Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011041.1 Kokia drynarioides strain JFW-HI SEQ_126012, 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: 389353
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:156 original size:86 final size:86
Alignment explanation
Indices: 1--231 Score: 311
Period size: 86 Copynumber: 2.7 Consensus size: 86
* * * * * *
1 CATCTAAGGTACCAAGGTGTCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTCAGTTACTG
1 CATCAAAGGCACCAAGGTGTCGATACTTTCCGATGGTCCCGCACCACCATCGGCCTTAGTTACCG
* **
66 ATGGTGTCCGATGCTCTTGCA
66 ATGGTGTCCGAGGCTCCCGCA
* *
87 CATCGAAGGCACCAAGGTGTCGATACTTTCCGATGGTCCCGCACCACCATCGACCTTAGTTACCG
1 CATCAAAGGCACCAAGGTGTCGATACTTTCCGATGGTCCCGCACCACCATCGGCCTTAGTTACCG
152 ATGGTGTCCGAGGCTCCCGCA
66 ATGGTGTCCGAGGCTCCCGCA
* * * *
173 CATCAAAGGCACCATGGTGCCGATAC-TTCTCGACGGTCCTGCACCACCATCGGCCTTAG
1 CATCAAAGGCACCAAGGTGTCGATACTTTC-CGATGGTCCCGCACCACCATCGGCCTTAG
232 CTGCCAATAC
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 3 0.02
86 125 0.98
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.23
Consensus pattern (86 bp):
CATCAAAGGCACCAAGGTGTCGATACTTTCCGATGGTCCCGCACCACCATCGGCCTTAGTTACCG
ATGGTGTCCGAGGCTCCCGCA
Found at i:378 original size:144 final size:144
Alignment explanation
Indices: 102--660 Score: 658
Period size: 144 Copynumber: 3.9 Consensus size: 144
92 AAGGCACCAA
* * * * * *
102 GGTGT-CGATACTTTCCGATGGTCCCGCACCACCATCGACCTTAGTTACCGATGGTGTCCGAGGC
1 GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGATGTCCGACGC
* * * *
166 TCCCGCACATCAAAGGCACCATGGTGCCGATACTTCTCGACGGTCCTGCACCACCATCGGCCTTA
66 TTCCGCACATCAAAGGCACCATGGTGCCGATACTTCACGATGGTCCCGCACCACCATCGGCCTTA
*
231 GCTGCCAATACAAT
131 GCTGCCAATACGAT
* * * * *** * *
245 GGTATCCGATGCTTCCAGATGGTCCCGCACCACCATCGTCCTAAGCTGTTGATGATGTTCGATGC
1 GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGATGTCCGACGC
* * * * * * *
310 TTCCGTACATCGAAGGCACCATGGTACTGATACTTCCCAATGGTCCCGCACCACCATTGGCCTTA
66 TTCCGCACATCAAAGGCACCATGGTGCCGATACTTCACGATGGTCCCGCACCACCATCGGCCTTA
375 GCTGCCAATACGAT
131 GCTGCCAATACGAT
389 GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGAT-AGTGTCCGACG
1 GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGA-TGTCCGACG
* * ** *
453 C-TCTCGCACATCCAAGGCACCAAGGTGCCGATAGATCACGATTGTCCCGCACCACCATCGGCCT
65 CTTC-CGCACATCAAAGGCACCATGGTGCCGATACTTCACGATGGTCCCGCACCACCATCGGCCT
517 TAGCTGCCAATACGAT
129 TAGCTGCCAATACGAT
* * * * *
533 GGTGTCCGATGCTTCCCGATGGTCCCGCACCATCATCGGCCTAAGTTATCGATGGTGTCTGATGC
1 GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGATGTCCGACGC
* * * *** * *
598 -TCTCGCACATCCAAGGCACCAAGGTGTCGATGGATCTCGATTGTCCCGCACCACCATCGGCCT
66 TTC-CGCACATCAAAGGCACCATGGTGCCGATACTTCACGATGGTCCCGCACCACCATCGGCCT
661 AAGTTGCCGA
Statistics
Matches: 360, Mismatches: 52, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
143 7 0.02
144 353 0.98
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (144 bp):
GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATGATGTCCGACGC
TTCCGCACATCAAAGGCACCATGGTGCCGATACTTCACGATGGTCCCGCACCACCATCGGCCTTA
GCTGCCAATACGAT
Found at i:646 original size:288 final size:287
Alignment explanation
Indices: 102--660 Score: 746
Period size: 288 Copynumber: 1.9 Consensus size: 287
92 AAGGCACCAA
* * * *
102 GGTGTCGATACTTTCCGATGGTCCCGCACCACCATCGACCTTAGTTACCGATGGTGTCCGAGGCT
1 GGTGTCGATACTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCGACGCT
* * * *
167 CCCGCACATCAAAGGCACCATGGTGCCGATACTTCTCGACGGTCCTGCACCACCATCGGCCTTAG
66 CCCGCACATCAAAGGCACCAAGGTGCCGATACATCACGACGGTCCCGCACCACCATCGGCCTTAG
* * *
232 CTGCCAATACAATGGTATCCGATGCTTCCAGATGGTCCCGCACCACCATCGTCCTAAGCTGTTGA
131 CTGCCAATACAATGGTATCCGATGCTTCCAGATGGTCCCGCACCACCATCGGCCTAAGCTATCGA
* * * *
297 TGATGTTCGATGCTTCCGTACATCGAAGGCACCATGGTACTGATACTTCCCAATGGTCCCGCACC
196 TGATGTTCGATGCTTCCGCACATCCAAGGCACCAAGGTACTGATACATCCCAATGGTCCCGCACC
*
362 ACCATTGGCCTTAGCTGCCAATACGAT
261 ACCATCGGCCTTAGCTGCCAATACGAT
* *
389 GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATAGTGTCCGACGC
1 GGTGT-CGATACTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCGACGC
* * * **
454 TCTCGCACATCCAAGGCACCAAGGTGCCGATAGATCACGATTGTCCCGCACCACCATCGGCCTTA
65 TCCCGCACATCAAAGGCACCAAGGTGCCGATACATCACGACGGTCCCGCACCACCATCGGCCTTA
* * * * *
519 GCTGCCAATACGATGGTGTCCGATGCTTCCCGATGGTCCCGCACCATCATCGGCCTAAGTTATCG
130 GCTGCCAATACAATGGTATCCGATGCTTCCAGATGGTCCCGCACCACCATCGGCCTAAGCTATCG
* * ** * * *
584 ATGGTG-TCTGATGC-TCTCGCACATCCAAGGCACCAAGGT-GTCGATGGATCTCGATTGTCCCG
195 ATGATGTTC-GATGCTTC-CGCACATCCAAGGCACCAAGGTACT-GATACATCCCAATGGTCCCG
646 CACCACCATCGGCCT
257 CACCACCATCGGCCT
661 AAGTTGCCGA
Statistics
Matches: 233, Mismatches: 35, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
287 10 0.04
288 223 0.96
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (287 bp):
GGTGTCGATACTTCCCGATGGTCCCGCACCACCATCGACCTAAGTTACCGATAGTGTCCGACGCT
CCCGCACATCAAAGGCACCAAGGTGCCGATACATCACGACGGTCCCGCACCACCATCGGCCTTAG
CTGCCAATACAATGGTATCCGATGCTTCCAGATGGTCCCGCACCACCATCGGCCTAAGCTATCGA
TGATGTTCGATGCTTCCGCACATCCAAGGCACCAAGGTACTGATACATCCCAATGGTCCCGCACC
ACCATCGGCCTTAGCTGCCAATACGAT
Found at i:684 original size:86 final size:85
Alignment explanation
Indices: 548--746 Score: 245
Period size: 86 Copynumber: 2.3 Consensus size: 85
538 CCGATGCTTC
* * * * *
548 CCGATGGTCCCGCACCATCATCGGCCTAAGTTATCGATGGTGTCTGATGCTCTCGCACATCCAAG
1 CCGATAGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATGCTCCCGCACATCCAAG
**
613 GCACCAAGGTGTCGATGGAT
66 GCACCAAGGTGTCGATACAT
* * **
633 CTCGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCCCGCACATTGAA
1 C-CGATAGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATGCTCCCGCACATCCAA
* * *
698 GGTACCATGGTGTCGATACTT
65 GGCACCAAGGTGTCGATACAT
*
719 CCTGATAGTCTCGCACCACCATCGGCCT
1 CC-GATAGTCCCGCACCACCATCGGCCT
747 TACCTGCCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 2 0.02
86 95 0.98
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (85 bp):
CCGATAGTCCCGCACCACCATCGGCCTAAGTTACCGATGGTGTCCGATGCTCCCGCACATCCAAG
GCACCAAGGTGTCGATACAT
Found at i:688 original size:43 final size:43
Alignment explanation
Indices: 548--691 Score: 134
Period size: 43 Copynumber: 3.3 Consensus size: 43
538 CCGATGCTTC
* * *
548 CCGATGGTCCCGCACCATCATCGGCCTAAGTTATCGATGGTGT
1 CCGATGCTCCCGCACCACCATCGGCCTAAGTTGTCGATGGTGT
* * * * * *
591 CTGATGCTCTCGCA-CATCCA-AGGCACCAAGGTGTCGATGG-AT
1 CCGATGCTCCCGCACCA-CCATCGGC-CTAAGTTGTCGATGGTGT
*
633 CTCGATTG-TCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGT
1 C-CGA-TGCTCCCGCACCACCATCGGCCTAAGTTGTCGATGGTGT
677 CCGATGCTCCCGCAC
1 CCGATGCTCCCGCAC
692 ATTGAAGGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
42 9 0.12
43 59 0.77
44 9 0.12
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (43 bp):
CCGATGCTCCCGCACCACCATCGGCCTAAGTTGTCGATGGTGT
Found at i:693 original size:230 final size:229
Alignment explanation
Indices: 402--972 Score: 836
Period size: 230 Copynumber: 2.5 Consensus size: 229
392 GTCCGATGCT
* * * * *
402 TCCCGATGGTCCCGCACCACCATCGGCCTAAGTTACCGATAGTGTCCGACGCTCTCGCACATCCA
1 TCCCGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCTCGCACATCGA
* * ** * * *
467 AGGCACCAAGGTGCCGATAGATCACGATTGTCCCGCACCACCATCGGCCTTAGCTGCCAATACGA
66 AGGTACCATGGTGCCGATACTTC-CGATAGTCTCGCACCACCATCGGCCTTACCTGCCAATACGA
* * * * *
532 TGGTGTCCGATGCTTCCCGATGGTCCCGCACCATCATCGGCCTAAGTTATCGATGGTGTCTGATG
130 TGGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCAGCCTAAGTTACCGATAGTGTCCGATG
*
597 CTCTCGCACATCCAAGGCACCAAGGTGTCGATGGA
195 CTCTCGCACATCCAAGGCACCAAGGTGCCGATGGA
* * *
632 TCTCGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCCCGCACATTGA
1 TCCCGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCTCGCACATCGA
*
697 AGGTACCATGGTGTCGATACTTCCTGATAGTCTCGCACCACCATCGGCCTTACCTGCCAATACGA
66 AGGTACCATGGTGCCGATACTTCC-GATAGTCTCGCACCACCATCGGCCTTACCTGCCAATACGA
* * *
762 TGGTGTCCGATGCTTCCCGATGGTCCCGTACCACCATCATCCTAAGTTGCCGATAGTGTCCGATG
130 TGGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCAGCCTAAGTTACCGATAGTGTCCGATG
*
827 CTCTTGCACATCCAAGGCACCAAGGTGCCGATGGA
195 CTCTCGCACATCCAAGGCACCAAGGTGCCGATGGA
* * * *
862 TCCCGATTGTCCTGCACCACCATAGGCCTAAGCTGCCGATGGTGTCCGATGCTCTTGCACATCGA
1 TCCCGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCTCGCACATCGA
*
927 AGGTACCATGGTGCTGATACTTCCCGATAGTCTCGCACCACCATCG
66 AGGTACCATGGTGCCGATACTT-CCGATAGTCTCGCACCACCATCG
973 ACCTCAGTTA
Statistics
Matches: 304, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
229 1 0.00
230 301 0.99
231 2 0.01
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.23
Consensus pattern (229 bp):
TCCCGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCTCGCACATCGA
AGGTACCATGGTGCCGATACTTCCGATAGTCTCGCACCACCATCGGCCTTACCTGCCAATACGAT
GGTGTCCGATGCTTCCCGATGGTCCCGCACCACCATCAGCCTAAGTTACCGATAGTGTCCGATGC
TCTCGCACATCCAAGGCACCAAGGTGCCGATGGA
Found at i:856 original size:43 final size:43
Alignment explanation
Indices: 809--945 Score: 122
Period size: 43 Copynumber: 3.2 Consensus size: 43
799 CATCCTAAGT
809 TGCCGATAGTGTCCGATGCTCTTGCACATCCAAGGCACCAAGG
1 TGCCGATAGTGTCCGATGCTCTTGCACATCCAAGGCACCAAGG
* * *
852 TGCCGAT-G-GATCCCGATTG-TCCTGCACCA-CCATAGGC-CTAAGC
1 TGCCGATAGTG-T-CCGA-TGCTCTTGCA-CATCCA-AGGCACCAAGG
* * * *
895 TGCCGATGGTGTCCGATGCTCTTGCACATCGAAGGTACCATGG
1 TGCCGATAGTGTCCGATGCTCTTGCACATCCAAGGCACCAAGG
*
938 TGCTGATA
1 TGCCGATA
946 CTTCCCGATA
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
41 1 0.01
42 9 0.12
43 52 0.71
44 10 0.14
45 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.23
Consensus pattern (43 bp):
TGCCGATAGTGTCCGATGCTCTTGCACATCCAAGGCACCAAGG
Found at i:898 original size:144 final size:144
Alignment explanation
Indices: 635--898 Score: 332
Period size: 144 Copynumber: 1.8 Consensus size: 144
625 CGATGGATCT
* * * **
635 CGATTGTCCCGCACCACCATCGGCCTAAGTTGCCGATGGTGTCCGATGCTCCCGCACATTGAAGG
1 CGATGGTCCCGCACCACCATCAGCCTAAGTTGCCGATAGTGTCCGATGCTCCCGCACATCCAAGG
* * * * * * *
700 TACCATGGTGTCGATACTTCCTGATAGTCTCGCACCACCATCGGCCTTACCTGCCAATACGATGG
66 CACCAAGGTGCCGATACATCCCGATAGTCTCGCACCACCATAGGCCTAACCTGCCAATACGATGG
