Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 17 of 163
Found at i:5768523 original size:45 final size:45
Alignment explanation
Indices: 5768456--5768662 Score: 159
Period size: 45 Copynumber: 4.6 Consensus size: 45
5768446 GTACTGGCGT
* * * * * *
5768456 GAAGTAGATCATAGATACCAGATCTTGTCTCCCCGTACAGGTGGT
1 GAAGCAGATCAAAGAAAGCAGATCTTGTCTCCCCATACAGGTGGC
* * * * * *
5768501 GGAGTAGATCGAAGAAAGCAGATCTTGCCTTCCCATACTGGTGGC
1 GAAGCAGATCAAAGAAAGCAGATCTTGTCTCCCCATACAGGTGGC
* * ** *
5768546 GAAGCAGATCAAAGAAAGTAGATCTTGTCT--TCATGTA-TTGGC
1 GAAGCAGATCAAAGAAAGCAGATCTTGTCTCCCCATACAGGTGGC
* * * * * * *
5768588 GTGAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGC
1 --GAAGCAGATCAAAGAAAGCAGATCTTGTCTCCCCATACAGGTGGC
5768635 GAAGCAGATCAAAGAAAGCAGATCTTGT
1 GAAGCAGATCAAAGAAAGCAGATCTTGT
5768663 TTTCATGTAC
Statistics
Matches: 121, Mismatches: 36, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
42 4 0.03
43 3 0.02
44 24 0.20
45 83 0.69
46 3 0.02
47 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (45 bp):
GAAGCAGATCAAAGAAAGCAGATCTTGTCTCCCCATACAGGTGGC
Found at i:5768688 original size:89 final size:89
Alignment explanation
Indices: 5768519--5768695 Score: 291
Period size: 89 Copynumber: 2.0 Consensus size: 89
5768509 TCGAAGAAAG
* *
5768519 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAT
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTAC
* ** *
5768584 TGGCGTGAAGTAGATCAGAGATAC
66 CGGCGTGAAACAGATCAAAGATAC
*
5768608 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTTTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTAC
5768673 CGGCGTGAAACAGATCAAAGATA
66 CGGCGTGAAACAGATCAAAGATA
5768696 GTAGGTCCTG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (89 bp):
CAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTAC
CGGCGTGAAACAGATCAAAGATAC
Found at i:5768728 original size:134 final size:134
Alignment explanation
Indices: 5768456--5768780 Score: 323
Period size: 134 Copynumber: 2.4 Consensus size: 134
5768446 GTACTGGCGT
* * * * * *
5768456 GAAGTAGATCATAGATACCAGATCTTGTCTCCCCGTACAGGTGGTGGAGTAGATCGAAGAAAGCA
1 GAAGTAGATCAGAGATACCAGATCTTGTCTTCCCGTACTGGTGGTGAAGCAGATCAAAGAAAGCA
* * * * * * *
5768521 GATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTATTG
66 GATCTTGCCTTCACATACCGGTCGCGAAACAGATCAAAGAAAGTAGATCCTGTCCTCATATATTG
* *
5768586 GCGT
131 GAGC
* * *
5768590 GAAGTAGATCAGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAGAAAGCA
1 GAAGTAGATCAGAGATACCAGATCTTGTCTTCCCGTACTGGTGGTGAAGCAGATCAAAGAAAGCA
** ** * * * *
5768655 GATCTTGTTTTCATGTACCGG-CGTGAAACAGATCAAAGATAGTAGGTCCTGTCCTCCTATATCT
66 GATCTTGCCTTCACATACCGGTCGCGAAACAGATCAAAGAAAGTAGATCCTGTCCTCATATAT-T
*
5768719 GTAGC
130 GGAGC
* * * * *
5768724 GAAGTGGATC-GA-ATATACAGATTTTATCTTCCCGTACTGATGGTGAAGCAGATCAAA
1 GAAGTAGATCAGAGATA-CCAGATCTTGTCTTCCCGTACTGGTGGTGAAGCAGATCAAA
5768781 TGTAACAGGT
Statistics
Matches: 154, Mismatches: 35, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
132 3 0.02
133 68 0.44
134 83 0.54
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (134 bp):
GAAGTAGATCAGAGATACCAGATCTTGTCTTCCCGTACTGGTGGTGAAGCAGATCAAAGAAAGCA
GATCTTGCCTTCACATACCGGTCGCGAAACAGATCAAAGAAAGTAGATCCTGTCCTCATATATTG
GAGC
Found at i:5768776 original size:89 final size:89
Alignment explanation
Indices: 5768677--5768872 Score: 261
Period size: 89 Copynumber: 2.2 Consensus size: 89
5768667 ATGTACCGGC
* ** * *
5768677 GTGAAACAGATCAAAGATAGTAGGTCCTGTCCTCCTATATCTG-TAGCGAAGTGGATCGAATATA
1 GTGAAGCAGATCAAAGATAACAGGTCCTGTCCTCCTATATC-GATAGCGAAATGGATCAAATATA
*
5768741 CAGATTTTATCTTCCCGTACTGATG
65 CAGATTTTATCTTCCCATACTGATG
*
5768766 GTGAAGCAGATCAAATG-TAACAGGTCCTGTCTTCCTATATCGATAGCGAAATGGATCAAATATA
1 GTGAAGCAGATCAAA-GATAACAGGTCCTGTCCTCCTATATCGATAGCGAAATGGATCAAATATA
*
5768830 CAGATTTTATCTTCCCATACTGGTG
65 CAGATTTTATCTTCCCATACTGATG
* * *
5768855 GCGAAGTAGATCGAAGAT
1 GTGAAGCAGATCAAAGAT
5768873 TACGGATCTT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
88 2 0.02
89 90 0.97
90 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (89 bp):
GTGAAGCAGATCAAAGATAACAGGTCCTGTCCTCCTATATCGATAGCGAAATGGATCAAATATAC
AGATTTTATCTTCCCATACTGATG
Found at i:5768859 original size:44 final size:44
Alignment explanation
Indices: 5768722--5768866 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
5768712 TATATCTGTA
* *
5768722 GCGAAGTGGATCGAATATACAGATTTTATCTTCCCGTACTGATG
1 GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
* ** * * ** * * *
5768766 GTGAAGCAGATCAAATGTAACAGGTCCTGTCTTCCTATA-TCGATA
1 GCGAAGTGGATCAAATAT-ACAGATTTTATCTTCCCATACT-GATG
* *
5768811 GCGAAATGGATCAAATATACAGATTTTATCTTCCCATACTGGTG
1 GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
*
5768855 GCGAAGTAGATC
1 GCGAAGTGGATC
5768867 GAAGATTACG
Statistics
Matches: 72, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
44 41 0.57
45 31 0.43
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
Found at i:5769298 original size:44 final size:44
Alignment explanation
Indices: 5769235--5769348 Score: 140
Period size: 44 Copynumber: 2.6 Consensus size: 44
5769225 CAGTGGAATC
* *
5769235 GATCGGA-AAAAGAAGATCTTGTCTTCATGTATTGACGTGAAGTA
1 GATCGGAGAAAA-AAGATCTTGTCTTCATGTACTGACATGAAGTA
* *
5769279 GATCGGAGAAAACAGATCTTGTCTTCATGTACTGGCATGAAGTA
1 GATCGGAGAAAAAAGATCTTGTCTTCATGTACTGACATGAAGTA
** **
5769323 GATCAAAGAAAGTAGATCTTGTCTTC
1 GATCGGAGAAAAAAGATCTTGTCTTC
5769349 CCATACCGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 57 0.93
45 4 0.07
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (44 bp):
GATCGGAGAAAAAAGATCTTGTCTTCATGTACTGACATGAAGTA
Found at i:5770950 original size:23 final size:22
Alignment explanation
Indices: 5770924--5770993 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 22
5770914 TTACATAATT
5770924 TGTATATATATGCATTTTTTTCA
1 TGTATATATATGCATTTTTTT-A
* *
5770947 TGTAGTACATACGCATATTTTTATA
1 TGTA-TATATATGCAT-TTTTT-TA
* *
5770972 TG-AAATATATACATTTTTTTA
1 TGTATATATATGCATTTTTTTA
5770993 T
1 T
5770994 ATGTATTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 3 0.08
22 5 0.13
23 11 0.29
24 10 0.26
25 8 0.21
26 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (22 bp):
TGTATATATATGCATTTTTTTA
Found at i:5771975 original size:3 final size:3
Alignment explanation
Indices: 5771969--5772116 Score: 68
Period size: 3 Copynumber: 48.7 Consensus size: 3
5771959 GTTTCGACAC
** * *
5771969 TTA TTA TTA TTA GCA TTA TTA TTA TTA TTA TTA GTA TTA TTG TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** * * * * *
5772016 TTG TTC CTA TTA ACA TAA TTA TAAA TTA TTG TTA ATA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * * *
5772062 TTA TTTA TTTA ATA TTA TTA ATA TT- TTCA CTGA -TA TTA CTA TTA TTA
1 TTA -TTA -TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA
5772109 TTA TTA TT
1 TTA TTA TT
5772117 TTCATATCTC
Statistics
Matches: 105, Mismatches: 33, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
2 5 0.05
3 89 0.85
4 10 0.10
5 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:5772645 original size:2 final size:2
Alignment explanation
Indices: 5772640--5772693 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
5772630 TTTATCTTCG
* * *
5772640 TA TA TA TA TA TA TA TA TA TA TA TC T- TC TA TC T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5772679 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5772694 CCTTATACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5772658 original size:35 final size:35
Alignment explanation
Indices: 5772607--5772693 Score: 102
Period size: 35 Copynumber: 2.5 Consensus size: 35
5772597 NNNNNNNTAT
* * * * * *
5772607 TATATATATCTTTATATACGTTTTTTATCTTCGTA
1 TATATATATATATATATACATCTTCTATCTTAGTA
* *
5772642 TATATATATATATATATATATCTTCTATCTTATTA
1 TATATATATATATATATACATCTTCTATCTTAGTA
5772677 TATATATATATATATAT
1 TATATATATATATATAT
5772694 CCTTATACAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.55
Consensus pattern (35 bp):
TATATATATATATATATACATCTTCTATCTTAGTA
Found at i:5772698 original size:25 final size:25
Alignment explanation
Indices: 5772650--5772699 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5772640 TATATATATA
* *
5772650 TATATATATATATCTTCTATCTTAT
1 TATATATATATATCATATATCTTAT
5772675 TATATATATATAT-ATATATCCTTAT
1 TATATATATATATCATATAT-CTTAT
5772700 ACACGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATATATATATCATATATCTTAT
Found at i:5776910 original size:18 final size:19
Alignment explanation
Indices: 5776887--5776924 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5776877 TTAAAATGGA
*
5776887 AAAATGTATATGTAT-TAT
1 AAAATGTAAATGTATATAT
5776905 AAAATGTAAATGTATATAT
1 AAAATGTAAATGTATATAT
5776924 A
1 A
5776925 TATAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
AAAATGTAAATGTATATAT
Found at i:5777072 original size:3 final size:3
Alignment explanation
Indices: 5777064--5777163 Score: 200
Period size: 3 Copynumber: 33.3 Consensus size: 3
5777054 ATGTATAAGT
5777064 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5777112 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5777160 ATA A
1 ATA A
5777164 ATTAAACTTA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5778881 original size:6 final size:7
Alignment explanation
Indices: 5778864--5778895 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5778854 TCAAGAAGAA
5778864 AAAAAAC
1 AAAAAAC
5778871 AAAAAAC
1 AAAAAAC
5778878 AAAAAAC
1 AAAAAAC
5778885 -AAAAAC
1 AAAAAAC
5778891 AAAAA
1 AAAAA
5778896 TAAGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:5778881 original size:14 final size:13
Alignment explanation
