Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006439.1 Hibiscus syriacus cultivar Beakdansim tig00015555_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: 467271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:373878 original size:19 final size:19
Alignment explanation
Indices: 373854--373892 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
373844 TTATTAAATC
373854 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
373873 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
373892 A
1 A
373893 ATGCATTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:378691 original size:148 final size:148
Alignment explanation
Indices: 378075--379970 Score: 3211
Period size: 148 Copynumber: 12.8 Consensus size: 148
378065 GCACAAACAT
* * *
378075 GATAAATATTTATAATTACATTTAAATAGAAACTTGAAAATTCAATTCAATTCGACTTAATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* * *
378140 ATTTTATAAACTCAGATCGAAAAAAATTTCAAGTCAACTATTTTATAAATGGAACTGAATTAGAA
66 ATTTTATAAACTCAAATCG-AAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAA
378205 TCAAATAATATTATAATAA
130 TCAAATAATATTATAATAA
378224 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378289 ATTTTACAAACTCAAATCG-AAAAATTTCGAGTCAACTATTTTATAAACGGAACTGCATTAGAAT
66 ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
378353 CAAATAATATTATAATAA
131 CAAATAATATTATAATAA
* * *
378371 GATAAATATTTATAATTACATTTAAATAGAAACTTGAAAATTCAATTCAATTCGACTTAATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378436 ATTTTATAAACTCAGATCGAAAAAAATTTCGAGTCAACTATTTTATAAATGGAACTGAATTAGAA
66 ATTTTATAAACTCAAATCG-AAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAA
378501 TCAAATAATATTATAATAA
130 TCAAATAATATTATAATAA
378520 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378585 ATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGCATTAGAAT
66 ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
378650 CAAATAATATTATAATAA
131 CAAATAATATTATAATAA
* * *
378668 GATAAATATTTATAATTACATTTAAATAGAAACTTGAAAATTCAATTCAATTCGACTTAATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378733 ATTTTATAAACTCAGATCGAAAAAAATTTCGAGTCAACTATTTTATAAATGGAACTGAATTAGAA
66 ATTTTATAAACTCAAATCG-AAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAA
378798 TCAAATAATATTATAATAA
130 TCAAATAATATTATAATAA
378817 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378882 ATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGCATTAGAAT
66 ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
378947 CAAATAATATTATAATAA
131 CAAATAATATTATAATAA
*
378965 GATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *** * *
379030 ATTTTATAAACTCAGATCGGAAATTTTTTTGAATCAACTATTTTATAAACGGAACTGAATTAGAA
66 ATTTTATAAACTCAAATC-GAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAA
379095 TCAAATAATATTATAATAA
130 TCAAATAATATTATAATAA
379114 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* * *
379179 ATTTTACAAACTCAAATCGAAAAAAATTCGAGTCAACTATTTTATAAACGGAACTGCATTAGAAT
66 ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
379244 CAAATAATATTATAATAA
131 CAAATAATATTATAATAA
*
379262 GATAAATATTTATAATTAAATTTAAACAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *** * *
379327 ATTTTATAAACTCAGATCGGAAATTTTTTTGAATCAACTATTTTATAAACGGAACTGAATTAGAA
66 ATTTTATAAACTCAAATC-GAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAA
379392 TCAAATAATATTATAATAA
130 TCAAATAATATTATAATAA
379411 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
379476 ATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGCATTAGAAT
66 ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
379541 CAAATAATATTATAATAA
131 CAAATAATATTATAATAA
*
379559 GATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *** * *
379624 ATTTTATAAACTCAGATCGGAAATTTTTTTTGAATCAACTATTTTATAAACGGAACTGAATTAGA
66 ATTTTATAAACTCAAATC-GAAA-AAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGA
379689 ATCAAATAATATTATAATAA
129 ATCAAATAATATTATAATAA
379709 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* * *
379774 ATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAATGAAACTGAATTAGAAT
66 ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
379839 CAAATAATATTATAATAA
131 CAAATAATATTATAATAA
379857 GATAAATATTTATAATTAAATTTAAACAGAAACTCT-AAAATTCAATTCAATTCGACTTGATTTA
1 GATAAATATTTATAATTAAATTTAAACAGAAACT-TGAAAATTCAATTCAATTCGACTTGATTTA
* * *
379921 AATTTTATAAACTCATATCGAAAAAAATTTTGAATCAACTATTTTATAAA
65 AATTTTATAAACTCAAATCG-AAAAAATTTCGAGTCAACTATTTTATAAA
379971 TTGAATTGAA
Statistics
Matches: 1641, Mismatches: 97, Indels: 18
0.93 0.06 0.01
Matches are distributed among these distances:
147 139 0.08
148 694 0.42
149 673 0.41
150 135 0.08
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (148 bp):
GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
ATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACGGAACTGAATTAGAAT
CAAATAATATTATAATAA
Found at i:378761 original size:297 final size:297
Alignment explanation
Indices: 378075--379981 Score: 3415
Period size: 297 Copynumber: 6.4 Consensus size: 297
378065 GCACAAACAT
* * *
378075 GATAAATATTTATAATTACATTTAAATAGAAACTTGAAAATTCAATTCAATTCGACTTAATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
*
378140 ATTTTATAAACTCAGATCGAAAAAAA-TTTCAAGTCAACTATTTTATAAATGGAACTGAATTAGA
66 ATTTTATAAACTCAGATCGAAAAAAATTTTGAA-TCAACTATTTTATAAATGGAACTGAATTAGA
378204 ATCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAA
130 ATCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAA
378269 TTCAATTCGACTTGATTTAAATTTTACAAACTCAAATCG-AAAAATTTCGAGTCAACTATTTTAT
195 TTCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTAT
378333 AAACGGAACTGCATTAGAATCAAATAATATTATAATAA
260 AAACGGAACTGCATTAGAATCAAATAATATTATAATAA
