Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001337.1 Hibiscus syriacus cultivar Beakdansim tig00002611_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: 79935
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:281 original size:11 final size:11
Alignment explanation
Indices: 265--324 Score: 65
Period size: 11 Copynumber: 5.8 Consensus size: 11
255 TAAAATTACA
265 ATATTAAAAAT
1 ATATTAAAAAT
276 ATATTAAAAAT
1 ATATTAAAAAT
**
287 ATA-TAATGAT
1 ATATTAAAAAT
*
297 A-ATTATAAA-
1 ATATTAAAAAT
306 AT-TTAAAAAT
1 ATATTAAAAAT
316 ATATTAAAA
1 ATATTAAAA
325 TTCTATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 8 0.21
10 11 0.28
11 20 0.51
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATATTAAAAAT
Found at i:758 original size:7 final size:7
Alignment explanation
Indices: 746--842 Score: 53
Period size: 7 Copynumber: 14.0 Consensus size: 7
736 TAATTAACCT
746 TAAATCC
1 TAAATCC
753 TAAATCC
1 TAAATCC
760 TAAATCC
1 TAAATCC
*
767 TAAACCC
1 TAAATCC
*
774 T--ATAC
1 TAAATCC
*
779 TATAAACC
1 TA-AATCC
*
787 ATAAACCC
1 -TAAATCC
795 TAAA--C
1 TAAATCC
*
800 TCAAAACC
1 T-AAATCC
808 ATAAA-CC
1 -TAAATCC
815 TTAAATCC
1 -TAAATCC
823 TAAA-CC
1 TAAATCC
*
829 TAAACCC
1 TAAATCC
836 TAAATCC
1 TAAATCC
843 AATTATATGA
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
5 5 0.07
6 9 0.12
7 43 0.60
8 12 0.17
9 3 0.04
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAATCC
Found at i:765 original size:14 final size:13
Alignment explanation
Indices: 741--839 Score: 67
Period size: 14 Copynumber: 7.2 Consensus size: 13
731 ATTTGTAATT
741 AACCTTAAATCCTA
1 AACC-TAAATCCTA
755 AATCCTAAATCCTA
1 AA-CCTAAATCCTA
* *
769 AACCCTATA-CTATA
1 AA-CCTAAATC-CTA
*
783 AACCATAAACCCTA
1 AACC-TAAATCCTA
*
797 AA-CTCAAAACCATA
1 AACCT-AAATCC-TA
811 AACCTTAAATCCTA
1 AACC-TAAATCCTA
*
825 AACCTAAACCCTA
1 AACCTAAATCCTA
838 AA
1 AA
840 TCCAATTATA
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
12 1 0.01
13 19 0.28
14 39 0.57
15 9 0.13
16 1 0.01
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.22
Consensus pattern (13 bp):
AACCTAAATCCTA
Found at i:775 original size:21 final size:22
Alignment explanation
Indices: 741--842 Score: 92
Period size: 21 Copynumber: 4.9 Consensus size: 22
731 ATTTGTAATT
* *
741 AACCTTAAATCCTAAATCCTAA
1 AACCATAAACCCTAAATCCTAA
* *
763 ATCC-TAAACCCT--ATACTATA
1 AACCATAAACCCTAAATCCTA-A
783 AACCATAAACCCTAAA--CTCAA
1 AACCATAAACCCTAAATCCT-AA
*
804 AACCATAAACCTTAAATCCT-A
1 AACCATAAACCCTAAATCCTAA
825 AACC-TAAACCCTAAATCC
1 AACCATAAACCCTAAATCC
843 AATTATATGA
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.07
20 17 0.25
21 38 0.57
22 4 0.06
23 3 0.04
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (22 bp):
AACCATAAACCCTAAATCCTAA
Found at i:2902 original size:14 final size:14
Alignment explanation
Indices: 2885--2912 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2875 ATATATATAT
2885 ATATGTGCGCGCGC
1 ATATGTGCGCGCGC
2899 ATATGTGCGCGCGC
1 ATATGTGCGCGCGC
2913 GCGCATGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.36, T:0.21
Consensus pattern (14 bp):
ATATGTGCGCGCGC
Found at i:5882 original size:18 final size:18
Alignment explanation
Indices: 5859--5916 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
5849 AAGAAGAAGA
5859 AAGTTAATTAATGTAATC
1 AAGTTAATTAATGTAATC
* * **
5877 AAGTT-ATTTACG-AAGA
1 AAGTTAATTAATGTAATC
5893 AAGTTAATTAATGTAATC
1 AAGTTAATTAATGTAATC
5911 AAGTTA
1 AAGTTA
5917 TTTACTTACA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
16 7 0.23
17 10 0.33
18 13 0.43
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (18 bp):
AAGTTAATTAATGTAATC
Found at i:5897 original size:34 final size:34
Alignment explanation
Indices: 5854--5921 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
5844 AGAAGAAGAA
5854 GAAGAAAGTTAATTAATGTAATCAAGTTATTTAC
1 GAAGAAAGTTAATTAATGTAATCAAGTTATTTAC
5888 GAAGAAAGTTAATTAATGTAATCAAGTTATTTAC
1 GAAGAAAGTTAATTAATGTAATCAAGTTATTTAC
5922 TTACAGAGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (34 bp):
GAAGAAAGTTAATTAATGTAATCAAGTTATTTAC
Found at i:10794 original size:3 final size:3
Alignment explanation
Indices: 10788--10843 Score: 78
Period size: 3 Copynumber: 18.0 Consensus size: 3
10778 ATATTTATAT
10788 TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
10834 TTA TATA TTA
1 TTA T-TA TTA
10844 CAGGCCCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.04
3 39 0.80
4 8 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:10794 original size:15 final size:15
Alignment explanation
Indices: 10776--10839 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
