Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003941.1 Hibiscus syriacus cultivar Beakdansim tig00008517_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: 147729
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3832 original size:20 final size:20
Alignment explanation
Indices: 3783--3850 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
3773 AAACTGCTCG
3783 TGGGTATCGATACTAAG-CTCC
1 TGGGTATCGATACT-AGCCT-C
**
3804 TCAGTATCGATACTAGCCTC
1 TGGGTATCGATACTAGCCTC
* * *
3824 TGGGTATCGATACCAACATC
1 TGGGTATCGATACTAGCCTC
3844 TGGGTAT
1 TGGGTAT
3851 TAATACTAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (20 bp):
TGGGTATCGATACTAGCCTC
Found at i:3936 original size:22 final size:21
Alignment explanation
Indices: 3890--3944 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3880 ACAAAAGGAT
* *
3890 GGTATTGATAC-TCTTTCTTG
1 GGTATCGATACTTCTTTCTGG
*
3910 AGTATCGATACTTCTATTCTGG
1 GGTATCGATACTTCT-TTCTGG
3932 GGTATCGATACTT
1 GGTATCGATACTT
3945 TCTTGAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.31
21 3 0.10
22 17 0.59
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (21 bp):
GGTATCGATACTTCTTTCTGG
Found at i:3954 original size:18 final size:19
Alignment explanation
Indices: 3891--3954 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 19
3881 CAAAAGGATG
*
3891 GTATTGATACTCTTTCTTGA
1 GTATCGATA-TCTTTCTTGA
* *
3911 GTATCGATACTTCTATTCTGGG
1 GTATCGATA--TCT-TTCTTGA
3933 GTATCGATA-CTTTCTTGA
1 GTATCGATATCTTTCTTGA
3951 GTAT
1 GTAT
3955 TTATACCAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.25
19 2 0.06
20 8 0.22
21 3 0.08
22 14 0.39
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (19 bp):
GTATCGATATCTTTCTTGA
Found at i:5270 original size:18 final size:17
Alignment explanation
Indices: 5249--5283 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5239 AGGTCATTTC
*
5249 AGTATCGATACTCATGGG
1 AGTATCAATACT-ATGGG
5267 AGTATCAATACTATGGG
1 AGTATCAATACTATGGG
5284 TAGAATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (17 bp):
AGTATCAATACTATGGG
Found at i:6116 original size:3 final size:3
Alignment explanation
Indices: 6026--6101 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
6016 ATCGGAAAAA
* *
6026 TAT TA- TAT TAT TAT TAAT TAT TAT TAT TAC TAT TAT TAT TAG TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
6071 TAC TAT TAC TAT TAT TAG TAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6102 GATCAAATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:8036 original size:29 final size:29
Alignment explanation
Indices: 8003--8062 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
7993 TTATATTTGA
8003 TTTACGTTTTATCAAAGAGGGAATATTCT
1 TTTACGTTTTATCAAAGAGGGAATATTCT
8032 TTTACGTTTTATCAAAGAGGGAATATTCT
1 TTTACGTTTTATCAAAGAGGGAATATTCT
8061 TT
1 TT
8063 ACGGATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (29 bp):
TTTACGTTTTATCAAAGAGGGAATATTCT
Found at i:8386 original size:16 final size:17
Alignment explanation
Indices: 8349--8386 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
8339 GCATACCAAC
8349 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
8366 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
8382 TTTTT
1 TTTTT
8387 AAAAGACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:11333 original size:18 final size:19
Alignment explanation
Indices: 11310--11349 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
11300 AGATCAAATC
*
11310 AAAACATAGAGCAAAGA-A
1 AAAACAAAGAGCAAAGAGA
11328 AAAACAAAGAGCAAAGAGA
1 AAAACAAAGAGCAAAGAGA
11347 AAA
1 AAA
11350 GAAACTAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.70, C:0.10, G:0.17, T:0.03
Consensus pattern (19 bp):
AAAACAAAGAGCAAAGAGA
Found at i:11385 original size:20 final size:20
Alignment explanation
Indices: 11360--11406 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11350 GAAACTAAGA
*
11360 AAAAAATCAAAGAAA-AAAG
1 AAAAAAGCAAAGAAAGAAAG
11379 AACAAAAGCAAAGAAAGAAAG
1 AA-AAAAGCAAAGAAAGAAAG
11400 AAAAAAG
1 AAAAAAG
11407 AAATATATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 6 0.24
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAAGCAAAGAAAGAAAG
Found at i:11739 original size:19 final size:19
Alignment explanation
Indices: 11715--11752 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11705 GAAGAGACTA
*
11715 TATTCATATTCCATCCCGC
1 TATTCAGATTCCATCCCGC
*
11734 TATTCAGATTTCATCCCGC
1 TATTCAGATTCCATCCCGC
11753 CCATCGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (19 bp):
TATTCAGATTCCATCCCGC
Found at i:12641 original size:22 final size:22
Alignment explanation
Indices: 12599--12641 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12589 ATATCCTTTG
* *
12599 ATGTTATTTCTCTCGAAACAAA
1 ATGTTATCTCGCTCGAAACAAA
12621 ATGTTATCTCGCT-GAAGACAA
1 ATGTTATCTCGCTCGAA-ACAA