765 TGTCCGATGCTTCC
131 TGTCCGATGCTTCC
* * **
779 CGATGGTCCCGTACCACCATCATCCTAAGTTGCCGATAGTGTCCGATGCTCTTGCACATCCAAGG
1 CGATGGTCCCGCACCACCATCAGCCTAAGTTGCCGATAGTGTCCGATGCTCCCGCACATCCAAGG
** * *
844 CACCAAGGTGCCGATGGATCCCGATTGTC-CTGCACCACCATAGGCCTAAGCTGCC
66 CACCAAGGTGCCGATACATCCCGATAGTCTC-GCACCACCATAGGCCTAACCTGCC
899 GATGGTGTCC
Statistics
Matches: 99, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
143 1 0.01
144 98 0.99
ACGTcount: A:0.20, C:0.34, G:0.23, T:0.23
Consensus pattern (144 bp):
CGATGGTCCCGCACCACCATCAGCCTAAGTTGCCGATAGTGTCCGATGCTCCCGCACATCCAAGG
CACCAAGGTGCCGATACATCCCGATAGTCTCGCACCACCATAGGCCTAACCTGCCAATACGATGG
TGTCCGATGCTTCC
Found at i:913 original size:86 final size:86
Alignment explanation
Indices: 776--1184 Score: 396
Period size: 86 Copynumber: 4.8 Consensus size: 86
766 GTCCGATGCT
* * * * *
776 TCCCGATGGTCCCGTACCACCATC-ATCCTAAGTTGCCGATAGTGTCCGATGCTCTTGCACATCC
1 TCCCGATGGTCCTGCACCACCATCGA-CCTAAGTTGTCGATGGTGTCCGATGCTCTCGCACATCC
**
840 AAGGCACCAAGGTGCCGATGGA
65 AAGGCACCAAGGTGCCGATACA
* * * * * * *
862 TCCCGATTGTCCTGCACCACCATAGGCCTAAGCTGCCGATGGTGTCCGATGCTCTTGCACATCGA
1 TCCCGATGGTCCTGCACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGCTCTCGCACATCCA
* * * *
927 AGGTACCATGGTGCTGATACT
66 AGGCACCAAGGTGCCGATACA
* * * *
948 TCCCGATAGT-CTCGCACCACCATCGACCTCAGTTATCGATGGTGTCCGATGCTCCCGCACATCC
1 TCCCGATGGTCCT-GCACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGCTCTCGCACATCC
* * * *
1012 AAGGCACCATGGTTCCAATACT
65 AAGGCACCAAGGTGCCGATACA
* * * * *
1034 TCCCGATGGTCTTGAACCACCATCGACCTCAGTTGTCGGTGGTGTCCGATGCTCTCGCACATCCG
1 TCCCGATGGTCCTGCACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGCTCTCGCACATCCA
* *
1099 AGGTACCAAGGTGCCGATGA-T
66 AGGCACCAAGGTGCCGAT-ACA
* * * * *
1120 TCTCGATGGT-CTCGTACCACCATCGACCTAAGCTGTCGATGGTGTCTGATGATC-CAGCACATC
1 TCCCGATGGTCCT-GCACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGCTCTC-GCACATC
1183 CA
64 CA
1185 GTGCACGAAC
Statistics
Matches: 269, Mismatches: 48, Indels: 12
0.82 0.15 0.04
Matches are distributed among these distances:
85 4 0.01
86 263 0.98
87 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (86 bp):
TCCCGATGGTCCTGCACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGCTCTCGCACATCCA
AGGCACCAAGGTGCCGATACA
Found at i:1079 original size:172 final size:173
Alignment explanation
Indices: 763--1184 Score: 494
Period size: 172 Copynumber: 2.5 Consensus size: 173
753 CCAATACGAT
* * *
763 GGTGTCCGATG-CTTCCCGATGGTCCCGTACCACCATC-ATCCTAAGTTGCCGATAGTGTCCGAT
1 GGTG-CCGATGACTTCCCGATGGTCTCGTACCACCATCGA-CCTAAGTTGTCGATGGTGTCCGAT
** * ** * * *
826 GCTCTTGCACATCCAAGGCACCAAGGTGCCGATGGATCCCGATTGTCCTGCACCACCATAGGCCT
64 GCTCCAGCACATCCAAGGCACCAAGGTGCCAATACATCCCGATGGTCCTGAACCACCATAGACCT
* *
891 AAGCTGCCGATGGTGTCCGATGCTCTTGCACAT-CGAAGGTACCAT
129 AAGCTGCCGATGGTGTCCGATGCTCTCGCACATCCG-AGGTACCAA
* * * * *
936 GGTGCTGAT-ACTTCCCGATAGTCTCGCACCACCATCGACCTCAGTTATCGATGGTGTCCGATGC
1 GGTGCCGATGACTTCCCGATGGTCTCGTACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGC
* * * * * * *
1000 TCCCGCACATCCAAGGCACCATGGTTCCAATACTTCCCGATGGTCTTGAACCACCATCGACCTCA
66 TCCAGCACATCCAAGGCACCAAGGTGCCAATACATCCCGATGGTCCTGAACCACCATAGACCTAA
* * *
1065 GTTGTCGGTGGTGTCCGATGCTCTCGCACATCCGAGGTACCAA
131 GCTGCCGATGGTGTCCGATGCTCTCGCACATCCGAGGTACCAA
* * * *
1108 GGTGCCGATGA-TTCTCGATGGTCTCGTACCACCATCGACCTAAGCTGTCGATGGTGTCTGATGA
1 GGTGCCGATGACTTCCCGATGGTCTCGTACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGC
1172 TCCAGCACATCCA
66 TCCAGCACATCCA
1185 GTGCACGAAC
Statistics
Matches: 208, Mismatches: 37, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
172 200 0.96
173 8 0.04
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.24
Consensus pattern (173 bp):
GGTGCCGATGACTTCCCGATGGTCTCGTACCACCATCGACCTAAGTTGTCGATGGTGTCCGATGC
TCCAGCACATCCAAGGCACCAAGGTGCCAATACATCCCGATGGTCCTGAACCACCATAGACCTAA
GCTGCCGATGGTGTCCGATGCTCTCGCACATCCGAGGTACCAA
Found at i:3794 original size:17 final size:17
Alignment explanation
Indices: 3774--3806 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3764 AGTTGAGAAA
3774 TAAAATGCAAAGACAAT
1 TAAAATGCAAAGACAAT
*
3791 TAAAATGCAATGACAA
1 TAAAATGCAAAGACAA
3807 CTATATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.18
Consensus pattern (17 bp):
TAAAATGCAAAGACAAT
Found at i:9095 original size:13 final size:13
Alignment explanation
Indices: 9077--9101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9067 ACAAACATTA
9077 GCCTCAACCTTGC
1 GCCTCAACCTTGC
9090 GCCTCAACCTTG
1 GCCTCAACCTTG
9102 TGGTCGCATT
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:0.16, C:0.44, G:0.16, T:0.24
Consensus pattern (13 bp):
GCCTCAACCTTGC
Found at i:11959 original size:18 final size:18
Alignment explanation
Indices: 11938--11988 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
11928 TGCAGTCTGT
11938 TGTGGCTGCATGC-GAGCA
1 TGTGGCTGCAT-CTGAGCA
* *
11956 TGTGGTTGCATCTGAGTA
1 TGTGGCTGCATCTGAGCA
*
11974 TGTGACTGCATCTGA
1 TGTGGCTGCATCTGA
11989 TCAGGATGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (18 bp):
TGTGGCTGCATCTGAGCA
Found at i:20889 original size:23 final size:23
Alignment explanation
Indices: 20863--20917 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
20853 AGTAAAAGAT
* * *
20863 GTAAATGTATCATGTTGACGAGC
1 GTAAACGTAGCATGCTGACGAGC
20886 GTAAACGTAGCATGCTGACGAGC
1 GTAAACGTAGCATGCTGACGAGC
20909 GTAAACGTA
1 GTAAACGTA
20918 AAGAAGTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (23 bp):
GTAAACGTAGCATGCTGACGAGC
Found at i:21902 original size:23 final size:23
Alignment explanation
Indices: 21875--21928 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
21865 ATTCTATCTA
21875 TTTCAAATAAGATTTTAAATTAT
1 TTTCAAATAAGATTTTAAATTAT
21898 TTTCAAATAAGATTTTAAATTAT
1 TTTCAAATAAGATTTTAAATTAT
21921 TTTCAAAT
1 TTTCAAAT
21929 TTGTACTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTCAAATAAGATTTTAAATTAT
Found at i:23916 original size:133 final size:135
Alignment explanation
Indices: 23675--23943 Score: 452
Period size: 133 Copynumber: 2.0 Consensus size: 135
23665 CCTATAGGAC
*
23675 AGAGTGTAATTGTTAACAAAGTTTGTAGGAATTGTCCATTGAAAGTTCAAAATTATGAGTTCCTT
1 AGAGTGTAATTGTTAACAAAGTCTGTAGGAATTGTCCATTGAAAGTTCAAAA-TATGAGTTCCTT
* *
23740 GTGGACTTAATGTTGTTACCCTTTGATGAATTTGACGTCATTTTGGAATGGATTGGTTAACCATG
65 GCGAACTTAATGTTGTTACCCTTTGATGAATTTGACGTCATTTTGGAATGGATTGGTTAACCATG
23805 CACGAT
130 CACGAT
**
23811 AGAGTGTAATTGTTAACAAAGTCTGTAGGAATTGTCCATTGAAAGTT-TGAA-ATGAGTTCCTTG
1 AGAGTGTAATTGTTAACAAAGTCTGTAGGAATTGTCCATTGAAAGTTCAAAATATGAGTTCCTTG
* *
23874 CGAACTTAATGTTGTTACCCTTTGATGAATTTGGCGTCATTTTGGAATGGATTGGTTAACTATGC
66 CGAACTTAATGTTGTTACCCTTTGATGAATTTGACGTCATTTTGGAATGGATTGGTTAACCATGC
23939 ACGAT
131 ACGAT
23944 GTAATGGTCA
Statistics
Matches: 126, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
133 78 0.62
135 2 0.02
136 46 0.37
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (135 bp):
AGAGTGTAATTGTTAACAAAGTCTGTAGGAATTGTCCATTGAAAGTTCAAAATATGAGTTCCTTG
CGAACTTAATGTTGTTACCCTTTGATGAATTTGACGTCATTTTGGAATGGATTGGTTAACCATGC
ACGAT
Found at i:27892 original size:23 final size:23
Alignment explanation
Indices: 27849--27893 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
27839 AGAAGAAAAT
** *
27849 GTATCATGCTGATGAGCGTAAAC
1 GTATCATGCTGACAAGAGTAAAC
27872 GTATCATGCTGACAAGAGTAAA
1 GTATCATGCTGACAAGAGTAAA
27894 TGTACTTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (23 bp):
GTATCATGCTGACAAGAGTAAAC
Found at i:49553 original size:21 final size:21
Alignment explanation
Indices: 49527--49566 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49517 TTAGCACACT
49527 CAGATGCATCCACAACAAAGC
1 CAGATGCATCCACAACAAAGC
*
49548 CAGATGCATCCACACCAAA
1 CAGATGCATCCACAACAAA
49567 ATCAGACGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.10
Consensus pattern (21 bp):
CAGATGCATCCACAACAAAGC
Found at i:49572 original size:21 final size:21
Alignment explanation
Indices: 49526--49572 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
49516 ATTAGCACAC
*
49526 TCAGATGCATCCACAACAAAG
1 TCAGATGCATCCACAACAAAA
* *
49547 CCAGATGCATCCACACCAAAA
1 TCAGATGCATCCACAACAAAA
49568 TCAGA
1 TCAGA
49573 CGCAACAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.32, G:0.13, T:0.13
Consensus pattern (21 bp):
TCAGATGCATCCACAACAAAA
Found at i:54679 original size:39 final size:39
Alignment explanation
Indices: 54636--54719 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
54626 ATGTAGATGA
54636 ACACTTCGAGTTTATTAAGGATATCACAGACGACAAAAG
1 ACACTTCGAGTTTATTAAGGATATCACAGACGACAAAAG
*
54675 ACACTCCGAGTTTATTAAGGATATCACAGACGACAAAAG
1 ACACTTCGAGTTTATTAAGGATATCACAGACGACAAAAG
*
54714 ATACTT
1 ACACTT
54720 GCTGGTAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (39 bp):
ACACTTCGAGTTTATTAAGGATATCACAGACGACAAAAG
Found at i:55468 original size:39 final size:39
Alignment explanation
Indices: 55425--55504 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
55415 ATCTGAGATT
55425 ATGAACTCTCATCAGTGGATGTTGACTTAAGGGACCAAG
1 ATGAACTCTCATCAGTGGATGTTGACTTAAGGGACCAAG
*
55464 ATGAACTCTTATCAGTGGATGTTGACTTAAGGGACCAAG
1 ATGAACTCTCATCAGTGGATGTTGACTTAAGGGACCAAG
55503 AT
1 AT
55505 AGATCTGTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (39 bp):
ATGAACTCTCATCAGTGGATGTTGACTTAAGGGACCAAG
Found at i:55709 original size:15 final size:15
Alignment explanation
Indices: 55691--55729 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
55681 AGGAAGAAGT
55691 TGCTGAGAAAGAATA
1 TGCTGAGAAAGAATA
* *
55706 TGCTAAGAAAGAATC
1 TGCTGAGAAAGAATA
*
55721 TACTGAGAA
1 TGCTGAGAA
55730 CATTGTCACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (15 bp):
TGCTGAGAAAGAATA
Found at i:57185 original size:43 final size:43
Alignment explanation
Indices: 57121--57433 Score: 283
Period size: 43 Copynumber: 7.3 Consensus size: 43
57111 CCAAAACTCT
* ** *
57121 CGCACATCCATGGCATTAAGGTGTCAATGCTGTCCGATGCTCC
1 CGCACATCCAAGGCACCAAGGTGTCGATGCTGTCCGATGCTCC
* * * * *
57164 CGGACATCCAAGGCACCAAGGTGCCGGTGGTGTCCGAGGCTCTC
1 CGCACATCCAAGGCACCAAGGTGTCGATGCTGTCCGATGCTC-C
* * * * * *