Indices: 5778864--5778895 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
5778854 TCAAGAAGAA
5778864 AAAAAACAAAAAAC
1 AAAAAAC-AAAAAC
5778878 AAAAAACAAAAAC
1 AAAAAACAAAAAC
5778891 AAAAA
1 AAAAA
5778896 TAAGAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:5778903 original size:14 final size:13
Alignment explanation
Indices: 5778865--5778906 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5778855 CAAGAAGAAA
*
5778865 AAAAACAAAAAAC
1 AAAAATAAAAAAC
5778878 AAAAA-ACAAAAAC
1 AAAAATA-AAAAAC
5778891 AAAAATAAGAAAAC
1 AAAAATAA-AAAAC
5778905 AA
1 AA
5778907 CCTTGAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 17 0.65
14 8 0.31
ACGTcount: A:0.83, C:0.12, G:0.02, T:0.02
Consensus pattern (13 bp):
AAAAATAAAAAAC
Found at i:5778903 original size:20 final size:20
Alignment explanation
Indices: 5778849--5778906 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
5778839 TTCGAAATAA
*
5778849 AAAAATCAAGAAGAAAAAAAAC
1 AAAAAT-AAGAA-AACAAAAAC
*
5778871 AAAAA-ACAAAAAACAAAAAC
1 AAAAATA-AGAAAACAAAAAC
5778891 AAAAATAAGAAAACAA
1 AAAAATAAGAAAACAA
5778907 CCTTGAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 22 0.71
21 4 0.13
22 5 0.16
ACGTcount: A:0.81, C:0.10, G:0.05, T:0.03
Consensus pattern (20 bp):
AAAAATAAGAAAACAAAAAC
Found at i:5779269 original size:21 final size:19
Alignment explanation
Indices: 5779219--5779269 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
5779209 CTTTCTGTTA
*
5779219 TGGGT-TTGGGCTAGGGTT
1 TGGGTATTGGGCCAGGGTT
*
5779237 TGGTTAGTTGGGCCAGGGTGGT
1 TGGGTA-TTGGGCCAGGGT--T
5779259 TGGGTATTGGG
1 TGGGTATTGGG
5779270 TTTGAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 4 0.15
20 11 0.42
21 5 0.19
22 6 0.23
ACGTcount: A:0.08, C:0.06, G:0.51, T:0.35
Consensus pattern (19 bp):
TGGGTATTGGGCCAGGGTT
Found at i:5783548 original size:72 final size:72
Alignment explanation
Indices: 5783454--5783615 Score: 207
Period size: 72 Copynumber: 2.2 Consensus size: 72
5783444 GAGGAAAAGT
* * * *
5783454 ACCATTTAATTGATTTTCTGAAACATCAAATACCTCCAAAGATGATAACTGCCCTATAGACGAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
*
5783519 GAATTTG
66 GAACTTG
* * * * * * * *
5783526 GCCGTTTAACTGATTTTTTGAAACATTAAACAACTTCAAAGATGATAGCTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
5783591 GAACTTG
66 GAACTTG
5783598 ACCATTTAATTGATTTTC
1 ACCATTTAATTGATTTTC
5783616 GAGATTGGTC
Statistics
Matches: 73, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGATAACTCCCCTATAGACAAGG
GAACTTG
Found at i:5786101 original size:7 final size:7
Alignment explanation
Indices: 5786089--5786114 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5786079 TTTTTGAGTT
5786089 AGAGAGA
1 AGAGAGA
5786096 AGAGAGA
1 AGAGAGA
5786103 AGAGAGA
1 AGAGAGA
5786110 AGAGA
1 AGAGA
5786115 AAGGGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AGAGAGA
Found at i:5789784 original size:19 final size:20
Alignment explanation
Indices: 5789760--5789801 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5789750 TATGTGAATA
*
5789760 AAATATT-TTTTAAAACTTC
1 AAATATTATTTTAAAAATTC
5789779 AAATATTACTTTTAAAAATTC
1 AAATATTA-TTTTAAAAATTC
5789800 AA
1 AA
5789802 CTTAAATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATATTATTTTAAAAATTC
Found at i:5790759 original size:26 final size:27
Alignment explanation
Indices: 5790730--5790780 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5790720 AAATTGAGCT
*
5790730 CAAAAAAAGAA-TAAAAACTAAATTGA
1 CAAAAAAAAAATTAAAAACTAAATTGA
*
5790756 CAAAAAAAAAATTGAAAACTAAATT
1 CAAAAAAAAAATTAAAAACTAAATT
5790781 CAATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.18
Consensus pattern (27 bp):
CAAAAAAAAAATTAAAAACTAAATTGA
Found at i:5794540 original size:72 final size:72
Alignment explanation
Indices: 5794413--5794729 Score: 438
Period size: 72 Copynumber: 4.4 Consensus size: 72
5794403 GAGGAAATGT
* * *
5794413 ACCATTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAAGG
5794478 GAATTTG
66 GAATTTG
* ** *
5794485 ACCATTTAATTGATTTTCTGAAACATTAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAGG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAAGG
5794550 GAATTTG
66 GAATTTG
* * * * *
5794557 GCCGTTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATG
1 ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAAGG
5794622 GAATTTG
66 GAATTTG
* ** *
5794629 ACCATTTAATTGGATTTTCTG-AGCATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACAAG
1 ACCATTTAATT-GATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAAG
5794693 GGAATTTG
65 GGAATTTG
* * * *
5794701 GCCGTTTAATTGATTTACTGAAAGATCAA
1 ACCATTTAATTGATTTTCTGAAACATCAA
5794730 GGTGAGTAAC
Statistics
Matches: 213, Mismatches: 30, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
71 8 0.04
72 196 0.92
73 9 0.04
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (72 bp):
ACCATTTAATTGATTTTCTGAAACATCAAACAACTCCAAAGATGACAACTCCCCTATAGACAAGG
GAATTTG
Found at i:5794635 original size:144 final size:144
Alignment explanation
Indices: 5794417--5794729 Score: 574
Period size: 144 Copynumber: 2.2 Consensus size: 144
5794407 AAATGTACCA
5794417 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
*
5794482 TTGACCATTTAATT-GATTTTCTGAAACATTAAACTCCTCCAAAGATGACAACTGCCCTATAGAC
66 TTGACCATTTAATTGGATTTTCTG-AACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGAC
5794546 AAGGGAATTTGGCCG
130 AAGGGAATTTGGCCG
5794561 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
1 TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
*
5794626 TTGACCATTTAATTGGATTTTCTGAGCATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
66 TTGACCATTTAATTGGATTTTCTGAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
5794691 AGGGAATTTGGCCG
131 AGGGAATTTGGCCG
* *
5794705 TTTAATTGATTTACTGAAAGATCAA
1 TTTAATTGATTTTCTGAAACATCAA
5794730 GGTGAGTAAC
Statistics
Matches: 164, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
144 155 0.95
145 9 0.05
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (144 bp):
TTTAATTGATTTTCTGAAACATCAAACAACTTCAAAGATGATAACTCCCCTATAGACAATGGAAT
TTGACCATTTAATTGGATTTTCTGAACATCAAACTCCTCCAAAGATGACAACTGCCCTATAGACA
AGGGAATTTGGCCG
Found at i:5820868 original size:178 final size:179
Alignment explanation
Indices: 5820645--5821006 Score: 717
Period size: 178 Copynumber: 2.0 Consensus size: 179
5820635 TTATTGAATA
5820645 AAAAGAATAATATAAAATAATAAGTAAATCAATAAAGGATATTTTTATTTTTATTTAAAAAATTA
1 AAAAGAATAATATAAAATAATAAGTAAATCAATAAAGGATATTTTTATTTTTATTTAAAAAATTA
5820710 ATAAATAAATTTTAAGAGTTAATATATATTTTTGGTGACAATAAAACATTACCTAACTAATTACA
66 ATAAATAAATTTTAAGAGTTAATATATATTTTTGGTGACAATAAAACATTACCTAACTAATTACA
5820775 TAGAAACACTGTGAAAAGAAAAAACACCCTTAGACTTGTCCATTACAAG
131 TAGAAACACTGTGAAAAGAAAAAACACCCTTAGACTTGTCCATTACAAG
5820824 AAAAGAATAATAT-AAATAATAAGTAAATCAATAAAGGATATTTTTATTTTTATTTAAAAAATTA
1 AAAAGAATAATATAAAATAATAAGTAAATCAATAAAGGATATTTTTATTTTTATTTAAAAAATTA
5820888 ATAAATAAATTTTAAGAGTTAATATATATTTTTGGTGACAATAAAACATTACCTAACTAATTACA
66 ATAAATAAATTTTAAGAGTTAATATATATTTTTGGTGACAATAAAACATTACCTAACTAATTACA
5820953 TAGAAACACTGTGAAAAGAAAAAACACCCTTAGACTTGTCCATTACAAG
131 TAGAAACACTGTGAAAAGAAAAAACACCCTTAGACTTGTCCATTACAAG
5821002 AAAAG
1 AAAAG
5821007 CTTGAACCAT
Statistics
Matches: 183, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
178 170 0.93
179 13 0.07
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.32
Consensus pattern (179 bp):
AAAAGAATAATATAAAATAATAAGTAAATCAATAAAGGATATTTTTATTTTTATTTAAAAAATTA
ATAAATAAATTTTAAGAGTTAATATATATTTTTGGTGACAATAAAACATTACCTAACTAATTACA
TAGAAACACTGTGAAAAGAAAAAACACCCTTAGACTTGTCCATTACAAG
Found at i:5823184 original size:22 final size:22
Alignment explanation
Indices: 5823159--5823202 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5823149 AACCCTTAAA
5823159 CCTTGTGT-TTCTTCTTTCTTTC
1 CCTT-TGTCTTCTTCTTTCTTTC
* *
5823181 CCTTTTTCTTTTTCTTTCTTTC
1 CCTTTGTCTTCTTCTTTCTTTC
5823203 TTTCTGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (22 bp):
CCTTTGTCTTCTTCTTTCTTTC
Found at i:5823243 original size:5 final size:6
Alignment explanation
Indices: 5823166--5823244 Score: 52
Period size: 6 Copynumber: 12.5 Consensus size: 6
5823156 AAACCTTGTG
** * *
5823166 TTTCTT CTTTCTT TCCCTT TTTCTT TTTCTT TCTT-TC TTTCTG TTTCGTT
1 TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT T-TTCTT TTTCTT TTTC-TT
**
5823216 TGGCTT CTTTCTT TTTCTTT TTTCTT TTT
1 TTTCTT -TTTCTT TTTC-TT TTTCTT TTT
5823245 ATTACTTGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
5 2 0.04
6 33 0.59
7 21 0.38
ACGTcount: A:0.00, C:0.22, G:0.05, T:0.73
Consensus pattern (6 bp):
TTTCTT
Found at i:5826530 original size:74 final size:75
Alignment explanation
Indices: 5826435--5826583 Score: 291
Period size: 74 Copynumber: 2.0 Consensus size: 75
5826425 CTAAGATAAA
5826435 TGCAACTTAACAAGCAAATACCTCTAAAATAATAACAAAATTAATAATAAAACAATAGTTATACA
1 TGCAACTTAACAAGCAAATACCTCTAAAATAATAACAAAATTAATAATAAAACAATAGTTATACA
5826500 ATATATAATC
66 ATATATAATC
5826510 TGCAACTTAA-AAGCAAATACCTCTAAAATAATAACAAAATTAATAATAAAACAATAGTTATACA
1 TGCAACTTAACAAGCAAATACCTCTAAAATAATAACAAAATTAATAATAAAACAATAGTTATACA
5826574 ATATATAATC
66 ATATATAATC
5826584 AATAACAATA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 64 0.86
75 10 0.14
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (75 bp):
TGCAACTTAACAAGCAAATACCTCTAAAATAATAACAAAATTAATAATAAAACAATAGTTATACA
ATATATAATC
Found at i:5827780 original size:2 final size:2
Alignment explanation
Indices: 5827770--5827813 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5827760 TAACAAAGTG
*
5827770 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5827810 TA TA
1 TA TA