12642 TTTTCTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
ATGTTATCTCGCTCGAAACAAA
Found at i:12823 original size:66 final size:65
Alignment explanation
Indices: 12683--12908 Score: 339
Period size: 66 Copynumber: 3.5 Consensus size: 65
12673 GACATAACCC
*
12683 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTC-TTGAGACAGTTTATTTTGAAGAAAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTTGAGACAGTTTCTTTTGAAGAAAA
* *
12747 ATATTTGAGTCTGATTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTGAAGAAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTC-TTTGAGACAGTTTCTTTTGAAGAAA
12812 A
65 A
* * * *
12813 ATCTTTGAGTCTGTTTATTTGGAAATAAAATTTTGTCTCTCTTAAGACAGTTTCTTTTGAAGGAA
1 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCT-TTGAGACAGTTTCTTTTGAAGAAA
12878 A
65 A
*
12879 ATCTTTGAGTCTTTTTCTCTT-GAAACAAAA
1 ATCTTTGAGTCTGTTTCT-TTGGAAACAAAA
12909 GTCTTTGAGT
Statistics
Matches: 146, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
64 37 0.25
65 1 0.01
66 106 0.73
67 2 0.01
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.43
Consensus pattern (65 bp):
ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTTGAGACAGTTTCTTTTGAAGAAAA
Found at i:12896 original size:29 final size:30
Alignment explanation
Indices: 12862--12963 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
12852 TCTTAAGACA
* **
12862 GTTTCTTTTGAAGGAAAA-TCTTTGAGTCTT
1 GTTTCTCTTGAAACAAAAGTCTTTGAGT-TT
12892 -TTTCTCTTGAAACAAAAGTCTTTGAGTTT
1 GTTTCTCTTGAAACAAAAGTCTTTGAGTTT
* * *
12921 GTTTCTCATGAAACAAACA-TCTTTGAGATC
1 GTTTCTCTTGAAACAAA-AGTCTTTGAGTTT
*
12951 GTTTCCCTTGAAA
1 GTTTCTCTTGAAA
12964 TGAATTTTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 16 0.26
30 44 0.72
31 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (30 bp):
GTTTCTCTTGAAACAAAAGTCTTTGAGTTT
Found at i:13160 original size:43 final size:43
Alignment explanation
Indices: 13051--13297 Score: 170
Period size: 43 Copynumber: 5.8 Consensus size: 43
13041 AAGATGGCTT
* * * **
13051 GTCGTCCTCATCGCGTAGAAACCATGTCATCCCCCGAT---CA
1 GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATAACCA
* *
13091 GACTTCCTCATCACGTAGGAGA-CGTGTCA-CCTCTAGATAACCA
1 GTCGTCCTCATCACGTAGGA-ACCGTGTCATCC-CTAGATAACCA
* **
13134 GTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCC-
1 GTCGTCCTCATCACGTAGGAACCGTG---TCATCCCT--AGATAACCA
* * **
13181 TTCCGTCCTCATCACGAAGGAACCGTGTCATCCC---CCAACCA
1 GT-CGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATAACCA
* * * *
13222 GACCTCCTCATCACGTAGGAGCCGTGTCAACCCTAGATAACCA
1 GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATAACCA
* * *
13265 GCCGTCCTCATCACATAAGAACCGTGTCATCCC
1 GTCGTCCTCATCACGTAGGAACCGTGTCATCCC
13298 CTTAGACGAC
Statistics
Matches: 158, Mismatches: 32, Indels: 31
0.71 0.14 0.14
Matches are distributed among these distances:
39 2 0.01
40 55 0.35
41 1 0.01
42 1 0.01
43 56 0.35
45 7 0.04
46 5 0.03
47 3 0.02
48 28 0.18
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (43 bp):
GTCGTCCTCATCACGTAGGAACCGTGTCATCCCTAGATAACCA
Found at i:13273 original size:131 final size:131
Alignment explanation
Indices: 13038--13291 Score: 359
Period size: 131 Copynumber: 1.9 Consensus size: 131
13028 ACCATTATCT
* * * * * *
13038 CTAAAGATGGCTTGTCGTCCTCATCGCGTAGAAACCATGTCATCCCCCGATCAGACTTCCTCATC
1 CTAAAGATGGCTTGCCGTCCTCATCACGAAGAAACCATGTCATCCCCCAACCAGACCTCCTCATC
* * *
13103 ACGTAGGAGACGTGTCACCTCTAGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATC
66 ACGTAGGAGACGTGTCACCTCTAGATAACCAGCCATCCTCATCACATAAGAACCGTGTTATCATC
13168 C
131 C
* *
13169 CTAAAGATGGCCTT-CCGTCCTCATCACGAAGGAACCGTGTCATCCCCCAACCAGACCTCCTCAT
1 CTAAAGATGG-CTTGCCGTCCTCATCACGAAGAAACCATGTCATCCCCCAACCAGACCTCCTCAT
* *
13233 CACGTAGGAGCCGTGTCAACC-CTAGATAACCAGCCGTCCTCATCACATAAGAACCGTGT
65 CACGTAGGAGACGTGTC-ACCTCTAGATAACCAGCCATCCTCATCACATAAGAACCGTGT
13292 CATCCCCTTA
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
131 102 0.94
132 6 0.06
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.22
Consensus pattern (131 bp):
CTAAAGATGGCTTGCCGTCCTCATCACGAAGAAACCATGTCATCCCCCAACCAGACCTCCTCATC
ACGTAGGAGACGTGTCACCTCTAGATAACCAGCCATCCTCATCACATAAGAACCGTGTTATCATC
C
Found at i:13561 original size:3 final size:3
Alignment explanation
Indices: 13492--13547 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
13482 CTCAGAAAAA
*
13492 TAT TA- TAT TAT TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAG
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
13537 TAT TAT TAT TA
1 TAT TAT TAT TA
13548 ATCAAATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:15959 original size:16 final size:17
Alignment explanation
Indices: 15922--15959 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
15912 GCATACCAGC
15922 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
15939 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
