Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002738.1 Hibiscus syriacus cultivar Beakdansim tig00005647_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: 74266
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:894 original size:2 final size:2
Alignment explanation
Indices: 889--971 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
879 ACCGAAGTAA
889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
931 AT AT 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 AT AT A
972 GGGTAGAGAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6746 original size:30 final size:31
Alignment explanation
Indices: 6712--6778 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
6702 TTGCCATACA
6712 GTCCCCCAATATTTAGTCTG-TTGCAATATG
1 GTCCCCCAATATTTAGTCTGTTTGCAATATG
*
6742 GTCCCCCAATATTTAGTTTGTTTGCAATATG
1 GTCCCCCAATATTTAGTCTGTTTGCAATATG
*
6773 CTCCCC
1 GTCCCC
6779 GACGTAACCG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (31 bp):
GTCCCCCAATATTTAGTCTGTTTGCAATATG
Found at i:9091 original size:19 final size:20
Alignment explanation
Indices: 9052--9095 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
9042 ACAATTGAAT
9052 TTGCCACGACATTTCATTCAA
1 TTGCCACGACA-TTCATTCAA
9073 CTTGCCACGACA-T-ATTCAA
1 -TTGCCACGACATTCATTCAA
9092 TTGC
1 TTGC
9096 AACCACACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 6 0.27
20 1 0.05
22 11 0.50
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.32
Consensus pattern (20 bp):
TTGCCACGACATTCATTCAA
Found at i:11231 original size:23 final size:23
Alignment explanation
Indices: 11178--11237 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
11168 ACAATCTTAT
*
11178 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
** * *
11201 GCGACACTTCGTTGCAATTCTAC
1 ATGGCACTTCGGTGCAATTCTAC
11224 ATGGCACTTCGGTG
1 ATGGCACTTCGGTG
11238 TATTTATACG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (23 bp):
ATGGCACTTCGGTGCAATTCTAC
Found at i:18166 original size:23 final size:22
Alignment explanation
Indices: 18140--18199 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
18130 AATCTTATAT
18140 GGCACTATGGTGCAATTCTACGC
1 GGCACT-TGGTGCAATTCTACGC
*
18163 GGCACTTTGGTGCAATTCTATGC
1 GGCAC-TTGGTGCAATTCTACGC
18186 GGCACTTCGGTGCA
1 GGCACTT-GGTGCA
18200 TTTATATGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.06
23 31 0.91
24 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACGC
Found at i:18207 original size:23 final size:23
Alignment explanation
Indices: 18140--18207 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
18130 AATCTTATAT
* *
18140 GGCACTAT-GGTGCAATTCTACGC
1 GGCACT-TCGGTGCAATTATATGC
* *
18163 GGCACTTTGGTGCAATTCTATGC
1 GGCACTTCGGTGCAATTATATGC
*
18186 GGCACTTCGGTGCATTTATATG
1 GGCACTTCGGTGCAATTATATG
18208 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 1 0.03
23 39 0.98
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATATGC
Found at i:22599 original size:59 final size:59
Alignment explanation
Indices: 22500--22628 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
22490 CAGCAGGCTG
** * * *
22500 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTGTGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
* ** * *
22559 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
*
22618 CATACTCGGGA
1 CATATTCGGGA
22629 TTGCATTACG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
Found at i:22727 original size:20 final size:20
Alignment explanation
Indices: 22687--22728 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
22677 TTATATATTG
* *
22687 GGCTATTGTCTATTGTTTAT
1 GGCTATTGTCTATGGTATAT
22707 GGCTATTGTCTATGGTATAT
1 GGCTATTGTCTATGGTATAT
22727 GG
1 GG
22729 TTATGGAATA
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:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (20 bp):
GGCTATTGTCTATGGTATAT
Found at i:22778 original size:44 final size:44
Alignment explanation
Indices: 22729--22967 Score: 399
Period size: 44 Copynumber: 5.4 Consensus size: 44
22719 TGGTATATGG
* *
22729 TTATGGA-ATAATGGCAAGTTTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
22773 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