* * *
378371 GATAAATATTTATAATTACATTTAAATAGAAACTTGAAAATTCAATTCAATTCGACTTAATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378436 ATTTTATAAACTCAGATCGAAAAAAATTTCGAGTCAACTATTTTATAAATGGAACTGAATTAGAA
66 ATTTTATAAACTCAGATCGAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAATTAGAA
378501 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
131 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
378566 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
196 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
378631 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
261 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
* * *
378668 GATAAATATTTATAATTACATTTAAATAGAAACTTGAAAATTCAATTCAATTCGACTTAATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *
378733 ATTTTATAAACTCAGATCGAAAAAAATTTCGAGTCAACTATTTTATAAATGGAACTGAATTAGAA
66 ATTTTATAAACTCAGATCGAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAATTAGAA
378798 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
131 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
378863 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
196 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
378928 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
261 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
*
378965 GATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *** *
379030 ATTTTATAAACTCAGATCGGAAATTTTTTTGAATCAACTATTTTATAAACGGAACTGAATTAGAA
66 ATTTTATAAACTCAGATCGAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAATTAGAA
379095 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
131 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
*
379160 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAAATTCGAGTCAACTATTTTATA
196 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
379225 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
261 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
*
379262 GATAAATATTTATAATTAAATTTAAACAGAAACTAGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
* *** *
379327 ATTTTATAAACTCAGATCGGAAATTTTTTTGAATCAACTATTTTATAAACGGAACTGAATTAGAA
66 ATTTTATAAACTCAGATCGAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAATTAGAA
379392 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
131 TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
379457 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
196 TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
379522 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
261 AACGGAACTGCATTAGAATCAAATAATATTATAATAA
*
379559 GATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAATTCAATTCAATTCGACTTGATTTAA
1 GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
**** *
379624 ATTTTATAAACTCAGATCGGAAATTTTTTTTGAATCAACTATTTTATAAACGGAACTGAATTAGA
66 ATTTTATAAACTCAGATC-GAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAATTAGA
379689 ATCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAA
130 ATCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAA
379754 TTCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTAT
195 TTCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTAT
* * *
379819 AAATGAAACTGAATTAGAATCAAATAATATTATAATAA
260 AAACGGAACTGCATTAGAATCAAATAATATTATAATAA
379857 GATAAATATTTATAATTAAATTTAAACAGAAACTCT-AAAATTCAATTCAATTCGACTTGATTTA
1 GATAAATATTTATAATTAAATTTAAACAGAAACT-TGAAAATTCAATTCAATTCGACTTGATTTA
* * *
379921 AATTTTATAAACTCATATCGAAAAAAATTTTGAATCAACTATTTTATAAATTGAATTGAAT
65 AATTTTATAAACTCAGATCGAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAAT
379982 ATTTAGGTCC
Statistics
Matches: 1575, Mismatches: 32, Indels: 7
0.98 0.02 0.00
Matches are distributed among these distances:
296 226 0.14
297 1060 0.67
298 289 0.18
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (297 bp):
GATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAATTCAATTCGACTTGATTTAA
ATTTTATAAACTCAGATCGAAAAAAATTTTGAATCAACTATTTTATAAATGGAACTGAATTAGAA
TCAAATAATATTATAATAAGATAAATATTTATAATTAAATTTAAACAGAAACTTGAAAATTCAAT
TCAATTCGACTTGATTTAAATTTTACAAACTCAAATCGAAAAAATTTCGAGTCAACTATTTTATA
AACGGAACTGCATTAGAATCAAATAATATTATAATAA
Found at i:380192 original size:35 final size:35
Alignment explanation
Indices: 380153--380232 Score: 135
Period size: 35 Copynumber: 2.3 Consensus size: 35
380143 GGGGTTGGGC
380153 ATGTAATTGAAGTATTTTGAAATTT-GAGGTTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTAG-GGTTTAGA
380188 ATGTAATTGAAGTATTTTGAAATTTAGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAAATTTAGGGTTTAGA
*
380223 ATATAATTGA
1 ATGTAATTGA
380233 TGATTGTGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
35 42 0.98
36 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAAATTTAGGGTTTAGA
Found at i:384716 original size:29 final size:28
Alignment explanation
Indices: 384679--384750 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
384669 AATGGGACCA
*
384679 TAACTGTAATGATTAAAAGAATAAGGCTC
1 TAACTGTAAT-ATTAAAAGAATAAGGCCC
* *
384708 TAATTGTAAATATTAAAAGAATAGGGCCC
1 TAACTGT-AATATTAAAAGAATAAGGCCC
384737 TAACTGTAAATATT
1 TAACTGT-AATATT
384751 GAAGGAGCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 35 0.92
30 3 0.08
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (28 bp):
TAACTGTAATATTAAAAGAATAAGGCCC
Found at i:386896 original size:24 final size:24
Alignment explanation
Indices: 386869--386915 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
386859 GCTTCTTCCC
*
386869 CTTCTTATCTTTCTT-TTTCTCTTT
1 CTTCTT-TCTCTCTTCTTTCTCTTT
*
386893 CTTCTTTGTCTCTTCTTTCTCTT
1 CTTCTTTCTCTCTTCTTTCTCTT
386916 CACCTTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.68
Consensus pattern (24 bp):
CTTCTTTCTCTCTTCTTTCTCTTT
