Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 24
Found at i:415872 original size:19 final size:19
Alignment explanation
Indices: 415830--415983 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
415820 TAGTTTACTT
* *
415830 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
415850 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
415869 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
415888 TCGCAACGCGAACTGAAAA
1 TCGCAACGCGAAATGAAAA
*
415907 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
415921 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
415940 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
415954 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
415973 TCGCAATGCGA
1 TCGCAACGCGA
415984 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.17
15 1 0.01
16 7 0.07
17 6 0.06
18 1 0.01
19 62 0.58
20 12 0.11
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:415924 original size:14 final size:14
Alignment explanation
Indices: 415905--415961 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
415895 GCGAACTGAA
*
415905 AATCGCAACGACAG
1 AATCGCAACGAAAG
415919 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
415936 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
415952 AATCGCAACG
1 AATCGCAACG
415962 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:415932 original size:33 final size:33
Alignment explanation
Indices: 415848--415978 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
415838 CGAAACTTAA
* *
415848 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
*
415886 AATCGCAACGCGAACTGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
415919 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
415952 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
415979 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 58 0.67
34 1 0.01
36 1 0.01
38 26 0.30
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:415975 original size:52 final size:51
Alignment explanation
Indices: 415847--415983 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 51
415837 ACGAAACTTA
* * * *
415847 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* * ** * * **
415898 AACT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
415950 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
415984 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
50 9 0.14
51 3 0.05
52 40 0.62
53 3 0.05
54 9 0.14
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:416014 original size:14 final size:14
Alignment explanation
Indices: 415995--416053 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
415985 TTTGGTTTCG
415995 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
416009 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
416026 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
416042 CGTTGCGATTTT
1 CGTTGCGATTTT
416054 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:416021 original size:33 final size:33
Alignment explanation
Indices: 415979--416102 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
415969 AAAATCGCAA
*
415979 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
416012 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
416045 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
416078 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
416103 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:416033 original size:19 final size:18
Alignment explanation
Indices: 415979--416070 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
415969 AAAATCGCAA
415979 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
415998 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
416012 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
416031 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
416045 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
416064 TGCGATT
1 TGCGATT
416071 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:416080 original size:14 final size:14
Alignment explanation
Indices: 416028--416084 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
416018 TTTGGTTTCG
*
416028 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
416042 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
416061 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
416075 CGTTGCGATT
1 CGTTGCGATT
416085 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:418083 original size:14 final size:14
Alignment explanation
Indices: 418064--418120 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
418054 TTTCATTTTG
418064 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
418078 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
418097 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
418111 CGTTGCGATT
1 CGTTGCGATT
418121 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:418092 original size:33 final size:33
Alignment explanation
Indices: 418050--418128 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
418040 ACAGTCGCAA
*
418050 CGATTTTCATTTTGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
418083 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
418116 CGATTTTCATTTC
1 CGATTTTCATTTC
418129 TCTCGTTGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (33 bp):
CGATTTTCATTTCGCGTTGCGATTCTCTCGTTG
Found at i:418100 original size:19 final size:19
Alignment explanation
Indices: 418075--418172 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 19
418065 GTTGCGATTC
418075 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
*
418094 TCGCGTTGCGA--TTC---
1 TCTCGTTGCGATTTTCATT
418108 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCA-TT
**
418128 CTCTCGTTGCAGATAGTCATTT
1 -TCTCGTTGC-GATTTTCA-TT
*
418150 TCACGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
418169 TCTC
1 TCTC
418173 TCGTTGCGAC
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
14 10 0.16
16 3 0.05
17 3 0.05
19 15 0.24
20 6 0.10
21 17 0.27
22 9 0.14
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.47
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:418131 original size:21 final size:21
Alignment explanation
Indices: 418105--418181 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
418095 CGCGTTGCGA
418105 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
418126 TTCTCTCGTTGCAGATAGTCAT
1 TTCTCTCGTTGC-GATTTTCAT
*
418148 TT-TCACGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
418168 TTCTCTCGTTGCGA
1 TTCTCTCGTTGCGA
418182 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.19
21 30 0.62
22 9 0.19
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:418736 original size:20 final size:20
Alignment explanation
Indices: 418711--418903 Score: 228
Period size: 20 Copynumber: 9.6 Consensus size: 20
418701 CTTTAAAAAT
418711 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
418731 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
418751 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
418772 CGCGTTGCGATGTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
418792 AGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
418812 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
418832 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
418852 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
418872 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
418892 CGCGTTGCGATT
1 CGCGTTGCGATT
418904 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
20 132 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:426844 original size:22 final size:22
Alignment explanation
Indices: 426782--426845 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
426772 GTAGTTGTCA
* *
426782 GATATTTAGTTAGTTAAGTTGTT
1 GATAATTAGTTAGTT-TGTTGTT
*
426805 GATAATTAGTTAGATTGTTGTT
1 GATAATTAGTTAGTTTGTTGTT
*
426827 GTTAATTAGTTAGTTTGTT
1 GATAATTAGTTAGTTTGTT
426846 AGTGAGGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 23 0.64
23 13 0.36
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (22 bp):
GATAATTAGTTAGTTTGTTGTT
Found at i:427743 original size:27 final size:27
Alignment explanation
Indices: 427652--427745 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
427642 ACATGAGAAC
* * *
427652 GACATACTGGGCAATGGCATTGCGCAT
1 GACATAATGGGTAATGGCATTGTGCAT
* *
427679 GACATAATGGATAATGGCATTGTGGAT
1 GACATAATGGGTAATGGCATTGTGCAT
* *
427706 GACATAATGGGTAATGACCTTGTGCAT
1 GACATAATGGGTAATGGCATTGTGCAT
427733 GACATAATGGGTA
1 GACATAATGGGTA
427746 GGTTGTTATG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (27 bp):
GACATAATGGGTAATGGCATTGTGCAT
Found at i:427855 original size:18 final size:18
Alignment explanation
Indices: 427832--427869 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
427822 TGTCTAATTC
427832 GGTCGTGTAATCTGAGGT
1 GGTCGTGTAATCTGAGGT
427850 GGTCGTGTAATCTGAGGT
1 GGTCGTGTAATCTGAGGT
427868 GG
1 GG
427870 CCATGTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.42, T:0.32
Consensus pattern (18 bp):
GGTCGTGTAATCTGAGGT
Found at i:432126 original size:2 final size:2
Alignment explanation
Indices: 432119--432174 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
432109 GAAAATTAAT
432119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
432161 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
432175 AAAGAAGAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432725 original size:25 final size:25
Alignment explanation
Indices: 432678--432725 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
432668 TTTCAAAAAT
* **
432678 ATAATATAGGATTATTTTTATTTAA
1 ATAAGATAGGATTATTTCCATTTAA
432703 ATAAGATAGGATTATTTCCATTT
1 ATAAGATAGGATTATTTCCATTT
432726 TTATTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (25 bp):
ATAAGATAGGATTATTTCCATTTAA
Found at i:433001 original size:25 final size:25