22817 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGA
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
22861 TTATGGATAAATGGTAAGTATAATGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
22905 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
22949 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
22968 ATATTGAACA
Statistics
Matches: 184, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 172 0.93
45 2 0.01
46 10 0.05
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:22783 original size:25 final size:25
Alignment explanation
Indices: 22755--22827 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
22745 AGTTTATTGG
22755 TAAAATAAGCTTACGAGCTTATGGA
1 TAAAATAAGCTTACGAGCTTATGGA
* **
22780 T-AAAT--G-GTA--AGTATATTGG-
1 TAAAATAAGCTTACGAGCTTA-TGGA
22799 TAAAATAAGCTTACGAGCTTATGGA
1 TAAAATAAGCTTACGAGCTTATGGA
22824 TAAA
1 TAAA
22828 TGGTAAGTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 2 0.06
22 2 0.06
23 2 0.06
24 7 0.21
25 9 0.26
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (25 bp):
TAAAATAAGCTTACGAGCTTATGGA
Found at i:22828 original size:24 final size:24
Alignment explanation
Indices: 22757--22828 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
22747 TTTATTGGTA
22757 AAATAAGCTTACGAGCTTATGGAT
1 AAATAAGCTTACGAGCTTATGGAT
*
22781 AAAT--G-GTA--AG-TATATTGG-T
1 AAATAAGCTTACGAGCT-TA-TGGAT
22800 AAAATAAGCTTACGAGCTTATGGAT
1 -AAATAAGCTTACGAGCTTATGGAT
22825 AAAT
1 AAAT
22829 GGTAAGTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 7 0.19
21 2 0.06
22 2 0.06
23 2 0.06
24 11 0.31
25 5 0.14
26 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (24 bp):
AAATAAGCTTACGAGCTTATGGAT
Found at i:22910 original size:24 final size:24
Alignment explanation
Indices: 22883--22956 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
22873 GGTAAGTATA
22883 ATGGTAAAATAAGCTTACGAGCTT
1 ATGGTAAAATAAGCTTACGAGCTT
* **
22907 ATGG-ATAAAT--G-GTA--AGTAT
1 ATGGTA-AAATAAGCTTACGAGCTT
22926 ATTGGTAAAATAAGCTTACGAGCTT
1 A-TGGTAAAATAAGCTTACGAGCTT
22951 ATGGTA
1 ATGGTA
22957 TTAAATGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 3 0.08
22 2 0.06
23 3 0.08
24 13 0.36
25 4 0.11
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGGTAAAATAAGCTTACGAGCTT
Found at i:24863 original size:23 final size:22
Alignment explanation
Indices: 24820--24863 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
24810 TACTGTAGTA
*
24820 GGGAATCGGTACCCTATAGCAG
1 GGGAATCGGTACCCTAAAGCAG
*
24842 GGGAATCGGTTCCCCTAAAGCA
1 GGGAATCGG-TACCCTAAAGCA
24864 ATCTGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.18
Consensus pattern (22 bp):
GGGAATCGGTACCCTAAAGCAG
Found at i:24939 original size:21 final size:18
Alignment explanation
Indices: 24909--24959 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 18
24899 GTATTATTCA
*
24909 TTACTATTCATACGGTATT
1 TTACTGTTCATACGGTA-T
*
24928 GTTCACTGTTCATACTGTAT
1 -TT-ACTGTTCATACGGTAT
24948 TTACTGTTCATA
1 TTACTGTTCATA
24960 AAACATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 10 0.36
19 2 0.07
20 3 0.11
21 13 0.46
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.47
Consensus pattern (18 bp):
TTACTGTTCATACGGTAT
Found at i:25839 original size:37 final size:36
Alignment explanation
Indices: 25793--25934 Score: 122
Period size: 36 Copynumber: 3.7 Consensus size: 36
25783 TTTTTGAAAG
* * **
25793 TATATTATATAATTTTTGAAAACATTTTGAAATTATA
1 TATAATATATAA-TTTTAAAAACATTTTGAAAACATA
25830 TATAATATATAATTTTAAAAACATTTTGAAAACATA
1 TATAATATATAATTTTAAAAACATTTTGAAAACATA
* *
25866 TATATATATATATATATATAATATATATAGTTTTGAAAACATATA
1 TATA-ATATATA-AT-TTTAA-A-A-ACA-TTTTGAAAAC--ATA
* *
25911 TATAATATATAGTTTTGAAAACAT
1 TATAATATATAATTTTAAAAACAT
25935 ATATAATATA
Statistics
Matches: 86, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
36 25 0.29
37 18 0.21
38 3 0.03
39 6 0.07
40 2 0.02
41 2 0.02
42 5 0.06
43 11 0.13
44 7 0.08
45 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (36 bp):
TATAATATATAATTTTAAAAACATTTTGAAAACATA
Found at i:25909 original size:27 final size:25
Alignment explanation
Indices: 25879--26010 Score: 167
Period size: 25 Copynumber: 5.1 Consensus size: 25