10766 TTTGGTTTTT
10776 TTATATTTATATTTA
1 TTATATTTATATTTA
10791 TTATATTTAT-TATTA
1 TTATATTTATAT-TTA
*
10806 TTAT-TAT-TA-TTA
1 TTATATTTATATTTA
10818 TTAT-TATTATTATTTA
1 TTATAT-TTA-TATTTA
10834 TTATAT
1 TTATAT
10840 ATTACAGGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
12 8 0.20
13 2 0.05
14 3 0.08
15 19 0.47
16 7 0.17
17 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTATATTTA
Found at i:10796 original size:9 final size:9
Alignment explanation
Indices: 10782--10839 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
10772 TTTTTTATAT
10782 TTATATTTA
1 TTATATTTA
10791 TTATATTTA
1 TTATATTTA
10800 -T-TA-TTA
1 TTATATTTA
10806 TTAT-TATTA
1 TTATAT-TTA
10815 TTAT-TATTA
1 TTATAT-TTA
10824 TTATTATTTA
1 TTA-TATTTA
10834 TTATAT
1 TTATAT
10840 ATTACAGGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 2 0.05
9 27 0.63
10 7 0.16
11 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATTTA
Found at i:12212 original size:22 final size:21
Alignment explanation
Indices: 12182--12235 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
12172 AATTTTATTT
12182 TTATATATTTAAATTAATAATAA
1 TTAT-TATTTAAA-TAATAATAA
* * *
12205 TTATTATTTTAATCATATTAA
1 TTATTATTTAAATAATAATAA
12226 TATATTATTT
1 T-TATTATTT
12236 GATTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATTTAAATAATAATAA
Found at i:12537 original size:140 final size:140
Alignment explanation
Indices: 12262--12529 Score: 312
Period size: 140 Copynumber: 1.9 Consensus size: 140
12252 AATTTTATAA
* * * *
12262 TAATGTTTATTTATTTTTTAATATCAAAGAAAATGGCAATCTTAAAGCAACTAGATGTCTGTTTT
1 TAATATTTATTTATTTTTTAATATCAAAGAAAATGGCAATCTTAAAACAACTAGAAGTCTCTTTT
* * * * *** *
12327 CTGATATTTTTAAATAAATAAATATTTTACTTTTATAAATTGTATATATTAATCTATTTTTTTAG
66 CTGATATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAG
12392 ATAAATATTT
131 ATAAATATTT
* ** *
12402 TAATATTTATTTATTTTTTAATATCAAAGGAAA-GAGCTGTCTTAAAACACCTAGAAG-CTCTTT
1 TAATATTTATTTATTTTTTAATATCAAAGAAAATG-GCAATCTTAAAACAACTAGAAGTCTCTTT
* *
12465 TCTGTTATTTCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAAT-TTACT-TAAAATTA
65 TCTGATATTTCTAAATAAATAAATATCTTACTTT-TATAAATT-ATAAATATTAATCTAAAATTA
12527 TAG
128 TAG
12530 TAATAAATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
138 10 0.09
139 45 0.42
140 52 0.49
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (140 bp):
TAATATTTATTTATTTTTTAATATCAAAGAAAATGGCAATCTTAAAACAACTAGAAGTCTCTTTT
CTGATATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAG
ATAAATATTT
Found at i:13070 original size:14 final size:15
Alignment explanation
Indices: 13044--13076 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
13034 TTAATATTTC
13044 ATTTTACTTACAAGT
1 ATTTTACTTACAAGT
*
13059 ATTTTA-TTACAATT
1 ATTTTACTTACAAGT
13073 ATTT
1 ATTT
13077 ATTTTTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTTACTTACAAGT
Found at i:14645 original size:14 final size:14
Alignment explanation
Indices: 14606--14660 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
14596 TTTACGTTTG
*
14606 TATTTACATTTACA
1 TATTTACATTTGCA
*
14620 TTTTTACATTTGCA
1 TATTTACATTTGCA
14634 TATTTACATTTGGCA
1 TATTTACATTT-GCA
* *
14649 TCTTTGCATTTG
1 TATTTACATTTG
14661 TATTTTCATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.53
Consensus pattern (14 bp):
TATTTACATTTGCA
Found at i:19795 original size:114 final size:114
Alignment explanation
Indices: 19595--19814 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
19585 CACGTTCTCA
* * *
19595 TAGTAGAAATAAGGAGACCTAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
19660 GGTATGAACCCCAAAATCAATCATTAGATTTGAAAGATGAATTTGCTCG
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCG
*
19709 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
19774 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAA
19815 CTGCATGATC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCG
Found at i:21968 original size:54 final size:53
Alignment explanation
Indices: 21884--22039 Score: 222
Period size: 54 Copynumber: 2.9 Consensus size: 53
21874 AGAAATCTTG
* * *
21884 GCAGAAACCACAGAAAATGATGAATGTGTTGTCAAACGCTTTACGAACATCTGA
1 GCAGAAACCACAG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
21938 GCAGAAACCACATGAAAGGATGAATTTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAACCACA-GAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * *
21992 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 GCAGAAACCACA-GAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
22040 CTGCTATTCT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
54 91 0.99
55 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (53 bp):
GCAGAAACCACAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:22437 original size:22 final size:22
Alignment explanation
Indices: 22406--22460 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
22396 ATCTACACTC
*
22406 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
22428 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
*
22450 TTCAAATATGA
1 TTCAAAGATGA
22461 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:23029 original size:113 final size:113
Alignment explanation
Indices: 22899--23410 Score: 794
Period size: 113 Copynumber: 4.5 Consensus size: 113
22889 AGTTCATAAT
* *
22899 AAGAACTCATCTAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCG
1 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCG
22964 AATTCATCATTTGATGGATCAGCATTACCAGGTCAAGTTCATAATGAG
66 AATTCATCATTTGATGGATCAGCATTACCAGGTCAAGTTCATAATGAG
* *
23012 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTTG
1 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCG
*
23077 AATTCATCATTTGATGGATCAGCATTACTAGGTCAAGTTCATAATGAG
66 AATTCATCATTTGATGGATCAGCATTACCAGGTCAAGTTCATAATGAG
* *
23125 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTG
1 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCG
* * *
23190 AATTCATCATTTGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAG
66 AATTCATCATTTGATGGATCAGCATTACCAGGTCAAGTTCATAATGAG
* *
23238 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCA
1 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCG
* * * * * * *
23303 AATTCATCACTCGATAGATCAACTTTTCCAGAG--AGAGTTTATAATGAG
66 AATTCATCATTTGATGGATCAGCATTACCAG-GTCA-AGTTCATAATGAG
* *
23351 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
1 AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTT
23411 GCATGATTCT
Statistics
Matches: 371, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
113 365 0.98
114 6 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTCGCTCG
AATTCATCATTTGATGGATCAGCATTACCAGGTCAAGTTCATAATGAG
Found at i:23687 original size:3 final size:3
Alignment explanation
Indices: 23681--23744 Score: 94
Period size: 3 Copynumber: 20.7 Consensus size: 3
23671 TTATATTTAA
23681 TAT TAT TAT TAT TAT T-T TAT TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
23726 TAT TATT TAT TAT ATAT TA
1 TAT TA-T TAT TAT -TAT TA
23745 CAGGCCCAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.04
3 46 0.81
4 9 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25424 original size:140 final size:140
Alignment explanation
Indices: 25149--25416 Score: 312
Period size: 140 Copynumber: 1.9 Consensus size: 140
25139 AATTTTATAA
* * * * *
25149 TAATGTTTATTTATTTTTTAATATCAAAGAAAATGACAGTCTTAAAGCAACTAGATGTCTGTTTT
1 TAATATTTATTTATATTTTAATATCAAAGAAAATGACAGTCTTAAAACAACTAGAAGTCTCTTTT
* * * * *** *
25214 CTGATATTTTTAAATAAATAAATATTTTACTTTTATAAATTGTATATATTAATCTATTTTTTTAG
66 CTGATATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAG
25279 ATAAATGTTT
131 ATAAATGTTT
* * * *
25289 TAATATTTATTTATATTTTAATATCAAAGGAAA-GAGCTGTCTTAAAATACCTAGAAG-CTCTTT
1 TAATATTTATTTATATTTTAATATCAAAGAAAATGA-CAGTCTTAAAACAACTAGAAGTCTCTTT
*
25352 TCTGATATTTCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAAT-TTACT-TAAAATTA
65 TCTGATATTTCTAAATAAATAAATATCTTACTTT-TATAAATT-ATAAATATTAATCTAAAATTA
25414 TAG
128 TAG
25417 TAATAAATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
138 10 0.09
139 47 0.44
140 50 0.47
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (140 bp):
TAATATTTATTTATATTTTAATATCAAAGAAAATGACAGTCTTAAAACAACTAGAAGTCTCTTTT
CTGATATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAAAATTATAG
ATAAATGTTT
Found at i:26143 original size:14 final size:14
Alignment explanation
Indices: 26109--26152 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
26099 CGATAATCCG
**
26109 TTCGTTTATGTTTG
1 TTCGTTTATGTTCA
*
26123 TTTGTTTATGTTCA
1 TTCGTTTATGTTCA
*
26137 TTCGTTTATGATCA
1 TTCGTTTATGTTCA
26151 TT
1 TT
26153 TATGCTCTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.61
Consensus pattern (14 bp):
TTCGTTTATGTTCA
Found at i:28086 original size:21 final size:21
Alignment explanation
Indices: 28062--28102 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28052 AATGTTACTT
*
28062 CTCTCTCTGCTTCTATCGCTG
1 CTCTATCTGCTTCTATCGCTG
*
28083 CTCTATCTGCTTCTCTCGCT
1 CTCTATCTGCTTCTATCGCT
28103 TCAGCTTCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.39, G:0.12, T:0.44
Consensus pattern (21 bp):
CTCTATCTGCTTCTATCGCTG
Found at i:32810 original size:21 final size:21
Alignment explanation
Indices: 32786--32826 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
