Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005975.1 Hibiscus syriacus cultivar Beakdansim tig00014048_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: 99997
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:11464 original size:31 final size:31
Alignment explanation
Indices: 11426--11598 Score: 256
Period size: 31 Copynumber: 5.6 Consensus size: 31
11416 TTCATAGATT
* * * *
11426 CCGAAGAACCTCGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
11457 CCGAAGAACATAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
* * *
11488 CCAAAGAACATATGTAAACAATCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
11519 CCGAAGAACATAGGTAAACAGTCTATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
* *
11550 CCGAAGAACATAGGTAAACAATCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCTATATGTC
*
11581 CCAAAGAACATAGGTAAA
1 CCGAAGAACATAGGTAAA
11599 TCCTCGACCC
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 129 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCTATATGTC
Found at i:11585 original size:93 final size:93
Alignment explanation
Indices: 11426--11598 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
11416 TTCATAGATT
* * * * *
11426 CCGAAGAACCTCGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCTATATGTCCCA
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCA
*
11491 AAGAACATATGTAAACAATCTATATGTC
66 AAGAACATAGGTAAACAATCTATATGTC
*
11519 CCGAAGAACATAGGTAAACAGTCTATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCA
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCA
11584 AAGAACATAGGTAAA
66 AAGAACATAGGTAAA
11599 TCCTCGACCC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (93 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCA
AAGAACATAGGTAAACAATCTATATGTC
Found at i:12979 original size:20 final size:20
Alignment explanation
Indices: 12954--12992 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12944 TTTTTCCATT
12954 AGGGGGAATC-GATACCCCCC
1 AGGGGGAATCTG-TACCCCCC
12974 AGGGGGAATCTGTACCCCC
1 AGGGGGAATCTGTACCCCC
12993 TGCGTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13
Consensus pattern (20 bp):
AGGGGGAATCTGTACCCCCC
Found at i:14194 original size:31 final size:31
Alignment explanation
Indices: 14156--14218 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
14146 CCCGAAGGAC
* *
14156 CAGTCCATA-GATCATGAAGAACCTAGGTAAA
1 CAGTCCATATGATC-CGAAGAACATAGGTAAA
*
14187 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGATCCGAAGAACATAGGTAAA
14218 C
1 C
14219 CCTCGACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGATCCGAAGAACATAGGTAAA
Found at i:14995 original size:64 final size:63
Alignment explanation
Indices: 14862--15018 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 63
14852 TAATGAAGGT
* * ** *
14862 ATGCATCGATGCACTACTGTTGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACT-TTGCATCGATGCACAAAATGCATTCGATGTTGTATTATTAAAGAG
* * *
14926 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTT-TGCATCGATGCACAAAATGCATTCGATGT-TGTATTATTAAAGAG
* *
14989 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCAC-TACTTTGCATCGAT
15019 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTTGCATCGATGCACAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:18121 original size:40 final size:41
Alignment explanation
Indices: 18064--18141 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
18054 ACAAGTTCGT
* *
18064 TCTAATTTTTGTTTTTGATCTCTTGTTTTGTTTTAAATAAG
1 TCTAATTTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
18105 TCTAA-TTTGGTTTTTGATCCCTTGTTTTGTTTTAAAT
1 TCTAATTTTGGTTTTTGATCCCTTGTTTTGTTTTAAAT
18142 TAGTTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 30 0.86
41 5 0.14
ACGTcount: A:0.18, C:0.09, G:0.13, T:0.60
Consensus pattern (41 bp):
TCTAATTTTGGTTTTTGATCCCTTGTTTTGTTTTAAATAAG
Found at i:18160 original size:40 final size:40
Alignment explanation
Indices: 18076--18161 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
18066 TAATTTTTGT
* **
18076 TTTTGATCTCTTGTTTTGTTTTAAATAAGTCTAATTTGGT
1 TTTTGATCCCTTGTTTTGTTTTAAATAAGTCTAATTTGCA
* * *
18116 TTTTGATCCCTTGTTTTGTTTTAAATTAGTTTTATTTGCA
1 TTTTGATCCCTTGTTTTGTTTTAAATAAGTCTAATTTGCA
18156 TTTTGA
1 TTTTGA
18162 CTCTTAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.59
Consensus pattern (40 bp):
TTTTGATCCCTTGTTTTGTTTTAAATAAGTCTAATTTGCA
Found at i:28429 original size:19 final size:19
Alignment explanation
Indices: 28384--28455 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
28374 TTTCGCCTGA
28384 AAAAAATGAAAAAGACAAAAATG
1 AAAAAATG--AAAGA-AAAAA-G
*
28407 -AAAAATGAAAGAAAAAGG
1 AAAAAATGAAAGAAAAAAG
28425 AAAAAATGAGAA-AAAAAAG
1 AAAAAATGA-AAGAAAAAAG
*
28444 AAAAAATAAAAG
1 AAAAAATGAAAG