25869 ATATATATAT
25879 ATATATAATATATATAGTTTTGAAAAC
1 ATATAT-A-ATATATAGTTTTGAAAAC
25906 ATATATATAATATATAGTTTTGAAAAC
1 --ATATATAATATATAGTTTTGAAAAC
25933 ATATATAATATATAGTTTTGAAAAC
1 ATATATAATATATAGTTTTGAAAAC
* *
25958 ATATATAATATATAGTTTTTAAAAT
1 ATATATAATATATAGTTTTGAAAAC
* * *
25983 AT-TTTGAAAACATAGTTTTGAAAAC
1 ATATAT-AATATATAGTTTTGAAAAC
26008 ATA
1 ATA
26011 AAACATTTTG
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
24 2 0.02
25 67 0.71
27 18 0.19
28 1 0.01
29 6 0.06
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.41
Consensus pattern (25 bp):
ATATATAATATATAGTTTTGAAAAC
Found at i:25914 original size:2 final size:2
Alignment explanation
Indices: 25863--25894 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
25853 TTTTGAAAAC
25863 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25895 GTTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:26066 original size:29 final size:29
Alignment explanation
Indices: 26016--26130 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 29
26006 ACATAAAACA
*
26016 TTTTGAAAACATATATATATATATATAGT
1 TTTTGAAAACATATATAAATATATATAGT
*
26045 TTTTGAAAACAT-TTTGAAATATATATA-T
1 TTTTGAAAACATATAT-AAATATATATAGT
* * * * *
26073 ATAT-ATATATATATATATATATAATATAGT
1 TTTTGA-AAACATATATAAATAT-ATATAGT
* * *
26103 TTTTTAAAACATTTTTTAAATATATATA
1 TTTTGAAAACA-TATATAAATATATATA
26131 ATATATAGTT
Statistics
Matches: 64, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
27 1 0.02
28 14 0.22
29 29 0.45
30 11 0.17
31 9 0.14
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTTGAAAACATATATAAATATATATAGT
Found at i:26070 original size:2 final size:2
Alignment explanation
Indices: 26063--26100 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
26053 ACATTTTGAA
26063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26101 GTTTTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:26173 original size:20 final size:20
Alignment explanation
Indices: 26140--26180 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
26130 AATATATAGT
** *
26140 TTTGAAAATGTTTTTGAAAA
1 TTTGAAAACATTTTAGAAAA
26160 TTTGAAAACATTTTAGAAAA
1 TTTGAAAACATTTTAGAAAA
26180 T
1 T
26181 ATATATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (20 bp):
TTTGAAAACATTTTAGAAAA
Found at i:26771 original size:7 final size:8
Alignment explanation
Indices: 26753--26778 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
26743 ACAGAGACAG
26753 AAAACATA
1 AAAACATA
26761 AAAACATA
1 AAAACATA
26769 AAAACATA
1 AAAACATA
26777 AA
1 AA
26779 GGGAGCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAACATA
Found at i:27462 original size:27 final size:26
Alignment explanation
Indices: 27421--27496 Score: 73
Period size: 32 Copynumber: 2.7 Consensus size: 26
27411 ATTTAACATT
27421 TTTATTTTTTATTTTATTTTCCCTTTGA
1 TTTA-TTTTT-TTTTATTTTCCCTTTGA
27449 TTTATTTAATTTTTTTTATTTTTTCCCTTTGA
1 TTTA--T--TTTTTTTTA--TTTTCCCTTTGA
27481 TTTA-TTTTTTTTATTT
1 TTTATTTTTTTTTATTT
27497 AATATTTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
25 3 0.07
27 9 0.21
28 4 0.09
29 2 0.05
30 5 0.12
31 4 0.09
32 16 0.37
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTATTTTTTTTTATTTTCCCTTTGA
Found at i:27473 original size:32 final size:33
Alignment explanation
Indices: 27424--27487 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
27414 TAACATTTTT
27424 ATTTTTTATTTTATTTTCCCTTTGATTTATTTA
1 ATTTTTTATTTTATTTTCCCTTTGATTTATTTA
27457 ATTTTTT-TTATT-TTTTCCCTTTGATTTATTT
1 ATTTTTTATT-TTATTTTCCCTTTGATTTATTT
27488 TTTTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 21 0.70
33 9 0.30
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (33 bp):
ATTTTTTATTTTATTTTCCCTTTGATTTATTTA
Found at i:27528 original size:25 final size:24
Alignment explanation
Indices: 27480--27528 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
27470 TTTCCCTTTG
* * *
27480 ATTTATTTTTTTTATTTAATATTT
1 ATTTATTTTTCTTATATAACATTT
27504 ATTTATTATTTCTTATATAACATTT
1 ATTTATT-TTTCTTATATAACATTT
27529 TTGAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTTATTTTTCTTATATAACATTT
Found at i:28671 original size:21 final size:20
Alignment explanation