32776 GGCTTAAAAT
*
32786 CACCCAAAAATAACCCCAAAC
1 CACCCAAAAACAACCCCAAAC
32807 CACCCAAAAACAACCCCAAA
1 CACCCAAAAACAACCCCAAA
32827 ACCTTTCGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.44, G:0.00, T:0.02
Consensus pattern (21 bp):
CACCCAAAAACAACCCCAAAC
Found at i:33652 original size:11 final size:11
Alignment explanation
Indices: 33622--33661 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
33612 GTAATTAATT
33622 TATAATAAATAA
1 TATAAT-AATAA
33634 TCATAATAATAA
1 T-ATAATAATAA
*
33646 TATAATAATAG
1 TATAATAATAA
33657 TATAA
1 TATAA
33662 AAATCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 14 0.54
12 7 0.27
13 5 0.19
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (11 bp):
TATAATAATAA
Found at i:39199 original size:41 final size:41
Alignment explanation
Indices: 39107--39287 Score: 136
Period size: 41 Copynumber: 4.3 Consensus size: 41
39097 CGAGTCTTTA
* * *
39107 GCGGCGTTTGTATAAAAACGCCACTATAGATAAT-CT-TATT
1 GCGGCATTTGTATAAAAACGCCACTACA-ATACTACTCTATT
* * *
39147 GTGGCATTTTGTATAAAAACGCCGCTA-AAGCACTACTCTATT
1 GCGGCA-TTTGTATAAAAACGCCACTACAA-TACTACTCTATT
* *
39189 GCGGCATTTGT-TGAAAAAACGCCACTACTATATATTAACCCTATT
1 GCGGCATTTGTAT--AAAAACGCCACTAC-A-ATACT-ACTCTATT
* * * *
39234 GCGTCATTTGTATAACAACGCCGCTACAATACTTCTCTATT
1 GCGGCATTTGTATAAAAACGCCACTACAATACTACTCTATT
**
39275 GCGGTGTTTGTAT
1 GCGGCATTTGTAT
39288 TCCAAACGAC
Statistics
Matches: 111, Mismatches: 19, Indels: 21
0.74 0.13 0.14
Matches are distributed among these distances:
39 1 0.01
40 8 0.07
41 42 0.38
42 25 0.23
43 1 0.01
44 15 0.14
45 18 0.16
46 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
GCGGCATTTGTATAAAAACGCCACTACAATACTACTCTATT
Found at i:39362 original size:20 final size:20
Alignment explanation
Indices: 39339--39380 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
39329 TAAAAACGCC
39339 GCTAAATTTACCATTTTATG
1 GCTAAATTTACCATTTTATG
* *
39359 GCTAAATTTACCCTTTTGTG
1 GCTAAATTTACCATTTTATG
39379 GC
1 GC
39381 ATTTAGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (20 bp):
GCTAAATTTACCATTTTATG
Found at i:42873 original size:22 final size:24
Alignment explanation
Indices: 42848--42897 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
42838 ATTTTAAAAA
*
42848 TTTTAAAGATTTAA-ATTA-ATTT
1 TTTTAAAGAGTTAATATTATATTT
* *
42870 TTTTGAAGAGTTAATTTTATATTT
1 TTTTAAAGAGTTAATATTATATTT
42894 TTTT
1 TTTT
42898 CAAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (24 bp):
TTTTAAAGAGTTAATATTATATTT
Found at i:42965 original size:27 final size:27
Alignment explanation
Indices: 42931--42983 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
42921 CTAACTAAAT
42931 TTTTTGAAAATTTAAAAGTTTGGGGAA
1 TTTTTGAAAATTTAAAAGTTTGGGGAA
*
42958 TTTTTGAAAATTTAGAAGTTTGGGGA
1 TTTTTGAAAATTTAAAAGTTTGGGGA
42984 CATGGTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.42
Consensus pattern (27 bp):
TTTTTGAAAATTTAAAAGTTTGGGGAA
Found at i:50234 original size:2 final size:2
Alignment explanation
Indices: 50229--50271 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
50219 TTTAAGGTAA
50229 AT AT AT 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 AT AT AT
50271 A
1 A
50272 ATAACATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51520 original size:3 final size:3
Alignment explanation
Indices: 51508--51554 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
51498 AAAATATTAG
51508 ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT ATT AATT A-T ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT -ATT
51552 ATT
1 ATT
51555 TTGCAAGACC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.15
3 27 0.69
4 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:51527 original size:14 final size:14
Alignment explanation
Indices: 51508--51553 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
51498 AAAATATTAG
51508 ATTATATTATTATT
1 ATTATATTATTATT
51522 ATTATATTATTATT
1 ATTATATTATTATT
51536 ATTA-ATTA-TATT
1 ATTATATTATTATT
51548 AATTAT
1 -ATTAT
51554 TTTGCAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.13
13 8 0.27
14 18 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATATTATTATT
Found at i:53762 original size:18 final size:17
Alignment explanation
Indices: 53723--53755 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53713 ACCTTTTTCC
*
53723 TTTAATTTTTATTTTAT
1 TTTACTTTTTATTTTAT
53740 TTTACTTTTT-TTTTAT
1 TTTACTTTTTATTTTAT
53756 CATTTACATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTACTTTTTATTTTAT
Found at i:55706 original size:14 final size:13
Alignment explanation
Indices: 55674--55717 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
