAC-TTTGATGACAT
64 TCGAAGGTCTTTTGTTGGCAA
* * *
31105 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTACCTTTGAGCTGAGTGTAATCAAACTT
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
*
31170 GAAGGTCTTTTTGTTGGCAG
66 GAAGGTC-TTTTGTTGGCAA
* * * *
31190 ACAACCCTTCTTGCCTTGAGTTATACTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
* *
31255 GAAGGTCTTTTGTTAGAAA
66 GAAGGTCTTTTGTTGGCAA
** * * *
31274 ATAACCCTTCTTTCCTTGAGCTATGTTGCAAATGGTGTGCCTTTGAGCTGAGTG-----GAACTC
1 ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
31334 GAAGGTC---T-TTGGCAA
66 GAAGGTCTTTTGTTGGCAA
* *
31349 ATAGCCCTTCTTGCCTTGAG
1 ATAACCCTTCTCGCCTTGAG
31369 CTTTGAATTG
Statistics
Matches: 227, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
75 23 0.10
76 1 0.00
79 13 0.06
83 30 0.13
84 57 0.25
85 103 0.45
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (84 bp):
ATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTC
GAAGGTCTTTTGTTGGCAA
Found at i:31319 original size:169 final size:170
Alignment explanation
Indices: 31022--31327 Score: 420
Period size: 169 Copynumber: 1.8 Consensus size: 170
31012 GCTGACTGAT
*
31022 AACCCTTCTCGCATTGAGTTATGCTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
1 AACCCTTCTCGCATTGAGTTATACTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
* *
31087 GAAGGACTTTGATGACATATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGTACCTTTGAG
66 GAAGGACTTTGATGACAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTACCTTTGAG
31152 CTGAGTGTAATCAAACTTGAAGGTCTTTTTGTTGGCAGAC
131 CTGAGTGTAATCAAACTTGAAGGTCTTTTTGTTGGCAGAC
* * ** ** *
31192 AACCCTTCTTGCCTTGAGTTATACTGTAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCGAACTC
1 AACCCTTCTCGCATTGAGTTATACTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
* * ** * * *
31255 GAAGGTCTTTTGTTAGA-AAATAACCCTTCTTTCCTTGAGCTATGTTGCAAATGGTGTGCCTTTG
66 GAAGGAC-TTTGAT-GACAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTACCTTTG
31319 AGCTGAGTG
129 AGCTGAGTG
31328 GAACTCGAAG
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
168 33 0.28
169 55 0.47
170 29 0.25
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (170 bp):
AACCCTTCTCGCATTGAGTTATACTGTAAATTGGATACGCCTCAGAGCTGAATGTAATCGAACTC
GAAGGACTTTGATGACAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGTACCTTTGAG
CTGAGTGTAATCAAACTTGAAGGTCTTTTTGTTGGCAGAC
Found at i:31761 original size:112 final size:112
Alignment explanation
Indices: 31553--31806 Score: 314
Period size: 112 Copynumber: 2.3 Consensus size: 112
31543 TGTTACTTAT
* * *
31553 GGCACGATATC-CTTCGTCGTGAAGTTGAAATCGTGGATGACCTATTCATTGTAAAGTTGAGCCT
1 GGCACGAT-TCACTTCGTCGTGAAGTTGAAACCATGGATGACCCATTCATTGTAAAGTTGAGCCT
* * *
31617 TGAATTGGATGTCTTTAATCGTGAAGTTGAAATCAAATGTTGTTGGTGA
65 TGAATTGGATATCCTTAATCGTGAAGTTGAAATCAAATGTTGCT-GTGA
* * * ** *
31666 -GCATGATTCACTTCGTCGTGAAGTTGAAACCATGGATGGCCCATTCGTTGTGTAGTTGAGTCTT
1 GGCACGATTCACTTCGTCGTGAAGTTGAAACCATGGATGACCCATTCATTGTAAAGTTGAGCCTT
** * *
31730 GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGTTGCTGTTA
66 GAATTGGATATCCTTAATCGTGAAGTTGAAATCAAATGTTGCTGTGA
* *
31777 GGCACGATTCCCTTCGTCGTGAAGTCGAAA
1 GGCACGATTCACTTCGTCGTGAAGTTGAAA
31807 TTAACTATGA
Statistics
Matches: 120, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
111 5 0.04
112 115 0.96
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (112 bp):
GGCACGATTCACTTCGTCGTGAAGTTGAAACCATGGATGACCCATTCATTGTAAAGTTGAGCCTT
GAATTGGATATCCTTAATCGTGAAGTTGAAATCAAATGTTGCTGTGA
Found at i:31972 original size:43 final size:44
Alignment explanation
Indices: 31925--32033 Score: 141
Period size: 43 Copynumber: 2.5 Consensus size: 44
31915 ATTCCCTTCG
* *
31925 TCGTGAAGTTGAAACCGTGGATGT-GTGGACACGATATCCTCCA
1 TCGTGGAGTTGAAATCGTGGATGTCGTGGACACGATATCCTCCA
* ** * *
31968 TCGTGGAGTTGAAATTGTGGAT-TCGTGGGTATGATATCCTCCG
1 TCGTGGAGTTGAAATCGTGGATGTCGTGGACACGATATCCTCCA
32011 TCGTGGAGTTGAAATCGTGGATG
1 TCGTGGAGTTGAAATCGTGGATG
32034 GCTCCTTCGT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (44 bp):
TCGTGGAGTTGAAATCGTGGATGTCGTGGACACGATATCCTCCA
Found at i:32193 original size:43 final size:43
Alignment explanation
Indices: 32146--32229 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
32136 CTGTGGTTGA
* * *
32146 GTGGGCACGATATTTTTCATCGTGGAGTTGAAATCGTGGATCC
1 GTGGGCACGATATTCTCCATCGTGGAGTTAAAATCGTGGATCC
* *
32189 GTGGGTACGATATTCTCCGTCGTGGAGTTAAAATCGTGGAT
1 GTGGGCACGATATTCTCCATCGTGGAGTTAAAATCGTGGAT
32230 GACCCCTTCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.32
Consensus pattern (43 bp):
GTGGGCACGATATTCTCCATCGTGGAGTTAAAATCGTGGATCC
Found at i:32525 original size:64 final size:64
