Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007981.1 Hibiscus syriacus cultivar Beakdansim tig00110422_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1405786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:847006 original size:19 final size:19
Alignment explanation
Indices: 846982--847061 Score: 107
Period size: 19 Copynumber: 4.5 Consensus size: 19
846972 AAAAAGTACT
*
846982 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
847001 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
847020 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
847034 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
847053 ATCGCAACG
1 ATCGCAACG
847062 AGAGAATCGC
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 37 0.70
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:847038 original size:14 final size:14
Alignment explanation
Indices: 847019--847075 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
847009 GCGAAATGAA
847019 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
847033 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
847052 AATCGCAACGAGAG
1 AATCGCAACGAGAG
847066 AATCGCAACG
1 AATCGCAACG
847076 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:847042 original size:33 final size:33
Alignment explanation
Indices: 847000--847090 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
846990 GCGAAATGAA
847000 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
847033 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
847066 AATCGCAACGCGAAATTAAATTCGC
1 AATCGCAACGCGAAATGAAAATCGC
847091 TTTGCGATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:847108 original size:19 final size:19
Alignment explanation
Indices: 847086--847180 Score: 84
Period size: 19 Copynumber: 5.5 Consensus size: 19
847076 CGAAATTAAA
*
847086 TTCGCTTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
847105 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
847121 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
847138 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
847154 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
847171 TTCGCATTGC
1 TTCGCATTGC
847181 AATAATAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 12 0.20
16 13 0.22
17 13 0.22
19 21 0.36
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:847134 original size:33 final size:33
Alignment explanation
Indices: 847092--847180 Score: 169
Period size: 33 Copynumber: 2.7 Consensus size: 33
847082 TAAATTCGCT
847092 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
*
847125 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
847158 TTGCGATTTTCATTTCGCATTGC
1 TTGCGATTTTCATTTCGCATTGC
847181 AATAATAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCG
Found at i:849493 original size:12 final size:12
Alignment explanation
Indices: 849476--849500 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
849466 TCTTCGGGGA
849476 CTTTTTCTTCTT
1 CTTTTTCTTCTT
849488 CTTTTTCTTCTT
1 CTTTTTCTTCTT
849500 C
1 C
849501 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:849709 original size:24 final size:24
Alignment explanation
Indices: 849675--849728 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
849665 CTGAAACATC
*
849675 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
849699 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
849723 ATCAAA
1 ATCAAA
849729 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:850538 original size:20 final size:21
Alignment explanation
Indices: 850513--850564 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
850503 TTTTCCTAAT
*
850513 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
850533 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
850554 TCGCAATGCGA
1 TCGCAATGCGA
850565 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:850586 original size:20 final size:20
Alignment explanation
Indices: 850553--850631 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
850543 AATTTGGAAA
* *
850553 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
850573 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
850594 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
850614 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
850632 AAATCGTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:850916 original size:20 final size:20
Alignment explanation
Indices: 850839--850908 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
850829 ATTCATTTGA
850839 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
** *
850859 CTATCGCAATTCG-AAATGAA
1 CTATCGCAACGCGAAAATG-G
**
850879 AAATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
850899 CTATCGCAAC
1 CTATCGCAAC
850909 TAGAAAATCG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
19 5 0.13
20 28 0.74
21 5 0.13
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:850980 original size:19 final size:17
Alignment explanation
Indices: 850935--850984 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 17
850925 GAAATGAAAA
850935 TCGCATTGCGATTTTCT
1 TCGCATTGCGATTTTCT
*
850952 T-G--TTGTGATTTTCATT
1 TCGCATTGCGATTTTC--T
850968 TCGCATTGCGATTTTCT
1 TCGCATTGCGATTTTCT
850985 CGTTGCGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
14 10 0.38
16 3 0.12
17 3 0.12
19 10 0.38
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.52
Consensus pattern (17 bp):
TCGCATTGCGATTTTCT
Found at i:853043 original size:20 final size:20
Alignment explanation
Indices: 853020--853073 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
853010 GAAACTTAAA
853020 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
853040 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
853060 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
853074 TGCAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:853082 original size:19 final size:18
Alignment explanation
Indices: 853018--853156 Score: 78
Period size: 19 Copynumber: 7.8 Consensus size: 18
853008 ACGAAACTTA
*
853018 AAATCGCAACGCGAAAATG
1 AAATCGCAATGCG-AAATG
* *
853037 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAATGC-GAAAT-G
**
853058 CTATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
853076 CAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
* *
853091 AAATTGTAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
853109 AAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
853124 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
853142 AAAGTCGCAATGCGA
1 AAA-TCGCAATGCGA
853157 TTTGTGTTTC
Statistics
Matches: 93, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
14 16 0.17
16 8 0.09
17 8 0.09
18 4 0.04
19 31 0.33
20 24 0.26
21 2 0.02
ACGTcount: A:0.42, C:0.21, G:0.22, T:0.15
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:853107 original size:33 final size:32
Alignment explanation
Indices: 853060--853151 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 32
853050 GGAAATGGCT
853060 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
* *
853093 ATTGTAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
853126 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAA-TCGCAA
853152 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 3 0.06
33 50 0.94
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:853168 original size:19 final size:18
Alignment explanation
Indices: 853163--853260 Score: 86
Period size: 18 Copynumber: 5.8 Consensus size: 18
853153 GCGATTTGTG
*
853163 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTTCA
853181 TTTCGCATTGCGATTT--
1 TTTCGCATTGCGATTTCA
*
853197 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
853214 TTTCGCATTGCGATTT--
1 TTTCGCATTGCGATTTCA
* *
853230 TGTCG--TTACGATTTTCA
1 TTTCGCATTGCGA-TTTCA
853247 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
853261 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 11 0.17
15 6 0.10
16 8 0.13
17 8 0.13
18 19 0.30
19 11 0.17
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.47
Consensus pattern (18 bp):
TTTCGCATTGCGATTTCA
Found at i:853207 original size:14 final size:14
Alignment explanation
Indices: 853188--853244 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
853178 TCATTTCGCA
853188 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
853202 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
853219 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
853235 TTACGATTTT
1 TTGCGATTTT
853245 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 15 0.43
15 3 0.09
16 4 0.11
17 4 0.11
18 3 0.09
19 6 0.17
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:853218 original size:33 final size:33
Alignment explanation
Indices: 853168--853260 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
853158 TTGTGTTTCG
853168 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