Found at i:387004 original size:33 final size:34
Alignment explanation
Indices: 386954--387061 Score: 111
Period size: 33 Copynumber: 3.3 Consensus size: 34
386944 TTTGTCTTTC
* *
386954 CTTC-CTTCCTTCACCTCTTTGCCTTTCTTCT-T
1 CTTCTCTTTCTTCTCCTCTTTGCCTTTCTTCTAT
*
386986 CTTCTCTTTCTTCTCCTCTTTGTCTTTCTTCTCAT
1 CTTCTCTTTCTTCTCCTCTTTGCCTTTCTTCT-AT
*
387021 CTT-TC-TTCTTCTCCTCTTTATCC-TTCTTCTTAT
1 CTTCTCTTTCTTCTCCTCTTT-GCCTTTCTTC-TAT
387054 CTT-TCTTT
1 CTTCTCTTT
387062 GTCTCTTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
32 4 0.06
33 51 0.78
34 6 0.09
35 4 0.06
ACGTcount: A:0.04, C:0.35, G:0.02, T:0.59
Consensus pattern (34 bp):
CTTCTCTTTCTTCTCCTCTTTGCCTTTCTTCTAT
Found at i:387017 original size:18 final size:18
Alignment explanation
Indices: 386962--387050 Score: 82
Period size: 18 Copynumber: 5.3 Consensus size: 18
386952 TCCTTCCTTC
* *
386962 CTTCACCTCTTTGCCTTT
1 CTTCTCCTCTTTGTCTTT
*
386980 CTTCT--TC-TTCTCTTT
1 CTTCTCCTCTTTGTCTTT
386995 CTTCTCCTCTTTGTCTTT
1 CTTCTCCTCTTTGTCTTT
*
387013 CTTCTCATC-TT-TC-TT
1 CTTCTCCTCTTTGTCTTT
* *
387028 CTTCTCCTCTTTATCCTT
1 CTTCTCCTCTTTGTCTTT
387046 CTTCT
1 CTTCT
387051 TATCTTTCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
15 21 0.36
16 6 0.10
17 6 0.10
18 26 0.44
ACGTcount: A:0.03, C:0.36, G:0.02, T:0.58
Consensus pattern (18 bp):
CTTCTCCTCTTTGTCTTT
Found at i:387136 original size:18 final size:18
Alignment explanation
Indices: 387101--387138 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
387091 TTCTACCTCA
*
387101 TCTTTCTTTTTCTTCTTT
1 TCTTTCTTTTTCTCCTTT
387119 TCTTTCTTCTTT-TCCTTT
1 TCTTTCTT-TTTCTCCTTT
387137 TC
1 TC
387139 ATCCTTGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTTCTTTTTCTCCTTT
Found at i:387150 original size:27 final size:25
Alignment explanation
Indices: 387120--387231 Score: 70
Period size: 27 Copynumber: 4.4 Consensus size: 25
387110 TTCTTCTTTT
387120 CTTTCTTCTTTTCCTTTTCATCCTTGC
1 CTTTCTTCTTTTCCTTTTCAT-CTT-C
* * *
387147 CTTTCTTCTTCTCC--ATC-TCTTT
1 CTTTCTTCTTTTCCTTTTCATCTTC
* * * *
387169 CTCTTCTCCCTCTTCCTCTTCATCTTT
1 CT-TTCT-TCTTTTCCTTTTCATCTTC
*
387196 C-ATCTTCTTTTCCTTTTCATCCTTGC
1 CTTTCTTCTTTTCCTTTTCAT-CTT-C
387222 CTTTCTTCTT
1 CTTTCTTCTT
387232 CTCCATCTCT
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
22 2 0.03
23 7 0.11
24 18 0.28
25 8 0.12
26 3 0.05
27 26 0.41
ACGTcount: A:0.04, C:0.37, G:0.02, T:0.57
Consensus pattern (25 bp):
CTTTCTTCTTTTCCTTTTCATCTTC
Found at i:387209 original size:24 final size:25
Alignment explanation
Indices: 387179--387279 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 25
387169 CTCTTCTCCC
387179 TCTTCCTCTTCATCTTTCATCTTCT
1 TCTTCCTCTTCATCTTTCATCTTCT
* * *
387204 T-TTCCTTTTCATCCTTGCCT-TTCT
1 TCTTCCTCTTCAT-CTTTCATCTTCT
*
387228 TCTT-CTCCATC-TCTTTC-TCTTCT
1 TCTTCCT-CTTCATCTTTCATCTTCT
387251 CCCTCTTCCTCTTCATCTTTCATCTTCT
1 ---TCTTCCTCTTCATCTTTCATCTTCT
387279 T
1 T
387280 TTTCTCCTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
22 1 0.02
23 8 0.14
24 18 0.31
25 11 0.19
26 7 0.12
27 8 0.14
28 6 0.10
ACGTcount: A:0.06, C:0.38, G:0.01, T:0.55
Consensus pattern (25 bp):
TCTTCCTCTTCATCTTTCATCTTCT
Found at i:387209 original size:75 final size:75
Alignment explanation
Indices: 387123--387281 Score: 318
Period size: 75 Copynumber: 2.1 Consensus size: 75
387113 TTCTTTTCTT
387123 TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
1 TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
387188 TCATCTTTCA
66 TCATCTTTCA
387198 TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
1 TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
387263 TCATCTTTCA
66 TCATCTTTCA
387273 TCTTCTTTT
1 TCTTCTTTT
387282 TCTCCTTATC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.05, C:0.38, G:0.01, T:0.56
Consensus pattern (75 bp):
TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
TCATCTTTCA
Found at i:387344 original size:75 final size:75
Alignment explanation
Indices: 387123--387309 Score: 293
Period size: 75 Copynumber: 2.5 Consensus size: 75
387113 TTCTTTTCTT
* *
387123 TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
1 TCTTCTTTTCCTTATCATCCTTACCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
387188 TCATCTTTCA
66 TCATCTTTCA
* *
387198 TCTTCTTTTCCTTTTCATCCTTGCCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
1 TCTTCTTTTCCTTATCATCCTTACCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
387263 TCATCTTTCA
66 TCATCTTTCA
* *
387273 TCTTCTTTTTCTCCTTATCCTCCTTATCTTTCTTCTT
1 TCTTC--TTT-TCCTTATCATCCTTACCTTTCTTCTT
387310 TTTCTTCTTC
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
75 80 0.76
77 3 0.03
78 22 0.21
ACGTcount: A:0.05, C:0.37, G:0.01, T:0.56
Consensus pattern (75 bp):
TCTTCTTTTCCTTATCATCCTTACCTTTCTTCTTCTCCATCTCTTTCTCTTCTCCCTCTTCCTCT
TCATCTTTCA
Found at i:388623 original size:80 final size:80
Alignment explanation
Indices: 388482--388814 Score: 540
Period size: 80 Copynumber: 4.2 Consensus size: 80
388472 CCCTCCAAAT
* * * * *
388482 ACATCATCAAGAATCAAAACAGAAGACATAGATATTCACCCGCATGATACTTATCAGTCCAGATC
1 ACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATC
388547 TTATTCAATCTATAC
66 TTATTCAATCTATAC
* * *
388562 ACAACAAAAAGAATCGAAACAGCAGACATAGATATTCACCCGCATGATACTAATCAGTCCAGATC
1 ACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATC
388627 TTATTCAATCTATAC
66 TTATTCAATCTATAC
*
388642 ACATCAACAAGAATCGAAACAGCAGACACATATATTCACCCGCATGATACTAATCAGTCCAGATC
1 ACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATC
* *
388707 GTATTCAATCTATAT
66 TTATTCAATCTATAC
388722 ACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATC
1 ACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATC
* *
388787 TAATTCAATCTATAT
66 TTATTCAATCTATAC