5827814 AAAAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5828231 original size:21 final size:22
Alignment explanation
Indices: 5828186--5828231 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
5828176 AAAAAAATTT
*
5828186 AAAATAATATTTATTACTTTATA
1 AAAATAATATTTATTAC-ATATA
*
5828209 AAAATAATATTTTTTA-ATATA
1 AAAATAATATTTATTACATATA
5828230 AA
1 AA
5828232 CTAGAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
23 15 0.71
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATAATATTTATTACATATA
Found at i:5830347 original size:18 final size:18
Alignment explanation
Indices: 5830316--5830350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5830306 TTTAGCAATG
5830316 TTTTTATCTCAAAAGTAT
1 TTTTTATCTCAAAAGTAT
* *
5830334 TTTTTGTCTTAAAAGTA
1 TTTTTATCTCAAAAGTA
5830351 CTTCTTAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTTTATCTCAAAAGTAT
Found at i:5835700 original size:14 final size:14
Alignment explanation
Indices: 5835664--5835697 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5835654 TCATCATTTA
5835664 CCTATAACCAAAAC
1 CCTATAACCAAAAC
5835678 CCTATAACCAAAAC
1 CCTATAACCAAAAC
5835692 CC-ATAA
1 CCTATAA
5835698 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:5835801 original size:11 final size:11
Alignment explanation
Indices: 5835787--5835827 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
5835777 AGGGAGAAGC
*
5835787 AAAAAAGAATG
1 AAAAAAGAAAG
*
5835798 AAAAAAAAAAG
1 AAAAAAGAAAG
5835809 AAAAAAGAAAG
1 AAAAAAGAAAG
5835820 AAAGAAAG
1 AAA-AAAG
5835828 TTAAAAGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 22 0.85
12 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:5837668 original size:126 final size:126
Alignment explanation
Indices: 5837456--5837691 Score: 328
Period size: 126 Copynumber: 1.9 Consensus size: 126
5837446 ACACGGCCGT
* * * *
5837456 GTGATTTTATATTACACGGGCACAGTGAGTTACACGGCTTACATACATGGGCATACGAAGCAGTC
1 GTGACTTTATATTACACGGGCACAGTGAGTTACACGACTTACATACACGGGCATACGAAGCAATC
*
5837521 ACATGGGCGTGTGGAGCAGCCACACAACCATGTCAAGAGCCACACGGTGCGACATGGTCGC
66 ACACGGGCGTGTGGAGCAGCCACACAACCATGTCAAGAGCCACACGGTGCGACATGGTCGC
* * * ** **
5837582 GTGACTTTATATTACACGGGCATAGTGAGTTATACGATTTATGTACACGGGCATGTGAAGCAATC
1 GTGACTTTATATTACACGGGCACAGTGAGTTACACGACTTACATACACGGGCATACGAAGCAATC
* ** *
5837647 ACACGGGCGTGTGGAGTAGCCACACGGCCATGTCAAGAGCGACAC
66 ACACGGGCGTGTGGAGCAGCCACACAACCATGTCAAGAGCCACAC
5837692 AGTTTGGGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
126 94 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (126 bp):
GTGACTTTATATTACACGGGCACAGTGAGTTACACGACTTACATACACGGGCATACGAAGCAATC
ACACGGGCGTGTGGAGCAGCCACACAACCATGTCAAGAGCCACACGGTGCGACATGGTCGC
Found at i:5842851 original size:3 final size:3
Alignment explanation
Indices: 5842843--5842888 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
5842833 TCCATCTCCC
* *
5842843 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAG CAT CAC CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5842889 TCCGTTGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.28
Consensus pattern (3 bp):
CAT
Found at i:5856322 original size:11 final size:11
Alignment explanation
Indices: 5856306--5856330 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5856296 AACGCAGTCT
5856306 TAACATCCATC
1 TAACATCCATC
5856317 TAACATCCATC
1 TAACATCCATC
5856328 TAA
1 TAA
5856331 TGCAATTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (11 bp):
TAACATCCATC
Found at i:5856615 original size:16 final size:15
Alignment explanation
Indices: 5856589--5856618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5856579 TATTTAATAT
5856589 GGGCTGGGTTGGGCC
1 GGGCTGGGTTGGGCC
5856604 GGGCTCGGGTTGGGC
1 GGGCT-GGGTTGGGC
5856619 TTGGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (15 bp):
GGGCTGGGTTGGGCC
Found at i:5866650 original size:24 final size:24
Alignment explanation
Indices: 5866590--5866658 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
5866580 GGCCCGAATT
*
5866590 ATATATTAAATATATATATTTTTAT
1 ATATATTAAATATATAT-TTTTTAC
* * *
5866615 TTTTAATCAAATATATATTTTTTAC
1 ATAT-ATTAAATATATATTTTTTAC
5866640 ATATATTAAATATATATTT
1 ATATATTAAATATATATTT
5866659 AATATGGGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 14 0.39
25 10 0.28
26 12 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATATTAAATATATATTTTTTAC
Found at i:5866690 original size:16 final size:15
Alignment explanation
Indices: 5866664--5866693 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5866654 TATTTAATAT
5866664 GGGCTGGGTTGGGCC
1 GGGCTGGGTTGGGCC
5866679 GGGCTCGGGTTGGGC
1 GGGCT-GGGTTGGGC
5866694 TTGGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (15 bp):
GGGCTGGGTTGGGCC
Found at i:5868190 original size:104 final size:104
Alignment explanation
Indices: 5868072--5868279 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
5868062 TTGTTTTATT
5868072 ATCTGAATGAATAATTTGAATGAAATTATTAATTTAGATCAGGATTGGGTGGAAAATCGAGGAAA
1 ATCTGAATGAATAATTTGAATGAAATTATTAATTTAGATCAGGATTGGGTGGAAAATCGAGGAAA
5868137 ATAGATAATTACCAAAATGCCCCTGAATCTTGGTATTTC
66 ATAGATAATTACCAAAATGCCCCTGAATCTTGGTATTTC
5868176 ATCTGAATGAATAATTTGAATGAAATTATTAATTTAGATCAGGATTGGGTGGAAAATCGAGGAAA
1 ATCTGAATGAATAATTTGAATGAAATTATTAATTTAGATCAGGATTGGGTGGAAAATCGAGGAAA
5868241 ATAGATAATTACCAAAATGCCCCTGAATCTTGGTATTTC
66 ATAGATAATTACCAAAATGCCCCTGAATCTTGGTATTTC
5868280 TGCAATTTAG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (104 bp):
ATCTGAATGAATAATTTGAATGAAATTATTAATTTAGATCAGGATTGGGTGGAAAATCGAGGAAA
ATAGATAATTACCAAAATGCCCCTGAATCTTGGTATTTC
Found at i:5868582 original size:25 final size:25
Alignment explanation
Indices: 5868554--5868605 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
5868544 CAGCTCTTAT
* *
5868554 GAGCGTCTCGATATTTGGCTCTCAC
1 GAGCGTCCCGATATTTGACTCTCAC
*
5868579 GAGCTTCCCGATATTTGACTCTCAC
1 GAGCGTCCCGATATTTGACTCTCAC
5868604 GA
1 GA
5868606 ACTTCCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCGTCCCGATATTTGACTCTCAC
Found at i:5868610 original size:25 final size:25
Alignment explanation
Indices: 5868562--5868611 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
5868552 ATGAGCGTCT
* *
5868562 CGATATTTGGCTCTCACGAGCTTCC
1 CGATATTTGACTCTCACGAACTTCC
5868587 CGATATTTGACTCTCACGAACTTCC
1 CGATATTTGACTCTCACGAACTTCC
5868612 TGATTAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (25 bp):
CGATATTTGACTCTCACGAACTTCC
Found at i:5868625 original size:25 final size:25
Alignment explanation
Indices: 5868562--5868626 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
5868552 ATGAGCGTCT
* *
5868562 CGATATTTGGCTCTCACGAGCTTCC
1 CGATATATGGCTCTCACGAACTTCC
* *
5868587 CGATATTTGACTCTCACGAACTTCC
1 CGATATATGGCTCTCACGAACTTCC
*
5868612 TGAT-TAATGGCTCTC
1 CGATAT-ATGGCTCTC
5868627 TTGAGCTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (25 bp):
CGATATATGGCTCTCACGAACTTCC
Found at i:5868649 original size:25 final size:25
Alignment explanation
Indices: 5868628--5868718 Score: 114
Period size: 25 Copynumber: 3.6 Consensus size: 25
5868618 ATGGCTCTCT
5868628 TGAGCTTCCCATTATACAGCTCACA
1 TGAGCTTCCCATTATACAGCTCACA
* * * *
5868653 TGAGCTTCCTGATAAT-TAGCTCGCAA
1 TGAGCTTCC-CATTATACAGCTCAC-A
5868679 T-AGCTTCCCATTATACAGCTCACA
1 TGAGCTTCCCATTATACAGCTCACA
5868703 TGAGCTTCCCATTATA
1 TGAGCTTCCCATTATA
5868719 TGGCTCGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
24 6 0.11
25 42 0.78
26 6 0.11
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (25 bp):
TGAGCTTCCCATTATACAGCTCACA
Found at i:5868661 original size:50 final size:50
Alignment explanation
Indices: 5868607--5868737 Score: 160
Period size: 50 Copynumber: 2.6 Consensus size: 50
5868597 CTCTCACGAA
* *
5868607 CTTCCTGATTAATGGCTCTC-TTGAGCTTCCCATTATACAGCTCACATGAG
1 CTTCCTGATTAATGGCTCGCAAT-AGCTTCCCATTATACAGCTCACATGAG
*
5868657 CTTCCTGA-TAATTAGCTCGCAATAGCTTCCCATTATACAGCTCACATGAG
1 CTTCCTGATTAA-TGGCTCGCAATAGCTTCCCATTATACAGCTCACATGAG
* * *
5868707 CTTCC-CATTATATGGCTCGAAAGAGCTTCCC
1 CTTCCTGATTA-ATGGCTCGCAATAGCTTCCC
5868738 CGTTTACATG
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
49 4 0.06
50 64 0.91
51 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.31
Consensus pattern (50 bp):
CTTCCTGATTAATGGCTCGCAATAGCTTCCCATTATACAGCTCACATGAG
Found at i:5868724 original size:25 final size:25
Alignment explanation
Indices: 5868628--5868737 Score: 109
Period size: 25 Copynumber: 4.4 Consensus size: 25
5868618 ATGGCTCTCT
*
5868628 TGAGCTTCCCATTATACAGCTCACA
1 TGAGCTTCCCATTATATAGCTCACA
* * *
5868653 TGAGCTTCCTGATAAT-TAGCTCGCAA
1 TGAGCTTCC-CATTATATAGCTCAC-A
*
5868679 T-AGCTTCCCATTATACAGCTCACA
1 TGAGCTTCCCATTATATAGCTCACA
*
5868703 TGAGCTTCCCATTATATGGCTCGA-A
1 TGAGCTTCCCATTATATAGCTC-ACA
*
5868728 AGAGCTTCCC
1 TGAGCTTCCC
5868738 CGTTTACATG
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
24 6 0.09
25 56 0.81
26 7 0.10
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (25 bp):
TGAGCTTCCCATTATATAGCTCACA
Found at i:5890250 original size:156 final size:153
Alignment explanation
Indices: 5890024--5890334 Score: 550
Period size: 156 Copynumber: 2.0 Consensus size: 153
5890014 GAAGCAATAA
* *
5890024 CTGAAAACTACTTGGAAATATTTGACCTACGTTACCACATGAAGCAGTTCGAGAAAGAGAATTAT
1 CTGAAAACTACTTGGAAATATTTGACCTACGTCACCACATGAAGCAGTTCGAGAAAGAGAATTAC
*
5890089 CAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGTTT
66 CAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGCTT
5890154 ACCTTTTCTTTTAAAGCAGAAAG
131 ACCTTTTCTTTTAAAGCAGAAAG
* *
5890177 CTGAAAGCTACTTGGAAATATTTGACCTACCTTGTCATCACATGAAGCAGTTCGAGAAAGAGAAT
1 CTGAAAACTACTTGGAAATATTTGACCTA-C--GTCACCACATGAAGCAGTTCGAGAAAGAGAAT