853200 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
853233 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
853261 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 8 0.14
33 51 0.86
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:853267 original size:19 final size:20
Alignment explanation
Indices: 853245--853288 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
853235 TTACGATTTT
853245 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
853264 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
853284 CATTT
1 CATTT
853289 TCATGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:853296 original size:20 final size:20
Alignment explanation
Indices: 853254--853299 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
853244 TCATTTCGCA
*
853254 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
853274 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
853294 TTGCGA
1 TTGCGA
853300 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:853807 original size:18 final size:18
Alignment explanation
Indices: 853781--853825 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
853771 GTCGATCAGA
*
853781 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
853799 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
853817 TGATGGCTC
1 TGATGGCTC
853826 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:855703 original size:20 final size:20
Alignment explanation
Indices: 855678--855729 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
855668 ATTATGTATT
855678 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
855698 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
855718 ATCTCGTTGCGA
1 ATCGCGTTGCGA
855730 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:855739 original size:61 final size:61
Alignment explanation
Indices: 855657--855794 Score: 177
Period size: 61 Copynumber: 2.3 Consensus size: 61
855647 CGCTTTGAAA
* * * *
855657 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * * *
855718 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCTCATTGTGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
855779 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
855795 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:855766 original size:20 final size:20
Alignment explanation
Indices: 855657--855791 Score: 85
Period size: 20 Copynumber: 6.7 Consensus size: 20
855647 CGCTTTGAAA
*
855657 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * * *
855678 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTAAGT
* * *
855698 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
855718 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
855739 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * *
855759 ATCTCATTGTGATAGTCAGT
1 ATCGCATTGCGATAGTAAGT
855779 ATCGCATTGCGAT
1 ATCGCATTGCGAT
855792 TTTCCCAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
19 5 0.05
20 62 0.67
21 23 0.25
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:855902 original size:21 final size:21
Alignment explanation
Indices: 855862--855902 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
855852 ACTGTAGACC
** *
855862 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
855883 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
855903 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:857526 original size:26 final size:28
Alignment explanation
Indices: 857464--857526 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
857454 AATTAAATAC
*
857464 AAATAAATATACAAGAGAATAAAAAATTG
1 AAATAAA-ATACAAAAGAATAAAAAATTG
* *
857493 AAA-GAAATA-AAAAGAATAATAAATT-
1 AAATAAAATACAAAAGAATAAAAAATTG
857518 AAATAAAAT
1 AAATAAAAT
857527 TGGATTCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 3 0.10
26 18 0.62
27 3 0.10
28 2 0.07
29 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (28 bp):
AAATAAAATACAAAAGAATAAAAAATTG
Found at i:858023 original size:21 final size:20
Alignment explanation
Indices: 857991--858029 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
857981 AAGGAAAAAT
857991 ATTAAAATAATT-TTTATAA
1 ATTAAAATAATTATTTATAA
858010 ATTATAAATAAATTATTTAT
1 ATTA-AAAT-AATTATTTAT
858030 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 4 0.24
22 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAAAATAATTATTTATAA
Found at i:858730 original size:21 final size:21
Alignment explanation
Indices: 858704--858748 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
858694 ATCCGAAAAA
*
858704 ATCGGATATCCGAAAT-TTCGG
1 ATCGGATATCC-AAATATCCGG
858725 ATCGGATATCCAAATATCCGG
1 ATCGGATATCCAAATATCCGG
858746 ATC
1 ATC
858749 CGAATCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (21 bp):
ATCGGATATCCAAATATCCGG
Found at i:858853 original size:25 final size:25
Alignment explanation
Indices: 858825--858875 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
858815 AAAAGATTAC
*
858825 ATATTTTGTAAACAAACAATAAAAT
1 ATATTATGTAAACAAACAATAAAAT
*
858850 ATATTATGTAAACAAGCAATAAAAT
1 ATATTATGTAAACAAACAATAAAAT
858875 A
1 A
858876 AGCGATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (25 bp):
ATATTATGTAAACAAACAATAAAAT
Found at i:860757 original size:137 final size:137
Alignment explanation
Indices: 860586--860960 Score: 572
Period size: 137 Copynumber: 2.7 Consensus size: 137
860576 AGTCGAGTAA
* * ** *
860586 AAGGCTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTGT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGT
*
860651 GAACTCCTTCTGGATATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAA
66 GAACTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAA
860716 TTAAGAC
131 TTAAGAC
* * *
860723 AAGGTTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCATCTTCAGATGAGTTTTTCTCATTGT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGT
860788 GAACTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAA
66 GAACTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAA
860853 TTAAGAC
131 TTAAGAC
* * * *
860860 AATGTTGAACAAGTTATTCTCATTATGAACTTATTCTTCCTCTTCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGT
** * * *
860925 GAA-TTTTCTCTGAAAATGTTGATCATCAAGAGAGGT
66 GAACTCCT-TCTGGAAATGTTGATCCTCAAAAGAGGT
860961 TCTTCTGGTT
Statistics
Matches: 217, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
136 2 0.01
137 215 0.99
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (137 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGT
GAACTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTGTCGTTGATTCAACTTCATATGTGATGAA
TTAAGAC
Found at i:865034 original size:80 final size:80
Alignment explanation
Indices: 864917--865075 Score: 239
Period size: 80 Copynumber: 2.0 Consensus size: 80
864907 GATCAAAATT
* * * *
864917 AAAAAAAATATATCAGAATAAGGATAGGATTTGATGTTCCAGTAAAGTTTAAAGGATAGGATCAG
1 AAAAAAAATATATCAGAATAAGAATAGGATTTAATGTTCCAGTAAACTTTAAAGGACAGGATCAG
864982 ATCAAAATTCAAAAAA
66 ATCAAAATT-AAAAAA
* * *
864998 AAAAAAAAT-TATCAGACTAAGAATATGATTTAATGTTCCAGTCAACTTTAAAGGACAGGATCAG
1 AAAAAAAATATATCAGAATAAGAATAGGATTTAATGTTCCAGTAAACTTTAAAGGACAGGATCAG
865062 ATCAAAATTAAAAA
66 ATCAAAATTAAAAA
865076 TATATATTTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
79 5 0.07
80 57 0.80
81 9 0.13
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.25
Consensus pattern (80 bp):
AAAAAAAATATATCAGAATAAGAATAGGATTTAATGTTCCAGTAAACTTTAAAGGACAGGATCAG
ATCAAAATTAAAAAA
Found at i:870339 original size:243 final size:245
Alignment explanation
Indices: 869734--870387 Score: 815
Period size: 243 Copynumber: 2.7 Consensus size: 245
869724 AGGAAAAATT
*
869734 TTTGCCACAGAATGGATAGTCTTCCTCATTCAGTGAAGAA-AG-AC-AAAAACATAATATGGCCA
1 TTTGCCACAGAATGAATAGTCTTCCTCATTCAGTGAAGAAGAGAACAAAAAACATAATATGGCCA
869796 TACATGTAGCTTATGAATATGTTATGTGCTGACGGAGAACAATCTAATCAGCACAGGACCGTCCA
66 TACATGTAGCTTATGAATATGTTATGTGCTGACGGAGAACAATCTAATCAGCACAGGACCGTCCA
* * **
869861 TAAGCACATTAATAACAAGGAACATACAAGATGAAGAGCGTAAGAATATCAATGACCACTAATGA
131 TAAGCACATTAATAACAAGGAACATACAAGATGAAGAGCGTAAGAATATCAACGACCACAAACCA
* * * *
869926 ACACTATGAAAGAAAAAAAACATAACGGGCATAAAGGTTAATAGGTATGTAATT
196 AAACTATGAAAG---AAAAACAGAAC-GGCATAAAGGTAAATAGGTATGTAATA
* * * * *
869980 TTTACCACTGAATGAATAGTCTTCCTCATTCACTGAATG--GCAAAACAAAAAACATAATATAGC
1 TTTGCCACAGAATGAATAGTCTTCCTCATTCAGTGAA-GAAG-AGAACAAAAAACATAATATGGC
** * * *
870043 CACGCATGCAGCTTATGAATATGTTATGTGGTGACGG-GAAACAATCTAATCAGCACAAGACCGT
64 CATACATGTAGCTTATGAATATGTTATGTGCTGACGGAG-AACAATCTAATCAGCACAGGACCGT
* * * *
870107 CCATAAGTACATTAATAACAAGGAACATACATGATGATGAGTGTAA-ACATATCAACGACCACAA
128 CCATAAGCACATTAATAACAAGGAACATACAAGATGAAGAGCGTAAGA-ATATCAACGACCACAA
* * * **
870171 ACCAAAACTGT-TATG-AGCACAGGAA-GGCATAAAGGTAAATAGGTATGTAATA
192 ACCAAAACTATGAAAGAAAAACA-GAACGGCATAAAGGTAAATAGGTATGTAATA
* * *
870223 TTTGCCACAGAATGAACAGTCTTCCTCATTCAGTGAAGAAGAGAACAAAAAACATAATGTGGACA
