Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007747.1 Hibiscus syriacus cultivar Beakdansim tig00110010_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: 73857
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1740 original size:33 final size:34
Alignment explanation
Indices: 1677--1742 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
1667 CTCATGTGCA
* *
1677 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAAATTTCCAAT
1711 AAGTTGGCCACCAACC-AAGATGAAATTTCCAA
1 AAGTTGGCCACCAACCAAAGATGAAATTTCCAA
1743 CTTGCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAAATTTCCAAT
Found at i:3141 original size:21 final size:21
Alignment explanation
Indices: 3115--3157 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3105 TCATTTCTCC
3115 GATTCTCAAACTGTAGAGTAG
1 GATTCTCAAACTGTAGAGTAG
*
3136 GATTCTCTAACTGTAGAGTAG
1 GATTCTCAAACTGTAGAGTAG
3157 G
1 G
3158 TTGTGGCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (21 bp):
GATTCTCAAACTGTAGAGTAG
Found at i:3869 original size:19 final size:19
Alignment explanation
Indices: 3845--3890 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
3835 AACTTGAGAC
3845 ATTGCTTAAACAATATCAA
1 ATTGCTTAAACAATATCAA
3864 ATTGCTTAAACAATATCAA
1 ATTGCTTAAACAATATCAA
3883 ATTGCTTA
1 ATTGCTTA
3891 TCACTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (19 bp):
ATTGCTTAAACAATATCAA
Found at i:5616 original size:17 final size:16
Alignment explanation
Indices: 5594--5627 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
5584 TAATATTGAG
5594 TTAACCAAGATTTCATA
1 TTAACCAAGATTT-ATA
5611 TTAACCAAGATTTATA
1 TTAACCAAGATTTATA
5627 T
1 T
5628 AATTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (16 bp):
TTAACCAAGATTTATA
Found at i:6148 original size:35 final size:35
Alignment explanation
Indices: 6100--6167 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
6090 TATTATTTTG
* * *
6100 ATTATTTTGGAATTTGGGGTTTAGAATGTAATTGA
1 ATTATTTTAGAATTTGGGATTTAGAATGAAATTGA
6135 ATTATTTTAGAATTTGGGATTTAGAATGAAATT
1 ATTATTTTAGAATTTGGGATTTAGAATGAAATT
6168 AAGGGAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (35 bp):
ATTATTTTAGAATTTGGGATTTAGAATGAAATTGA
Found at i:7902 original size:42 final size:42
Alignment explanation
Indices: 7831--7912 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
7821 GAAAGGCGAA
* * **
7831 TAAAGTAAAACGACAGGAGGCATCCCACTTTCGATTCTCGTC
1 TAAAGTAAAACGAAAGGAAGCATAACACTTTCGATTCTCGTC
* *
7873 TAAAGTAGAACGAAAGGAAGCATAACACTTTCTATTCTCG
1 TAAAGTAAAACGAAAGGAAGCATAACACTTTCGATTCTCG
7913 ATGAATCACC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (42 bp):
TAAAGTAAAACGAAAGGAAGCATAACACTTTCGATTCTCGTC
Found at i:10554 original size:130 final size:130
Alignment explanation
Indices: 10321--10559 Score: 444
Period size: 130 Copynumber: 1.8 Consensus size: 130
10311 ATGTCCATGC
10321 CTGACAGTAAAGTGATTGGTGTCAGTAATAGGGTTGATGGCTATTAATAGATCGACAGATGGACG
1 CTGACAGTAAAGTGATTGGTGTCAGTAATAGGGTTGATGGCTATTAATAGATCGACAGATGGACG
10386 TATCATGCTATTAGTAGATAACAGATGATGAGATTGAAAGCGGTAAAGTGATGGCTATTAATAGA
66 TATCATGCTATTAGTAGATAACAGATGATGAGATTGAAAGCGGTAAAGTGATGGCTATTAATAGA
* *
10451 CTGACAGTAAAGTGATTGGTGTCAGTCAA-AGGGTTGATGGCTATTAATAGATTGACAGATGGGC
1 CTGACAGTAAAGTGATTGGTGTCAGT-AATAGGGTTGATGGCTATTAATAGATCGACAGATGGAC
10515 GTATCATGCTATTAGTAGATAACAGATGATGAGATTGAAAGCGGT
65 GTATCATGCTATTAGTAGATAACAGATGATGAGATTGAAAGCGGT
10560 TATGACGAGT
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
130 104 0.98
131 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (130 bp):
CTGACAGTAAAGTGATTGGTGTCAGTAATAGGGTTGATGGCTATTAATAGATCGACAGATGGACG
TATCATGCTATTAGTAGATAACAGATGATGAGATTGAAAGCGGTAAAGTGATGGCTATTAATAGA
Found at i:19036 original size:60 final size:59
Alignment explanation
Indices: 18903--19052 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 59
18893 TTTGGATGAA
* *
18903 TTTGGTGATGAAATTAGAATATTCAAAAG-TTTGGGACCAATTTAGAAAGTGATTCATAG
1 TTTGG-GATGAAATTAGAATATTCAAAAGTTTTGGGACCAATTTAGAAAGAGAATCATAG
* *