15955 TTTTT
1 TTTTT
15960 AAAATACGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:21446 original size:29 final size:29
Alignment explanation
Indices: 21395--21452 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
21385 GTGTTGGTCG
*
21395 TAGGTCGCCATGCCATCCGGGCGACCTAC
1 TAGGTCGCCATGCCATCCCGGCGACCTAC
** * *
21424 TAGGTCGCCATTTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCATCCCGGCGACCTAC
21453 GAGATATTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCATCCCGGCGACCTAC
Found at i:33708 original size:31 final size:31
Alignment explanation
Indices: 33645--33722 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
33635 AGAGTCGAGG
* *
33645 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATGAACA
* *
33676 GTTTACCTAGGT-TCTTCGGGACCTATGAACA
1 GTTTACCTAGGTCT-TTCGAGACATATGAACA
*
33707 G-TTACCGAGGATCTTT
1 GTTTACCTAGG-TCTTT
33723 ATGACCTCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 9 0.23
31 29 0.74
32 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGAACA
Found at i:33760 original size:30 final size:30
Alignment explanation
Indices: 33695--33793 Score: 137
Period size: 30 Copynumber: 3.3 Consensus size: 30
33685 GGTTCTTCGG
* *
33695 GACCTATGAACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
33725 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * * *
33755 GACCTCTGGATAGTTATCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
33784 GACCTCTGGA
1 GACCTCTGGA
33794 TAGGTCCTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 18 0.29
30 45 0.71
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:33790 original size:29 final size:30
Alignment explanation
Indices: 33706--33796 Score: 139
Period size: 30 Copynumber: 3.1 Consensus size: 30
33696 ACCTATGAAC
*
33706 AGTTACCGAGGATCTTTATGACCTCTGGAC
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
33736 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
* * *
33766 AGTTATCG-GGGTCTTTGTGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
33795 AG
1 AG
33797 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 21 0.37
30 36 0.63
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:37590 original size:64 final size:65
Alignment explanation
Indices: 37517--37678 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 65
37507 ATTGCTTGAA
* ***
37517 GGTGTATCGATGCACAAGTAGTGCATCGATGCACT-CTTTTAATATAA-AAACATAAAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATA-AACAAACATAAAATGCAAT
37580 T
65 T
* * * * *
37581 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCAAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAACAAACATAAAATGCAAT
37644 T
65 T
* * *
37645 TGTGCACCGATGCACAGGTAGTGCATCGATGCAC
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCAC
37679 CGATAGGGAA
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
63 5 0.06
64 72 0.91
65 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATAAAATGCAATT
Found at i:38670 original size:30 final size:29
Alignment explanation
Indices: 38636--38704 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
38626 GGTTCTTCGG
*
38636 GACCTATGGCCAGTTACCGAGGATCTTTAT
1 GACCTATGGACAGTTACCG-GGATCTTTAT
* * * *
38666 GACCTCTGGATAGTTACCGGGGTCTTTGT
1 GACCTATGGACAGTTACCGGGATCTTTAT
*
38695 GACCTCTGGA
1 GACCTATGGA
38705 TAGGTCCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (29 bp):
GACCTATGGACAGTTACCGGGATCTTTAT
Found at i:38700 original size:29 final size:30
Alignment explanation
Indices: 38647--38707 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
38637 ACCTATGGCC
38647 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
* *
38677 AGTTACCG-GGGTCTTTGTGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
38706 AG
1 AG
38708 GTCCTTCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:48349 original size:6 final size:6
Alignment explanation
Indices: 48332--48361 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
48322 AAGATTCCGC
*
48332 AACGGA ATCGGA AACGGA AACGGA AACGGA
1 AACGGA AACGGA AACGGA AACGGA AACGGA
48362 TTCCGTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.17, G:0.33, T:0.03
Consensus pattern (6 bp):
AACGGA
Found at i:53428 original size:17 final size:17
Alignment explanation
Indices: 53408--53460 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
53398 ATATTTTTTA
53408 AATATTTTTAATAAAGT
1 AATATTTTTAATAAAGT
53425 AATA--TTT-A-AAA-T
1 AATATTTTTAATAAAGT
*
53437 ATTATTTTTAATAAAGT
1 AATATTTTTAATAAAGT
53454 AATATTT
1 AATATTT
53461 AAAATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 4 0.14
13 3 0.10
14 4 0.14
15 4 0.14
16 3 0.10
17 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
AATATTTTTAATAAAGT
Found at i:53450 original size:29 final size:29
Alignment explanation
Indices: 53410--53474 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
