Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008292.1 Hibiscus syriacus cultivar Beakdansim tig00110956_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: 1591938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 4 of 8
Found at i:736265 original size:12 final size:12
Alignment explanation
Indices: 736232--736288 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
736222 CACAACTTGT
* *
736232 AAAGAGAGAAAA
1 AAAGAGAGAGAG
736244 AAAGAGAGAGAG
1 AAAGAGAGAGAG
736256 AAAGAGAGAGAG
1 AAAGAGAGAGAG
*
736268 AGAGAGTA-AGAAG
1 AAAGAG-AGAG-AG
736281 AAAGAGAG
1 AAAGAGAG
736289 CGACTAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
12 30 0.79
13 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:736269 original size:14 final size:14
Alignment explanation
Indices: 736234--736270 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
736224 CAACTTGTAA
*
736234 AGAGAGAAAAAAAG
1 AGAGAGAGAAAAAG
*
736248 AGAGAGAGAAAGAG
1 AGAGAGAGAAAAAG
736262 AGAGAGAGA
1 AGAGAGAGA
736271 GAGTAAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAAAAAG
Found at i:757685 original size:16 final size:17
Alignment explanation
Indices: 757635--757686 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
757625 TAAAAAATTA
757635 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
757652 GA-TT-AAA-TTATGAGT
1 AATTTGAAAGTTA-GAGT
757667 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
757683 AATT
1 AATT
757687 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:757878 original size:6 final size:7
Alignment explanation
Indices: 757853--757877 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
757843 ATACTTTAAA
757853 AAAAATT
1 AAAAATT
757860 AAAAATT
1 AAAAATT
757867 AAAAATT
1 AAAAATT
757874 AAAA
1 AAAA
757878 TAGATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:763743 original size:10 final size:10
Alignment explanation
Indices: 763728--763756 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
763718 ATGTATAGAG
763728 ATAAATAAAA
1 ATAAATAAAA
763738 ATAAATAAAA
1 ATAAATAAAA
763748 ATAAATAAA
1 ATAAATAAA
763757 GTAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:763767 original size:19 final size:19
Alignment explanation
Indices: 763728--763768 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
763718 ATGTATAGAG
*
763728 ATAAATAAAAATAAATAAAA
1 ATAAAT-AAAGTAAATAAAA
763748 ATAAATAAAGTAAATGAAAA
1 ATAAATAAAGTAAAT-AAAA
763768 A
1 A
763769 ATATAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAATAAAGTAAATAAAA
Found at i:763774 original size:19 final size:18
Alignment explanation
Indices: 763730--763776 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
763720 GTATAGAGAT
*
763730 AAATA-AAAATAAATAAA
1 AAATATAAAGTAAATAAA
*
763747 AATAAATAAAGTAAATGAAA
1 AA-ATATAAAGTAAAT-AAA
763767 AAATATAAAG
1 AAATATAAAG
763777 AATATACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 2 0.08
19 15 0.62
20 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAATATAAAGTAAATAAA
Found at i:763880 original size:145 final size:144
Alignment explanation
Indices: 763587--764012 Score: 730
Period size: 145 Copynumber: 2.9 Consensus size: 144
763577 AAGGAAACGC
*
763587 AATAGAATAAAAATAAATAAAGTAAATGAAAAAAAATAAAGAATATACATATAATAATAAAAGAA
1 AATA-AATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAG--
*
763652 AACAAAAAAATATATGTTTATATACGCTATCAATAATACCTAAAAATAATAAAATTAACGATGGT
63 -A-AAAAAAATATATGTTTATATACGCTATCAATAATA-CTTAAAATAATAAAATTAACGATGGT
763717 TATGTATAGAGATAAATAAA
125 TATGTATAGAGATAAATAAA
763737 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
1 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
*
763802 AAAATATATATGTTTATATACGTTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGT
66 AAAA-ATATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGT
763867 ATAGAGATAAATAAA
130 ATAGAGATAAATAAA
763882 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAA-AAAA-ATA
1 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGA-A
*
763945 AAAAAATATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGGTTATGT
65 AAAAAATATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGT
764010 ATA
130 ATA
764013 TATATATATA
Statistics
Matches: 269, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
143 62 0.23
144 10 0.04
145 107 0.40
146 29 0.11
149 57 0.21
150 4 0.01
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.27
Consensus pattern (144 bp):
AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
AAAAATATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGTA
TAGAGATAAATAAA
Found at i:763888 original size:10 final size:10
Alignment explanation
Indices: 763873--763901 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
763863 ATGTATAGAG
763873 ATAAATAAAA
1 ATAAATAAAA
763883 ATAAATAAAA
1 ATAAATAAAA
763893 ATAAATAAA
1 ATAAATAAA
763902 GTAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:763912 original size:19 final size:19
Alignment explanation
Indices: 763873--763913 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
763863 ATGTATAGAG
*
763873 ATAAATAAAAATAAATAAAA
1 ATAAAT-AAAGTAAATAAAA
763893 ATAAATAAAGTAAATGAAAA
1 ATAAATAAAGTAAAT-AAAA
763913 A
1 A
763914 ATATAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAATAAAGTAAATAAAA
Found at i:763919 original size:19 final size:18
Alignment explanation
Indices: 763875--763921 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
763865 GTATAGAGAT
*
763875 AAATA-AAAATAAATAAA
1 AAATATAAAGTAAATAAA
*
763892 AATAAATAAAGTAAATGAAA
1 AA-ATATAAAGTAAAT-AAA
763912 AAATATAAAG
1 AAATATAAAG
763922 AATATACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 2 0.08
19 15 0.62
20 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAATATAAAGTAAATAAA
Found at i:764016 original size:2 final size:2
Alignment explanation
Indices: 764009--764092 Score: 86
Period size: 2 Copynumber: 44.0 Consensus size: 2
763999 GATGGTTATG
764009 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
764050 -A AA TA -A AA TA AA AA TA TA CA TA -A GA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
764089 TA TA
1 TA TA
764093 AATAAAGGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
1 4 0.06
2 67 0.94
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:764128 original size:50 final size:50
Alignment explanation
Indices: 764024--764135 Score: 131
Period size: 50 Copynumber: 2.2 Consensus size: 50
764014 ATATATATAT
* *
764024 ATATATATATATATATATATATAATAAAATAAAATAAAAATATACATAAG
1 ATATATATATATATATATAAATAATAAAATAAAATAAAAATATACATAAA
* *
764074 ATATATATATATATATATAAATAA-AGGAATAAAAT-ATAATAATA-ATGAAA
1 ATATATATATATATATATAAATAATA-AAATAAAATAAAAAT-ATACAT-AAA
764124 ATATAGTATATA
1 ATATA-TATATA
764136 ATAATAGTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
49 7 0.13
50 41 0.76
51 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (50 bp):
ATATATATATATATATATAAATAATAAAATAAAATAAAAATATACATAAA
Found at i:765945 original size:105 final size:105
Alignment explanation
Indices: 765758--766424 Score: 1129
Period size: 105 Copynumber: 6.3 Consensus size: 105
765748 TGTTTCGAGG
* * * * * *
765758 CCAATATCTTTCGCTATGAAGTTGAAATTGGCTCCGAAAT-TGGGAAATTATTTGTTGACAACCA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATCTGAGAAA-TGTTTGTTGACAACCA
* *
765822 GCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTAGAGT
64 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
765864 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
765929 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
765969 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
766034 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
766074 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTAAGAAATATTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
*
766139 GGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
766179 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
*
766244 GATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
766284 CTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
*
766349 GGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
766389 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
766425 GGTAAAACCT
Statistics
Matches: 537, Mismatches: 23, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
105 499 0.93
106 38 0.07
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:767187 original size:9 final size:8
Alignment explanation
Indices: 767166--767214 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
767156 ACCCGTATTA
*
767166 TTTTCTCT
1 TTTTTTCT
*
767174 TTTTTTGT
1 TTTTTTCT
767182 TCTTTTTCCT
1 T-TTTTT-CT
767192 TTTTTTCT
1 TTTTTTCT
767200 TTTTTTCT
1 TTTTTTCT
767208 CTTTTTT
1 -TTTTTT
767215 TTCAACTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 17 0.49
9 16 0.46
10 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:767193 original size:18 final size:18
Alignment explanation
Indices: 767166--767215 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
767156 ACCCGTATTA
*
767166 TTTTCTCTTTTTTTGTTCT
1 TTTTCTCTTTTTTTCTT-T
767185 TTTTC-CTTTTTTTCTTT
1 TTTTCTCTTTTTTTCTTT
767202 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
767216 TCAACTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTCTCTTTTTTTCTTT
Found at i:767197 original size:10 final size:9
Alignment explanation
Indices: 767166--767215 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
767156 ACCCGTATTA
767166 TTTTCTCTTT
1 TTTTC-CTTT
*
767176 TTTT-GTTCT
1 TTTTCCTT-T
767185 TTTTCCTTT
1 TTTTCCTTT
767194 TTTT-CTTT
1 TTTTCCTTT
767202 TTTTCTCTTT