18962 TTTAGGGCTGAAATTAGAATGA-TCAAAAGTTTATGGG-CTAATTTA-AAATGAGAATCATAG
1 TTT-GGGATGAAATTAGAAT-ATTCAAAAGTTT-TGGGACCAATTTAGAAA-GAGAATCATAG
* *
19022 TTTGGAGATAAAATTAAAATATTCAAAAGTT
1 TTTGG-GATGAAATTAGAATATTCAAAAGTT
19053 CAAGGGTCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
59 29 0.38
60 44 0.57
61 4 0.05
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (59 bp):
TTTGGGATGAAATTAGAATATTCAAAAGTTTTGGGACCAATTTAGAAAGAGAATCATAG
Found at i:24322 original size:64 final size:64
Alignment explanation
Indices: 24221--24346 Score: 243
Period size: 64 Copynumber: 2.0 Consensus size: 64
24211 GGAGGGGAAA
24221 ATTATAAACTGGTCATCAAATTTCAACCGAAATCATTACCAGTTATTTGATCGCAGCCGTCAGT
1 ATTATAAACTGGTCATCAAATTTCAACCGAAATCATTACCAGTTATTTGATCGCAGCCGTCAGT
*
24285 ATTATAAACTGGTCATCAAATTTCAACCGAAATCATTACCAGTTATTTGATCGTAGCCGTCA
1 ATTATAAACTGGTCATCAAATTTCAACCGAAATCATTACCAGTTATTTGATCGCAGCCGTCA
24347 AACTGACGGC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (64 bp):
ATTATAAACTGGTCATCAAATTTCAACCGAAATCATTACCAGTTATTTGATCGCAGCCGTCAGT
Found at i:27423 original size:65 final size:65
Alignment explanation
Indices: 27348--27477 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
27338 AAATAAAAAC
27348 AATTGTTTCTGTTTTGGATAAATGTGATTGAAATAAAGATGGAATATTAGTTCACATTAGGGATG
1 AATTGTTTCTGTTTTGGATAAATGTGATTGAAATAAAGATGGAATATTAGTTCACATTAGGGATG
27413 AATTGTTTCTGTTTTGGATAAATGTGATTGAAATAAAGATGGAATATTAGTTCACATTAGGGATG
1 AATTGTTTCTGTTTTGGATAAATGTGATTGAAATAAAGATGGAATATTAGTTCACATTAGGGATG
27478 GGCATAGGTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (65 bp):
AATTGTTTCTGTTTTGGATAAATGTGATTGAAATAAAGATGGAATATTAGTTCACATTAGGGATG
Found at i:28158 original size:2 final size:2
Alignment explanation
Indices: 28151--28186 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28141 CGACCCGACC
28151 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
28187 TAAGAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28473 original size:21 final size:21
Alignment explanation
Indices: 28447--28495 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28437 ACGGCCAAAA
*
28447 ACTCATCTCAACCCGCCCCAT
1 ACTCATCCCAACCCGCCCCAT
*
28468 ACTCATCCCAACCCGCGCCAT
1 ACTCATCCCAACCCGCCCCAT
*
28489 GCTCATC
1 ACTCATC
28496 ATTATCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.51, G:0.08, T:0.18
Consensus pattern (21 bp):
ACTCATCCCAACCCGCCCCAT
Found at i:40675 original size:176 final size:176
Alignment explanation
Indices: 40381--40736 Score: 685
Period size: 176 Copynumber: 2.0 Consensus size: 176
40371 GTAGTCCACG
*
40381 ATGTCTGATTGTTGTGTGGAATAGAGGTTTATTGAATGAGGGTAATTTTTGCCGTTGAACCCGCC
1 ATGTCTGATTGTTGTGTGGAATAGAGGTTTATTGAATGAGGATAATTTTTGCCGTTGAACCCGCC
40446 AAACTCTGGAAGTAACATGTTATAGTCAGCTGATTTTTACTACTTTGAGCTATCTCTTGGAAGGT
66 AAACTCTGGAAGTAACATGTTATAGTCAGCTGATTTTTACTACTTTGAGCTATCTCTTGGAAGGT
40511 TTGAGGATTATATTGCTTTGAAGTTTATGATCGATTTCATCACCGA
131 TTGAGGATTATATTGCTTTGAAGTTTATGATCGATTTCATCACCGA
40557 ATGTCTGATTGTTGTGTGGAATAGAGGTTTATTGAATGAGGATAATTTTTGCCGTTGAACCCGCC
1 ATGTCTGATTGTTGTGTGGAATAGAGGTTTATTGAATGAGGATAATTTTTGCCGTTGAACCCGCC
*
40622 AAACTCTGGAAGTAACATGTTATAGTCAGCTGATTTTTACTGCTTTGAGCTATCTCTTGGAAGGT
66 AAACTCTGGAAGTAACATGTTATAGTCAGCTGATTTTTACTACTTTGAGCTATCTCTTGGAAGGT
*
40687 TTGAGGATTATATTGCTTTGAAGTTTATGATCGATTTTATCACCGA
131 TTGAGGATTATATTGCTTTGAAGTTTATGATCGATTTCATCACCGA
40733 ATGT
1 ATGT
40737 GCTGCTGGGT
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
176 177 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (176 bp):
ATGTCTGATTGTTGTGTGGAATAGAGGTTTATTGAATGAGGATAATTTTTGCCGTTGAACCCGCC
AAACTCTGGAAGTAACATGTTATAGTCAGCTGATTTTTACTACTTTGAGCTATCTCTTGGAAGGT
TTGAGGATTATATTGCTTTGAAGTTTATGATCGATTTCATCACCGA
Found at i:42759 original size:2 final size:2
Alignment explanation
Indices: 42752--42777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42742 TCTTTTGTAA
42752 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
42778 TTAGAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46376 original size:15 final size:16