53400 ATTTTTTAAA
53410 TATTTTTAATAAAGTAATATTTAAAATAT
1 TATTTTTAATAAAGTAATATTTAAAATAT
53439 TATTTTTAATAAAGTAATATTTAAAATAT
1 TATTTTTAATAAAGTAATATTTAAAATAT
53468 TATTTTT
1 TATTTTT
53475 TATCGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TATTTTTAATAAAGTAATATTTAAAATAT
Found at i:53633 original size:68 final size:69
Alignment explanation
Indices: 53516--53647 Score: 169
Period size: 68 Copynumber: 1.9 Consensus size: 69
53506 TCGCTTGTTC
* * *
53516 CCAATATTAGCATTTTCAATAGAAAAAATAATGTTTTAGATAATACTTTACT-AGAAATGTTAAA
1 CCAATATTAACATTTTCAATAGAAAAAATAATATTTTAAATAATACTTTACTGA-AAATGTTAAA
53580 TGCGT
65 TGCGT
* * * * *
53585 CCAATATTAATATTTTCGATA-AACAAATAATATTTTAAATAGTGCTTTACTGAAAATGTTAAA
1 CCAATATTAACATTTTCAATAGAAAAAATAATATTTTAAATAATACTTTACTGAAAATGTTAAA
53648 CATTTTAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
68 35 0.65
69 19 0.35
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (69 bp):
CCAATATTAACATTTTCAATAGAAAAAATAATATTTTAAATAATACTTTACTGAAAATGTTAAAT
GCGT
Found at i:53694 original size:21 final size:21
Alignment explanation
Indices: 53665--53705 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53655 AATAGCGCCT
* *
53665 AATATTAATATTTTAGATAAA
1 AATAATAATATTTTAAATAAA
53686 AATAATAATATTTTAAATAA
1 AATAATAATATTTTAAATAA
53706 CACATTATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAATAATATTTTAAATAAA
Found at i:53719 original size:78 final size:77
Alignment explanation
Indices: 53575--53719 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 77
53565 ACTAGAAATG
* * *** * *
53575 TTAAATGCGTCCAATATTAATATTTTCGATAAACAAATAATATTTTAAATAGTGCTTTACTGAAA
1 TTAAATGCGTCCAATATTAATATTTTAGATAAAAAAATAATATTTTAAATAACACATTACTCAAA
53640 ATGTTAAACATT
66 ATGTTAAACATT
53652 TTAAATAGCG-CCTAATATTAATATTTTAGATAAAAATAATAATATTTTAAATAACACATTA-TC
1 TTAAAT-GCGTCC-AATATTAATATTTTAGATAAAAA-AATAATATTTTAAATAACACATTACTC
53715 AAAAT
63 AAAAT
53720 AATTAACATA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
77 8 0.14
78 30 0.52
79 20 0.34
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.38
Consensus pattern (77 bp):
TTAAATGCGTCCAATATTAATATTTTAGATAAAAAAATAATATTTTAAATAACACATTACTCAAA
ATGTTAAACATT
Found at i:54726 original size:21 final size:21
Alignment explanation
Indices: 54697--54749 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
54687 ATTCTGACTA
54697 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
54718 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
54739 TCGCAATGCGA
1 TCGCATTGCGA
54750 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:54764 original size:20 final size:20
Alignment explanation
Indices: 54739--54905 Score: 196
Period size: 20 Copynumber: 8.3 Consensus size: 20
54729 TTTTCCTAAT
54739 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * **
54759 TCGCAACGCAAATTTGGTAAA
1 TCGCAATGCGAA-TACGTAAA
*
54780 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
54800 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
54820 TCGCAATGCGAAT-C-TGACTA
1 TCGCAATGCGAATACGT-A-AA
*
54840 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
54860 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
54880 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
54900 TCGCAA
1 TCGCAA
54906 CGAGATTATG
Statistics
Matches: 125, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 103 0.82
21 17 0.14
22 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:54913 original size:60 final size:60
Alignment explanation
Indices: 54739--54905 Score: 255
Period size: 60 Copynumber: 2.8 Consensus size: 60
54729 TTTTCCTAAT
* * *
54739 TCGCAATGCGAATACGTAAATCGCAACGCAAATTTGGTAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCT-GTAAATCGCAATGCGATTACGTAAA
* *
54800 TCGCAATGCGATTACGTAAATCGCAATGCGAATCTG-ACTATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTA-AATCGCAATGCGATTACGTAAA
*
54860 TCGCAATGCAAATACGTAAATCGCAATGCGAATCTGTAAATCGCAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAA
54906 CGAGATTATG
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.01
60 63 0.66
61 32 0.33
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAATGCGATTACGTAAA
Found at i:55809 original size:24 final size:24
Alignment explanation
Indices: 55758--55811 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
55748 GTATTCGAAA
*
55758 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCAGGAC
* *
55782 TTTGATCTTGGTCAATACTAGGAT
1 TTTGATCTTGGTCAATACCAGGAC
55806 TTTGAT
1 TTTGAT
55812 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGGAC
Found at i:58258 original size:20 final size:19
Alignment explanation
Indices: 58233--58353 Score: 92
Period size: 20 Copynumber: 6.5 Consensus size: 19
58223 CAACGCGGAA
58233 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAA-ATGACT
*
58253 ATCGCAACACAGAAATGACT
1 ATCGCAACGC-GAAATGACT