57208 AG-ACATCCAAGGCAGCAAGGT-TCTGATGATATCCGATACTGC
1 CGCACATCCAAGGCACCAAGGTGTC-GATGCTGTCCGATGCTCC
*
57250 CACACATCCAAGGCACCAAGGTGTCGATGCT-TCTCGATGCTCC
1 CGCACATCCAAGGCACCAAGGTGTCGATGCTGTC-CGATGCTCC
* * * **
57293 CGCACATCCAAGGTACCAAGGTGTCGGTGGTGTCTAATGCTCC
1 CGCACATCCAAGGCACCAAGGTGTCGATGCTGTCCGATGCTCC
* * * * * * *
57336 TGCACATCCAAGGCACTAAGGTGTCGGTGGTTTTCAATGCTCC
1 CGCACATCCAAGGCACCAAGGTGTCGATGCTGTCCGATGCTCC
* *
57379 CGCACATTCGAGGCACCAAGGTGTCGATGCT-TCTCGATGCTCC
1 CGCACATCCAAGGCACCAAGGTGTCGATGCTGTC-CGATGCTCC
*
57422 TGCACATCCAAG
1 CGCACATCCAAG
57434 CATGAAAATT
Statistics
Matches: 216, Mismatches: 47, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
42 5 0.02
43 205 0.95
44 6 0.03
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (43 bp):
CGCACATCCAAGGCACCAAGGTGTCGATGCTGTCCGATGCTCC
Found at i:57357 original size:129 final size:129
Alignment explanation
Indices: 57123--57433 Score: 360
Period size: 129 Copynumber: 2.4 Consensus size: 129
57113 AAAACTCTCG
* ** * *
57123 CACATCCATGGCATTAAGGTGTCAATGCTGTC-CGATGCTCCCGGACATCCAAGGCACCAAGGTG
1 CACATCCAAGGCACCAAGGTGTCGATGCT-TCTCGATGCTCCCGCACATCCAAGGCACCAAGGTG
* * *
57187 CCGGTGGTGTCCGAGGCTCTCAGACATCCAAGGCAGCAAGGT-TCTGATGATATCCGATACTGCC
65 CCGGTGGTGTCCAAGGCTCTCAGACATCCAAGGCAGCAAGGTGTC-GATGATATCCAATACTCCC
57251 A
129 A
* *
57252 CACATCCAAGGCACCAAGGTGTCGATGCTTCTCGATGCTCCCGCACATCCAAGGTACCAAGGTGT
1 CACATCCAAGGCACCAAGGTGTCGATGCTTCTCGATGCTCCCGCACATCCAAGGCACCAAGGTGC
* * * * * * * *
57317 CGGTGGTGTCTAATGCTC-CTGCACATCCAAGGCA-CTAAGGTGTCGGTGGTTTTCAATGCTCCC
66 CGGTGGTGTCCAAGGCTCTCAG-ACATCCAAGGCAGC-AAGGTGTCGATGATATCCAATACTCCC
*
57380 G
129 A
* * *
57381 CACATTCGAGGCACCAAGGTGTCGATGCTTCTCGATGCTCCTGCACATCCAAG
1 CACATCCAAGGCACCAAGGTGTCGATGCTTCTCGATGCTCCCGCACATCCAAG
57434 CATGAAAATT
Statistics
Matches: 156, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
128 5 0.03
129 149 0.96
130 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (129 bp):
CACATCCAAGGCACCAAGGTGTCGATGCTTCTCGATGCTCCCGCACATCCAAGGCACCAAGGTGC
CGGTGGTGTCCAAGGCTCTCAGACATCCAAGGCAGCAAGGTGTCGATGATATCCAATACTCCCA
Found at i:67956 original size:13 final size:13
Alignment explanation
Indices: 67914--67956 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
67904 TCGCATAAAG
67914 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
* *
67927 GAAAGAA-AAAGAG
1 AAAAGAAGAAA-AA
67940 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
67953 AAAA
1 AAAA
67957 TATATATACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.12
13 18 0.75
14 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAAA
Found at i:68321 original size:13 final size:13
Alignment explanation
Indices: 68303--68327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68293 CCTTTTGTAT
68303 CATTTTTAGCATA
1 CATTTTTAGCATA
68316 CATTTTTAGCAT
1 CATTTTTAGCAT
68328 TTCATACTTA
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATA
Found at i:80584 original size:17 final size:17
Alignment explanation
Indices: 80557--80589 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
80547 TTCTAATTAG
80557 ACCCAAAAAATTTATTTT
1 ACCCAAAAAA-TTATTTT
80575 ACCC-AAAAATTATTT
1 ACCCAAAAAATTATTT
80590 AAAACCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (17 bp):
ACCCAAAAAATTATTTT
Found at i:88544 original size:27 final size:22
Alignment explanation
Indices: 88479--88541 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
88469 CATACAACAT
88479 ATCACAA-CACAAATGCAATAAA
1 ATCACAAGCAC-AATGCAATAAA
88501 ATCACAAGCACAATGCAATAAA
1 ATCACAAGCACAATGCAATAAA
*
88523 ATCACAAGTACAATGCAAT
1 ATCACAAGCACAATGCAAT
88542 GCACCTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 36 0.92
23 3 0.08
ACGTcount: A:0.54, C:0.22, G:0.08, T:0.16
Consensus pattern (22 bp):
ATCACAAGCACAATGCAATAAA
Found at i:92199 original size:13 final size:14
Alignment explanation
Indices: 92181--92212 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
92171 GTCAACGTAA
92181 TTAGA-GTTAAATG
1 TTAGAGGTTAAATG
92194 TTAGAGGTTAAATG
1 TTAGAGGTTAAATG
92208 TTAGA
1 TTAGA
92213 ACAACTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (14 bp):
TTAGAGGTTAAATG
Found at i:106634 original size:14 final size:14
Alignment explanation
Indices: 106615--106649 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
106605 AAGCCCGACC
*
106615 CGTTGACCGTTGAT
1 CGTTGACCATTGAT
106629 CGTTGACCATTGAT
1 CGTTGACCATTGAT
106643 CGTTGAC
1 CGTTGAC
106650 TTTTTCTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (14 bp):
CGTTGACCATTGAT
Found at i:115085 original size:2 final size:2
Alignment explanation
Indices: 115078--115114 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
115068 AATTAGAGAT
* *
115078 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
115115 GTGAATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:115429 original size:24 final size:24
Alignment explanation
Indices: 115399--115466 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 24
115389 TTGAAATTTA
*
115399 ATAAAAGAAAAATAATTAATAATT
1 ATAAAAGAAAAATAATTAATAAAT
* *
115423 GTAAAAGATAAATATAATTATTAAAT
1 ATAAAAGA-AAA-ATAATTAATAAAT
* *
115449 ATTAAATAAAAATAATTA
1 ATAAAAGAAAAATAATTA
115467 TATTTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 14 0.39
25 6 0.17
26 16 0.44
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
ATAAAAGAAAAATAATTAATAAAT
Found at i:121763 original size:24 final size:24
Alignment explanation
Indices: 121745--121795 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
121735 AGTTTGACTT
121745 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAACAAAGTTTAATTG
* *
121769 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAAAGTTTAATTG
121793 AAA
1 AAA
121796 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAAAGTTTAATTG
Found at i:122131 original size:31 final size:29
Alignment explanation
Indices: 122093--122168 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
122083 TAAATATAAA
122093 ATTGGTACTCAAACTTGTTCACTTCTCCCAG
1 ATTGGTACTCAAACTTGTT--CTTCTCCCAG
* * * *
122124 ATTGGTACTTAAAGTTTGTTTTTGTCCCAG
1 ATTGGTACTCAAA-CTTGTTCTTCTCCCAG
*
122154 ATTGGTACTCGAACT
1 ATTGGTACTCAAACT
122169 ATTTTTTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 19 0.51
31 12 0.32
32 5 0.14
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.39
Consensus pattern (29 bp):
ATTGGTACTCAAACTTGTTCTTCTCCCAG
Found at i:123261 original size:34 final size:34
Alignment explanation
Indices: 123235--123301 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
123225 AAATGGGAAA
*
123235 AATAAAAGGGAAGGGAAAAACGGGAAAATAAAAT
1 AATAAAAGAGAAGGGAAAAACGGGAAAATAAAAT
**
123269 AATAAAAGAGAAGGGAAAATGGGGAAAAATAAA
1 AATAAAAGAGAAGGGAAAAACGGG-AAAATAAA
123302 TGACATCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.63, C:0.01, G:0.27, T:0.09
Consensus pattern (34 bp):
AATAAAAGAGAAGGGAAAAACGGGAAAATAAAAT
Found at i:130891 original size:11 final size:11
Alignment explanation
Indices: 130875--130913 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
130865 ATTTCCCACA
*
130875 AAAAAAGTGAT
1 AAAAAAGTGAG
130886 AAAAAAGTCGAG
1 AAAAAAGT-GAG
*
130898 AAAAAAATGAG
1 AAAAAAGTGAG
130909 AAAAA
1 AAAAA
130914 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (11 bp):
AAAAAAGTGAG
Found at i:134365 original size:20 final size:20
Alignment explanation
Indices: 134340--134378 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
134330 GCTAAGAATC
134340 TGAAACAACAT-AAAGAAAAG
1 TGAAACAA-ATAAAAGAAAAG
134360 TGAAACAAATAAAAGAAAA
1 TGAAACAAATAAAAGAAAA
134379 TAAAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.69, C:0.08, G:0.13, T:0.10
Consensus pattern (20 bp):
TGAAACAAATAAAAGAAAAG
Found at i:139469 original size:12 final size:12
Alignment explanation
Indices: 139452--139483 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
139442 TCGGCATATT
139452 AAATTGCAAAAC
1 AAATTGCAAAAC
139464 AAATTGCAAAAC
1 AAATTGCAAAAC
139476 AAATTGCA
1 AAATTGCA
139484 TTGTTAACGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (12 bp):
AAATTGCAAAAC
Found at i:140777 original size:24 final size:24
Alignment explanation
Indices: 140745--140793 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
140735 ACCGTATCTC
140745 TCAAAATTAGTTAGATTACAGCTG
1 TCAAAATTAGTTAGATTACAGCTG
*
140769 TCAAAATTAGTTAGATTATAGCTG
1 TCAAAATTAGTTAGATTACAGCTG
140793 T
1 T
140794 GCACTCACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (24 bp):
TCAAAATTAGTTAGATTACAGCTG
Found at i:145020 original size:15 final size:16
Alignment explanation
Indices: 144985--145019 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
144975 GAATAAAGTG
*
144985 TTTTGAGACTTTTAAT
1 TTTTGAGACTTGTAAT
145001 TTTTGAGACTTGTAAT
1 TTTTGAGACTTGTAAT
145017 TTT
1 TTT
145020 GGGGTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (16 bp):
TTTTGAGACTTGTAAT
Found at i:161027 original size:20 final size:21
Alignment explanation
Indices: 160993--161031 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
160983 CATTTTTCTA
*
160993 TTTACTTTTATTTATTTCACT
1 TTTACTTTTAGTTATTTCACT
161014 TTTACTTTT-GTTATTTCA
1 TTTACTTTTAGTTATTTCA
161032 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTATTTCACT
Found at i:163358 original size:17 final size:18
Alignment explanation
Indices: 163336--163376 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
163326 AGATAGTTTT
*
163336 TGCATTTT-TATTGTCCC
1 TGCATTTTATATTGTCAC
*
163353 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
163371 TGCATT
1 TGCATT
163377 CCTTTTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.15, C:0.20, G:0.12, T:0.54
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:163981 original size:14 final size:14
Alignment explanation
Indices: 163961--164012 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
163951 AATCAGTTGA
163961 AAAAGAAAAAATGAG
1 AAAAGAAAAAA-GAG
163976 -AAAGAAGAAAAGAG
1 AAAAGAA-AAAAGAG
163990 AAAAG-AAAAAGAAG
1 AAAAGAAAAAAG-AG
164004 AAAA-AAAAA
1 AAAAGAAAAA
164013 TTATAATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.15
14 20 0.61
15 8 0.24