1 TTTTC-CTTT
767212 TTTT
1 TTTT
767216 TCAACTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 10 0.29
9 10 0.29
10 14 0.41
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:767217 original size:19 final size:19
Alignment explanation
Indices: 767166--767217 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
767156 ACCCGTATTA
767166 TTTTCTCTTTTTTTGT-TCT
1 TTTTCTCTTTTTTT-TCTCT
*
767185 TTTTC-C-TTTTTTTCTTT
1 TTTTCTCTTTTTTTTCTCT
767202 TTTTCTCTTTTTTTTC
1 TTTTCTCTTTTTTTTC
767218 AACTTAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.45
18 2 0.07
19 13 0.45
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTCTCTTTTTTTTCTCT
Found at i:777983 original size:10 final size:10
Alignment explanation
Indices: 777968--778007 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
777958 GTATAGAGAT
777968 AATAAAAATA
1 AATAAAAATA
777978 AATAAAAATA
1 AATAAAAATA
*
777988 AAT-AAAGTA
1 AATAAAAATA
777997 AATGAAAAATA
1 AAT-AAAAATA
778008 TAAAGAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.31
10 13 0.50
11 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (10 bp):
AATAAAAATA
Found at i:778012 original size:18 final size:18
Alignment explanation
Indices: 777966--778012 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
777956 ATGTATAGAG
*
777966 ATAATAAAAATAAATAAAA
1 ATAAT-AAAGTAAATAAAA
777985 ATAAATAAAGTAAATGAAAA
1 AT-AATAAAGTAAAT-AAAA
778005 AT-ATAAAG
1 ATAATAAAG
778013 AATACATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 10 0.40
20 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
ATAATAAAGTAAATAAAA
Found at i:778117 original size:10 final size:10
Alignment explanation
Indices: 778102--778130 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
778092 ATGTATAGAG
778102 ATAAATAAAA
1 ATAAATAAAA
778112 ATAAATAAAA
1 ATAAATAAAA
778122 ATAAATAAA
1 ATAAATAAA
778131 GTAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:778141 original size:19 final size:19
Alignment explanation
Indices: 778102--778142 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
778092 ATGTATAGAG
*
778102 ATAAATAAAAATAAATAAAA
1 ATAAAT-AAAGTAAATAAAA
778122 ATAAATAAAGTAAATGAAAA
1 ATAAATAAAGTAAAT-AAAA
778142 A
1 A
778143 ATATAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAATAAAGTAAATAAAA
Found at i:778148 original size:19 final size:18
Alignment explanation
Indices: 778104--778150 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
778094 GTATAGAGAT
*
778104 AAATA-AAAATAAATAAA
1 AAATATAAAGTAAATAAA
*
778121 AATAAATAAAGTAAATGAAA
1 AA-ATATAAAGTAAAT-AAA
778141 AAATATAAAG
1 AAATATAAAG
778151 AATATACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 2 0.08
18 2 0.08
19 15 0.62
20 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAATATAAAGTAAATAAA
Found at i:778215 original size:143 final size:141
Alignment explanation
Indices: 777832--778241 Score: 683
Period size: 143 Copynumber: 2.9 Consensus size: 141
777822 AAGGAAACGC
777832 AATAGAATAAAAAT-AATAAAGTAAATGAAAAAA-ATAAAGAATATACATATAATAATAAAAGAA
1 AATA-AATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAG-A
*
777895 AACAAAAATATGTTTATATACGCTATCAATAATACCTAAAAATAATAAAATT-ACGATGGTTATG
64 AA-AAAAATATGTTTATATACGCTATCAATAATA-CTTAAAATAATAAAATTAACGATGGTTATG
777959 TATAGAGATAATAAA
127 TATAGAGATAATAAA
777974 AATAAATAAAAATAAATAAAGTAAATG-AAAAATATAAAG-A-ATACATATAATAATAAAAGAAA
1 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
*
778036 AAAAATATG-TT-TATACGTTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGTATA
66 AAAAATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGTATA
778099 GAGATAAATAAA
131 GAGAT-AATAAA
778111 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
1 AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
*
778176 AAAATATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAAATAACGATGGTTATGTAT
66 AAAA-ATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGTAT
778241 A
130 A
778242 TATATATATA
Statistics
Matches: 254, Mismatches: 4, Indels: 19
0.92 0.01 0.07
Matches are distributed among these distances:
135 16 0.06
136 38 0.15
137 35 0.14
138 21 0.08
139 4 0.02
140 45 0.18
141 20 0.08
142 25 0.10
143 50 0.20
ACGTcount: A:0.60, C:0.05, G:0.09, T:0.27
Consensus pattern (141 bp):
AATAAATAAAAATAAATAAAGTAAATGAAAAAATATAAAGAATATACATATAATAATAAAAGAAA
AAAAATATGTTTATATACGCTATCAATAATACTTAAAATAATAAAATTAACGATGGTTATGTATA
GAGATAATAAA
Found at i:778245 original size:2 final size:2
Alignment explanation
Indices: 778238--778280 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
778228 GATGGTTATG
778238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
778279 TA
1 TA
778281 AATAAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:778328 original size:39 final size:40
Alignment explanation
Indices: 778261--778361 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 40
778251 ATATATATAT
* *
778261 ATATATATATATAATATATAAATAAAAATAAAATACATAAG
1 ATATATATATATAATAAAGAAATAAAAATAAAATA-ATAAG
* *
778302 ATATATATATA-AATAAAGGAATAAAATATAATAATAATGAAA
1 ATATATATATATAATAAAGAAATAAAA-ATAA-AATAAT-AAG
778344 ATATAGTATATAATAATA
1 ATATA-TATAT-ATAATA
778362 GTAGGGATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
40 12 0.24
41 17 0.34
42 11 0.22
43 5 0.10
44 1 0.02
45 4 0.08
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (40 bp):
ATATATATATATAATAAAGAAATAAAAATAAAATAATAAG
Found at i:779791 original size:16 final size:16
Alignment explanation
Indices: 779770--779805 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
779760 TTAGAATCTG
*
779770 TGAAGGAATCGGAATC
1 TGAAGGAATCAGAATC
*
779786 TGAAGGAATTAGAATC
1 TGAAGGAATCAGAATC
779802 TGAA
1 TGAA
779806 TTTGAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.28, T:0.22
Consensus pattern (16 bp):
TGAAGGAATCAGAATC
Found at i:780370 original size:32 final size:32
Alignment explanation
Indices: 780328--780477 Score: 174
Period size: 33 Copynumber: 4.5 Consensus size: 32
780318 CCTAAACCTG
*
780328 AACCTGACCCGACCCGAATATCACACTTAAAAA
1 AACC-GACCCGACCCGAATATCAAACTTAAAAA
* * *
780361 AACCTACCCGACCCAAATATCACACTTAAAAA
1 AACCGACCCGACCCGAATATCAAACTTAAAAA
* *
780393 AATCAGACCCGACCCGAATATCAAACTTTAAAGA
1 AA-CCGACCCGACCCGAATATCAAAC-TTAAAAA
* *
780427 ACCCGACCTCAACCCGAATATCAAACTTAAAAA
1 AACCGACC-CGACCCGAATATCAAACTTAAAAA
*
780460 CACTCGACCCGACCCGAA
1 AAC-CGACCCGACCCGAA
780478 CCCGAATTTT
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
32 28 0.28
33 43 0.43
34 28 0.28
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.15
Consensus pattern (32 bp):
AACCGACCCGACCCGAATATCAAACTTAAAAA
Found at i:780471 original size:67 final size:65
Alignment explanation
Indices: 780333--780477 Score: 184
Period size: 67 Copynumber: 2.2 Consensus size: 65
780323 ACCTGAACCT
* * * *
780333 GACCCGACCCGAATATCACACTTAAAAAAACCTACCCGACCCAAATATCACACTTAAAAAAATCA
1 GACCCGACCCGAATATCAAACTTAAAAAAACCGACCCAACCCAAATATCAAACTTAAAAAAATCA
* * * *
780398 GACCCGACCCGAATATCAAACTTTAAAGAACCCGACCTCAACCCGAATATCAAACTTAAAAACAC
1 GACCCGACCCGAATATCAAAC-TTAAAAAAACCGACC-CAACCCAAATATCAAACTTAAAAA-AA
780463 TC-
63 TCA
780465 GACCCGACCCGAA
1 GACCCGACCCGAA
780478 CCCGAATTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
65 20 0.29
66 12 0.17
67 34 0.49
68 3 0.04
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.14
Consensus pattern (65 bp):
GACCCGACCCGAATATCAAACTTAAAAAAACCGACCCAACCCAAATATCAAACTTAAAAAAATCA
Found at i:785629 original size:2 final size:2
Alignment explanation
Indices: 785622--785657 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
785612 CCCTAACAGC
785622 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
785658 GCTTTTAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:790819 original size:15 final size:14
Alignment explanation
Indices: 790795--790825 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
790785 ATACAATAAT
790795 ATAACAATTTTCTA
1 ATAACAATTTTCTA
790809 ATAACCAATTTTCTA
1 ATAA-CAATTTTCTA
790824 AT
1 AT
790826 TATAACACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAACAATTTTCTA
Found at i:792056 original size:22 final size:22
Alignment explanation
Indices: 792026--792081 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
792016 ACTCTCTACG
*
792026 GCGACATCCGTCCCCATCTCC-
1 GCGAAATCCGTCCCCATCTCCA
*
792047 GACGAAATCCATCCCCATCTCCA
1 G-CGAAATCCGTCCCCATCTCCA
792070 GCGAAATCCGTC
1 GCGAAATCCGTC
792082 TATCTCCATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
GCGAAATCCGTCCCCATCTCCA
Found at i:792472 original size:20 final size:20
Alignment explanation
Indices: 792438--792540 Score: 109
Period size: 20 Copynumber: 5.2 Consensus size: 20
792428 AAAATCGCAA
**
792438 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
* *
792458 CGATAATCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
**
792478 CGATTTTCA-TTTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
**
792497 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTG
* *
792517 TGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTG
792537 CGAT
1 CGAT
792541 TTTAAGTTTC
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 16 0.24
20 51 0.76
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (20 bp):
CGATAGTCATTTTCGCGTTG
Found at i:792527 original size:39 final size:39
Alignment explanation
Indices: 792438--792540 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
792428 AAAATCGCAA
* ** *
792438 CGATAGTCAAATTCGCGTTGCGATAATCATTTTCGTGTTG
1 CGATAGTC-ATTTCGCGTTGCGATAATCAAATTCGCGTTG
** *
792478 CGATTTTCATTTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTCGCGTTGCGATAATCAAATTCGCGTTG