5890242 TACCAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAG
63 TACCAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAG
5890307 CTTACCTTTTCTTTTAAAGCAGAAAG
128 CTTACCTTTTCTTTTAAAGCAGAAAG
5890333 CT
1 CT
5890335 ACTAAGAGAA
Statistics
Matches: 150, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
153 28 0.19
154 1 0.01
156 121 0.81
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (153 bp):
CTGAAAACTACTTGGAAATATTTGACCTACGTCACCACATGAAGCAGTTCGAGAAAGAGAATTAC
CAGGGACCGATTCTTCCGTATCCTTTGGACTACTTTTAATCTGTCAGATAACCCAAACTAAGCTT
ACCTTTTCTTTTAAAGCAGAAAG
Found at i:5892835 original size:20 final size:20
Alignment explanation
Indices: 5892810--5892868 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
5892800 ACCTTTCTTC
*
5892810 TTTTTTATTTATTTTTTCTA
1 TTTTTTATTTATTTTTACTA
* *
5892830 TTTTTTGCTTT-TTTTTACTT
1 TTTTTT-ATTTATTTTTACTA
5892850 TTTTATGTATTTATTTTTA
1 TTTT-T-TATTTATTTTTA
5892869 GGTTATTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 17 0.55
21 7 0.23
22 7 0.23
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTATTTTTACTA
Found at i:5911761 original size:24 final size:24
Alignment explanation
Indices: 5911734--5911779 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5911724 ATTGTATTGG
*
5911734 ATGAAGAGGAGGAAGATGAAGATT
1 ATGAAGAGGAGGAAGAAGAAGATT
* *
5911758 ATGAGGTGGAGGAAGAAGAAGA
1 ATGAAGAGGAGGAAGAAGAAGA
5911780 AGATGACGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.41, T:0.13
Consensus pattern (24 bp):
ATGAAGAGGAGGAAGAAGAAGATT
Found at i:5911782 original size:33 final size:33
Alignment explanation
Indices: 5911731--5911794 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
5911721 AAAATTGTAT
* * * *
5911731 TGGATGAAGAGGAGGAAGATGAAGATTATGAGG
1 TGGAGGAAGAAGAAGAAGATGAAGATGATGAGG
*
5911764 TGGAGGAAGAAGAAGAAGATGACGATGATGA
1 TGGAGGAAGAAGAAGAAGATGAAGATGATGA
5911795 TGATGAAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.41, T:0.16
Consensus pattern (33 bp):
TGGAGGAAGAAGAAGAAGATGAAGATGATGAGG
Found at i:5918865 original size:27 final size:28
Alignment explanation
Indices: 5918817--5918875 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
5918807 AATCGCCTAA
*
5918817 AAATTTTAAAAAATAGAAAAATA-AAAG
1 AAATTCTAAAAAATAGAAAAATACAAAG
** * *
5918844 AAATTCTAAAAAATTTATAAATACAAAT
1 AAATTCTAAAAAATAGAAAAATACAAAG
5918872 AAAT
1 AAAT
5918876 AATAATTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.27
Consensus pattern (28 bp):
AAATTCTAAAAAATAGAAAAATACAAAG
Found at i:5929034 original size:19 final size:18
Alignment explanation
Indices: 5929010--5929068 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 18
5929000 TTGAATTTTC
5929010 AAAAATTCAAAATAATTAT
1 AAAAATTCAAAA-AATTAT
*
5929029 AAAAATTCCAAAAATTAT
1 AAAAATTCAAAAAATTAT
* * *
5929047 -ATATTTTAAAAAA-TAT
1 AAAAATTCAAAAAATTAT
5929063 AAAAAT
1 AAAAAT
5929069 ATAAAAAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 3 0.09
17 12 0.38
18 6 0.19
19 11 0.34
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTCAAAAAATTAT
Found at i:5929044 original size:18 final size:19
Alignment explanation
Indices: 5929010--5929047 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5929000 TTGAATTTTC
5929010 AAAAATTCAAAATAATTAT
1 AAAAATTCAAAATAATTAT
*
5929029 AAAAATTCCAAA-AATTAT
1 AAAAATTCAAAATAATTAT
5929047 A
1 A
5929048 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATTCAAAATAATTAT
Found at i:5929190 original size:3 final size:3
Alignment explanation
Indices: 5929182--5929211 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5929172 TTTAGTTTCT
5929182 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5929212 AATTTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5930439 original size:16 final size:16
Alignment explanation
Indices: 5930415--5930463 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
5930405 TTCGCTGTAT
5930415 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
5930431 TGGATTAGAGGCGTAA
1 TGGAATAGAGGCGTAA
5930447 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
5930463 T
1 T
5930464 AGCAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:5930718 original size:18 final size:17
Alignment explanation
Indices: 5930697--5930731 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5930687 TTATTATTAA
*
5930697 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5930715 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5930732 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5933672 original size:23 final size:23
Alignment explanation
Indices: 5933644--5933690 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5933634 GGGCAGAGGG
*
5933644 ACAGAGGGAGCAAATCGGCAGAA
1 ACAGAGGGAGCAAATCGACAGAA
5933667 ACAGAGGGAGCAAATCGACAGAA
1 ACAGAGGGAGCAAATCGACAGAA
5933690 A
1 A
5933691 AGAAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.32, T:0.04
Consensus pattern (23 bp):
ACAGAGGGAGCAAATCGACAGAA
Found at i:5936395 original size:13 final size:13
Alignment explanation
Indices: 5936379--5936404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5936369 CTTTGCATAT
5936379 TGTCTTCAACAGG
1 TGTCTTCAACAGG
5936392 TGTCTTCAACAGG
1 TGTCTTCAACAGG
5936405 CTCGCACTTT
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:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:5947516 original size:23 final size:23
Alignment explanation
Indices: 5947474--5947517 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5947464 GTAAAACCGA
*
5947474 ATAATTGTCACATGTTTATTACC
1 ATAATTGTCACATGTATATTACC
5947497 ATAATTG-CACATGTAATATTA
1 ATAATTGTCACATGT-ATATTA
5947518 TTAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
ATAATTGTCACATGTATATTACC
Found at i:5952417 original size:22 final size:23
Alignment explanation
Indices: 5952360--5952417 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
5952350 ATAAAATCTG
*
5952360 AAATGTATATTTTAAATATTTTATA
1 AAAT-TAT-TTTTAAAAATTTTATA
*
5952385 ATATTATTTTTAAAAATTTTA-A
1 AAATTATTTTTAAAAATTTTATA
5952407 AAATTATTTTT
1 AAATTATTTTT
5952418 TAATATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.37
23 13 0.43
24 3 0.10
25 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AAATTATTTTTAAAAATTTTATA
Found at i:5953039 original size:24 final size:26
Alignment explanation
Indices: 5952981--5953041 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
5952971 TAAATAAAGG
*
5952981 ACAAATAAAAATACTTAAAAAGTAAAT
1 ACAAA-AAAAATACTTAAAAAGTAAAA
* *
5953008 A-AAGAAAAA-ACTTAAAATG-AAAA
1 ACAAAAAAAATACTTAAAAAGTAAAA
5953031 ACAAAAAAAAT
1 ACAAAAAAAAT
5953042 GAAAAAAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
23 4 0.14
24 16 0.57
25 5 0.18
26 2 0.07
27 1 0.04
ACGTcount: A:0.72, C:0.07, G:0.05, T:0.16
Consensus pattern (26 bp):
ACAAAAAAAATACTTAAAAAGTAAAA
Found at i:5956899 original size:20 final size:20
Alignment explanation
Indices: 5956890--5956940 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
5956880 CCTCTACAAG
5956890 GTATTGATACCTCATAGCAA
1 GTATTGATACCTCATAGCAA
5956910 GTATTGATACCTCATAGCAA
1 GTATTGATACCTCATAGCAA
5956930 GTATTGATACC
1 GTATTGATACC
5956941 ATAGGCTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATTGATACCTCATAGCAA
Found at i:5968633 original size:17 final size:17
Alignment explanation
Indices: 5968607--5968639 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5968597 ATTAACTCTG
5968607 TTAAACAGTAAATATTT
1 TTAAACAGTAAATATTT
*
5968624 TTAAATAGTAAATATT
1 TTAAACAGTAAATATT
5968640 ATCTCTATTT
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:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAAACAGTAAATATTT
Found at i:5968999 original size:2 final size:2
Alignment explanation
Indices: 5968992--5969018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5968982 TTATTTTAAT
5968992 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
5969019 GAAATTAAAT
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:5974631 original size:42 final size:42
Alignment explanation
Indices: 5974574--5974691 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
5974564 GTTTACAAAC
* * *
5974574 AAAAACGCCGCTAAAGACCGTGTTCTTTAGCGGTGCTTCGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
5974616 AAAAAGGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
5974658 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
5974692 ATTTTTTCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:5974709 original size:42 final size:42
Alignment explanation
Indices: 5974663--5974800 Score: 206
Period size: 42 Copynumber: 3.3 Consensus size: 42
5974653 TAGATAAAAA
* *
5974663 CGCCGCTAAAGATCATGTTCTTTAGCGGCATTTTTTCTTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTTAAG
* *
5974705 CGCCGCTAAAAAACATGGTCTTTAGCGGCGTTTTTT-TCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCT-TAAG
* *
5974747 CGCCTCTAAAGAACATGTTCTTTAGCGGCGTTTATTCTTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTTAAG
5974789 CGCCGCTAAAGA
1 CGCCGCTAAAGA
5974801 CGTGTTTTCT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 83 0.98
43 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCTTAAG
Found at i:5974727 original size:84 final size:84
Alignment explanation
Indices: 5974622--5974798 Score: 219
Period size: 84 Copynumber: 2.1 Consensus size: 84
5974612 CGAAAAAAAG
* * * *
5974622 GCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGATAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCCGCTAAAAAACATGGTCTTTAGAGGCGCTTAGATAAAAACGCCGCTAAAGAACATGTTCTTTA
*
5974687 GCGGCATTTTTTCTTAAGC
66 GCGGCATTTATTCTTAAGC
* * *** ** * *