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAAGAG
Found at i:173015 original size:10 final size:10
Alignment explanation
Indices: 173002--173040 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
172992 AAAAGTTTTA
173002 TATAGTTTCC
1 TATAGTTTCC
173012 TATAGTTTCC
1 TATAGTTTCC
173022 TATAGTTTCC
1 TATAGTTTCC
173032 TATAGTTTC
1 TATAGTTTC
173041 ACAATCACGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (10 bp):
TATAGTTTCC
Found at i:174253 original size:2 final size:2
Alignment explanation
Indices: 174246--174272 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
174236 AATAATAGGT
174246 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
174273 TGATATGCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:175780 original size:31 final size:31
Alignment explanation
Indices: 175742--175821 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 31
175732 TTTTGCGCAC
175742 TTATTTTAAAATATAAGAACTAGCAGTCTCA
1 TTATTTTAAAATATAAGAACTAGCAGTCTCA
** **
175773 TTATTTTAGGATACTAATTACTAGCAGTCTCA
1 TTATTTTAAAATA-TAAGAACTAGCAGTCTCA
175805 TTATTTTAAAATATAAG
1 TTATTTTAAAATATAAG
175822 CAAAATTTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 14 0.34
32 27 0.66
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (31 bp):
TTATTTTAAAATATAAGAACTAGCAGTCTCA
Found at i:179723 original size:31 final size:31
Alignment explanation
Indices: 179688--179748 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
179678 TTCAAAACAG
*
179688 CAATTAGTTGCTCCTCTTGATCTTTTGTCAA
1 CAATTAGTTACTCCTCTTGATCTTTTGTCAA
179719 CAATTAGTTACTCCTCTTGATCTTTTGTCA
1 CAATTAGTTACTCCTCTTGATCTTTTGTCA
179749 GTTCTGCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46
Consensus pattern (31 bp):
CAATTAGTTACTCCTCTTGATCTTTTGTCAA
Found at i:184500 original size:26 final size:26
Alignment explanation
Indices: 184471--184533 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
184461 AATTCTAGGC
184471 ACAATTCTGGACACATTCATGCAGCG
1 ACAATTCTGGACACATTCATGCAGCG
* **
184497 ACAATTCTGTACATGTTCATGCAGCG
1 ACAATTCTGGACACATTCATGCAGCG
184523 AC-ATTCCTGGA
1 ACAATT-CTGGA
184534 TGCAATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 3 0.09
26 29 0.91
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (26 bp):
ACAATTCTGGACACATTCATGCAGCG
Found at i:184557 original size:37 final size:38
Alignment explanation
Indices: 184515--184600 Score: 129
Period size: 37 Copynumber: 2.3 Consensus size: 38
184505 GTACATGTTC
*
184515 ATGCAGCGACATTCCTGGATGCAA-TTGAAGAATACTT
1 ATGCAGCGACATTCCTAGATGCAATTTGAAGAATACTT
** *
184552 ATGCAGTAACATTCCTAGATGCAATTTGAAGAATATTT
1 ATGCAGCGACATTCCTAGATGCAATTTGAAGAATACTT
184590 ATGCAGCGACA
1 ATGCAGCGACA
184601 GTCTTGGGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 21 0.50
38 21 0.50
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (38 bp):
ATGCAGCGACATTCCTAGATGCAATTTGAAGAATACTT
Found at i:184592 original size:38 final size:37
Alignment explanation
Indices: 184523--184595 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 37
184513 TCATGCAGCG
*
184523 ACATTCCTGGATGCAATTGAAGAATACTTATGCAGTA
1 ACATTCCTAGATGCAATTGAAGAATACTTATGCAGTA
*
184560 ACATTCCTAGATGCAATTTGAAGAATATTTATGCAG
1 ACATTCCTAGATGCAA-TTGAAGAATACTTATGCAG
184596 CGACAGTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (37 bp):
ACATTCCTAGATGCAATTGAAGAATACTTATGCAGTA
Found at i:190492 original size:92 final size:92
Alignment explanation
Indices: 190350--190552 Score: 309
Period size: 92 Copynumber: 2.2 Consensus size: 92
190340 AGTTGGGATA
* * *
190350 CTTGAATCGGTAGAAGTTGCAGGATTAAACTTCTTAGCTCTCTGGAGTTTTTAGTAGCTGTAGAT
1 CTTGTATCGGTAGAAGTTGTAGGATTAAACTTCTTAGCTCTCTGGAGTTTTTAGTAGCGGTAGAT
*
190415 GTATGACTTGTTTCGGTAGAAGAGTCT
66 GTATGACTTGTTTCAGTAGAAGAGTCT
* * * * *
190442 CTTGTATCGGTAGAAGTTGTAGGGTTAAATTTCTTATCTCTCTGGAGTTTTTCGTATCGGTAGAT
1 CTTGTATCGGTAGAAGTTGTAGGATTAAACTTCTTAGCTCTCTGGAGTTTTTAGTAGCGGTAGAT
190507 GTATGACTTGTTTCAGTAGAAGAGTCT
66 GTATGACTTGTTTCAGTAGAAGAGTCT
*
190534 TTTGTATCGGTAGAA-TTGT
1 CTTGTATCGGTAGAAGTTGT
190553 CACTTGTATC
Statistics
Matches: 101, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 4 0.04
92 97 0.96
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.40
Consensus pattern (92 bp):
CTTGTATCGGTAGAAGTTGTAGGATTAAACTTCTTAGCTCTCTGGAGTTTTTAGTAGCGGTAGAT
GTATGACTTGTTTCAGTAGAAGAGTCT
Found at i:211551 original size:2 final size:2
Alignment explanation
Indices: 211544--211579 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
211534 TTTGAATGCT
*
211544 TA TA TA TA TA TA TA TA TA TG 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
211580 AGCAGAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:211683 original size:41 final size:41
Alignment explanation
Indices: 211637--211728 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
211627 AAAATTTTTT
211637 TATTTAAATTTTTTATCATTTATAAAATTTTAAATTAGTAA
1 TATTTAAATTTTTTATCATTTATAAAATTTTAAATTAGTAA
*
211678 TATTTAAGTTTTTTATCATTTATAAAATTTTAAATTAGTAA
1 TATTTAAATTTTTTATCATTTATAAAATTTTAAATTAGTAA
* *
211719 TGTTAAAATT
1 TATTTAAATT
211729 ACATTTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (41 bp):
TATTTAAATTTTTTATCATTTATAAAATTTTAAATTAGTAA
Found at i:212013 original size:114 final size:114
Alignment explanation
Indices: 211888--212102 Score: 421
Period size: 114 Copynumber: 1.9 Consensus size: 114
211878 TTGCCCTCTA
211888 AATTTTTTTAGATAATTACGTTTATTTTCTTTAAATTAAGAGTTATTTTTTAATTTAATGTATTA
1 AATTTTTTTAGATAATTACGTTTATTTTCTTTAAATTAAGAGTTATTTTTTAATTTAATGTATTA
211953 TTTATTTTATTATTTTTCACATGTAATTATCTTATTGAGTTATATAGGT
66 TTTATTTTATTATTTTTCACATGTAATTATCTTATTGAGTTATATAGGT
*
212002 AATTTTTTTAGATAATTACGTTTATTTTCTTTAAATTAAGAGTTATTTTTTGATTTAATGTATTA
1 AATTTTTTTAGATAATTACGTTTATTTTCTTTAAATTAAGAGTTATTTTTTAATTTAATGTATTA
212067 TTTATTTTATTATTTTTCACATGTAATTATCTTATT
66 TTTATTTTATTATTTTTCACATGTAATTATCTTATT
212103 TCACATATGA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (114 bp):
AATTTTTTTAGATAATTACGTTTATTTTCTTTAAATTAAGAGTTATTTTTTAATTTAATGTATTA
TTTATTTTATTATTTTTCACATGTAATTATCTTATTGAGTTATATAGGT
Found at i:218793 original size:36 final size:38
Alignment explanation
Indices: 218726--218805 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 38
218716 GAGCAATTTA
*
218726 ATTTTTTTTCTTTTATGTTCTTTAAACTTTCT-CTTCT
1 ATTTTTTTTCTTTTATATTCTTTAAACTTTCTCCTTCT
* * *
218763 TTTTTTTTTTTTTTA-ATTCTCTT-AAGTTTCTCCTTCT
1 ATTTTTTTTCTTTTATATTCT-TTAAACTTTCTCCTTCT
218800 ATTTTT
1 ATTTTT
218806 CTACCTTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.70
Consensus pattern (38 bp):
ATTTTTTTTCTTTTATATTCTTTAAACTTTCTCCTTCT
Found at i:220490 original size:43 final size:44
Alignment explanation
Indices: 220418--220542 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 44
220408 GACATTGAGA
* * * * *
220418 GGAACATTGTTTCCTAAAATTGAATGTATGAGATTGATTATG-T
1 GGAACACTATTTCCTAATATTGAAAGTATGTGATTGATTATGAT
* * **
220461 GGAACACTATTTCCTATTATTTAAAGTATGTGA--GAAAATGATT
1 GGAACACTATTTCCTAATATTGAAAGTATGTGATTGATTATGA-T
* *
220504 GGAACATTATTTCCTAATATTGATAGTATGTGATTGATT
1 GGAACACTATTTCCTAATATTGAAAGTATGTGATTGATT
220543 GAGAGCATGA
Statistics
Matches: 63, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
41 5 0.08
43 56 0.89
45 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (44 bp):
GGAACACTATTTCCTAATATTGAAAGTATGTGATTGATTATGAT
Found at i:228095 original size:24 final size:24
Alignment explanation
Indices: 228063--228116 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
228053 GTTGGGTGAT
228063 GCGCGTGCGACGGGATCGACGACG
1 GCGCGTGCGACGGGATCGACGACG
228087 GCGCGTGCGACGGGATCGACGACG
1 GCGCGTGCGACGGGATCGACGACG
228111 GCGCGT
1 GCGCGT
228117 TGACAGAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.30, G:0.46, T:0.09
Consensus pattern (24 bp):
GCGCGTGCGACGGGATCGACGACG
Found at i:228754 original size:29 final size:28
Alignment explanation
Indices: 228711--228938 Score: 126
Period size: 29 Copynumber: 7.8 Consensus size: 28
228701 GAAGGTCCCT
228711 AAACTATCCAAAAATTCCATTTTGACCCC
1 AAACT-TCCAAAAATTCCATTTTGACCCC
* **
228740 AAAACTTTCAAAAATTATAATTTT-ACTCCC
1 -AAACTTCCAAAAATT-CCATTTTGAC-CCC
* *
228770 TAACTTCCAAAAATTCCATTTTCACCCTC
1 AAACTTCCAAAAATTCCATTTTGACCC-C
* * *
228799 GAACCTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCA-TTTTGACCC-C
* *
228829 AAACTTCCGAAAATTACCATTTT-ACCACT
1 AAACTTCCAAAAATT-CCATTTTGACC-CC
** *
228858 GGA-TATCCAAAAACTCCATTTTTGACCCC
1 AAACT-TCCAAAAATTCCA-TTTTGACCCC
*
228887 GAAAC-TCTAAAAAATTACCATTTT-ACCCCC
1 -AAACTTC-CAAAAATT-CCATTTTGA-CCCC
* *
228917 GAA-TGTCCAAAAATTCCGTTTT
1 AAACT-TCCAAAAATTCCATTTT
228939 TTTATCCCGA
Statistics
Matches: 154, Mismatches: 27, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
28 17 0.11
29 72 0.47
30 59 0.38
31 6 0.04
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTGACCCC
Found at i:228867 original size:59 final size:58
Alignment explanation
Indices: 228771--229056 Score: 179
Period size: 59 Copynumber: 4.8 Consensus size: 58
228761 TTTACTCCCT
* *
228771 AACTTCCAAAAATT-CCATTTTCACCCTCGA-ACCTCCAAAAATTCCATTTTTGACCCTAA
1 AACTTCCAAAAATTACCATTTT-ACCCTGGATA--TCCAAAAATTCCATTTTTGACCCCAA
* * *
228830 AACTTCCGAAAATTACCATTTTACCACTGGATATCCAAAAACTCCATTTTTGACCCCGA
1 AACTTCCAAAAATTACCATTTTACC-CTGGATATCCAAAAATTCCATTTTTGACCCCAA
* * * * * * * *
228889 AAC-TCTAAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCGTTTTTTTATCCCGA
1 AACTTC-CAAAAATTACCATTTTA-CCCTGGATATCCAAAAATTCC-ATTTTTGACCCCAA
*** * * * * * * * **
228949 TTTTTCTAAAAATTACCGTTTTACCCTCGA-ATGTCTAATATTCTATTTTAAACCCCAA
1 AACTTCCAAAAATTACCATTTTACCCTGGATAT-CCAAAAATTCCATTTTTGACCCCAA
** *
229007 ATTTTCCCAAAATTACCATTTTACCCTCGAGA-ATCC-AAAATTACCATTTT
1 AACTTCCAAAAATTACCATTTTACCCT-G-GATATCCAAAAATT-CCATTTT
229057 GCCCCCCGGG
Statistics
Matches: 176, Mismatches: 40, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
58 40 0.23
59 90 0.51
60 43 0.24
61 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (58 bp):
AACTTCCAAAAATTACCATTTTACCCTGGATATCCAAAAATTCCATTTTTGACCCCAA
Found at i:228867 original size:88 final size:88
Alignment explanation