55664 ACAAAAAGAG
55674 AAAAGAAGAAAAAA
1 AAAAG-AGAAAAAA
*
55688 TAAAGAGAAAATAA
1 AAAAGAGAAAA-AA
55702 AAAAGAGAAACAAA
1 AAAAGAGAAA-AAA
55716 AA
1 AA
55718 CAAATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 6 0.23
14 19 0.73
15 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAGAGAAAAAA
Found at i:55716 original size:13 final size:12
Alignment explanation
Indices: 55674--55742 Score: 50
Period size: 12 Copynumber: 5.5 Consensus size: 12
55664 ACAAAAAGAG
55674 AAAAGAAGAAAAA
1 AAAAG-AGAAAAA
55687 ATAAAGAGAAAATAA
1 A-AAAGAG-AAA-AA
*
55702 AAAAGAGAAACA
1 AAAAGAGAAAAA
* **
55714 AAAACA-AATGA
1 AAAAGAGAAAAA
*
55725 AAAAGAGAAGAA
1 AAAAGAGAAAAA
55737 AAAAGA
1 AAAAGA
55743 CAAGACGCAC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
11 8 0.18
12 15 0.33
13 6 0.13
14 13 0.29
15 3 0.07
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAAGAGAAAAA
Found at i:55739 original size:35 final size:35
Alignment explanation
Indices: 55666--55742 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
55656 CAATCAGAAC
* *
55666 AAAAAGAGAAAAGAAGAAAAAATAAAGAGAAAATA
1 AAAAAGAGAAAAGAAGAAAAAATAAAAAGAAAAGA
* *
55701 AAAAAGAGAAACA-AA-AACAAATGAAAAAGAGAAGA
1 AAAAAGAGAAA-AGAAGAAAAAAT-AAAAAGAAAAGA
55736 AAAAAGA
1 AAAAAGA
55743 CAAGACGCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.17
35 29 0.81
36 1 0.03
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.04
Consensus pattern (35 bp):
AAAAAGAGAAAAGAAGAAAAAATAAAAAGAAAAGA
Found at i:56857 original size:32 final size:32
Alignment explanation
Indices: 56788--56865 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
56778 ATGAGGAACA
56788 ATTGGGGCATCTTTGAAGATTCAACATCAAAT
1 ATTGGGGCATCTTTGAAGATTCAACATCAAAT
* **
56820 GTTGGGGCATCTTATG-AGATTCAACATTGAAT
1 ATTGGGGCATCTT-TGAAGATTCAACATCAAAT
*
56852 ATT-GGGAATCTTTG
1 ATTGGGGCATCTTTG
56866 GGAATTCAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.05
31 8 0.20
32 28 0.70
33 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (32 bp):
ATTGGGGCATCTTTGAAGATTCAACATCAAAT
Found at i:57198 original size:64 final size:64
Alignment explanation
Indices: 57089--57393 Score: 454
Period size: 64 Copynumber: 4.8 Consensus size: 64
57079 GTGAAGGGTA
*
57089 TTTC-AGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAAC
1 TTTCTAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC
** *
57152 TTTCTAGTTTCATTCAGAGTCAATTTCAACTTCTTAGCGAATGATATTGGACTCAACAAACAAC
1 TTTCTAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC
* *
57216 TTTCTATTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT-GACTCAACAAACAAC
1 TTTCTAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC
* * * * *
57279 TTTCTATTTTCATTCAGATTCAATTTCAACTTTACAACGAAGGATATTGGACTCAACAAATAAC
1 TTTCTAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC
* * *
57343 TTT-TCAGTTTCATTCAGAGTTAATTTCAACTTCACAACGAAGTATATTGGA
1 TTTCT-AGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGA
57394 TTCGAAACAA
Statistics
Matches: 221, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
63 65 0.29
64 156 0.71
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (64 bp):
TTTCTAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC
Found at i:57325 original size:127 final size:127
Alignment explanation
Indices: 57089--57391 Score: 457
Period size: 127 Copynumber: 2.4 Consensus size: 127
57079 GTGAAGGGTA
* *
57089 TTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAACTT
1 TTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT-GACTCAACAAACAACTT
* * *
57154 TCTAGTTTCATTCAGAGTCAATTTCAACTTCTTAGCGAATGATATTGGACTCAACAAACAAC-
65 TCTAGTTTCATTCAGAGTCAATTTCAACTTCTCAACGAAGGATATTGGACTCAACAAACAACT
* *
57216 TTTCTATTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATTGACTCAACAAACAACTT
1 TTTC-AGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGACTCAACAAACAACTT
* * *
57281 TCTATTTTCATTCAGATTCAATTTCAACTT-TACAACGAAGGATATTGGACTCAACAAATAACT
65 TCTAGTTTCATTCAGAGTCAATTTCAACTTCT-CAACGAAGGATATTGGACTCAACAAACAACT
* *
57344 TTTCAGTTTCATTCAGAGTTAATTTCAACTTCACAACGAAGTATATTG
1 TTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTG
57392 GATTCGAAAC
Statistics
Matches: 160, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
126 1 0.01
127 114 0.71
128 45 0.28
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (127 bp):
TTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGACTCAACAAACAACTTT
CTAGTTTCATTCAGAGTCAATTTCAACTTCTCAACGAAGGATATTGGACTCAACAAACAACT
Found at i:57895 original size:156 final size:156
Alignment explanation
Indices: 57611--57943 Score: 479
