Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003424.1 Hibiscus syriacus cultivar Beakdansim tig00007211_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: 149099
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2637 original size:12 final size:11
Alignment explanation
Indices: 2599--2644 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
2589 TGATTACTAC
2599 TTTC-TATT-T
1 TTTCTTATTCT
* *
2608 TTTCTTCTTAT
1 TTTCTTATTCT
2619 TTTCTTATTCT
1 TTTCTTATTCT
2630 TTTCCTTATTCT
1 TTT-CTTATTCT
2642 TTT
1 TTT
2645 GGAGTTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 13 0.42
12 11 0.35
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTCTTATTCT
Found at i:5762 original size:21 final size:20
Alignment explanation
Indices: 5715--5762 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
5705 GATGAAGAAC
*
5715 AAGTTGGATTTGGATGATTT
1 AAGTTGGATTTGGATGATTG
5735 AAGGTTGGATTT-GATGTTATTG
1 AA-GTTGGATTTGGATG--ATTG
5757 AAGTTG
1 AAGTTG
5763 TAAAGTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.25
21 13 0.54
22 5 0.21
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (20 bp):
AAGTTGGATTTGGATGATTG
Found at i:17271 original size:13 final size:13
Alignment explanation
Indices: 17206--17270 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
17196 TTGTATATCG
17206 ATAGTAAGGCATA
1 ATAGTAAGGCATA
17219 ATAGTAAGGCATA
1 ATAGTAAGGCATA
17232 ATAGTAAGGCATA
1 ATAGTAAGGCATA
17245 ATAGTAAGGCATA
1 ATAGTAAGGCATA
* *
17258 TTAGTGAGGCATA
1 ATAGTAAGGCATA
17271 TCAGGTGAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.25
Consensus pattern (13 bp):
ATAGTAAGGCATA
Found at i:22546 original size:117 final size:117
Alignment explanation
Indices: 22340--22590 Score: 319
Period size: 117 Copynumber: 2.1 Consensus size: 117
22330 AACGCAAGGT
* * * *
22340 ACCCAATAAGCACCTAAGTGCCCCAATGACGTATAGGTACTATAGTATAGAGTGACCTTATATTA
1 ACCCAATAAGAACCTAAGTGCCACAATGACGTATAGGTACTATAGTATAGAGCGACCTTATAGTA
* *
22405 ATAATTCTAGAGTGATAATTCATTATGAATACCATCCTCACACACAAAGTGC
66 ACAATTCTAGAGTGATAATTCATTATGAATACCATACTCACACACAAAGTGC
* *
22457 ACCCAATAAGAATCTAAGTGCCACAATGATGTATAGGTACTATAGTAT-GTAGCGACAC-TATAG
1 ACCCAATAAGAACCTAAGTGCCACAATGACGTATAGGTACTATAGTATAG-AGCGAC-CTTATAG
* * ** * *
22520 TAACAGTTCTAGAGT-AGTAATTCATTATGAATGCCATACTTTCACATAATGTGC
64 TAACAATTCTAGAGTGA-TAATTCATTATGAATACCATACTCACACACAAAGTGC
*
22574 ATCCAATAAGAACCTAA
1 ACCCAATAAGAACCTAA
22591 ATGCAGTAGT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
116 2 0.02
117 112 0.97
118 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (117 bp):
ACCCAATAAGAACCTAAGTGCCACAATGACGTATAGGTACTATAGTATAGAGCGACCTTATAGTA
ACAATTCTAGAGTGATAATTCATTATGAATACCATACTCACACACAAAGTGC
Found at i:22749 original size:26 final size:26
Alignment explanation
Indices: 22676--22750 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
22666 GGCATCTCAC
22676 TTGCACTTGAAAGTGCCATTTATCAA
1 TTGCACTTGAAAGTGCCATTTATCAA
* * * *
22702 TTTCACTTTAAGGTTCCATTTATCAA
1 TTGCACTTGAAAGTGCCATTTATCAA
* *
22728 TTGCACTTGAAAATGCCCTTTAT
1 TTGCACTTGAAAGTGCCATTTAT
22751 ACCAAAGGCT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (26 bp):
TTGCACTTGAAAGTGCCATTTATCAA
Found at i:24044 original size:19 final size:20
Alignment explanation
Indices: 24020--24066 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24010 CCAAAGTGGC
*
24020 TCAATTTC-ACACTCTAGCA
1 TCAATTTCAACACTCTAACA
*
24039 TCAATTTCAACATTCTAACA
1 TCAATTTCAACACTCTAACA
*
24059 TTAATTTC
1 TCAATTTC
24067 CAGCATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (20 bp):