* *
792517 TGATAGTCATTTTCGTGTTGCGAT
1 CGATAGTCA-TTTCGCGTTGCGAT
792541 TTTAAGTTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 32 0.63
40 19 0.37
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.40
Consensus pattern (39 bp):
CGATAGTCATTTCGCGTTGCGATAATCAAATTCGCGTTG
Found at i:794460 original size:19 final size:20
Alignment explanation
Indices: 794436--794481 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
794426 AGAAGAATAG
*
794436 TCGCAACAC-GAAACTTA-AA
1 TCGCAACACAGAAA-TGACAA
794455 TCGCAACACAGAAATGACAA
1 TCGCAACACAGAAATGACAA
794475 TCGCAAC
1 TCGCAAC
794482 GCAAATTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.46, C:0.28, G:0.13, T:0.13
Consensus pattern (20 bp):
TCGCAACACAGAAATGACAA
Found at i:794612 original size:19 final size:20
Alignment explanation
Indices: 794574--794612 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
794564 GCAACGCGAA
* *
794574 TTTAGTTTCGCGTTGTGATT
1 TTTAGTTTCGCATTGCGATT
794594 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
794613 ATCCCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.54
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:794680 original size:19 final size:20
Alignment explanation
Indices: 794652--794694 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
794642 CGATAGTCAT
794652 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
794671 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
794691 TTTC
1 TTTC
794695 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:794847 original size:13 final size:13
Alignment explanation
Indices: 794829--794854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
794819 TATGTTGTCC
794829 TTGAACATGCACT
1 TTGAACATGCACT
794842 TTGAACATGCACT
1 TTGAACATGCACT
794855 AAACCTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TTGAACATGCACT
Found at i:795239 original size:21 final size:20
Alignment explanation
Indices: 795187--795275 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 20
795177 AACTCACCTG
*
795187 TCATCGCTCAAGAGGCCTCT
1 TCATCCCTCAAGAGGCCTCT
* **
795207 CCTATCGTTCAAGAGGCCTCT
1 TC-ATCCCTCAAGAGGCCTCT
* *
795228 ATCATCCCTCAAGAGTCCCCT
1 -TCATCCCTCAAGAGGCCTCT
*
795249 CTCA-CCGTTCAAGAGGCCTCT
1 -TCATCC-CTCAAGAGGCCTCT
795270 GTCATC
1 -TCATC
795276 ATTGAAGAGG
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 3 0.06
21 48 0.91
22 2 0.04
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (20 bp):
TCATCCCTCAAGAGGCCTCT
Found at i:795284 original size:42 final size:42
Alignment explanation
Indices: 795187--795305 Score: 125
Period size: 42 Copynumber: 2.8 Consensus size: 42
795177 AACTCACCTG
* * *
795187 TCATCGCTCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCTCTA
1 TCATCACTCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCTCTA
* * *
795229 TCATCCCTCAAGA-GTCCCCTCTCACCGTTCAAGAGGCCTCTG
1 TCATCACTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCTCTA
* * *
795271 TCATCATTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCACTCAAGAGGTCCCTCCCACCGTTCAAGAG
795306 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 59 0.92
43 4 0.06
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCACTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCTCTA
Found at i:796715 original size:14 final size:14
Alignment explanation
Indices: 796696--796758 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
796686 TTTACTTTTT
796696 AAATTGATTTGTAA
1 AAATTGATTTGTAA
796710 AAATTGATTTGTAA
1 AAATTGATTTGTAA
* *
796724 AAGTTGATTTGTTTA
1 AAATTGATTTG-TAA
* *
796739 ATATTGATGTGTAA
1 AAATTGATTTGTAA
796753 ATAATT
1 A-AATT
796759 CTTATTTGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 27 0.68
15 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (14 bp):
AAATTGATTTGTAA
Found at i:796733 original size:28 final size:29
Alignment explanation
Indices: 796699--796753 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
796689 ACTTTTTAAA
*
796699 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
796727 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
796754 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:796882 original size:20 final size:20
Alignment explanation
Indices: 796857--796910 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
796847 AGGTACACTT
*
796857 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
796877 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
796897 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
796911 TCAATTCGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:796979 original size:34 final size:34
Alignment explanation
Indices: 796920--797089 Score: 128
Period size: 34 Copynumber: 4.8 Consensus size: 34
796910 GTCAATTCGT
* *
796920 GTTGCGATAGTCTAATACGCTTTGCGATTTTCTC
1 GTTGCGATAGTCAAATACGCATTGCGATTTTCTC
* * *
796954 GTTGCGATAGTCAAATACCCATTGCGATAATCAAATCCAC
1 GTTGCGATAGTCAAATACGCATTGCGAT--T----TTCTC
* *
796994 GTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGC
1 GTTGCGATAGTCAAATACGCATTGCGATTTTCT-C
* * * *
797028 GTTGCGATAGTCAAATTCGCGTTGTGATTTT-TGA
1 GTTGCGATAGTCAAATACGCATTGCGATTTTCT-C
* * *
797062 GTTGCGATAATCAAATTCGCGTTGCGAT
1 GTTGCGATAGTCAAATACGCATTGCGAT
797090 AGTCAAATTC
Statistics
Matches: 115, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
34 85 0.74
36 1 0.01
38 1 0.01
40 28 0.24
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (34 bp):
GTTGCGATAGTCAAATACGCATTGCGATTTTCTC
Found at i:797016 original size:20 final size:20
Alignment explanation
Indices: 796953--797117 Score: 138
Period size: 20 Copynumber: 8.8 Consensus size: 20
796943 GCGATTTTCT
* *
796953 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* * * *
796973 CATTGCGATAATCAAATCCA
1 CGTTGCGATAGTCAAATTCG
796993 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
797013 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
797027 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
797047 CGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
797061 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
797081 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
797101 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
797118 GAATGTGTAA
Statistics
Matches: 115, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 22 0.19
16 2 0.02
18 2 0.02
20 89 0.77
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:797340 original size:140 final size:140
Alignment explanation
Indices: 797088--797370 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
797078 TCGCGTTGCG
797088 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAATGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAATGATAACAACTGAACAGATCA
* * * *
797153 TAGCAATGTTTAGACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAAATGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
797218 AATGCACATA
131 AATACACATA
*
797228 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAATGATAACAACTGAACAGATCA
797293 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
797358 AATACACATA
131 AATACACATA
797368 ATA
1 ATA
797371 CAACGTTTGC
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAATGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:797451 original size:18 final size:18
Alignment explanation
Indices: 797428--797462 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
797418 AAGCCGGTTG
*
797428 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
797446 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
797463 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:799763 original size:24 final size:24
Alignment explanation
Indices: 799736--799782 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
799726 CAAAATCCGA
799736 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
799760 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
799783 AATACCGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:811654 original size:2 final size:2
Alignment explanation
Indices: 811649--811696 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
811639 CATAAAAAAT
811649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
811691 CA TA TA
1 TA TA TA
811697 CTTGATACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:815614 original size:24 final size:24
Alignment explanation
Indices: 815587--815634 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
815577 CCTCATCCAG
815587 CTCCACTTCCT-CTTCTTCTTCAAC
1 CTCCACTT-CTACTTCTTCTTCAAC
*
815611 CTCCTCTTCTACTTCTTCTTCAAC
1 CTCCACTTCTACTTCTTCTTCAAC
815635 TTCCTCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (24 bp):
CTCCACTTCTACTTCTTCTTCAAC
Found at i:815618 original size:12 final size:12
Alignment explanation
Indices: 815598--815651 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
815588 TCCACTTCCT
*
815598 CTTCTTCTTCAA
1 CTTCCTCTTCAA
* *
815610 CCTCCTCTTCTA
1 CTTCCTCTTCAA
*
815622 CTTCTTCTTCAA
1 CTTCCTCTTCAA
*
815634 CTTCCTCCTCAA
1 CTTCCTCTTCAA
815646 CTTCCT
1 CTTCCT
815652 GGGGTTGTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTCCTCTTCAA
Found at i:815639 original size:24 final size:24
Alignment explanation
Indices: 815598--815649 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
815588 TCCACTTCCT
* *
815598 CTTCTTCTTCAACCTCCTCTTCTA
1 CTTCTTCTTCAACCTCCTCCTCAA
*
815622 CTTCTTCTTCAACTTCCTCCTCAA
1 CTTCTTCTTCAACCTCCTCCTCAA
815646 CTTC
1 CTTC
815650 CTGGGGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.44
Consensus pattern (24 bp):
CTTCTTCTTCAACCTCCTCCTCAA
Found at i:816408 original size:14 final size:14
Alignment explanation