28456 GAGGATTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.07
19 26 0.60
20 7 0.16
22 7 0.16
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAAATGAAAGAAAAAAG
Found at i:28429 original size:26 final size:26
Alignment explanation
Indices: 28382--28448 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
28372 TATTTCGCCT
*
28382 GAAAAAAATGAAAAAGACAAAAATGA
1 GAAAAAAAAGAAAAAGACAAAAATGA
*
28408 -AAAATGAAAGAAAAAGGA-AAAAATGA
1 GAAAA-AAAAGAAAAA-GACAAAAATGA
28434 GAAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
28449 ATAAAAGGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 4 0.11
26 25 0.71
27 6 0.17
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.06
Consensus pattern (26 bp):
GAAAAAAAAGAAAAAGACAAAAATGA
Found at i:29683 original size:46 final size:46
Alignment explanation
Indices: 29574--29710 Score: 202
Period size: 46 Copynumber: 2.9 Consensus size: 46
29564 CAACTTCTCT
* * *
29574 AGATTTGATATTCCCTTCAGAGTAAGTGGAATATGTCTCTCTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAG--TCTCTTCTCCA
*
29622 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
*
29668 AGATTTGATAGTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTC
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT-CTTC
29711 GATTCAATGG
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
46 46 0.56
47 4 0.05
48 32 0.39
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (46 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
Found at i:29823 original size:113 final size:111
Alignment explanation
Indices: 29622--29933 Score: 486
Period size: 113 Copynumber: 2.8 Consensus size: 111
29612 CTCTTCTTCA
* * * *
29622 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG-TCTCTTCTCCAAGATTTGATAGTCCCTTC
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAAC-AGTTCTCTTCTTCAAGATTTGATATTCCCTTC
29686 AGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTACCCC
65 AGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTACCCC
**
29733 AGATCTGATATTCCCTTGGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACA-GT-TCTCTTCTTCAAGATTTGATATTCCCTT
*
29798 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCCCC
64 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTACCCC
*
29846 AGATCTGATATTCCCTTCAGAGTAAGTGGAACA-TGTCTCTTCTTCAAGATTTGATATTCCCCTC
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGT-TCTCTTCTTCAAGATTTGATATTCCCTTC
*
29910 AGAATAAGTGGAACAAGTCT-CTTC
65 AGAGTAAGTGGAACAAGTCTGCTTC
29934 TCCAAGATTT
Statistics
Matches: 186, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
110 5 0.03
111 77 0.41
113 104 0.56
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (111 bp):
AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGTTCTCTTCTTCAAGATTTGATATTCCCTTCA
GAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTACCCC
Found at i:29918 original size:46 final size:46
Alignment explanation
Indices: 29846--29980 Score: 216
Period size: 46 Copynumber: 2.9 Consensus size: 46
29836 CAACTCCCCC
* * *
29846 AGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTTCTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
* *
29892 AGATTTGATATTCCCCTCAGAATAAGTGGAACAAGTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
29938 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACTTC
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT-CTTC
29981 GATTCAATGG
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 77 0.95
47 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (46 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTTCTCCA
Found at i:29965 original size:157 final size:158
Alignment explanation
Indices: 29755--30136 Score: 588
Period size: 157 Copynumber: 2.4 Consensus size: 158
29745 CCCTTGGGAG
* * *
29755 TAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTG
1 TAAGTGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTA
29820 CTTCGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTC
64 CTTCGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTC
29885 -TTCTTCAAGATTTGATATTCCCCTCAGAA
129 TTTCTTCAAGATTTGATATTCCCCTCAGAA
29914 TAAGTGGAACAAGTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACT
1 TAAGTGGAACAAGTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACT
* * *
29979 TCGATTCAATGGATTAACTTCCCCAGATCTGATATTCCCTTCGGAGTAAGTGGAACATGTCTCTT
66 TCGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTC-T
* *
30044 TTCTTCAAGATTTGATATTCCCTTCAGAG
130 TTCTTCAAGATTTGATATTCCCCTCAGAA
* * * *
30073 TAAGCGGAACAGATCTCTCTTCTCCAAGATTTGATATTCCCTTC-GTAGTAAGCGAAACAAGTCT
1 TAAGTGGAACA-A-GTCTCTTCTCCAAGATTTGATATTCCCTTCAG-AGTAAGTGGAACAAGTCT
30137 TTCTTCTTCA
Statistics
Matches: 206, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