TCAATTTCAACACTCTAACA
Found at i:26629 original size:25 final size:25
Alignment explanation
Indices: 26567--26615 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
26557 CTTTGTCCAT
26567 TTAGCATACAACTTTTATTTATAAC
1 TTAGCATACAACTTTTATTTATAAC
26592 TTAGCATACAACTTTTATTTATAA
1 TTAGCATACAACTTTTATTTATAA
26616 GCATTAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (25 bp):
TTAGCATACAACTTTTATTTATAAC
Found at i:28103 original size:5 final size:5
Alignment explanation
Indices: 28093--28146 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
28083 ATGCAATTTA
* * * * *
28093 ATAAC ATAAC ATAAC ATAAC ATAGC ATAGC ATAGC ATAGC ATAAC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
28143 ATAA
1 ATAA
28147 TATATACTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.52, C:0.19, G:0.09, T:0.20
Consensus pattern (5 bp):
ATAAC
Found at i:28106 original size:10 final size:10
Alignment explanation
Indices: 28093--28146 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
28083 ATGCAATTTA
*
28093 ATAACATAAC
1 ATAACATAGC
*
28103 ATAACATAAC
1 ATAACATAGC
*
28113 ATAGCATAGC
1 ATAACATAGC
*
28123 ATAGCATAGC
1 ATAACATAGC
28133 ATAACATAGC
1 ATAACATAGC
28143 ATAA
1 ATAA
28147 TATATACTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.52, C:0.19, G:0.09, T:0.20
Consensus pattern (10 bp):
ATAACATAGC
Found at i:51925 original size:20 final size:20
Alignment explanation
Indices: 51899--51951 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
51889 AAAGTTGTCC
51899 CGAAGGACCTATGTATATC-
1 CGAAGGACCTATGTATATCT
* *
51918 CAGAAGGATCTCTGTATATCT
1 C-GAAGGACCTATGTATATCT
*
51939 CGAAAGACCTATG
1 CGAAGGACCTATG
51952 AACGCTCGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
CGAAGGACCTATGTATATCT
Found at i:52820 original size:64 final size:64
Alignment explanation
Indices: 52706--52825 Score: 161
Period size: 64 Copynumber: 1.9 Consensus size: 64
52696 ACATAAATCT
* * *
52706 CATTCGATGTTTGTATTTTAAGGGGATGCATCGATACACTACTTATGCATCAATACTCTGATGG
1 CATTCGATGTTTGTATTTTAAGGAGATGCATCGATACACTACATAGGCATCAATACTCTGATGG
* * * *
52770 CATTCGATGTTTTTATTTTAAATGAG-TGCATCGATACACTTCATAGGCATCGATAC
1 CATTCGATGTTTGTATTTT-AAGGAGATGCATCGATACACTACATAGGCATCAATAC
52826 ACCATGAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
64 44 0.92
65 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAGGAGATGCATCGATACACTACATAGGCATCAATACTCTGATGG
Found at i:59509 original size:20 final size:20
Alignment explanation
Indices: 59472--59528 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 20
59462 GATACCAATT
* *
59472 GGTCTCCAAATCAAAGGACC
1 GGTCTCCATACCAAAGGACC
* **
59492 GGTCTCCATACCATAGGATT
1 GGTCTCCATACCAAAGGACC
* *
59512 GTTCTCCATACCGAAGG
1 GGTCTCCATACCAAAGG
59529 CTTTATATCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
GGTCTCCATACCAAAGGACC
Found at i:64698 original size:20 final size:19
Alignment explanation
Indices: 64653--64691 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
64643 CAAGATGACC
*
64653 CAATTTCACACTCTAATAT
1 CAATTTCACACTCTAACAT
64672 CAATTTCAACACTCTAACAT
1 CAATTTC-ACACTCTAACAT
64692 TAGTTTCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (19 bp):
CAATTTCACACTCTAACAT
Found at i:71816 original size:29 final size:31
Alignment explanation
Indices: 71752--71817 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 31
71742 TTTCAAAAAC
* *
71752 TTTTAGTCCCTAAACTTTTACAAAATTTATA
1 TTTTGGTCACTAAACTTTTACAAAATTTATA
*
71783 CTTTGGTCACTAAAC-TTT-CAAAATTT-TCA
1 TTTTGGTCACTAAACTTTTACAAAATTTAT-A
71812 TTTTGG
1 TTTTGG