1 TTTGCCACAGAATGAATAGTCTTCCTCATTCAGTGAAGAAGAGAACAAAAAACATAATATGGCCA
* * * * *
870288 TATATGTAGCTTCTGAATATGTTATGTGCTGATGGAGAACAACCAAATCAGCACAGGACCGTCCA
66 TACATGTAGCTTATGAATATGTTATGTGCTGACGGAGAACAATCTAATCAGCACAGGACCGTCCA
* *
870353 TAAGCACATTACTAACAAGGAAAATACAAGATGAA
131 TAAGCACATTAATAACAAGGAACATACAAGATGAA
870388 AGAGGACGAC
Statistics
Matches: 346, Mismatches: 51, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
242 1 0.00
243 161 0.47
244 6 0.02
245 2 0.01
246 33 0.10
247 2 0.01
248 6 0.02
249 135 0.39
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (245 bp):
TTTGCCACAGAATGAATAGTCTTCCTCATTCAGTGAAGAAGAGAACAAAAAACATAATATGGCCA
TACATGTAGCTTATGAATATGTTATGTGCTGACGGAGAACAATCTAATCAGCACAGGACCGTCCA
TAAGCACATTAATAACAAGGAACATACAAGATGAAGAGCGTAAGAATATCAACGACCACAAACCA
AAACTATGAAAGAAAAACAGAACGGCATAAAGGTAAATAGGTATGTAATA
Found at i:887303 original size:29 final size:28
Alignment explanation
Indices: 887219--887303 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
887209 CTAAAAATTT
*
887219 AAACGAACATGAACACCTTAAAAACAA-AC
1 AAACAAACATGAACA-CTTAAAAA-AACAC
* **
887248 AAACAAACATGAACATTTAAACGAACAC
1 AAACAAACATGAACACTTAAAAAAACAC
* *
887276 GAATCAAACATTAACACTTAAAAAAACA
1 -AAACAAACATGAACACTTAAAAAAACA
887304 ATCAAACTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
27 2 0.04
28 7 0.16
29 36 0.80
ACGTcount: A:0.59, C:0.21, G:0.06, T:0.14
Consensus pattern (28 bp):
AAACAAACATGAACACTTAAAAAAACAC
Found at i:889557 original size:16 final size:16
Alignment explanation
Indices: 889536--889574 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
889526 GGTATTACCC
889536 GACCTGTTATGAACCT
1 GACCTGTTATGAACCT
889552 GACCTGTTATGAACCT
1 GACCTGTTATGAACCT
889568 GACCTGT
1 GACCTGT
889575 AACTAACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (16 bp):
GACCTGTTATGAACCT
Found at i:890406 original size:23 final size:23
Alignment explanation
Indices: 890380--890430 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
890370 CAGCAAACAA
*
890380 CAACAGGCAGCATTGAATCAATT
1 CAACAAGCAGCATTGAATCAATT
*** *
890403 CAACAAGCATTGTTGCATCAATT
1 CAACAAGCAGCATTGAATCAATT
890426 CAACA
1 CAACA
890431 TTTTTGCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (23 bp):
CAACAAGCAGCATTGAATCAATT
Found at i:893230 original size:46 final size:46
Alignment explanation
Indices: 893180--893507 Score: 306
Period size: 46 Copynumber: 7.0 Consensus size: 46
893170 GAGACAGAAG
* *
893180 AAGATGAAGAGTCTCAGTTATATTTAGGGTTAGAGAATATGAACAA
1 AAGATGAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
* *
893226 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATAAACAA
1 AAGATGAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
* * * *
893272 AAGATAAAGAGTCTCAGTTAGATTTAGGGTTAAAAAAGATGAACAT
1 AAGATGAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
* * * * * *
893318 AAGATAAAGA-TC-CTTGATTAGATTTAGGGTTAAAGAAAATAAACAG
1 AAGATGAAGAGTCTC-AG-TTAGATTTAGGGTTAGAGAAGATGAACAA
* * * *
893364 AAGAATAAGAAGAGTCTC-GATTAGATTCAAGGTTATAGAAGAT-AAAAA
1 AAG-AT--GAAGAGTCTCAG-TTAGATTTAGGGTTAGAGAAGATGAACAA
* *
893412 GAAGAAGAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATGAACAAAAA
1 -AAGATGAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAAC---AA
* * * *
893462 AAGAGGAAGAGTCTC-GATTAGATTTGGGGTTAGAAAATATGAACAA
1 AAGATGAAGAGTCTCAG-TTAGATTTAGGGTTAGAGAAGATGAACAA
893508 TACTCTGTTA
Statistics
Matches: 237, Mismatches: 31, Indels: 28
0.80 0.10 0.09
Matches are distributed among these distances:
44 1 0.00
45 3 0.01
46 153 0.65
47 5 0.02
48 5 0.02
49 65 0.27
50 4 0.02
51 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (46 bp):
AAGATGAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGATGAACAA
Found at i:893300 original size:92 final size:92
Alignment explanation
Indices: 893180--893507 Score: 317
Period size: 95 Copynumber: 3.5 Consensus size: 92
893170 GAGACAGAAG
* * * *
893180 AAGATGAAGAGTCTC-AGTTATATTTAGGGTTAGAGAATATGAACAAAAGATAAAGAGTCTCAGT
1 AAGATAAAGAGTCTCGA-TTAGATTTAGGGTTAGAAAAGATGAACAAAAGATAAAGAGTCTCAGT
893244 TAGATTTAGGGTTAGAGAAGATAAACAA
65 TAGATTTAGGGTTAGAGAAGATAAACAA
* * *
893272 AAGATAAAGAGTCTC-AGTTAGATTTAGGGTTAAAAAAGATGAACATAAGATAAAGA-TC-CTTG
1 AAGATAAAGAGTCTCGA-TTAGATTTAGGGTTAGAAAAGATGAACAAAAGATAAAGAGTCTC-AG
* * *
893334 ATTAGATTTAGGGTTAAAGAAAATAAACAG
64 -TTAGATTTAGGGTTAGAGAAGATAAACAA
* * * * *
893364 AAGAATAAGAAGAGTCTCGATTAGATTCAAGGTTATAGAAGAT-AAAAAGAAGA-AGAAGAGTCT
1 AAG-AT-A-AAGAGTCTCGATTAGATTTAGGGTTAGAAAAGATGAACAA-AAGATA-AAGAGTCT
* *
893427 TAGTTAGATTTAGGGTTAGAGAAGATGAACAAAAA
61 CAGTTAGATTTAGGGTTAGAGAAGAT--A-AACAA
** * *
893462 AAGAGGAAGAGTCTCGATTAGATTTGGGGTTAGAAAATATGAACAA
1 AAGATAAAGAGTCTCGATTAGATTTAGGGTTAGAAAAGATGAACAA
893508 TACTCTGTTA
Statistics
Matches: 191, Mismatches: 31, Indels: 24
0.78 0.13 0.10
Matches are distributed among these distances:
90 1 0.01
91 3 0.02
92 79 0.41
93 2 0.01
94 5 0.03
95 85 0.45
96 8 0.04
97 2 0.01
98 6 0.03
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (92 bp):
AAGATAAAGAGTCTCGATTAGATTTAGGGTTAGAAAAGATGAACAAAAGATAAAGAGTCTCAGTT
AGATTTAGGGTTAGAGAAGATAAACAA
Found at i:893432 original size:141 final size:138
Alignment explanation
Indices: 893201--893457 Score: 349
Period size: 141 Copynumber: 1.8 Consensus size: 138
893191 TCTCAGTTAT
* * * * *
893201 ATTTAGGGTTAGAGAATATGAACAAAAGATAAAGAGTCTCAGTTAGATTTAGGGTTAGAGAAGAT
1 ATTTAGGGTTAAAGAAAATAAACAAAAGATAAAGAGTCTCAGTTAGATTCAAGGTTAGAGAAGAT
893266 AAACAAAAGATAAAGAGTCTCAGTTAGATTTAGGGTTAAAAAAGATGAACATAAGATAAAGATCC
66 AAACAAAAGATAAAGAGTCTCAGTTAGATTTAGGGTTAAAAAAGATGAACATAAGATAAAGATCC
893331 TTGATTAG
131 TTGATTAG
* *
893339 ATTTAGGGTTAAAGAAAATAAACAGAAGAATAAGAAGAGTCTC-GATTAGATTCAAGGTTATAGA
1 ATTTAGGGTTAAAGAAAATAAACAAAAG-AT-A-AAGAGTCTCAG-TTAGATTCAAGGTTAGAGA
* * *
893403 AGATAAA-AAGAAGA-AGAAGAGTCTTAGTTAGATTTAGGGTTAGAGAAGATGAACA
62 AGATAAACAA-AAGATA-AAGAGTCTCAGTTAGATTTAGGGTTAAAAAAGATGAACA
893458 AAAAAAGAGG
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
138 24 0.23
139 2 0.02
140 5 0.05
141 72 0.70
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (138 bp):
ATTTAGGGTTAAAGAAAATAAACAAAAGATAAAGAGTCTCAGTTAGATTCAAGGTTAGAGAAGAT
AAACAAAAGATAAAGAGTCTCAGTTAGATTTAGGGTTAAAAAAGATGAACATAAGATAAAGATCC
TTGATTAG
Found at i:893862 original size:94 final size:93
Alignment explanation
Indices: 893737--893985 Score: 269
Period size: 93 Copynumber: 2.7 Consensus size: 93
893727 ACAAGTTGGG
* * * * *
893737 TATTGGGTTTTT-GTGTTTGTAAAGATTGAATGAGGATTTTGGGGATGAACAAGGGTTGAGTTTT
1 TATT-GGTTTTTGGTGTTTGTAAAGATCGAATGAGGGTTTTGGGGATAAACAAGAGTTGAATTTT
* *
893801 --GTGTGTTGTATTGAAAAAAA-ATTGGTTTGA
65 AGGAGT-TTG-ATCGAAAAAAACA-T-GTTTGA
* *
893831 TATTGGTTTTTGGTGTTTGTGAAGATCGAATGAGGGTTTT-GGGATAAACACGAGTTGAATTTTA
1 TATTGGTTTTTGGTGTTTGTAAAGATCGAATGAGGGTTTTGGGGATAAACAAGAGTTGAATTTTA
893895 GGAGTTTGATCGAAAAAAACATGTTTGA
66 GGAGTTTGATCGAAAAAAACATGTTTGA
* * * *
893923 TATT-GTGTTTTGGTGTTTGTAAAGGTCAAATAAGGGTTTTGGGGATACACATAG-GTTGAATTT
1 TATTGGT-TTTTGGTGTTTGTAAAGATCGAATGAGGGTTTTGGGGATAAACA-AGAGTTGAATTT
893986 GGGTTTATTG
Statistics
Matches: 133, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
91 2 0.02
92 39 0.29
93 55 0.41
94 34 0.26
95 3 0.02
ACGTcount: A:0.27, C:0.04, G:0.29, T:0.40
Consensus pattern (93 bp):
TATTGGTTTTTGGTGTTTGTAAAGATCGAATGAGGGTTTTGGGGATAAACAAGAGTTGAATTTTA
GGAGTTTGATCGAAAAAAACATGTTTGA
Found at i:894437 original size:13 final size:15
Alignment explanation
Indices: 894406--894543 Score: 56
Period size: 16 Copynumber: 9.9 Consensus size: 15
894396 CTATATAATT
*
894406 TATATAGTATATAAT
1 TATATAGTATATAAC
894421 TATATAGT-T-TAAC
1 TATATAGTATATAAC
* *
894434 TATA-A--AAATTA-
1 TATATAGTATATAAC
894445 TAT--AGTATATAAAC
1 TATATAGTATAT-AAC
*
894459 TATATA-TAGTTTAAC
1 TATATAGTA-TATAAC
894474 TATAT--TATATAAAC
1 TATATAGTATAT-AAC
*
894488 TATATAGTATATAAAT
1 TATATAGTATAT-AAC
894504 TATATAGT-T-T-A-
1 TATATAGTATATAAC
*
894515 TATATAGTTCATATAAA
1 TATATAG-T-ATATAAC
894532 T-TATAGTATATA
1 TATATAGTATATA
894544 GTTTATATAA
Statistics
Matches: 97, Mismatches: 8, Indels: 37
0.68 0.06 0.26
Matches are distributed among these distances:
10 1 0.01
11 10 0.10
12 8 0.08
13 10 0.10
14 21 0.22
15 21 0.22
16 25 0.26
17 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (15 bp):
TATATAGTATATAAC
Found at i:894449 original size:22 final size:22
Alignment explanation
Indices: 894418--894477 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
894408 TATAGTATAT
894418 AATTATATAGTTTAACTATAAA
1 AATTATATAGTTTAACTATAAA
894440 AATTATATAG--T-A-TAT-AA
1 AATTATATAGTTTAACTATAAA
*
894457 ACTATATATAGTTTAACTATA
1 AAT-TATATAGTTTAACTATA
894478 TTATATAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
17 4 0.13
18 10 0.32
19 1 0.03
20 2 0.06
21 1 0.03
22 13 0.42
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (22 bp):
AATTATATAGTTTAACTATAAA
Found at i:894518 original size:11 final size:11
Alignment explanation