157 110 0.53
159 49 0.24
160 2 0.01
161 45 0.22
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (158 bp):
TAAGTGGAACAAGTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTACT
TCGATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGTCTCTT
TCTTCAAGATTTGATATTCCCCTCAGAA
Found at i:30050 original size:270 final size:271
Alignment explanation
Indices: 29553--30083 Score: 902
Period size: 270 Copynumber: 2.0 Consensus size: 271
29543 TTTGATCCCA
* * * * *
29553 ATTCAATGGATCAACTTCTCTAGATTTGATATTCCCTTCAGAGTAAGTGGAATATGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATG-CTCTCTTC
* *
29618 TTCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCTCCAAGATTTGATAGTCCC
65 TTCAAGATTTGATATTCCCCTCAGAATAAGCGGAACAAGTCTCTTCTCCAAGATTTGATAGTCCC
*
29683 TTCAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTACCCCAGATCTGATATTCCC
130 TTCAGAGTAAGTGGAACAAGTCTACTTCGATTCAATGGATCAACTACCCCAGATCTGATATTCCC
* *
29748 TTGGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGTGGAAC
195 TTCGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGCGGAAC
29813 AAGTCTGCTTCG
260 AAGTCTGCTTCG
29825 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATG-TCTCTTCT
1 ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGCTCTCTTCT
* *
29889 TCAAGATTTGATATTCCCCTCAGAATAAGTGGAACAAGTCTCTTCTCCAAGATTTGATATTCCCT
66 TCAAGATTTGATATTCCCCTCAGAATAAGCGGAACAAGTCTCTTCTCCAAGATTTGATAGTCCCT
* *
29954 TCAGAGTAAGTGGAACAAGTCTACTTCGATTCAATGGATTAACTTCCCCAGATCTGATATTCCCT
131 TCAGAGTAAGTGGAACAAGTCTACTTCGATTCAATGGATCAACTACCCCAGATCTGATATTCCCT
* *
30019 TCGGAGTAAGTGGAACATGTCTCTTTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACA
196 TCGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACA
30084 GATCTCTCTT
Statistics
Matches: 243, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
270 192 0.79
272 51 0.21
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (271 bp):
ATTCAATGGATCAACTCCCCCAGATCTGATATTCCCTTCAGAGTAAGTGGAACATGCTCTCTTCT
TCAAGATTTGATATTCCCCTCAGAATAAGCGGAACAAGTCTCTTCTCCAAGATTTGATAGTCCCT
TCAGAGTAAGTGGAACAAGTCTACTTCGATTCAATGGATCAACTACCCCAGATCTGATATTCCCT
TCGGAGTAAGTGGAACAGGTCTCTCTTCTTCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACA
AGTCTGCTTCG
Found at i:30082 original size:48 final size:49
Alignment explanation
Indices: 30003--30210 Score: 223
Period size: 48 Copynumber: 4.3 Consensus size: 49
29993 TAACTTCCCC
* * * *
30003 AGATCTGATATTCCCTTC-GGAGTAAGTGGAACATGTCTCTTTTCTTCA
1 AGATTTGATATTCCCTTCAGCAGTAAGCGGAACAAGTCTCTTTTCTTCA
* *
30051 AGATTTGATATTCCCTTCAG-AGTAAGCGGAAC-AGATCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGCAGTAAGCGGAACAAG-TCTCTTTTCTTCA
* *
30099 AGATTTGATATTCCCTTC-GTAGTAAGCGAAACAAGTCT-TTCTTCTTCA
1 AGATTTGATATTCCCTTCAGCAGTAAGCGGAACAAGTCTCTT-TTCTTCA
* * * * *
30147 AGATTTGATATACCCTTCAGCA-AAAGTGGAACAAATC-CCTTTCATTCA
1 AGATTTGATATTCCCTTCAGCAGTAAGCGGAACAAGTCTCTTTTC-TTCA
30195 AGATTTGATATTCCCT
1 AGATTTGATATTCCCT
30211 GAGTGGCAGT
Statistics
Matches: 136, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
47 6 0.04
48 125 0.92
49 5 0.04
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (49 bp):
AGATTTGATATTCCCTTCAGCAGTAAGCGGAACAAGTCTCTTTTCTTCA
Found at i:30178 original size:96 final size:96
Alignment explanation
Indices: 30003--30210 Score: 269
Period size: 96 Copynumber: 2.2 Consensus size: 96
29993 TAACTTCCCC
* * * * *
30003 AGATCTGATATTCCCTTCGGAGTAAGTGGAACATGTCTCTTTTCTTCAAGATTTGATATTCCCTT
1 AGATTTGATATTCCCTTCGGAGTAAGCGAAACAAGTCTCTTTTCTTCAAGATTTGATATACCCTT
* * *
30068 CAGAGTAAGCGGAACAGATCTCTCTTC-TCCA
66 CAGAGAAAGCGGAACAAATCCCT-TTCATCCA
*
30099 AGATTTGATATTCCCTTCGTAGTAAGCGAAACAAGTCT-TTCTTCTTCAAGATTTGATATACCCT
1 AGATTTGATATTCCCTTCGGAGTAAGCGAAACAAGTCTCTT-TTCTTCAAGATTTGATATACCCT
* *
30163 TCAGCA-AAAGTGGAACAAATCCCTTTCATTCA
65 TCAG-AGAAAGCGGAACAAATCCCTTTCATCCA
30195 AGATTTGATATTCCCT
1 AGATTTGATATTCCCT
30211 GAGTGGCAGT
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
95 5 0.05
96 92 0.94
97 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (96 bp):
AGATTTGATATTCCCTTCGGAGTAAGCGAAACAAGTCTCTTTTCTTCAAGATTTGATATACCCTT
CAGAGAAAGCGGAACAAATCCCTTTCATCCA
Found at i:34681 original size:31 final size:31
Alignment explanation
Indices: 34645--34703 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
34635 AACTTAAAAG
*
34645 AGTTTTGCAATACCGAAATTTAAATAATTTT
1 AGTTTTACAATACCGAAATTTAAATAATTTT
* *
34676 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACCGAAATTTAAATAAT
34704 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACCGAAATTTAAATAATTTT
Found at i:34752 original size:22 final size:22
Alignment explanation
Indices: 34727--35290 Score: 698
Period size: 22 Copynumber: 25.6 Consensus size: 22