*
388802 ACATCAGCAAGAA
1 ACATCAACAAGAA
388815 GGTAGTTGAA
Statistics
Matches: 237, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 237 1.00
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.23
Consensus pattern (80 bp):
ACATCAACAAGAATCGAAACAGCAGACACAGATATTCACCCGCATGATACTAATCAGTCCAGATC
TTATTCAATCTATAC
Found at i:388981 original size:251 final size:252
Alignment explanation
Indices: 388682--389137 Score: 842
Period size: 251 Copynumber: 1.8 Consensus size: 252
388672 TATATTCACC
388682 CGCATGATACTAATCAGTCCAGATCGTATTCAATCTATATACATCAACAAGAATCGAAACAGCAG
1 CGCATGATACTAATCAGTCCAGATCGTATTCAATCTATATACATCAACAAGAATCGAAACAGCAG
388747 ACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTAATTCAATCTATATACATCAGCAA
66 ACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTAATTCAATCTATATACATCAGCAA
* * *
388812 GAAGGTAGTTGAAAAC-ACACACACACACATGTTTCGAAGTCTGTTTATTATCTATTCAACCTGT
131 GAAGATAGTTGAAAACAACACACACACACATGTTTCGAAGTCTGTTTATTATCTATTCAACATGC
388876 AAGAAAATCGAAACGATCTAAAATAAGATTAACATGGTAGTTGAAAACACACACACA
196 AAGAAAATCGAAACGATCTAAAATAAGATTAACATGGTAGTTGAAAACACACACACA
* *
388933 CGCATGATACTAATCAGTCCAGATCTTATTCAATCTATATACATCAACAAGAATTGAAACAGCAG
1 CGCATGATACTAATCAGTCCAGATCGTATTCAATCTATATACATCAACAAGAATCGAAACAGCAG
*
388998 ACACAGATATTCACCCGCATGATACTAATCAGTCCTGATCTAATTCAATCTATATACATCAGCAA
66 ACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTAATTCAATCTATATACATCAGCAA
389063 GAAGATAGTTGAAAACAAACACACACACACATGTTTCGAAGTCTGTTTATTATCTATTCAACATG
131 GAAGATAGTTGAAAAC-AACACACACACACATGTTTCGAAGTCTGTTTATTATCTATTCAACATG
389128 CAAGAAAATC
195 CAAGAAAATC
389138 TAAGATTAAC
Statistics
Matches: 197, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
251 142 0.72
253 55 0.28
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (252 bp):
CGCATGATACTAATCAGTCCAGATCGTATTCAATCTATATACATCAACAAGAATCGAAACAGCAG
ACACAGATATTCACCCGCATGATACTAATCAGTCCAGATCTAATTCAATCTATATACATCAGCAA
GAAGATAGTTGAAAACAACACACACACACATGTTTCGAAGTCTGTTTATTATCTATTCAACATGC
AAGAAAATCGAAACGATCTAAAATAAGATTAACATGGTAGTTGAAAACACACACACA
Found at i:390722 original size:35 final size:35
Alignment explanation
Indices: 390682--390758 Score: 154
Period size: 35 Copynumber: 2.2 Consensus size: 35
390672 TGTATTTTTT
390682 TAATATTATTATGTTATAGACTTTAGTTTTGTTTA
1 TAATATTATTATGTTATAGACTTTAGTTTTGTTTA
390717 TAATATTATTATGTTATAGACTTTAGTTTTGTTTA
1 TAATATTATTATGTTATAGACTTTAGTTTTGTTTA
390752 TAATATT
1 TAATATT
390759 GTTTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (35 bp):
TAATATTATTATGTTATAGACTTTAGTTTTGTTTA
Found at i:391373 original size:6 final size:6
Alignment explanation
Indices: 391358--391399 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
391348 ACGTGTCGAA
391358 GACC-C GACCAC GACCAC GACCAC GACCAC GACCAC GA-CAC GA
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GA
391400 AACGAGACGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 9 0.25
6 27 0.75
ACGTcount: A:0.33, C:0.48, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:391917 original size:6 final size:6
Alignment explanation
Indices: 391906--391958 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
391896 CGTCTCGTCT
*
391906 GTGGTC GTGGTC GTGGTC GTGGTC CTGGTC GTGGTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
391954 GTGGT
1 GTGGT
391959 AATACGTGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.17, G:0.49, T:0.34
Consensus pattern (6 bp):
GTGGTC
Found at i:392067 original size:21 final size:21
Alignment explanation
Indices: 392044--392191 Score: 133
Period size: 21 Copynumber: 7.0 Consensus size: 21
392034 CGTTGCGATT
*
392044 TTGGACTATCGCAACGCGAAT
1 TTGGACTATCGCAACGCGAAC
*
392065 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
392088 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
392107 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
392130 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
392149 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
392172 TTAGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
392192 TATGTAAATC
Statistics
Matches: 102, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
19 19 0.19
21 46 0.45
23 37 0.36
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:392114 original size:42 final size:42
Alignment explanation
Indices: 392047--392185 Score: 242
Period size: 42 Copynumber: 3.3 Consensus size: 42
392037 TGCGATTTTG
392047 GACTATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
392091 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
392133 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
392175 GACTATCGCAA
1 GACTATCGCAA
392186 TGCGAATATG
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
42 82 0.88
44 11 0.12
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:394371 original size:28 final size:27
Alignment explanation
Indices: 394318--394369 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 27
394308 AATTTAAAAC
394318 AAAATAGAAAATAAATAATAAATATAT
1 AAAATAGAAAATAAATAATAAATATAT
394345 AAAATAG--AA-AAATAATAAATATAT
1 AAAATAGAAAATAAATAATAAATATAT
394369 A
1 A
394370 TACATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 16 0.64
25 2 0.08
27 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAATAGAAAATAAATAATAAATATAT
Found at i:394395 original size:12 final size:13
Alignment explanation
Indices: 394362--394395 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
394352 AAAAATAATA
394362 AATATATATACAT
1 AATATATATACAT
394375 -ATATATATACAT
1 AATATATATACAT
394387 AATAT-TATA
1 AATATATATA
394396 AATATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATATATACAT
Found at i:395665 original size:13 final size:13
Alignment explanation