71818 GCAATTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 14 0.47
30 3 0.10
31 12 0.40
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTTGGTCACTAAACTTTTACAAAATTTATA
Found at i:84866 original size:7 final size:7
Alignment explanation
Indices: 84850--84899 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
84840 GTCAAAGAAA
*
84850 GTCAAGG
1 GTCAACG
84857 GTCAACG
1 GTCAACG
84864 GTC-ACG
1 GTCAACG
84870 GTCAACG
1 GTCAACG
84877 GTC-ACG
1 GTCAACG
84883 GTCAACG
1 GTCAACG
84890 GTCAACG
1 GTCAACG
84897 GTC
1 GTC
84900 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 12 0.30
7 28 0.70
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:84874 original size:13 final size:13
Alignment explanation
Indices: 84856--84899 Score: 79
Period size: 13 Copynumber: 3.3 Consensus size: 13
84846 GAAAGTCAAG
84856 GGTCAACGGTCAC
1 GGTCAACGGTCAC
84869 GGTCAACGGTCAC
1 GGTCAACGGTCAC
84882 GGTCAACGGTCAAC
1 GGTCAACGGTC-AC
84896 GGTC
1 GGTC
84900 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 24 0.80
14 6 0.20
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTCAACGGTCAC
Found at i:84879 original size:20 final size:20
Alignment explanation
Indices: 84850--84899 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
84840 GTCAAAGAAA
*
84850 GTCAAGGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
84870 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
84890 GTCAACGGTC
1 GTCAACGGTC
84900 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:84935 original size:10 final size:10
Alignment explanation
Indices: 84908--84967 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
84898 TCGGGTCGGG
*
84908 TCAACCCGGT
1 TCAAACCGGT
* *
84918 TTAGACCGGT
1 TCAAACCGGT
*
84928 TCGAACCGG-
1 TCAAACCGGT
84937 TCAAACCGGT
1 TCAAACCGGT
*
84947 TCGAACCTGG-
1 TCAAACC-GGT
84957 TCAAACCGGT
1 TCAAACCGGT
84967 T
1 T
84968 TTCCAGCAGC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
9 10 0.26
10 26 0.68
11 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:84946 original size:19 final size:20
Alignment explanation
Indices: 84922--84967 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
84912 CCCGGTTTAG
84922 ACCGGTTCGAACC-GGTCAA
1 ACCGGTTCGAACCTGGTCAA
84941 ACCGGTTCGAACCTGGTCAA
1 ACCGGTTCGAACCTGGTCAA
84961 ACCGGTT
1 ACCGGTT
84968 TTCCAGCAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.20
Consensus pattern (20 bp):
ACCGGTTCGAACCTGGTCAA
Found at i:92144 original size:7 final size:7
Alignment explanation
Indices: 92133--92183 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
92123 GTCAAAGAAA
*
92133 GTCAACA
1 GTCAACG
92140 GTCAACG
1 GTCAACG
92147 GTC-ACG
1 GTCAACG
92153 GTCAACG
1 GTCAACG
92160 GTC-ACG
1 GTCAACG
92166 GTCAACG
1 GTCAACG
92173 GTCAACG
1 GTCAACG
92180 GTCA
1 GTCA
92184 GGTCGGGTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:92158 original size:13 final size:13
Alignment explanation
Indices: 92140--92183 Score: 79
Period size: 13 Copynumber: 3.3 Consensus size: 13
92130 AAAGTCAACA
92140 GTCAACGGTCACG
1 GTCAACGGTCACG
92153 GTCAACGGTCACG
1 GTCAACGGTCACG
92166 GTCAACGGTCAACG
1 GTCAACGGTC-ACG
92180 GTCA
1 GTCA
92184 GGTCGGGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 23 0.77
14 7 0.23
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:92158 original size:20 final size:21
Alignment explanation
Indices: 92133--92183 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
92123 GTCAAAGAAA
*
92133 GTCAACAGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