Indices: 28632--28671 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28622 TCTAATTTTA
* *
28632 AAAAAATTAATGTGTCATTT
1 AAAAAATTAATATGCCATTT
28652 AAAAAATTAATATGACCATT
1 AAAAAATTAATATG-CCATT
28672 GTATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAAAATTAATATGCCATTT
Found at i:28957 original size:22 final size:22
Alignment explanation
Indices: 28932--28980 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
28922 GATGTATTTA
*
28932 ATTTT-CTATACATATATAAATT
1 ATTTTACTATAAATATA-AAATT
*
28954 ATTTTAATTATAAATATAAAATT
1 ATTTT-ACTATAAATATAAAATT
28977 ATTT
1 ATTT
28981 AAATATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 9 0.39
24 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTACTATAAATATAAAATT
Found at i:28990 original size:23 final size:23
Alignment explanation
Indices: 28943--29020 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
28933 TTTTCTATAC
*
28943 ATATATAAATTATTTTAAT-TATAA
1 ATATA-AAATTATTTAAATAT-TAA
28967 ATATAAAATTATTTAAATATTAAA
1 ATATAAAATTATTTAAATATT-AA
* * *
28991 AAATTAAA-TATTAAAATATTTAA
1 ATATAAAATTATTTAAATA-TTAA
29014 A-ATAAAA
1 ATATAAAA
29021 ATTAAATTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.11
23 25 0.54
24 16 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAAATTATTTAAATATTAA
Found at i:28999 original size:15 final size:15
Alignment explanation
Indices: 28979--29027 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
28969 ATAAAATTAT
28979 TTAAATATTAAAAAA
1 TTAAATATTAAAAAA
*
28994 TTAAATATTAAAATAT
1 TTAAATATTAAAA-AA
29010 TTAAA-A-T-AAAAA
1 TTAAATATTAAAAAA
29022 TTAAAT
1 TTAAAT
29028 TACTAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 6 0.20
13 3 0.10
14 1 0.03
15 14 0.47
16 6 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAATATTAAAAAA
Found at i:29093 original size:2 final size:2
Alignment explanation
Indices: 29086--29126 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
29076 TAAAATTAGA
29086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29127 CATAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29131 original size:8 final size:7
Alignment explanation
Indices: 29085--29131 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 7
29075 TTAAAATTAG
29085 AATATAT
1 AATATAT
29092 -ATATAT
1 AATATAT
29098 ATATATAT
1 A-ATATAT
29106 ATATATAT
1 A-ATATAT
29114 ATATATAT
1 A-ATATAT
29122 AATATCAT
1 AATAT-AT
29130 AA
1 AA
29132 AATAATTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.16
7 4 0.11
8 27 0.73
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (7 bp):
AATATAT
Found at i:29455 original size:24 final size:24
Alignment explanation
Indices: 29428--29484 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 24
29418 AATTAGTCTA
29428 AAATTTTTAACTCTCGACTAATTT
1 AAATTTTTAACTCTCGACTAATTT
* *
29452 AAATTTTACAAGTCTCGACTAATTT
1 AAATTTT-TAACTCTCGACTAATTT
29477 AAATTTTT
1 AAATTTTT
29485 TAAATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (24 bp):
AAATTTTTAACTCTCGACTAATTT
Found at i:29881 original size:25 final size:25
Alignment explanation
Indices: 29853--29911 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
29843 AGAAAACATA
*
29853 ATAAATTTCGACTAATCCAAAATTT
1 ATAAATCTCGACTAATCCAAAATTT
* ** *
29878 ATAAGTCTCGACTAATTTAAATTTT
1 ATAAATCTCGACTAATCCAAAATTT
29903 ATAAATCTC
1 ATAAATCTC
29912 AATTAATCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (25 bp):
ATAAATCTCGACTAATCCAAAATTT
Found at i:35533 original size:18 final size:20
Alignment explanation
Indices: 35519--35560 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
35509 AATTTATTTA
35519 AAAAATATTATTTATAATAT
1 AAAAATATTATTTATAATAT
*
35539 AAATATATTATTTATAGATAT
1 AAAAATATTATTTATA-ATAT
35560 A
1 A
35561 TTATTTGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAAATATTATTTATAATAT
Found at i:35559 original size:15 final size:15
Alignment explanation
Indices: 35536--35566 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35526 TTATTTATAA
35536 TATAAATATATTATT
1 TATAAATATATTATT
*
35551 TATAGATATATTATT
1 TATAAATATATTATT
35566 T
1 T
35567 GGGGTGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATAAATATATTATT
Found at i:35634 original size:13 final size:13
Alignment explanation
Indices: 35616--35640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35606 TTAGATATTA
35616 ATTGTTATAATTT
1 ATTGTTATAATTT
35629 ATTGTTATAATT
1 ATTGTTATAATT
35641 GAGCGCTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATTGTTATAATTT
Found at i:37779 original size:75 final size:75
Alignment explanation
Indices: 37625--37806 Score: 206
Period size: 75 Copynumber: 2.4 Consensus size: 75
37615 TGATTTGGGT
* * *
37625 TTAATATTATGGTTTGAGT-TTTAAGATTTAACACTTTAATATTATGATTTTATTATGGATTTCA
1 TTAATATTATGGTTTGAATCTTGAA-ATTTGACACTTTAATATTATGATTTTATTATGGATTTCA
* *
37689 TTATTCCAGAG
65 TTATTCCAAAC
* * *
37700 TTAATATTATGGTTTGAATCTTGAAATTTGACATTTTAATATTATGGTTTGT-TTATGGATTTTA
1 TTAATATTATGGTTTGAATCTTGAAATTTGACACTTTAATATTATGATTT-TATTATGGATTTCA
* *
37764 TTGTTCTAAAC
65 TTATTCCAAAC
* * * *
37775 TTAATATTGTTGTTTGACTCTTGATATTTGAC
1 TTAATATTATGGTTTGAATCTTGAAATTTGAC
37807 TTTATTTATA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
75 86 0.95
76 5 0.05
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (75 bp):
TTAATATTATGGTTTGAATCTTGAAATTTGACACTTTAATATTATGATTTTATTATGGATTTCAT
TATTCCAAAC
Found at i:38046 original size:21 final size:21
Alignment explanation
Indices: 38022--38073 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
38012 CAGTTTTCAA
38022 ATTCGCAACGTGAATATCCAG
1 ATTCGCAACGTGAATATCCAG
38043 ATTCGCAACGTGAATATCCAG
1 ATTCGCAACGTGAATATCCAG
38064 ATTCGCAACG
1 ATTCGCAACG
38074 CGATTGTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (21 bp):
ATTCGCAACGTGAATATCCAG
Found at i:38127 original size:19 final size:19
Alignment explanation
Indices: 38103--38207 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 19
38093 GCGATTTTGA
38103 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
38122 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
**
38141 AAAATGTGTTGCGCGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
38161 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
38185 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
38204 AAAA
1 AAAA
38208 ATCCAAAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
19 51 0.69
20 3 0.04
22 8 0.11
24 3 0.04
25 9 0.12
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:38197 original size:63 final size:60
Alignment explanation
Indices: 38092--38207 Score: 169
Period size: 63 Copynumber: 1.9 Consensus size: 60
38082 AGATTCGCAA
* * * *
38092 CGCGATTTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGATAGTTAAAATGTGTTG
1 CGCGAGTTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGATAGTGAAAATGTGTTG
38152 CGCGAGTTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGATAGTGAAAA
1 CGCGAGTTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGATAGTGAAAA
38208 ATCCAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 14 0.29
62 2 0.04
63 33 0.67
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (60 bp):
CGCGAGTTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGATAGTGAAAATGTGTTG
Found at i:38646 original size:19 final size:19
Alignment explanation
Indices: 38602--38750 Score: 115
Period size: 19 Copynumber: 7.8 Consensus size: 19
38592 TCGTTGCGAT
*
38602 TTTGGAAAATCGCAACGCGAA
1 TTTGGAATATCGCAA--CGAA
* *
38623 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
38642 TTTGGAAAATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* * *
38661 CTTCGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* * *
38680 TTTGGACTAACG-TA--AA
1 TTTGGAATATCGCAACGAA
*
38696 TTTGGAAAATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
38715 TTTGGAAAATCGCAACGCGAA
1 TTTGGAATATCGCAA--CGAA
* *
38736 CTTGGATTATCGCAA
1 TTTGGAATATCGCAA
38751 AAATCGCGTT
Statistics
Matches: 102, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
16 11 0.11
17 1 0.01
18 1 0.01
19 61 0.60
21 28 0.27
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:38727 original size:54 final size:56
Alignment explanation
Indices: 38602--38750 Score: 158
Period size: 54 Copynumber: 2.6 Consensus size: 56
38592 TCGTTGCGAT
*
38602 TTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGAA
1 TTTGGAAAATCGCAA--CGAACTTGGACTAACGCAAC-AATTTGGAAAATCGCAACGAA
* * ** * *
38661 CTTCGACTATCGCAACGAATTTGGACTAACG-TA-AATTTGGAAAATCGCAACGAA
1 TTTGGAAAATCGCAACGAACTTGGACTAACGCAACAATTTGGAAAATCGCAACGAA
* *
38715 TTTGGAAAATCGCAACGCGAACTTGGATTATCGCAA
1 TTTGGAAAATCGCAA--CGAACTTGGACTAACGCAA
38751 AAATCGCGTT
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
54 32 0.44
56 14 0.19
57 15 0.21
59 11 0.15
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (56 bp):
TTTGGAAAATCGCAACGAACTTGGACTAACGCAACAATTTGGAAAATCGCAACGAA
Found at i:39060 original size:33 final size:33
Alignment explanation
Indices: 39015--39082 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
39005 TTCTTTTTTC
39015 GATTTCTATGACTTATATCAAGTTATTGATGCA
1 GATTTCTATGACTTATATCAAGTTATTGATGCA
*
39048 GATTTCTCTGACTTATATCAAGTTATTGATGCA
1 GATTTCTATGACTTATATCAAGTTATTGATGCA
39081 GA
1 GA
39083 AACTAGACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (33 bp):
GATTTCTATGACTTATATCAAGTTATTGATGCA
Found at i:45414 original size:25 final size:25
Alignment explanation
Indices: 45334--45414 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 25
45324 TTGAATGGTT
45334 ATTTATCTATCATAGTTCATATAAA
1 ATTTATCTATCATAGTTCATATAAA
* *
45359 A-TT-TCTATCATACATGCCAATATAAA
1 ATTTATCTATCATA-GT-TC-ATATAAA
45385 TATTTATCTATCATAGTTCATATAAA
1 -ATTTATCTATCATAGTTCATATAAA
45411 ATTT
1 ATTT
45415 CTAATTTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
23 9 0.20
24 3 0.07
25 6 0.13
26 14 0.30
27 2 0.04
28 3 0.07
29 9 0.20
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.43
Consensus pattern (25 bp):
ATTTATCTATCATAGTTCATATAAA
Found at i:55601 original size:22 final size:21
Alignment explanation
Indices: 55576--55628 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
55566 TTATATATTT
*
55576 TTATAAAAGTTATATAAAATAA
1 TTATAAAAATTATATAAAAT-A
* *
55598 TTATAAAAATTATTTATAATA
1 TTATAAAAATTATATAAAATA
*
55619 TTATTAAAAT
1 TTATAAAAAT
55629 ATTTATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTATAAAAATTATATAAAATA
Found at i:55624 original size:24 final size:24
Alignment explanation
Indices: 55565--55637 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
55555 TATAGGATAC
* *
55565 TTTAT-ATATTTTTATAAAAGTTA
1 TTTATAATATTATTATAAAAATTA
* *
55588 --TATAAAATAATTATAAAAATTA
1 TTTATAATATTATTATAAAAATTA
*
55610 TTTATAATATTATTA-AAATATTTA
1 TTTATAATATTATTATAAA-AATTA
55634 TTTA
1 TTTA
55638 ATTTTAACAT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.08
22 14 0.36
23 3 0.08
24 19 0.49
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
TTTATAATATTATTATAAAAATTA
Found at i:55663 original size:29 final size:29
Alignment explanation
Indices: 55620--55702 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
55610 TTTATAATAT
*
55620 TATTAAAATATTTATTTAATTTTAACATCA
1 TATT-AAATAATTATTTAATTTTAACATCA
* * * *
55650 TATTAATTAATTATTTAA-ATTAATATTA
1 TATTAAATAATTATTTAATTTTAACATCA
* *
55678 TTTTAAATGATCTATTTAATTTTAA
1 TATTAAATAAT-TATTTAATTTTAA
55703 ATAATTTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
28 15 0.36
29 19 0.45
30 8 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (29 bp):
TATTAAATAATTATTTAATTTTAACATCA
Found at i:55709 original size:29 final size:29
Alignment explanation
Indices: 55625--55714 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
55615 AATATTATTA
* * *
55625 AAATATTTATTTAATTTTAACATCATATT
1 AAATAATTATTTAATTTTAACATAATTTT
* * * *
55654 AATTAATTATTTAA-ATTAATATTATTTT
1 AAATAATTATTTAATTTTAACATAATTTT
* *
55682 AAATGATCTATTTAATTTTAA-ATAATTTA
1 AAATAAT-TATTTAATTTTAACATAATTTT
55711 AAAT
1 AAAT
55715 TTAAGTAAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
28 15 0.31
29 29 0.60
30 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (29 bp):
AAATAATTATTTAATTTTAACATAATTTT
Found at i:55832 original size:17 final size:18
Alignment explanation
Indices: 55812--55857 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
55802 TTATTTAAAA
55812 TAAATAATTAACAT-TTT
1 TAAATAATTAACATATTT
* *
55829 TAAATAAATAATATGATTT
1 TAAATAATTAACAT-ATTT
55848 TAAA-AATTAA
1 TAAATAATTAA
55858 ATAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 12 0.50
18 5 0.21