34717 ATAATAAATT
34727 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
34749 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
34771 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
34793 TTTTAAAATAAA--ATTTTACATA
1 TTTTAAAATAAATCA-ATT-CATA
34815 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
34837 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
**
34859 TTTTAAAATAAAT-TTTTCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
34881 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* ***
34903 TTTTAAAATAATTTTTTTTCATA
1 TTTTAAAATAA-ATCAATTCATA
34926 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
34948 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
34970 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
34992 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* * *
35014 TTTTAATATAAATCAATCCACA
1 TTTTAAAATAAATCAATTCATA
*
35036 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
35058 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
35080 TTTTAAAATAAAT-TTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
35102 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* * ***
35124 TTTTCAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
35146 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
35168 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
35190 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
35212 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
***
35234 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
35256 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
35278 TTTTAAAATAAAT
1 TTTTAAAATAAAT
35291 TTTAAAATAG
Statistics
Matches: 476, Mismatches: 47, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
20 2 0.00
21 8 0.02
22 437 0.92
23 28 0.06
24 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:36978 original size:38 final size:36
Alignment explanation
Indices: 36912--36986 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
36902 ATTGAAAAAT
* *
36912 ATTTATATATTTTCTTTAAAAAAATGAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAAATGAAAAT-ATAAA
* *
36949 ATTTATATAATTTCTTTTACAAAATTGAAAATATAAA
1 ATTTATATAATTTC-TTTAAAAAAATGAAAATATAAA
36986 A
1 A
36987 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (36 bp):
ATTTATATAATTTCTTTAAAAAAATGAAAATATAAA
Found at i:37806 original size:18 final size:19
Alignment explanation
Indices: 37783--37827 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
37773 CAAGTAATCC
*
37783 TATTCC-CTGGTAATCTTA
1 TATTCCACTGATAATCTTA
37801 TATTCCCACTGATAATCTTA
1 TATT-CCACTGATAATCTTA
*
37821 CATTCCA
1 TATTCCA
37828 TAAACCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 5 0.22
20 14 0.61
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Found at i:41393 original size:60 final size:59
Alignment explanation
Indices: 41337--41475 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 59
41327 AGAAGTTTGG
*
41337 GGACCAATTTAGAAA-GAGTGTCAAAGTTTAGGGATGAAATTAGAATGTTCAAAAGTTTAA
1 GGACCAATTTA-AAATGAGAGTCAAAGTTT-GGGATGAAATTAGAATGTTCAAAAGTTTAA
* *
41397 GGACTAATTTAAAATGAGAGTCAAAGTTTGAGGATGACATTAGAATGTTCAAAAGTTTAA
1 GGACCAATTTAAAATGAGAGTCAAAGTTTG-GGATGAAATTAGAATGTTCAAAAGTTTAA
* * *
41457 AGATCAAATTAAAATGAGA
1 GGACCAATTTAAAATGAGA
41476 ATTATAGCTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 4 0.06
60 66 0.94
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (59 bp):
GGACCAATTTAAAATGAGAGTCAAAGTTTGGGATGAAATTAGAATGTTCAAAAGTTTAA
Found at i:41467 original size:29 final size:29
Alignment explanation
Indices: 41359--41472 Score: 88
Period size: 29 Copynumber: 3.9 Consensus size: 29
41349 AAAGAGTGTC
* * *
41359 AAAGTTTAGGGATGAAATTAGAATGTTCA
1 AAAGTTTAAGGATCAAATTAAAATGTTCA
* *
41388 AAAGTTTAAGGA-CTAATTTAAAATGAGAGTC-
1 AAAGTTTAAGGATC-AAATTAAAAT--G-TTCA
* * * *
41419 AAAGTTTGAGGATGACATTAGAATGTTCA
1 AAAGTTTAAGGATCAAATTAAAATGTTCA
*
41448 AAAGTTTAAAGATCAAATTAAAATG
1 AAAGTTTAAGGATCAAATTAAAATG
41473 AGAATTATAG
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
28 2 0.03
29 40 0.63
31 19 0.30
32 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (29 bp):
AAAGTTTAAGGATCAAATTAAAATGTTCA
Found at i:42172 original size:83 final size:83
Alignment explanation
Indices: 42077--42302 Score: 319
Period size: 82 Copynumber: 2.7 Consensus size: 83
42067 AACGCCACAG
* * * * *
42077 TAGGGTTCATCTATAGTAGCATTTTTTCAACAAATACCGCAAAATAGTAGTACTTTAGCGGTGTT
1 TAGGGTTCATCTATAGTGGCATTTTTTCAACAAACACCGTAATAGAGTAGTACTTTAGCGGTGTT
*
42142 TTTATACAAATGCTGTAA
66 TTTATACAAATGCCGTAA
* * *
42160 TAGGGTTTATCTATAGTGGCA-TTTTTCAACAAACACCATAATAGAGTAGTACTTTAACGGTGTT
1 TAGGGTTCATCTATAGTGGCATTTTTTCAACAAACACCGTAATAGAGTAGTACTTTAGCGGTGTT