58273 ATCGCAACTTG-GAAATGACT
1 ATCGCAAC--GCGAAATGACT
*
58293 ATCGCAA--CGAGA-GA--
1 ATCGCAACGCGAAATGACT
* **
58307 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
* **
58326 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
58345 ATCGCAACG
1 ATCGCAACG
58354 AGTGAATCGC
Statistics
Matches: 87, Mismatches: 5, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
17 5 0.06
19 27 0.31
20 39 0.45
21 3 0.03
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:58330 original size:19 final size:19
Alignment explanation
Indices: 58306--58382 Score: 101
Period size: 19 Copynumber: 4.3 Consensus size: 19
58296 GCAACGAGAG
58306 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
58325 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
58344 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
58358 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
58378 AATCG
1 AATCG
58383 TTCGCATTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
14 8 0.16
16 5 0.10
17 2 0.04
18 3 0.06
19 27 0.54
20 5 0.10
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:58563 original size:14 final size:14
Alignment explanation
Indices: 58544--58580 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
58534 CATCAATTAA
58544 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
58558 ACAAATCATCTTTT
1 ACAAATCAACATTT
58572 ACAAATCAA
1 ACAAATCAA
58581 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:60041 original size:42 final size:42
Alignment explanation
Indices: 59934--60041 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
59924 TCTAGAATGT
* * *
59934 TGGGAG-GGACCTCTTCAACGATGATAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGATAGGGGCCTCTTGAACGA
* * **
59976 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
60018 TAGGG-GAGGCCTCTTGAACGATGA
1 T-GGGAGAGGCCTCTTGAACGATGA
60042 CAGGTGAGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 49 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:60612 original size:20 final size:20
Alignment explanation
Indices: 60587--60635 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
60577 CAACAACAAA
*
60587 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATAACT
* **
60607 ATCGCAATGCGAATTTAACT
1 ATCGCAACGCGAAAATAACT
60627 ATCGCAACG
1 ATCGCAACG
60636 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:60705 original size:20 final size:20
Alignment explanation
Indices: 60680--60749 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
60670 GATTATTTCG
**
60680 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
60700 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
60720 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
60740 TTGCGATAGT
1 TTGCGATAGT
60750 AAACTATTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:62687 original size:39 final size:40
Alignment explanation
Indices: 62627--62751 Score: 166
Period size: 39 Copynumber: 3.2 Consensus size: 40
62617 CTGAAACTTT
* *
62627 AAATCGCAACACGTAAATGAAAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGAAAATCGCAACGCGAAAATGA
** *
62667 CTATCGCAACGCG-AAATGAAAATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGAAAATCGCAACGCGAAAATGA
**
62705 AAATCGCAACACGAAAATGACTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGAAAATCGCAACGCGAAAATGA
62744 AAATCGCA
1 AAATCGCA
62752 TTGCGATTCT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
38 16 0.21
39 49 0.65
40 10 0.13
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (40 bp):
AAATCGCAACACGAAAATGAAAATCGCAACGCGAAAATGA
Found at i:62718 original size:58 final size:59
Alignment explanation
Indices: 62627--62751 Score: 234
Period size: 58 Copynumber: 2.1 Consensus size: 59
62617 CTGAAACTTT
62627 AAATCGCAACACGTAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGA
1 AAATCGCAACACGTAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGA
*
62686 AAATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGA
1 AAATCGCAACACGTAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGA
62744 AAATCGCA
1 AAATCGCA
62752 TTGCGATTCT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
58 53 0.82
59 12 0.18
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (59 bp):
AAATCGCAACACGTAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAAATGA
Found at i:62757 original size:19 final size:19
Alignment explanation
Indices: 62627--62751 Score: 160
Period size: 19 Copynumber: 6.4 Consensus size: 19
62617 CTGAAACTTT
*
62627 AAATCGCAACACGTAAATGA
1 AAATCGCAACGCG-AAATGA
*
62647 AAATCGCAACACGAAAATGA
1 AAATCGCAACGCG-AAATGA
**
62667 CTATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
62686 AAATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
*
62705 AAATCGCAACACGAAAATGA
1 AAATCGCAACGCG-AAATGA
**
62725 CTATCGCAACGCGAAATGA
1 AAATCGCAACGCGAAATGA
62744 AAATCGCA
1 AAATCGCA