Indices: 395647--395671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
395637 TGTAAAACAT
395647 AAAATAAATTAAA
1 AAAATAAATTAAA
395660 AAAATAAATTAA
1 AAAATAAATTAA
395672 TTAAGCGGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATTAAA
Found at i:404706 original size:16 final size:16
Alignment explanation
Indices: 404681--404721 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
404671 TCATTAGATA
*
404681 TACGAATTAAAAAATG
1 TACGATTTAAAAAATG
404697 TACGATTTAAAAAATG
1 TACGATTTAAAAAATG
404713 TACGATTTA
1 TACGATTTA
404722 TACAAGTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (16 bp):
TACGATTTAAAAAATG
Found at i:407873 original size:30 final size:30
Alignment explanation
Indices: 407806--407905 Score: 146
Period size: 31 Copynumber: 3.3 Consensus size: 30
407796 GTACATATAT
*
407806 CACATTAGGAATTTTGTCGAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
* *
407836 GCACATTAGGAATTATGTCAAAGTATAGGTA
1 -CACATTAGGAATTTTGTCAAAGTATAAGTA
*
407867 CACATTAGGCATTTTGTCAAAGTATAAGTA
1 CACATTAGGAATTTTGTCAAAGTATAAGTA
407897 CAACATTAG
1 C-ACATTAG
407906 ACTTTTTTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
30 28 0.45
31 34 0.55
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (30 bp):
CACATTAGGAATTTTGTCAAAGTATAAGTA
Found at i:408720 original size:22 final size:22
Alignment explanation
Indices: 408692--408757 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
408682 AGAGGTACTG
* *
408692 ATACCCCTATCAATGGGCATCA
1 ATACCCCTATAAATGGGTATCA
* *
408714 ATACCCCTATAAATGGGTACCG
1 ATACCCCTATAAATGGGTATCA
*
408736 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATAAATGGGTATCA
408758 TGAAGGCTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (22 bp):
ATACCCCTATAAATGGGTATCA
Found at i:409094 original size:20 final size:20
Alignment explanation
Indices: 409042--409087 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
409032 ACACTTGAAG
*
409042 AAGCAAGAAAACAACTATCC
1 AAGCAAGAAAACAACTATAC
*
409062 AATCAAGAAAACAACTATAC
1 AAGCAAGAAAACAACTATAC
409082 AAGCAA
1 AAGCAA
409088 ACAAACACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.11
Consensus pattern (20 bp):
AAGCAAGAAAACAACTATAC
Found at i:411128 original size:88 final size:85
Alignment explanation
Indices: 410978--411161 Score: 305
Period size: 88 Copynumber: 2.1 Consensus size: 85
410968 CTTCAACTTT
* *
410978 ATCATATAAAATATGTAATCAGATAAGATTTTATAGTCTGAAAACGACAAAGTATTTTCTAAAGT
1 ATCATATAAAATATGTAATCAGAAAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
411043 TTCCAACTTTAATTTTTTTA
66 TTCCAACTTTAATTTTTTTA
411063 ATCATATAAAATATGTAATCAGAAAAGATTTTTTTATAGTCTGAAAACGACAAAGTATTTCCTAA
1 ATCATATAAAATATGTAATCAGAAAAGA---TTTTATAGTCTGAAAACGACAAAGTATTTCCTAA
* *
411128 AGTTTTCAATTTTAATTTTTTTA
63 AGTTTCCAACTTTAATTTTTTTA
411151 ATCATATAAAA
1 ATCATATAAAA
411162 GAAAAAAAGT
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
85 27 0.29
88 65 0.71
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (85 bp):
ATCATATAAAATATGTAATCAGAAAAGATTTTATAGTCTGAAAACGACAAAGTATTTCCTAAAGT
TTCCAACTTTAATTTTTTTA
Found at i:416415 original size:13 final size:13
Alignment explanation
Indices: 416378--416442 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
416368 TTAGCATATT
*
416378 TTATTTATAATAA
1 TTATTAATAATAA
* *
416391 -TAATAGTAATAA
1 TTATTAATAATAA
416403 TTATTAATAATAA
1 TTATTAATAATAA
* *
416416 TAATTAATAATTA
1 TTATTAATAATAA
* *
416429 TTATCATTAATAA
1 TTATTAATAATAA
416442 T
1 T
416443 AAACAATCAA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
12 9 0.22
13 31 0.77
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
TTATTAATAATAA
Found at i:416416 original size:16 final size:16
Alignment explanation
Indices: 416384--416444 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
416374 TATTTTATTT
*
416384 ATAA-TAATAATAGTA
1 ATAATTAATAATAATA
*
416399 ATAATTATTAATAATA
1 ATAATTAATAATAATA
* *
416415 ATAATTAATAATTATT
1 ATAATTAATAATAATA
*
416431 ATCATTAATAATAA
1 ATAATTAATAATAA
416445 ACAATCAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
15 4 0.11
16 34 0.89
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
ATAATTAATAATAATA
Found at i:416444 original size:3 final size:3
Alignment explanation
Indices: 416384--416426 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
416374 TATTTTATTT
* *
416384 ATA ATA ATA ATA GTA ATA ATTA TTA ATA ATA ATA ATTA ATA AT
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA A-TA ATA AT
416427 TATTATCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 29 0.85
4 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:417856 original size:31 final size:31
Alignment explanation
Indices: 417821--417885 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
417811 ATTTGGTCGG
* *
417821 ATTCAAGGGTTAAAATCATATTTTATTTAAA
1 ATTCAAGGGTCAAAATCATATTTTATATAAA
* * * *
417852 ATTCAATGGTCACATTGATATTTTATATAAA
1 ATTCAAGGGTCAAAATCATATTTTATATAAA
417883 ATT
1 ATT
417886 TAGGGATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (31 bp):
ATTCAAGGGTCAAAATCATATTTTATATAAA
Found at i:423914 original size:2 final size:2
Alignment explanation
Indices: 423907--424132 Score: 121
Period size: 2 Copynumber: 118.5 Consensus size: 2
423897 ATTTTTATTC
*
423907 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TT TA TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
423948 T- TA TA TGG TA TGG TA T- TA TA TA GCA TA TA TA T- TA TA -A TA
1 TA TA TA T-A TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
423987 TG TA TA TA GCA T- TA TA TA T- TA TG TT TA TG T- TA T- TCA TA T-
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
424026 TA TA TA T- TA TA T- TA -A TA TA T- TA TA GTA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