Indices: 816372--816411 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
816362 CATCTCAAAC
*
816372 CTCTAAATATATAAA
1 CTCTAAAT-TTTAAA
816387 CTTCTAAATTTTAAA
1 C-TCTAAATTTTAAA
816402 CTCTAAATTT
1 CTCTAAATTT
816412 AGTGGGTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 7 0.30
16 7 0.30
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (14 bp):
CTCTAAATTTTAAA
Found at i:817621 original size:27 final size:27
Alignment explanation
Indices: 817583--817647 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
817573 AGAACATTGA
817583 TTATTTTCTTTAATTGATATTTATTTG
1 TTATTTTCTTTAATTGATATTTATTTG
817610 TTATTTTCTTTAATTGATATTTATTTG
1 TTATTTTCTTTAATTGATATTTATTTG
817637 TTATTTTCTTT
1 TTATTTTCTTT
817648 TTACCTACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.20, C:0.05, G:0.06, T:0.69
Consensus pattern (27 bp):
TTATTTTCTTTAATTGATATTTATTTG
Found at i:819775 original size:18 final size:18
Alignment explanation
Indices: 819752--819803 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
819742 GACCGGTCCT
*
819752 GACCCGACTCGTTGATCC
1 GACCCGACTCGTTGACCC
*
819770 GACCCGACCCGTTGACCC
1 GACCCGACTCGTTGACCC
819788 GACCCGA-TCGTTGACC
1 GACCCGACTCGTTGACC
819804 GTTGATCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 8 0.26
18 23 0.74
ACGTcount: A:0.17, C:0.42, G:0.23, T:0.17
Consensus pattern (18 bp):
GACCCGACTCGTTGACCC
Found at i:819858 original size:29 final size:28
Alignment explanation
Indices: 819816--819913 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 28
819806 TGATCGATGT
*
819816 TATTCTGGTAAATAATTCAGTTTTGGTGC
1 TATTTTGGTAAATAATTC-GTTTTGGTGC
* *
819845 TATTTTGGTAAATAATTTGGTTTTGGTAC
1 TATTTTGGTAAATAA-TTCGTTTTGGTGC
* * ** *
819874 TATTATGGTAATTAATTCGAAATGGGTGC
1 TATTTTGGTAAATAATTCG-TTTTGGTGC
819903 TATTTTGGTAA
1 TATTTTGGTAA
819914 TTATTTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 3 0.05
29 51 0.91
30 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (28 bp):
TATTTTGGTAAATAATTCGTTTTGGTGC
Found at i:827204 original size:17 final size:18
Alignment explanation
Indices: 827172--827206 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
827162 TGACCGGTCA
827172 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
827190 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
827207 GTTGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:827256 original size:29 final size:29
Alignment explanation
Indices: 827214--827294 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
827204 ACCGTTGACC
*
827214 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTATGGTAAATAATTCAGTTTT
**
827243 GGTGCTATTATGGTAAATAATTTGGTTTT
1 GGTGCTATTATGGTAAATAATTCAGTTTT
*
827272 GGTGCTA-TACTGGTAATTAATTC
1 GGTGCTATTA-TGGTAAATAATTC
827295 GAAATGGGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 2 0.04
29 44 0.96
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (29 bp):
GGTGCTATTATGGTAAATAATTCAGTTTT
Found at i:839061 original size:20 final size:20
Alignment explanation
Indices: 838922--839072 Score: 96
Period size: 20 Copynumber: 7.6 Consensus size: 20
838912 AAATGACCAA
*
838922 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
838942 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
*
838961 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
* ** *
838984 -AAA-TCGGATTGCGATTTTT
1 CAAATTCGCAACGCGA-ATTT
* * **
839003 CAAATTTGCAACGCAAAAGT
1 CAAATTCGCAACGCGAATTT
*
839023 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
839042 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
839062 -AATTTCGCAAC
1 CAAATTCGCAAC
839073 AGGTTTTAGT
Statistics
Matches: 97, Mismatches: 26, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
19 30 0.31
20 53 0.55
21 12 0.12
22 1 0.01
23 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:839832 original size:12 final size:12
Alignment explanation
Indices: 839811--839844 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
839801 ACCACATTTC
*
839811 CAATACCAAACA
1 CAATATCAAACA
839823 CAATATCAAACA
1 CAATATCAAACA
*
839835 CAATCTCAAA
1 CAATATCAAA
839845 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:842632 original size:20 final size:20
Alignment explanation
Indices: 842604--842653 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
842594 ATGTTGCGAT
* *
842604 CAACACGAAAGTTAAATTGG
1 CAACGCGAAAGTAAAATTGG
*
842624 CAACGCGAAAGTAAAATTTG
1 CAACGCGAAAGTAAAATTGG
842644 CAACGCGAAA
1 CAACGCGAAA
842654 TAAGCGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (20 bp):
CAACGCGAAAGTAAAATTGG
Found at i:842685 original size:20 final size:20
Alignment explanation
Indices: 842662--842721 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
842652 AATAAGCGTT
842662 GCAATAGTCAAATTCGCAAC
1 GCAATAGTCAAATTCGCAAC
* *
842682 GCAAAAGACAAATTCGCAAC
1 GCAATAGTCAAATTCGCAAC
*
842702 GCGATAGTCAAATTCGCAAC
1 GCAATAGTCAAATTCGCAAC
842722 ACGAAATCGC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
GCAATAGTCAAATTCGCAAC
Found at i:842808 original size:20 final size:20
Alignment explanation
Indices: 842780--842821 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
842770 GCAACGCTTA
*
842780 TTTCACGTTGCGAATTTACC
1 TTTCACGTTGCGAAATTACC
*
842800 TTTCGCGTTGCGAAATTACC
1 TTTCACGTTGCGAAATTACC
842820 TT
1 TT
842822 CAACATAATG
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:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTCACGTTGCGAAATTACC
Found at i:842903 original size:25 final size:25
Alignment explanation
Indices: 842862--842910 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
842852 AAATCAATTA
* *
842862 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGAGTACATTATTTG
842887 AACATTGTTATGAGTACATTATTT
1 AACATTGTTATGAGTACATTATTT
842911 AGAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (25 bp):
AACATTGTTATGAGTACATTATTTG
Found at i:843671 original size:39 final size:39
Alignment explanation
Indices: 843628--843716 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
843618 TACGATGCTC
843628 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
843667 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
843706 ATCAAAATCTA
1 ATCAAAATCTA
843717 CAACTGGAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:844075 original size:66 final size:60
Alignment explanation
Indices: 843995--844134 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
843985 TTTTAAAAAC
*
843995 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACAAATC-AATT
844060 A
60 A
* * **
844061 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
844121 AACAAATCAACTTT
1 AACAAATCAACTTT
844135 CAATATAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 19 0.28
61 21 0.30
62 3 0.04
66 26 0.38
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:845540 original size:21 final size:21
Alignment explanation
Indices: 845493--845610 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
845483 GTGAATCGGG
* * * *
845493 CTCTTGAACGGTGGGCGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
845514 CACTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
845535 CTCTTGAACGGTG-GAAGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
845555 TTCTTCG-ATGATGAGAGGGTC
1 CTCTT-GAACGATGAGAGGGGC
*
845576 CTCTTGAACGAT-AGGAGGTGC
1 CTCTTGAACGATGA-GAGGGGC
*
845597 CTCTTGAATGATGA
1 CTCTTGAACGATGA
845611 TAGGTGCATC
Statistics
Matches: 72, Mismatches: 20, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
20 15 0.21
21 56 0.78
22 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:848103 original size:22 final size:22
Alignment explanation
Indices: 848075--848128 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
848065 GATGGAGATA
**
848075 GACGGATTTTGTCGAAAATGGG
1 GACGGATTTCATCGAAAATGGG
* *
848097 GACGGATTTCATCGGATATGGG
1 GACGGATTTCATCGAAAATGGG
848119 GACGGATTTC
1 GACGGATTTC
848129 GCCGTAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.35, T:0.28
Consensus pattern (22 bp):
GACGGATTTCATCGAAAATGGG
Found at i:848278 original size:20 final size:20
Alignment explanation
Indices: 848253--848301 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
848243 GCGTAAAAAC
848253 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
848273 ATTTGACTATCGCGTTTCGA
1 ATTTGACTTTCGCGTTGCGA
848293 ATTTGACTT
1 ATTTGACTT
848302 CTGTGTTGCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:851379 original size:32 final size:32
Alignment explanation
Indices: 851338--851401 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
851328 GCAATAACAC
851338 CCGCGATGGCCACAATCATGATAAATCCGAAA
1 CCGCGATGGCCACAATCATGATAAATCCGAAA
851370 CCGCGATGGCCACAATCATGATAAATCCGAAA
1 CCGCGATGGCCACAATCATGATAAATCCGAAA
851402 TTACCGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.16
Consensus pattern (32 bp):
CCGCGATGGCCACAATCATGATAAATCCGAAA
Found at i:856805 original size:15 final size:15
Alignment explanation
Indices: 856769--856820 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
856759 TTACAAAAAA
*
856769 TATATTTTTATTATAAT
1 TATATTTTT-TT-TATT
856786 TATATTTTTTTTATT
1 TATATTTTTTTTATT
*
856801 TATATTTTTTATATT
1 TATATTTTTTTTATT
856816 T-TATT
1 TATATT
856821 ATATTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 4 0.12
15 18 0.55
16 2 0.06
17 9 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATATTTTTTTTATT
Found at i:857030 original size:13 final size:14
Alignment explanation
Indices: 857006--857064 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
856996 TATATTTTTG
*
857006 TTATAATTATATTT
1 TTATATTTATATTT
857020 TT-TATTTATATTT
1 TTATATTTATATTT
*