Indices: 894504--894660 Score: 95
Period size: 11 Copynumber: 13.2 Consensus size: 11
894494 GTATATAAAT
894504 TATATAGTTTA
1 TATATAGTTTA
*
894515 TATATAGTTCA
1 TATATAGTTTA
*
894526 TATA-AATTATA
1 TATATAGTT-TA
894537 GTATATAGTTTA
1 -TATATAGTTTA
*
894549 TATA-A-TATA
1 TATATAGTTTA
*
894558 TATATAATTTAA
1 TATATAGTTT-A
894570 CTATATAGTGTATAAA
1 -TATATAGT-T-T--A
894586 TTATATAGTTTA
1 -TATATAGTTTA
894598 TATATAGTTTA
1 TATATAGTTTA
* * *
894609 TATAAACTATAA
1 TATATAGT-TTA
894621 TATATAGTATATAAA
1 TATATAGT-T-T--A
894636 TTATATAGTTTA
1 -TATATAGTTTA
894648 TATATAGTTTA
1 TATATAGTTTA
894659 TA
1 TA
894661 CATATTATAT
Statistics
Matches: 117, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
9 7 0.06
10 5 0.04
11 51 0.44
12 19 0.16
13 10 0.09
14 3 0.03
15 4 0.03
16 18 0.15
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:894572 original size:83 final size:79
Alignment explanation
Indices: 894485--894670 Score: 250
Period size: 83 Copynumber: 2.3 Consensus size: 79
894475 ATATTATATA
* *
894485 AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAATTATAGTATATAGTTTAT
1 AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAACTATAATATATAG--TAT
894550 ATAATATATATATAATTT
64 ATAA-AT-TATATAATTT
* *
894568 AACTATATAGTGTATAAATTATATAGTTTATATATAGTTTATATAAACTATAATATATAGTATAT
1 AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAACTATAATATATAGTATAT
*
894633 AAATTATATAGTTT
66 AAATTATATAATTT
*
894647 -A-TATATAGTTTATACATATTATAT
1 AACTATATAGTATATA-A-ATTATAT
894671 TATTATATAA
Statistics
Matches: 95, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
77 12 0.13
78 2 0.02
79 16 0.17
80 2 0.02
81 7 0.07
83 56 0.59
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (79 bp):
AACTATATAGTATATAAATTATATAGTTTATATATAGTTCATATAAACTATAATATATAGTATAT
AAATTATATAATTT
Found at i:894643 original size:50 final size:51
Alignment explanation
Indices: 894538--894669 Score: 182
Period size: 50 Copynumber: 2.6 Consensus size: 51
894528 TAAATTATAG
* * *
894538 TATATAGTTTATATA-A-TATATATATAATTTAACTATATAGTGTATAAAT
1 TATATAGTTTATATATAGTTTATATATAATATAACTATATAGTATATAAAT
894587 TATATAGTTTATATATAGTTTATATA-AACTATAA-TATATAGTATATAAAT
1 TATATAGTTTATATATAGTTTATATATAA-TATAACTATATAGTATATAAAT
* *
894637 TATATAGTTTATATATAGTTTATACATATTATA
1 TATATAGTTTATATATAGTTTATATATAATATA
894670 TTATTATATA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
49 15 0.20
50 47 0.64
51 12 0.16
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (51 bp):
TATATAGTTTATATATAGTTTATATATAATATAACTATATAGTATATAAAT
Found at i:896230 original size:64 final size:64
Alignment explanation
Indices: 896051--896211 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
896041 GAATAAATTG
* *
896051 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATACACTCATGGTTTTATGAA
1 AACATCAAATGCATTTTATGCATCGATGCACATA-CATGCATCGATGCACTCATGGTTTTATGAA
* *
896116 AACATCAAATGCATTTAATGCATCGATGCACAAGACATGCATCGATGCACTCA-GGCTATTT-TG
1 AACATCAAATGCATTTTATGCATCGATGCAC-ATACATGCATCGATGCACTCATGG-T-TTTATG
896179 -A
63 AA
896180 AACATCAAATGCATTTTATGCATCGATGCACA
1 AACATCAAATGCATTTTATGCATCGATGCACA
896212 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
63 1 0.01
64 33 0.38
65 49 0.56
66 5 0.06
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (64 bp):
AACATCAAATGCATTTTATGCATCGATGCACATACATGCATCGATGCACTCATGGTTTTATGAA
Found at i:904814 original size:64 final size:65
Alignment explanation
Indices: 904658--904818 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 65
904648 GAATAAATTG
* * *
904658 AACATCGAATGCATTTTATGCATCGATACACATACCATACATCGATGCACTCAGGGTTTTATGAA
1 AACATCGAATGCATTTTATGCATCGATGCACATAACATACATCGATGCACTCAGGCTTTTATGAA
* *
904723 AACATCGAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
1 AACATCGAATGCATTTTATGCATCGATGCACATA-ACATACATCGATGCACTCAGGCT-TTTATG
904786 -A
64 AA
904787 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
904819 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
64 33 0.38
65 52 0.59
66 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTTATGCATCGATGCACATAACATACATCGATGCACTCAGGCTTTTATGAA
Found at i:904833 original size:64 final size:66
Alignment explanation
Indices: 904658--904836 Score: 235
Period size: 65 Copynumber: 2.8 Consensus size: 66
904648 GAATAAATTG
* *
904658 AACATCGAATGCATTTTATGCATCGAT--ACACATACCATACATCGATGCACTCAGGGTTTTATG
1 AACATCGAATGCATTTTATGCATCGATGCACACATA-CATGCATCGATGCACTCAGGCTTTTATG
904721 AA
65 AA
* *
904723 AACATCGAATGCATTTGATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGCTATTT-TG
1 AACATCGAATGCATTTTATGCATCGATGCACACATACATGCATCGATGCACTCAGGCT-TTTATG
904786 -A
65 AA
* * *
904787 AACATCGAATGCATTTTATGCATCGATGCACACTTA-GTGCACCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCACACATACATGCATCGATGCAC
904837 CTTGTGTATG
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
64 44 0.44
65 49 0.49
66 5 0.05
67 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (66 bp):
AACATCGAATGCATTTTATGCATCGATGCACACATACATGCATCGATGCACTCAGGCTTTTATGA
A
Found at i:906817 original size:25 final size:23
Alignment explanation
Indices: 906773--906822 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
906763 CGGGACATAC
*
906773 AGTGATCATTCGGGATATTTCAT
1 AGTGATCATTCGGGAAATTTCAT
*
906796 AGTGGTCATTCGGGACAAATTTCAT
1 AGTGATCATTCGGG--AAATTTCAT
906821 AG
1 AG
906823 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (23 bp):
AGTGATCATTCGGGAAATTTCAT
Found at i:915460 original size:18 final size:18
Alignment explanation
Indices: 915437--915471 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
915427 TTCCATCCGG
*
915437 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
915455 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
915472 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:916643 original size:19 final size:19
Alignment explanation
Indices: 916621--916703 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
916611 CTAGGCGGCT
*
916621 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
916640 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
916659 CGGCTCGGCT----T-AAA
1 CGGCTCGGCTCAGCTCAAA
*
916673 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
916692 CGGCTCGGCTCA
1 CGGCTCGGCTCA
916704 AACGGCTCCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.35, G:0.29, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:916650 original size:14 final size:14
Alignment explanation
Indices: 916645--916711 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
916635 TCAAACGGCT
*
916645 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
*
916659 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
916673 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
916691 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
916706 CGGCTC
1 CGGCTC
916712 CTCAGGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 29 0.64
15 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.16
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:916674 original size:33 final size:33
Alignment explanation
Indices: 916627--916711 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
916617 GGCTCGGCTT
*
916627 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
916660 GGCTCGGCTTAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
916693 GGCTCGGCTCAAACGGCTC
1 GGCTCGGCTCAAACGGCTC
916712 CTCAGGCTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.16
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:918409 original size:17 final size:17
Alignment explanation
Indices: 918389--918421 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
918379 ATATTTATTT
918389 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
918406 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
918422 TGTGATCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:918523 original size:17 final size:16
Alignment explanation
Indices: 918498--918533 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
918488 TTAAATATTA
918498 TTTTAAATAATAATAT
1 TTTTAAATAATAATAT
918514 TTTTACAATAATAATAT
1 TTTTA-AATAATAATAT
918531 TTT
1 TTT
918534 CACCTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAATAATAATAT
Found at i:919445 original size:24 final size:24
Alignment explanation
Indices: 919414--919475 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
919404 ACAACCGTCT
919414 TCTCTTCCTCTTTCTTCTTCTGGC
1 TCTCTTCCTCTTTCTTCTTCTGGC
919438 TCTCTTCCTCTTTCTTCTTCTGGC
1 TCTCTTCCTCTTTCTTCTTCTGGC
*
919462 ACTCTTCCTCTTTC
1 TCTCTTCCTCTTTC
919476 AATCCATTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.02, C:0.39, G:0.06, T:0.53
Consensus pattern (24 bp):
TCTCTTCCTCTTTCTTCTTCTGGC
Found at i:920491 original size:20 final size:20
Alignment explanation
Indices: 920451--920492 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
920441 TTTATTTTAA
*