5974706 GCCGCTAAAAAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCTCTAAAGAACATGTTCTTTA
1 GCCGCTAAAAAACATGGTCTTTAGAGGCGCTTAGATAAAAACGCCGCTAAAGAACATGTTCTTTA
*
5974771 GCGGCGTTTATTCTTAAGC
66 GCGGCATTTATTCTTAAGC
5974790 GCCGCTAAA
1 GCCGCTAAA
5974799 GACGTGTTTT
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (84 bp):
GCCGCTAAAAAACATGGTCTTTAGAGGCGCTTAGATAAAAACGCCGCTAAAGAACATGTTCTTTA
GCGGCATTTATTCTTAAGC
Found at i:5975070 original size:21 final size:21
Alignment explanation
Indices: 5975032--5975076 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5975022 CTCTACTCTA
* *
5975032 CTTCTCTCGCTGTAGCCTCCG
1 CTTCCCTCGCTGCAGCCTCCG
* *
5975053 CTTCCCTCGCTGCCGCCTCTG
1 CTTCCCTCGCTGCAGCCTCCG
5975074 CTT
1 CTT
5975077 TAAGTTGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCCG
Found at i:5979171 original size:19 final size:19
Alignment explanation
Indices: 5979147--5979185 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5979137 GTAATGTATG
5979147 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
5979166 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
5979185 T
1 T
5979186 GTAAGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:5979190 original size:87 final size:89
Alignment explanation
Indices: 5979049--5979488 Score: 400
Period size: 87 Copynumber: 4.9 Consensus size: 89
5979039 TAAGTAAATT
* * * * * * * * **
5979049 ATGTAAGTTATGTACGTGTATAAGTTATGTAAGTTATCAAAGTAAGCTATGTAAGTTGCGTATTA
1 ATGTATGTTATGTAAGTATGTAAGTTATGTATG-TAT-TATGTAAGTTATGTAAGTTATGTATTA
5979114 TGTAAGTTATGTAAGTTATCAAAGTA
64 TGTAAGTTATGTAAGTTATCAAAGTA
5979140 ATGTATGTTATGTAAGT-TGTAAGTTAT-TATGTATTATGTAAGTTATGTAAGTTATGTATTATG
1 ATGTATGTTATGTAAGTATGTAAGTTATGTATGTATTATGTAAGTTATGTAAGTTATGTATTATG
* *
5979203 TAGGTTATGTAATTTATCAAAGTA
66 TAAGTTATGTAAGTTATCAAAGTA
5979227 ATGTATGTTATGTAAGT-TGTAAGTTAT-TATGTATTATGTAAGTTATGT-A-TTATGTAGGTTA
1 ATGTATGTTATGTAAGTATGTAAGTTATGTATGTATTATGTAAGTTATGTAAGTTATGTA--TTA
* * ** *
5979288 TGTAAGTTGTGTAAGATATTTAAGTT
64 TGTAAGTTATGTAAGTTATCAAAGTA
* *
5979314 ATGTAAGTTTGTATTATGTAAGTTATGTAAGTTATGTATGTA--ATGTATGTTATGTAAGTTTTG
1 ATGT-A---TG--TTATGTAAG-TATGTAAGTTATGTATGTATTATGTAAGTTATGTAAGTTATG
* * **
5979377 TATTATGTGAG-TATTTAAGTTATGTAAGTTATA
59 TATTATGTAAGTTATGTAAGTTATCAAAG---TA
* * * * * *
5979410 ATGTAAGTTATGT-ATTATGTAGGTTATGTAAG--TTATGTAAGTTATGTAATTTTTGTATTATG
1 ATGTATGTTATGTAAGTATGTAAGTTATGTATGTATTATGTAAGTTATGTAAGTTATGTATTATG
*
5979472 TAAGTTGTGTAAGTTAT
66 TAAGTTATGTAAGTTAT
5979489 GTATGCTATG
Statistics
Matches: 295, Mismatches: 35, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
85 7 0.02
86 1 0.00
87 120 0.41
88 48 0.16
89 14 0.05
90 15 0.05
91 17 0.06
92 1 0.00
93 22 0.07
94 21 0.07
95 12 0.04
96 17 0.06
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.46
Consensus pattern (89 bp):
ATGTATGTTATGTAAGTATGTAAGTTATGTATGTATTATGTAAGTTATGTAAGTTATGTATTATG
TAAGTTATGTAAGTTATCAAAGTA
Found at i:5979258 original size:19 final size:19
Alignment explanation
Indices: 5979234--5979272 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5979224 GTAATGTATG
5979234 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
5979253 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
5979272 T
1 T
5979273 GTATTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:5979471 original size:43 final size:43
Alignment explanation
Indices: 5979047--5979613 Score: 355
Period size: 43 Copynumber: 13.7 Consensus size: 43
5979037 ATTAAGTAAA
* *
5979047 TTATGTAAGTTATGTACGTGTA--TAAGTTATGTAAGTTAT-CA
1 TTATGTAAGTTATGTAAGT-TATGTAAGTTATGTAAGTTATGTA
* * **
5979088 --AAGTAAGCTATGTAAGTTGCGT-A-TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT-A
** * *
5979128 GTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTATTATGTA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAG---TTATGTA
*
5979173 TTATGTAAGTTATGTAAGTTATGT-A-TTATGTAGGTTATGTAA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT-A
** * *
5979215 TTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAG---T-TA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
*
5979253 TTATGT-A-TTATGTAAGTTATGT-A-TTATGTAGGTTATGTAA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT-A
* * *
5979293 GTTGTGTAAGATATTTAAGTTATGTAAGTT-TGT-A-TTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT-A
* * * *
5979335 GTTATGTAAGTTATGTATGTAATGTATGTTATGTAAGTTTTGTA
1 -TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* *
5979379 TTATGTGAG-TATTTAAGTTATGTAAGTTATAATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAG-T-T-ATGTAAGTTATGTA
* * *
5979424 TTATGTAGGTTATGTAAGTTATGTAAGTTATGTAATTTTTGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* * * *
5979467 TTATGTAAGTTGTGTAAGTTATGTATGCTATGTAAGTAATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* * *
5979510 TTATGTAAGTTTATATAAG---T-TAA--TACGTAAGTAATGTA
1 TTATGTAAG-TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
* ** * *
5979548 TTATGTAAGTTTATATAA-AAAT-T---TTATATAAGTCATGTA
1 TTATGTAAG-TTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
5979587 TTATGTAAGTTATGT-A-TTATGTAAGTT
1 TTATGTAAGTTATGTAAGTTATGTAAGTT
5979614 TACATGTAAG
Statistics
Matches: 413, Mismatches: 67, Indels: 92
0.72 0.12 0.16
Matches are distributed among these distances:
34 2 0.00
35 18 0.04
36 1 0.00
37 7 0.02
38 54 0.13
39 38 0.09
40 8 0.02
41 14 0.03
42 47 0.11
43 129 0.31
44 44 0.11
45 29 0.07
46 22 0.05
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTA
Found at i:5979591 original size:39 final size:37
Alignment explanation
Indices: 5979499--5979597 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 37
5979489 GTATGCTATG
5979499 TAAGTAATGTATTATGTAAGTTTATATAAGTTAATAC
1 TAAGTAATGTATTATGTAAGTTTATATAAGTTAATAC
* *
5979536 GTAAGTAATGTATTATGTAAGTTTATATAAAAATTTTATA-
1 -TAAGTAATGTATTATGTAAGTTTATAT---AAGTTAATAC
*
5979576 TAAGTCATGTATTATGTAAGTT
1 TAAGTAATGTATTATGTAAGTT
5979598 ATGTATTATG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
38 27 0.49
39 21 0.38
41 7 0.13
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.44
Consensus pattern (37 bp):
TAAGTAATGTATTATGTAAGTTTATATAAGTTAATAC
Found at i:5979646 original size:21 final size:20
Alignment explanation
Indices: 5979620--5979669 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
5979610 AGTTTACATG
5979620 TAAGTTTATGTG-ATAGTTATA
1 TAAGTTTATGTGAATA-TTA-A
5979641 TAAGTTTAT-TGAATATTAA
1 TAAGTTTATGTGAATATTAA
5979660 TAAG-TTATGT
1 TAAGTTTATGT
5979670 AAGTTCTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 5 0.19
21 12 0.44
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (20 bp):
TAAGTTTATGTGAATATTAA
Found at i:5979674 original size:9 final size:9
Alignment explanation
Indices: 5979042--5979646 Score: 374
Period size: 9 Copynumber: 67.8 Consensus size: 9
5979032 TATGTATTAA
*
5979042 GTAAATTAT
1 GTAAGTTAT
5979051 GTAAGTTAT
1 GTAAGTTAT
*
5979060 GTACGTGTA-
1 GTAAGT-TAT
5979069 -TAAGTTAT
1 GTAAGTTAT
5979077 GTAAGTTAT
1 GTAAGTTAT
*
5979086 CAAAGTAAGCTAT
1 ----GTAAGTTAT
**
5979099 GTAAGTTGC
1 GTAAGTTAT
5979108 GT-A-TTAT
1 GTAAGTTAT
5979115 GTAAGTTAT
1 GTAAGTTAT
5979124 GTAAGTTAT
1 GTAAGTTAT
** *
5979133 CAAAGTAAT
1 GTAAGTTAT
*
5979142 GTATGTTAT
1 GTAAGTTAT
5979151 GTAAG-T-T
1 GTAAGTTAT
5979158 GTAAGTTAT
1 GTAAGTTAT
*
5979167 -TATGTATTAT
1 GTAAG--TTAT
5979177 GTAAGTTAT
1 GTAAGTTAT
5979186 GTAAGTTAT
1 GTAAGTTAT
5979195 GT-A-TTAT
1 GTAAGTTAT
*
5979202 GTAGGTTAT
1 GTAAGTTAT
*
5979211 GTAATTTAT
1 GTAAGTTAT
** *
5979220 CAAAGTAAT
1 GTAAGTTAT
*
5979229 GTATGTTAT
1 GTAAGTTAT
5979238 GTAAG-T-T
1 GTAAGTTAT
5979245 GTAAGTTAT
1 GTAAGTTAT
*
5979254 -TATGTATTAT
1 GTAAG--TTAT
5979264 GTAAGTTAT
1 GTAAGTTAT
5979273 GT-A-TTAT
1 GTAAGTTAT
*
5979280 GTAGGTTAT
1 GTAAGTTAT
*
5979289 GTAAGTTGT
1 GTAAGTTAT
*
5979298 GTAAGATAT
1 GTAAGTTAT
*
5979307 TTAAGTTAT
1 GTAAGTTAT
5979316 GTAAGTT-T
1 GTAAGTTAT
5979324 GT-A-TTAT
1 GTAAGTTAT
5979331 GTAAGTTAT
1 GTAAGTTAT
5979340 GTAAGTTAT
1 GTAAGTTAT
* *
5979349 GTATGTAAT
1 GTAAGTTAT
*
5979358 GTATGTTAT
1 GTAAGTTAT
*
5979367 GTAAGTTTT
1 GTAAGTTAT
5979376 GT-A-TTAT
1 GTAAGTTAT
*
5979383 GTGAG-TAT
1 GTAAGTTAT
*
5979391 TTAAGTTAT
1 GTAAGTTAT
5979400 GTAAGTTATAAT
1 GTAAG-T-T-AT
5979412 GTAAGTTAT
1 GTAAGTTAT
5979421 GT-A-TTAT
1 GTAAGTTAT
*
5979428 GTAGGTTAT
1 GTAAGTTAT
5979437 GTAAGTTAT
1 GTAAGTTAT
5979446 GTAAGTTAT
1 GTAAGTTAT
* *
5979455 GTAATTTTT
1 GTAAGTTAT
5979464 GT-A-TTAT
1 GTAAGTTAT
*
5979471 GTAAGTTGT
1 GTAAGTTAT
5979480 GTAAGTTAT
1 GTAAGTTAT
* *
5979489 GTATGCTAT
1 GTAAGTTAT
*
5979498 GTAAGTAAT
1 GTAAGTTAT
5979507 GT-A-TTAT
1 GTAAGTTAT
5979514 GTAAGTTTAT
1 GTAAG-TTAT
*
5979524 ATAAGTTAAT
1 GTAAGTT-AT
*
5979534 ACGTAAGTAAT
1 --GTAAGTTAT
5979545 GT-A-TTAT
1 GTAAGTTAT
5979552 GTAAGTTTAT
1 GTAAG-TTAT
* *
5979562 ATAAAAATTTTAT
1 GT---AA-GTTAT
* *
5979575 ATAAGTCAT
1 GTAAGTTAT
5979584 GT-A-TTAT
1 GTAAGTTAT
5979591 GTAAGTTAT
1 GTAAGTTAT
5979600 GT-A-TTAT
1 GTAAGTTAT
5979607 GTAAGTTTACAT
1 GTAAG-TT--AT
5979619 GTAAGTTTAT
1 GTAAG-TTAT
5979629 GTGATAGTTAT
1 GT-A-AGTTAT
*
5979640 ATAAGTT
1 GTAAGTT
5979647 TATTGAATAT
Statistics
Matches: 464, Mismatches: 74, Indels: 116
0.71 0.11 0.18
Matches are distributed among these distances:
6 2 0.00
7 71 0.15
8 41 0.09
9 258 0.56
10 36 0.08
11 16 0.03
12 24 0.05
13 16 0.03
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:5981473 original size:53 final size:53
Alignment explanation
Indices: 5981391--5981497 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
5981381 AATAAATGTT
* * *
5981391 AAACATTTTTGTGGCGTTTTAAGCAAAGCGCCACAAACTATAAGTCAAAACGC
1 AAACATTTTTGCGGCGTTTCAAACAAAGCGCCACAAACTATAAGTCAAAACGC