424065 GTA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TT TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
424106 TA T- TA TT TA TT TA TA TA TT TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
424133 TATGTTATAT
Statistics
Matches: 172, Mismatches: 25, Indels: 54
0.69 0.10 0.22
Matches are distributed among these distances:
1 19 0.11
2 142 0.83
3 11 0.06
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:424009 original size:21 final size:24
Alignment explanation
Indices: 423964--424108 Score: 85
Period size: 21 Copynumber: 6.2 Consensus size: 24
423954 GGTATGGTAT
423964 TATATAGCATATATATTATAATATG
1 TATATAGCATATATATTAT-ATATG
423989 TATATAGCAT-TATA-TAT-TATG
1 TATATAGCATATATATTATATATG
* *
424010 TTTAT-G-TTATTCATATTATATAT-
1 TATATAGCATA-T-ATATTATATATG
** * *
424033 TATATTAATATATTATAGTATATATT
1 TATA-TAGCATA-TATATTATATATG
*
424059 TATATAG--TATATA-TATATATA
1 TATATAGCATATATATTATATATG
* *
424080 TATATA-TATATATATTATATTATT
1 TATATAGCATATATATTATA-TATG
424104 TATAT
1 TATAT
424109 TATTTATTTA
Statistics
Matches: 98, Mismatches: 9, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 22 0.22
22 13 0.13
23 15 0.15
24 16 0.16
25 22 0.22
26 8 0.08
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (24 bp):
TATATAGCATATATATTATATATG
Found at i:424048 original size:29 final size:30
Alignment explanation
Indices: 423997--424161 Score: 125
Period size: 29 Copynumber: 5.5 Consensus size: 30
423987 TGTATATAGC
* * *
423997 ATTATATATTATGTT--TATGTTAT-TCAT
1 ATTATATATTATATTAATATATTATATTAT
424024 ATTATATATTATATTAATATATTATAGTATAT
1 ATTATATATTATATTAATATATTATA-T-TAT
*
424056 ATTTATATAGTATA-T-ATATA-TATATATAT
1 A-TTATATATTATATTAATATATTATAT-TAT
*
424085 ATATATATATTATATTATTTATATTAT-TTAT
1 AT-TATATATTATATTA-ATATATTATATTAT
*
424116 -TTATATATT-TATTATATTATGTTATATTAT
1 ATTATATATTATATTA-A-TATATTATATTAT
424146 ATTAT-TATTAATATTA
1 ATTATATATT-ATATTA
424162 TTTTTTTTAG
Statistics
Matches: 114, Mismatches: 8, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
27 14 0.12
28 7 0.06
29 38 0.33
30 14 0.12
31 13 0.11
32 14 0.12
33 14 0.12
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.58
Consensus pattern (30 bp):
ATTATATATTATATTAATATATTATATTAT
Found at i:424130 original size:95 final size:95
Alignment explanation
Indices: 423963--424134 Score: 226
Period size: 95 Copynumber: 1.8 Consensus size: 95
423953 TGGTATGGTA
* *
423963 TTATATAGCATATATATTATAATATGTATATAGCATTATATATTATGTTTATGTTATTCATATTA
1 TTATATAGCATATATATTATAATATATATATAGCATTATATATTATGATTATGTTATTCATATTA
424028 TATATTATATTAATATATTATAGTATATAT
66 TATATTATATTAATATATTATAGTATATAT
* * *
424058 TTATATAGTATATATATATATATATATATATATA-TATTATATTATTTAT-ATTAT-TTATTTAT
1 TTATATAGCATATATAT-TATA-ATATATATATAGCATTATA-TA-TTATGATTATGTTATTCAT
*
424120 A-TATTTATTATATTA
62 ATTATATATTATATTA
424135 TGTTATATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
95 29 0.43
96 18 0.27
97 16 0.24
98 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (95 bp):
TTATATAGCATATATATTATAATATATATATAGCATTATATATTATGATTATGTTATTCATATTA
TATATTATATTAATATATTATAGTATATAT
Found at i:424135 original size:8 final size:8
Alignment explanation
Indices: 424023--424153 Score: 87
Period size: 8 Copynumber: 15.8 Consensus size: 8
424013 ATGTTATTCA
424023 TATTATA-
1 TATTATAT
424030 TATTATAT
1 TATTATAT
*
424038 TAATATAT
1 TATTATAT
424046 TA-TAGTAT
1 TATTA-TAT
424054 ATATT-TAT
1 -TATTATAT
*
424062 ATAGTATAT
1 -TATTATAT
424071 ATATATATAT
1 -TAT-TATAT
424081 ATATATATAT
1 -TAT-TATAT
424091 ATATTATAT
1 -TATTATAT
424100 TATTTATAT
1 TA-TTATAT
424109 TATT-TAT
1 TATTATAT
424116 T-TATATATT
1 TAT-TATA-T
424125 TATTATAT
1 TATTATAT
424133 TATGT-TA-
1 TAT-TATAT
424140 TATTATAT
1 TATTATAT
424148 TATTAT
1 TATTAT
424154 TAATATTATT
Statistics
Matches: 107, Mismatches: 3, Indels: 27
0.78 0.02 0.20
Matches are distributed among these distances:
6 2 0.02
7 19 0.18
8 37 0.35
9 28 0.26
10 21 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TATTATAT
Found at i:424152 original size:51 final size:55
Alignment explanation
Indices: 423907--424164 Score: 173
Period size: 53 Copynumber: 4.7 Consensus size: 55
423897 ATTTTTATTC
* * * *
423907 TATATATATATATATATA-TATATTATT-TTATATAGTATATA-TTATATGGTATGG
1 TATATATATATATATATATTATATTATTATT-TATATTATTTATTTATATAGTAT-A
* * * * * * * *
423961 TAT-TATATAGCATATATATTATAATATGTATATAGCATTATATA-TTATGT-TTATG
1 TATATATATA-TATATATATTATATTAT-TATTTA-TATTATTTATTTATATAGTATA
* * *
424016 T-TAT-TCATAT-TATATATTATATTAATATATTATAGTATATATTTATATAGTATA
1 TATATAT-ATATATATATATTATATTATTAT-TTATATTATTTATTTATATAGTATA
*
424070 TATATATATATATATATATATATATTATATTATTTATATTATTTATTTATATA-TTTA
1 TATATATATATATATATAT-TATA-T-TATTATTTATATTATTTATTTATATAGTATA
* *
424127 T-TATAT-TATGT-TATATTATATTATTATTAATATTATTT
1 TATATATATATATATATATTATATTATTATTTATATTATTT
424165 TTTTTAGTTT
Statistics
Matches: 166, Mismatches: 22, Indels: 35
0.74 0.10 0.16
Matches are distributed among these distances:
51 16 0.10
52 11 0.07
53 30 0.18
54 21 0.13
55 24 0.14
56 19 0.11
57 21 0.13
58 19 0.11
59 5 0.03
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (55 bp):
TATATATATATATATATATTATATTATTATTTATATTATTTATTTATATAGTATA
Found at i:424161 original size:12 final size:13
Alignment explanation
Indices: 424011--424164 Score: 102
Period size: 13 Copynumber: 11.5 Consensus size: 13
424001 TATATTATGT
*
424011 TTATGTTATTCATA
1 TTAT-TTATTTATA
*
424025 TTATATA-TTATA
1 TTATTTATTTATA
*
424037 TTAATATATTATAGTA
1 TT-ATTTATT-TA-TA
*
424053 TATATTTATATAGTA
1 T-TATTTATTTA-TA
* *
424068 -TATATATATATA
1 TTATTTATTTATA
* *
424080 TATATATATATATA
1 T-TATTTATTTATA
424094 TTATATTATTTATA
1 TTAT-TTATTTATA
424108 TTATTTATTTATA