920451 TTCTATTCAATTTAGTCGTG
1 TTCTATTCAATTTAATCGTG
*
920471 TTCTATTCAATTTAATTGTG
1 TTCTATTCAATTTAATCGTG
920491 TT
1 TT
920493 GATGCTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (20 bp):
TTCTATTCAATTTAATCGTG
Found at i:926015 original size:17 final size:17
Alignment explanation
Indices: 925993--926031 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
925983 TGAATCAAAT
925993 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
926010 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
926027 -AATTA
1 TAATTA
926032 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:926089 original size:18 final size:18
Alignment explanation
Indices: 926063--926142 Score: 56
Period size: 21 Copynumber: 4.1 Consensus size: 18
926053 TAAAAAATAT
926063 TAAAATATTT-TATATTAA
1 TAAAATATTTATA-ATTAA
*
926081 TAAAGTATTTATAATTAATA
1 TAAAATATTTATAATT-A-A
*
926101 TTAAAATAATTATATATT-A
1 -TAAAATATTTATA-ATTAA
926120 TAATTAATATATTATAATTAA
1 TAA--AATAT-TTATAATTAA
926141 TA
1 TA
926143 TTAATTTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
18 15 0.31
19 4 0.08
20 8 0.16
21 19 0.39
22 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
TAAAATATTTATAATTAA
Found at i:926103 original size:39 final size:41
Alignment explanation
Indices: 926058--926160 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
926048 TTAATTAAAA
* *
926058 AATATTAAAAT-ATTTTATATTAATAA-AGTAT-TTATAATT
1 AATATTAAAATAATTATATATT-ATAATAATATATTATAATT
926097 AATATTAAAATAATTATATATTATAATTAATATATTATAATT
1 AATATTAAAATAATTATATATTATAA-TAATATATTATAATT
**
926139 AATATTAATTTAATTA-ATATTA
1 AATATTAAAATAATTATATATTA
926161 ACTTATATTA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
39 15 0.27
40 9 0.16
41 10 0.18
42 22 0.39
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (41 bp):
AATATTAAAATAATTATATATTATAATAATATATTATAATT
Found at i:926189 original size:7 final size:7
Alignment explanation
Indices: 926177--926201 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
926167 ATTAATATAA
926177 TATAGTT
1 TATAGTT
926184 TATAGTT
1 TATAGTT
926191 TATAGTT
1 TATAGTT
926198 TATA
1 TATA
926202 ATTTGTAATT
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:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
TATAGTT
Found at i:926288 original size:14 final size:14
Alignment explanation
Indices: 926271--926332 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
926261 ATGTTATAAA
926271 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
926285 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
926299 TCATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
926314 TAATATAGTATAGT
1 TTATATAGTATAGT
926328 TTATA
1 TTATA
926333 AACTATATAC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.62
15 8 0.22
16 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:926322 original size:43 final size:40
Alignment explanation
Indices: 926273--926363 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
926263 GTTATAAATT
* *
926273 ATATAGTATAGTTTATAAACTATAGTTCATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA-TAC-TAT-ATTAATATAA
926316 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
926356 ATTATAGT
1 A-TATAGT
926364 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 9 0.20
42 2 0.04
43 24 0.53
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
Found at i:926361 original size:15 final size:15
Alignment explanation
Indices: 926343--926393 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
926333 AACTATATAC
926343 TATATTAATATAAAT
1 TATATTAATATAAAT
*
926358 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
926373 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
926389 TATAT
1 TATAT
926394 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:926400 original size:22 final size:22
Alignment explanation
Indices: 926375--926477 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
926365 AAGATAATTA
926375 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
926397 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
926417 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
926439 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
926461 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
926478 TGTTTATAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
20 10 0.15
21 22 0.34
22 28 0.43
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:926433 original size:21 final size:21
Alignment explanation
Indices: 926404--926456 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
926394 AGTACATTAA
* *
926404 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
926425 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
926446 TATAAACTATA
1 TATAAACTATA
926457 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:926492 original size:21 final size:20
Alignment explanation
Indices: 926402--926493 Score: 78
Period size: 21 Copynumber: 4.3 Consensus size: 20
926392 ATAGTACATT
926402 AATATAAACTATAGTTTATA
1 AATATAAACTATAGTTTATA
* *
926422 AATTATATACTATAGGTTATA
1 AA-TATAAACTATAGTTTATA
* *
926443 AAGTATAAACTATA-TAGTACA
1 AA-TATAAACTATAGT-TTATA
*
926464 CTAATATAAACTATTGTTTATA
1 --AATATAAACTATAGTTTATA
926486 AACTATAA
1 AA-TATAA
926494 GTTACATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
20 4 0.07
21 36 0.64
22 13 0.23
23 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (20 bp):
AATATAAACTATAGTTTATA
Found at i:926526 original size:20 final size:19
Alignment explanation
Indices: 926499--926591 Score: 52
Period size: 20 Copynumber: 4.8 Consensus size: 19
926489 TATAAGTTAC
926499 ATAT-ATAGTTTATATAAA
1 ATATAATAGTTTATATAAA
*
926517 ATATAAATAGATTGTATATATAC
1 ATAT-AATAG-TT-TATATA-AA
*
926540 ATATACTATAGGTTATAT---
1 ATATA--ATAGTTTATATAAA
*
926558 ATAT-ATAGTTTATATATA
1 ATATAATAGTTTATATAAA
*
926576 GTATACATAGTTTATA
1 ATATA-ATAGTTTATA
926592 CATACATGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
15 10 0.17
18 11 0.19
20 14 0.24
21 2 0.03
22 12 0.20
23 6 0.10
24 4 0.07
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (19 bp):
ATATAATAGTTTATATAAA
Found at i:926560 original size:57 final size:55
Alignment explanation
Indices: 926487--926624 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 55
926477 TTGTTTATAA
*
926487 ACTATAAGTTACATATATAGTTTATATAAAATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATAGTTTATATAAAATATAAATAG-TT-TATACATACATAT
* * * * * *
926544 ACTATAGGTTATATATATATAGTTTATATATAGTATACATAGTTTATACATACATGT
1 ACTATAAG-T-TACATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
926601 ACTATAAGTTACATATATAGTTTA
1 ACTATAAGTTACATATATAGTTTA
926625 CATGTATACA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 14 0.20
56 1 0.01
57 25 0.36
58 3 0.04
59 27 0.39
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.42
Consensus pattern (55 bp):
ACTATAAGTTACATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
Found at i:926564 original size:15 final size:16
Alignment explanation
Indices: 926540--926580 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
926530 GTATATATAC
926540 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
926556 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
*
926571 ATATAGTATA
1 ATATACTATA
926581 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:926570 original size:59 final size:57
Alignment explanation
Indices: 926487--926619 Score: 171
Period size: 57 Copynumber: 2.3 Consensus size: 57
926477 TTGTTTATAA
*
926487 ACTATAAGTTAC--ATATATAGTTTATATAAAATATAAATAGATTGTATATATACATAT
1 ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAG-TT-TATACATACATAT
* * * * * *
926544 ACTATAGGTTATATATATATAGTTTATATATAGTATACATAGTTTATACATACATGT
1 ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
926601 ACTATAAGTTACATATATA
1 ACTATAAGTTACATATATA
926620 GTTTACATGT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 38 0.58
58 2 0.03
59 25 0.38
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (57 bp):
ACTATAAGTTACATATATATAGTTTATATAAAATATAAATAGTTTATACATACATAT
Found at i:926621 original size:35 final size:36
Alignment explanation
Indices: 926582--926655 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
926572 TATAGTATAC
*
926582 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
926617 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
926654 AT
1 AT
926656 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:926689 original size:7 final size:7
Alignment explanation
Indices: 926677--926716 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
926667 TATGCATAAT
926677 GTTTAGG
1 GTTTAGG
*
926684 GTTTAGA
1 GTTTAGG
926691 GTTTATGG
1 GTTTA-GG
926699 G-TTAGG
1 GTTTAGG
926705 GTTTAGG
1 GTTTAGG
926712 GTTTA
1 GTTTA
926717 TATTTTAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 3 0.10
7 24 0.83
8 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:926778 original size:35 final size:36