Indices: 228717--228910 Score: 216
Period size: 88 Copynumber: 2.2 Consensus size: 88
228707 CCCTAAACTA
* * *
228717 TCCAAAAATTCCA-TTTTGACCCCAAAACTTTCAAAAATTATAATTTTACTCCCTAACTTCCAAA
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACAATTTTACTCACTAACTTCCAAA
* *
228781 AATTCCA-TTTTCACCCTCGAACC
66 AACTCCATTTTTCACCC-CGAAAC
* * * *
228804 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCGAAAATTACCATTTTAC-CACTGGA-TATCCA
1 TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACAATTTTACTCACT-AACT-TCCA
*
228867 AAAACTCCATTTTTGACCCCGAAAC
64 AAAACTCCATTTTTCACCCCGAAAC
*
228892 TCTAAAAAATTACCATTTT
1 TC-CAAAAATT-CCATTTT
228911 ACCCCCGAAT
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
87 17 0.19
88 51 0.57
89 15 0.17
90 7 0.08
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (88 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACAATTTTACTCACTAACTTCCAAA
AACTCCATTTTTCACCCCGAAAC
Found at i:228929 original size:30 final size:30
Alignment explanation
Indices: 228838--228929 Score: 75
Period size: 30 Copynumber: 3.1 Consensus size: 30
228828 AAAACTTCCG
* * *
228838 AAAATTACCATTTTACCACTGGATATCC-A
1 AAAATTACCATTTTACCCCCGAATATCCAA
* *
228867 AAAACT-CCATTTTTGA-CCCCGAA-ACTCTAA
1 AAAATTACCA-TTTT-ACCCCCGAATA-TCCAA
*
228897 AAAATTACCATTTTACCCCCGAATGTCCAA
1 AAAATTACCATTTTACCCCCGAATATCCAA
228927 AAA
1 AAA
228930 TTCCGTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
28 4 0.08
29 16 0.33
30 25 0.52
31 3 0.06
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (30 bp):
AAAATTACCATTTTACCCCCGAATATCCAA
Found at i:228985 original size:29 final size:28
Alignment explanation
Indices: 228877--228986 Score: 78
Period size: 29 Copynumber: 3.7 Consensus size: 28
228867 AAAACTCCAT
** *
228877 TTTTGACCCCGAAACTCTAAAAAATTACCA
1 TTTT-ACCCCGAATGTCT-AAAAATTACCG
*
228907 TTTTACCCCCGAATGTCCAAAAATT-CCG
1 TTTTA-CCCCGAATGTCTAAAAATTACCG
* * *
228935 TTTTTTTATCCCGATTTTTCTAAAAATTACCG
1 ---TTTTACCCCGA-ATGTCTAAAAATTACCG
228967 TTTTACCCTCGAATGTCTAA
1 TTTTACCC-CGAATGTCTAA
228987 TATTCTATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
28 2 0.03
29 21 0.34
30 21 0.34
31 15 0.24
32 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.36
Consensus pattern (28 bp):
TTTTACCCCGAATGTCTAAAAATTACCG
Found at i:240361 original size:18 final size:18
Alignment explanation
Indices: 240338--240381 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
240328 CAATCTATTA
240338 TTCGAATTGTTTGAATTT
1 TTCGAATTGTTTGAATTT
240356 TTCGAATTGTTTGAATTT
1 TTCGAATTGTTTGAATTT
*
240374 TTCAAATT
1 TTCGAATT
240382 ATTCAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.55
Consensus pattern (18 bp):
TTCGAATTGTTTGAATTT
Found at i:240362 original size:9 final size:10
Alignment explanation
Indices: 240338--240381 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
240328 CAATCTATTA
240338 TTCGAATTGT
1 TTCGAATTGT
240348 TT-GAATT-T
1 TTCGAATTGT
240356 TTCGAATTGT
1 TTCGAATTGT
240366 TT-GAATT-T
1 TTCGAATTGT
*
240374 TTCAAATT
1 TTCGAATT
240382 ATTCAAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 6 0.20
9 19 0.63
10 5 0.17
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.55
Consensus pattern (10 bp):
TTCGAATTGT
Found at i:242194 original size:30 final size:30
Alignment explanation
Indices: 242158--242219 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
242148 AAAAATTTTA
* *
242158 TTGTTAATTTT-TCTATTATTTTAGAGGCAT
1 TTGTTAATTTTGT-TACTATTTTAGAGACAT
242188 TTGTTAATTTTGTTACTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
242218 TT
1 TT
242220 ATTTGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGACAT
Found at i:242925 original size:15 final size:15
Alignment explanation
Indices: 242905--242933 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
242895 ATGACAAATC
242905 ACATTTTTCTTCTTT
1 ACATTTTTCTTCTTT
242920 ACATTTTTCTTCTT
1 ACATTTTTCTTCTT
242934 GATTTTCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (15 bp):
ACATTTTTCTTCTTT
Found at i:252074 original size:18 final size:18
Alignment explanation
Indices: 252051--252103 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
252041 ACAGCTTACA
252051 CTTTGATGAGCTTGCAAT
1 CTTTGATGAGCTTGCAAT
*
252069 CTTTGATGAGCTCG-AAT
1 CTTTGATGAGCTTGCAAT
*
252086 CTTTAGGTGAGCTTGCAA
1 CTTT-GATGAGCTTGCAA
252104 ATGTAGAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.23
18 21 0.70
19 2 0.07
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.36
Consensus pattern (18 bp):
CTTTGATGAGCTTGCAAT
Found at i:253408 original size:20 final size:20
Alignment explanation
Indices: 253383--253425 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
253373 AGTTCTCGTA
253383 GTCAGTAGCAGTCTAATGGT
1 GTCAGTAGCAGTCTAATGGT
253403 GTCAGTAGCAGTCTAATGGT
1 GTCAGTAGCAGTCTAATGGT
253423 GTC
1 GTC
253426 TAATCCTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (20 bp):
GTCAGTAGCAGTCTAATGGT
Found at i:259117 original size:11 final size:11
Alignment explanation
Indices: 259101--259130 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
259091 TACTACGATC
*
259101 AAATAATAACA
1 AAATAATAAAA
259112 AAATAATAAAA
1 AAATAATAAAA
259123 AAATAATA
1 AAATAATA
259131 GTAGTGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:259374 original size:12 final size:12
Alignment explanation
Indices: 259359--259391 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
259349 TAAATAAAAA
259359 TAAAAGTAAACG
1 TAAAAGTAAACG
*
259371 TAAACGTAAACG
1 TAAAAGTAAACG
259383 TAAAA-TAAA
1 TAAAAGTAAA
259392 GCAATAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (12 bp):
TAAAAGTAAACG
Found at i:261233 original size:100 final size:99
Alignment explanation
Indices: 261076--262290 Score: 751
Period size: 100 Copynumber: 12.1 Consensus size: 99
261066 AGAAAGACAT
* * * * * **
261076 GATTTGATATTGTAGCTTCATCTTGCTCC-TCTACATCTTCAGGGAGATAGGACTTGCTAATGTA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCAT-TGCATCTTCAGGGAGATAAGATTTGCTTTTGTA
*
261140 GTTTCAATCCGATCCACTGCAACTTAAGAGATATAG
65 GCTTCAATCCGATCCACTGCAACTTAAG-GATATAG
* * *
261176 GGTTTGATGTCGTAACTTCATCTTGCTCCATTG-AGTCTTCAGGGAGATAAGATTTGCTTCTGTA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCA-TCTTCAGGGAGATAAGATTTGCTTTTGTA
* * * *
261240 GCTTCAATCTGA-CCTACTACAACTTCAGGGGTATAG
65 GCTTCAATCCGATCC-ACTGCAACTT-AAGGATATAG
* * ** * * * * *
261276 GATTTGATGTC--A-CTTCAACTTGCTCCACTATAACTTTAAGAAGATAAGGTTTGCTTTTGTAG
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGATAAGATTTGCTTTTGTAG
* * * * *
261338 CTTCAATCCGACCCACCGTAACTTCAGGGCTATAG
66 CTTCAATCCGATCCACTGCAACTT-AAGGATATAG
* * * * * * *
261373 GACTTGATGTTGTAGTTTCATCTTACTTCATTGTATCTT-TGAGGAGATAAGATTTGCTTTTGTA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAG-GGAGATAAGATTTGCTTTTGTA
* *
261437 GCTTCAATCCGACCCATTGCAACTTTAGAGG-TATAG
65 GCTTCAATCCGATCCACTGCAAC-TTA-AGGATATAG
* * * * * * * ** *
261473 GATTTGATATTGTAGCTTCATTTTCCTCCACTGCAACTTCAGGGAGATAAGATTTACCATCGTAG
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGATAAGATTTGCTTTTGTAG
* * * *
261538 TTTCAATCCTATCCACTACAACTTCAAGGATGTAG
66 CTTCAATCCGATCCACTGCAACTT-AAGGATATAG
* * * * * ** * * *
261573 AATTTGGTGTGGTAGCTTTATCTTGCTCAATTATAACTTTAGGGAGATAAGACTTGCTATTTGTA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGATAAGATTTGCT-TTTGTA
** * * **
261638 ATTTCATTCCGACCCACTGCAACTTCAAGGGGACT-G
65 GCTTCAATCCGATCCACTGCAACTT-AAGGATA-TAG
* * * * * * * * * ** *
261674 GA-AT-AT-T--T-GTTTCATC-CGATCTACTACATCTTCAGGGATATAGGATTTAATTTTCTTC
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGATAAGATTTGCTTTT-GT-
* * * * * *
261732 ATCTTGCTCTATTGCTCTGATCCAGTGCATCTTTAGGGATATAA
64 AGC-T--TC-AAT-C-C-GATCCACTGCAAC-TTAAGGATATAG
* * * ** * * * *
261776 GATTTTATGTCGTAACTTCATCTTACTCTGTTGCAACTTCAGAGAGATAAAGATATGCTTTCGTA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGAT-AAGATTTGCTTTTGTA
*
261841 GCTTCAATCCAAT-CACTGCAACTTCAAGGATATAG
65 GCTTCAATCCGATCCACTGCAACTT-AAGGATATAG
*
261876 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATC-TCTAAGGAGATAAGATTTGCTTTTGTA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTC-AGGGAGATAAGATTTGCTTTTGTA
* * * * * *
261940 GCTTCAATTCAACCCACTACAACTTCAGGGGTATAG
65 GCTTCAATCCGATCCACTGCAACTT-AAGGATATAG
* * * * * * * * * ** *
261976 GATTTGATGTGGTAGCTTCAACTTGCTCTACTGCAACTTTAGAGAGAAAAATATTTGCTACTATA
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAG-ATAAGATTTGCTTTTGTA
* * * *
262041 GCTTTAATCCGATCC-TTGTAACTTCATGGATATAG
65 GCTTCAATCCGATCCACTGCAACTT-AAGGATATAG
* * * *
262076 GATTTGATGTCGTAACTTCATCTTGCTCCACTGCATCTTTAGGGAGATAAGATTTGCTTCTGTAG
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGATAAGATTTGCTTTTGTAG
* *
262141 CTTCAATCTGA-CCAACTGCAACTTCAAGGGTATAG
66 CTTCAATCCGATCC-ACTGCAACTT-AAGGATATAG
* ** * * * ** *
262176 GATTCGATGTTATAGCTTCATCTTGCTCTACTGCAACTTCAAAGAGATAAAGATTTGCTTTTGTG
1 GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGAT-AAGATTTGCTTTTGTA
* **
262241 GTTTCAATTTGATCCACTGCAACTTTAAGGATATAG
65 GCTTCAATCCGATCCACTGCAAC-TTAAGGATATAG
*
262277 GATTTTATGTCGTA
1 GATTTGATGTCGTA
262291 CTGATCCCTC
Statistics
Matches: 855, Mismatches: 214, Indels: 91
0.74 0.18 0.08
Matches are distributed among these distances:
93 3 0.00
94 24 0.03
95 7 0.01
96 2 0.00
97 75 0.09
98 9 0.01
99 66 0.08
100 482 0.56
101 119 0.14
102 22 0.03
103 4 0.00
104 4 0.00
105 3 0.00
107 2 0.00
108 8 0.01
109 17 0.02
110 8 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (99 bp):
GATTTGATGTCGTAGCTTCATCTTGCTCCATTGCATCTTCAGGGAGATAAGATTTGCTTTTGTAG
CTTCAATCCGATCCACTGCAACTTAAGGATATAG
Found at i:261477 original size:50 final size:51
Alignment explanation
Indices: 261306--261492 Score: 152
Period size: 50 Copynumber: 3.7 Consensus size: 51
261296 TGCTCCACTA
* * **
261306 TAACTTTAAGAAGATA-AGG-TTTGCTTTTGTAGCTTCAATCCGACCCACCG
1 TAACTTT-AGAGGATATAGGATTTGATTTTGTAGCTTCAATCCGACCCATTG
* * * * * ** *
261356 TAACTTCAG-GGCTATAGGACTTGATGTTGTAGTTTC-ATCTTACTTCATTG
1 TAACTTTAGAGGATATAGGATTTGATTTTGTAGCTTCAATCCGAC-CCATTG
* * * *
261406 TATCTTT-GAGGAGATAAGATTTGCTTTTGTAGCTTCAATCCGACCCATTG
1 TAACTTTAGAGGATATAGGATTTGATTTTGTAGCTTCAATCCGACCCATTG