19 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAATAATTAACATATTT
Found at i:55854 original size:21 final size:20
Alignment explanation
Indices: 55808--55872 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
55798 GGTATTATTT
*
55808 AAAATAAATAATTAACATTTT-
1 AAAATAAATAA-T-ATATTTTA
*
55829 TAAATAAATAATATGATTTTA
1 AAAATAAATAATAT-ATTTTA
55850 AAAATTAAATAA-ATATTTTA
1 AAAA-TAAATAATATATTTTA
55870 AAA
1 AAA
55873 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.03
20 15 0.39
21 15 0.39
22 7 0.18
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATAAATAATATATTTTA
Found at i:55867 original size:20 final size:22
Alignment explanation
Indices: 55833--55872 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
55823 CATTTTTAAA
55833 TAAATAATATGATTTTAAAAAT
1 TAAATAATATGATTTTAAAAAT
55855 TAAATAA-AT-ATTTTAAAA
1 TAAATAATATGATTTTAAAA
55873 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAATAATATGATTTTAAAAAT
Found at i:55872 original size:19 final size:21
Alignment explanation
Indices: 55805--55873 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
55795 AATGGTATTA
**
55805 TTTAAAA-TAAATAATTAACAT
1 TTTAAAATTAAATAA-TATGAT
*
55826 TTTTAAA-TAAATAATATGAT
1 TTTAAAATTAAATAATATGAT
55846 TTTAAAAATTAAATAA-AT-AT
1 TTT-AAAATTAAATAATATGAT
55866 TTTAAAAT
1 TTTAAAAT
55874 ATTTTTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 5 0.12
20 12 0.29
21 18 0.43
22 7 0.17
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (21 bp):
TTTAAAATTAAATAATATGAT
Found at i:55931 original size:22 final size:22
Alignment explanation
Indices: 55883--55946 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
55873 TATTTTTAAA
55883 AAAT-ATTATAATATAATATTT
1 AAATAATTATAATATAATATTT
*
55904 AGAATAATT-TAATATAAATTTTT
1 A-AATAATTATAATAT-AATATTT
55927 AAAT-A-TATAA-ATAATTATTT
1 AAATAATTATAATATAA-TATTT
55947 TTATTTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
19 2 0.06
20 7 0.19
21 5 0.14
22 12 0.33
23 10 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATAATTATAATATAATATTT
Found at i:56601 original size:2 final size:2
Alignment explanation
Indices: 56596--56651 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
56586 ACACTCTAAT
56596 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
56638 CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA
56652 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:56656 original size:2 final size:2
Alignment explanation
Indices: 56651--56678 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
56641 ACACACACAC
56651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56679 TTCGAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57519 original size:56 final size:57
Alignment explanation
Indices: 57425--57531 Score: 157
Period size: 56 Copynumber: 1.9 Consensus size: 57
57415 TGCACATACT
*
57425 ATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCACCAGCC
1 ATGCATCGATACACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCACCAGCC
*
57482 ATGCATCGATACACTCAG-GCTATTT-TG-AAACATCGAATGCATTTTATGCA
1 ATGCATCGATACACTCAGAG-T-TTTATGAAAACATCGAATGCATTTGATGCA
57532 TCGATGCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
56 23 0.50
57 20 0.43
58 3 0.07
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (57 bp):
ATGCATCGATACACTCAGAGTTTTATGAAAACATCGAATGCATTTGATGCACCAGCC
Found at i:58337 original size:14 final size:14
Alignment explanation
Indices: 58315--58350 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
58305 AGTTTAATAA
58315 ATTCAAGTCGAGAT
1 ATTCAAGTCGAGAT
* *
58329 ATTCGAGTCGAGTT
1 ATTCAAGTCGAGAT
58343 ATTCAAGT
1 ATTCAAGT
58351 TTCTATGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (14 bp):
ATTCAAGTCGAGAT
Found at i:60643 original size:14 final size:14
Alignment explanation
Indices: 60624--60652 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60614 CATTCAGATC
60624 TGAATCTAACTAAT
1 TGAATCTAACTAAT
60638 TGAATCTAACTAAT
1 TGAATCTAACTAAT
60652 T
1 T
60653 AAGTAATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TGAATCTAACTAAT
Found at i:67534 original size:13 final size:13
Alignment explanation
Indices: 67511--67573 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