Alignment explanation
Indices: 926700--926785 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 36
926690 AGTTTATGGG
* * *
926700 TTAGGG-TTTAGGGTTTATATTTTAATGTTTATGAT
1 TTAGGGATTTAGGGTTTATAGTATAATGTTTAGGAT
* *
926735 TTA-TGATTTAGGGTTTAT-GTATATTGTTTAGGAT
1 TTAGGGATTTAGGGTTTATAGTATAATGTTTAGGAT
926769 TTAGGGATTTAGGGTTT
1 TTAGGGATTTAGGGTTT
926786 CTATAAACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
34 16 0.37
35 27 0.63
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (36 bp):
TTAGGGATTTAGGGTTTATAGTATAATGTTTAGGAT
Found at i:927146 original size:2 final size:2
Alignment explanation
Indices: 927139--927277 Score: 66
Period size: 2 Copynumber: 72.0 Consensus size: 2
927129 GCATAGTGTT
* *
927139 TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
927179 TA T- TA GT- TA -A CA TA CA TA TA TA TA CTA TA T- TA -A TA TA -A
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * * *
927217 TT TA TA AA CTA TA TA T- TT TA TA TA GT- TA TA CA TA TA TA GTT
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
927258 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
927278 ATTAAAAGTA
Statistics
Matches: 104, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
1 11 0.11
2 86 0.83
3 7 0.07
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:927252 original size:23 final size:23
Alignment explanation
Indices: 927226--927277 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
927216 ATTTATAAAC
*
927226 TATATATTTTATATAGT-TATACA
1 TATATAGTTTATATA-TATATACA
*
927249 TATATAGTTTATATATATATATA
1 TATATAGTTTATATATATATACA
927272 TATATA
1 TATATA
927278 ATTAAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
TATATAGTTTATATATATATACA
Found at i:927253 original size:21 final size:22
Alignment explanation
Indices: 927137--927277 Score: 68
Period size: 23 Copynumber: 6.0 Consensus size: 22
927127 ATGCATAGTG
*
927137 TTTATATATATATATATATATA
1 TTTATATATATATACATATATA
* * * *
927159 TATAATCTATAGATTACTTATATTA
1 T-TTATATATATA-TACATATA-TA
* * * *
927184 GTTAACATACATATATATACTATA
1 -TTTATATATATATACATA-TATA
* * *
927208 TTAATATAATTTATAAACTATATA
1 TTTATAT-ATATATACA-TATATA
927232 TTT-TATATAGTTATACATATATA
1 TTTATATATA--TATACATATATA
*
927255 GTTTATATATATATATATATATA
1 -TTTATATATATATACATATATA
927278 ATTAAAAGTA
Statistics
Matches: 89, Mismatches: 19, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
22 3 0.03
23 34 0.38
24 32 0.36
25 19 0.21
26 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTATATATATATACATATATA
Found at i:927260 original size:15 final size:14
Alignment explanation
Indices: 927235--927269 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
927225 CTATATATTT
927235 TATATAGTTATACA
1 TATATAGTTATACA
*
927249 TATATAGTTTATATA
1 TATATAG-TTATACA
927264 TATATA
1 TATATA
927270 TATATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
TATATAGTTATACA
Found at i:927704 original size:15 final size:15
Alignment explanation
Indices: 927684--927715 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
927674 ATATACTTTT
927684 TATAGTTTATACATA
1 TATAGTTTATACATA
*
927699 TATAGTTTATATATA
1 TATAGTTTATACATA
927714 TA
1 TA
927716 CTTGCTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATAGTTTATACATA
Found at i:930078 original size:18 final size:18
Alignment explanation
Indices: 930034--930117 Score: 82
Period size: 18 Copynumber: 4.6 Consensus size: 18
930024 AAACATAATT
*
930034 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
930052 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
930070 TATAAATATAGTTTATATA
1 TATATATATAGTTTATA-A
* *
930089 TAAATTTATA-TTATATATA
1 TATATATATAGTT-TATA-A
930108 TATATATATA
1 TATATATATA
930118 TATTATTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.02
18 31 0.56
19 23 0.42
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:930079 original size:36 final size:38
Alignment explanation
Indices: 930034--930117 Score: 104
Period size: 36 Copynumber: 2.3 Consensus size: 38
930024 AAACATAATT
930034 TATATATATAGCTTATA-AT-AATTATATAGTT-TATA-A
1 TATATATATAGCTTATATATAAATT-TATA-TTATATATA
* *
930070 TATAAATATAGTTTATATATAAATTTATATTATATATA
1 TATATATATAGCTTATATATAAATTTATATTATATATA
930108 TATATATATA
1 TATATATATA
930118 TATTATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 17 0.41
37 10 0.24
38 14 0.34
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (38 bp):
TATATATATAGCTTATATATAAATTTATATTATATATA
Found at i:930090 original size:2 final size:2
Alignment explanation
Indices: 930065--930120 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
930055 TTATATAGTT
* * * *
930065 TA TA -A TA TA AA TA TA GTT TA TA TA TA AA TT TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
930106 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
930121 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.93
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:930107 original size:21 final size:21
Alignment explanation
Indices: 930083--930123 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
930073 AAATATAGTT
*
930083 TATATATAAATTTATATTATA
1 TATATATAAATATATATTATA
*
930104 TATATATATATATATATTAT
1 TATATATAAATATATATTAT
930124 TTTTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATATAAATATATATTATA
Found at i:932135 original size:20 final size:20
Alignment explanation
Indices: 932110--932154 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
932100 TAATTCAAAA
932110 CTTTCATTTTCACTCATATT
1 CTTTCATTTTCACTCATATT
932130 CTTTCATTTTCACTCATATT
1 CTTTCATTTTCACTCATATT
*
932150 TTTTC
1 CTTTC
932155 CTTTCAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (20 bp):
CTTTCATTTTCACTCATATT
Found at i:937143 original size:15 final size:17
Alignment explanation
Indices: 937120--937153 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
937110 TTAAGATATG
937120 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
937136 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
937152 TT
1 TT
937154 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:947282 original size:18 final size:18
Alignment explanation
Indices: 947248--947284 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
947238 GAATGCTCGG
947248 AGGGAACCGATTCCCCCC
1 AGGGAACCGATTCCCCCC
947266 AGGGATACCGATTCCCCCC
1 AGGGA-ACCGATTCCCCCC
947285 TTGTATAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.22, C:0.43, G:0.22, T:0.14
Consensus pattern (18 bp):
AGGGAACCGATTCCCCCC
Found at i:950255 original size:15 final size:15
Alignment explanation
Indices: 950235--950264 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
950225 AATTACCAAT
*
950235 TTCCATTGAAATATC
1 TTCCATTAAAATATC
950250 TTCCATTAAAATATC
1 TTCCATTAAAATATC
950265 CATAGTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:950915 original size:18 final size:18
Alignment explanation
Indices: 950892--950926 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
950882 GACCTAACCT
950892 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
950910 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
950927 TAATAAAAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:951255 original size:14 final size:14
Alignment explanation
Indices: 951232--951263 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
951222 CGTTCGTGAA
951232 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
*
951246 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
951260 CGTT
1 CGTT
951264 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:951893 original size:10 final size:10
Alignment explanation
Indices: 951878--951951 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
951868 GGTCTCCAAT
951878 GTTTATGTTC
1 GTTTATGTTC
951888 GTTTATGTTC
1 GTTTATGTTC
*
951898 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
951910 GTTCT-TGTTC
1 GTT-TATGTTC
951920 GTTTA---T-
1 GTTTATGTTC
*
951926 GTTTGTGTTC
1 GTTTATGTTC
951936 GTTTATGTTC
1 GTTTATGTTC
951946 GTTTAT
1 GTTTAT
951952 TTATTAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
6 4 0.08
7 1 0.02
9 2 0.04
10 31 0.62
11 7 0.14
12 5 0.10
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.61
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:951902 original size:16 final size:16
Alignment explanation
Indices: 951883--951947 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
951873 CCAATGTTTA
951883 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
951899 TGTTCATTTATGTTCT
1 TGTTCGTTTATGTTCG
*
951915 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
951931 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
951947 T
1 T
951948 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.08, C:0.11, G:0.22, T:0.60
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:952042 original size:16 final size:16
Alignment explanation