* *
261456 CAACTTTAGAGG-TATAGGATTTGATATTGTAGCTTCA
1 TAACTTTAGAGGATATAGGATTTGATTTTGTAGCTTCA
261493 TTTTCCTCCA
Statistics
Matches: 101, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
48 3 0.03
49 11 0.11
50 78 0.77
51 9 0.09
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (51 bp):
TAACTTTAGAGGATATAGGATTTGATTTTGTAGCTTCAATCCGACCCATTG
Found at i:262013 original size:50 final size:50
Alignment explanation
Indices: 261854--262216 Score: 177
Period size: 50 Copynumber: 7.3 Consensus size: 50
261844 TCAATCCAAT
* * * *
261854 CACTGCAACTTCAAGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTC
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCAACTTGCTC
* * * * * * * *
261904 CATTGCATCTCTAAGGAG-ATAAGATTTGCTTTTGTAGCTTCAA-TT-CAACC
1 CACTGCAACT-TCAGGGGTATAGGATTTGATGTTGTAGCTTCAACTTGC--TC
* *
261954 CACTACAACTTCAGGGGTATAGGATTTGATGTGGTAGCTTCAACTTGCTC
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCAACTTGCTC
* * * * * ** * ** * * * *
262004 TACTGCAACTTTAGAGAGAAAAATATTTGCTACTATAGCTTTAA-TCCGATC
1 CACTGCAACTTCAG-GGGTATAGGATTTGATGTTGTAGCTTCAACT-TGCTC
* * * * * * *
262055 C-TTGTAACTTCATGGATATAGGATTTGATGTCGTAACTTCATCTTGCTC
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCAACTTGCTC
* * * *
262104 CACTGCATCTTTAGGGAG-ATAAGATTTGCT-TCTGTAGCTTCAA-TCTGAC-C
1 CACTGCAACTTCAGGG-GTATAGGATTTGATGT-TGTAGCTTCAACT-TG-CTC
* * * * *
262154 AACTGCAACTTCAAGGGTATAGGATTCGATGTTATAGCTTCATCTTGCTC
1 CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCAACTTGCTC
*
262204 TACTGCAACTTCA
1 CACTGCAACTTCA
262217 AAGAGATAAA
Statistics
Matches: 215, Mismatches: 80, Indels: 36
0.65 0.24 0.11
Matches are distributed among these distances:
48 1 0.00
49 30 0.14
50 154 0.72
51 29 0.13
52 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (50 bp):
CACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCAACTTGCTC
Found at i:263146 original size:10 final size:9
Alignment explanation
Indices: 263129--263170 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
263119 TCTCCTTTTC
263129 TTTTTTCTT
1 TTTTTTCTT
263138 TTCTTTTCTT
1 TT-TTTTCTT
*
263148 TTATTTCTT
1 TTTTTTCTT
263157 TTATTTT-TT
1 TT-TTTTCTT
263166 TTTTT
1 TTTTT
263171 GGTGAAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 3 0.10
9 14 0.48
10 12 0.41
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:263156 original size:19 final size:18
Alignment explanation
Indices: 263123--263170 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
263113 TCAACATCTC
263123 CTTTTC-TTTTTTCTTTT
1 CTTTTCTTTTTTTCTTTT
263140 CTTTTCTTTTATTTCTTTT
1 CTTTTCTTTT-TTTCTTTT
*
263159 ATTTT-TTTTTTT
1 CTTTTCTTTTTTT
263171 GGTGAAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.32
18 7 0.25
19 12 0.43
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.83
Consensus pattern (18 bp):
CTTTTCTTTTTTTCTTTT
Found at i:263167 original size:9 final size:10
Alignment explanation
Indices: 263131--263167 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
263121 TCCTTTTCTT
*
263131 TTTTCTTTTC
1 TTTTCTTTTA
263141 TTTTCTTTTA
1 TTTTCTTTTA
263151 -TTTCTTTTA
1 TTTTCTTTTA
263160 TTTT-TTTT
1 TTTTCTTTT
263168 TTTGGTGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:267440 original size:18 final size:17
Alignment explanation
Indices: 267356--267477 Score: 68
Period size: 17 Copynumber: 7.0 Consensus size: 17
267346 TAAATAGTGT
* *
267356 AAAATAAAAGTACTAAA
1 AAAATAAAAGAAATAAA
*
267373 GATAAATAAAATAAAT-AA
1 -A-AAATAAAAGAAATAAA
* *
267391 AAAATAAAAGTAAA-CAT
1 AAAATAAAAG-AAATAAA
*
267408 AAAATAAAAGTAATAAA
1 AAAATAAAAGAAATAAA
*
267425 ACAAATAATAGAAATAAGA
1 A-AAATAAAAGAAATAA-A
* ** **
267444 TAAAGGATTGAAATAAA
1 AAAATAAAAGAAATAAA
*
267461 AAAATAAAAGAGATAAA
1 AAAATAAAAGAAATAAA
267478 GTGTAAATTA
Statistics
Matches: 78, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
16 10 0.13
17 29 0.37
18 28 0.36
19 11 0.14
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAATAAAAGAAATAAA
Found at i:267696 original size:5 final size:5
Alignment explanation
Indices: 267686--267710 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
267676 TAACATGAAA
267686 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
267711 GACTAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:268777 original size:17 final size:18
Alignment explanation
Indices: 268755--268794 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
268745 TCTTCAATAG
268755 TCTTT-GATGAGCTTGCA
1 TCTTTGGATGAGCTTGCA
*
268772 TCTTTGGGTGAGCTTGCA
1 TCTTTGGATGAGCTTGCA
*
268790 ACTTT
1 TCTTT
268795 AGGTGAAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.42
Consensus pattern (18 bp):
TCTTTGGATGAGCTTGCA
Found at i:268785 original size:18 final size:18
Alignment explanation
Indices: 268762--268800 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
268752 TAGTCTTTGA
* *
268762 TGAGCTTGCATCTTTGGG
1 TGAGCTTGCAACTTTAGG
268780 TGAGCTTGCAACTTTAGG
1 TGAGCTTGCAACTTTAGG
268798 TGA
1 TGA
268801 AGTCGCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (18 bp):
TGAGCTTGCAACTTTAGG
Found at i:269777 original size:24 final size:24
Alignment explanation
Indices: 269749--269814 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
269739 GATGTTAATT
*
269749 TTTTATCTTATTCAACCTTTCACC
1 TTTTATCTTCTTCAACCTTTCACC
* *
269773 TTTTATCTTCTTTAACTTTTCACC
1 TTTTATCTTCTTCAACCTTTCACC
*
269797 TTTCATCTTCTTCTAACC
1 TTTTATCTTCTTC-AACC
269815 CCTTTCCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 32 0.91
25 3 0.09
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTATCTTCTTCAACCTTTCACC
Found at i:277193 original size:5 final size:5
Alignment explanation
Indices: 277183--277256 Score: 78
Period size: 5 Copynumber: 13.6 Consensus size: 5
277173 AATAGTGCAT
277183 AATAA AATAA AATTGAA AATAA AATAA AACTAA AATAA AACTAAA AATAA
1 AATAA AATAA AA-T-AA AATAA AATAA AA-TAA AATAA AA-T-AA AATAA
277233 AA-AA AATGAA AATGAA AATAA AAT
1 AATAA AAT-AA AAT-AA AATAA AAT
277257 GGAAAATGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 14
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.06
5 30 0.48
6 20 0.32
7 8 0.13
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:277205 original size:17 final size:15
Alignment explanation
Indices: 277183--277256 Score: 78
Period size: 17 Copynumber: 4.5 Consensus size: 15
277173 AATAGTGCAT
277183 AATAAAATAAAATTGAA
1 AATAAAATAAAA-T-AA
277200 AATAAAATAAAACTAA
1 AATAAAATAAAA-TAA
277216 AATAAAACTAAAAATAA
1 AATAAAA-T-AAAATAA
277233 AA-AAAATGAAAATGAA
1 AATAAAAT-AAAAT-AA
277249 AATAAAAT
1 AATAAAAT
277257 GGAAAATGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
15 6 0.12
16 17 0.33
17 24 0.47
18 4 0.08
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (15 bp):
AATAAAATAAAATAA
Found at i:277235 original size:6 final size:6
Alignment explanation
Indices: 277186--277418 Score: 178
Period size: 6 Copynumber: 38.3 Consensus size: 6
277176 AGTGCATAAT
* * * *
277186 AAAATA AAATTG AAAAT- AAAATA AAACT- AAAATA AAACTA AAAAT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
277231 -AAA-A AAAATG AAAATG AAAAT- AAAATGG AAAATGA AAAATGA AAAATGA
1 AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAAT-A AAAAT-A AAAAT-A
* *
277280 AAAATGA AAAATGA AAAATGA AAAATGA AAAATGA AAACTAAA AAAATG
1 AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAA--ATA AAAATA
* * * *
277329 AAAATGA AAAAGA AAAAGA AAAAGA AAAA-G AAAAT- AAAA-A AAAATA
1 AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
277375 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
277419 TCTACTAATT
Statistics
Matches: 199, Mismatches: 15, Indels: 26
0.83 0.06 0.11
Matches are distributed among these distances:
4 3 0.02
5 29 0.15
6 100 0.50
7 62 0.31
8 4 0.02
9 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:277244 original size:7 final size:7
Alignment explanation
Indices: 277234--277415 Score: 181
Period size: 6 Copynumber: 28.9 Consensus size: 7
277224 TAAAAATAAA
277234 AAAAATG
1 AAAAATG
277241 -AAAATG
1 AAAAATG
277247 -AAAAT-
1 AAAAATG
277252 -AAAATG
1 AAAAATG
*
277258 GAAAATG
1 AAAAATG
277265 AAAAATG
1 AAAAATG
277272 AAAAATG
1 AAAAATG
277279 AAAAATG
1 AAAAATG
277286 AAAAATG
1 AAAAATG
277293 AAAAATG
1 AAAAATG
277300 AAAAATG
1 AAAAATG
277307 AAAAATG
1 AAAAATG
* *
277314 AAAACTAA
1 AAAAAT-G
277322 AAAAATG
1 AAAAATG
277329 -AAAATG
1 AAAAATG
277335 AAAAA-G
1 AAAAATG
277341 AAAAA-G
1 AAAAATG
277347 AAAAA-G
1 AAAAATG
277353 AAAAA-G
1 AAAAATG
277359 -AAAAT-
1 AAAAATG
277364 -AAAA--
1 AAAAATG
277368 AAAAAT-
1 AAAAATG
277374 AAAAAT-
1 AAAAATG
277380 AAAAAT-
1 AAAAATG
277386 AAAAAT-
1 AAAAATG
277392 AAAAAT-
1 AAAAATG
277398 AAAAAT-
1 AAAAATG
277404 AAAAAT-
1 AAAAATG
277410 AAAAAT
1 AAAAAT
277416 AAATCTACTA
Statistics
Matches: 163, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
5 17 0.10
6 78 0.48
7 63 0.39
8 5 0.03
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:277339 original size:1 final size:1
Alignment explanation
Indices: 277335--277414 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
277325 AATGAAAATG
* * * * * * * * * *
277335 AAAAAGAAAAAGAAAAAGAAAAAGAAAATAAAAAAAAATAAAAATAAAAATAAAAATAAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
277400 AAATAAAAATAAAAA
1 AAAAAAAAAAAAAAA
277415 TAAATCTACT
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (1 bp):
A
Found at i:277419 original size:28 final size:28
Alignment explanation
Indices: 277186--277419 Score: 124
Period size: 28 Copynumber: 8.0 Consensus size: 28
277176 AGTGCATAAT
* *
277186 AAAATAAAATTGAAAAT-AAAATAAA-A
1 AAAATAAAAATAAAAATAAAAATAAATA
* *
277212 CTAAAATAAAACTAAAAATAAAAA-AAATG
1 --AAAATAAAAATAAAAATAAAAATAAATA
* *
277241 AAAATGAAAAT-AAAATGGAAAATGAAAAATGA
1 AAAATAAAAATAAAAAT--AAAA--ATAAAT-A
277273 AAAATGAAAAATGAAAAATGAAAAATGAAAAATGA
1 AAAAT-AAAAAT-AAAAAT-AAAAAT---AAAT-A
* **
277308 AAAATGAAAACTAAAAA-AATGA-AAATGA
1 AAAAT-AAAAATAAAAATAAAAATAAAT-A
* * * *
277336 AAAAGAAAAAGAAAAAGAAAAAGAAA-A
1 AAAATAAAAATAAAAATAAAAATAAATA
277363 TAAAA-AAAAATAAAAATAAAAATAAAAATA
1 -AAAATAAAAATAAAAATAAAAAT--AAATA