857033 TTATATTTAAATTAT
1 TTATATTTATATT-T
*
857048 AATTATAATTATATTT
1 --TTATATTTATATTT
857064 T
1 T
857065 ATTATTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 12 0.32
14 12 0.32
15 1 0.03
16 1 0.03
17 11 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATATTTATATTT
Found at i:857040 original size:111 final size:110
Alignment explanation
Indices: 856700--857047 Score: 314
Period size: 114 Copynumber: 3.1 Consensus size: 110
856690 TTAATAATTT
* *
856700 TTTTAATTATTAAAAATAAATAAAATTCATGATTTATATATTAAAATATTAATAGTGATTTACAA
1 TTTTAATTATTAAAAATAAATAAAATTCAAGATTTATATATTAAAATATTAATAGTGA-TTACAT
856765 AAAATATATTTTTATTATAATTATATTTTTTTTATTTATATTTTTTATA
65 AAAATATATTTTTATTATAATTATA--TTTTTTATTTATA-TTTTTATA
** ** * * * * * * * *
856814 TTTT-ATTATATTTAAATTGATATAATTCATACATAATATTTTTTAAAAAATTTATTA-TAATT-
1 TTTTAATTAT-TAAAAATAAATAAAATTCA-AGAT-TTATATATTAAAATA-TTAATAGTGATTA
* * * * **
856876 --TAAATTGATATTATTCATATATAAATATAATTTATTACTTT-TAATAATT-TA
62 CATAAAAT-ATATT-TTTAT-TATAATTAT-ATTTTTTA-TTTAT-ATTTTTATA
856927 TTTTAATTATTAAAAATAAATAAAATTCAAGATTTATATATTAAAATATTAATAGTGATGTACAT
1 TTTTAATTATTAAAAATAAATAAAATTCAAGATTTATATATTAAAATATTAATAGTGAT-TACAT
*
856992 AAAATATATTTTTGTTATAATTATATTTTTTATTTATATTTTTATA
65 AAAATATATTTTTATTATAATTATATTTTTTATTTATATTTTTATA
*
857038 TTTAAATTAT
1 TTTTAATTAT
857048 AATTATAATT
Statistics
Matches: 176, Mismatches: 40, Indels: 39
0.69 0.16 0.15
Matches are distributed among these distances:
110 12 0.07
111 33 0.19
112 16 0.09
113 33 0.19
114 42 0.24
115 21 0.12
116 14 0.08
117 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (110 bp):
TTTTAATTATTAAAAATAAATAAAATTCAAGATTTATATATTAAAATATTAATAGTGATTACATA
AAATATATTTTTATTATAATTATATTTTTTATTTATATTTTTATA
Found at i:857066 original size:38 final size:41
Alignment explanation
Indices: 857006--857086 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 41
856996 TATATTTTTG
* *
857006 TTATAATTATATTTTTTATTTA-TA-TTT-TTATATTTAAA
1 TTATAATTATATTATATATTTATTATTTTATTATATTTAAA
857044 TTATAATTATAATTATAT-TTTATTATTTTATTATATTTAAA
1 TTATAATTAT-ATTATATATTTATTATTTTATTATATTTAAA
857085 TT
1 TT
857087 GATATAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
38 14 0.38
39 7 0.19
40 3 0.08
41 13 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (41 bp):
TTATAATTATATTATATATTTATTATTTTATTATATTTAAA
Found at i:857095 original size:38 final size:42
Alignment explanation
Indices: 857006--857086 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 42
856996 TATATTTTTG
857006 TTATAATTATATTTTTTATTTATATTTTTATATTTAAATTATAA
1 TTATAATTATATTTTTTATTTATA--TTTATATTTAAATTATAA
857050 TTATAATTATATTTTATTATTT-TA-TTATATTTAAATT
1 TTATAATTATATTTT-TTATTTATATTTATATTTAAATT
857087 GATATAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
41 13 0.36
44 17 0.47
45 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (42 bp):
TTATAATTATATTTTTTATTTATATTTATATTTAAATTATAA
Found at i:857102 original size:41 final size:40
Alignment explanation
Indices: 857007--857102 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 40
856997 ATATTTTTGT
*
857007 TATAATTATATTTTTTATTTATATTTTTATATTTAAATTA
1 TATAATTATATATTTTATTTATATTTTTATATTTAAATTA
* *
857047 TAATTATAATTATATTTTA-TTAT-TTTATTATATTTAAATTGA
1 T-ATAATTA-TATATTTTATTTATATTT-TTATATTTAAATT-A
857089 TATAATTGATATAT
1 TATAATT-ATATAT
857103 ATTAATTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
40 4 0.09
41 31 0.67
42 11 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (40 bp):
TATAATTATATATTTTATTTATATTTTTATATTTAAATTA
Found at i:857149 original size:48 final size:47
Alignment explanation
Indices: 857051--857149 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 47
857041 AAATTATAAT
** *
857051 TATAATTATATTTTATTATTTTATTATATTTAAATTGATATAATTGA
1 TATAATTATATTTTAAAATTTTATTATATTTAAATTGATATAATTCA
* *
857098 TATATATTA-ATTTTAAAATTTTATTATAATTTAAGTTGATATTATTCA
1 TATA-ATTATATTTTAAAATTTTATTAT-ATTTAAATTGATATAATTCA
857146 TATA
1 TATA
857150 CAATTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 20 0.44
48 25 0.56
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (47 bp):
TATAATTATATTTTAAAATTTTATTATATTTAAATTGATATAATTCA
Found at i:866498 original size:28 final size:28
Alignment explanation
Indices: 866467--866531 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
866457 AAATTACACT
* *
866467 ATGGTCACTAATATTGATTTATCACAAA
1 ATGGTCACTAACATCGATTTATCACAAA
866495 ATGGTCACTAACATCGATTTATCACAAA
1 ATGGTCACTAACATCGATTTATCACAAA
*
866523 ATGATCACT
1 ATGGTCACT
866532 CATTCATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (28 bp):
ATGGTCACTAACATCGATTTATCACAAA
Found at i:869935 original size:20 final size:20
Alignment explanation
Indices: 869910--869963 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
869900 GACCAACAAA
869910 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
869930 TTCGCAAC-CTAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
869950 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
869964 ATGTAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:872672 original size:42 final size:42
Alignment explanation
Indices: 872625--872723 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
872615 GATGCACCTA
* * *
872625 TCATCATTCAAGAGGCACCTCCTATCGTTTAAGAGGCCCCTC-
1 TCATCATTCAAGAGGCACCTCCCATCGTTCAAAAGGCCCC-CG
* *
872667 TCATCA-TCGAAGATGCCCCTCCCATCGTTCAAAAGGCCCCCG
1 TCATCATTC-AAGAGGCACCTCCCATCGTTCAAAAGGCCCCCG
*
872709 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
872724 TCCCGCTCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
41 3 0.06
42 42 0.89
43 2 0.04
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCACCTCCCATCGTTCAAAAGGCCCCCG
Found at i:872705 original size:21 final size:21
Alignment explanation
Indices: 872626--872723 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
872616 ATGCACCTAT
* *
872626 CATCATTCAAGAGGCACCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * *
872647 TATCGTTTAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
* *
872668 CATC-ATCGAAGATGCCCCTCC
1 CATCGTTC-AAGAGGCCCCTCC
* *
872689 CATCGTTCAAAAGGCCCC-CGT
1 CATCGTTCAAGAGGCCCCTC-C
872710 CATCGTTCAAGAGG
1 CATCGTTCAAGAGG
872724 TCCCGCTCGC
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:874381 original size:39 final size:39
Alignment explanation
Indices: 874327--874410 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
874317 TCAAGTTGTA
*
874327 GATTTTGATTTCCTTTTGCATGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCATGACACCATATGAGATTTG
*
874366 GATTTTGATTTCCTTTTGCTTGACACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCATGACACCATATGAGATTTG
874405 GATTTT
1 GATTTT
874411 AATGAGCATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.46
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCATGACACCATATGAGATTTG
Found at i:874746 original size:18 final size:18
Alignment explanation
Indices: 874723--874759 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
874713 CGAAATTTAT
874723 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
874741 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
874759 A
1 A
874760 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:875180 original size:25 final size:25
Alignment explanation
Indices: 875146--875195 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
875136 ATTATTTTTC
875146 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCATAACAATGTT
875171 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCATAACAATGTT
875196 TAATTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCATAACAATGTT
Found at i:875290 original size:34 final size:29
Alignment explanation
Indices: 875247--875325 Score: 106
Period size: 28 Copynumber: 2.6 Consensus size: 29
875237 AGGTGAAGGT
875247 AAATTCGCAACGCGAATTAAGCATTGCGATAGTC
1 AAATTCGCAACGCGAA--AAG---TGCGATAGTC
875281 AAATTCGCAACGCG-AAAGTGCGATAGTC
1 AAATTCGCAACGCGAAAAGTGCGATAGTC
875309 AAATTCGCAACGCGAAA
1 AAATTCGCAACGCGAAA
875326 GTCAAATTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
28 24 0.55
29 2 0.05
31 3 0.07
33 1 0.02
34 14 0.32
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (29 bp):
AAATTCGCAACGCGAAAAGTGCGATAGTC
Found at i:875311 original size:28 final size:28
Alignment explanation
Indices: 875271--875327 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
875261 AATTAAGCAT
875271 TGCGATAGTCAAATTCGCAACGCGAAAG
1 TGCGATAGTCAAATTCGCAACGCGAAAG
875299 TGCGATAGTCAAATTCGCAACGCGAAAG
1 TGCGATAGTCAAATTCGCAACGCGAAAG
875327 T
1 T
875328 CAAATTCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (28 bp):
TGCGATAGTCAAATTCGCAACGCGAAAG
Found at i:875373 original size:20 final size:20
Alignment explanation
Indices: 875348--875407 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
875338 TTGCGATTTT
875348 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
* *
875368 GCGTTGCGAATTTGTCTTTC
1 GCGTTGCGAATTTGACTATC
875388 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
875408 ATAACGCTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:878218 original size:12 final size:12
Alignment explanation
Indices: 878185--878219 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
878175 AGGTTTTGGG
*
878185 GTTTGAGATTGT
1 GTTTGATATTGT
878197 GTTTGATATTGT
1 GTTTGATATTGT
*
878209 GTTTGGTATTG
1 GTTTGATATTG
878220 GAAATGTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (12 bp):
GTTTGATATTGT
Found at i:878991 original size:19 final size:20
Alignment explanation
Indices: 878964--879014 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
878954 ACTAAAACCT
*