Alignment explanation
Indices: 46356--46390 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
46346 ATTCAAGGAA
46356 AAAAAAT-AAATAAAT
1 AAAAAATAAAATAAAT
*
46371 AAAAAATAAAATAAGT
1 AAAAAATAAAATAAAT
46387 AAAA
1 AAAA
46391 CGAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAAATAAAATAAAT
Found at i:47997 original size:283 final size:283
Alignment explanation
Indices: 47490--48054 Score: 1049
Period size: 283 Copynumber: 2.0 Consensus size: 283
47480 CACCATGTGG
*
47490 TTGACAGGCCCTCGAGCTGAATGAAATCGAACTCGAAAGGTCCTCGTTGACAAATATATTTTCTC
1 TTGACAGGCCCTCGAGCTAAATGAAATCGAACTCGAAAGGTCCTCGTTGACAAATATATTTTCTC
* *
47555 GACTTAAGCTATGCTGTTAGAAAACCGATTTTTTTGCCACTATGGCACGGTTAACCTAGATCTTC
66 GACTTAAGCTATGCTGTCAGAAAACCGATTTTTTTGCCACTATGGCACGGTTAACCTAGATATTC
*
47620 TTCTCGACTTGAAAACCCTGATTACATCCAGACAGTAGTGTGATTGAGGTGTCATCGAGCTGAAT
131 TTCTCGACTTGAAAACCCCGATTACATCCAGACAGTAGTGTGATTGAGGTGTCATCGAGCTGAAT
* *
47685 GGAATCGAACTCGATAATTTATTGACAGATAACCCTTCTTGCCTTAAGCTATGCTGTAAATTTGG
196 GGAATCGAACTCGACAATTTATTGACAGATAACCCTTATTGCCTTAAGCTATGCTGTAAATTTGG
47750 TTTGCCTCTAAGCTGAATGTAAA
261 TTTGCCTCTAAGCTGAATGTAAA
47773 TTGACAGGCCCTCGAGCTAAATGAAATCGAACTCGAAAGGTCCTCGTTGACAAATATATTTTCTC
1 TTGACAGGCCCTCGAGCTAAATGAAATCGAACTCGAAAGGTCCTCGTTGACAAATATATTTTCTC
*
47838 GACTTAAGTTATGCTGTCAGAAAACCGATTTTTTTGCCACTATGGCACGGTTAACCTAGATATTC
66 GACTTAAGCTATGCTGTCAGAAAACCGATTTTTTTGCCACTATGGCACGGTTAACCTAGATATTC
*
47903 TTTTCGACTTGAAAACCCCGATTACATCCAGACAGTAGTGTGATTGAGGTGTCATCGAGCTGAAT
131 TTCTCGACTTGAAAACCCCGATTACATCCAGACAGTAGTGTGATTGAGGTGTCATCGAGCTGAAT
*
47968 GGAATCGAACTCGACAATTTATTGACAGATAACCCTTATTGCCTTGAGCTATGCTGTAAATTTGG
196 GGAATCGAACTCGACAATTTATTGACAGATAACCCTTATTGCCTTAAGCTATGCTGTAAATTTGG
48033 TTTGCCTCTAAGCTGAATGTAA
261 TTTGCCTCTAAGCTGAATGTAA
48055 TCGAACTCAG
Statistics
Matches: 273, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
283 273 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (283 bp):
TTGACAGGCCCTCGAGCTAAATGAAATCGAACTCGAAAGGTCCTCGTTGACAAATATATTTTCTC
GACTTAAGCTATGCTGTCAGAAAACCGATTTTTTTGCCACTATGGCACGGTTAACCTAGATATTC
TTCTCGACTTGAAAACCCCGATTACATCCAGACAGTAGTGTGATTGAGGTGTCATCGAGCTGAAT
GGAATCGAACTCGACAATTTATTGACAGATAACCCTTATTGCCTTAAGCTATGCTGTAAATTTGG
TTTGCCTCTAAGCTGAATGTAAA
Found at i:48144 original size:84 final size:83
Alignment explanation
Indices: 48055--48777 Score: 610
Period size: 84 Copynumber: 8.7 Consensus size: 83
48045 CTGAATGTAA
* * * *
48055 TCGAACTCAGAGGTCTTCGGTTGGCAGATATCCCTTCTCGACTTAAGCTATACTACAAATGATGT
1 TCGAACTC-GAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
48120 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * ** * * *
48139 TCGAACTCGAAAGTCTTTGG-TGACAGATAACCATTCAAGCCTTGAGTTATACTGTAAATGATGT
1 TCGAACTCG-AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
* * * *
48203 GCCCTCGAAGCTGAGTGTAA
65 G-CCTTGGAGCTGAGCGTAG
* * * * * * * *
48223 TCGAACTAGAGGGTC--T--TCGGCAGATAGCCTTTCTCGACTTAAGCTATGCTGTAAATGATAT
1 TCGAACTCGA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
*
48284 ACCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * *
48303 TAGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACCAATGATAT
1 TCGAACTCG-AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
48368 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * * * **
48387 TCGAACTCGAAGGTTTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAACTGGCG
1 TCGAACTCG-AGG-TCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATG
* * * * *
48451 TGCCCTCGAAGTTGAGTGTAA
64 TG-CCTTGGAGCTGAGCGTAG
*
48472 TCGAACTCGAGGGTC--T--TTGGAAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
1 TCGAACTCGA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
*
48533 GCCTTGGAGCTGAGTGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * *
48552 TCGAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGT
1 TCGAACTC-GAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
* * * *
48617 GCCCTCGAAGCTGAGTGTAA