277393 AAAATAAAAATAAAAATAAAAATAAAT
1 AAAATAAAAATAAAAATAAAAATAAAT
277420 CTACTAATTT
Statistics
Matches: 166, Mismatches: 19, Indels: 42
0.73 0.08 0.19
Matches are distributed among these distances:
26 5 0.03
27 34 0.20
28 43 0.26
29 14 0.08
30 20 0.12
31 4 0.02
32 9 0.05
33 5 0.03
34 10 0.06
35 22 0.13
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (28 bp):
AAAATAAAAATAAAAATAAAAATAAATA
Found at i:299390 original size:19 final size:19
Alignment explanation
Indices: 299363--299403 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
299353 AATATAGGGA
299363 TAAAAATGAGC-ATGCAAAT
1 TAAAAATGAGCTATGC-AAT
*
299382 TAAATATGAGCTATGCAAT
1 TAAAAATGAGCTATGCAAT
299401 TAA
1 TAA
299404 TGATAAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (19 bp):
TAAAAATGAGCTATGCAAT
Found at i:299503 original size:19 final size:18
Alignment explanation
Indices: 299481--299517 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
299471 AGTTATGAAT
299481 CAAAATAAATTAGAAAATA
1 CAAAATAAATTA-AAAATA
*
299500 CAAAATTAATTAAAAATA
1 CAAAATAAATTAAAAATA
299518 AAGGAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
CAAAATAAATTAAAAATA
Found at i:299601 original size:28 final size:28
Alignment explanation
Indices: 299570--299639 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
299560 AAGGGGGTCG
* *
299570 AAAATG-AAGTTTT-GGATAGTTTGGGGTT
1 AAAATGTAA-TTTTGGGAAAGTTT-GAGTT
299598 AAAATGTAATTTTGGGAAAGTTTGAGTT
1 AAAATGTAATTTTGGGAAAGTTTGAGTT
*
299626 AAAAATGTGATTTT
1 -AAAATGTAATTTT
299640 TTGAAGTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 14 0.39
29 22 0.61
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (28 bp):
AAAATGTAATTTTGGGAAAGTTTGAGTT
Found at i:299659 original size:29 final size:29
Alignment explanation
Indices: 299593--299917 Score: 194
Period size: 29 Copynumber: 11.1 Consensus size: 29
299583 GGATAGTTTG
* ** *
299593 GGGTTAAAATGTAATTTTGGGAAAGTTTGA
1 GGGTAAAAATGTAATTTTTAG-AAGTTCGA
* * *
299623 -GTTAAAAATGTGATTTTTTGAAGTTCGA
1 GGGTAAAAATGTAATTTTTAGAAGTTCGA
* *
299651 GGGTTAAAAAATGTGATTTTTAGAAGTTCAA
1 GGG-T-AAAAATGTAATTTTTAGAAGTTCGA
* * *
299682 GGGTCAAAATGTGATTTTT-GTATGTTCGA
1 GGGTAAAAATGTAATTTTTAG-AAGTTCGA
* **
299711 GGGAAAAAATGTAATTTTTGAGAAGTTTAA
1 GGGTAAAAATGTAATTTTT-AGAAGTTCGA
** * * *
299741 GGACAAAAATGTAATCTTTGGAAGTTTG-
1 GGGTAAAAATGTAATTTTTAGAAGTTCGA
** * **
299769 GGGGCAAAAGGTAATTTTTGAGAAGTTTAA
1 GGGTAAAAATGTAATTTTT-AGAAGTTCGA
* * * *
299799 GGGTAAAAAAGCAAATTTTTGAGAAGTTTGG
1 GGGTAAAAATG-TAATTTTT-AGAAGTTCGA
* * * *
299830 GGGTCAAAATGTGATTTTTGGAGGTTCGA
1 GGGTAAAAATGTAATTTTTAGAAGTTCGA
* *
299859 GGGTAAAAATGTAATTTTAAGAAGGTC-A
1 GGGTAAAAATGTAATTTTTAGAAGTTCGA
* *
299887 GGGGTTAAAATGTGA-TTTTAGAAGTTC-A
1 -GGGTAAAAATGTAATTTTTAGAAGTTCGA
299915 GGG
1 GGG
299918 ACCTTTTAGG
Statistics
Matches: 231, Mismatches: 54, Indels: 23
0.75 0.18 0.07
Matches are distributed among these distances:
27 3 0.01
28 34 0.15
29 105 0.45
30 37 0.16
31 52 0.23
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTAGAAGTTCGA
Found at i:301505 original size:6 final size:6
Alignment explanation
Indices: 301496--301574 Score: 65
Period size: 6 Copynumber: 13.0 Consensus size: 6
301486 TAAATCTAAA
* *
301496 TAAATT TAAACT TAAATT TACAA-- TAAATT TAAATT TCAAATAAA TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAAT--T TAAATT
* *
301546 TAAACT TAAA-G TAAATT TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT
301575 CTTTGGGTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.03
5 6 0.10
6 40 0.68
7 6 0.10
8 4 0.07
9 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:301505 original size:10 final size:10
Alignment explanation
Indices: 301486--301529 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
301476 TGGACATTAG
*
301486 TAAATCTAAA
1 TAAATTTAAA
301496 TAAATTTAAA
1 TAAATTTAAA
301506 CTTAAATTTACAA
1 --TAAATTTA-AA
301519 TAAATTTAAA
1 TAAATTTAAA
301529 T
1 T
301530 TTCAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 12 0.40
11 8 0.27
12 8 0.27
13 2 0.07
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:301527 original size:17 final size:16
Alignment explanation
Indices: 301502--301573 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 16
301492 TAAATAAATT
*
301502 TAAACTTAAATTTACAA
1 TAAATTTAAATTTA-AA
301519 TAAATTTAAATTTCAAATAAA
1 TAAATTTAAA-TT----TAAA
*
301540 TAAATTTAAACTTAAA
1 TAAATTTAAATTTAAA
301556 GTAAATTTAAATTTAAA
1 -TAAATTTAAATTTAAA
301573 T
1 T
301574 TCTTTGGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.11
17 24 0.52
18 2 0.04
20 1 0.02
21 12 0.26
22 2 0.04
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:307855 original size:275 final size:275
Alignment explanation
Indices: 307346--307893 Score: 970
Period size: 275 Copynumber: 2.0 Consensus size: 275
307336 TGATACGCTA
* *
307346 CAATACCCCTATCATCTAAGACATAAAGTGCTTAACTCTACCCATTTGAGCATCATCATACAACT
1 CAATACCCCTATCATCTAAGACATAAAGTGCTTAACTCGACCCATTTGAGCATCATCACACAACT
* *
307411 ACGATGACGTATCTCCAAGCGACGACAATGGTTTATCTTCATGTGGTTATGGTGGTGTCAGCACT
66 ACGATGACGTATCTCCAAGCGACGACAATGGTTCATCTTCATGTGGTTATAGTGGTGTCAGCACT
*
307476 GCATCGTGACCACCTCGTCCTCGTCGCTGAGGCATAACATAGATCGAATACTAAAGAAAAGGTAG
131 GCATCGTGACCACCTCGTCCTCGTCGCCGAGGCATAACATAGATCGAATACTAAAGAAAAGGTAG
*
307541 AGAAAATGTACCAGGAGTCAGTAGCGGTAAGTGATCCAAGACTTAACTAAGTATAATTTCTAATA
196 AGAAAATGTACCAGGAGTCAGTAGCGGCAAGTGATCCAAGACTTAACTAAGTATAATTTCTAATA
307606 GGGCATTGTGATCTG
261 GGGCATTGTGATCTG
* * * *
307621 CAATGCCCCTGTCATCTGAGACATAAAGTGCTTAACTCGACCCATTTGAGCATCATCACACGACT
1 CAATACCCCTATCATCTAAGACATAAAGTGCTTAACTCGACCCATTTGAGCATCATCACACAACT
307686 ACGATGACGTATCTCCAAGCGACGACAATGGTTCATCTTCATGTGGTTATAGTGGTGTCAGCACT
66 ACGATGACGTATCTCCAAGCGACGACAATGGTTCATCTTCATGTGGTTATAGTGGTGTCAGCACT
* *
307751 GCATCGTGACCACCTCGTCCTCGTTGCCGAGGCATAACGTAGATCGAATACTAAAGAAAAGGTAG
131 GCATCGTGACCACCTCGTCCTCGTCGCCGAGGCATAACATAGATCGAATACTAAAGAAAAGGTAG
* *
307816 AGAAAATGTACCAGGAGTGAGTAGCGGCAAGTGATCCAAGACTTAACTAAGTATAATTTTTAATA
196 AGAAAATGTACCAGGAGTCAGTAGCGGCAAGTGATCCAAGACTTAACTAAGTATAATTTCTAATA
307881 GGGCATTGTGATC
261 GGGCATTGTGATC
307894 CCAATTCATA
Statistics
Matches: 259, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
275 259 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (275 bp):
CAATACCCCTATCATCTAAGACATAAAGTGCTTAACTCGACCCATTTGAGCATCATCACACAACT
ACGATGACGTATCTCCAAGCGACGACAATGGTTCATCTTCATGTGGTTATAGTGGTGTCAGCACT
GCATCGTGACCACCTCGTCCTCGTCGCCGAGGCATAACATAGATCGAATACTAAAGAAAAGGTAG
AGAAAATGTACCAGGAGTCAGTAGCGGCAAGTGATCCAAGACTTAACTAAGTATAATTTCTAATA
GGGCATTGTGATCTG
Found at i:310169 original size:29 final size:29
Alignment explanation
Indices: 310136--310443 Score: 178
Period size: 29 Copynumber: 10.7 Consensus size: 29
310126 TCACTTATCT
*
310136 TTCCAAAAATTA-CATTTTTATCCCTAAAC
1 TTCCAAAAATTACCA-TTTTACCCCTAAAC
* * *
310165 TTCCAAAAATTATCATTTTGCCCC-GAAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
* *
310193 TTTCCAAAAA-T-GCATTTTTA-CCCTCGAAC
1 -TTCCAAAAATTACCA-TTTTACCCCT-AAAC
*
310222 TTCCAAAAATTACCATTTTACCCCCAAAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
* *
310251 CTCCAAAACTTACCATTTTACCCCTAAAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
* * *
310280 TTCCAAAAA-TATCATTTTA-ACCTCAAATT
1 TTCCAAAAATTACCATTTTACCCCT-AAA-C
*** * *
310309 TTTTGAAAATTACAATTTTGACCCC-GAAC
1 TTCCAAAAATTACCATTTT-ACCCCTAAAC
*
310338 TTTCC-AAAATTACCATTTTA-CCCTCAGA-
1 -TTCCAAAAATTACCATTTTACCCCT-AAAC
* * *
310366 TGTCCAAAAATTA-CATTTTTGCCCC-CAAG
1 T-TCCAAAAATTACCA-TTTTACCCCTAAAC
* *
310395 TGTCCAAAAAATTACCA-TTTACCCTCGAATC
1 T-TCC-AAAAATTACCATTTTACCC-CTAAAC
310426 -TCCAAAAATTACCATTTT
1 TTCCAAAAATTACCATTTT
310444 GTCCCTTGGT
Statistics
Matches: 217, Mismatches: 36, Indels: 52
0.71 0.12 0.17
Matches are distributed among these distances:
27 12 0.06
28 47 0.22
29 122 0.56
30 30 0.14
31 4 0.02
32 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCCTAAAC
Found at i:310376 original size:58 final size:58
Alignment explanation
Indices: 310137--310444 Score: 238
Period size: 58 Copynumber: 5.3 Consensus size: 58
310127 CACTTATCTT
* ** * * * *
310137 TCCAAAAATTAC-ATTTTTATCCCTAAACTTCCAAAAATTATCATTTTGCCC-CGAACTT
1 TCCAAAAATTACAATTTTGA-CCCCGAACTTCCAAAAATTACCATTTTACCCTC-AAATC
* * * *
310195 TCCAAAAA-TGC-ATTTTTACCCTCGAACTTCCAAAAATTACCATTTTACCCCCAAACC
1 TCCAAAAATTACAATTTTGACCC-CGAACTTCCAAAAATTACCATTTTACCCTCAAATC
* * * * * *
310252 TCCAAAACTTACCATTTT-ACCCCTAAACTTCCAAAAA-TATCATTTTAACCTCAAATTT
1 TCCAAAAATTACAATTTTGACCCC-GAACTTCCAAAAATTACCATTTTACCCTCAAA-TC
*** * *
310310 TTTGAAAATTACAATTTTGACCCCGAACTTTCC-AAAATTACCATTTTACCCTCAGATG
1 TCCAAAAATTACAATTTTGACCCCGAAC-TTCCAAAAATTACCATTTTACCCTCAAATC
* * * *
310368 TCCAAAAATTACATTTTTG-CCCCCAAGTGTCCAAAAAATTACCA-TTTACCCTCGAATC
1 TCCAAAAATTACAATTTTGACCCCGAACT-TCC-AAAAATTACCATTTTACCCTCAAATC
*
310426 TCCAAAAATTACCATTTTG
1 TCCAAAAATTACAATTTTG
310445 TCCCTTGGTA
Statistics
Matches: 201, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
56 4 0.02
57 67 0.33
58 91 0.45
59 39 0.19
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTACAATTTTGACCCCGAACTTCCAAAAATTACCATTTTACCCTCAAATC
Found at i:318747 original size:9 final size:8
Alignment explanation
Indices: 318729--318759 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
318719 ACTATAGCCT
318729 AAAAATAA
1 AAAAATAA
318737 AAAAATAA
1 AAAAATAA
318745 AAAAATAA
1 AAAAATAA
318753 AGAAAAT
1 A-AAAAT
318760 TGTATCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:320432 original size:20 final size:21
Alignment explanation
Indices: 320398--320453 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
320388 TGATTGTCCT
* *
320398 CAAGCAAGCAAAACAAGTAAAG
1 CAAGAAAG-AAAACAAGTAAAA
*
320420 CAA-TAAGAAAAC-AGTAAAA
1 CAAGAAAGAAAACAAGTAAAA
320439 CAAGAAAGAAAACAA
1 CAAGAAAGAAAACAA
320454 AAGAGCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.31
20 13 0.45
21 4 0.14
22 3 0.10
ACGTcount: A:0.66, C:0.14, G:0.14, T:0.05
Consensus pattern (21 bp):
CAAGAAAGAAAACAAGTAAAA
Found at i:324722 original size:18 final size:18
Alignment explanation