62752 TTGCGATTCT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
19 47 0.51
20 45 0.49
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (19 bp):
AAATCGCAACGCGAAATGA
Found at i:62791 original size:20 final size:20
Alignment explanation
Indices: 62766--62812 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
62756 GATTCTCTCG
62766 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
62786 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
62806 TTGCGAT
1 TTGCGAT
62813 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:63417 original size:20 final size:20
Alignment explanation
Indices: 63372--63525 Score: 197
Period size: 20 Copynumber: 7.7 Consensus size: 20
63362 GCGCTATGTA
63372 AATCGCATTGCGATAGTTA-G-
1 AATCGCATTGCGAT--TTACGT
*
63392 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
63412 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
63432 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
63452 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* *
63472 AATCGCATTGCGATTTTTC-A
1 AATCGCATTGCGA-TTTACGT
* *
63492 AATTCGCGTTGTGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
63513 ATTCGCATTGCGA
1 AATCGCATTGCGA
63526 ATTAGGAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
20 100 0.85
21 14 0.12
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:63546 original size:21 final size:21
Alignment explanation
Indices: 63522--63567 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
63512 TATTCGCATT
63522 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
63543 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
63564 GCGA
1 GCGA
63568 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:64415 original size:11 final size:10
Alignment explanation
Indices: 64387--64445 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
64377 ATTTATTTTT
*
64387 TAAAAATAAA
1 TAAAAATGAA
*
64397 TAATAATGCAA
1 TAAAAATG-AA
64408 TAAAAATGAA
1 TAAAAATGAA
64418 TTAAAAATGAA
1 -TAAAAATGAA
* * *
64429 TACAATTCAA
1 TAAAAATGAA
64439 TAAAAAT
1 TAAAAAT
64446 ATAATGTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 20 0.51
11 19 0.49
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.25
Consensus pattern (10 bp):
TAAAAATGAA
Found at i:64430 original size:21 final size:21
Alignment explanation
Indices: 64387--64445 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
64377 ATTTATTTTT
*
64387 TAAAAATAAATAATAATGCAA
1 TAAAAATAAATAAAAATGCAA
*
64408 TAAAAATGAATTAAAAATG-AA
1 TAAAAAT-AAATAAAAATGCAA
* * *
64429 TACAATTCAATAAAAAT
1 TAAAAATAAATAAAAAT
64446 ATAATGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 8 0.26
21 14 0.45
22 9 0.29
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.25
Consensus pattern (21 bp):
TAAAAATAAATAAAAATGCAA
Found at i:64443 original size:31 final size:32
Alignment explanation
Indices: 64386--64445 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
64376 TATTTATTTT
*
64386 TTAAAAATAAATAATAATGCAATAAAAATGAA
1 TTAAAAATAAATAACAATGCAATAAAAATGAA
* *
64418 TTAAAAATGAAT-ACAATTCAATAAAAAT
1 TTAAAAATAAATAACAATGCAATAAAAAT
64446 ATAATGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (32 bp):
TTAAAAATAAATAACAATGCAATAAAAATGAA
Found at i:64990 original size:10 final size:10
Alignment explanation
Indices: 64975--65008 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
64965 TACATTATAT
64975 TTTTATTGAA
1 TTTTATTGAA
64985 TTTTATTGAA
1 TTTTATTGAA
*
64995 TTTTATTGTA
1 TTTTATTGAA
65005 TTTT
1 TTTT
65009 TATTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (10 bp):
TTTTATTGAA
Found at i:65020 original size:11 final size:11
Alignment explanation
Indices: 64972--65019 Score: 57
Period size: 10 Copynumber: 4.6 Consensus size: 11
64962 TTTTACATTA
64972 TATTTTTATTG
1 TATTTTTATTG
*
64983 -AATTTTATTG
1 TATTTTTATTG
*
64993 -AATTTTATTG
1 TATTTTTATTG
65003 TATTTTTATT-
1 TATTTTTATTG
65013 TATTTTT
1 TATTTTT
65020 TTAAAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (11 bp):
TATTTTTATTG
Found at i:67654 original size:18 final size:18
Alignment explanation
Indices: 67631--67673 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
67621 AGTATCTATG
67631 TTTAAAAATTAAAAAATA
1 TTTAAAAATTAAAAAATA
*
67649 TTT-AAAATTAAAAATTA
1 TTTAAAAATTAAAAAATA
*
67666 ATTAAAAA
1 TTTAAAAA
67674 AATTAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAATTAAAAAATA
Found at i:67719 original size:88 final size:90
Alignment explanation
Indices: 67610--67787 Score: 288
Period size: 90 Copynumber: 2.0 Consensus size: 90
67600 TAAGAAAGAA
*
67610 ATTTTTTATTAAGTATCTATGTTTAAAAATT-AAAAAA-TATTTAAAATTAAAAATTAATTAAAA
1 ATTTTTTATTAAGTATCTATGTTTAAAAATTAAAAAAATTAATTAAAATTAAAAATTAATTAAAA
67673 AAATTAAAAAGTAATCATATTAATT
66 AAATTAAAAAGTAATCATATTAATT
* * * *
67698 ATTTTTTATTAGGTATTTATGTTTAAAAATTAAAAAAATTAATTAATATTTAAAATTAATTAAAA