Alignment explanation
Indices: 432939--432991 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
432929 AAATTTTATA
**
432939 TATATTAACTTTAAGAAATATACTTT
1 TATATTAAC-TTATTAAATATACTTT
432965 TATATTAACTTATTAAATATA-TTT
1 TATATTAACTTATTAAATATACTTT
432989 TAT
1 TAT
432992 GGTTATCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
25 10 0.40
26 9 0.36
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
TATATTAACTTATTAAATATACTTT
Found at i:433018 original size:21 final size:20
Alignment explanation
Indices: 432974--433022 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
432964 TTATATTAAC
* *
432974 TTATTAAATATATTTTATGG
1 TTATTTAATTTATTTTATGG
**
432994 TTATCTTAATTTATTTTATTT
1 TTAT-TTAATTTATTTTATGG
433015 TTATTTAA
1 TTATTTAA
433023 AAATATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (20 bp):
TTATTTAATTTATTTTATGG
Found at i:433057 original size:31 final size:33
Alignment explanation
Indices: 433004--433069 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 33
432994 TTATCTTAAT
*
433004 TTATTTTATTTTTATTTAAAAATATATTTTATTA
1 TTATTTTATTTTTATTTAAAAATATATATT-TTA
433038 TTATTTTA-TTTT-TTT-AAAATATATATTTTA
1 TTATTTTATTTTTATTTAAAAATATATATTTTA
433068 TT
1 TT
433070 TTAATTTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 5 0.16
31 11 0.35
32 3 0.10
33 4 0.13
34 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (33 bp):
TTATTTTATTTTTATTTAAAAATATATATTTTA
Found at i:433067 original size:33 final size:33
Alignment explanation
Indices: 433003--433077 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
432993 GTTATCTTAA
433003 TTTATTTTATTTTTATTTAAAAATATATTTTAT
1 TTTATTTTATTTTTATTTAAAAATATATTTTAT
433036 TATTATTTTA-TTTT-TTTAAAATATATATTTTAT
1 T-TTATTTTATTTTTATTTAAAA-ATATATTTTAT
*
433069 TTTAATTTA
1 TTTATTTTA
433078 CTAAATATGC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 14 0.36
33 17 0.44
34 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (33 bp):
TTTATTTTATTTTTATTTAAAAATATATTTTAT
Found at i:433613 original size:23 final size:23
Alignment explanation
Indices: 433571--433619 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
433561 TAACCTACTA
*
433571 AAAAACAGAGAAAAATATGCCAC
1 AAAAACAGAGAAAAACATGCCAC
* *
433594 AAAAACATAGATAAACATGCCAC
1 AAAAACAGAGAAAAACATGCCAC
433617 AAA
1 AAA
433620 GGTAGATAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.10
Consensus pattern (23 bp):
AAAAACAGAGAAAAACATGCCAC
Found at i:433638 original size:20 final size:21
Alignment explanation
Indices: 433601--433639 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
433591 CACAAAAACA
*
433601 TAGATAAACATGCCACAAAGG
1 TAGATAAACATGCAACAAAGG
*
433622 TAGAT-AACATGTAACAAA
1 TAGATAAACATGCAACAAA
433640 AAAACATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (21 bp):
TAGATAAACATGCAACAAAGG
Found at i:436569 original size:22 final size:22
Alignment explanation
Indices: 436544--436603 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
436534 GTCTTGTAAT
* *
436544 TGATGACGGTGACAACGACTAA
1 TGATGACAGTGACAACGACGAA
* * *
436566 TGATGATAGTGACAATGACGGA
1 TGATGACAGTGACAACGACGAA
*
436588 TGATAACAGTGACAAC
1 TGATGACAGTGACAAC
436604 AACAACAACA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (22 bp):
TGATGACAGTGACAACGACGAA
Found at i:437676 original size:9 final size:9
Alignment explanation
Indices: 437662--437720 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
437652 GCTGCGGGAA
437662 ACCGGTTTG
1 ACCGGTTTG
**
437671 ACCGGTTCAA
1 ACCGGTT-TG
437681 ACCGGTTTG
1 ACCGGTTTG
*
437690 ACCGGTCTG
1 ACCGGTTTG
*
437699 AATCGGTTTG
1 -ACCGGTTTG
*
437709 ACCGGTCTG
1 ACCGGTTTG
437718 ACC
1 ACC
437721 CGACCCGACC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 25 0.64
10 14 0.36
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:437715 original size:19 final size:19
Alignment explanation
Indices: 437661--437718 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
437651 GGCTGCGGGA
*
437661 AACCGGTTTGACCGGT-TCA
1 AACCGGTTTGACCGGTCT-G
437680 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
437699 AATCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
437718 A
1 A
437719 CCCGACCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 35 0.97
20 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:437741 original size:22 final size:22
Alignment explanation
Indices: 437716--437762 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
437706 TTGACCGGTC
* * *
437716 TGACCCGACCCGACCTGACTGT
1 TGACACGACCCGACCGGACCGT
437738 TGACACGACCCGACCGGACCGT
1 TGACACGACCCGACCGGACCGT
437760 TGA
1 TGA
437763 TTGTTGACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (22 bp):
TGACACGACCCGACCGGACCGT
Found at i:445004 original size:22 final size:22
Alignment explanation
Indices: 444978--445042 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
444968 TGACCGGTCT
444978 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
445000 GACCCGACCCGACCGTTAACCC
1 GACCCGACCCGACCGTTGACCC
*
445022 GACCCAACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
445043 GTTGACTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.22, C:0.49, G:0.20, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:446657 original size:15 final size:15
Alignment explanation
Indices: 446639--446705 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
446629 TTCCGGAAAA
*
446639 TGAATTATTGGAATT
1 TGAATTACTGGAATT
446654 TGAATTACTGGAATT
1 TGAATTACTGGAATT
446669 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
446684 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
446698 TGAATTAC
1 TGAATTAC
446706 ATTTCTGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:447090 original size:23 final size:23
Alignment explanation
Indices: 447041--447103 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
447031 GTGTTATATT
* **
447041 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
447064 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
447087 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
447104 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:447131 original size:19 final size:20
Alignment explanation
Indices: 447079--447131 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
447069 TTAAATATCT
447079 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
447098 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
447119 TTATTAAATATAT
1 TTATTAAATATAT
447132 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:447222 original size:31 final size:33
Alignment explanation
Indices: 447176--447255 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
447166 ATAATATCTT
* *
447176 ATATTATTATAATATAATTGATTATTTTA-TAT-A
1 ATATTAATA-AATATAATT-ATTATATTATTATAA
447209 ATATTAA-AAATATAA-TATTATATTATTATAA
1 ATATTAATAAATATAATTATTATATTATTATAA
447240 ATATTAATAAAT-TAAT
1 ATATTAATAAATATAAT
447256 AAATAATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 8 0.20
30 4 0.10
31 18 0.44
32 5 0.12
33 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
ATATTAATAAATATAATTATTATATTATTATAA
Found at i:447230 original size:22 final size:23
Alignment explanation
Indices: 447205--447248 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
447195 GATTATTTTA
447205 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
447227 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
447249 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:447262 original size:52 final size:52
Alignment explanation
Indices: 447159--447262 Score: 122
Period size: 54 Copynumber: 2.0 Consensus size: 52
447149 ATTATTAAAA
** * *
447159 TAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATAATA-CTTATATTATTATAATATAATAAATTA-TATAAATAATAT
447213 TAAAAATATAATA-TTATATTATTATAAATATTAATAAATTA-ATAAATAAT
1 TAAAAATATAATACTTATATTATTAT-AATA-TAATAAATTATATAAATAAT
447263 GTTTTGATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
52 19 0.43
53 4 0.09
54 21 0.48
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (52 bp):
TAAAAATATAATACTTATATTATTATAATATAATAAATTATATAAATAATAT
Found at i:447559 original size:42 final size:42
Alignment explanation
Indices: 447440--447559 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
447430 ATGAATTACG
*
447440 TTCCGGAAAACGAATTACGTGAAACAAACACAGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
447482 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
447524 TTCCGGAAAACGAATTACGTGAAATAAACATGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
447560 TTCGGGGAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:448762 original size:12 final size:13
Alignment explanation
Indices: 448735--448788 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
448725 CATTTGTTAG
* *
448735 AATATAAAATAAA
1 AATAAAAAACAAA
*
448748 AATAAAAAAC-CA
1 AATAAAAAACAAA
*
448760 AATACAAAACAAA
1 AATAAAAAACAAA
448773 AATAAAAAACATAA
1 AATAAAAAACA-AA
448787 AA
1 AA
448789 AAACATAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.30
13 19 0.58
14 4 0.12
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (13 bp):
AATAAAAAACAAA
Found at i:448763 original size:25 final size:25
Alignment explanation
Indices: 448735--448782 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
448725 CATTTGTTAG
* *
448735 AATATAAAATAAAAATAAAAAACCA
1 AATACAAAACAAAAATAAAAAACCA
448760 AATACAAAACAAAAATAAAAAAC
1 AATACAAAACAAAAATAAAAAAC
448783 ATAAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.12
Consensus pattern (25 bp):
AATACAAAACAAAAATAAAAAACCA
Found at i:448802 original size:25 final size:26
Alignment explanation
Indices: 448746--448823 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
448736 ATATAAAATA
448746 AAAATAAAAAACCA-AATACAAAACA-
1 AAAATAAAAAA-CATAATACAAAACAT
448771 AAAATAAAAAACATAA-A-AAAACAT
1 AAAATAAAAAACATAATACAAAACAT
*
448795 AAACATAAATCAACATAATACAAAA-AT
1 AAA-ATAAA-AAACATAATACAAAACAT