1 TTATTTATTTATA
424121 -TATTTA-TTATA
1 TTATTTATTTATA
424132 TTATGTTATATTATA
1 TTAT-TTAT-TTATA
*
424147 TTA-TTATTAATA
1 TTATTTATTTATA
424159 TTATTT
1 TTATTT
424165 TTTTTAGTTT
Statistics
Matches: 119, Mismatches: 8, Indels: 27
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.04
12 24 0.20
13 37 0.31
14 29 0.24
15 15 0.13
16 8 0.07
17 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (13 bp):
TTATTTATTTATA
Found at i:427080 original size:31 final size:29
Alignment explanation
Indices: 427018--427093 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 29
427008 CTTTCGAACA
*
427018 AAAGAAAAAGAGAGAAAAAAAAAACAAAAG
1 AAAGAACAA-AGAGAAAAAAAAAACAAAAG
* *
427048 AAA-AATCAAAGAGAAAAACAAATCAACCAAG
1 AAAGAA-CAAAGAGAAAAAAAAAACAA--AAG
427079 AAAGAACAAAGAGAA
1 AAAGAACAAAGAGAA
427094 GAGGTTCTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 17 0.44
30 5 0.13
31 15 0.38
32 2 0.05
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (29 bp):
AAAGAACAAAGAGAAAAAAAAAACAAAAG
Found at i:428934 original size:22 final size:19
Alignment explanation
Indices: 428884--428936 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
428874 AGGGTTCTGT
*
428884 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
428903 -GTCCTACGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
428923 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
428937 GAATACTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:435741 original size:15 final size:15
Alignment explanation
Indices: 435723--435755 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
435713 CGAGGGTTCT
435723 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
435738 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
435753 GTA
1 GTA
435756 ATGGTCCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.27
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:435790 original size:22 final size:19
Alignment explanation
Indices: 435740--435792 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
435730 TTCGGGACGT
*
435740 AGTCCTTCGGGACGTAATG
1 AGTCCTTCGGGACATAATG
*
435759 -GTCCTACGGGACATATATAG
1 AGTCCTTCGGGACATA-AT-G
435779 CAGTCCTTCGGGAC
1 -AGTCCTTCGGGAC
435793 GAATATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 13 0.48
19 2 0.07
20 1 0.04
22 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (19 bp):
AGTCCTTCGGGACATAATG
Found at i:435798 original size:22 final size:20
Alignment explanation
Indices: 435740--435798 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 20
435730 TTCGGGACGT
*
435740 AGTCCTTCGGGACGTA-ATG
1 AGTCCTTCGGGACGAATATG
*
435759 -GTCCTACGGGAC-ATATATAG
1 AGTCCTTCGGGACGA-ATAT-G
435779 CAGTCCTTCGGGACGAATAT
1 -AGTCCTTCGGGACGAATAT
435799 TGAACAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
18 12 0.39
19 2 0.06
20 1 0.03
22 15 0.48
23 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (20 bp):
AGTCCTTCGGGACGAATATG
Found at i:441065 original size:6 final size:6
Alignment explanation
Indices: 441054--441122 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
441044 CTCTATTTTT
* *
441054 ATGTAG ATGTAG ATGTAG ATTTAG ATGTAG ATGTAG ATGTCG ATGTAG
1 ATGTAG ATGTAG ATGTAG ATGTAG ATGTAG ATGTAG ATGTAG ATGTAG
*
441102 ATGTCG ATGTAG ATGTAG ATG
1 ATGTAG ATGTAG ATGTAG ATG
441123 ATATATCATA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (6 bp):
ATGTAG
Found at i:445142 original size:24 final size:25
Alignment explanation
Indices: 445102--445150 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
445092 CATAATTAAT
*
445102 TTATTAAAGTTTATTATAATAAAAA
1 TTATTAAAGTTTATTATAAAAAAAA
445127 TTATTAACA-TTT-TTATAAAAAAAA
1 TTATTAA-AGTTTATTATAAAAAAAA
445151 CATTTAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
25 10 0.45
26 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
TTATTAAAGTTTATTATAAAAAAAA
Found at i:445783 original size:14 final size:15
Alignment explanation
Indices: 445757--445786 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
445747 TTTGGACATT
445757 TATTTTATAATTAAA
1 TATTTTATAATTAAA
445772 TATTTT-TAATTAAA
1 TATTTTATAATTAAA
445786 T
1 T
445787 TTATATTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTTATAATTAAA
Found at i:445971 original size:14 final size:14
Alignment explanation
Indices: 445949--445994 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
445939 GTAATTGATT
*
445949 TTCTAGAAATTGAA
1 TTCTGGAAATTGAA
*
445963 TTCTGGAAAATGAA
1 TTCTGGAAATTGAA
*
445977 TTACTGGAATTTGAA
1 TT-CTGGAAATTGAA
445992 TTC
1 TTC
445995 AGAAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (14 bp):
TTCTGGAAATTGAA
Found at i:446230 original size:21 final size:20
Alignment explanation
Indices: 446192--446245 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
446182 AACATAATAT
* *
446192 TATTATTTTTAAAATATTAAA
1 TATTATTTTT-TACTATTAAA
446213 -ATTAATTTATTTACTATTAAA
1 TATT-ATTT-TTTACTATTAAA
446234 TATTATTTTTTA
1 TATTATTTTTTA
446246 TAATTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 7 0.25
21 16 0.57
22 5 0.18
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTTACTATTAAA
Found at i:446267 original size:30 final size:31
Alignment explanation
Indices: 446231--446303 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
446221 ATTTACTATT
**
446231 AAATATTAT-TTTTTATAATTTTATT-AATAA
1 AAATATTATATTGGTAT-ATTTTATTAAATAA
446261 AAATATTAATATTGGTATATTTTATTGAAATAA
1 AAATATT-ATATTGGTATATTTTATT-AAATAA
446294 AAATATTATA
1 AAATATTATA
446304 AATTATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 7 0.19
31 10 0.27
32 8 0.22
33 12 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (31 bp):
AAATATTATATTGGTATATTTTATTAAATAA
Found at i:446311 original size:31 final size:29