92153 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
92173 GTCAACGGTCA
1 GTCAACGGTCA
92184 GGTCGGGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:92194 original size:17 final size:17
Alignment explanation
Indices: 92152--92212 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
92142 CAACGGTCAC
*
92152 GGTCAACGGTCACGGTCAAC
1 GGTCAACGGTCA-GGTC--G
92172 GGTCAACGGTCAGGTCG
1 GGTCAACGGTCAGGTCG
* * *
92189 GGTCAATGGCCGGGTCG
1 GGTCAACGGTCAGGTCG
92206 GGTCAAC
1 GGTCAAC
92213 CCGGTTCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 20 0.56
19 4 0.11
20 12 0.33
ACGTcount: A:0.20, C:0.26, G:0.38, T:0.16
Consensus pattern (17 bp):
GGTCAACGGTCAGGTCG
Found at i:92236 original size:9 final size:9
Alignment explanation
Indices: 92206--92275 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
92196 GGCCGGGTCG
*
92206 GGTCAACCC
1 GGTCAAACC
*
92215 GGTTCAGACC
1 GG-TCAAACC
92225 GGTCAAACC
1 GGTCAAACC
**
92234 GGTTTGAACC
1 GG-TCAAACC
92244 GGTCAAACC
1 GGTCAAACC
* *
92253 GATTCAAAACT
1 G-GTC-AAACC
92264 GGTCAAACC
1 GGTCAAACC
92273 GGT
1 GGT
92276 TTTCCAGCAG
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 23 0.50
10 18 0.39
11 5 0.11
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:92244 original size:19 final size:19
Alignment explanation
Indices: 92206--92277 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
92196 GGCCGGGTCG
* * *
92206 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTTAAACC
*
92225 GGTCAAACCGGTTTGAACC
1 GGTCAAACCGGTTTAAACC
* * *
92244 GGTCAAACCGATTCAAAACT
1 GGTCAAACCGGTT-TAAACC
92264 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
92278 TCCAGCAGCT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (19 bp):
GGTCAAACCGGTTTAAACC
Found at i:99570 original size:47 final size:50
Alignment explanation
Indices: 99455--99577 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 50
99445 TTTTTTCCTT
* * * * *
99455 TATGACATCCATTCATACCAATTATGCATTGTTTTACACTATATATGTATA
1 TATGGCATCCTTTCATACCACTTATACATTGTTGTACACTATATA-GTATA
*
99506 TATGGCATCCTTTCATACCACTTATATATTGTTGTACA-T-TATA-TATA
1 TATGGCATCCTTTCATACCACTTATACATTGTTGTACACTATATAGTATA
99553 TATGGCATCCTTTCATACCACTTAT
1 TATGGCATCCTTTCATACCACTTAT
99578 GCAATGCTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
47 29 0.44
49 4 0.06
50 1 0.02
51 32 0.48
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (50 bp):
TATGGCATCCTTTCATACCACTTATACATTGTTGTACACTATATAGTATA
Found at i:99841 original size:81 final size:81
Alignment explanation
Indices: 99615--101806 Score: 2646
Period size: 81 Copynumber: 27.1 Consensus size: 81
99605 ATTCTTTTAG
* * * * * * * *
99615 TCTTTTACCCAAAGGCATTTAACCTTTCATCAAACTTGCATAATTGA-ACCTTTTTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
99679 ACAGCTAGACCATTAA
66 ACAGCTAGGCCATTAA
* * * *
99695 TCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGTATAATTGAAACTTTTATGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
99759 ACAACTAGGCAATTAA
66 ACAGCTAGGCCATTAA
* * *
99775 TCATTTACTCAACGGTATTTAACCGTTCATCTAATTGGCAAAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
99840 ACAACTAGTCCATTAA
66 ACAGCTAGGCCATTAA
* *** * * * * *
99856 TCTTTCACTCAATAATATTTAACCGTTAATTTAACCGTCATAATTGACACTTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
99921 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * ** *
99937 TCTTTTACTCTACAGTATTTAACCGTTCATCTAA-TAAGCATAATTGAAACCTTTCTATCAAATT
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACT-GGCATAATTGACACCTTTCTGCCAAATG
* *
100001 CATAGCTAAGCCATTAA