Period size: 156 Copynumber: 2.1 Consensus size: 156
57601 AGATTGGATT
* * * ** *
57611 TCAACTTCACAGCGAAGGAGCGTCTGTCAACAAATAACTTTCCAGTTTCATTCAGAGTTAATTTT
1 TCAACTTCACAGCGAAGGAGCGTATGTCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATTTC
* * * *
57676 AACTTCACAGTGAAGGATATTGGACTTGAAAAAATGCAACTTACACAAGATTGAATTTTAACTTA
66 AACTTCACAGTGAAGGATATTAGACTCGAAAAAATACAACTTACACAAGATTGAATTTCAACTTA
* * *
57741 ACGACGAATGATATCCAATTCAAAGC
131 ACAACGAAAGATATCAAATTCAAAGC
*
57767 TCAACTTCACAGCGAAGGAGCGTATGTCAACAAACAACTTCCCAGTTTCATTCGGAGCCAATTTC
1 TCAACTTCACAGCGAAGGAGCGTATGTCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATTTC
* *
57832 AACTTCATAGTGAAGGATATTAGACTCGAAACAATACAACTTACACAAGATT-AGATTTCAACTT
66 AACTTCACAGTGAAGGATATTAGACTCGAAAAAATACAACTTACACAAGATTGA-ATTTCAACTT
*
57896 CACAACGAAAGATATCAAATTCAAAGC
130 AACAACGAAAGATATCAAATTCAAAGC
* *
57923 TCAACTTTACAGCGAATGAGC
1 TCAACTTCACAGCGAAGGAGC
57944 CATCCACGAT
Statistics
Matches: 157, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
155 1 0.01
156 156 0.99
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (156 bp):
TCAACTTCACAGCGAAGGAGCGTATGTCAACAAACAACTTCCCAGTTTCATTCAGAGCCAATTTC
AACTTCACAGTGAAGGATATTAGACTCGAAAAAATACAACTTACACAAGATTGAATTTCAACTTA
ACAACGAAAGATATCAAATTCAAAGC
Found at i:58194 original size:85 final size:84
Alignment explanation
Indices: 58062--58318 Score: 325
Period size: 85 Copynumber: 3.0 Consensus size: 84
58052 TACAACATAG
* * * * *
58062 CTCAAGGTGATAAGGGCTATCTGTCAACTAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGAC
1 CTCAAGGCGAGAAGGGCTATCTGTC-ACAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGC
58127 ATATCAAATTTACAGTATAA
65 ATATCAAATTTACAGTATAA
* *
58147 CTCAAGGCGAGAAGGGTTATCTGTCAGCAAAGACCTTTGAGTTCGATTACATTTAGCTCAAAGGC
1 CTCAAGGCGAGAAGGGCTATCTGTCA-CAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGC
* * ** *
58212 ATATTAAATTTGCAACATAG
65 ATATCAAATTTACAGTATAA
* * * * *
58232 CTCAAGGCGAGAAGGACTATCTGTCCACAAATACCTTTGAGTTTGATTCCATTCAGCTCAAGGGC
1 CTCAAGGCGAGAAGGGCTATCTGT-CACAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGC
*
58297 ATGTCAAATTTACAGTATAA
65 ATATCAAATTTACAGTATAA
58317 CT
1 CT
58319 TAAGTTGGGA
Statistics
Matches: 145, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 142 0.98
86 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (84 bp):
CTCAAGGCGAGAAGGGCTATCTGTCACAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCA
TATCAAATTTACAGTATAA
Found at i:59642 original size:13 final size:13
Alignment explanation
Indices: 59626--59672 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
59616 CATAATGAAA
*
59626 ATAAATAAATAGT
1 ATAAATAAATAAT
59639 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
59653 A-AAATAAA-AAT
1 ATAAATAAATAAT
*
59664 ATATATAAA
1 ATAAATAAA
59673 ATATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 4 0.13
12 9 0.30
13 10 0.33
14 7 0.23
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:59659 original size:17 final size:17
Alignment explanation
Indices: 59639--59682 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
59629 AATAAATAGT
59639 ATAAATAAAATA-ATAAA
1 ATAAA-AAAATATATAAA
*
59656 ATAAAAATATATATAAA
1 ATAAAAAAATATATAAA
*
59673 ATATAAAAAT
1 ATAAAAAAAT
59683 GTATGTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAAATATATAAA
Found at i:59678 original size:19 final size:19
Alignment explanation
Indices: 59656--59697 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
59646 AAATAATAAA
59656 ATAAAAATATATATAAAAT
1 ATAAAAATATATATAAAAT
* * *
59675 ATAAAAATGTATGTATAAT
1 ATAAAAATATATATAAAAT
59694 ATAA
1 ATAA
59698 TAAAATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAAAAATATATATAAAAT
Found at i:59682 original size:25 final size:26
Alignment explanation
Indices: 59628--59680 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
59618 TAATGAAAAT
*
59628 AAATAAATAGTATAAATAAAATAATA
1 AAATAAATAATATAAATAAAATAATA
*
59654 AAATAAA-AATATATATAAAAT-ATA
1 AAATAAATAATATAAATAAAATAATA
59678 AAA
1 AAA
59681 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 12 0.48
26 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (26 bp):
AAATAAATAATATAAATAAAATAATA
Found at i:59960 original size:23 final size:24
Alignment explanation
Indices: 59925--59972 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
59915 ACGCAAAGAA
59925 AAATGAAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAAA-TATAATTAAAT
*
59949 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
59972 A
1 A
59973 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:60429 original size:37 final size:37
Alignment explanation