42224 TTTATACAAATGCCGTAA
66 TTTATACAAATGCCGTAA
* * * * *
42242 TAGAGTTCATATATAGTGGCGTTTTTTCAATAAACACCGTAATAGAGTAATACTTTAGCGG
1 TAGGGTTCATCTATAGTGGCATTTTTTCAACAAACACCGTAATAGAGTAGTACTTTAGCGG
42303 CATTTCTACA
Statistics
Matches: 125, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
82 71 0.57
83 54 0.43
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (83 bp):
TAGGGTTCATCTATAGTGGCATTTTTTCAACAAACACCGTAATAGAGTAGTACTTTAGCGGTGTT
TTTATACAAATGCCGTAA
Found at i:42266 original size:41 final size:40
Alignment explanation
Indices: 42139--42267 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 40
42129 CTTTAGCGGT
* * *
42139 GTTTTTATACAAATGCTGTAATAGGGTTTATCTATAGTGGC
1 GTTTTTATACAAATGCCGTAATAGAG-TTATATATAGTGGC
* ** * * ** *
42180 ATTTTTCA-ACAAACACCATAATAGAG-TAGTACTTTAACGGT
1 GTTTTT-ATACAAATGCCGTAATAGAGTTA-TA-TATAGTGGC
42221 GTTTTTATACAAATGCCGTAATAGAGTTCATATATAGTGGC
1 GTTTTTATACAAATGCCGTAATAGAGTT-ATATATAGTGGC
42262 GTTTTT
1 GTTTTT
42268 TCAATAAACA
Statistics
Matches: 63, Mismatches: 19, Indels: 12
0.67 0.20 0.13
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 54 0.86
42 4 0.06
43 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (40 bp):
GTTTTTATACAAATGCCGTAATAGAGTTATATATAGTGGC
Found at i:42327 original size:83 final size:82
Alignment explanation
Indices: 42048--42328 Score: 283
Period size: 83 Copynumber: 3.4 Consensus size: 82
42038 AATGGTACAA
* * * * *
42048 TTAGCGGCGTTTATACACAAACGCCACAGTAGGGTTCATCTATAGTAGCATTTTTTCAACAAATA
1 TTAGCGGCGTTTTTACACAAACGCCGCAATAGGGTTCATCTATAGTGGC-TTTTTTCAACAAACA
* * *
42113 CCGCAAAATAGTAGTACT
65 CCGTAATAGAGTAGTACT
* * * * * * *
42131 TTAGCGGTGTTTTTATACAAATGCTGTAATAGGGTTTATCTATAGTGGCATTTTTCAACAAACAC
1 TTAGCGGCGTTTTTACACAAACGCCGCAATAGGGTTCATCTATAGTGGCTTTTTTCAACAAACAC
*
42196 CATAATAGAGTAGTACT
66 CGTAATAGAGTAGTACT
* * * * * * * *
42213 TTAACGGTGTTTTTATACAAATGCCGTAATAGAGTTCATATATAGTGGCGTTTTTTCAATAAACA
1 TTAGCGGCGTTTTTACACAAACGCCGCAATAGGGTTCATCTATAGTGGC-TTTTTTCAACAAACA
*
42278 CCGTAATAGAGTAATACT
65 CCGTAATAGAGTAGTACT
* * **
42296 TTAGCGGCATTTCTACACAAACGTTGCAATAGG
1 TTAGCGGCGTTTTTACACAAACGCCGCAATAGG
42329 TATAATCTAT
Statistics
Matches: 162, Mismatches: 35, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
82 71 0.44
83 91 0.56
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (82 bp):
TTAGCGGCGTTTTTACACAAACGCCGCAATAGGGTTCATCTATAGTGGCTTTTTTCAACAAACAC
CGTAATAGAGTAGTACT
Found at i:42616 original size:20 final size:20
Alignment explanation
Indices: 42588--42722 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
42578 AATTGGGAAA
*
42588 ATCGAAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
42608 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
42628 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
42649 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
42669 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * * *
42689 TTCGCAACGCAATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
42709 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
42723 TTTCAAAGCG
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.69
21 23 0.25
22 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:42632 original size:61 final size:61
Alignment explanation
Indices: 42585--42713 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 61
42575 GCGAATTGGG
* * * * *
42585 AAAATCGAAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGAAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
42646 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCAATAATAC
1 AAAATCGAAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
42707 ATAATCG
1 AAAATCG
42714 CAATGCGATT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.24
Consensus pattern (61 bp):
AAAATCGAAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:42714 original size:61 final size:61
Alignment explanation
Indices: 42598--42716 Score: 166
Period size: 61 Copynumber: 2.0 Consensus size: 61
42588 ATCGAAATGC
* * * *
42598 GATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAATCGCAACGA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCAATAATACAAAATCGCAACGA
* * * *
42659 GATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCAATAATACATAATCGCAA
1 GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCAATAATACAAAATCGCAA
42717 TGCGATTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (61 bp):
GATACTGACTATCGCAACGCGATACTGACTATCGCAACGCAATAATACAAAATCGCAACGA
Found at i:43249 original size:20 final size:20
Alignment explanation
Indices: 43195--43253 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
43185 GCGATTCTCT
**
43195 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