Indices: 952017--952049 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
952007 AAAAACATTT
*
952017 TGTTCGTTTATGTTCG
1 TGTTCCTTTATGTTCG
952033 TGTTCCTTTATGTTCG
1 TGTTCCTTTATGTTCG
952049 T
1 T
952050 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCCTTTATGTTCG
Found at i:957407 original size:30 final size:33
Alignment explanation
Indices: 957339--957409 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
957329 TTGTCTGTGC
* * *
957339 TATATGATTAATATAAATATATGATTATGTGAT
1 TATATGATGAATATAAATATAAGATTATGTAAT
*
957372 AATATGA-GAATAT-AATATAAG-TTATGTAAT
1 TATATGATGAATATAAATATAAGATTATGTAAT
957402 TATATGAT
1 TATATGAT
957410 CATAAGAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 14 0.44
31 7 0.22
32 5 0.16
33 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (33 bp):
TATATGATGAATATAAATATAAGATTATGTAAT
Found at i:957723 original size:21 final size:21
Alignment explanation
Indices: 957697--957736 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
957687 TTCTACGTGG
*
957697 TCCTTTGGGACATATATGTAA
1 TCCTTTGGAACATATATGTAA
957718 TCCTTTGGAACATATATGT
1 TCCTTTGGAACATATATGT
957737 GGTACTTCGG
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:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TCCTTTGGAACATATATGTAA
Found at i:957842 original size:21 final size:21
Alignment explanation
Indices: 957816--957856 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
957806 ATATGTGTTA
*
957816 TATGTGGTCTTTCGGGACATC
1 TATGTGGTCATTCGGGACATC
*
957837 TATGTGGTCATTCGTGACAT
1 TATGTGGTCATTCGGGACAT
957857 TTCTACGCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATC
Found at i:959062 original size:18 final size:18
Alignment explanation
Indices: 959039--959081 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
959029 TCTACTTTAA
959039 GAATAAATTAGTGCATTT
1 GAATAAATTAGTGCATTT
959057 GAATAAATTAGTGCATTT
1 GAATAAATTAGTGCATTT
959075 GAATAAA
1 GAATAAA
959082 GAGAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (18 bp):
GAATAAATTAGTGCATTT
Found at i:959253 original size:21 final size:21
Alignment explanation
Indices: 959227--959279 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
959217 GTTTCCAGAT
959227 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
959248 TCGCAACGCAAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
959269 TCGCAATGCGA
1 TCGCAACGCGA
959280 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:959332 original size:42 final size:42
Alignment explanation
Indices: 959275--959672 Score: 492
Period size: 42 Copynumber: 9.5 Consensus size: 42
959265 ACTATCGCAA
* *
959275 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
959315 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTT--CGT
1 TGCGATTTATTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGT
* * * * *
959357 TGCGA--TAGTCGAAGTTCACGTTGCGATTTATTCCAAATT--CGT
1 TGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGT
* * * *
959399 TGTGA--TAGTCCAAGTTCGCGTTGCGATAGTTGAAATTCGCGT
1 TGCGATTTATTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGT
959441 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
959483 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
959525 TGCGATTTATTCCAAGTACGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* *
959567 TGCGATTTATTCCAAGGTCGTTGCGATAGTCAAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
959609 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCTT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
959651 TGCGATTTATTCCAAATTCGTT
1 TGCGATTTATTCCAAGTTCGTT
959673 TGATTATTAC
Statistics
Matches: 324, Mismatches: 24, Indels: 18
0.89 0.07 0.05
Matches are distributed among these distances:
40 30 0.09
41 2 0.01
42 263 0.81
44 29 0.09
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:959379 original size:63 final size:62
Alignment explanation
Indices: 959283--959614 Score: 363
Period size: 63 Copynumber: 5.3 Consensus size: 62
959273 AATGCGATTT
* * *
959283 TCCAAATT-CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAG
* * *
959346 TCCAAGTT-CGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTGTGATAG
1 TCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
* *
959407 TCCAAGTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
1 TCCAAGTTC-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
* * * * *
959470 TCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGAT
1 TCCAAGTTC-CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGA-
*
959531 TTAT
60 -TAG
* *
959535 TCCAAG-TACGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGGTCGTTGCGATAG
1 TCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
*
959596 TCAAAGTTCGCGTTGCGAT
1 TCCAAGTTC-CGTTGCGAT
959615 TTATTCCAAG
Statistics
Matches: 228, Mismatches: 27, Indels: 28
0.81 0.10 0.10
Matches are distributed among these distances:
61 43 0.19
62 1 0.00
63 161 0.71
64 1 0.00
65 22 0.10
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (62 bp):
TCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
Found at i:959409 original size:105 final size:105
Alignment explanation
Indices: 959275--959572 Score: 421
Period size: 105 Copynumber: 2.9 Consensus size: 105
959265 ACTATCGCAA
959275 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGT
959338 TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCACGT
66 TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCACGT
* *
959378 TGCGATTTATTCCAAATTCGTTGTGATAGTCCAAGTTCGCGTTGCGA--TAGTT-GAAATTCGCG
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA-TTCCAAATTCGCG
* *
959440 TTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
65 TTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCACGT
* * * *
959483 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC-AAGT-ACGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGT
*
959546 TGCGATAGTCGAAGTTCGCGTTGCGAT
66 TGCGATAGTCCAAGTT--CGTTGCGAT
959573 TTATTCCAAG
Statistics
Matches: 173, Mismatches: 12, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
103 31 0.18
104 4 0.02
105 131 0.76
106 5 0.03
107 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (105 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGT
TGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCACGT
Found at i:960330 original size:21 final size:20
Alignment explanation
Indices: 960304--960490 Score: 81
Period size: 21 Copynumber: 9.1 Consensus size: 20
960294 CGCAAATCAG
960304 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
**
960325 TTTCCAATTTCGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
*
960346 TTTCCCAATTCGCAATGCGAA
1 TTT-CCAATTCGCAATGCGAT
**** *
960367 TAAGTAAATCGCAATGCGAAT
1 TTTCCAATTCGCAATGCG-AT
*** *
960388 TTGGAAAATCGCAATGCGAT
1 TTTCCAATTCGCAATGCGAT
** * * *
960408 ACT-GACTATCGCAATGCAAT
1 TTTCCAAT-TCGCAATGCGAT
*
960428 TTTCCTAATTCGCATTGCGAT
1 TTTCC-AATTCGCAATGCGAT
* **
960449 TTACGTATTCGCAATGCGAAT
1 TTTCCAATTCGCAATGCG-AT
* * *
960470 CTTACTA-TCGCAATGCGAT
1 TTTCCAATTCGCAATGCGAT
960489 TT
1 TT
960491 ACATAGCGCC
Statistics
Matches: 123, Mismatches: 36, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
19 4 0.03
20 48 0.39
21 65 0.53
22 6 0.05
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:960460 original size:20 final size:19
Alignment explanation
Indices: 960396--960492 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 19
960386 ATTTGGAAAA
*
960396 TCGCAATGCGATACTGACTA-
1 TCGCAATGCGAT--TTACTAT
* *
960416 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGA-TTTACT-AT
*
960437 TCGCATTGCGATTTACGTAT
1 TCGCAATGCGATTTAC-TAT
960457 TCGCAATGCGAATCTTACTA-
1 TCGCAATGCG-AT-TTACTAT
960477 TCGCAATGCGATTTAC
1 TCGCAATGCGATTTAC
960493 ATAGCGCCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
18 4 0.06
19 5 0.08
20 36 0.56
21 15 0.23
22 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (19 bp):
TCGCAATGCGATTTACTAT
Found at i:961045 original size:19 final size:19
Alignment explanation
Indices: 961007--961073 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
960997 TTCGAGAATG
961007 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
961027 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
961046 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
961065 AAAATCGCA
1 AAAATCGCA
961074 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:961114 original size:20 final size:19
Alignment explanation
Indices: 961069--961119 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
961059 GAAACCAAAA
* **
961069 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
961088 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
961107 TCCGCGTTGCGAT
1 T-CGCGTTGCGAT
961120 TTTCATTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:961125 original size:20 final size:19
Alignment explanation
Indices: 961069--961148 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 19
961059 GAAACCAAAA
*