67501 CGTCACACCC
67511 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
67524 TACCTGACCCGTT
1 GACCCGACCCGTT
67537 GACCCGACCCAACCTGTT
1 GACCCGA--C--CC-GTT
67555 GACCCGACCCGTT
1 GACCCGACCCGTT
67568 GACCCG
1 GACCCG
67574 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 25 0.61
14 2 0.05
15 1 0.02
16 1 0.02
17 2 0.05
18 10 0.24
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:67545 original size:31 final size:31
Alignment explanation
Indices: 67507--67573 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
67497 TGATCGTCAC
* * *
67507 ACCCGACCCGACCCGTTTACCTGACCCGTTG
1 ACCCGACCCAACCCGTTGACCCGACCCGTTG
*
67538 ACCCGACCCAACCTGTTGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTGACCCGACCCGTTG
67569 ACCCG
1 ACCCG
67574 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.16
Consensus pattern (31 bp):
ACCCGACCCAACCCGTTGACCCGACCCGTTG
Found at i:67583 original size:15 final size:17
Alignment explanation
Indices: 67563--67596 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
67553 TTGACCCGAC
67563 CCGTTGACC-C-GTTGA
1 CCGTTGACCACTGTTGA
67578 CCGTTGACCACTGTTGA
1 CCGTTGACCACTGTTGA
67595 CC
1 CC
67597 AAAACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (17 bp):
CCGTTGACCACTGTTGA
Found at i:68899 original size:18 final size:18
Alignment explanation
Indices: 68873--68907 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68863 TCAAAATGAC
*
68873 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
68891 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
68908 CCGGATGGCA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:69911 original size:12 final size:11
Alignment explanation
Indices: 69886--69952 Score: 53
Period size: 12 Copynumber: 5.7 Consensus size: 11
69876 AGTTACCTGA
*
69886 ATTCTGTTCTG
1 ATTCTGATCTG
69897 ATTCTGATCTGG
1 ATTCTGATCT-G
*
69909 ATTCTGTTCTG
1 ATTCTGATCTG
*
69920 ATATCTGATATG
1 AT-TCTGATCTG
* *
69932 AATTCTGTTTTG
1 -ATTCTGATCTG
69944 ATTTCTGAT
1 A-TTCTGAT
69953 ATCTCCGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
11 13 0.29
12 30 0.67
13 2 0.04
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (11 bp):
ATTCTGATCTG
Found at i:69936 original size:24 final size:23
Alignment explanation
Indices: 69883--69954 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 23
69873 GATAGTTACC
*
69883 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATTCTGATA
*
69906 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
69930 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGA-TTCTGATA
69954 T
1 T
69955 CTCCGTTTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 15 0.35
24 27 0.63
25 1 0.02
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:72135 original size:29 final size:29
Alignment explanation
Indices: 72079--72135 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
72069 TCCTTCAATT
* *
72079 ATAATTAAAGTTTTATTTTATATTTTTAA
1 ATAATTAAAATTTTATTTTATATATTTAA
72108 ATAATTAAAATTTTATTTTA-ATAATTTA
1 ATAATTAAAATTTTATTTTATAT-ATTTA
72136 TGGTCCTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
ATAATTAAAATTTTATTTTATATATTTAA
Found at i:73898 original size:26 final size:27
Alignment explanation
Indices: 73862--73920 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
73852 TTAACCTAAA
73862 GAACCTTACCATCAAA-CCAAATGACT
1 GAACCTTACCATCAAACCCAAATGACT
73888 GAACCTTACCATCAAACCCAAATGACT
1 GAACCTTACCATCAAACCCAAATGACT
73915 -AACCTT
1 GAACCTT
73921 GAAAACAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.41, C:0.32, G:0.07, T:0.20
Consensus pattern (27 bp):
GAACCTTACCATCAAACCCAAATGACT
Found at i:73929 original size:26 final size:27
Alignment explanation
Indices: 73862--73930 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
73852 TTAACCTAAA
* *
73862 GAACCTTACCATCAAA-CCAAATGACT
1 GAACCTTACAAACAAACCCAAATGACT
* *
73888 GAACCTTACCATCAAACCCAAATGACT
1 GAACCTTACAAACAAACCCAAATGACT
73915 -AACCTTGA-AAACAAAC
1 GAACCTT-ACAAACAAAC
73931 AAAACAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 28 0.72
27 11 0.28
ACGTcount: A:0.45, C:0.30, G:0.07, T:0.17
Consensus pattern (27 bp):
GAACCTTACAAACAAACCCAAATGACT
Done.