1 ATTTTTTATTAAGTATCTATGTTTAAAAATTAAAAAAATTAATTAAAATTAAAAATTAATTAAAA
*
67763 AAATTAAAAATTAATCATATTAATT
66 AAATTAAAAAGTAATCATATTAATT
67788 TATTAATTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 29 0.35
89 6 0.07
90 47 0.57
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (90 bp):
ATTTTTTATTAAGTATCTATGTTTAAAAATTAAAAAAATTAATTAAAATTAAAAATTAATTAAAA
AAATTAAAAAGTAATCATATTAATT
Found at i:67743 original size:13 final size:13
Alignment explanation
Indices: 67725--67769 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
67715 TATGTTTAAA
67725 AATTAAAAAAATT
1 AATTAAAAAAATT
67738 AATTAATATTTAAAATT
1 AATTAA-A---AAAATT
67755 AATTAAAAAAATT
1 AATTAAAAAAATT
67768 AA
1 AA
67770 AAATTAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 14 0.50
14 1 0.04
16 1 0.04
17 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAAAAAAATT
Found at i:68534 original size:2 final size:2
Alignment explanation
Indices: 68529--68558 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
68519 TTAAAAAATA
68529 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 A
68559 GGGTAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:70652 original size:20 final size:20
Alignment explanation
Indices: 70609--70657 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
70599 ATTCAAGCCG
*
70609 CCGGCTACCCATTAATTTTT
1 CCGGCTGCCCATTAATTTTT
70629 -CGGCTGCCCATTAATTTTT
1 CCGGCTGCCCATTAATTTTT
*
70648 CCGGCCGCCC
1 CCGGCTGCCC
70658 CATTTGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.14, C:0.37, G:0.16, T:0.33
Consensus pattern (20 bp):
CCGGCTGCCCATTAATTTTT
Found at i:74162 original size:23 final size:23
Alignment explanation
Indices: 74132--74190 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
74122 CGTATAAATG
74132 CACCGAAGTGCCACATAGAATTA
1 CACCGAAGTGCCACATAGAATTA
* *
74155 CACCGAAGTGCCGCGTAGAATTA
1 CACCGAAGTGCCACATAGAATTA
74178 CACCGAAGTGCCA
1 CACCGAAGTGCCA
74191 TATAAAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (23 bp):
CACCGAAGTGCCACATAGAATTA
Found at i:78203 original size:74 final size:74
Alignment explanation
Indices: 78082--78234 Score: 261
Period size: 74 Copynumber: 2.1 Consensus size: 74
78072 TGAGATGATC
*
78082 CCATATCTCCTTAGATGTCTTCTTCTCCTCGATGCTTGACAATACTTCATCTGCTAATGCTAGAT
1 CCATATCTCCTTAGATGTCTTCTTCTCCTCGATGCTTGACAATACTTCATCTCCTAATGCTAGAT
*
78147 GAAAGTTTT
66 GAAAGTTTG
* * *
78156 CCATATCTCCTTAGCTGTCTTCTTCTCCTCGATGCTTGACAATACTTCATCTCCTAGTGCTAGTT
1 CCATATCTCCTTAGATGTCTTCTTCTCCTCGATGCTTGACAATACTTCATCTCCTAATGCTAGAT
78221 GAAAGTTTG
66 GAAAGTTTG
78230 CCATA
1 CCATA
78235 GCATTCCCAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.39
Consensus pattern (74 bp):
CCATATCTCCTTAGATGTCTTCTTCTCCTCGATGCTTGACAATACTTCATCTCCTAATGCTAGAT
GAAAGTTTG
Found at i:81082 original size:13 final size:13
Alignment explanation
Indices: 81064--81088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81054 ATTAATTAAT
81064 TAAAATTTTTATA
1 TAAAATTTTTATA
81077 TAAAATTTTTAT
1 TAAAATTTTTAT
81089 TTTATAATTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAAATTTTTATA
Found at i:81092 original size:186 final size:185
Alignment explanation
Indices: 80772--81137 Score: 624
Period size: 186 Copynumber: 2.0 Consensus size: 185
80762 AAATTTTAAA
* * * *
80772 TTTTAAATATATTATATATAACATATGGGTTTAGCCCAAACTATTTAAAACTCAATTAATAATTT
1 TTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACTCAATTAATAATTT
*
80837 AAGATCCAATAACTTTTAATCCTAAATCAATATTAATTAATTAAAAAATTTATATAAAACTTATA
66 AAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAACTTATA
*
80902 TTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTGAATTAATTTT
131 TTTTATAATTATATATTATTTAAATTAATTATAAACTG-TTTTTTGAATTAATTTT
80958 TTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACTCAATTAATAATTT
1 TTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACTCAATTAATAATTT
* ** * *
81023 AAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAATTTTTATATAAAATTTTTA
66 AAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAACTTATA
81088 TTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTA
131 TTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTA
81138 TAAAATATTT
Statistics
Matches: 169, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
185 12 0.07
186 157 0.93
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (185 bp):
TTTTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACTCAATTAATAATTT
AAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAACTTATA
TTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTAATTTT
Found at i:84360 original size:13 final size:13
Alignment explanation
Indices: 84342--84370 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
84332 CCACCGTACT
84342 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
84355 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