43215 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
43235 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
43254 AGAAATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:43444 original size:25 final size:24
Alignment explanation
Indices: 43390--43444 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
43380 TGTTTATTAT
* *
43390 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
43414 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
43440 TGTTT
1 TGTTT
43445 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:44827 original size:21 final size:21
Alignment explanation
Indices: 44782--44828 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
44772 GTTAGGGTAG
* *
44782 TTACGTGATGAGGTCAATGCC
1 TTACGTGAGGAGGTCAATACC
* *
44803 TTACGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACC
44824 TTACG
1 TTACG
44829 CAAAGACGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACC
Found at i:45152 original size:19 final size:20
Alignment explanation
Indices: 45109--45153 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
45099 TGCAACACGA
45109 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
45129 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
45148 AAATGA
1 AAATGA
45154 AAATTGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:45176 original size:14 final size:14
Alignment explanation
Indices: 45153--45209 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
45143 ATGCGAAATG
*
45153 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
45167 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
45183 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
45199 AAAATCGCAAC
1 AAAATCGCAAC
45210 ACGAAATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:45200 original size:32 final size:33
Alignment explanation
Indices: 45137--45227 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
45127 GGAAATGGCT
*
45137 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
45170 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
**
45202 ATCGCAACACGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
45228 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:45265 original size:14 final size:14
Alignment explanation
Indices: 45246--45334 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
45236 GTGTTTCGCA
45246 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
45260 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
45276 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
45292 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
45309 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
45325 TTGCGATTTT
1 TTGCGATTTT
45335 CATTTCGCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 25 0.40
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:45308 original size:33 final size:33
Alignment explanation
Indices: 45239--45350 Score: 217
Period size: 33 Copynumber: 3.4 Consensus size: 33
45229 GCGATTTGTG
45239 TTTCGCATTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
45271 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
45304 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
45337 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
45351 AGCCATTTCC
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
32 27 0.34
33 52 0.66
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:45369 original size:20 final size:19
Alignment explanation
Indices: 45335--45390 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
45325 TTGCGATTTT
*
45335 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
45354 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
45374 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
45391 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:47278 original size:14 final size:14
Alignment explanation
Indices: 47259--47294 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47249 ATTGTTTAAT
47259 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
47273 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
47287 TGATTTGT
1 TGATTTGT
47295 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:47440 original size:14 final size:14
Alignment explanation
Indices: 47421--47474 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
47411 GAAACTGACT
47421 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
47435 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
47454 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
47468 ATCGCAA
1 ATCGCAA
47475 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:47523 original size:20 final size:20
Alignment explanation
Indices: 47506--47593 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