65 G-CCTTGGAGCTGAGCGTAG
* * * * * **
48637 TCGAACTCGAGGGTC--T--TCGGCAGATAGCCCTTTTCGACTTAAGCTATGCTGCAAATGATAC
1 TCGAACTCGA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGT
*
48698 GCCTTGGAGCTGAGCATAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * *
48717 TCAAACTCGAAGGTATTTTGTTAGCAGATAACCCTTCTCAACTTAAGTTATACTGGAAATG
1 TCGAACTCG-AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATG
48778 TTGTCTTAAA
Statistics
Matches: 504, Mismatches: 110, Indels: 50
0.76 0.17 0.08
Matches are distributed among these distances:
80 75 0.15
81 109 0.22
82 5 0.01
83 38 0.08
84 221 0.44
85 56 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
TCGAACTCGAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:48499 original size:165 final size:165
Alignment explanation
Indices: 48079--48777 Score: 617
Period size: 165 Copynumber: 4.2 Consensus size: 165
48069 CTTCGGTTGG
* * * * ** * * * * *
48079 CAGATATCCCTTCTCGACTTAAGCTATACTACAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGA
** * ** * * * *
48143 ACTCGAAAGTCTTTGGTGACAGATAACCATTCAAGCCTTGAGTTATACTGTAAATGATGTGCCCT
66 ACTCGAGGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATG-CCT
* * * * * * * *
48208 CGAAGCTGAGTGTAATCGAACTAG-AGG-GTCTTCG-G-
127 TGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGA
* * * * ** * * * * * *
48243 CAGATAGCCTTTCTCGACTTAAGCTATGCTGTAAATGATAT-ACCTTGGAGCTGAGCGTAGTAGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGA
* * *
48307 ACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACCAATGATATGCCT
66 ACTCGAGGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCT
48372 TGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGA
127 TGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGA
* * * * *
48411 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAACTGGCGTGCCCTCGAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGA
* *
48476 ACTCGAGGGTCTTTGGAAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGA
66 ACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGA
* * *
48541 GCTGAGTGTAGTCGAACTCAAAGG-TCTTTGGTTGGA
131 GCTGAGCGTAGTCGAACTCGAAGGTTTTTTGG-T-GA
* *
48577 -AGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGA
* * * * * *
48641 ACTCGAGGGTCTTCGGCAGATAGCCCTTTTCGACTTAAGCTATGCTGCAAATGATACGCCTTGGA
66 ACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGA
* * * *
48706 GCTGAGCATAGTCAAACTCGAAGGTATTTT-GTTA
131 GCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGA
* *
48740 GCAGATAACCCTTCTCA-ACTTAAGTTATACTGGAAATG
1 -CAGATAACCCTTCT-AGACTTAAGTTATGCTGTAAATG
48778 TTGTCTTAAA
Statistics
Matches: 444, Mismatches: 75, Indels: 31
0.81 0.14 0.06
Matches are distributed among these distances:
163 1 0.00
164 95 0.21
165 275 0.62
166 11 0.02
167 3 0.01
168 33 0.07
169 26 0.06
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (165 bp):
CAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGA
ACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGA
GCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGA
Found at i:48508 original size:249 final size:247
Alignment explanation
Indices: 48057--48646 Score: 811
Period size: 249 Copynumber: 2.4 Consensus size: 247
48047 GAATGTAATC
* * * *
48057 GAACTCAGAGGTCTTCGGTTGGCAGATATCCCTTCTCGACTTAAGCTATACTACAAATGATGTGC
1 GAACTCA-AGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGC
48122 CTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTGGTGACAGATAACCATTCAAGCCTTGAGTT
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTGGTGACAGATAACCATTCAAGCCTTGAGTT
* * *
48187 ATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAGGGTCTTCGGCAGATAGCC
130 ATACTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAGGGTCTTCGGAAGATAACC
* * *
48252 TTTCTCGACTTAAGCTATGCTGTAAATGATATACCTTGGAGCTGAGCGTAGTA
195 CTTCTCGACTTAAGCTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGTA
* *
48305 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACCAATGATATGC
1 GAACTC-AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGC
* * * *
48370 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
65 CTTGGAGCTGAGCGTAGTCGAACTCGAAAG-TCTTTGGTGACAGATAACCATTCAAGCCTTGAGT
* * * * * *
48435 TATGCTGTAACTGGCGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCTTTGGAAGATAAC
129 TATACTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAGGGTCTTCGGAAGATAAC
* * * * *
48500 CCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTC
194 CCTTCTCGACTTAAGCTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGTA
* * ** *
48554 GAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGC
1 GAACTC-AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATG-
* * * *
48619 CCTCGAAGCTGAGTGTAATCGAACTCGA
64 CCTTGGAGCTGAGCGTAGTCGAACTCGA
48647 GGGTCTTCGG
Statistics
Matches: 300, Mismatches: 39, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
248 86 0.29
249 190 0.63
250 24 0.08
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (247 bp):
GAACTCAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGCC
TTGGAGCTGAGCGTAGTCGAACTCGAAAGTCTTTGGTGACAGATAACCATTCAAGCCTTGAGTTA
TACTGTAAATGACGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAGGGTCTTCGGAAGATAACCC
TTCTCGACTTAAGCTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGTA
Found at i:48748 original size:249 final size:249
Alignment explanation
Indices: 48057--48777 Score: 664
Period size: 249 Copynumber: 2.9 Consensus size: 249
48047 GAATGTAATC
* * * * * *
48057 GAACTCAGAGGTCTTCGGTTGGCAGATATCCCTTCTCGACTTAAGCTATACTACAAATGATGTGC
1 GAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGC
* * * * * * * * * * *
48122 CTTGGAGCTGAGCGTAGTCGAACTCGAAAGTCT-TTGGTGACAGATAACCATTCAAGCCTTGAGT
66 CTCGAAGCTGAGCGTAATCGAACTCGAAGGTGTCTTCGTGACAGATAACCCTTCTAGACTTAAGC
* * *** * ** * * * * *
48186 TATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTAGAGGGTCTTCGGCAGATAGC
131 TATGCTGCAAATGGCATACCCTCGAAGCTGAGCATAATCAAACTCGAAGGTCTTTGGCAGATAAC
* * * *
48251 CTTTCTCGACTTAAGCTATGCTGTAAATGATATACCTTGGAGCTGAGCGTAGTA
196 CCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGTA
* * * *
48305 GAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATACTACCAATGATATGC
1 GAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGC
* * * * * * * * *
48370 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
66 CTCGAAGCTGAGCGTAATCGAACTCGAAGGTGTCTTCGTGACAGATAACCCTTCTAGACTTAAGC
* * * * * ** * * *
48435 TATGCTGTAACTGGCGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCTTTGGAAGATAAC
131 TATGCTGCAAATGGCATACCCTCGAAGCTGAGCATAATCAAACTCGAAGGTCTTTGGCAGATAAC
* * * *
48500 CCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGTGTAGTC
196 CCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGTA
* ** *
48554 GAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGC
1 GAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATG-
* * * *
48619 CCTCGAAGCTGAGTGTAATCGAACTCG-AGG-GTCTTCG-G-CAGATAGCCCTTTTCGACTTAAG
65 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTGTCTTCGTGACAGATAACCCTTCTAGACTTAAG
* * * *
48680 CTATGCTGCAAAT-G-ATACGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTATTTTGTTAGCA
130 CTATGCTGCAAATGGCATAC-CCTCGAAGCTGAGCATAATCAAACTCGAAGGT-CTTTG---GCA
* *
48743 GATAACCCTTCTCAACTTAAGTTATACTGGAAATG
190 GATAACCCTTCTCGACTTAAGTTATACTGCAAATG
48778 TTGTCTTAAA
Statistics
Matches: 400, Mismatches: 66, Indels: 13
0.84 0.14 0.03
Matches are distributed among these distances:
244 2 0.00
245 25 0.06
246 32 0.08
247 1 0.00
248 92 0.23
249 225 0.56
250 23 0.06
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (249 bp):
GAACTCAAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGC
CTCGAAGCTGAGCGTAATCGAACTCGAAGGTGTCTTCGTGACAGATAACCCTTCTAGACTTAAGC
TATGCTGCAAATGGCATACCCTCGAAGCTGAGCATAATCAAACTCGAAGGTCTTTGGCAGATAAC
CCTTCTCGACTTAAGTTATACTGCAAATGATATACCTTGGAGCTGAGCGTAGTA
Found at i:50638 original size:14 final size:14
Alignment explanation
Indices: 50598--50638 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