* *
5981444 AAACATTTTTGCGGCGTTTCAAACGAAGCGCCACTAACTATAAGTCAAAACGC
1 AAACATTTTTGCGGCGTTTCAAACAAAGCGCCACAAACTATAAGTCAAAACGC
5981497 A
1 A
5981498 GTCGCTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.23
Consensus pattern (53 bp):
AAACATTTTTGCGGCGTTTCAAACAAAGCGCCACAAACTATAAGTCAAAACGC
Found at i:5982208 original size:7 final size:7
Alignment explanation
Indices: 5982198--5982222 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5982188 TATAAATTCT
5982198 AAACCCC
1 AAACCCC
5982205 AAACCCC
1 AAACCCC
5982212 AAACCCC
1 AAACCCC
5982219 AAAC
1 AAAC
5982223 ATTAAAAGTC
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:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACCCC
Found at i:5983198 original size:18 final size:18
Alignment explanation
Indices: 5983175--5983210 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5983165 ATTGAATTTT
5983175 AATT-AATATAAATAAACA
1 AATTAAATATAAA-AAACA
5983193 AATTAAATATAAAAAACA
1 AATTAAATATAAAAAACA
5983211 TATAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AATTAAATATAAAAAACA
Found at i:5983218 original size:18 final size:19
Alignment explanation
Indices: 5983179--5983218 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5983169 AATTTTAATT
*
5983179 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
5983198 AATATAAA-AAACATATAA
1 AATATAAATAAACAAATAA
5983216 AAT
1 AAT
5983219 GATTTTGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:5983966 original size:114 final size:113
Alignment explanation
Indices: 5983317--5983951 Score: 565
Period size: 113 Copynumber: 5.6 Consensus size: 113
5983307 TCGGGAAAAG
* * * ** * *
5983317 CGCCGCTAATACTATGCTTTAGCGGCATTTTCCCGTGTGCGCCACTAATTCCAGTATACATCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCAAG
* * * * * * * *
5983382 AACTAAACGCTGTGTTTTCGTTAATATCTTTTGGCGGCACTTACCA-AAAA
65 -ACCAAACTCTGCGTTTTGGTTAAGATCTTTT-GCAGCGCTTACCACTAAA
* ** * *
5983432 GCGCCGC-AA-GC---A--TTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACCTCAA
1 -CGCCGCTAATACTATACTTTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATCAA
* * *
5983490 GGCCAAACTCTGCGTTTTGGTTAAGATAC-TTTGCGGCGCTTTCCAC-AAA
64 GACCAAACTCTGCGTTTTGGTTAAGAT-CTTTTGCAGCGCTTACCACTAAA
* *
5983539 CGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATCAAG
* * *
5983604 ATCAAACTCTGCGTTTTGGTTAAGATATTTTG-AGGCGCTTACCACCAAA
65 ACCAAACTCTGCGTTTTGGTTAAGATCTTTTGCA-GCGCTTACCACTAAA
* * * * * * *
5983653 CGCTGCTATTACTATGCTTTAGCGGCGTTTTCCTTAAACGCCACTAATTATAGTATACATCAAGA
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
* * * * * * * *
5983718 CCAAAACGCTGCGTTTTGGTTAAGATGTTTTGCGGCGTTTAACGCTCAG
66 CC-AAACTCTGCGTTTTGGTTAAGATCTTTTGCAGCGCTTACCACTAAA
* * * *
5983767 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTACAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACTTTAGCGGCGTTTTC--CATAAGCGCCACTAATTCTAATATACATCAA
* * * * *
5983832 GATCAAACTCTGCGTTTTGGTTAACATCTTTTGCAACGCTT-CCGCTAAG
64 GACCAAACTCTGCGTTTTGGTTAAGATCTTTTGCAGCGCTTACCACTAAA
* * * * *
5983881 CTCCGCTAATACTATGCGTTAGCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAG
1 CGCCGCTAATACTATACTTTAGCGGCGTTT-TCCATAAGCGCCACTAATTCTAATATACATCAAG
5983946 ACCAAA
65 ACCAAA
5983952 ACGCTACGTG
Statistics
Matches: 424, Mismatches: 77, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
106 6 0.01
107 15 0.04
108 24 0.06
109 37 0.09
111 1 0.00
113 142 0.33
114 131 0.31
115 34 0.08
116 34 0.08
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (113 bp):
CGCCGCTAATACTATACTTTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCAAGA
CCAAACTCTGCGTTTTGGTTAAGATCTTTTGCAGCGCTTACCACTAAA
Found at i:5983979 original size:114 final size:112
Alignment explanation
Indices: 5983314--5983966 Score: 543
Period size: 114 Copynumber: 5.8 Consensus size: 112
5983304 GTTTCGGGAA
* * * ** * *
5983314 AAGCGCCGCTAATACTATGCTTTAGCGGCATTTTCCCGTGTGCGCCACTAATTCCAGTATACATC
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATC
* * * * * * ***
5983379 AAGAACTAAACGCTGTGTTTTCGTTAATATCTTTTGGCGGCACTTACCAAA
65 AAG-ACCAAACGCTGCGTTTTGGTTAAGAT-TTTT-GCAGCGCTTACCGCT
* ** * *
5983430 AAGCGCCGC-AA-GC---A--TTAGCGGCGTTTTGAAATAAGCGCCACTAACTCTAATATACCTC
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTT-CCATAAGCGCCACTAATTCTAATATACATC
* * * * * *
5983488 AAGGCCAAACTCTGCGTTTTGGTTAAGATACTTTGCGGCGCTTTCCAC-
65 AAGACCAAACGCTGCGTTTTGGTTAAGAT-TTTTGCAGCGCTTACCGCT
* * *
5983536 AAACGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTC
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTCC-ATAAGCGCCACTAATTCTAATATACATC
* * * *
5983601 AAGATCAAACTCTGCGTTTTGGTTAAGATATTTTG-AGGCGCTTACCACC
65 AAGACCAAACGCTGCGTTTTGGTTAAGAT-TTTTGCA-GCGCTTACCGCT
* * * * * * * *
5983650 AAACGCTGCTATTACTATGCTTTAGCGGCGTTTTCCTTAAACGCCACTAATTATAGTATACATCA
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCA
* * *
5983715 AGACCAAAACGCTGCGTTTTGGTTAAGATGTTTTGCGGCGTTTAACGCT
66 AGACC-AAACGCTGCGTTTTGGTTAAGAT-TTTTGCAGCGCTTACCGCT
* * * * *
5983764 CAGCGCCGCTAATACTATACATTAGCGGCGTTTTCTTTACAAGCGCCACTAATTGTAATATACAT
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTC--CATAAGCGCCACTAATTCTAATATACAT
* * * *
5983829 CAAGATCAAACTCTGCGTTTTGGTTAACATCTTTTGCAACGCTT-CCGCT
64 CAAGACCAAACGCTGCGTTTTGGTTAAGAT-TTTTGCAGCGCTTACCGCT
* * * * *
5983878 AAGCTCCGCTAATACTATGCGTTAGCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATC
1 AAGCGCCGCTAATACTATACTTTAGCGGCGTTT-TCCATAAGCGCCACTAATTCTAATATACATC
* *
5983943 AAGACCAAAACGCTACGTGTTGGT
65 AAGACC-AAACGCTGCGTTTTGGT
5983967 CTTGAGATTT
Statistics
Matches: 437, Mismatches: 84, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
106 8 0.02
107 12 0.03
108 24 0.05
109 36 0.08
111 1 0.00
113 140 0.32
114 145 0.33
115 34 0.08
116 37 0.08
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (112 bp):
AAGCGCCGCTAATACTATACTTTAGCGGCGTTTTCCATAAGCGCCACTAATTCTAATATACATCA
AGACCAAACGCTGCGTTTTGGTTAAGATTTTTGCAGCGCTTACCGCT
Found at i:5983980 original size:229 final size:227
Alignment explanation
Indices: 5983539--5983983 Score: 590
Period size: 229 Copynumber: 1.9 Consensus size: 227
5983529 TTTCCACAAA
* * * *
5983539 CGCCGCTACTACTATACTTTAGCGGCGTTTTCCAATAAGCGCCACTAATTCTAATATACCTCAAG
1 CGCCGCTAATACTATACATTAGCGGCGTTTTCCAACAAGCGCCACTAATTCTAATATACATCAAG
* * * *
5983604 ATCAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACCAAACGCTGCTATTACTATG
66 ATCAAACTCTGCGTTTTGGTTAACATATTTTGAGACGCTTACCACCAAACGCCGCTAATACTATG
* * * * *
5983669 CTTTAGCGGCGTTTTCCTTAAACGCCACTAATTATAGTATACATCAAGACCAAAACGCTGCGTTT
131 CGTTAGCGGCGTTTTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTACGTGT
5983734 TGGTTAAGATGTTTTGCGGCGTTTAACGCTCAG
196 TGGTTAAGA-GTTTTGCGGCGTTTAACGCTCAG
** *
5983767 CGCCGCTAATACTATACATTAGCGGCGTTTTCTTTACAAGCGCCACTAATTGTAATATACATCAA
1 CGCCGCTAATACTATACATTAGCGGCGTTTTC-CAACAAGCGCCACTAATTCTAATATACATCAA
* * * * *
5983832 GATCAAACTCTGCGTTTTGGTTAACATCTTTTGCA-ACGCTT-CCGCTAAGCTCCGCTAATACTA
65 GATCAAACTCTGCGTTTTGGTTAACATATTTTG-AGACGCTTACCACCAAACGCCGCTAATACTA
* * *
5983895 TGCGTTAGCGGCGTTTGTTCGTAAGCGCCACTAATTCTAATATACATCAAGACCAAAACGCTACG
129 TGCGTTAGCGGCGTTT-TCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTACG
*
5983960 TGTTGGTCT-TGAGATTTTGCGGCG
193 TGTTGGT-TAAGAG-TTTTGCGGCG
5983984 CTGTGTGGTA
Statistics
Matches: 187, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
228 62 0.33
229 123 0.66
230 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (227 bp):
CGCCGCTAATACTATACATTAGCGGCGTTTTCCAACAAGCGCCACTAATTCTAATATACATCAAG
ATCAAACTCTGCGTTTTGGTTAACATATTTTGAGACGCTTACCACCAAACGCCGCTAATACTATG
CGTTAGCGGCGTTTTCCGTAAACGCCACTAATTATAATATACATCAAGACCAAAACGCTACGTGT
TGGTTAAGAGTTTTGCGGCGTTTAACGCTCAG
Found at i:5994721 original size:2 final size:2
Alignment explanation
Indices: 5994714--5994741 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5994704 TGAAATCTTC
5994714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5994742 GATAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6000823 original size:16 final size:18
Alignment explanation
Indices: 6000802--6000844 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
6000792 CTTCAATAAG
6000802 ATATTTTTA-TATAATA-
1 ATATTTTTATTATAATAT
*
6000818 ATATTTTTATTTTAATAT
1 ATATTTTTATTATAATAT
6000836 ATATTTTTA
1 ATATTTTTA
6000845 AAATATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 6 0.25
18 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTTTTATTATAATAT
Found at i:6003128 original size:22 final size:22
Alignment explanation
Indices: 6003103--6003149 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
6003093 AAATGACAGT
*
6003103 AAAACAATAGGAAAACAACAAC
1 AAAACAATAGAAAAACAACAAC
* * *
6003125 AAAACAGTAGAAAAATAACAGC
1 AAAACAATAGAAAAACAACAAC
6003147 AAA
1 AAA
6003150 TTAATAGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.68, C:0.15, G:0.11, T:0.06
Consensus pattern (22 bp):
AAAACAATAGAAAAACAACAAC
Found at i:6007547 original size:37 final size:37
Alignment explanation
Indices: 6007506--6007579 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
6007496 TTGAGTTGGA
6007506 AATTTCACCATATTCACAATGTAGTTGACAATGTGTT
1 AATTTCACCATATTCACAATGTAGTTGACAATGTGTT
6007543 AATTTCACCATATTCACAATGTAGTTGACAATGTGTT
1 AATTTCACCATATTCACAATGTAGTTGACAATGTGTT
6007580 CTATCATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (37 bp):
AATTTCACCATATTCACAATGTAGTTGACAATGTGTT
Found at i:6008065 original size:76 final size:77
Alignment explanation
Indices: 6007959--6008113 Score: 303
Period size: 76 Copynumber: 2.0 Consensus size: 77
6007949 CGGCGGAATA
6007959 ATTATTCTCTAAACTTAATTTAATAAATAATAAATTATATAATTAAATAATTAAATAAAAATAAA