878964 GTTGTGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
** *
878983 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGA
879003 GTTGCGAATTTG
1 GTTGCGAATTTG
879015 GAAAATCACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:879087 original size:20 final size:21
Alignment explanation
Indices: 879038--879093 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
879028 CGATTTACAT
879038 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGGAA
* *
879059 ACTAG-GTTGCGAAATTGG-A
1 ATTCGCGTTGCGAAATTGGAA
879078 ATTCGCGTTGC-AAATT
1 ATTCGCGTTGCGAAATT
879094 TGTTGGTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.30
20 18 0.60
21 3 0.10
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:879743 original size:12 final size:12
Alignment explanation
Indices: 879719--879753 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
879709 CTTTAACTCG
879719 TTATTATTTAAAA
1 TTATTA-TTAAAA
*
879732 TTGTTATTAAAA
1 TTATTATTAAAA
879744 TTATTATTAA
1 TTATTATTAA
879754 TAAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TTATTATTAAAA
Found at i:881295 original size:33 final size:33
Alignment explanation
Indices: 881211--881296 Score: 81
Period size: 33 Copynumber: 2.6 Consensus size: 33
881201 TGGTCACTAA
*
881211 TGTAAATTATTTTTTA-TT-TTATTTTTATTTCT
1 TGTAAATT-TTATTTATTTCTTATTTTTATTTCT
* * *
881243 TTTATAATTTAATAT-TTTCTTATTTTTATTT-T
1 TGTA-AATTTTATTTATTTCTTATTTTTATTTCT
881275 TCGTAAATTTTATTTATTTCTT
1 T-GTAAATTTTATTTATTTCTT
881297 CTGTGGCATT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
32 18 0.43
33 24 0.57
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (33 bp):
TGTAAATTTTATTTATTTCTTATTTTTATTTCT
Found at i:881497 original size:12 final size:12
Alignment explanation
Indices: 881480--881506 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
881470 GAATTGAATT
881480 TTTAAATTTCAA
1 TTTAAATTTCAA
881492 TTTAAATTTCAA
1 TTTAAATTTCAA
881504 TTT
1 TTT
881507 TCGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTTCAA
Found at i:885578 original size:31 final size:32
Alignment explanation
Indices: 885529--885615 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 32
885519 TGAGAGACAA
* * *
885529 TGGGGCATCTTTGAAGATTCAACATC-AA-AT
1 TGGGCCATATTTGGAGATTCAACATCGAATAT
885559 GTGGGCCAT-TATTGGAGATTCAACATCGAATAT
1 -TGGGCCATAT-TTGGAGATTCAACATCGAATAT
* *
885592 TGGGGCATATTTGGGGATTCAACA
1 TGGGCCATATTTGGAGATTCAACA
885616 CCCTGATGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 1 0.02
31 22 0.46
32 22 0.46
33 3 0.06
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (32 bp):
TGGGCCATATTTGGAGATTCAACATCGAATAT
Found at i:885898 original size:64 final size:64
Alignment explanation
Indices: 885795--885961 Score: 226
Period size: 64 Copynumber: 2.6 Consensus size: 64
885785 TACAGCTTTT
* * * ** * ** *
885795 AGAGTCAATTTCAACTTTACAATGAAGGGTATTAAACTCAACAAATAACTTTTTAGTTTTATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
885859 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
885923 AGAGTCAATTTCAGCTACACAGCGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
885962 GAAGCAATGT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 91 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:886111 original size:121 final size:121
Alignment explanation
Indices: 885964--886555 Score: 968
Period size: 121 Copynumber: 4.9 Consensus size: 121
885954 TTGGACTCGA
* * * * *
885964 AGCAATGTAACTCTTGGATTTTAACTTCATGACGAAGGATATCCAATTCAAAACTCAACTTCACA
1 AGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
*
886029 ACGAATGAGCCATCCACGATTTCAACTTCATGACGAAGGATATCGTGCCCACAAGC
66 ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
* * *
886085 AGCAATGCAACCTTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAATCTCAACTTCACA
1 AGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
*
886150 ACGAATGAGTCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
66 ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
* * *
886206 AACAAAGCAACCCTTGGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACA
1 AGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
*
886271 ACAAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
66 ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
*
886327 AGCAATACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
1 AGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
* * *
886392 ACGAATGAGCCATCCAGGATTTTAACTTCACGACGAAGGATATCGTGCCCATAAGC
66 ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
* * *
886448 AGCAATACAACCCTTGGATTTCAACTTCACGGCGAAGAATATCCAATTCAAAGCTCAACTTCACA
1 AGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
* * *
886513 ACGAATAAGCCATCCACGATTTTAACTTCACGACGAAAGATAT
66 ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATAT
886556 TTAATTAAAA
Statistics
Matches: 441, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 441 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (121 bp):
AGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACA
ACGAATGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGC
Found at i:886177 original size:66 final size:64
Alignment explanation
Indices: 886101--886984 Score: 363
Period size: 66 Copynumber: 14.4 Consensus size: 64
886091 GCAACCTTTG
* *
886101 GATTTCAACTTCACGATGAAGGATATCCAATTCAAATCTCAACTTCACAACGAATGAGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886166 C
64 C
* * * * * *
886167 GATTTCAACTTCACGACGAAGGATAT-C-GTGC---C-C-AC--AAGCAACAA--AGCAACCCTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCA-CAACAATGAGCCATCC-A
*
886221 G
64 C
*
886222 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACAACAAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886287 C
64 C
* * * * * * *
886288 GATTTCAACTTCACGACGAAGGATAT-C-GTGC---C-C-AC--AAGCAGCAAT-A-CAACCCTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCA-CAACAATGAGCCATCC-A
*
886342 G
64 C
886343 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
*
886408 G
64 C
* * * * * * * *
886409 GATTTTAACTTCACGACGAAGGATAT-C-GTGC---C-C-A--TAAGCAGCAAT-A-CAACCCTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCA-CAACAATGAGCCATCC-A
*
886463 G
64 C
* * *
886464 GATTTCAACTTCACGGCGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886529 C
64 C
* * ** * * *
886530 GATTTTAACTTCACGACGAAAGATATTTAATTAAAAGCTCAATTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886595 C
64 C
* * * * * * * **
886596 GATTTTAACTTCACGACGAAAGATAT-C-GTGC---C-C-AC--AAGCAGCAATGCAACC--CTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCA-CAACAATG-AGCCATCCA
*
886650 G
64 C
*
886651 GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886716 C
64 C
* * * * * **
886717 GATTTCAA-TTCACGACGAAGGATAT-C-GTGC---C-C-AC--AAGCATCAATGCAACC--CTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCA-CAACAATG-AGCCATCCA
*
886770 G
64 C
* * * * *
886771 GATTTCAACTTCACAACGAAGAATATCCAATTCAAAGCTCAACTTCACATCAAAGGAGCCATCAA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886836 C
64 C
* * * * * * * **
886837 GATTTTAACTTCACGACGAAGGATAT-C-GTGC---C-C-AC--AAGCAGCAATTCAACC--CTT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCA-CAACAA-TGAGCCATCCA
*
886891 G
64 C
* *
886892 GATTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAACTTCACAAC-AATGAGCCATCCA
886957 C
64 C
* *
886958 AATTTCAACTTCACGATGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
886985 GTGCCCAACG
Statistics
Matches: 595, Mismatches: 132, Indels: 182
0.65 0.15 0.20
Matches are distributed among these distances:
54 22 0.04
55 146 0.25
56 31 0.05
57 36 0.06
58 9 0.02
59 6 0.01
60 5 0.01
61 6 0.01
62 6 0.01
63 13 0.02
64 39 0.07
65 44 0.07
66 218 0.37
67 14 0.02
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23
Consensus pattern (64 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAACTTCACAACAATGAGCCATCCAC
Found at i:886233 original size:55 final size:55
Alignment explanation
Indices: 886167--886369 Score: 178
Period size: 55 Copynumber: 3.5 Consensus size: 55
886157 AGTCATCCAC
886167 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAAAGCAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAAAGCAACCCTTG
* * * * *
886222 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCA-CAACAAATG-AGCCATC
1 GATTTCAACTTCACGACGAAGGATAT-C--GT----GC-CCAC--AAGCAACAAA-GCAACC--C
***
886285 CAC
53 TTG
*
886288 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATA-CAACCCTTG
1 GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAA-AGCAACCCTTG
886343 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
886370 CAATTCAAAG
Statistics
Matches: 115, Mismatches: 17, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
55 53 0.46
56 2 0.02
57 8 0.07
58 5 0.04
59 2 0.02
62 2 0.02
63 4 0.03
64 10 0.09
65 3 0.03
66 26 0.23
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (55 bp):
GATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAACAAAGCAACCCTTG
Found at i:886569 original size:308 final size:307
Alignment explanation
Indices: 886222--886863 Score: 1050
Period size: 308 Copynumber: 2.1 Consensus size: 307
886212 GCAACCCTTG
* * * *
886222 GATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACAACAAATGAGCCATCCA
1 GATTTTAACTTCACGACGAAAGATATCCAATTAAAAGCTCAACTTCACAACAAAGGAGCCATCCA
*
886287 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
66 CGATTTCAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
* * *
886352 TTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAGGATTTTAA
131 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAA
* **
886417 CTTCACGACGAAGGATATCGTGCCCATAAGCAGCAATACAACCCTTGGATTTCAACTTCACGGCG