448822 AA
1 AA
448824 GAGATTTGCA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
23 6 0.13
24 6 0.13
25 18 0.39
26 7 0.15
27 5 0.11
28 4 0.09
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (26 bp):
AAAATAAAAAACATAATACAAAACAT
Found at i:449597 original size:103 final size:103
Alignment explanation
Indices: 449379--450024 Score: 526
Period size: 103 Copynumber: 6.4 Consensus size: 103
449369 ATCAAGAAAA
* * * * * * * * *
449379 GATCGAATGGTTTATTTAGGGATGAATAGATAAAGAACAGGGGTTAGGGTTTGTGTTTTAATCGA
1 GATCAAATGGGTTATTTAGGGAAGAACATATGAAGAACAAGAGTTAGGGTTTGTGTTTTGATCGA
** *
449444 GAAAAACAGAAATCAAATGAA-ATTTTGTGTTTATTTTG
66 GAAAAACAGAAATTGAAGGAAGA-TTTGTGTTTATTTTG
* * * * *
449482 GATCGAATGGTTTATTAAGGGAAGAACATATGAAGAACAAGAATTATGGTTTGTGTTTTGATCGA
1 GATCAAATGGGTTATTTAGGGAAGAACATATGAAGAACAAGAGTTAGGGTTTGTGTTTTGATCGA
* *
449547 GAAAAACA-AAATTGAAGGAAGATTTGTGTTTGTTTTA
66 GAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTG
* *
449584 AATCAAATGGG---TTTAGGGAAGAACATATGAAGAA-AATGGGTTAGGGTTTGTGTTTTGATCG
1 GATCAAATGGGTTATTTAGGGAAGAACATATGAAGAACAA-GAGTTAGGGTTTGTGTTTTGATCG
** *
449645 AGAAAAAC-GTAAAAAGAATGAAGATTTGTGTTTATTTTG
65 AGAAAAACAG-AAATTGAAGGAAGATTTGTGTTTATTTTG
** * * * * *
449684 GATCAAATGGGTTATTTTTGGAAGAATAAATGAAGAACGAGAGTTAGGGTTTATGTTTTGATAGA
1 GATCAAATGGGTTATTTAGGGAAGAACATATGAAGAACAAGAGTTAGGGTTTGTGTTTTGATCGA
* *
449749 GAAAAATAGAAATTGAAGGATGATTTGTGTTTATTTTG
66 GAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTG
* * * *
449787 GATCGAATGAGTTATTTAGGGAAG-AC-TA--AATGAACAGGGGTTAGGGTTTGTGTTTTGAT--
1 GATCAAATGGGTTATTTAGGGAAGAACATATGAA-GAACAAGAGTTAGGGTTTGTGTTTTGATCG
* * * * *
449846 AAAAAAATAGAAATCGAATGAAGGTTTGTGTTTATTTTG
65 AGAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTG
** * * * * * *
449885 GATTGAATAGGCT-TTTAGAGATGAACAAATGAAGAATACAA-A--T-GGATTTTTGTGTTTTGA
1 GATCAAATGGGTTATTTAGGGAAGAACATATGAAG-A-ACAAGAGTTAGG--GTTTGTGTTTTGA
** * *
449945 TCGA-AAAAAC-GCAAAAGGGATGAAGAATTT-TGTTTATTTTG
62 TCGAGAAAAACAG-AAATTGAAGGAAG-ATTTGTGTTTATTTTG
* * *
449986 GATCAAATGAGCTT-TTTAGGGATGAACATGTGAAGAACA
1 GATCAAATG-GGTTATTTAGGGAAGAACATATGAAGAACA
450025 CAGATGAATT
Statistics
Matches: 441, Mismatches: 79, Indels: 49
0.78 0.14 0.09
Matches are distributed among these distances:
97 8 0.02
98 49 0.11
99 55 0.12
100 76 0.17
101 37 0.08
102 58 0.13
103 156 0.35
104 2 0.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (103 bp):
GATCAAATGGGTTATTTAGGGAAGAACATATGAAGAACAAGAGTTAGGGTTTGTGTTTTGATCGA
GAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTG
Found at i:449743 original size:202 final size:202
Alignment explanation
Indices: 449409--449887 Score: 541
Period size: 202 Copynumber: 2.4 Consensus size: 202
449399 GATGAATAGA
* * *
449409 TAAA-GAACAGGGGTTAGGGTTTGTGTTTTAATCGAGAAAAACAG-AAATCA-AATGAA-ATTTT
1 TAAATGAAAAGGGGTTAGGGTTTGTGTTTTGATCGAGAAAAAC-GTAAA-AAGAATGAAGA-TTT
* * * * *
449470 GTGTTTATTTTGGATCGAATGGTTTATTAAGGGAAGAACATATGAAGAACAAGAATTATGGTTTG
63 GTGTTTATTTTGGATCAAATGGGTTATTAAGGGAAGAACAAATGAAGAACAAGAATTAGGGTTTA
* * *
449535 TGTTTTGATCGAGAAAAACA-AAATTGAAGGAAGATTTGTGTTTGTTTTAAATCAAATG-G-GTT
128 TGTTTTGATAGAGAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTAAATCAAATGAGTATT
449597 TAGGGAAGAAC
193 TAGGGAAG-AC
*
449608 ATATGAA-GAAAATGGGTTAGGGTTTGTGTTTTGATCGAGAAAAACGTAAAAAGAATGAAGATTT
1 -TA--AATGAAAAGGGGTTAGGGTTTGTGTTTTGATCGAGAAAAACGTAAAAAGAATGAAGATTT
*** * * *
449672 GTGTTTATTTTGGATCAAATGGGTTATTTTTGGAAGAATAAATGAAGAACGAGAGTTAGGGTTTA
63 GTGTTTATTTTGGATCAAATGGGTTATTAAGGGAAGAACAAATGAAGAACAAGAATTAGGGTTTA
* * ** *
449737 TGTTTTGATAGAGAAAAATAGAAATTGAAGGATGATTTGTGTTTATTTTGGATCGAATGAGTTAT
128 TGTTTTGATAGAGAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTAAATCAAATGAG-TAT
449802 TTAGGGAAGAC
192 TTAGGGAAGAC
* * * *
449813 TAAATGAACAGGGGTTAGGGTTTGTGTTTTGAT--A-AAAAA-ATAGAAATCGAATGAAGGTTTG
1 TAAATGAAAAGGGGTTAGGGTTTGTGTTTTGATCGAGAAAAACGTA-AAA-AGAATGAAGATTTG
449874 TGTTTATTTTGGAT
64 TGTTTATTTTGGAT
449888 TGAATAGGCT
Statistics
Matches: 239, Mismatches: 28, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
199 2 0.01
200 10 0.04
201 29 0.12
202 123 0.51
203 60 0.25
204 3 0.01
205 2 0.01
206 10 0.04
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (202 bp):
TAAATGAAAAGGGGTTAGGGTTTGTGTTTTGATCGAGAAAAACGTAAAAAGAATGAAGATTTGTG
TTTATTTTGGATCAAATGGGTTATTAAGGGAAGAACAAATGAAGAACAAGAATTAGGGTTTATGT
TTTGATAGAGAAAAACAGAAATTGAAGGAAGATTTGTGTTTATTTTAAATCAAATGAGTATTTAG
GGAAGAC
Found at i:450382 original size:34 final size:36
Alignment explanation
Indices: 450343--450464 Score: 161
Period size: 34 Copynumber: 3.6 Consensus size: 36
450333 AATCCCACAA
* *
450343 ATATATACTAT-ATAC-TTAT-TTTACACTTATATT
1 ATATATACTATAATACATTATAATTAAACTTATATT
*
450376 -TATATATTATAATACATTATAATTAAACTTATA-T
1 ATATATACTATAATACATTATAATTAAACTTATATT
450410 -TATATACTATAATACATTATAATTAAACTTATATT
1 ATATATACTATAATACATTATAATTAAACTTATATT
450445 ATATAT--TATAATACATTATA
1 ATATATACTATAATACATTATA
450465 GTTTATAGAT
Statistics
Matches: 80, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
32 9 0.11
33 4 0.05
34 51 0.64
35 11 0.14
36 5 0.06
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (36 bp):
ATATATACTATAATACATTATAATTAAACTTATATT
Found at i:450391 original size:24 final size:24
Alignment explanation
Indices: 450364--450498 Score: 83
Period size: 24 Copynumber: 5.8 Consensus size: 24
450354 ATACTTATTT
450364 TACACTTATATTTATATATTATAA
1 TACACTTATATTTATATATTATAA
*
450388 TACA-TTATAATTA-A-ACTTATATTA
1 TACACTTATATTTATATA-TTATA--A
* *
450412 TATAC-TATA---ATACATTATAA
1 TACACTTATATTTATATATTATAA
*
450432 TTAAACTTATA-TTATATATTATAA
1 -TACACTTATATTTATATATTATAA
*
450456 TACA-TTATAGTTTATAGATTATATA
1 TACACTTATA-TTTATATATTATA-A
* *
450481 TA-AATTATATGTATATAT
1 TACACTTATATTTATATAT
450499 ATAGTTTATA
Statistics
Matches: 89, Mismatches: 8, Indels: 28
0.71 0.06 0.22
Matches are distributed among these distances:
20 1 0.01
21 6 0.07
22 21 0.24
23 12 0.13
24 41 0.46
25 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (24 bp):
TACACTTATATTTATATATTATAA
Found at i:450395 original size:17 final size:17
Alignment explanation
Indices: 450375--450464 Score: 89
Period size: 17 Copynumber: 5.3 Consensus size: 17
450365 ACACTTATAT
450375 TTATATATTATAATACA
1 TTATATATTATAATACA
*
450392 TTATA-ATTA-AACTTATA
1 TTATATATTATAA--TACA
*
450409 TTATATACTATAATACA
1 TTATATATTATAATACA
*
450426 TTATA-ATTA-AACTTATA
1 TTATATATTATAA--TACA
450443 TTATATATTATAATACA
1 TTATATATTATAATACA
450460 TTATA
1 TTATA
450465 GTTTATAGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
15 4 0.07
16 7 0.12
17 37 0.63
18 7 0.12
19 4 0.07
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATATATTATAATACA
Found at i:450396 original size:10 final size:10
Alignment explanation
Indices: 450381--450464 Score: 51
Period size: 10 Copynumber: 7.6 Consensus size: 10
450371 ATATTTATAT
450381 ATTATAATAC
1 ATTATAATAC
*
450391 ATTATAATTAA
1 ATTATAA-TAC
*
450402 ACTTATATTATAT
1 A-TTATA--ATAC
*
450415 ACTATAATAC
1 ATTATAATAC
*
450425 ATTATAATTAA
1 ATTATAA-TAC
*
450436 ACTTATATTATAT
1 A-TTATA--ATAC
450449 ATTATAATAC
1 ATTATAATAC
450459 ATTATA
1 ATTATA
450465 GTTTATAGAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
10 25 0.43
11 6 0.10
12 19 0.33
13 6 0.10
14 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTATAATAC
Found at i:450533 original size:14 final size:12
Alignment explanation
Indices: 450504--450546 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
450494 TATATATAGT
*
450504 TTATATATAAAC
1 TTATAAATAAAC
450516 TTATACAATAATAC
1 TTATA-AATAA-AC
*
450530 TTATAATTAAAC
1 TTATAAATAAAC
450542 TTATA
1 TTATA
450547 GTTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 12 0.44
13 8 0.30
14 7 0.26
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (12 bp):
TTATAAATAAAC
Found at i:450647 original size:44 final size:45
Alignment explanation
Indices: 450581--450668 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
450571 TTTATAGTTT
*
450581 ATATATAGTATATATGGGTTAGGATTTAGTATATAGTTTATATAAA
1 ATATATAG-ATATATGGGTTAGGATTTAGTATATAATTTATATAAA
* *
450627 ATATATAG-TATATGGTTTAGGGTTTAGTATATAATTTATATA
1 ATATATAGATATATGGGTTAGGATTTAGTATATAATTTATATA
450669 TAGTATTTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 31 0.79
46 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (45 bp):
ATATATAGATATATGGGTTAGGATTTAGTATATAATTTATATAAA
Found at i:450725 original size:81 final size:78
Alignment explanation
Indices: 450635--450798 Score: 215
Period size: 81 Copynumber: 2.1 Consensus size: 78
450625 AAATATATAG
* *
450635 TATATGGTTTAGGGTTTAGTATATAATTTATATATAGTATTTAGTTTATA-TATATTATATA-AA
1 TATATGGTTTAAGGTTTAATATATAATTTATATATAGTA--TAGTTTATAGTATA-TATATAGAA
450698 TAAACTATATATAATTTA
63 TAAA--ATATATAATTTA
* * *
450716 TATATGGTTTAAGGTTTAATATATAGTTTATATATAGTATAGTTTATAGTTTATATATAGTATAA
1 TATATGGTTTAAGGTTTAATATATAATTTATATATAGTATAGTTTATAGTATATATATAGAATAA
*
450781 AATATATAGTTTA
66 AATATATAATTTA
450794 TATAT
1 TATAT
450799 AAACTATAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
78 16 0.21
79 15 0.20
80 8 0.11
81 36 0.48
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.49
Consensus pattern (78 bp):
TATATGGTTTAAGGTTTAATATATAATTTATATATAGTATAGTTTATAGTATATATATAGAATAA
AATATATAATTTA
Found at i:450756 original size:7 final size:7
Alignment explanation
Indices: 450744--450882 Score: 66
Period size: 7 Copynumber: 20.9 Consensus size: 7
450734 ATATATAGTT
450744 TATATA-
1 TATATAG
450750 TAGTATAG
1 TA-TATAG
*
450758 TTTATAG
1 TATATAG
450765 T-T-TA-
1 TATATAG
450769 TATATAG
1 TATATAG
* *
450776 TATAAAA
1 TATATAG
450783 TATATAG
1 TATATAG
*
450790 TTTATA-
1 TATATAG
* *
450796 TATAAAC
1 TATATAG
450803 TATA-AG
1 TATATAG
450809 TATATATAG
1 --TATATAG
450818 TATATAG
1 TATATAG
450825 TATATAG
1 TATATAG
*
450832 TTTATA-
1 TATATAG
450838 TATATAG