50588 ACAAAAAACT
50598 TGAGAAAAA-AAAA
1 TGAGAAAAAGAAAA
*
50611 GGA-AAAAAGAAAA
1 TGAGAAAAAGAAAA
50624 TGAGAAAAAGAAAA
1 TGAGAAAAAGAAAA
50638 T
1 T
50639 TCAGATAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 8 0.33
14 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (14 bp):
TGAGAAAAAGAAAA
Found at i:55000 original size:2 final size:2
Alignment explanation
Indices: 54983--55016 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
54973 TAAGTAAATT
54983 TA TA T- TA TA T- 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
55017 ACAGTAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:56322 original size:39 final size:39
Alignment explanation
Indices: 56279--56682 Score: 603
Period size: 39 Copynumber: 10.4 Consensus size: 39
56269 CGCGAGGCGA
* *
56279 CTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
**
56318 CTTCTGTTTCAAGAAAAACTATCTCAAGCGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
56357 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
* *
56396 CTTCCT-TTTCAAGGGAAACTATATCAAGCGAGACAAAAT
1 CTT-CTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
* * **
56435 CTTTTGTTTCAAGGGAAACTATCTCAAGAGAGGCAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
* *
56474 CTTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
**
56513 CTTCTGTTTCAAGGGAAACTATCTCCTGCGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
* *
56552 CTTTTGTTTCAAGAGAAACTATCTCAAGCGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
*
56591 TTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
* **
56630 CTTCTGTTTCGATAGAAACTATCTCAAGCGAGATAAAAT
1 CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
*
56669 CTTATGTTTCAAGG
1 CTTCTGTTTCAAGG
56683 AAAAACAATC
Statistics
Matches: 330, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
38 1 0.00
39 327 0.99
40 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (39 bp):
CTTCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
Found at i:56777 original size:75 final size:75
Alignment explanation
Indices: 56651--56933 Score: 251
Period size: 76 Copynumber: 3.7 Consensus size: 75
56641 ATAGAAACTA
* * * *
56651 TCTCAAGCGAGATAAAATCTTATGTTTCAAGGAAAAACAATCTTG-AGTGAAAT-AAATCTTCTT
1 TCTCAAGCGAGA-CAAATC-T-TGTTTTAA-GAAAAACAATCATGTAGTGAAATGAAAT-GTCTT
*
56714 ATTTTGAGTAAAAAAG
61 -TTTTGAGTAAAATAG
* *
56730 TCTCTAGCAAGACAAATCTTGTTTTAAGAAAAACAA-CATGTAGTGAAATGAAATGTCATTTTTT
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCATGTAGTGAAATGAAATGTC-TTTTTT
*
56794 GAATAAAACTTA-
65 GAGTAAAA--TAG
* * ** * *
56806 TCCCAAGCGAGACAAATCTTATTTTAAGAAAAACAAT-ATCCAGTCAAATGAAATGTCTCTTTTC
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCATGTAGTGAAATGAAATGTCT-TTTTT
*
56870 AAGTAAAATAG
65 GAGTAAAATAG
*
56881 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAATC-T-TCAGTGAAAT-AAAT
1 TCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAATCATGT-AGTGAAATGAAAT
56934 CCTCCATATT
Statistics
Matches: 170, Mismatches: 23, Indels: 27
0.77 0.10 0.12
Matches are distributed among these distances:
74 9 0.05
75 70 0.41
76 74 0.44
77 2 0.01
78 5 0.03
79 10 0.06
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (75 bp):
TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCATGTAGTGAAATGAAATGTCTTTTTTG
AGTAAAATAG
Found at i:60399 original size:15 final size:15
Alignment explanation
Indices: 60372--60415 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
60362 TGCAATGAAT
60372 AATG-AATGTATGCAA
1 AATGCAATG-ATGCAA
60387 AATGCAATGATGC-A
1 AATGCAATGATGCAA
60401 AATGC-A-GATGCAA
1 AATGCAATGATGCAA
60414 AA
1 AA
60416 ATGTTGATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 6 0.22
15 8 0.30
16 4 0.15
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.20
Consensus pattern (15 bp):
AATGCAATGATGCAA
Found at i:61147 original size:27 final size:28
Alignment explanation
Indices: 61117--61169 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
61107 ATGAAAAATG
*