196 -TTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAACTTCACAACG
* * *
886482 AAGAATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCAC
260 AAGAATATCCAATTCAAAGCTCAACTTCACAACAAAGAAGCCATCAAC
** * *
886530 GATTTTAACTTCACGACGAAAGATATTTAATTAAAAGCTCAATTTCACAACGAAGGAGCCATCCA
1 GATTTTAACTTCACGACGAAAGATATCCAATTAAAAGCTCAACTTCACAACAAAGGAGCCATCCA
* *
886595 CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAAC
66 CGATTTCAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
886660 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAA
131 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAA
* *
886725 TTCACGACGAAGGATATCGTGCCCACAAGCATCAATGCAACCCTTGGATTTCAACTTCACAACGA
196 TTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAACTTCACAACGA
* *
886790 AGAATATCCAATTCAAAGCTCAACTTCACATCAAAGGAGCCATCAAC
261 AGAATATCCAATTCAAAGCTCAACTTCACAACAAAGAAGCCATCAAC
*
886837 GATTTTAACTTCACGACGAAGGATATC
1 GATTTTAACTTCACGACGAAAGATATC
886864 GTGCCCACAA
Statistics
Matches: 308, Mismatches: 26, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
307 127 0.41
308 181 0.59
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (307 bp):
GATTTTAACTTCACGACGAAAGATATCCAATTAAAAGCTCAACTTCACAACAAAGGAGCCATCCA
CGATTTCAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAA
TTCACGACGAAGGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAACTTCACAACGA
AGAATATCCAATTCAAAGCTCAACTTCACAACAAAGAAGCCATCAAC
Found at i:886591 original size:187 final size:187
Alignment explanation
Indices: 886343--886742 Score: 676
Period size: 187 Copynumber: 2.1 Consensus size: 187
886333 ACAACCCTTG
* *
886343 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTAAAAGCTCAACTTCACAACGAAGGAGCCATCCA
* * *
886408 GGATTTTAACTTCACGACGAAGGATATCGTGCCCATAAGCAGCAATACAACCCTTGGATTTCAAC
66 CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
*
886473 TTCACGGCGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCAC
131 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCAC
* * ** *
886530 GATTTTAACTTCACGACGAAAGATATTTAATTAAAAGCTCAATTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTAAAAGCTCAACTTCACAACGAAGGAGCCATCCA
*
886595 CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAAC
66 CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
*
886660 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
131 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCAC
886717 GATTTCAA-TTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
886743 GTGCCCACAA
Statistics
Matches: 197, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
186 16 0.08
187 181 0.92
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (187 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTAAAAGCTCAACTTCACAACGAAGGAGCCATCCA
CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATACAACCCTTGGATTTCAAC
TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATAAGCCATCCAC
Found at i:886677 original size:55 final size:55
Alignment explanation
Indices: 886596--886797 Score: 142
Period size: 55 Copynumber: 3.5 Consensus size: 55
886586 AGCCATCCAC
* *
886596 GATTTTAACTTCACGACGAA-AGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
1 GATTTCAACTTCACGACGAAGA-ATATCGTGCCCACAAGCAACAATGCAACCCTTG
* * * *
886651 GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCA-CAACGAATG-AGCCATC
1 GATTTCAACTTCACGACGAAGAATAT-C--GT----GC-CCAC--AAGCAAC-AATGCAACC--C
***
886714 CAC
53 TTG
* *
886717 GATTTCAA-TTCACGACGAAGGATATCGTGCCCACAAGCATCAATGCAACCCTTG
1 GATTTCAACTTCACGACGAAGAATATCGTGCCCACAAGCAACAATGCAACCCTTG
*
886771 GATTTCAACTTCACAACGAAGAATATC
1 GATTTCAACTTCACGACGAAGAATATC
886798 CAATTCAAAG
Statistics
Matches: 110, Mismatches: 20, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
54 9 0.08
55 44 0.40
56 8 0.07
57 3 0.03
58 3 0.03
62 3 0.03
63 3 0.03
64 7 0.06
65 21 0.19
66 9 0.08
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.22
Consensus pattern (55 bp):
GATTTCAACTTCACGACGAAGAATATCGTGCCCACAAGCAACAATGCAACCCTTG
Found at i:886776 original size:120 final size:121
Alignment explanation
Indices: 886530--886991 Score: 712
Period size: 121 Copynumber: 3.8 Consensus size: 121
886520 AGCCATCCAC
* ** * *
886530 GATTTTAACTTCACGACGAA-AGATATTTAATTAAAAGCTCAATTTCACAACGAAGGAGCCATCC
1 GATTTCAACTTCACGACGAAGA-ATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCC
* *
886594 ACGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
65 ACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
*
886651 GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
*
886716 CGATTTCAA-TTCACGACGAAGGATATCGTGCCCACAAGCATCAATGCAACCCTTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
* * * *
886771 GATTTCAACTTCACAACGAAGAATATCCAATTCAAAGCTCAACTTCACATCAAAGGAGCCATCAA
1 GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
* *
886836 CGATTTTAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATTCAACCCTTG
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
* * * *
886892 GATTTCAACTTCATGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCCA
1 GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
* *
886957 CAATTTCAACTTCACGATGAAGGATATCGTGCCCA
66 CGATTTCAACTTCACGACGAAGGATATCGTGCCCA
886992 ACGGATCGAC
Statistics
Matches: 311, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
120 112 0.36
121 198 0.64
122 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (121 bp):
GATTTCAACTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
CGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTG
Found at i:886965 original size:241 final size:242
Alignment explanation
Indices: 886530--886991 Score: 757
Period size: 241 Copynumber: 1.9 Consensus size: 242
886520 AGCCATCCAC
* * ** * * *
886530 GATTTTAACTTCACGACGAAAGATATTTAATTAAAAGCTCAATTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACAACGAAAGATATCCAATTAAAAGCTCAACTTCACAACAAAGGAGCCATCAA
886595 CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAAC
66 CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAAC
*
886660 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACGATTTCAA
131 TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACAATTTCAA
886725 -TTCACGACGAAGGATATCGTGCCCACAAGCATCAATGCAACCCTTG
196 CTTCACGACGAAGGATATCGTGCCCACAAGCATCAATGCAACCCTTG
* *
886771 GATTTCAACTTCACAACG-AAGAATATCCAATTCAAAGCTCAACTTCACATCAAAGGAGCCATCA
1 GATTTCAACTTCACAACGAAAG-ATATCCAATTAAAAGCTCAACTTCACAACAAAGGAGCCATCA
* *
886835 ACGATTTTAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATTCAACCCTTGGATTTCAA
65 ACGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAA
* * *
886900 CTTCATGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCCACAATTTCA
130 CTTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACAATTTCA
*
886965 ACTTCACGATGAAGGATATCGTGCCCA
195 ACTTCACGACGAAGGATATCGTGCCCA
886992 ACGGATCGAC
Statistics
Matches: 203, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
240 3 0.01
241 176 0.87
242 24 0.12
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (242 bp):
GATTTCAACTTCACAACGAAAGATATCCAATTAAAAGCTCAACTTCACAACAAAGGAGCCATCAA
CGATTTTAACTTCACGACGAAAGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAAC
TTCACGACGAAGAATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACAATTTCAA
CTTCACGACGAAGGATATCGTGCCCACAAGCATCAATGCAACCCTTG
Found at i:887280 original size:84 final size:83
Alignment explanation
Indices: 887089--887533 Score: 323
Period size: 84 Copynumber: 5.3 Consensus size: 83
887079 AAAGGCTATT
* * * * * * * *
887089 TGTCATCAAAGATCTTCGAGTTCGATTACATTCAGCTTAAAGGCAT-ATCAATTTACAGTATAAC
1 TGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGC-TCATC-ATTTGCAGCATAGC
* *
887153 TCAAGGCTAGAAGGATTATC
64 TCAAGGCAAGAAGGGTTATC
* * * * *
887173 TATCAACAATGACCTTCTAGTTCGATTACACTCAACTCAAAAGCTCATCATTTGCAGCATAGCTC
1 TGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCTCATCATTTGCAGCATAGCTC
*
887238 AAGGCAAGAAGGGCTATC
66 AAGGCAAGAAGGGTTATC
* * *
887256 TGCCAACAAAAGACCTTCAAGTTCGATTATACTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
1 TGTCAAC-AAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCTCATCATTTGCAGCATAGCT
* *
887321 C-AGAGAAAGAAAGGTTATC
65 CAAG-GCAAGAAGGGTTATC
** * **
887340 TGTCAATGAA-ACCTTCAAGTTCGATTACATTCAGCTC-AAGGACAT-ATCAAATTCACAGCATA
1 TGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGG-C-TCATC--ATTTGCAGCATA
* * *
887402 ACTCAAGGCGATAAGGGTTATC
62 GCTCAAGGCAAGAAGGGTTATC
* * * * * * * * *
887424 TGTCAGC-AA-ACCTTCGAGTTCAATTACATTCAACTCATAGACAT-ATCAAATTTACAACATAG
1 TGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGC-TCATC--ATTTGCAGCATAG
* * * *
887486 CTCAAGACGATAAGGGCTATC
63 CTCAAGGCAAGAAGGGTTATC
**
887507 TGTCAAC-AAGAATTTTCAAGTTCGATT
1 TGTCAACAAAG-ACCTTCAAGTTCGATT
887534 TCATTCAGTT
Statistics
Matches: 294, Mismatches: 56, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
81 4 0.01
82 29 0.10
83 109 0.37
84 138 0.47
85 14 0.05
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (83 bp):
TGTCAACAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCTCATCATTTGCAGCATAGCTC
AAGGCAAGAAGGGTTATC
Found at i:888008 original size:27 final size:27
Alignment explanation
Indices: 887978--888034 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
887968 TACTCCAAAG
887978 AAATCATCACATGCAACAACCATTATA
1 AAATCATCACATGCAACAACCATTATA
*
888005 AAATCATCACATGCAACAACTATTATA
1 AAATCATCACATGCAACAACCATTATA
888032 AAA
1 AAA
888035 AGAGGGGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.51, C:0.23, G:0.04, T:0.23
Consensus pattern (27 bp):
AAATCATCACATGCAACAACCATTATA