1 TATATAG
*
450845 T-T-TAT
1 TATATAG
*
450850 TATTTTA-
1 TA-TATAG
450857 TATATAG
1 TATATAG
*
450864 TACATAG
1 TATATAG
*
450871 TTTATA-
1 TATATAG
450877 TATATA
1 TATATA
450883 TAGTTCATAT
Statistics
Matches: 102, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
4 1 0.01
5 6 0.06
6 24 0.24
7 62 0.61
8 7 0.07
9 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (7 bp):
TATATAG
Found at i:450776 original size:11 final size:11
Alignment explanation
Indices: 450648--450942 Score: 97
Period size: 11 Copynumber: 26.9 Consensus size: 11
450638 ATGGTTTAGG
450648 GTTTAGTATATA
1 GTTTA-TATATA
*
450660 ATTTATATATA
1 GTTTATATATA
450671 G--TAT-T-TA
1 GTTTATATATA
450678 GTTTATATATA
1 GTTTATATATA
*
450689 -TTATATAAATA
1 GTT-TATATATA
***
450700 AACTATATATA
1 GTTTATATATA
*
450711 ATTTATATAT-
1 GTTTATATATA
* *
450721 GGTT-TA-A-G
1 GTTTATATATA
450729 GTTTAATATATA
1 GTTT-ATATATA
450741 GTTTATATATA
1 GTTTATATATA
* *
450752 GTATAGTTTATA
1 GTTTA-TATATA
450764 GTTTATATATA
1 GTTTATATATA
*
450775 GTATAAAATATATA
1 GT-T--TATATATA
450789 GTTTATATATA
1 GTTTATATATA
*
450800 ---AACTATA-A
1 GTTTA-TATATA
450808 G--TATATATA
1 GTTTATATATA
450817 GTATATAGTATATA
1 GT-T-TA-TATATA
450831 GTTTATATATATA
1 G-TT-TATATATA
450844 GTTTAT-TAT-
1 GTTTATATATA
450853 -TTTATATATA
1 GTTTATATATA
** *
450863 GTACATAGTTTA
1 GTTTATA-TATA
*
450875 -TATATATATA
1 GTTTATATATA
* *
450885 GTTCATATGCAGA
1 GTTTATAT--ATA
*
450898 CTATATATATATA
1 GT-T-TATATATA
*
450911 GTTCATATATA
1 GTTTATATATA
450922 GTTTATATATA
1 GTTTATATATA
* *
450933 ATTCATATAT
1 GTTTATATAT
450943 TTTATACTTA
Statistics
Matches: 214, Mismatches: 36, Indels: 67
0.68 0.11 0.21
Matches are distributed among these distances:
7 3 0.01
8 16 0.07
9 18 0.08
10 13 0.06
11 98 0.46
12 24 0.11
13 16 0.07
14 21 0.10
15 5 0.02
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (11 bp):
GTTTATATATA
Found at i:450779 original size:9 final size:9
Alignment explanation
Indices: 450734--450930 Score: 56
Period size: 9 Copynumber: 22.8 Consensus size: 9
450724 TTAAGGTTTA
450734 ATATATAGT
1 ATATATAGT
450743 -T-TATA-T
1 ATATATAGT
450749 ATAGTATAGT
1 ATA-TATAGT
450759 -T-TATAGTTT
1 ATATATAG--T
450768 ATATATAGT
1 ATATATAGT
450777 ATA-A-A--
1 ATATATAGT
450782 ATATATAGT
1 ATATATAGT
*
450791 TTATATA-T
1 ATATATAGT
*
450799 AAACTATAAGT
1 ATA-TAT-AGT
450810 ATATATAGT
1 ATATATAGT
450819 ATATAGTA-T
1 ATATA-TAGT
*
450828 ATAGTTTA-T
1 ATA-TATAGT
450837 ATATATAGT
1 ATATATAGT
* *
450846 TTAT-TATT
1 ATATATAGT
*
450854 TTATATA-T
1 ATATATAGT
*
450862 AGTACATAGT
1 A-TATATAGT
450872 -T-TATA-T
1 ATATATAGT
450878 ATATATAGT
1 ATATATAGT
*
450887 -TCATAT-GC
1 AT-ATATAGT
*
450895 AGACTATA-T
1 ATA-TATAGT
450904 ATATATAGTT
1 ATATATAG-T
450914 CATATATAGT
1 -ATATATAGT
*
450924 TTATATA
1 ATATATA
450931 TAATTCATAT
Statistics
Matches: 141, Mismatches: 16, Indels: 62
0.64 0.07 0.28
Matches are distributed among these distances:
5 3 0.02
6 3 0.02
7 16 0.11
8 27 0.19
9 64 0.45
10 12 0.09
11 16 0.11
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (9 bp):
ATATATAGT
Found at i:450954 original size:22 final size:21
Alignment explanation
Indices: 450903--450948 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
450893 GCAGACTATA
*
450903 TATATATAGTTCATATATAGTT
1 TATATATAATTCATATATA-TT
450925 TATATATAATTCATATAT-TT
1 TATATATAATTCATATATATT
450945 TATA
1 TATA
450949 CTTATATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
22 17 0.74
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
TATATATAATTCATATATATT
Found at i:459433 original size:2 final size:2
Alignment explanation
Indices: 459426--459460 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
459416 ACATTTTAAA
459426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
459461 GTTTTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:459554 original size:39 final size:37
Alignment explanation
Indices: 459444--459952 Score: 613
Period size: 37 Copynumber: 13.6 Consensus size: 37
459434 ATATATATAT
**
459444 ATATATATATATATATAGTTTTTGAAACATTTTTAAAAA
1 ATATATATA-ATATATAG-TTTTGAAACATTTTTTGAAA
* * *
459483 AAATACATAGTATATAGTTTTTGAAACATTTTTTGAAA
1 ATATATATAATATATAG-TTTTGAAACATTTTTTGAAA
459521 ATATATATAATATATAGTTGTTGAAACATTTTTTGAAA
1 ATATATATAATATATAGTT-TTGAAACATTTTTTGAAA
*
459559 ATATATATAATATATAGTTTTGGAAAACATTTTTCGAAA
1 ATATATATAATATATAGTTTT-G-AAACATTTTTTGAAA
**
459598 ACGTATATAATATATAGTTTTGGAAAACATTTTTTGAAA
1 ATATATATAATATATAGTTTT-G-AAACATTTTTTGAAA
*
459637 ATATATATAATATATAGTTTAGAAA-ATATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAACAT-TTTTTGAAA
*
459674 ACATATATAATATATAGTTTTGAAA-ATATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAACAT-TTTTTGAAA
*
459711 ATATATATAATATATAGTTTTGGAAAACATTTTTCGAAA
1 ATATATATAATATATAGTTTT-G-AAACATTTTTTGAAA
**
459750 ACGTATATAATATATAGTTTTGGAAACATTTTTTGAAA
1 ATATATATAATATATAGTTTT-GAAACATTTTTTGAAA
**
459788 ATATATATAATATATAGTTTTGAAA-ACGTTTTGAAA
1 ATATATATAATATATAGTTTTGAAACATTTTTTGAAA
* *
459824 ATATATATAATACATAGTTTAGAAA-ATATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAACAT-TTTTTGAAA
* *
459861 ACATATATAATATATAGTTTTGAAATC-GTTTTTG-AA
1 ATATATATAATATATAGTTTTGAAA-CATTTTTTGAAA
* * *
459897 A-ATATATAATAGATAATTTAGAAAACA-TTTTTGAAA
1 ATATATATAATATATAGTTTTG-AAACATTTTTTGAAA
459933 ATATATATAATATAT-GTTTT
1 ATATATATAATATATAGTTTT
459953 TATAAAATAT
Statistics
Matches: 416, Mismatches: 40, Indels: 31
0.85 0.08 0.06
Matches are distributed among these distances:
35 24 0.06
36 47 0.11
37 123 0.30
38 113 0.27
39 107 0.26
40 2 0.00
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAACATTTTTTGAAA
Found at i:459642 original size:37 final size:38
Alignment explanation
Indices: 459444--459952 Score: 630
Period size: 38 Copynumber: 13.6 Consensus size: 38
459434 ATATATATAT
**
459444 ATATATATATATATATAGTTTTTG-AAACATTTTTAAAAA
1 ATATATATA-ATATATAG-TTTTGAAAACATTTTTTGAAA
* * *
459483 AAATACATAGTATATAGTTTTTG-AAACATTTTTTGAAA
1 ATATATATAATATATAG-TTTTGAAAACATTTTTTGAAA
459521 ATATATATAATATATAGTTGTTG-AAACATTTTTTGAAA
1 ATATATATAATATATAGTT-TTGAAAACATTTTTTGAAA
*
459559 ATATATATAATATATAGTTTTGGAAAACATTTTTCGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTTGAAA
**
459598 ACGTATATAATATATAGTTTTGGAAAACATTTTTTGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTTGAAA
* *
459637 ATATATATAATATATAGTTTAGAAAATA-TTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
* *
459674 ACATATATAATATATAGTTTTGAAAATA-TTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
*
459711 ATATATATAATATATAGTTTTGGAAAACATTTTTCGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTTGAAA
** *
459750 ACGTATATAATATATAGTTTTGGAAACATTTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
*
459788 ATATATATAATATATAGTTTTGAAAAC--GTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
* * *
459824 ATATATATAATACATAGTTTAGAAAATA-TTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
* * *
459861 ACATATATAATATATAGTTTTGAAATC-GTTTTTG-AA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
* * *
459897 A-ATATATAATAGATAATTTAGAAAACA-TTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
459933 ATATATATAATATAT-GTTTT
1 ATATATATAATATATAGTTTT
459953 TATAAAATAT
Statistics
Matches: 415, Mismatches: 45, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
35 27 0.07
36 41 0.10
37 116 0.28
38 129 0.31
39 102 0.25
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTTGAAA
Found at i:459708 original size:12 final size:12
Alignment explanation
Indices: 459658--459714 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
459648 ATATAGTTTA
459658 GAAAATATTTTT
1 GAAAATATTTTT
* * *
459670 GAAAACATATAT
1 GAAAATATTTTT
*
459682 -AATATATAGTTTT
1 GAA-A-ATATTTTT
459695 GAAAATATTTTT
1 GAAAATATTTTT
459707 GAAAATAT
1 GAAAATAT
459715 ATATAATATA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
11 2 0.06
12 25 0.74
13 5 0.15
14 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (12 bp):
GAAAATATTTTT
Found at i:459941 original size:113 final size:112
Alignment explanation
Indices: 459444--459952 Score: 658
Period size: 113 Copynumber: 4.5 Consensus size: 112
459434 ATATATATAT
* * * * *
459444 ATATATATATATATATAGTTTTTG-AAACATTTTTAAAAAAAATACATAGTATATAGTTTTTG-A
1 ATATATATA-ATATATAG-TTTTGAAAACATTTTT-GAAAATATATATAATATATAGTTTTGGAA
*
459507 AACATTTTTTGAAAATATATATAATATATAGTTGTTGAAACATTTTTTGAAA
63 AACA-TTTTTGAAAACATATATAATATATAGTT-TTGAAACATTTTTTGAAA
**
459559 ATATATATAATATATAGTTTTGGAAAACATTTTTCGAAAACGTATATAATATATAGTTTTGGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTT-GAAAATATATATAATATATAGTTTTGGAAA
* *
459624 ACATTTTTTGAAAATATATATAATATATAGTTTAGAAA-ATATTTTTGAAA
64 ACA-TTTTTGAAAACATATATAATATATAGTTTTGAAACAT-TTTTTGAAA
* *
459674 ACATATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTGGAAAAC
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGGAAAAC
*
459739 ATTTTTCGAAAACGTATATAATATATAGTTTTGGAAACATTTTTTGAAA
66 ATTTTT-GAAAACATATATAATATATAGTTTT-GAAACATTTTTTGAAA
* * * *
459788 ATATATATAATATATAGTTTTGAAAAC-GTTTTGAAAATATATATAATACATAG-TTTAGAAAAT
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGGAAAAC
*
459851 ATTTTTGAAAACATATATAATATATAGTTTTGAAATC-GTTTTTG-AA
66 ATTTTTGAAAACATATATAATATATAGTTTTGAAA-CATTTTTTGAAA
* * *
459897 A-ATATATAATAGATAATTTAGAAAACATTTTTGAAAATATATATAATATAT-GTTTT
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTT
459953 TATAAAATAT
Statistics
Matches: 356, Mismatches: 28, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
108 23 0.06
109 28 0.08
110 10 0.03
111 25 0.07
112 19 0.05
113 81 0.23
114 60 0.17
115 76 0.21
116 34 0.10
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (112 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGTTTTGGAAAAC
ATTTTTGAAAACATATATAATATATAGTTTTGAAACATTTTTTGAAA
Found at i:459970 original size:15 final size:17
Alignment explanation