Alignment explanation
Indices: 446243--446373 Score: 70
Period size: 31 Copynumber: 4.3 Consensus size: 29
446233 ATATTATTTT
*
446243 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
446273 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
* * * * * *
446306 TTATATTAATTATTTATTAAAGTAATAGT-T
1 TTATATT--TTATTAATAAAAATATTAATAA
* * *
446336 TTATATTATATT-TTAAAAATATTAATTA
1 TTATATTTTATTAATAAAAATATTAATAA
*
446364 GTATATTTTA
1 TTATATTTTA
446374 ACTATCTTTA
Statistics
Matches: 76, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
27 9 0.12
28 12 0.16
30 8 0.11
31 22 0.29
32 6 0.08
33 19 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:446531 original size:53 final size:53
Alignment explanation
Indices: 446422--446531 Score: 118
Period size: 53 Copynumber: 2.1 Consensus size: 53
446412 TATTAAATAT
* * **
446422 ATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTCTATGAAATTA
1 ATAAATAATATAATT-ATTATTAATAATTTAATAATATTATTTCAAAAAAATTA
*
446476 ATAAATAATATAAATT-TTATTAATAATTTATTATATATTA-TT-AAAAAAATGTA
1 ATAAATAATAT-AATTATTATTAATAATTTAATA-ATATTATTTCAAAAAAAT-TA
446529 ATA
1 ATA
446532 TCTTATATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
52 5 0.10
53 23 0.48
54 17 0.35
55 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (53 bp):
ATAAATAATATAATTATTATTAATAATTTAATAATATTATTTCAAAAAAATTA
Found at i:447791 original size:21 final size:21
Alignment explanation
Indices: 447766--447813 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
447756 TTTGTTGCTT
447766 CAGCTTGTGACTTTAACTTCA
1 CAGCTTGTGACTTTAACTTCA
447787 CAGCTTGTGACTTTAACTTCA
1 CAGCTTGTGACTTTAACTTCA
447808 CAGCTT
1 CAGCTT
447814 CCTTCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (21 bp):
CAGCTTGTGACTTTAACTTCA
Found at i:462089 original size:21 final size:21
Alignment explanation
Indices: 462063--462129 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
462053 AATATCATTG
*
462063 AAAAATTATTGAAAATTAATT
1 AAAAATTAATGAAAATTAATT
462084 AAAAATTAATGAAAATTAATT
1 AAAAATTAATGAAAATTAATT
* *
462105 AAAAATTAATAAAAATTTATT
1 AAAAATTAATGAAAATTAATT
462126 AAAA
1 AAAA
462130 TAAAAAGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (21 bp):
AAAAATTAATGAAAATTAATT
Found at i:462130 original size:10 final size:11
Alignment explanation
Indices: 462063--462129 Score: 86
Period size: 11 Copynumber: 6.4 Consensus size: 11
462053 AATATCATTG
462063 AAAAATT-ATT
1 AAAAATTAATT
*
462073 GAAAATTAATT
1 AAAAATTAATT
462084 AAAAATTAA-T
1 AAAAATTAATT
*
462094 GAAAATTAATT
1 AAAAATTAATT
462105 AAAAATTAA-T
1 AAAAATTAATT
*
462115 AAAAATTTATT
1 AAAAATTAATT
462126 AAAA
1 AAAA
462130 TAAAAAGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
10 24 0.49
11 25 0.51
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
AAAAATTAATT
Found at i:462454 original size:82 final size:82
Alignment explanation
Indices: 462162--462722 Score: 694
Period size: 82 Copynumber: 6.8 Consensus size: 82
462152 ACATGTCACC
* *
462162 CAGTTTATCTGAGTTGATGTGATATGTCAATGAAAAGCAAAGGACATGAATAGTGTAGATTCTCT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
* *
462227 GATT-TGAATGGAAATTATTT
66 GATTCT--CT-AAAATT-TTT
* * * * *
462247 CAGTTTATCTGAATTGATGTGAAATGTCAATGAATAGAAAAGGACGTGAATAGTATAGATTATCT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
* *
462312 GATTCTATAAATTTTTTT
66 GATTCTCTAAA-ATTTTT
* * * *
462330 CA-TTTCATCTAAGTTGATGTGAAATGTCAATGAAAAGAAAATGACATGAATAGTGTAGATTCTC
1 CAGTTT-ATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTC
462394 TGATTCTCTAAAATTTTT
65 TGATTCTCTAAAATTTTT
* * * * *
462412 AAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAATGATGTGAATAGTGTAAATTCTTT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
462477 GATTCTCTAAAATTTTT
66 GATTCTCTAAAATTTTT
* * * * *
462494 CATTTTATCTGAGTTGACGTGAAATGTCAATGAAAAGCACAGGACGTGAATAGTGTAAATTATCT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
*
462559 GATTCTCTAAAAATTTT
66 GATTCTCTAAAATTTTT
* * * * * * * *
462576 CATTTTATCTAAGTTGATGTGAAATGTAAATGAAAAGCACAGAACGTGAATAATGTATATTCTCC
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
462641 GATTCTCTAAAATTTTT
66 GATTCTCTAAAATTTTT
* * ** * *
462658 CATTTTATTTGAGTAAATGTGAAATGTCAATGAAAAACAAATGACGTGAATAGTGTAGATTCTCT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
462723 ACAAGGGATG
Statistics
Matches: 417, Mismatches: 55, Indels: 11
0.86 0.11 0.02
Matches are distributed among these distances:
82 278 0.67
83 72 0.17
84 4 0.01
85 62 0.15
86 1 0.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (82 bp):
CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGCAAAGGACGTGAATAGTGTAGATTCTCT
GATTCTCTAAAATTTTT
Found at i:462794 original size:25 final size:25
Alignment explanation
Indices: 462760--462813 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
462750 ATCATAGTCA
*
462760 ATCTCTTACACAACACATTCCTTTC
1 ATCTCTTACACAACACACTCCTTTC
*
462785 ATCTCTTACACAACACACTCTTTTC
1 ATCTCTTACACAACACACTCCTTTC
462810 ATCT
1 ATCT
462814 TTAATCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.37
Consensus pattern (25 bp):
ATCTCTTACACAACACACTCCTTTC
Found at i:462821 original size:32 final size:31
Alignment explanation
Indices: 462759--462844 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 31
462749 GATCATAGTC
462759 AATCTCTTACACAACACA----TTC--CTTT
1 AATCTCTTACACAACACATCTTTTCATCTTT
*
462784 CATCTCTTACACAACACACTCTTTTCATCTTT
1 AATCTCTTACACAACACA-TCTTTTCATCTTT
*
462816 AATCTCTTACACAACACATTTTTTCATCT
1 AATCTCTTACACAACACATCTTTTCATCT
462845 AACGAAATAC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 17 0.33
30 3 0.06
31 10 0.20
32 21 0.41
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (31 bp):
AATCTCTTACACAACACATCTTTTCATCTTT
Done.