47496 CGATTTTCTA
*
47506 GTTGCGATAGCTATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
47526 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
47546 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
47566 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
47586 GTTGCGAT
1 GTTGCGAT
47594 TTCCCCGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 3 0.05
20 50 0.91
21 2 0.04
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:47832 original size:20 final size:20
Alignment explanation
Indices: 47807--47874 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
47797 TTGAAGATGA
47807 TTGCGATTTTTAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
*** *
47827 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTTAGAATCTCG
**
47847 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-TAGAATCTCG
47868 TTGCGAT
1 TTGCGAT
47875 AGTCAGTATC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCGATTTTTAGAATCTCG
Found at i:47871 original size:41 final size:40
Alignment explanation
Indices: 47806--47897 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
47796 TTTGAAGATG
*
47806 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
* ** * *
47846 GTTGCGATTTTGTATTATCTCGTTGCGATAGTCAGTATCGC
1 ATTGCGATTTT-TAGAATCTCGTTGCGAAAGTCAGAATCGC
47887 ATTGCGATTTT
1 ATTGCGATTTT
47898 CCAAATTCGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (40 bp):
ATTGCGATTTTTAGAATCTCGTTGCGAAAGTCAGAATCGC
Found at i:47927 original size:20 final size:21
Alignment explanation
Indices: 47883--47934 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
47873 ATAGTCAGTA
*
47883 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
47904 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
47924 TCGCATTGCGA
1 TCGCATTGCGA
47935 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:48746 original size:24 final size:24
Alignment explanation
Indices: 48719--48772 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
48709 GTATTCGAAA
* * *
48719 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTAGTCAACACCCGGAC
* *
48743 TTTGATATTAGTCAACACTCGGAT
1 TTTGATATTAGTCAACACCCGGAC
48767 TTTGAT
1 TTTGAT
48773 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTAGTCAACACCCGGAC
Found at i:48962 original size:6 final size:6
Alignment explanation
Indices: 48951--48983 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
48941 AATCCTGAAG
*
48951 AAGAAA AAGAAA AAGAAA AAGAAG AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
48984 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:51139 original size:42 final size:41
Alignment explanation
Indices: 51080--51285 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
51070 GTGAATCGGG
* *
51080 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
51122 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
51164 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAATGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
51206 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
51248 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
51286 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:51146 original size:21 final size:21
Alignment explanation
Indices: 51080--51146 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
51070 GTGAATCGGG
*
51080 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
51100 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
51122 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
51143 CTCT
1 CTCT
51147 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:51221 original size:84 final size:84
Alignment explanation
Indices: 51110--51284 Score: 341
Period size: 84 Copynumber: 2.1 Consensus size: 84
51100 CCTCTTCAAC
*
51110 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
51175 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
51194 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
51259 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
51278 GATGACA
1 GATGACA
51285 GGCGAGTCGG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (84 bp):
GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:51681 original size:91 final size:92
Alignment explanation
Indices: 51504--51688 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 92
51494 ATTTTAAACT
51504 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAGAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACA-AGTTTAGC
51569 AGAATTGGCAGCAACCGAATAAATTTAC
65 AGAATTGGCAGCAACCGAATAAATTTAC
*
51597 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-AC-AGTTTAG
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTTAG
*
51659 CAGTATTGGCAGCAACCGAATAAATTTAC