Indices: 459936--459968 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
459926 TTTGAAAATA
*
459936 TATATAATATATGTTTT
1 TATAAAATATATGTTTT
459953 TATAAAATATA-GTTTT
1 TATAAAATATATGTTTT
459969 ATTTACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
TATAAAATATATGTTTT
Found at i:459984 original size:15 final size:14
Alignment explanation
Indices: 459966--460002 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
459956 AAAATATAGT
459966 TTTATTTACATTATA
1 TTTATTTACATT-TA
*
459981 TTTATTTATATTTA
1 TTTATTTACATTTA
459995 TTTATTTA
1 TTTATTTA
460003 TTCATTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATTTACATTTA
Found at i:459998 original size:14 final size:15
Alignment explanation
Indices: 459966--460003 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
459956 AAAATATAGT
*
459966 TTTATTTACATTATA
1 TTTATTTATATTATA
459981 TTTATTTATATT-TA
1 TTTATTTATATTATA
459995 TTTATTTAT
1 TTTATTTAT
460004 TCATTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTTATATTATA
Found at i:460024 original size:35 final size:36
Alignment explanation
Indices: 459979--460046 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
459969 ATTTACATTA
459979 TATTTATTTATATTTATT-TATTTATTCATTTTGTT
1 TATTTATTTATATTTATTCTATTTATTCATTTTGTT
* * * *
460014 TATTTCTTTATTTTTATTCTATTTTTTCTTTTT
1 TATTTATTTATATTTATTCTATTTATTCATTTT
460047 TAGGGTCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 16 0.57
36 12 0.43
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (36 bp):
TATTTATTTATATTTATTCTATTTATTCATTTTGTT
Found at i:460909 original size:22 final size:21
Alignment explanation
Indices: 460871--460911 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
460861 TAATTCCTTT
460871 TTTAAATTTGTTTTTATTTAC
1 TTTAAATTTGTTTTTATTTAC
460892 TTTAATATTT-TTTATTATTT
1 TTTAA-ATTTGTTT-TTATTT
460912 TATTTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTAAATTTGTTTTTATTTAC
Found at i:466210 original size:11 final size:11
Alignment explanation
Indices: 466194--466219 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
466184 GAAATATGAC
466194 AATTTAATTTA
1 AATTTAATTTA
466205 AATTTAATTTA
1 AATTTAATTTA
466216 AATT
1 AATT
466220 CAATAGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:468091 original size:22 final size:22
Alignment explanation
Indices: 468066--468155 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 22
468056 TGGTATATTT
*
468066 TATTGAAATAAATATTATAAAA
1 TATTGAAATATATATTATAAAA
* * *
468088 TATT-AATTATTTATTAAAATAA
1 TATTGAAATATATATTATAA-AA
468110 TATTG--ATATATATT-TAAAA
1 TATTGAAATATATATTATAAAA
* *
468129 TATT-AATTAGTATATTTTAAATA
1 TATTGAAATA-TATATTATAAA-A
468152 TATT
1 TATT
468156 TATTAAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
19 6 0.11
20 4 0.08
21 24 0.45
22 14 0.26
23 5 0.09
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
TATTGAAATATATATTATAAAA
Found at i:468107 original size:19 final size:22
Alignment explanation
Indices: 468077--468160 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 22
468067 ATTGAAATAA
468077 ATATTATAAAATATTAATTAT-T
1 ATATT-TAAAATATTAATTATAT
*
468099 -TA-TTAAAATAAT-ATTGATAT
1 ATATTTAAAATATTAATT-ATAT
468119 ATATTTAAAATATTAATTAGTAT
1 ATATTTAAAATATTAATTA-TAT
*
468142 AT-TTTAAATATATTTATTA
1 ATATTTAAA-ATATTAATTA
468161 AAATTTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
18 3 0.06
19 10 0.19
20 2 0.04
21 4 0.08
22 16 0.31
23 17 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATATTTAAAATATTAATTATAT
Found at i:468142 original size:21 final size:20
Alignment explanation
Indices: 468077--468152 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
468067 ATTGAAATAA
468077 ATATTATAAAATATTAATTAT
1 ATATT-TAAAATATTAATTAT
* * *
468098 TTA-TTAAAATAATATTGATAT
1 ATATTTAAAATATTAAT--TAT
468119 ATATTTAAAATATTAATTAGT
1 ATATTTAAAATATTAATTA-T
*
468140 ATATTTTAAATAT
1 ATATTTAAAATAT
468153 ATTTATTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 10 0.23
20 3 0.07
21 20 0.45
22 11 0.25
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATTTAAAATATTAATTAT
Found at i:468258 original size:50 final size:49
Alignment explanation
Indices: 468154--468275 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 49
468144 TTTAAATATA
* * *
468154 TTTATTAAAATTTTATTATTATTTATATAATTATATAAATAATATTATC
1 TTTATTAAAAATTTAATATTATTTATATAATTATATAAATAATATAATC
* *
468203 ATTATTAAAAATTTAATATTATTTCTATGAAATTA-ATAAATAATATAAAT-
1 TTTATTAAAAATTTAATATTATTTATAT--AATTATATAAATAATAT-AATC
*
468253 TTTATTAATAATATT-ATATTATT
1 TTTATTAAAAAT-TTAATATTATT
468276 AAAATAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
49 24 0.39
50 29 0.47
51 9 0.15
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (49 bp):
TTTATTAAAAATTTAATATTATTTATATAATTATATAAATAATATAATC
Found at i:468349 original size:21 final size:20
Alignment explanation
Indices: 468317--468362 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
468307 TATAATTGAT
*
468317 TATTTTATTAATATTAAAAA
1 TATTATATTAATATTAAAAA
*
468337 TATTATATATAATATTAGAAA
1 TATTATAT-TAATATTAAAAA
468358 TATTA
1 TATTA
468363 ATAACATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TATTATATTAATATTAAAAA
Found at i:468678 original size:42 final size:42
Alignment explanation
Indices: 468601--468683 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
468591 ACACTAAAAT
* *
468601 AATATTTTATAAAAAATAAATTACATGAAATAAATAAGAGAA
1 AATATTTTATAAAAAATAAATTACACGAAACAAATAAGAGAA
* *
468643 AATATTTT-TCAAAAAACT-AATTACACGTAACAAATATGAGA
1 AATATTTTAT-AAAAAA-TAAATTACACGAAACAAATAAGAGA
468684 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 1 0.03
42 33 0.94
43 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (42 bp):
AATATTTTATAAAAAATAAATTACACGAAACAAATAAGAGAA
Found at i:470371 original size:10 final size:10
Alignment explanation
Indices: 470358--470479 Score: 51
Period size: 10 Copynumber: 11.8 Consensus size: 10
470348 TACGTATATA
470358 TTATTTATTT
1 TTATTTATTT
470368 TTATTTTTATTAT
1 TTA--TTTATT-T
470381 TCT-TTTATATT
1 T-TATTTAT-TT
*
470392 TTA-TTATAT
1 TTATTTATTT
*
470401 TTAATTATATT
1 TTATTTAT-TT
470412 TTA-TTATTT
1 TTATTTATTT
470421 TCTA-TTATTT
1 T-TATTTATTT
470431 ATTATTT-TCGTT
1 -TTATTTAT--TT
* *
470443 TTATTCATTA
1 TTATTTATTT
470453 TTA-TTA-TT
1 TTATTTATTT
*
470461 ATATTATATTT
1 TTATT-TATTT
470472 TTATTTAT
1 TTATTTAT
470480 ATATTTTGTC
Statistics
Matches: 87, Mismatches: 8, Indels: 34
0.67 0.06 0.26
Matches are distributed among these distances:
8 3 0.03
9 10 0.11
10 36 0.41
11 25 0.29
12 10 0.11
13 2 0.02
14 1 0.01
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (10 bp):
TTATTTATTT
Found at i:470388 original size:17 final size:17
Alignment explanation
Indices: 470352--470438 Score: 81
Period size: 17 Copynumber: 4.9 Consensus size: 17
470342 TATATATACG
*
470352 TATATATTATT-TATTTT
1 TATATTTTATTAT-TTTT
470369 TAT-TTTTATTATTCTTT
1 TATATTTTATTATT-TTT
470386 TATATTTTATTATATTTAAT
1 TATATTTTATTAT-TTT--T
*
470406 TATATTTTATTATTTTC
1 TATATTTTATTATTTTT
470423 TAT-TATTTATTATTTT
1 TATAT-TTTATTATTTT
470439 CGTTTTATTC
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
16 8 0.13
17 24 0.39
18 11 0.18
19 4 0.07
20 14 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTTATTATTTTT
Found at i:470416 original size:54 final size:58
Alignment explanation
Indices: 470329--470479 Score: 147
Period size: 54 Copynumber: 2.6 Consensus size: 58
470319 ACATTTTTTA
* ** *
470329 TTTT-TATTTTATATATATATACGTATATATTATTTATTTT-TATT-TTTATTA-TTC-
1 TTTTATATTTTAT-TATATTTAATTATATTTTATTTATTTTCTATTATTTATTATTTCG
470383 TTTTATATTTTATTATATTTAATTATATTTTA-TTATTTTCTATTATTTATTATTTTCG
1 TTTTATATTTTATTATATTTAATTATATTTTATTTATTTTCTATTATTTATTA-TTTCG
*
470441 TTTTAT-TCATTATTAT-TATTATATTATATTTTTATTTAT
1 TTTTATAT-TTTATTATAT-TTA-ATTATA-TTTTATTTAT
470480 ATATTTTGTC
Statistics
Matches: 81, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
53 7 0.09
54 23 0.28
55 15 0.19
57 5 0.06
58 16 0.20
59 6 0.07
60 5 0.06
61 4 0.05
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (58 bp):
TTTTATATTTTATTATATTTAATTATATTTTATTTATTTTCTATTATTTATTATTTCG
Found at i:470446 original size:18 final size:17
Alignment explanation
Indices: 470356--470454 Score: 67
Period size: 18 Copynumber: 5.4 Consensus size: 17
470346 TATACGTATA
470356 TATTATTTAT-TTTTATT
1 TATTATTT-TCTTTTATT
470373 T-TTATTATTCTTTTATATTT
1 TATTATT-TTC-TTT-TA-TT
* *
470393 TATTATATTTAATTATATTT
1 TATTAT-TTT-CTTTTA-TT
*
470413 TATTATTTTCTATTATT
1 TATTATTTTCTTTTATT
470430 TATTATTTTCGTTTTATT
1 TATTATTTTC-TTTTATT
*
470448 CATTATT
1 TATTATT
470455 ATTATTATAT
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
16 6 0.09
17 14 0.21
18 18 0.27
19 5 0.08
20 14 0.21
21 8 0.12
22 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (17 bp):
TATTATTTTCTTTTATT
Found at i:470531 original size:51 final size:51
Alignment explanation
Indices: 470390--470531 Score: 131
Period size: 51 Copynumber: 2.8 Consensus size: 51
470380 TTCTTTTATA
* *
470390 TTTTATTATATTTA-ATTATAT-TTTATTATTTTCT-ATTATTTATTATTTTCG
1 TTTTATTATATATATATTATATATATATTATTTT-TAATTA--TATTATTTTCG
*
470441 TTTTATTCAT-TAT-TATTAT-TATAT-TATATTTTTATTTATA-TATTTT-G
1 TTTTATT-ATATATATATTATATATATAT-TATTTTTAATTATATTATTTTCG
470488 TCTTTATTATATATATATATATATATATATTATTTTTAATTATA
1 T-TTTATTATATATATAT-TATATATATATTATTTTTAATTATA
470532 ATACCTACCT
Statistics
Matches: 76, Mismatches: 4, Indels: 22
0.75 0.04 0.22
Matches are distributed among these distances:
47 4 0.05
48 15 0.20
49 5 0.07
50 6 0.08
51 43 0.57
52 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (51 bp):
TTTTATTATATATATATTATATATATATTATTTTTAATTATATTATTTTCG
Found at i:470675 original size:10 final size:11
Alignment explanation
Indices: 470631--470676 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
470621 TGGGGGGTGT
470631 TTAAATAT-TA
1 TTAAATATATA
*
470641 TTATATATATA
1 TTAAATATATA
*