61117 ACACAAACAAAAG-AAAGAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAGTGT
61144 ACACAAACAAAAGAAAAGAAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAGT
61170 TAGTACATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.13
Consensus pattern (28 bp):
ACACAAACAAAAGAAAAGAAATTAGTGT
Found at i:62628 original size:2 final size:2
Alignment explanation
Indices: 62616--62674 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
62606 CAAGTAAATT
62616 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
62657 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
62675 ACAGTGGAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66099 original size:20 final size:20
Alignment explanation
Indices: 66074--66166 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
66064 TTTTCCCAAT
*
66074 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
66094 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
66115 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* *
66135 TCGCAACGCGAATAGGGAAAA
1 TCGCAATGCGAATA-AGAAAA
66156 TCGCAATGCGA
1 TCGCAATGCGA
66167 TACTTACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 29 0.49
21 30 0.51
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:66119 original size:41 final size:41
Alignment explanation
Indices: 66074--66166 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
66064 TTTTCCCAAT
*
66074 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATAGGGAAAA
66115 TCGCAATGCGAATAAGTAAATCGCAACGCGAATAGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATAGGGAAAA
66156 TCGCAATGCGA
1 TCGCAATGCGA
66167 TACTTACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATAGGGAAAA
Found at i:66179 original size:41 final size:41
Alignment explanation
Indices: 66093--66227 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
66083 GAATAAGTAA
* ** *
66093 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATAGGGAAAATCGCAATGCG-ATACTTACT
66134 ATCGCAACGCGAATAGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATAGGGAAAATCGCAATGCGATACTTACT
* * * *
66175 ATCGCAATGCGATAATA--CAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCG--AATAGGGAAAATCGCAATGCGATACTTACT
*
66216 TTCGCAACGCGA
1 ATCGCAACGCGA
66228 TACTGACTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.01
40 5 0.06
41 71 0.88
43 4 0.05
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATAGGGAAAATCGCAATGCGATACTTACT
Found at i:66180 original size:20 final size:20
Alignment explanation
Indices: 66155--66244 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
66145 AATAGGGAAA
*
66155 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
66175 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
66196 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
66216 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
66236 TTCGCAACG
1 ATCGCAACG
66245 TGATTTACAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 40 0.69
21 12 0.21
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:66464 original size:22 final size:22
Alignment explanation
Indices: 66436--66479 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
66426 CACTCTCTCA
66436 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
66458 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
66480 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:66766 original size:20 final size:20
Alignment explanation
Indices: 66741--66778 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
66731 CGATTCTCTC
66741 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
66761 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
66779 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:68114 original size:18 final size:18
Alignment explanation
Indices: 68093--68137 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
68083 TCCACTTCGG
* *
68093 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
68111 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
68129 GAGCCATCA
1 GAGCCATCA