65 CACAGCTAGGCCATTAA
* * * * * *
100018 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATAATTGACAACTTTCTACAAAATAC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
100083 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* ** * * * * *
100099 TCTTTTACTTTATGACATTTTTTAACCTTTCATCTAACTGGTATAATTGACACATTTCTTCCAAA
1 TCTTTTAC-TCA--ACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAA
* *
100164 TACACAGCTAGTCCATTAA
63 TGCACAGCTAGGCCATTAA
* ** *
100183 TCTGTTACTCAACGGTATTTAACCGTTCATCTAACTACCATAATTGACACCTTTCGGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
100248 ACAGTTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * ** * *
100264 TCTTTTACTTAACGGTATTTAACAGTTCATTTAACTAGCATAATTGACACAATTATGCAAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
100329 ACAGCTAGACCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
100345 TCATTTACTCAACGGTATTTAACCATTCATCTAACTGGAATAATTGATACCTTTATGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
100410 ACAACTAGGCCTTTAA
66 ACAGCTAGGCCATTAA
* * * ** *
100426 TCTTTTACTCGACAGTATTTAACCGTTCATCTAACTGGCATAATGGACAGATTTCTACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
100491 ACAGAC-AGTCCATTAA
66 ACAG-CTAGGCCATTAA
* * * * ** * *
100507 TTTTTTACTCGACGATATTTAACCATTCATCTAACTACCATACTTTACACCTTTCTG-CAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
100571 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * * *
100587 TCTTTTACTCAACGGTATTTAACAGTTCATTTAACTGGCAT-ATTGACACCTTTTTACAAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
100651 ACAGGTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
100667 TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
100732 ATAGCTAGTCCATTAA
66 ACAGCTAGGCCATTAA
* ** **
100748 TCTTTTACACAACGGTATTTAACCGTTCATCTAACTACCATAATTGACACCTTTCTTTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
**
100813 TTAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
100829 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTT-TGCAAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
100893 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
100909 TCTTTCACTCAACGGTATTTAAACGTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
100974 ACGGCTAGGCCATTAT
66 ACAGCTAGGCCATTAA
* * * * **
100990 TCTTTTACTCAACGGTATTTAATCATTCATCTAACTGCCATAATTGACACCTTTATGAGAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
**
101055 ACAATTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
101071 TCTTTTACTCAACGGTATTTAA-CGTTCATCTATA-TGGCATAATTGACACCTTTATGCCAAATG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTA-ACTGGCATAATTGACACCTTTCTGCCAAATG
*
101134 CATAGCTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * * *
101151 TCTTTTACTCAGCGGTATTTAACCGTTCATCTAACTGTCATAATTAACACATTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
101216 -CAGCTAGTCCCTTAA
66 ACAGCTAGGCCATTAA
* ** *
101231 TCTTTTACTCAACGGTATTTAACCGCTCATCTAACAT-ATATAATTGTCACCTTTCTGCCAAATG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAAC-TGGCATAATTGACACCTTTCTGCCAAATG
*
101295 CACAGCTAGTCCATTAA
65 CACAGCTAGGCCATTAA
* * ** * *
101312 TCTTTTACTCAATGGTATTTAATCGTTCATCTAACTACCATAATTGACACCTTTCTTCCAGATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
**
101377 ATTGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
101393 TCTTTTACTCAACGGTAGTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
101458 ACAGCTAGGCCATTGA
66 ACAGCTAGGCCATTAA
* * *
101474 TCTTTTACTCAACGATATTTAACCGTTCATCTAACT-GCAATAATTGACACCTTTTTGCCAACTG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGC-ATAATTGACACCTTTCTGCCAAATG