Alignment explanation
Indices: 32387--32526 Score: 192
Period size: 64 Copynumber: 2.2 Consensus size: 64
32377 ACTCTCGAGC
* * *
32387 AAATTGTATGTTGAGTTCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
1 AAATTGTTTGTTGAGTACAATATCCTTCGACGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
* * * *
32451 AAATTATTTGTTGAGTACAATATCCTTC-ACCGTGAAGTTGAAATTGACTCTTAATGAAATTGGA
1 AAATTGTTTGTTGAGTACAATATCCTTCGA-CGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
*
32515 AAGTTGTTTGTT
1 AAATTGTTTGTT
32527 AACAGAAGCT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 1 0.02
64 65 0.98
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (64 bp):
AAATTGTTTGTTGAGTACAATATCCTTCGACGTGAAGTTGAAATTGACTCTGAATGAAACTAGA
Found at i:32853 original size:32 final size:32
Alignment explanation
Indices: 32784--32872 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
32774 TAGCATTAGT
* *
32784 ATGTTGAATCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
* **
32816 ATGTTGAATCTCCAAATATGCCTCAACATTTG
1 ATGTTGAATCTCCAAATATGCCCCAACATTCA
* ** *
32848 TTGTTGAATCTTTAAAGATGCCCCA
1 ATGTTGAATCTCCAAATATGCCCCA
32873 TTGTTCCTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (32 bp):
ATGTTGAATCTCCAAATATGCCCCAACATTCA
Found at i:34095 original size:2 final size:2
Alignment explanation
Indices: 34088--34121 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
34078 ACAACAAGGG
*
34088 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34122 GGATAAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38612 original size:22 final size:21
Alignment explanation
Indices: 38587--38632 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
38577 TATAGTTTTC
38587 TTTCTTCTATAAAGTTTTTACT
1 TTTCTT-TATAAAGTTTTTACT
* **
38609 TTTCTTTTTCTAGTTTTTACT
1 TTTCTTTATAAAGTTTTTACT
38630 TTT
1 TTT
38633 ATACTTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTCTTTATAAAGTTTTTACT
Found at i:39277 original size:16 final size:17
Alignment explanation
Indices: 39256--39289 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
39246 TGAATTTTAC
39256 TTCAAA-ATTACTTTCT
1 TTCAAATATTACTTTCT
*
39272 TTCAAATTTTACTTTCT
1 TTCAAATATTACTTTCT
39289 T
1 T
39290 CGAACACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCAAATATTACTTTCT
Found at i:39365 original size:29 final size:29
Alignment explanation
Indices: 39332--39390 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
39322 CAATTTCCGC
*
39332 CTAGCCCAGACA-CAAGACCAATTCATCGA
1 CTAGCCCAGA-AGCAAAACCAATTCATCGA
39361 CTAGCCCAGAAGCAAAACCAATTCATCGA
1 CTAGCCCAGAAGCAAAACCAATTCATCGA
39390 C
1 C
39391 AATTTCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.39, C:0.34, G:0.14, T:0.14
Consensus pattern (29 bp):
CTAGCCCAGAAGCAAAACCAATTCATCGA
Found at i:43906 original size:20 final size:21
Alignment explanation
Indices: 43881--43932 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
43871 TTTTCCCAAT
*
43881 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
43901 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
43922 TCGCAATGCGA
1 TCGCAATGCGA
43933 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:43946 original size:20 final size:19
Alignment explanation
Indices: 43921--44035 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 19
43911 AATTGGGAAA
43921 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
* *
43941 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
43962 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATAC-TACT
*
43982 TTCGCAACT-CGATACTGACT
1 ATCGCAA-TGCGATACT-ACT
* * *
44002 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
44022 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
44036 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
19 5 0.07
20 43 0.58
21 23 0.31
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:44231 original size:22 final size:22
Alignment explanation
Indices: 44203--44246 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44193 CACTCTCTCA
44203 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
44225 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
44247 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:44535 original size:20 final size:20
Alignment explanation
Indices: 44510--44547 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44500 CGATTCTCTC
44510 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
44530 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
44548 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:45888 original size:18 final size:18
Alignment explanation
Indices: 45867--45911 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