Indices: 60388--60480 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
60378 ATGCTTGTGG
* * *
60388 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* * ** *
60425 ATCCTATTTTTAGAAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
60462 ATCATATTTTTAGGAGTTT
1 ATCCTATTTTTAGGAGTTT
60481 GAATCCTAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:61292 original size:20 final size:20
Alignment explanation
Indices: 61267--61312 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
61257 TCGTGAAGTT
61267 GAAATTGGCTCTGGAATCGG
1 GAAATTGGCTCTGGAATCGG
61287 GAAATTGGCTCTGGAATCGG
1 GAAATTGGCTCTGGAATCGG
61307 GAAATT
1 GAAATT
61313 ATTTGTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (20 bp):
GAAATTGGCTCTGGAATCGG
Found at i:61472 original size:106 final size:106
Alignment explanation
Indices: 61287--62428 Score: 1827
Period size: 106 Copynumber: 10.8 Consensus size: 106
61277 CTGGAATCGG
* * * * * *
61287 GAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACAACCAGCCGTCCCTCCGTTGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* * *
61352 ACTTGTGTTGTCTCGAGTCCAATATCCTTTGTTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* * *
61393 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACTAGCAGTCCCTTCATCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
61458 ACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* * *
61499 GAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACTAGCGGTCCCTTCGTTGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
61564 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* *
61605 GAAATTGGCTCTGAAATTGAGAATTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
61670 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* *
61711 GAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
61776 ACTTGCGTTGTCTGGAGTCTAATATCTTTCGTTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* *
61817 GAAATTGGCTCCGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* * *
61882 ACTTGCGTTGTATCGAGTCCAATATCCTTCGCTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* *
61923 GAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
61988 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* * * * *
62029 GAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACTAGCGGTCCCTTCGTCATGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
** *
62094 ACTTGCGTTGTCTTAAGTCCAATATCCTTCATTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* *
62135 GAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
62199 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
*
62240 GAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
62305 ACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTT
66 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
* * * * *
62346 GAAATTAGCTCTGAATTTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGA
1 GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
62411 ACTTGTGTTGTCTCGAGT
66 ACTTGCGTTGTCTGGAGT
62429 GGCACGATAT
Statistics
Matches: 970, Mismatches: 65, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
105 98 0.10
106 872 0.90
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
Found at i:63428 original size:22 final size:21
Alignment explanation
Indices: 63373--63428 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
63363 ATTGTGTTTG
*
63373 GTCAAAGGTTTGGCATTTGAT
1 GTCAAAAGTTTGGCATTTGAT
*
63394 GTTAAAAGATTTGGCATTTGAT
1 GTCAAAAG-TTTGGCATTTGAT
*
63416 GCTCAAATGTTTG
1 G-TCAAAAGTTTG
63429 ATGGGGTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 6 0.21
22 18 0.62
23 5 0.17
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (21 bp):
GTCAAAAGTTTGGCATTTGAT
Found at i:64077 original size:15 final size:14
Alignment explanation
Indices: 64049--64098 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 14
64039 TTCTTTTTGA
*
64049 TTTTTGTTCTTTCT
1 TTTTTGTTTTTTCT
64063 TTTTTGTTTTCTTCT
1 TTTTTGTTTT-TTCT
64078 TTTTTGCTTCTTTTCT
1 TTTTTG-TT-TTTTCT
64094 TTTTT
1 TTTTT
64099 TTATTTTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 9 0.28
15 10 0.31
16 11 0.34
17 2 0.06
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTTTGTTTTTTCT
Found at i:64106 original size:15 final size:15
Alignment explanation
Indices: 64049--64098 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
64039 TTCTTTTTGA
*
64049 TTTTTG-TTCTTTCT
1 TTTTTGTTTTTTTCT
*
64063 TTTTTGTTTTCTTCT
1 TTTTTGTTTTTTTCT
*
64078 TTTTTGCTTCTTTTCT
1 TTTTTG-TTTTTTTCT
64094 TTTTT
1 TTTTT
64099 TTATTTTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 6 0.20
15 12 0.40
16 12 0.40