1 ATTATTCTCTAAACTTAATTTAATAAATAATAAATTATATAATTAAATAATTAAATAAAAATAAA
6008024 ATTTTCATATAT
66 ATTTTCATATAT
6008036 ATTATTCTCT-AACTTAATTTAATAAATAATAAATTATATAATTAAATAATTAAATAAAAATAAA
1 ATTATTCTCTAAACTTAATTTAATAAATAATAAATTATATAATTAAATAATTAAATAAAAATAAA
6008100 ATTTTCATATAT
66 ATTTTCATATAT
6008112 AT
1 AT
6008114 ATATAGATCA
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 68 0.87
77 10 0.13
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (77 bp):
ATTATTCTCTAAACTTAATTTAATAAATAATAAATTATATAATTAAATAATTAAATAAAAATAAA
ATTTTCATATAT
Found at i:6012622 original size:27 final size:27
Alignment explanation
Indices: 6012592--6012644 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
6012582 TCAGTCTATT
6012592 AGAATATCAGATTTCATGCATTAGGGC
1 AGAATATCAGATTTCATGCATTAGGGC
6012619 AGAATATCAGATTTCATGCATTAGGG
1 AGAATATCAGATTTCATGCATTAGGG
6012645 TTTGGTTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (27 bp):
AGAATATCAGATTTCATGCATTAGGGC
Found at i:6026070 original size:25 final size:25
Alignment explanation
Indices: 6025999--6026078 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
6025989 TACCCATTAT
*
6025999 TGGCTCACATAAGCTTCCCGATT--A
1 TGGCTCACATGAGCTTCCCG-TTACA
* **
6026023 TGACTCTTATGAGCTTCCCGTTACA
1 TGGCTCACATGAGCTTCCCGTTACA
* * *
6026048 TGGCTCACATGAGCTTTCTGTTATA
1 TGGCTCACATGAGCTTCCCGTTACA
6026073 TGGCTC
1 TGGCTC
6026079 GAGAGACGGT
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
23 2 0.05
24 16 0.36
25 26 0.59
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCGTTACA
Found at i:6029375 original size:22 final size:22
Alignment explanation
Indices: 6029346--6029401 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
6029336 TGCACTAATG
**
6029346 AACAGAGAGCATTGAAGTGCTA
1 AACAGAGAGCACAGAAGTGCTA
* *
6029368 TACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGAAGTGCTA
6029390 AACAGAGAGCAC
1 AACAGAGAGCAC
6029402 TGGCGTGCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.18, G:0.27, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACAGAAGTGCTA
Found at i:6029474 original size:25 final size:25
Alignment explanation
Indices: 6029340--6029470 Score: 123
Period size: 25 Copynumber: 5.5 Consensus size: 25
6029330 TTGTTATGCA
* *
6029340 CTAATGAA-CAGAGAGCATTGAAGTG
1 CTAAT-AATCAGAGAGCACTGACGTG
* *
6029365 CT-AT-A-CAGAGAGCACAGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
*
6029387 CT-A-AA-CAGAGAGCACTGGCGTG
1 CTAATAATCAGAGAGCACTGACGTG
* *
6029409 CTAGTAATCAGAGAGCACTGACATG
1 CTAATAATCAGAGAGCACTGACGTG
* *
6029434 CTAATAATCAGATAGCACTGATGTG
1 CTAATAATCAGAGAGCACTGACGTG
6029459 CTAATAATCAGA
1 CTAATAATCAGA
6029471 TAGCGCACTA
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
22 35 0.39
24 4 0.04
25 50 0.56
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTGACGTG
Found at i:6030354 original size:13 final size:13
Alignment explanation
Indices: 6030336--6030375 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
6030326 TTAATTTTCC
6030336 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
6030349 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
* *
6030362 C-CTTCTTTCCTT
1 CTTTTCTTTCTTT
6030374 CT
1 CT
6030376 CTGTTTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:6030516 original size:23 final size:23
Alignment explanation
Indices: 6030486--6030532 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
6030476 AATAAGTATG
6030486 TACATATATTAATTACAAATGTA
1 TACATATATTAATTACAAATGTA
* *
6030509 TACATATATTTATTACACATGTA
1 TACATATATTAATTACAAATGTA
6030532 T
1 T
6030533 TTATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TACATATATTAATTACAAATGTA
Found at i:6033660 original size:31 final size:31
Alignment explanation
Indices: 6033616--6033686 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
6033606 AATGTTAATG
*
6033616 AGTGACTAATTTG-TAACTTTTTGATAACGTT-
1 AGTGACTGATTTGTTAACTTTTTGA-AA-GTTA
* **
6033647 AGTGACTGTTTTGTTATTTTTTTGAAAGTTA
1 AGTGACTGATTTGTTAACTTTTTGAAAGTTA
6033678 AGTGACTGA
1 AGTGACTGA
6033687 ATTAAAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 3 0.09
31 21 0.64
32 9 0.27
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (31 bp):
AGTGACTGATTTGTTAACTTTTTGAAAGTTA
Found at i:6034336 original size:39 final size:38
Alignment explanation
Indices: 6034253--6034338 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
6034243 CGCATAAGTG
*
6034253 TATT-TTATTATAAAACTTAAAGTTAAAATATATAATA
1 TATTATTATAATAAAACTTAAAGTTAAAATATATAATA
* * *
6034290 TAATATTATAATAAAACTTAAATGTT-AAGTGTATATATA
1 TATTATTATAATAAAACTTAAA-GTTAAAATATATA-ATA
6034329 TATTATTATA
1 TATTATTATA
6034339 TTATATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.07
38 23 0.56
39 15 0.37
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (38 bp):
TATTATTATAATAAAACTTAAAGTTAAAATATATAATA
Found at i:6034432 original size:25 final size:23
Alignment explanation
Indices: 6034365--6034440 Score: 71
Period size: 25 Copynumber: 3.1 Consensus size: 23
6034355 AGTAAAAGAA
*
6034365 AAAGAAATAGAAAAAGAAGGAGAG
1 AAAGAAATA-AAAAAGAAGGAAAG
* *
6034389 AAAGAAACGAAATATAGAAGGAAAG
1 AAAGAAA-TAAA-AAAGAAGGAAAG
*
6034414 AAAGGAAATAAAAAGAGAAAGAAAG
1 AAA-GAAATAAAAA-AGAAGGAAAG
6034439 AA
1 AA
6034441 GGAGAAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
24 10 0.24
25 28 0.67
26 4 0.10
ACGTcount: A:0.68, C:0.01, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAGAAATAAAAAAGAAGGAAAG
Found at i:6034438 original size:21 final size:22
Alignment explanation
Indices: 6034385--6034438 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
6034375 AAAAAGAAGG
* *
6034385 AGAGAAAGAAACGAAATATAGA
1 AGAGAAAGAAAGGAAATATAAA
6034407 AG-GAAAGAAAGGAAATA-AAA
1 AGAGAAAGAAAGGAAATATAAA
6034427 AGAGAAAGAAAG
1 AGAGAAAGAAAG
6034439 AAGGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 23 0.79
22 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.06
Consensus pattern (22 bp):
AGAGAAAGAAAGGAAATATAAA
Found at i:6035640 original size:21 final size:22
Alignment explanation
Indices: 6035615--6035657 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6035605 AGCTATTTGT
*
6035615 ATAGCAAGT-ATGAGATTTGAA
1 ATAGCAAGTGATGAGAATTGAA
6035636 ATAGCAAGTGATGAGAATTGAA
1 ATAGCAAGTGATGAGAATTGAA
6035658 TATGTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26
Consensus pattern (22 bp):
ATAGCAAGTGATGAGAATTGAA
Found at i:6043908 original size:7 final size:7
Alignment explanation
Indices: 6043896--6043921 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6043886 TCGATTATTG
6043896 GGGCAAT
1 GGGCAAT
6043903 GGGCAAT
1 GGGCAAT
6043910 GGGCAAT
1 GGGCAAT
6043917 GGGCA
1 GGGCA
6043922 GTTTATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.46, T:0.12
Consensus pattern (7 bp):
GGGCAAT
Found at i:6057016 original size:5 final size:5
Alignment explanation
Indices: 6057006--6057030 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6056996 TTTATTGGTG
6057006 AGTGA AGTGA AGTGA AGTGA AGTGA
1 AGTGA AGTGA AGTGA AGTGA AGTGA
6057031 GGAAGCTTTG
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:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (5 bp):
AGTGA
Found at i:6069185 original size:19 final size:19
Alignment explanation
Indices: 6069161--6069198 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6069151 GCAACTAAAA
6069161 ATTTCAAAGCTTAACATGT
1 ATTTCAAAGCTTAACATGT
6069180 ATTTCAAAGCTTAACATGT
1 ATTTCAAAGCTTAACATGT
6069199 TTACATTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
ATTTCAAAGCTTAACATGT
Found at i:6072537 original size:27 final size:27
Alignment explanation
Indices: 6072506--6072562 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
6072496 TTATAATTTG
*
6072506 GACAGCATCAATGCATGTTTTAATTCA
1 GACAGCATCAATGCATGTTTTAAGTCA
6072533 GACAGCATCAATGCATGTTTTAAGTCA
1 GACAGCATCAATGCATGTTTTAAGTCA
6072560 GAC
1 GAC
6072563 CTATTAACTA
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:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (27 bp):
GACAGCATCAATGCATGTTTTAAGTCA
Found at i:6081025 original size:19 final size:18
Alignment explanation
Indices: 6080988--6081022 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6080978 AAATTTTGGA
*
6080988 ATTTTTATAAATAATTTG
1 ATTTTTAAAAATAATTTG
*
6081006 ATTTTTAAAAATCATTT
1 ATTTTTAAAAATAATTT
6081023 TGAAAATTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTTAAAAATAATTTG
Found at i:6087373 original size:26 final size:28
Alignment explanation
Indices: 6087344--6087403 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
6087334 AATATATGAT
6087344 ATATATATTAT-TGTATA-TT-CAAGTTA
1 ATATATATTATGT-TATATTTACAAGTTA
6087370 ATATATATTATGTTATATTTACAAGTTA
1 ATATATATTATGTTATATTTACAAGTTA
6087398 ATATAT
1 ATATAT
6087404 TAAATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.48
27 3 0.10
28 13 0.42
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (28 bp):
ATATATATTATGTTATATTTACAAGTTA
Found at i:6087645 original size:16 final size:16
Alignment explanation
Indices: 6087624--6087654 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6087614 TTAAATAAAT
6087624 ATATATACAAAAATTA
1 ATATATACAAAAATTA
*
6087640 ATATATAGAAAAATT
1 ATATATACAAAAATT
6087655 CCGTGTGTTG
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:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATATACAAAAATTA
Found at i:6090904 original size:14 final size:14
Alignment explanation
Indices: 6090887--6090914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6090877 TTGAAAACTT
6090887 CTTATTGTATACTC
1 CTTATTGTATACTC
6090901 CTTATTGTATACTC
1 CTTATTGTATACTC