470652 TATATATATATA
1 T-TAAATATATA
470664 TTAAATAT-TA
1 TTAAATATATA
470674 TTA
1 TTA
470677 TGTTTAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 12 0.38
11 9 0.28
12 11 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTAAATATATA
Found at i:470696 original size:19 final size:19
Alignment explanation
Indices: 470668--470715 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
470658 TATATATTAA
470668 ATAT-TATTATGTTTAAAT
1 ATATGTATTATGTTTAAAT
470686 ATATGTATTATGTTTAAAT
1 ATATGTATTATGTTTAAAT
*
470705 GTATGTATTAT
1 ATATGTATTAT
470716 TTATTGCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (19 bp):
ATATGTATTATGTTTAAAT
Found at i:470957 original size:20 final size:19
Alignment explanation
Indices: 470908--470958 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
470898 ATTAATAAAA
470908 TATTTATTTTATTTTTATTT
1 TATTT-TTTTATTTTTATTT
* **
470928 CATTCATTTATTTTTATTT
1 TATTTTTTTATTTTTATTT
470947 GTATTTTTTTAT
1 -TATTTTTTTAT
470959 CTAATACATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (19 bp):
TATTTTTTTATTTTTATTT
Found at i:481408 original size:10 final size:10
Alignment explanation
Indices: 481395--481420 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
481385 AATAAAAAAG
481395 AAAAAAAGAA
1 AAAAAAAGAA
481405 AAAAAAAGAA
1 AAAAAAAGAA
481415 AAAAAA
1 AAAAAA
481421 TAATAAGGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:484233 original size:2 final size:2
Alignment explanation
Indices: 484228--484262 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
484218 TTTTATTATT
484228 TA TA TA TA 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 TA TA TA TA T
484263 TACGTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:484446 original size:16 final size:16
Alignment explanation
Indices: 484425--484510 Score: 53
Period size: 16 Copynumber: 5.7 Consensus size: 16
484415 GTTTTTATTC
484425 ATTATTATTATATTAT
1 ATTATTATTATATTAT
484441 ATTATT-TT-T-TTAT
1 ATTATTATTATATTAT
*
484454 ATT-TT-TTATATTTT
1 ATTATTATTATATTAT
*
484468 GTCT-TTATTATA-TAT
1 AT-TATTATTATATTAT
484483 A-TATATATATATATTAT
1 ATTAT-TAT-TATATTAT
* *
484500 TTTATAATTAT
1 ATTATTATTAT
484511 TATAATACCT
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
12 4 0.07
13 9 0.16
14 6 0.11
15 10 0.18
16 18 0.33
17 5 0.09
18 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (16 bp):
ATTATTATTATATTAT
Found at i:484496 original size:54 final size:53
Alignment explanation
Indices: 484389--484502 Score: 135
Period size: 53 Copynumber: 2.1 Consensus size: 53
484379 ATAGTTCTAT
*
484389 TTATTTTCTATATATTTATTATTTTCGTTTTTATTCATTATTATTATATTATA
1 TTATTTTCTATATATTTATTATTTTCGTCTTTATTCATTATTATTATATTATA
* * *
484442 TTATTTT-TTTATATTTTTTATATTTTGTCTTTATT-A-TATATATATATATATATA
1 TTATTTTCTATATATTTATTAT-TTTCGTCTTTATTCATTAT-TAT-TATAT-TATA
484496 TTATTTT
1 TTATTTT
484503 ATAATTATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
51 3 0.06
52 16 0.30
53 23 0.43
54 11 0.21
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (53 bp):
TTATTTTCTATATATTTATTATTTTCGTCTTTATTCATTATTATTATATTATA
Found at i:490738 original size:55 final size:54
Alignment explanation
Indices: 490679--490978 Score: 307
Period size: 54 Copynumber: 5.5 Consensus size: 54
490669 TAGAATTAAC
*
490679 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAA-T
* **
490734 GATTGAGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAG---CCAAAAT
* ** * * * *
490791 GACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAAT
* *
490845 GATTGAGCACCTCTGTACTTCAATCGAG-GACTGACACCTCTGTGCAGCCAACTAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGACACCTCTGTGCAGCCAA-AAT
* * * * * * ****
490900 GACTGAGCACCTTTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA-TTGGAAT
1 GATTGAGCACCTCTGTGCTTCAATCGAGA-GCTGACACCTCTGTGCAGCCAAAAT
*
490954 GATTGAGCACCTCTGTGCTACAATC
1 GATTGAGCACCTCTGTGCTTCAATC
490979 TAAAATCAAG
Statistics
Matches: 202, Mismatches: 36, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
53 1 0.00
54 70 0.35
55 70 0.35
56 15 0.07
57 42 0.21
58 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (54 bp):
GATTGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGCAGCCAAAAT
Found at i:490777 original size:27 final size:27
Alignment explanation
Indices: 490686--490778 Score: 91
Period size: 27 Copynumber: 3.4 Consensus size: 27
490676 AACGATTGAG
*
490686 CACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTTCAATCGAGAACTGA
* ** * *
490713 CACCTCTGTG-TAGCCAAAAGTG-ATTGA
1 CACCTCTGTGCT--TCAATCGAGAACTGA
490740 GCACCTCTGTGCTTCAATCGAGAACTGA
1 -CACCTCTGTGCTTCAATCGAGAACTGA
490768 CACCTCTGTGC
1 CACCTCTGTGC
490779 AGTAAAAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
26 1 0.02
27 29 0.58
28 19 0.38
29 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (27 bp):
CACCTCTGTGCTTCAATCGAGAACTGA
Found at i:490978 original size:109 final size:110
Alignment explanation
Indices: 490682--490978 Score: 330
Period size: 109 Copynumber: 2.7 Consensus size: 110
490672 AATTAACGAT
* * * * *
490682 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGA-TGATTGAGCACCTC
490747 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAAATGAC
65 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG-AAAAAAAATGAC
* ** *
490794 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
* * ** **
490859 GTACTTCAATCGAGGACTGACACCTCTGTGCAG-CCAACTATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
* * * * * **
490903 TGAGCACCTTTGTGCTTCAATCTAAATTCTGGCACCTCTGTGCA--TTGGAATGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAACCGAAA-GCTGACACCTCTGTGCAGCTAAG-ATGATTGAGCACCT
*
490966 CTGTGCTACAATC
64 CTGTGCTTCAATC
490979 TAAAATCAAG
Statistics
Matches: 159, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
108 2 0.01
109 52 0.33
110 14 0.09
111 46 0.29
112 45 0.28
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGAAAAAAAATGAC
Found at i:492004 original size:30 final size:30
Alignment explanation
Indices: 491968--492030 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
491958 GAGCTCAATA
491968 TTGAATACACATTGCTGCATTTATTTTAGT
1 TTGAATACACATTGCTGCATTTATTTTAGT
491998 TTGAATACACATTGCTGCATTTATTTTAGT
1 TTGAATACACATTGCTGCATTTATTTTAGT
492028 TTG
1 TTG
492031 CATTTCTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48
Consensus pattern (30 bp):
TTGAATACACATTGCTGCATTTATTTTAGT
Found at i:498925 original size:2 final size:2
Alignment explanation
Indices: 498918--498954 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
498908 CGTAATTAAG
498918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
498955 GTATGGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:499134 original size:16 final size:16
Alignment explanation
Indices: 499089--499148 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
499079 CGGCGTTTTT
499089 AACGCCGCTAAAAACACA
1 AACGCCGCTAAAAA-A-A
* *
499107 TACGGCG-T-AAAAAA
1 AACGCCGCTAAAAAAA
*
499121 AACGCCGCTAAAAAAT
1 AACGCCGCTAAAAAAA
*
499137 AGCGCCGCTAAA
1 AACGCCGCTAAA
499149 GTTTGCGGCG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 20 0.59
17 1 0.03
18 5 0.15
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.10
Consensus pattern (16 bp):
AACGCCGCTAAAAAAA
Found at i:499135 original size:14 final size:16
Alignment explanation
Indices: 499114--499148 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
499104 ACATACGGCG
*
499114 TAAAAAA-AACGCCGC
1 TAAAAAATAGCGCCGC
499129 TAAAAAATAGCGCCGC
1 TAAAAAATAGCGCCGC
499145 TAAA
1 TAAA
499149 GTTTGCGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.51, C:0.23, G:0.14, T:0.11
Consensus pattern (16 bp):
TAAAAAATAGCGCCGC
Found at i:499817 original size:21 final size:20
Alignment explanation
Indices: 499772--499847 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 20
499762 CTCTGTTCTA
* *
499772 CCGCTGCTCTCTCTGTGATGT
1 CCGCTGCTCTCTCTCTGCT-T
499793 -CGCTGCTTCTCTCTCTGCTT
1 CCGCTGC-TCTCTCTCTGCTT
**
499813 CCGCTGCTGCTCTAGCTGCTT
1 CCGCTGCT-CTCTCTCTGCTT
499834 CCGCTGCTCTCTCT
1 CCGCTGCTCTCTCT
499848 GTTTCCCTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.26
21 34 0.74
ACGTcount: A:0.03, C:0.39, G:0.20, T:0.38
Consensus pattern (20 bp):
CCGCTGCTCTCTCTCTGCTT
Found at i:499853 original size:18 final size:18
Alignment explanation
Indices: 499761--499853 Score: 69
Period size: 21 Copynumber: 4.6 Consensus size: 18
499751 GATATATTCT
499761 TCTCTGTTCTACCGCTGCTC
1 TCTCTGTT-T-CCGCTGCTC
*
499781 TCTCTGTGATGTCGCTGCTTCTC
1 TCTCTGT--T-TC-C-GCTGCTC
*
499804 TCTCTGCTTCCGCTGCTGC
1 TCTCTGTTTCCGCTGCT-C
*
499823 TCTAGCTGCTTCCGCTGCTC
1 TCT--CTGTTTCCGCTGCTC
499843 TCTCTGTTTCC
1 TCTCTGTTTCC
499854 CTTGCTTCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
18 12 0.20
19 5 0.08
20 13 0.21
21 16 0.26
22 3 0.05
23 12 0.20
ACGTcount: A:0.03, C:0.38, G:0.18, T:0.41
Consensus pattern (18 bp):
TCTCTGTTTCCGCTGCTC
Found at i:500897 original size:29 final size:31
Alignment explanation
Indices: 500845--500916 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
500835 ATTATAATAT
*
500845 TTATAATATTG-ACATTTTAATTTGTTT-AA
1 TTATAATATTGAACATTTGAATTTGTTTCAA
*
500874 TTATAATATTGAAC-TTTGATTTTGTTTCAA
1 TTATAATATTGAACATTTGAATTTGTTTCAA
500904 TTAT-ATCATTGAA
1 TTATAAT-ATTGAA
500917 TCGTTAAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 24 0.63
30 14 0.37
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (31 bp):
TTATAATATTGAACATTTGAATTTGTTTCAA
Found at i:501090 original size:29 final size:30
Alignment explanation
Indices: 501023--501090 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
501013 AACAACCCAT
*
501023 TAGAATAATTGAAATGAAAATAAAAATTCAG
1 TAGAATAATTGAAA-GAAAATAAAAATTCAA
** * *
501054 TATTATAATTGACA-AAATTAAAAATTCAA
1 TAGAATAATTGAAAGAAAATAAAAATTCAA
501083 TAGAATAA
1 TAGAATAA
501091 ATGATACAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 19 0.63