*
101538 CACATCTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * ** * * * * *
101555 TGTTTTACTCGACAATATTTAACCATTCATCTAATTAGCATAATTGACACATTTCTACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
101620 ACATCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
101636 TCTTTTACTCAACGATATTTAACCGTTCATCTAACT-GCAATAATTGACACCTTTATACCAAATG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGC-ATAATTGACACCTTTCTGCCAAATG
* *
101700 CACAACAAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * *
101717 TGTTTTACTCAATGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
101782 ATAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
101798 TCTTTTACT
1 TCTTTTACT
101807 TTATAAATGT
Statistics
Matches: 1802, Mismatches: 288, Indels: 43
0.84 0.14 0.02
Matches are distributed among these distances:
79 32 0.02
80 392 0.22
81 1303 0.72
82 8 0.00
83 2 0.00
84 65 0.04
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:100767 original size:403 final size:403
Alignment explanation
Indices: 99615--101806 Score: 2635
Period size: 403 Copynumber: 5.4 Consensus size: 403
99605 ATTCTTTTAG
* * * * * * * *
99615 TCTTTTACCCAAAGGCATTTAACCTTTCATCAAACTTGCATAATTGA-ACCTTTTTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAAC-TGCATAATTGACACATTTCTACCAAATGC
* * * *
99679 ACAGCTAGACCATTAATCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGTATAATTGAAA
65 ACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACA
* * * * *
99743 CTTTTATGCCAAATGCACAACTAGGCAATTAATCATTTACTCAACGGTATTTAACCGTTCATCTA
130 CCTTTCT-CCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTA
* * * * * **
99808 ATTGGCAAAATTGACACCTTTCTGCCAAATGCACAACTAGTCCATTAATCTTTCACTCAATAATA
194 ACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGATA
* * * * * * *
99873 TTTAACCGTTAATTTAACCGTCATAATTGACACTTTTCTGCCAAATGCACAACTAGGCCATTAAT
259 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGCACAGCTAGGCCATTAAT
* * * * *
99938 CTTTTACTCTACAGTATTTAACCGTTCATCTAA-TAAGCATAATTGAAACCTTTCTATCAAATTC
324 CTTTTACTCAACGGTATTTAACCGTTCATCTAACT-AGCATAATTGACACCTTTCTACCAAATGC
* *
100002 ATAGCTAAGCCATTAA
388 ACAGCTAGGCCATTAA
* * *
100018 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTTGCATAATTGACA-ACTTTCTACAAAATA
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAAC-TGCATAATTGACACA-TTTCTACCAAATG
* * ** * * * *
100082 CACAACTAGGCCATTAATCTTTTACTTTATGACATTTTTTAACCTTTCATCTAACTGGTATAATT
64 CACAGCTAGGCCATTAATCTTTTAC-TCA--ACGGTATTTAACCGTTCATCTAACTAGCATAATT
* * * *
100147 GACACATTTCTTCCAAATACACAGCTAGTCCATTAATCTGTTACTCAACGGTATTTAACCGTTCA
126 GACACCTTTC-TCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCA
** * * *
100212 TCTAACTACCATAATTGACACCTTTCGGCCAAATGCACAGTTAGGCCATTAATCTTTTACTTAAC
190 TCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAC
* * * * * * *
100277 GGTATTTAACAGTTCATTTAACTAGCATAATTGACACAATTATGCAAAATGCACAGCTAGACCAT
255 GATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGCACAGCTAGGCCAT
* * * * * * *
100342 TAATCATTTACTCAACGGTATTTAACCATTCATCTAACTGGAATAATTGATACCTTTATGCCAAA
320 TAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTACCAAA
* *
100407 TGCACAACTAGGCCTTTAA
385 TGCACAGCTAGGCCATTAA
* * * *
100426 TCTTTTACTCGACAGTATTTAACCGTTCATCTAACTGGCATAATGGACAGATTTCTACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACT-GCATAATTGACACATTTCTACCAAATGC
* * * * * * * *
100491 ACAGAC-AGTCCATTAATTTTTTACTCGACGATATTTAACCATTCATCTAACTACCATACTTTAC
65 ACAG-CTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGAC
* * * *
100555 ACCTTTCTGCAAATGCATAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACAGTTCATTTA
129 ACCTTTCTCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTA
* * * *
100620 ACTGGCAT-ATTGACACCTTTTTACAAAATGCACAGGTAGGCCATTAATCTTTTACTCAACGATA
194 ACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGATA
* * *
100684 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCATAGCTAGTCCATTAAT
259 TTTAACCGTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGCACAGCTAGGCCATTAAT
* * ** *
100749 CTTTTACACAACGGTATTTAACCGTTCATCTAACTACCATAATTGACACCTTTCTTTCAAATGCT
324 CTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCA
*
100814 TAGCTAGGCCATTAA
389 CAGCTAGGCCATTAA
* * *
100829 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTT-TGCAAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACT-GCATAATTGACACATTTCTACCAAATGC
* *
100893 ACAGCTAGGCCATTAATCTTTCACTCAACGGTATTTAAACGTTCATCTAACTAGCATAATTGACA
65 ACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACA
* * * *
100958 CCTTTCTACCAAATGCACGGCTAGGCCATTATTCTTTTACTCAACGGTATTTAATCATTCATCTA
130 CCTTTCT-CCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTA
* * ** ** *
101023 ACTGCCATAATTGACACCTTTATGAGAAATGCACAATTAGGCCATTAATCTTTTACTCAACGGTA
194 ACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGATA
* *
101088 TTTAA-CGTTCATCTATA-TGGCATAATTGACACCTTTATGCCAAATGCATAGCTAGGCCATTAA
259 TTTAACCGTTCATCTA-ACTGGCATAATTGACACATTTATGCCAAATGCACAGCTAGGCCATTAA
* * * *
101151 TCTTTTACTCAGCGGTATTTAACCGTTCATCTAACT-GTCATAATTAACACATTTCTGCCAAATG
323 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAG-CATAATTGACACCTTTCTACCAAATG
* *
101215 C-CAGCTAGTCCCTTAA
387 CACAGCTAGGCCATTAA
* ** * * *
101231 TCTTTTACTCAACGGTATTTAACCGCTCATCTAACATATATAATTGTCACCTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAAC-TGCATAATTGACACATTTCTACCAAATGC
* * * *
101296 ACAGCTAGTCCATTAATCTTTTACTCAATGGTATTTAATCGTTCATCTAACTACCATAATTGACA
65 ACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACA
* ** *
101361 CCTTTCTTCCAGATGCATTGCTAGGCCATTAATCTTTTACTCAACGGTAGTTAACCGTTCATCTA
130 CCTTTC-TCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTA
* *
101426 ACTAGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTGATCTTTTACTCAACGATA
194 ACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGATA
* * * *
101491 TTTAACCGTTCATCTAACT-GCAATAATTGACACCTTTTTGCCAACTGCACATCTAGGCCATTAA
259 TTTAACCGTTCATCTAACTGGC-ATAATTGACACATTTATGCCAAATGCACAGCTAGGCCATTAA
* * ** * * *
101555 TGTTTTACTCGACAATATTTAACCATTCATCTAATTAGCATAATTGACACATTTCTACCAAATGC
323 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGC
*
101620 ACATCTAGGCCATTAA
388 ACAGCTAGGCCATTAA
* * *
101636 TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGCAATAATTGACACCTTTATACCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGC-ATAATTGACACATTTCTACCAAATGC
* * * * * *
101701 ACAACAAGGCCATTAATGTTTTACTCAATGGTATTTAACCATTCATCTAACTGGCATAATTGACA
65 ACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACA
*
101766 CCTTTCTGCCAAATGCATAGCTAGGCCATTAATCTTTTACT
130 CCTTTCT-CCAAATGCACAGCTAGGCCATTAATCTTTTACT
101807 TTATAAATGT
Statistics
Matches: 1532, Mismatches: 231, Indels: 50
0.85 0.13 0.03
Matches are distributed among these distances:
401 1 0.00
402 126 0.08
403 619 0.40
404 251 0.16
405 199 0.13
407 10 0.01
408 322 0.21
409 4 0.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (403 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGCATAATTGACACATTTCTACCAAATGCA
CAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACAC
CTTTCTCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGGTATTTAACCGTTCATCTAAC
TGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAACGATATT
TAACCGTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGCACAGCTAGGCCATTAATCT
TTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTACCAAATGCACA
GCTAGGCCATTAA
Found at i:102013 original size:57 final size:57
Alignment explanation
Indices: 101913--102062 Score: 223
Period size: 57 Copynumber: 2.6 Consensus size: 57
101903 TAATTCATAT
* *
101913 AATTTCTTAACTTTTGGCACACAAAGTGGCC-ATATGGAAATTCATAAACCAATCATG
1 AATTTCTTAACTTTTTGCACACAAAGT-GCCTATGTGGAAATTCATAAACCAATCATG
* * *
101970 AATTTCTTAACTTTTTGCACACAAAGTGCCTATGTGGATATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCTATGTGGAAATTCATAAACCAATCATG
*
102027 AATTTCTTAACTTTTTGTACACAAAGTGCCTA-GTGG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCTATGTGG
102063 GTAATCGTCA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
56 7 0.08
57 79 0.92
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (57 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCTATGTGGAAATTCATAAACCAATCATG
Found at i:116234 original size:22 final size:21
Alignment explanation
Indices: 116209--116249 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
116199 TGGTTCAGCT
116209 AATAGGTGTTCCAATGATAATA
1 AATA-GTGTTCCAATGATAATA
* *
116231 AATATTGTTTCAATGATAA
1 AATAGTGTTCCAATGATAA
116250 ATGATGTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
AATAGTGTTCCAATGATAATA
Found at i:124037 original size:22 final size:22
Alignment explanation
Indices: 124012--124059 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
124002 ATCAATTATT
*
124012 ATATATATGATATTTATCATAA
1 ATATATATAATATTTATCATAA
* * *
124034 ATATATATAATGTTTATTATGA
1 ATATATATAATATTTATCATAA
124056 ATAT
1 ATAT
124060 TACTTCAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (22 bp):
ATATATATAATATTTATCATAA
Found at i:124315 original size:61 final size:61
Alignment explanation
Indices: 124230--124360 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 61
124220 AAGGACAAAA
* * * * **
124230 AGTGGAGGTGGAGGGAACAACCTTATGTGTCATATCCGGATTAGCCCTAGAGTGTAAACCT
1 AGTGTAGGTGGAGGGAACAACCTTATGAGTCATATCCGAATTAGCACTAGAGCATAAACCT
* * * * * *
124291 AGTGTAGGTGGTGGGCACGACCTTATGAGTCATATCTGAATTAGCACTAGAGCATAAGCTT
1 AGTGTAGGTGGAGGGAACAACCTTATGAGTCATATCCGAATTAGCACTAGAGCATAAACCT
124352 AGTGTAGGT
1 AGTGTAGGT
124361 TTAGCACTAC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (61 bp):
AGTGTAGGTGGAGGGAACAACCTTATGAGTCATATCCGAATTAGCACTAGAGCATAAACCT
Found at i:133894 original size:17 final size:17
Alignment explanation
Indices: 133853--133894 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
133843 CAGATTCCTG
133853 ATCTAGAAATTGTGTTAA
1 ATCTAGAAA-TGTGTTAA
133871 ATACTAGAAA-GTGTTAA
1 AT-CTAGAAATGTGTTAA
133888 AGTCTAG
1 A-TCTAG
133895 TAAAAATTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 12 0.55
18 3 0.14
19 7 0.32
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (17 bp):
ATCTAGAAATGTGTTAA
Found at i:143839 original size:5 final size:5
Alignment explanation
Indices: 143829--143878 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
143819 AACGGTCAAT
143829 GGTCG GGTCG GGTCG GGTCG GGTTAAC- GGTCG GGTC- GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTCG GG-T--CG GGTCG GGTCG GGTCG GGTCG
143875 GGTC
1 GGTC
143879 AGACCGGTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
4 5 0.12
5 30 0.75
6 2 0.05
7 2 0.05
8 1 0.03
ACGTcount: A:0.04, C:0.20, G:0.54, T:0.22
Consensus pattern (5 bp):
GGTCG
Done.