Found at i:889074 original size:24 final size:24
Alignment explanation
Indices: 889030--889078 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
889020 GGTGGTTGGC
*
889030 TTAATGGATGTTTAAACTTTATTT
1 TTAATGGATATTTAAACTTTATTT
*
889054 TTAATGGTATATTT-AAGTTTATTT
1 TTAATGG-ATATTTAAACTTTATTT
889078 T
1 T
889079 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (24 bp):
TTAATGGATATTTAAACTTTATTT
Found at i:894643 original size:24 final size:24
Alignment explanation
Indices: 894598--894647 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
894588 TGGTGGTTGG
894598 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
894622 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
894646 TT
1 TT
894648 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:895931 original size:17 final size:16
Alignment explanation
Indices: 895909--895943 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
895899 GAAATTAATA
*
895909 TTTTCTTATTTTCTTAT
1 TTTTCTTAATTT-TTAT
895926 TTTTCTTAATTTTTAT
1 TTTTCTTAATTTTTAT
895942 TT
1 TT
895944 ATTTCTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTAATTTTTAT
Found at i:897542 original size:40 final size:40
Alignment explanation
Indices: 897497--897589 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
897487 AAATGACCAA
* *
897497 CAAATTCGCAACGCGAACTCCAATTTCGCAATAC-AATTT
1 CAAATTCGCAACGCGAACTCCAAATTCGCAACACGAATTT
**
897536 CTAAATTCGCAACGCGATTTCCAAATTCGCAACACTGAATTT
1 C-AAATTCGCAACGCGAACTCCAAATTCGCAACAC-GAATTT
897578 CAAATTCGCAAC
1 CAAATTCGCAAC
897590 TCGATTTCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 29 0.62
41 11 0.23
42 6 0.13
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (40 bp):
CAAATTCGCAACGCGAACTCCAAATTCGCAACACGAATTT
Found at i:897583 original size:21 final size:20
Alignment explanation
Indices: 897497--897664 Score: 99
Period size: 20 Copynumber: 8.3 Consensus size: 20
897487 AAATGACCAA
* * *
897497 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* *
897517 CAATTTCGCAATAC-AATTT
1 CAAATTCGCAACACGAATTT
*
897536 CTAAATTCGCAACGCG-ATTT
1 C-AAATTCGCAACACGAATTT
897556 CCAAATTCGCAACACTGAATTT
1 -CAAATTCGCAACAC-GAATTT
*
897578 CAAATTCGCAACTCG-ATTT
1 CAAATTCGCAACACGAATTT
* * *
897597 CTGAATTTGCAACGCGAATTT
1 C-AAATTCGCAACACGAATTT
**** * *
897618 TGTTTTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
* **
897638 CGAATTCATAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
897658 TAAATTC
1 CAAATTC
897665 ACACCAGTTT
Statistics
Matches: 113, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
19 9 0.08
20 81 0.72
21 19 0.17
22 4 0.04
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:897597 original size:61 final size:60
Alignment explanation
Indices: 897497--897613 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 60
897487 AAATGACCAA
* *
897497 CAAATTCGCAACGCGAACTCCAATTTCGCAATACAATTTCTAAATTCGCAACGCGATTTC
1 CAAATTCGCAACACGAACTCCAAATTCGCAATACAATTTCTAAATTCGCAACGCGATTTC
* * * * *
897557 CAAATTCGCAACACTGAATTTCAAATTCGCAACT-CGATTTCTGAATTTGCAACGCGA
1 CAAATTCGCAACAC-GAACTCCAAATTCGCAA-TACAATTTCTAAATTCGCAACGCGA
897614 ATTTTGTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 13 0.27
61 34 0.71
62 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.27
Consensus pattern (60 bp):
CAAATTCGCAACACGAACTCCAAATTCGCAATACAATTTCTAAATTCGCAACGCGATTTC
Found at i:898648 original size:24 final size:24
Alignment explanation
Indices: 898590--898636 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
898580 AGTCAGTATT
*
898590 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
898614 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
898637 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:901212 original size:20 final size:20
Alignment explanation
Indices: 901189--901237 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
901179 TCATATTCAA
901189 AACGCGAAAGTAAAATGCGC
1 AACGCGAAAGTAAAATGCGC
* *
901209 AACGCGAAATTAAAATTCGC
1 AACGCGAAAGTAAAATGCGC
901229 AACGCGAAA
1 AACGCGAAA
901238 ATCGAAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (20 bp):
AACGCGAAAGTAAAATGCGC
Found at i:901272 original size:20 final size:20
Alignment explanation
Indices: 901247--901290 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
901237 AATCGAAACA
*
901247 CGAATTTGATTTTCGCGTTG
1 CGAATTTGAATTTCGCGTTG
* *
901267 CGAATTTTAATTTCGTGTTG
1 CGAATTTGAATTTCGCGTTG
901287 CGAA
1 CGAA
901291 AGTGTACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (20 bp):
CGAATTTGAATTTCGCGTTG
Found at i:901872 original size:207 final size:207
Alignment explanation
Indices: 901510--902110 Score: 987
Period size: 207 Copynumber: 2.9 Consensus size: 207
901500 ACATTCACGT
901510 AGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTACACATCTA
1 AGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTACACATCTA
901575 AAACCAACAAACAACAAATTATTGAATTATAGGTACTTAAACCAAACATTTTCAAACCAACAAGT
66 AAACCAACAAACAACAAATTATTGAATTATAGGTACTTAAACCAAACATTTTCAAACCAACAAGT
901640 ATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAACTGGTTATTTATGCACAAATACA
131 ATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAACTGGTTATTTATGCACAAATACA
901705 TCAATTTCACAC
196 TCAATTTCACAC
* * *
901717 AGCTCATTTCAGGATTAACCTGTAGAAACCAAACATTTGCTCAAACAACACTTTCTACATATCTA
1 AGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTACACATCTA
* *
901782 AAACCAACAAACAACAAATTATTGAATTCTAGGCACTTAAACCAAACATTTTCAAACCAACAAGT
66 AAACCAACAAACAACAAATTATTGAATTATAGGTACTTAAACCAAACATTTTCAAACCAACAAGT
*
901847 ATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAACTGATTATTTATGCACAAATACA
131 ATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAACTGGTTATTTATGCACAAATACA
*
901912 TCAATTTCACGC
196 TCAATTTCACAC
* *
901924 AGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTTCTCAAACAACACTTTCTATACATCT-
1 AGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTACACATCTA
* *
901988 AAACCAACAAACAACAAATTATTGAATTATAGGTACTT-AACC-AATATTTTCAAACCAGCAAAG
66 AAACCAACAAACAACAAATTATTGAATTATAGGTACTTAAACCAAACATTTTCAAACCAAC-AAG
* * * * * *
902051 -AGTATATA-TGTTAACAACACGTGCTCAAACTTACCAACAACAAATGGTTGTTTATGCACA
130 TA-TATA-ACAGTTAACAACACTTGCACAAACTTACCAATAACAACTGGTTATTTATGCACA
902111 CTTTCAGCAC
Statistics
Matches: 368, Mismatches: 23, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
204 16 0.04
205 56 0.15
206 37 0.10
207 259 0.70
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (207 bp):
AGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTACACATCTA
AAACCAACAAACAACAAATTATTGAATTATAGGTACTTAAACCAAACATTTTCAAACCAACAAGT
ATATAACAGTTAACAACACTTGCACAAACTTACCAATAACAACTGGTTATTTATGCACAAATACA
TCAATTTCACAC
Found at i:903132 original size:21 final size:21
Alignment explanation
Indices: 903106--903224 Score: 123
Period size: 21 Copynumber: 5.7 Consensus size: 21
903096 GTGACTCGGG
* * *
903106 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGGC
* *
903127 CTCTTGAATGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
903148 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
903169 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
903190 TTCTTGAATGAT-ATGATGGGC
1 CTCTTGAACGATGA-GAGGGGC
*
903211 CTCTTGAATGATGA
1 CTCTTGAACGATGA
903225 CAGGTGAATC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
20 1 0.01
21 79 0.98
22 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:903165 original size:42 final size:41
Alignment explanation
Indices: 903106--903228 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 41
903096 GTGACTCGGG
903106 CTCTTGAACGGTGGGAGGGACCTCTTGAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAATGATGACAGGGGC
* *
903148 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAATGATGACAGGGGC
* * * **
903190 TTCTTGAATGATATGATGGGCCTCTTGAATGATGACAGG
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAATGATGACAGG
903229 TGAATCGGGC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
42 67 0.96
43 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAATGATGACAGGGGC
Found at i:903656 original size:21 final size:21
Alignment explanation
Indices: 903632--903681 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
903622 ACCATTATCG
*
903632 TCACGTAAAGTACTGAACTCA
1 TCACGTAAAGCACTGAACTCA
* *
903653 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACTGAACTCA
903674 TCACGTAA
1 TCACGTAA
903682 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACTGAACTCA
Found at i:903871 original size:42 final size:42
Alignment explanation
Indices: 903796--903894 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
903786 GTGATGGAAT
* * * * * *
903796 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGACTCGATC
*
903838 AGGTGATGGCTCTGGGTGTCGAGCTATAGAATCGACTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGACTCGATC
903880 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
903895 AAGTAGGGGG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTATAGAATCGACTCGATC
Found at i:905247 original size:20 final size:20
Alignment explanation
Indices: 905224--905326 Score: 163
Period size: 20 Copynumber: 5.2 Consensus size: 20
905214 AAACTTAATT
905224 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
905244 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
905264 TCGCAACGCAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
905284 TCGCAACACGAAAATAAAAA
1 TCGCAACGCGAAAATGAAAA
*
905304 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
905323 TCGC
1 TCGC
905327 GTTGCGATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
19 8 0.10
20 69 0.90
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Done.