31 11 0.37
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.29
Consensus pattern (30 bp):
TAGAATAATTGAAAGAAAATAAAAATTCAA
Found at i:503469 original size:43 final size:44
Alignment explanation
Indices: 503422--503603 Score: 151
Period size: 43 Copynumber: 4.2 Consensus size: 44
503412 AAACCATTTA
* *
503422 ATTATTGGGTTGCCAAA-TAAAATCAAAAGATTAATTCCTTTTG
1 ATTATTGGGTTGCCAAACTAAAATCAAATGATTAGTTCCTTTTG
* * *
503465 ATTATT--ATTGCCAAAAAC-AAAATCAAATGATTAGTTCATTTTT
1 ATTATTGGGTTGCC--AAACTAAAATCAAATGATTAGTTCCTTTTG
* * * * * *
503508 AATATTGAGTTGTCAAATTAAAAATCAAAGGATTGGTTCC-TTTG
1 ATTATTGGGTTGCCAAACT-AAAATCAAATGATTAGTTCCTTTTG
* * * *
503552 A-TATTTGGCTGCAGAAACTAAAATCAAATGATTAGTTCCTTTCG
1 ATTATTGGGTTGC-CAAACTAAAATCAAATGATTAGTTCCTTTTG
503596 ATTATTGG
1 ATTATTGG
503604 TTGTGAAAAT
Statistics
Matches: 106, Mismatches: 23, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
41 5 0.05
43 63 0.59
44 12 0.11
45 26 0.25
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (44 bp):
ATTATTGGGTTGCCAAACTAAAATCAAATGATTAGTTCCTTTTG
Found at i:503530 original size:87 final size:87
Alignment explanation
Indices: 503418--503589 Score: 208
Period size: 88 Copynumber: 2.0 Consensus size: 87
503408 ATCAAAACCA
* *
503418 TTTAATTATTGGGTTGCCAAAT-AAAATCAAAAGATTAATTCCTTTTGATTATTATTGC-CAAAA
1 TTTAATTATTGAGTTGCCAAATAAAAATCAAAAGATTAATTCC-TTTGA-TATT-TGGCGCAAAA
503481 AC-AAAATCAAATGATTAGTTCATT
63 ACTAAAATCAAATGATTAGTTCATT
* * ** *
503505 TTTAA-TATTGAGTTGTCAAATTAAAAATCAAAGGATTGGTTCCTTTGATATTTGGCTGCAGAAA
1 TTTAATTATTGAGTTGCCAAA-TAAAAATCAAAAGATTAATTCCTTTGATATTTGGC-GCAAAAA
503569 CTAAAATCAAATGATTAGTTC
64 CTAAAATCAAATGATTAGTTC
503590 CTTTCGATTA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
85 3 0.04
86 17 0.23
87 17 0.23
88 36 0.49
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (87 bp):
TTTAATTATTGAGTTGCCAAATAAAAATCAAAAGATTAATTCCTTTGATATTTGGCGCAAAAACT
AAAATCAAATGATTAGTTCATT
Found at i:503624 original size:44 final size:41
Alignment explanation
Indices: 503439--503625 Score: 124
Period size: 43 Copynumber: 4.3 Consensus size: 41
503429 GGTTGCCAAA
* * * * *
503439 TAAAATCAAAAGATTAATTCCTTTTGATTATT-ATTGCCAAAAA
1 TAAAATCAAATGATTAGTTCC-TTTGA-TATTGGTTG-TAAAAT
* * * *
503482 CAAAATCAAATGATTAGTTCATTTTTAATATTGAGTTGTCAAAT
1 TAAAATCAAATGATTAGTTC--CTTTGATATTG-GTTGTAAAAT
* * * * *
503526 TAAAAATCAAAGGATTGGTTCCTTTGATATTTGGCTGCAGAAAC
1 T-AAAATCAAATGATTAGTTCCTTTGATA-TTGGTTGTA-AAAT
503570 TAAAATCAAATGATTAGTTCCTTTCGATTATTGGTTGTGAAAAT
1 TAAAATCAAATGATTAGTTCCTTT-GA-TATTGGTTGT-AAAAT
*
503614 TATAATCAAATG
1 TAAAATCAAATG
503626 TTGTGATATA
Statistics
Matches: 110, Mismatches: 24, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
43 51 0.46
44 36 0.33
45 23 0.21
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (41 bp):
TAAAATCAAATGATTAGTTCCTTTGATATTGGTTGTAAAAT
Found at i:503891 original size:53 final size:54
Alignment explanation
Indices: 503799--503947 Score: 135
Period size: 53 Copynumber: 2.7 Consensus size: 54
503789 CTTTGTAAGA
* * **
503799 AAATAAATTATCGAA-TTATTTCTTGAGAATCGTGGATGAT-AATCCTT-TAAAAG-
1 AAATAAATTAT-TAATTTATTTTTTGAGAATC-TTAATGATCAAT-CTTGTAAAAGT
* *
503852 AAATAAATTATTAATTTATTTTTTGAGAATCTTAAATGATTCTATTTTGTAAAAGT
1 AAATAAATTATTAATTTATTTTTTGAGAATCTT-AATGA-TCAATCTTGTAAAAGT
* * *
503908 TAATAAACTATTAAATTTATCTTTTGAGAATCTTAATGAT
1 AAATAAATTATT-AATTTATTTTTTGAGAATCTTAATGAT
503948 TCTATTTGTT
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
52 3 0.04
53 30 0.38
54 3 0.04
55 9 0.11
56 15 0.19
57 20 0.25
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.43
Consensus pattern (54 bp):
AAATAAATTATTAATTTATTTTTTGAGAATCTTAATGATCAATCTTGTAAAAGT
Found at i:504076 original size:37 final size:36
Alignment explanation
Indices: 503983--504088 Score: 108
Period size: 37 Copynumber: 2.9 Consensus size: 36
503973 GAATCTTGAA
**
503983 TAAAT-AAATAAATTGTTGAATTTATTGATTTTATTTT
1 TAAATGAAATAAATTGTTGAATTTATT--TCCTATTTT
* * **
504020 TAAAAGGAA-AAATCATTGAATTTATTTCCTATTTT
1 TAAATGAAATAAATTGTTGAATTTATTTCCTATTTT
504055 GTAAATGAAATAAATTGTTGAATTTATTTTCCTA
1 -TAAATGAAATAAATTGTTGAATTTA-TTTCCTA
504089 AGAATCTCAC
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
35 7 0.13
36 7 0.13
37 32 0.58
38 9 0.16
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (36 bp):
TAAATGAAATAAATTGTTGAATTTATTTCCTATTTT
Found at i:504182 original size:38 final size:38
Alignment explanation
Indices: 504140--504372 Score: 181
Period size: 38 Copynumber: 5.9 Consensus size: 38
504130 TAATTTAATT
* *
504140 TATTTTGT-AAATGAAATAAATCGTTGGATTTAGTTTCC
1 TATTTTGTAAAAAGAAATAAATCGTTAGATTTA-TTTCC
* * *
504178 TATTTTATAAAAAAAATAAATCGAAACAAATCGTTTGATTTATTTTCC
1 TATTTTGT---AAAAAGAAAT----A-A-ATCGTTAGATTTA-TTTCC
*
504226 TGTTTTGTAAAAAGAAATAAATCGTT-GATTTATTTTCC
1 TATTTTGTAAAAAGAAATAAATCGTTAGATTTA-TTTCC
* *
504264 TATTTTGTAAAAGGAAATAAATCATTAGATTTATTT--
1 TATTTTGTAAAAAGAAATAAATCGTTAGATTTATTTCC
* * *
504300 TTTTTTGT-AAAAGCAAATAAATTGTTAGATTTATTT-T
1 TATTTTGTAAAAAG-AAATAAATCGTTAGATTTATTTCC
* * *
504337 TCTTTTGTAAAAGGAAATAAATCATTAGATTTATTT
1 TATTTTGTAAAAAGAAATAAATCGTTAGATTTATTT
504373 TTTGGGAATC
Statistics
Matches: 162, Mismatches: 19, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
35 4 0.02
36 27 0.17
37 27 0.17
38 49 0.30
39 12 0.07
40 1 0.01
41 1 0.01
42 7 0.04
45 9 0.06
46 1 0.01
47 1 0.01
48 23 0.14
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (38 bp):
TATTTTGTAAAAAGAAATAAATCGTTAGATTTATTTCC
Found at i:504209 original size:48 final size:49
Alignment explanation
Indices: 504147--504249 Score: 147
Period size: 48 Copynumber: 2.1 Consensus size: 49
504137 ATTTATTTTG
*
504147 TAAAT-GAAATAAATCGTTGGATTTAGTTTCCTATTTTATAAAAA-AAA
1 TAAATCGAAACAAATCGTTGGATTTAGTTTCCTATTTTATAAAAAGAAA
* * * *
504194 TAAATCGAAACAAATCGTTTGATTTATTTTCCTGTTTTGTAAAAAGAAA
1 TAAATCGAAACAAATCGTTGGATTTAGTTTCCTATTTTATAAAAAGAAA
504243 TAAATCG
1 TAAATCG
504250 TTGATTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
47 5 0.10
48 34 0.69
49 10 0.20
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.38
Consensus pattern (49 bp):
TAAATCGAAACAAATCGTTGGATTTAGTTTCCTATTTTATAAAAAGAAA
Found at i:504351 original size:73 final size:73
Alignment explanation
Indices: 504200--504375 Score: 239
Period size: 73 Copynumber: 2.4 Consensus size: 73
504190 AAAATAAATC
* * *
504200 GAAACAAATCGTTTGATTTATTTTCCTGTTTTGTAAAAAGAAATAAATCGTTGATTTATTTTCCT
1 GAAATAAATCATTAGATTTATTTT--T-TTTTGTAAAAAGAAATAAATCGTTGATTTATTTT-CT
504265 ATTTTGTAAAAG
62 ATTTTGTAAAAG
* *
504277 GAAATAAATCATTAGATTTATTTTTTTTTGT-AAAAGCAAATAAATTGTTAGATTTATTTT-TCT
1 GAAATAAATCATTAGATTTATTTTTTTTTGTAAAAAG-AAATAAATCGTT-GATTTATTTTCTAT
504340 TTTGTAAAAG
64 TTTGTAAAAG
504350 GAAATAAATCATTAGATTTATTTTTT
1 GAAATAAATCATTAGATTTATTTTTT
504376 GGGAATCTTG
Statistics
Matches: 92, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
73 43 0.47
74 17 0.18
75 11 0.12
77 21 0.23
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (73 bp):
GAAATAAATCATTAGATTTATTTTTTTTTGTAAAAAGAAATAAATCGTTGATTTATTTTCTATTT
TGTAAAAG
Found at i:504355 original size:37 final size:36
Alignment explanation
Indices: 504200--504375 Score: 219
Period size: 38 Copynumber: 4.7 Consensus size: 36
504190 AAAATAAATC
* * *
504200 GAAACAAATCGTTTGATTTATTTTCCTGTTTTGTAAAAA
1 GAAATAAATCGTTAGATTTATTTT--T-TTTTGTAAAAG
504239 GAAATAAATCGTT-GATTTATTTTCCTATTTTGTAAAAG
1 GAAATAAATCGTTAGATTTATTTT--T-TTTTGTAAAAG
*
504277 GAAATAAATCATTAGATTTATTTTTTTTTGTAAAAG
1 GAAATAAATCGTTAGATTTATTTTTTTTTGTAAAAG
* *
504313 CAAATAAATTGTTAGATTTATTTTTCTTTTGTAAAAG
1 GAAATAAATCGTTAGATTTATTTTT-TTTTGTAAAAG
*
504350 GAAATAAATCATTAGATTTATTTTTT
1 GAAATAAATCGTTAGATTTATTTTTT
504376 GGGAATCTTG
Statistics
Matches: 125, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
36 34 0.27
37 34 0.27
38 35 0.28
39 22 0.18
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (36 bp):
GAAATAAATCGTTAGATTTATTTTTTTTTGTAAAAG
Found at i:505338 original size:14 final size:14
Alignment explanation
Indices: 505319--505355 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
505309 GTTTAACGAA
505319 AGGTTGAAACAAAG
1 AGGTTGAAACAAAG
505333 AGGTTGAAACAAAG
1 AGGTTGAAACAAAG
505347 AGGTTGAAA
1 AGGTTGAAA
505356 TCCTCAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.30, T:0.16
Consensus pattern (14 bp):
AGGTTGAAACAAAG
Found at i:508161 original size:25 final size:25
Alignment explanation
Indices: 508082--508175 Score: 68
Period size: 25 Copynumber: 3.6 Consensus size: 25
508072 ATTTAGTTTT
*
508082 TATATTAATTATAATT-TGTATATTA
1 TATATTATTTATAATTCT-TATATTA
*
508107 TA-ATTTGATTTTTATAATTCTAAT-TCTA
1 TATA-TT-A--TTTATAATTCTTATAT-TA
508135 TATATTATTTATAATTCTTATATTA
1 TATATTATTTATAATTCTTATATTA
* *
508160 TAAATTTTATTATAAT
1 TATATTAT-TTATAAT
508176 CACTAAATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
24 1 0.02
25 25 0.45
26 9 0.16
27 2 0.04
28 16 0.29
29 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TATATTATTTATAATTCTTATATTA
Found at i:508162 original size:14 final size:13
Alignment explanation
Indices: 508089--508175 Score: 63
Period size: 14 Copynumber: 6.6 Consensus size: 13
508079 TTTTATATTA
508089 ATTATAATTTGTAT
1 ATTATAATTT-TAT
*
508103 ATTATAATTTGATT
1 ATTATAATTTTA-T
* *
508117 TTTATAATTCTA-
1 ATTATAATTTTAT
* *
508129 ATTCTATATATTAT
1 ATTATA-ATTTTAT
508143 -TTATAATTCTTAT
1 ATTATAATT-TTAT
*
508156 ATTATAAATTT-T
1 ATTATAATTTTAT
508168 ATTATAAT
1 ATTATAAT
508176 CACTAAATTA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
12 14 0.25
13 15 0.27
14 27 0.48
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.57
Consensus pattern (13 bp):
ATTATAATTTTAT
Found at i:511167 original size:23 final size:22
Alignment explanation
Indices: 511135--511177 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
511125 CTAATGAACT
* *
511135 ATATATATAGTTTGTATATATC
1 ATATATATAGGTTATATATATC