68138 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:68702 original size:19 final size:19
Alignment explanation
Indices: 68613--68711 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 19
68603 TTTACTTTCA
* **
68613 CAACACGAAATGACTATCG
1 CAACGCGAAATGAAAATCG
***
68632 CAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGAAAATCG
*
68652 CAATGCGAAATGAAAATCG
1 CAACGCGAAATGAAAATCG
*
68671 CAA--CG--A-CAAAATCG
1 CAACGCGAAATGAAAATCG
68685 CAACGCGAAATGAAAATCG
1 CAACGCGAAATGAAAATCG
*
68704 CAATGCGA
1 CAACGCGA
68712 TTTGTGTTTC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 32 0.49
20 17 0.26
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
CAACGCGAAATGAAAATCG
Found at i:68742 original size:14 final size:14
Alignment explanation
Indices: 68723--68780 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
68713 TTGTGTTTCG
68723 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
68737 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
68753 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
68769 CGTTGCGATTTT
1 CGTTGCGATTTT
68781 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:68757 original size:32 final size:33
Alignment explanation
Indices: 68718--68796 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
68708 GCGATTTGTG
68718 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
68750 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
68783 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
68797 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:68795 original size:19 final size:19
Alignment explanation
Indices: 68737--68854 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
68727 GCGATTTTGT
68737 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
68755 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
68769 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
68788 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
68808 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
68827 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
68847 TGTTGCGA
1 CGTTGCGA
68855 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 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:70838 original size:19 final size:19
Alignment explanation
Indices: 70814--70884 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
70804 AAAACAGACT
70814 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
70833 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
70852 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
70871 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
70885 ATCGCAATGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.48, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:70890 original size:33 final size:36
Alignment explanation
Indices: 70814--70896 Score: 118
Period size: 38 Copynumber: 2.3 Consensus size: 36
70804 AAAACAGACT
*
70814 ATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
70852 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
70885 ATCGCAATGCGA
1 ATCGCAATGCGA
70897 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
33 16 0.36
34 1 0.02
36 2 0.05
38 25 0.57
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:70972 original size:20 final size:20
Alignment explanation
Indices: 70923--70972 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
70913 CGATTTTCTG
*
70923 GTTGCGATAACCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
70943 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
70963 GTTGCGATAG
1 GTTGCGATAG
70973 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:72047 original size:24 final size:24
Alignment explanation
Indices: 72020--72073 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
72010 GTATTCGAAA
* *
72020 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
72044 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
72068 TTTGAT
1 TTTGAT
72074 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
Done.