6090915 TTTACGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
CTTATTGTATACTC
Found at i:6093101 original size:113 final size:113
Alignment explanation
Indices: 6092975--6093214 Score: 453
Period size: 113 Copynumber: 2.1 Consensus size: 113
6092965 ACCTCGGGAA
6092975 CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
1 CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
* *
6093040 ATAATGGCTTTTTTATATTGCGCCGCTACTGCCACTATTCGTGAAGGT
66 ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
*
6093088 CAAACGATGCGTTTTGGCTAACATTTTTTGCGGCGCTTACAAATAAACGCCGCTAATTGTGCTAT
1 CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
6093153 ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
66 ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
6093201 CAAACGATGCGTTT
1 CAAACGATGCGTTT
6093215 AGTCAGTTTT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 124 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (113 bp):
CAAACGATGCGTTTTGGCTAACATTTTTTGCGACGCTTACAAATAAACGCCGCTAATTGTGCTAT
ATAATGGCGTTTTTATATTACGCCGCTACTGCCACTATTCGTGAAGGT
Found at i:6094353 original size:23 final size:23
Alignment explanation
Indices: 6094317--6094361 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6094307 AATCATTTCA
*
6094317 TATACTATTGTCAATTCATAATAT
1 TATACCATTGTCAATTCA-AATAT
6094341 TATACCATT-TCAATTCAAATA
1 TATACCATTGTCAATTCAAATA
6094362 ATACATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (23 bp):
TATACCATTGTCAATTCAAATAT
Found at i:6095015 original size:38 final size:38
Alignment explanation
Indices: 6095000--6095212 Score: 417
Period size: 38 Copynumber: 5.6 Consensus size: 38
6094990 AGATTATGTT
6095000 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
6095038 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
6095076 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
6095114 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
6095152 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCATATCATATCTAAGATTACA
*
6095190 TATGATATCTAAGATTGCATATC
1 TATCATATCTAAGATTGCATATC
6095213 CTTGAAGATT
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 174 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (38 bp):
TATCATATCTAAGATTGCATATCATATCTAAGATTACA
Found at i:6095022 original size:19 final size:19
Alignment explanation
Indices: 6095000--6095212 Score: 372
Period size: 19 Copynumber: 11.2 Consensus size: 19
6094990 AGATTATGTT
6095000 TATCATATCTAAGATTGCA
1 TATCATATCTAAGATTGCA
*
6095019 TATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCA
6095038 TATCATATCTAAGATTGCA
1 TATCATATCTAAGATTGCA
*
6095057 TATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCA
6095076 TATCATATCTAAGATTGCA
1 TATCATATCTAAGATTGCA
*
6095095 TATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCA
6095114 TATCATATCTAAGATTGCA
1 TATCATATCTAAGATTGCA
*
6095133 TATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCA
6095152 TATCATATCTAAGATTGCA
1 TATCATATCTAAGATTGCA
*
6095171 TATCATATCTAAGATTACA
1 TATCATATCTAAGATTGCA
*
6095190 TATGATATCTAAGATTGCA
1 TATCATATCTAAGATTGCA
6095209 TATC
1 TATC
6095213 CTTGAAGATT
Statistics
Matches: 182, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 182 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.37
Consensus pattern (19 bp):
TATCATATCTAAGATTGCA
Found at i:6095040 original size:57 final size:59
Alignment explanation
Indices: 6094946--6095212 Score: 352
Period size: 57 Copynumber: 4.6 Consensus size: 59
6094936 AAATTAAATC
* * * **
6094946 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCCT-T-GAAGATTATGTTTATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATATCTAAGATTATGCATATCATA
* *
6095007 TCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGA-T-TGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTATGCATATCATA
6095064 TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTA--CATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTATGCATATCATA
* *
6095121 TCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGA-T-TGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTATGCATATCATA
*
6095178 TCTAAGATTACATATGATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
6095213 CTTGAAGATT
Statistics
Matches: 186, Mismatches: 14, Indels: 16
0.86 0.06 0.07
Matches are distributed among these distances:
56 1 0.01
57 161 0.87
58 3 0.02
59 4 0.02
60 7 0.04
61 10 0.05
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (59 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGATTATGCATATCATA
Found at i:6105776 original size:34 final size:35
Alignment explanation
Indices: 6105733--6105809 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
6105723 TTACTGGTGT
* * *
6105733 CAGGTGTCAAG-TTGAGAGGATAGATATCTTGTTA
1 CAGGTGTCAAGTTTAAGAGGATAGATATATTATTA
*
6105767 CAGGTGTCAAGTTTTAAGGGGATAGATATATTATTA
1 CAGGTGTCAAG-TTTAAGAGGATAGATATATTATTA
6105803 CAGGTGT
1 CAGGTGT
6105810 AGGCGTATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 11 0.30
36 26 0.70
ACGTcount: A:0.30, C:0.08, G:0.29, T:0.34
Consensus pattern (35 bp):
CAGGTGTCAAGTTTAAGAGGATAGATATATTATTA
Found at i:6111234 original size:31 final size:31
Alignment explanation
Indices: 6111191--6111263 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
6111181 AACTTAACTG
*
6111191 AATTACTATTAATTGAATTAACTAAAATTTTT
1 AATT-CTATTAATCGAATTAACTAAAATTTTT
* *
6111223 AATTCTATTAATCGAATTAACTGAATTTTTT
1 AATTCTATTAATCGAATTAACTAAAATTTTT
6111254 AATTCT-TTAA
1 AATTCTATTAA
6111264 CAGTTAATCG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 4 0.11
31 30 0.79
32 4 0.11
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (31 bp):
AATTCTATTAATCGAATTAACTAAAATTTTT
Found at i:6111908 original size:4 final size:4
Alignment explanation
Indices: 6111899--6111944 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
6111889 CCATCAATAA
6111899 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC
6111945 TGTAGTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:6118084 original size:17 final size:17
Alignment explanation
Indices: 6118059--6118099 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
6118049 ATTATGTAGT
*
6118059 AATACTTTTATTTTAAA
1 AATACTTTTATTTCAAA
*
6118076 AATATTTTTATTTCAAA
1 AATACTTTTATTTCAAA
6118093 AATACTT
1 AATACTT
6118100 CTGAAAAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (17 bp):
AATACTTTTATTTCAAA
Found at i:6123725 original size:22 final size:21
Alignment explanation
Indices: 6123700--6123743 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
6123690 AAGCATATGA
*
6123700 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
6123722 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
6123743 A
1 A
6123744 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:6126518 original size:20 final size:21
Alignment explanation
Indices: 6126484--6126522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6126474 TACAAAACTT
6126484 CTCAATTTCAGTTCTAAATAA
1 CTCAATTTCAGTTCTAAATAA
*
6126505 CTCATTTTCA-TTCTAAAT
1 CTCAATTTCAGTTCTAAAT
6126523 GTTTGCTTCA
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:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (21 bp):
CTCAATTTCAGTTCTAAATAA
Found at i:6132261 original size:134 final size:130
Alignment explanation
Indices: 6131948--6132340 Score: 439
Period size: 133 Copynumber: 3.0 Consensus size: 130
6131938 ACCAAAAGGG
6131948 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGTGGATCCTTCATTGTTCTTAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGT-GATCCTTCATTGTT-TTAACAG
** ** * * *
6132013 CTAAAGCTTGATGTTTCTTAGACTGTTTCATGTATTTCTTTCAT-TTTTTATCCTCCCAGCCTGA
64 CTAAAGCTCAATAATGCTTAGA-TGTTTCATGTACTTCTTTCATGTTTTTA-CCTCCCAGCCTAA
*
6132077 GGAA
127 AGAA
* * *
6132081 AATTTTTTGATGCACTTAGGCGGGAACTTGAGTGAGTCTTGTTGATCCTTCATTGATTTCAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTG-TGATCCTTCATTG-TTTTAACAG
* * * * *
6132146 CTGAAGCTCAAAAATGCTTAGATGGTTTCGTGTCCTTCTTTCATGTTCTTACCTTCCCAGCCTAA
64 CTAAAGCTCAATAATGCTTAGAT-GTTTCATGTACTTCTTTCATGTTTTTACC-TCCCAGCCTAA
6132211 AGAA
127 AGAA
* * * **
6132215 AATTGTTTGATGCACTTAAGCAGGAACTTGAGTGACTGTTGCTGAT-CTTTGTTGTTTTTAACAG
1 AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTG-TGATCCTTCATTG-TTTTAACAG
* * * * *
6132279 CTAAAGTTCAATAATGCTTTAGATATTTCATGTGCTTCTTTCATGTTTTTACGTCCCGGCCT
64 CTAAAGCTCAATAATGC-TTAGATGTTTCATGTACTTCTTTCATGTTTTTACCTCCCAGCCT
6132341 GTAGTTTATC
Statistics
Matches: 219, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
132 9 0.04
133 143 0.65
134 67 0.31
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (130 bp):
AATTGTTTGATGCACTTAGGCAGGAACTTGAGTGAGTCTTGTGATCCTTCATTGTTTTAACAGCT
AAAGCTCAATAATGCTTAGATGTTTCATGTACTTCTTTCATGTTTTTACCTCCCAGCCTAAAGAA
Found at i:6133798 original size:20 final size:20
Alignment explanation
Indices: 6133769--6133808 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6133759 ATTTTTATAG
* *
6133769 AATAATATAATATTAAAATA
1 AATAAAATAAAATTAAAATA
*
6133789 AATAAAATAAAATTGAAATA
1 AATAAAATAAAATTAAAATA
6133809 TTTTTCATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
AATAAAATAAAATTAAAATA
Found at i:6136844 original size:6 final size:6
Alignment explanation
Indices: 6136830--6136886 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
6136820 CATCGGTGGT
* * * * * *
6136830 TGCTCC TGCTGC TGCTGT TCCTGC TGCTGC TGCTCC TGCTCC TGCTCC
1 TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC TGCTGC
*
6136878 TGTTGC TGC
1 TGCTGC TGC
6136887 ATAAAGGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.00, C:0.39, G:0.25, T:0.37
Consensus pattern (6 bp):
TGCTGC
Done.