45857 TTCACTTCGG
*
45867 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
45885 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
45903 GAGCCATCA
1 GAGCCATCA
45912 TCTGATCGAC
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:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:46384 original size:19 final size:19
Alignment explanation
Indices: 46342--46395 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
46332 AGTTTACTTT
* *
46342 CGCAACACGAAAATGACTAT
1 CGCAACGCG-AAATGACTAA
*
46362 CGCAACGCGAAATGGCTAA
1 CGCAACGCGAAATGACTAA
*
46381 CGCAATGCGAAATGA
1 CGCAACGCGAAATGA
46396 AATCGCAACG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (19 bp):
CGCAACGCGAAATGACTAA
Found at i:46422 original size:32 final size:32
Alignment explanation
Indices: 46381--46500 Score: 213
Period size: 32 Copynumber: 3.7 Consensus size: 32
46371 AAATGGCTAA
46381 CGCAATGCGAAATGAAATCGCAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
*
46413 CGCAATGCGAAATGAAATCACAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
46445 CGCAATGCGAAATGAAATCGCAACGACAAAAT
1 CGCAATGCGAAATGAAATCGCAACGACAAAAT
*
46477 CGCAACGCGAAATGAAAATCGCAA
1 CGCAATGCGAAATG-AAATCGCAA
46501 TGCGATTTGT
Statistics
Matches: 84, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
32 75 0.89
33 9 0.11
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (32 bp):
CGCAATGCGAAATGAAATCGCAACGACAAAAT
Found at i:46494 original size:19 final size:19
Alignment explanation
Indices: 46381--46505 Score: 79
Period size: 14 Copynumber: 7.5 Consensus size: 19
46371 AAATGGCTAA
46381 CGCAATGCGAAATG-AAAT
1 CGCAATGCGAAATGAAAAT
*
46399 CGCAA--CG--A-CAAAAT
1 CGCAATGCGAAATGAAAAT
46413 CGCAATGCGAAATG-AAAT
1 CGCAATGCGAAATGAAAAT
* *
46431 CACAA--CG--A-CAAAAT
1 CGCAATGCGAAATGAAAAT
46445 CGCAATGCGAAATG-AAAT
1 CGCAATGCGAAATGAAAAT
*
46463 CGCAA--CG--A-CAAAAT
1 CGCAATGCGAAATGAAAAT
*
46477 CGCAACGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
46496 CGCAATGCGA
1 CGCAATGCGA
46506 TTTGTGTTTC
Statistics
Matches: 80, Mismatches: 9, Indels: 35
0.65 0.07 0.28
Matches are distributed among these distances:
14 29 0.36
16 12 0.15
18 25 0.31
19 14 0.17
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.12
Consensus pattern (19 bp):
CGCAATGCGAAATGAAAAT
Found at i:46536 original size:14 final size:14
Alignment explanation
Indices: 46517--46574 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
46507 TTGTGTTTCG
46517 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
46531 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
46547 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
46563 CGTTGCGATTTT
1 CGTTGCGATTTT
46575 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:46551 original size:32 final size:33
Alignment explanation
Indices: 46512--46590 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
46502 GCGATTTGTG
46512 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
46544 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
46577 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
46591 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:46589 original size:19 final size:19
Alignment explanation
Indices: 46531--46648 Score: 86
Period size: 20 Copynumber: 6.4 Consensus size: 19
46521 GCGATTTTGT
46531 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
46549 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
46563 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
46582 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
46602 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
46621 TGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
46641 TGTTGCGA
1 CGTTGCGA
46649 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 25 0.31
20 30 0.37
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:48516 original size:14 final size:14
Alignment explanation
Indices: 48497--48532 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
48487 ATTGTTTAAT
48497 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
48511 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
48525 TGATTTGT
1 TGATTTGT
48533 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48671 original size:19 final size:19
Alignment explanation
Indices: 48649--48716 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
48639 ATCGCAACGA
48649 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
48668 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
48687 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
48701 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