961069 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
961088 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
961107 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
* *
961127 ATCTCGTTACGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
961147 TC
1 TC
961149 AACCAAAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 19 0.37
20 32 0.62
21 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:964729 original size:14 final size:14
Alignment explanation
Indices: 964710--964745 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
964700 ATTGTTTAAT
964710 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
964724 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
964738 TGATTTGT
1 TGATTTGT
964746 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:964876 original size:19 final size:18
Alignment explanation
Indices: 964852--964910 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
964842 AAAAAGTACT
964852 ATCGCAATACGAAATGAAA
1 ATCGCAA-ACGAAATGAAA
*
964871 ATCGC-AACG--A-GAGA
1 ATCGCAAACGAAATGAAA
*
964885 ATCGCAACGCGAAATGAAA
1 ATCGCAA-ACGAAATGAAA
964904 ATCGCAA
1 ATCGCAA
964911 CGAGAGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 2 0.06
17 3 0.09
18 2 0.06
19 15 0.47
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (18 bp):
ATCGCAAACGAAATGAAA
Found at i:964889 original size:14 final size:14
Alignment explanation
Indices: 964870--964926 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
964860 ACGAAATGAA
964870 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
964884 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
964903 AATCGCAACGAGAG
1 AATCGCAACGAGAG
964917 AATCGCAACG
1 AATCGCAACG
964927 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:964898 original size:33 final size:33
Alignment explanation
Indices: 964852--964932 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
964842 AAAAAGTACT
**
964852 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
964885 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
964918 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
964933 TAAATTCTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:964911 original size:19 final size:19
Alignment explanation
Indices: 964861--964912 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
964851 TATCGCAATA
964861 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAACG
*
964878 CG--A-GAGAATCGCAACG
1 CGAAATGAAAATCGCAACG
964894 CGAAATGAAAATCGCAACG
1 CGAAATGAAAATCGCAACG
964913 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (19 bp):
CGAAATGAAAATCGCAACG
Found at i:964991 original size:33 final size:32
Alignment explanation
Indices: 964939--965067 Score: 179
Period size: 33 Copynumber: 3.9 Consensus size: 32
964929 AAATTAAATT
*
964939 CTCGTTGCGATTTTCATTTCGCATTACGATTCC
1 CTCGTTGCGATTTTCATTTCGCATTGCGATT-C
* *
964972 CTCGCTGCGATTTTTATTTCGCATTGCGAAATT-
1 CTCGTTGCGATTTTCATTTCGCATTGCG--ATTC
*
965005 CGCGTTGCGATTTTCATTTCGCATTGCGATTC
1 CTCGTTGCGATTTTCATTTCGCATTGCGATTC
965037 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 -CTCGTTGCGATTTTCATTTCGCATTGCGAT
965068 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (32 bp):
CTCGTTGCGATTTTCATTTCGCATTGCGATTC
Found at i:965018 original size:66 final size:66
Alignment explanation
Indices: 964934--965066 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
964924 ACGCGAAATT
* *
964934 AAATTCTCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGCTGCGATTTTTATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGCTGCGATTTTCATTTCGCATTGC
964999 G
66 G
* * *
965000 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGCTGCGATTTTCATTTCGCATTGC
965065 G
66 G
965066 A
1 A
965067 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGCTGCGATTTTCATTTCGCATTGC
G
Found at i:965031 original size:19 final size:19
Alignment explanation
Indices: 964943--965067 Score: 82
Period size: 19 Copynumber: 7.4 Consensus size: 19
964933 TAAATTCTCG
964943 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* **
964962 TTACGA--TTC-CCTCGC-
1 TTGCGATTTTCATTTCGCA
*
964977 -TGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
964995 TTGCGA-----AATTCGCG
1 TTGCGATTTTCATTTCGCA
965009 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
965028 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
965042 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
965061 TTGCGAT
1 TTGCGAT
965068 AGTAATTTCC
Statistics
Matches: 78, Mismatches: 13, Indels: 30
0.64 0.11 0.25
Matches are distributed among these distances:
14 22 0.28
16 13 0.17
17 14 0.18
19 29 0.37
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:967378 original size:12 final size:12
Alignment explanation
Indices: 967361--967385 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
967351 TCTTCGGGGA
967361 CTTTTTCTTCTT
1 CTTTTTCTTCTT
967373 CTTTTTCTTCTT
1 CTTTTTCTTCTT
967385 C
1 C
967386 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:967594 original size:24 final size:24
Alignment explanation
Indices: 967560--967613 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
967550 CTGAAACATC
*
967560 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
967584 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
967608 ATCAAA
1 ATCAAA
967614 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:968191 original size:12 final size:12
Alignment explanation
Indices: 968167--968200 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
968157 TGCCGGATGG
*
968167 GGAA-GGATGTA
1 GGAACGGATATA
968178 GGAACGGATATA
1 GGAACGGATATA
968190 GGAACGGATAT
1 GGAACGGATAT
968201 CACCGGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.18
Consensus pattern (12 bp):
GGAACGGATATA
Found at i:968421 original size:20 final size:21
Alignment explanation
Indices: 968396--968447 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
968386 TTTTCCTAAT
*
968396 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
968416 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
968437 TCGCAATGCGA
1 TCGCAATGCGA
968448 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:968521 original size:20 final size:20
Alignment explanation
Indices: 968432--968523 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
968422 TGCGAATTTG
* *
968432 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
968452 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
968472 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
968493 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
968513 GAAAATCGCAA
1 GAAAATCGCAA
968524 TCATCTTTAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:968815 original size:14 final size:16
Alignment explanation
Indices: 968795--968868 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
968785 TGAAAATCGC
968795 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
968810 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
968827 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
968846 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
968862 -TTGCGAT
1 ATTGCGAT
968869 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:968832 original size:19 final size:19
Alignment explanation
Indices: 968791--968858 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
968781 GAAATGAAAA
968791 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
968807 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
968824 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
968843 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
968859 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:970921 original size:20 final size:20
Alignment explanation
Indices: 970898--970948 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
970888 ACTTAAAATT
970898 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
970918 GCAACGCGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
970938 GCAATGCGAAA
1 GCAACGCGAAA
970949 TGCAAATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.14
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:970957 original size:19 final size:18
Alignment explanation
Indices: 970915--971025 Score: 94
Period size: 19 Copynumber: 6.4 Consensus size: 18
970905 GAAAATGACT
* *
970915 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGA-A
970935 ATCGCAATGCGAAATGCAA
1 ATCGCAATGCGAAATG-AA
*
970954 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
970968 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
970987 ATCGCAAT--GAAA--AA
1 ATCGCAATGCGAAATGAA
*
971001 ATCGCAATGTGAAATGAA
1 ATCGCAATGCGAAATGAA
971019 ATCGCAA
1 ATCGCAA
971026 CGACAAAATC
Statistics
Matches: 77, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
14 19 0.25
16 8 0.10
17 8 0.10
18 9 0.12
19 23 0.30
20 10 0.13
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Done.