64 CAGAATTGGCAGCAACCGAATAAATTTAC
51688 T
1 T
51689 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 36 0.41
93 21 0.24
94 4 0.05
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTTAC
Found at i:53474 original size:19 final size:19
Alignment explanation
Indices: 53452--53497 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
53442 GCGACGAGAG
53452 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
53471 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
53490 AATCGCAA
1 AATCGCAA
53498 TACGATTTTG
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:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:53476 original size:33 final size:33
Alignment explanation
Indices: 53382--53480 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
53372 ACGAGATAAT
*
53382 GAGAATCGCAACGCGGAAATGACTATCACAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
53416 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
53449 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
53481 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:54162 original size:20 final size:20
Alignment explanation
Indices: 54134--54187 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
54124 GATTTTGTAT
*
54134 TATCACATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
54154 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
54174 TATCGCATTGCGAT
1 TATCGCATTGCGAT
54188 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:54318 original size:20 final size:20
Alignment explanation
Indices: 54293--54338 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
54283 CAACGCGAAT
*
54293 TTGCGATAATAGAGATCGCG
1 TTGCGATAATAGAGATCGCA
* *
54313 TTGCGA-ATTAGCGATCGCA
1 TTGCGATAATAGAGATCGCA
54332 TTGCGAT
1 TTGCGAT
54339 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCA
Found at i:57666 original size:43 final size:45
Alignment explanation
Indices: 57582--57673 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 45
57572 AAAGTAATTA
*
57582 GCGGCGTTTGTATCAAAAAAACGCCGCTATAAATATCGACCTTTT
1 GCGGCGTTTGTATCAAAAAAACGCCGCTATAAATATCGACCTGTT
* * * * *
57627 GCGGCGTTTGT-TC-CAAAAATGCCGCTATAGATCTTGACCTGTT
1 GCGGCGTTTGTATCAAAAAAACGCCGCTATAAATATCGACCTGTT
57670 GCGG
1 GCGG
57674 TATTTTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 28 0.68
44 2 0.05
45 11 0.27
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (45 bp):
GCGGCGTTTGTATCAAAAAAACGCCGCTATAAATATCGACCTGTT
Found at i:64742 original size:6 final size:6
Alignment explanation
Indices: 64731--64809 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
64721 GACACGTATT
* *
64731 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
64779 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
64810 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:64817 original size:5 final size:5
Alignment explanation
Indices: 64807--64845 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
64797 ACCACGACCA
* * *
64807 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
64846 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:70707 original size:6 final size:6
Alignment explanation
Indices: 70696--70872 Score: 327
Period size: 6 Copynumber: 29.5 Consensus size: 6
70686 GACACGTATT
70696 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
70744 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
70792 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
70840 ACCTCG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
70873 TCGAGCCGAG
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 169 1.00
ACGTcount: A:0.32, C:0.50, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:70884 original size:5 final size:5
Alignment explanation
Indices: 70874--70912 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
70864 ACCACGACCT
* * *
70874 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
70913 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:88834 original size:2 final size:2
Alignment explanation
Indices: 88829--88869 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
88819 TGTTTTTTTA
88829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88870 GTTTTTTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94105 original size:30 final size:28
Alignment explanation
Indices: 94052--94108 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
94042 ATAGAACCCA
* *
94052 AAATAAAAACCGGATATCCTAATGGGCT
1 AAATAAAAACCGAATACCCTAATGGGCT
94080 AAATAAAAAACCCGAATACCCTAATGGGC
1 AAAT-AAAAA-CCGAATACCCTAATGGGC
94109 CAAAAATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 16 0.64
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.18
Consensus pattern (28 bp):
AAATAAAAACCGAATACCCTAATGGGCT
Done.