511157 ATATACTATAGGTTATATATA
1 ATATA-TATAGGTTATATATA
511178 CTAATGAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (22 bp):
ATATATATAGGTTATATATATC
Found at i:511192 original size:17 final size:17
Alignment explanation
Indices: 511170--511227 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
511160 TACTATAGGT
511170 TATATATACTAATGAAC
1 TATATATACTAATGAAC
**
511187 TATATA-A-TATAT-AGTT
1 TATATATACTA-ATGA-AC
511203 TATATATACTAATGAAC
1 TATATATACTAATGAAC
511220 TATATATA
1 TATATATA
511228 ATGTATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAC
Found at i:511206 original size:33 final size:33
Alignment explanation
Indices: 511163--511306 Score: 143
Period size: 33 Copynumber: 4.3 Consensus size: 33
511153 TATCATATAC
*
511163 TATAGGTTATATATACTAATGAACTATATAATA
1 TATAGTTTATATATACTAATGAACTATATAATA
*
511196 TATAGTTTATATATACTAATGAACTATATATAATG
1 TATAGTTTATATATACTAATGAAC--TATATAATA
* *
511231 TATAATTTAAATATAC-AAT-ATAGTCTATATATATTA
1 TATAGTTTATATATACTAATGA-A--CTATATA-A-TA
*
511267 TATAG-TT-TATATACTAATAAACTATATAATA
1 TATAGTTTATATATACTAATGAACTATATAATA
*
511298 TATACTTTA
1 TATAGTTTA
511307 GGGTTTAGGG
Statistics
Matches: 92, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
31 6 0.07
32 3 0.03
33 31 0.34
34 16 0.17
35 29 0.32
36 7 0.08
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
TATAGTTTATATATACTAATGAACTATATAATA
Found at i:511245 original size:102 final size:101
Alignment explanation
Indices: 511089--511306 Score: 232
Period size: 102 Copynumber: 2.1 Consensus size: 101
511079 ATTAATAAAT
** * * * *
511089 TAATATATAGTTTATATATACTATATAGTTTATATACTAATGAACTATATATAT-AGT-TTGTAT
1 TAATATATAGTTTATATATACTATATAGACTATATACTAATGAAATATAAATATAAATATAGTAT
*
511152 ATATCATA-TACTATAGGTTATATATACTAATGAACTATA
66 ATAT-ATATTA-TATA-GTT-TATATACTAATAAACTATA
*
511191 TAATATATAGTTTATATATACTA-AT-GAACTATATA-TAATGTATAATTTAAATATACAATATA
1 TAATATATAGTTTATATATACTATATAG-ACTATATACTAATG-A-AATATAAATATA-AATATA
*
511253 GTCTATATATATTATATAGTTTATATACTAATAAACTATA
62 GTATATATATATTATATAGTTTATATACTAATAAACTATA
*
511293 TAATATATACTTTA
1 TAATATATAGTTTA
511307 GGGTTTAGGG
Statistics
Matches: 99, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
100 6 0.06
101 9 0.09
102 62 0.63
103 3 0.03
104 9 0.09
105 10 0.10
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (101 bp):
TAATATATAGTTTATATATACTATATAGACTATATACTAATGAAATATAAATATAAATATAGTAT
ATATATATTATATAGTTTATATACTAATAAACTATA
Found at i:511253 original size:86 final size:82
Alignment explanation
Indices: 511103--511263 Score: 193
Period size: 86 Copynumber: 1.9 Consensus size: 82
511093 ATATAGTTTA
* *
511103 TATATACTATATAGTTTATATACTAATGAACTATATATATAGTTTGTATATATCATATACTATAG
1 TATATAATATATAGTTTATATACTAATGAACTATATATATA--TTGTATATATAATATACTATA-
511168 GT-TATATATACTAATGAAC
63 GTCTATATATACTAATGAAC
*
511187 TATATAATATATAGTTTATATATACTAATGAACTATATATA-A-TGTATAATTTAAATATACAAT
1 TATATAATATATAG-TT-TATATACTAATGAACTATATATATATTGTAT-ATAT-AATATAC--T
511250 ATAGTCTATATATA
60 ATAGTCTATATATA
511264 TTATATAGTT
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
82 5 0.07
83 3 0.04
84 19 0.28
85 5 0.07
86 35 0.52
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (82 bp):
TATATAATATATAGTTTATATACTAATGAACTATATATATATTGTATATATAATATACTATAGTC
TATATATACTAATGAAC
Found at i:511358 original size:2 final size:2
Alignment explanation
Indices: 511341--511412 Score: 54
Period size: 2 Copynumber: 33.0 Consensus size: 2
511331 ATATGTAAAT
* *
511341 TA TA CTA TA TA GTA TA TA TA GTT TT TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
511384 GTA TA AA TA TA CTA TA GTA TA TA TT TA TA
1 -TA TA TA TA TA -TA TA -TA TA TA TA TA TA
511413 GGTCACATGT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 47 0.81
3 11 0.19
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:511359 original size:25 final size:26
Alignment explanation
Indices: 511321--511407 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 26
511311 TTAGGGTTTT
511321 TATATAGT-TCATAT-GTAAATTATAC
1 TATATAGTAT-ATATAGTAAATTATAC
**
511346 TATATAGTATATATAGT-TTTTATA-
1 TATATAGTATATATAGTAAATTATAC
*
511370 TATATA-TATATATAGTATAAATATAC
1 TATATAGTATATATAGTA-AATTATAC
511396 --TATAGTATATAT
1 TATATAGTATATAT
511408 TTATAGGTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
23 10 0.20
24 10 0.20
25 28 0.55
26 3 0.06
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (26 bp):
TATATAGTATATATAGTAAATTATAC
Found at i:511379 original size:23 final size:25
Alignment explanation
Indices: 511340--511407 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 25
511330 CATATGTAAA
511340 TTATACTATATAGTATATATAGTTT
1 TTATACTATATAGTATATATAGTTT
*
511365 TTATA-TATATA-TATATATAGTAT
1 TTATACTATATAGTATATATAGTTT
**
511388 AAATA-TACTATAGTATATAT
1 TTATACTA-TATAGTATATAT
511408 TTATAGGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 16 0.42
24 10 0.26
25 12 0.32
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (25 bp):
TTATACTATATAGTATATATAGTTT
Found at i:511431 original size:57 final size:56
Alignment explanation
Indices: 511370--511502 Score: 160
Period size: 57 Copynumber: 2.3 Consensus size: 56
511360 AGTTTTTATA
* * *
511370 TATATA-TATATATAGTATAAATATACTATAGTATATATTTATAGGTCACATGTAAAC
1 TATATAGTATATATA-TATAAATATACTATA-CATATATATATAAGTCACATGTAAAC
* * * *
511427 TATATAGTATATAAATATCAACTATAGTATACATATATATATAAGTCATATGTAAAC
1 TATATAGTATATATATAT-AAATATACTATACATATATATATAAGTCACATGTAAAC
*
511484 TATATAGTTTATATATATA
1 TATATAGTATATATATATA
511503 GTTCATATGT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
56 1 0.02
57 47 0.72
58 17 0.26
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.41
Consensus pattern (56 bp):
TATATAGTATATATATATAAATATACTATACATATATATATAAGTCACATGTAAAC
Found at i:511433 original size:33 final size:31
Alignment explanation
Indices: 511368--511520 Score: 108
Period size: 33 Copynumber: 5.1 Consensus size: 31
511358 ATAGTTTTTA
** *
511368 TATATA-TATATATATA-GT-ATAAATATAC
1 TATATAGTATATATATAGGTCATATGTAAAC
* *
511396 TATAGTA-TATATTTATAGGTCACATGTAAAC
1 TATA-TAGTATATATATAGGTCATATGTAAAC
* * * *
511427 TATATAGTATATAAATA--TCA-A-CTATAG
1 TATATAGTATATATATAGGTCATATGTAAAC
* *
511454 TATACA-TATATATATAAGTCATATGTAAAC
1 TATATAGTATATATATAGGTCATATGTAAAC
*
511484 TATATAGTTTATATATATAGTTCATATGTAAAC
1 TATATAG--TATATATATAGGTCATATGTAAAC
511517 TATA
1 TATA
511521 GTTCATATGT
Statistics
Matches: 96, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
26 9 0.09
27 8 0.08
28 8 0.08
29 15 0.16
30 12 0.12
31 18 0.19
33 26 0.27
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (31 bp):
TATATAGTATATATATAGGTCATATGTAAAC
Found at i:511521 original size:31 final size:32
Alignment explanation
Indices: 511460--511528 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
511450 ATAGTATACA
511460 TATATATATAAGTCATATGTAAACTATATAGTT
1 TATATATATAAGTCATATGTAAAC-ATATAGTT
511493 TATATATAT-AGTTCATATGTAAAC-TATAGTT
1 TATATATATAAG-TCATATGTAAACATATAGTT
*
511524 CATAT
1 TATAT
511529 GTAAATATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 11 0.32
32 2 0.06
33 21 0.62
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (32 bp):
TATATATATAAGTCATATGTAAACATATAGTT
Found at i:511522 original size:18 final size:18
Alignment explanation
Indices: 511499--511570 Score: 81
Period size: 18 Copynumber: 3.7 Consensus size: 18
511489 AGTTTATATA
511499 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
511517 TATAGTTCATATGTAAATATTAAC
1 TATAGTTCATATG----TA--AAC
*
511541 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
511559 TATAGTTCATAT
1 TATAGTTCATAT
511571 ATAATATCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 27 0.59
20 2 0.04
22 2 0.04
24 15 0.33
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:511659 original size:32 final size:32
Alignment explanation
Indices: 511618--511683 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
511608 AGTTCATATG
* *
511618 TAAACTATAGTTCATATATATAATATATAATA
1 TAAACTATAGTTCATATAAATAATATAAAATA
*
511650 TAAACTATAGTTTATATAAATAATATAAAATA
1 TAAACTATAGTTCATATAAATAATATAAAATA
511682 TA
1 TA
511684 GTATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAAATAATATAAAATA
Found at i:511672 original size:25 final size:23
Alignment explanation
Indices: 511631--511694 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
511621 ACTATAGTTC
*
511631 ATATA-TATAATATATAATATAAA
1 ATATAGTAT-ATAAATAATATAAA
*
511654 CTATAGTTTATATAAATAATATAAA
1 ATATAG--TATATAAATAATATAAA
511679 ATATAGTATATAAATA
1 ATATAGTATATAAATA
511695 TAAATTATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 14 0.40
25 18 0.51
26 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (23 bp):
ATATAGTATATAAATAATATAAA
Found at i:511697 original size:25 final size:26
Alignment explanation
Indices: 511632--511730 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 26
511622 CTATAGTTCA
*
511632 TATATATAATATATAATATAAACTATAG
1 TATATA-AATATA-AATATAAAATATAG
*
511660 TTTATATAA-AT-AATATAAAATATAG
1 TATATA-AATATAAATATAAAATATAG
** *
511685 TATATAAATATAAATTATAGTATGTAG
1 TATATAAATATAAA-TATAAAATATAG
*
511712 TTTATAAATATAAATATAA
1 TATATAAATATAAATATAA
511731 CCCTAAATCT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
24 2 0.03
25 20 0.33
26 6 0.10
27 24 0.40
28 8 0.13
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (26 bp):
TATATAAATATAAATATAAAATATAG
Found at i:511785 original size:21 final size:23
Alignment explanation
Indices: 511761--511808 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
511751 ACATATATAC
*
511761 TATATAT-ATAA-ATTATATAAT
1 TATATATAATAATACTATATAAT
*
511782 TATATATAATAATACTATATATT
1 TATATATAATAATACTATATAAT
511805 TATA
1 TATA
511809 CAATACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 4 0.17
23 12 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATAATAATACTATATAAT
Done.