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTTGTTTTTTTCT
Found at i:67469 original size:19 final size:19
Alignment explanation
Indices: 67436--67472 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
67426 TGCAGATGAT
67436 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
67455 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
67473 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:68767 original size:13 final size:13
Alignment explanation
Indices: 68751--68805 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
68741 CATAATGAAA
*
68751 ATAAATAAATAGT
1 ATAAATAAATAAT
68764 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
*
68778 A-AAATAAA-AAA
1 ATAAATAAATAAT
*
68789 ATATATAAA-AAT
1 ATAAATAAATAAT
68801 ATAAA
1 ATAAA
68806 AATGTATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 3 0.09
12 15 0.43
13 10 0.29
14 7 0.20
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:68786 original size:47 final size:47
Alignment explanation
Indices: 68735--68830 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 47
68725 GCAAAGAAAC
* *
68735 TAAAAACATA-ATGAAAATA-AATAAATAGTATAAATAAAATAATAAAA
1 TAAAAAAATATATAAAAATATAA-AAAT-GTATAAATAAAATAATAAAA
** *
68782 TAAAAAAATATATAAAAATATAAAAATGTATGTATAATATAATAAAA
1 TAAAAAAATATATAAAAATATAAAAATGTATAAATAAAATAATAAAA
68829 TA
1 TA
68831 CTAAATAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
47 28 0.67
48 12 0.29
49 2 0.05
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (47 bp):
TAAAAAAATATATAAAAATATAAAAATGTATAAATAAAATAATAAAA
Found at i:68801 original size:18 final size:16
Alignment explanation
Indices: 68735--68808 Score: 55
Period size: 17 Copynumber: 4.6 Consensus size: 16
68725 GCAAAGAAAC
*
68735 TAAAAACATAATGAAAA
1 TAAAAAAATAAT-AAAA
* *
68752 TAAATAAATAGT---A
1 TAAAAAAATAATAAAA
68765 TAAATAAAATAATAAAA
1 TAAA-AAAATAATAAAA
68782 TAAAAAAATATATAAAAA
1 TAAAAAAATA-AT-AAAA
*
68800 TATAAAAAT
1 TAAAAAAAT
68809 GTATGTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
16 6 0.13
17 16 0.36
18 12 0.27
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATAATAAAA
Found at i:68900 original size:28 final size:28
Alignment explanation
Indices: 68833--68900 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
68823 ATAAAATACT
68833 AAATAGTAA-CA-ATAATAATAAATAAA
1 AAATAGTAATCATATAATAATAAATAAA
* * * *
68859 AAAAAAT-ATACATATAATATTAACTAAA
1 AAATAGTAAT-CATATAATAATAAATAAA
68887 AAATAGTAATCATA
1 AAATAGTAATCATA
68901 GAAATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.16
27 2 0.06
28 22 0.69
29 2 0.06
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (28 bp):
AAATAGTAATCATATAATAATAAATAAA
Found at i:69002 original size:2 final size:2
Alignment explanation
Indices: 68997--69021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68987 ATAAAAAATA
68997 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 A
69022 ATAATAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69039 original size:25 final size:24
Alignment explanation
Indices: 69011--69059 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
69001 ATATATATAT
69011 ATATATATATAA-TAATAGAAAAATA
1 ATATA-ATATAACTAA-AGAAAAATA
69036 ATATAATATAACGTAAAGAAAAAT
1 ATATAATATAAC-TAAAGAAAAAT
69060 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 13 0.59
26 3 0.14
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (24 bp):
ATATAATATAACTAAAGAAAAATA
Found at i:69609 original size:37 final size:37
Alignment explanation
Indices: 69516--69617 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
69506 ATGCTTGTGG
* * ** * * *
69516 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
*
69553 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
69590 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
69618 TAGGACAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTAT
Found at i:76722 original size:21 final size:21
Alignment explanation
Indices: 76680--76723 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
76670 ACTCCGAGAG
* *
76680 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
76701 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
76722 CT
1 CT
76724 CCTCCAGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:79500 original size:13 final size:15
Alignment explanation
Indices: 79473--79505 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
79463 TAAAAAAAAC
79473 ATTATATATTATATT
1 ATTATATATTATATT
79488 ATTATA-ATT-TATT
1 ATTATATATTATATT
79501 ATTAT
1 ATTAT
79506 TTGCAGGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 3 0.17
15 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATATATTATATT
Done.