Indices: 324699--324738 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
324689 ATGAGAGTAT
324699 CTTTCATTGTTAGAATTA
1 CTTTCATTGTTAGAATTA
324717 CTTTCATTGTTAGAATTA
1 CTTTCATTGTTAGAATTA
324735 CTTT
1 CTTT
324739 GATTCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (18 bp):
CTTTCATTGTTAGAATTA
Found at i:333293 original size:21 final size:21
Alignment explanation
Indices: 333259--333302 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
333249 TGTTTTGAAG
* *
333259 GATAAGAAGAGGAAGCGCAAA
1 GATAAGAAGAGGAAACACAAA
333280 GATAAGAA-ACGGAAACACAAA
1 GATAAGAAGA-GGAAACACAAA
333301 GA
1 GA
333303 GGAAGGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.57, C:0.11, G:0.27, T:0.05
Consensus pattern (21 bp):
GATAAGAAGAGGAAACACAAA
Found at i:334068 original size:10 final size:11
Alignment explanation
Indices: 334035--334077 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
334025 TTAGTCACAT
334035 AAAGAAAAATGAA
1 AAAGAAAAA--AA
*
334048 AGAGAAAAAAA
1 AAAGAAAAAAA
334059 AAAGAAAAAAA
1 AAAGAAAAAAA
334070 AAAGAAAA
1 AAAGAAAA
334078 GAGAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 20 0.71
13 8 0.29
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:334071 original size:16 final size:18
Alignment explanation
Indices: 334052--334085 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
334042 AATGAAAGAG
334052 AAAAA-AAAA-AGAAAAA
1 AAAAAGAAAAGAGAAAAA
334068 AAAAAGAAAAGAGAAAAA
1 AAAAAGAAAAGAGAAAAA
334086 TATTGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAGAAAAA
Found at i:340244 original size:21 final size:21
Alignment explanation
Indices: 340189--340244 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
340179 TTTGTGATAG
*
340189 TTCTACCGATACAAGTGTAAC
1 TTCTACCGATACTAGTGTAAC
* * * *
340210 ATCTATCGAAACTAGT-TATGC
1 TTCTACCGATACTAGTGTA-AC
340231 TTCTACCGATACTA
1 TTCTACCGATACTA
340245 AAAACTCCAA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (21 bp):
TTCTACCGATACTAGTGTAAC
Found at i:340954 original size:42 final size:42
Alignment explanation
Indices: 340907--341045 Score: 181
Period size: 42 Copynumber: 3.3 Consensus size: 42
340897 TAGAGTCATA
* * *
340907 AGTCTTCCTTTAGTCATATTCTCATTCTTATCTCAAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTTATCTCGAGACATG
* *
340949 AGTCTTTCGTTAATCATAATCTCATTCTCT-TCTCGAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCT-TATCTCGAGACATG
* * *
340991 AGTCTTCCATTAATCATAATCTCATTCTCATCTTGAGACATG
1 AGTCTTCCTTTAATCATAATCTCATTCTTATCTCGAGACATG
341033 AGTCTTCCATTTA
1 AGTCTTCC-TTTA
341046 TACAAATTCT
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
42 80 0.95
43 4 0.05
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (42 bp):
AGTCTTCCTTTAATCATAATCTCATTCTTATCTCGAGACATG
Found at i:341071 original size:43 final size:43
Alignment explanation
Indices: 340942--341094 Score: 143
Period size: 42 Copynumber: 3.6 Consensus size: 43
340932 TCTTATCTCA
* * * * **
340942 AGACATGAGTCTTTCGTTAAT-CATAATCTCATTCTC-TTCTCG
1 AGACATGAGTCTTCCATTTATACATAATCTCATGCTCAACCT-G
* * * *
340984 AGACATGAGTCTTCCATTAAT-CATAATCTCATTCTCATCTTG
1 AGACATGAGTCTTCCATTTATACATAATCTCATGCTCAACCTG
341026 AGACATGAGTCTTCCATTTATACA-AATTCTCATGCTCAACCTG
1 AGACATGAGTCTTCCATTTATACATAA-TCTCATGCTCAACCTG
* *
341069 AGACATTAGTCTTCCTTTTTATACAT
1 AGACATGAGTCTTCC-ATTTATACAT
341095 CAAATGTTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
42 57 0.59
43 31 0.32
44 8 0.08
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (43 bp):
AGACATGAGTCTTCCATTTATACATAATCTCATGCTCAACCTG
Found at i:342260 original size:12 final size:12
Alignment explanation
Indices: 342243--342267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
342233 TTGTGTGGAG
342243 GAAGAAAAAGAT
1 GAAGAAAAAGAT
342255 GAAGAAAAAGAT
1 GAAGAAAAAGAT
342267 G
1 G
342268 TCAAGGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (12 bp):
GAAGAAAAAGAT
Found at i:344079 original size:37 final size:37
Alignment explanation
Indices: 344025--344095 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
344015 AATGTTGCTG
* *
344025 CATGAGCACTTCTAGATTGC-GTCCAAAACTGTCGCCA
1 CATGAGCACTTCCAGATTGCACT-CAAAACTGTCGCCA
344062 CATGAGCACTTCCAGATTGCACTCAAAACTGTCG
1 CATGAGCACTTCCAGATTGCACTCAAAACTGTCG
344096 TCGTAGGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (37 bp):
CATGAGCACTTCCAGATTGCACTCAAAACTGTCGCCA
Found at i:344209 original size:37 final size:38
Alignment explanation
Indices: 344128--344215 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
344118 CACCCAAGAC
* * * *
344128 TATCACTGCATAAGTATTCTTCAAATTGCATCTAGATC
1 TATCGCTGCATAAGTATTCTTCAAATTGCACCCAGATA
344166 TATCGCTGCATAAGTATTCTTC-AATTGCACCCAGGA-A
1 TATCGCTGCATAAGTATTCTTCAAATTGCACCCA-GATA
*
344203 TGTCGCTGCATAA
1 TATCGCTGCATAA
344216 ACATGTCCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
37 21 0.48
38 23 0.52
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (38 bp):
TATCGCTGCATAAGTATTCTTCAAATTGCACCCAGATA
Found at i:345081 original size:16 final size:16
Alignment explanation
Indices: 345060--345090 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
345050 TTGTGGATCC
345060 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
345076 CATTTTATCTTTATT
1 CATTTTACCTTTATT
345091 TCACATTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:347137 original size:41 final size:41
Alignment explanation
Indices: 347027--347144 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
347017 GACATCTTCA
* * * *
347027 GGGTTGGTCGCGACATAGACA-TGTTGTGTTGCGACATAGG
1 GGGTTGGTCGCGACATAGACATTCTTATGTTGCAACATAAG
* * *
347067 GGGTTCGTCGTGACATAGACATTCCTATGTTGCAACATAAG
1 GGGTTGGTCGCGACATAGACATTCTTATGTTGCAACATAAG
* * * *
347108 GGGTTGGTTGCAACATAGACATTTTTATGTCGCAACA
1 GGGTTGGTCGCGACATAGACATTCTTATGTTGCAACA
347145 AAGAAGGAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 19 0.30
41 44 0.70
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (41 bp):
GGGTTGGTCGCGACATAGACATTCTTATGTTGCAACATAAG
Found at i:354296 original size:21 final size:20
Alignment explanation
Indices: 354247--354306 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
354237 ATTAGCACAC
354247 TCAAATGCATCCACAATAAA
1 TCAAATGCATCCACAATAAA
* *
354267 GCTAGATGCATCCACACCA-AAA
1 TC-AAATGCATCCACA--ATAAA
*
354289 TCAAATGCAGCCACAATA
1 TCAAATGCATCCACAATA
354307 CTCTTCAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 23 0.74
22 4 0.13
23 1 0.03
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (20 bp):
TCAAATGCATCCACAATAAA
Found at i:360193 original size:23 final size:22
Alignment explanation
Indices: 360157--360200 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
360147 TAAATATTTC
*
360157 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
360180 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
360201 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:365108 original size:19 final size:20
Alignment explanation
Indices: 365081--365124 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
365071 TCACATGGAT
*
365081 GTGTTCCTGTCCAC-CGAGC
1 GTGTGCCTGTCCACACGAGC
*
365100 GTGTGCCTGTCCACATGAGC
1 GTGTGCCTGTCCACACGAGC
365120 GTGTG
1 GTGTG
365125 GGTTTTGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.11, C:0.30, G:0.32, T:0.27
Consensus pattern (20 bp):
GTGTGCCTGTCCACACGAGC
Found at i:366587 original size:20 final size:20
Alignment explanation
Indices: 366564--366601 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
366554 TGAAACAAAC
366564 ATATAT-AAT-TTTTATATA
1 ATATATAAATATTTTATATA
*
366582 ATATATAAATATTTTTTATA
1 ATATATAAATATTTTATATA
366602 TTTAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATAAATATTTTATATA
Found at i:369451 original size:18 final size:19
Alignment explanation
Indices: 369419--369454 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
369409 CTAATCAAAA
*
369419 TTTTATTTTTTATATATAT
1 TTTTATTTTTAATATATAT
369438 TTTTA-TTTTAATATATA
1 TTTTATTTTTAATATATA
369455 CAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTTTTAATATATAT
Found at i:370693 original size:22 final size:22
Alignment explanation
Indices: 370668--370739 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
370658 TAACTTACAT
370668 AATTTTATAGTGATAATTCTCA
1 AATTTTATAGTGATAATTCTCA
** * * *
370690 AA-TTTATTTTCAACAACTT-ACA
1 AATTTTATAGT-GATAA-TTCTCA
370712 TAATTTTATAGTGATAATTCTCA
1 -AATTTTATAGTGATAATTCTCA
370735 AATTT
1 AATTT
370740 ATTTTCAACT
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 6 0.17
22 14 0.40
23 9 0.26
24 6 0.17
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.46
Consensus pattern (22 bp):
AATTTTATAGTGATAATTCTCA
Found at i:370696 original size:21 final size:21
Alignment explanation
Indices: 370671--370741 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
370661 CTTACATAAT
370671 TTTATAGTGATAATTCTCAAA
1 TTTATAGTGATAATTCTCAAA
** * * *
370692 TTTATTTTCAACAACTTACAT-AAT
1 TTTATAGT-GATAA-TT-C-TCAAA
370716 TTTATAGTGATAATTCTCAAA
1 TTTATAGTGATAATTCTCAAA
370737 TTTAT
1 TTTAT
370742 TTTCAACTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 1 0.03
21 14 0.40
22 5 0.14
23 5 0.14
24 9 0.26
25 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (21 bp):
TTTATAGTGATAATTCTCAAA
Found at i:370710 original size:45 final size:45
Alignment explanation
Indices: 370659--370748 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
370649 AATGGCTAAT
370659 AACTTACATAATTTTATAGTGATAATTCTCAAATTTATTTTCAAC
1 AACTTACATAATTTTATAGTGATAATTCTCAAATTTATTTTCAAC
370704 AACTTACATAATTTTATAGTGATAATTCTCAAATTTATTTTCAAC
1 AACTTACATAATTTTATAGTGATAATTCTCAAATTTATTTTCAAC
370749 TTTATAAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (45 bp):
AACTTACATAATTTTATAGTGATAATTCTCAAATTTATTTTCAAC
Found at i:371024 original size:17 final size:17
Alignment explanation
Indices: 370981--371024 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
370971 ATAATTTACG
* *
370981 AAAATTTA-ATTAAATT
1 AAAATTTATATAAAATC
370997 AAAATTT-TATAAAATC
1 AAAATTTATATAAAATC
371013 AAAATTTATATA
1 AAAATTTATATA
371025 TTATATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAATTTATATAAAATC
Done.