48717 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:48792 original size:20 final size:20
Alignment explanation
Indices: 48735--48792 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
48725 TCGCATTGCG
* *
48735 ATTTTCTCGTTGCGATAACC
1 ATTTTCACGTTGCGATAGCC
*
48755 ATTTTCGCGTTGCGATAGCC
1 ATTTTCACGTTGCGATAGCC
48775 ATTTTCACGTTGCGATAG
1 ATTTTCACGTTGCGATAG
48793 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCACGTTGCGATAGCC
Found at i:49876 original size:24 final size:24
Alignment explanation
Indices: 49849--49902 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49839 GTATTCGAAA
* *
49849 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
49873 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
49897 TTTGAT
1 TTTGAT
49903 GATGTTTCAG
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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:52401 original size:19 final size:18
Alignment explanation
Indices: 52379--52509 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 18
52369 GGAAATTACT
52379 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
52398 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
52412 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
52431 ATCGCAA-CG--CT-AAT
1 ATCGCAAGCGAAATGAAA
*
52445 TTCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
52464 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
52478 ATCGTAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
52497 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
52510 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:52421 original size:33 final size:33
Alignment explanation
Indices: 52379--52505 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
52369 GGAAATTACT
52379 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
52412 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
52444 TTTCGCAACGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
52478 ATCGTAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
52506 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:52487 original size:66 final size:66
Alignment explanation
Indices: 52380--52512 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
52370 GAAATTACTA
* *
52380 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
52445 T
66 T
* *
52446 TCGCAACGCGAAATGAAAATCGCAACGAGGGAATCGTAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
52511 T
66 T
52512 T
1 T
52513 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:52527 original size:19 final size:19
Alignment explanation
Indices: 52505--52546 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
52495 AAATCGCAAC
52505 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
52524 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
52543 GCGA
1 GCGA
52547 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:52547 original size:19 final size:19
Alignment explanation
Indices: 52514--52580 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
52504 CGCGAATTTA
52514 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
52533 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
52550 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
52566 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
52581 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:52705 original size:14 final size:14
Alignment explanation
Indices: 52686--52722 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
52676 CATCAATTAA
52686 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
52700 ACAAATCACCTTTT
1 ACAAATCAACTTTT
52714 ACAAATCAA
1 ACAAATCAA
52723 TTAAACAATA
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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:54117 original size:21 final size:21
Alignment explanation
Indices: 54051--54117 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
54041 GTGAATCGGG
*
54051 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
54071 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
54093 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
54114 CTCT
1 CTCT
54118 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:54136 original size:42 final size:41
Alignment explanation
Indices: 54051--54173 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
54041 GTGAATCGGG
* * * * *
54051 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
54093 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
54135 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
54174 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Done.