84368 CCG
1 CCG
84371 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:86063 original size:76 final size:76
Alignment explanation
Indices: 85323--86036 Score: 1338
Period size: 76 Copynumber: 9.4 Consensus size: 76
85313 GAAATATTGA
*
85323 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85388 AGGCTTTTTGG
66 AGGCTTTTTGG
*
85399 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85464 AGGCTTTTTGG
66 AGGCTTTTTGG
*
85475 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCACGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85540 AGGCTTTTTGG
66 AGGCTTTTTGG
85551 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85616 AGGCTTTTTGG
66 AGGCTTTTTGG
**
85627 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTTTAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85692 AGGCTTTTTGG
66 AGGCTTTTTGG
**
85703 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTTTAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85768 AGGCTTTTTGG
66 AGGCTTTTTGG
85779 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85844 AGGCTTTTTGG
66 AGGCTTTTTGG
85855 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
85920 AGGCTTTTTGG
66 AGGCTTTTTGG
85931 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
85996 ATGCTTTTTGG
66 AGGCTTTTTGG
* *
86007 AAACATCATGCACTGAATGACTTACAGATG
1 AAACATCATGCACTGAAGGGCTTACAGATG
86037 TGGGAAATAG
Statistics
Matches: 628, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 628 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:89492 original size:114 final size:113
Alignment explanation
Indices: 89267--89484 Score: 337
Period size: 114 Copynumber: 1.9 Consensus size: 113
89257 GATCATGCAG
* * **
89267 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCAAATTAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
89332 ACACTTCCAGAAGATGCTATTGGGTCTCCTTGTTTCTACCATGAGCAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCAA
* * *
89380 TTCATCTTTCAAATCCAATGATTGTTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATCG-GTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
89445 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTAC
65 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTAC
89485 TTTGAGCACA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
113 22 0.23
114 72 0.77
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATCGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACCATGAGCAA
Found at i:92948 original size:15 final size:15
Alignment explanation
Indices: 92928--92958 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
92918 TTTCTTGATC
92928 ATTTCTTGTGTCAAA
1 ATTTCTTGTGTCAAA
92943 ATTTCTTGTGTCAAA
1 ATTTCTTGTGTCAAA
92958 A
1 A
92959 CCCTTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (15 bp):
ATTTCTTGTGTCAAA
Found at i:94464 original size:145 final size:147
Alignment explanation
Indices: 94201--94492 Score: 554
Period size: 145 Copynumber: 2.0 Consensus size: 147
94191 TTTCATGATG
94201 ACAGTAAAGTAATTGAATGAATGACCTTGGTTTTACTGTTACAAAACCTTTCATTAATTATTAAC
1 ACAGTAAAGTAATTGAATGAATGACCTTGGTTTTACTGTTACAAAACCTTTCATTAATTATTAAC
94266 ATGTTTTTATAATTAAGTATATGACAATACTTAAATAAAAATGTGAAAAATGCAT-AATTGAAAA
66 ATGTTTTTATAATTAAGTATATGACAATACTTAAATAAAAATGTGAAAAATGCATAAATTGAAAA
94330 ATAA-AATGCAAAATGT
131 ATAAGAATGCAAAATGT
94346 ACAGTAAAGTAATTGAATGAATGACC-TGGTTTTACTGTTACAAAACCTTTCATTAATTATTAAC
1 ACAGTAAAGTAATTGAATGAATGACCTTGGTTTTACTGTTACAAAACCTTTCATTAATTATTAAC
94410 ATGTTTTTATAATTAAAGTATATGACAATACTTAAATAAAAATGTGAAAAATGCATAAATTGAAA
66 ATGTTTTTATAATT-AAGTATATGACAATACTTAAATAAAAATGTGAAAAATGCATAAATTGAAA
94475 AATAAGAATGCAAAATGT
130 AATAAGAATGCAAAATGT
94493 GCAATTCAAA
Statistics
Matches: 144, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
144 52 0.36
145 67 0.47
146 13 0.09
147 12 0.08
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (147 bp):
ACAGTAAAGTAATTGAATGAATGACCTTGGTTTTACTGTTACAAAACCTTTCATTAATTATTAAC
ATGTTTTTATAATTAAGTATATGACAATACTTAAATAAAAATGTGAAAAATGCATAAATTGAAAA
ATAAGAATGCAAAATGT
Found at i:97854 original size:13 final size:13
Alignment explanation
Indices: 97836--97864 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
97826 CCACCGTACT
97836 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
97849 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
97862 CCG
1 CCG
97865 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:98493 original size:39 final size:35
Alignment explanation
Indices: 98444--98517 Score: 94
Period size: 39 Copynumber: 2.0 Consensus size: 35
98434 TTATTATTTT
*
98444 TTTTATTTAATGATAATAATATATATATATAATAATATA
1 TTTTATTTAATAATAATAATA-AT-TA-A-AATAATATA
*
98483 TTTTATTTAATAATATTAATAATTAAAATAATATA
1 TTTTATTTAATAATAATAATAATTAAAATAATATA
98518 ATGAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 9 0.27
36 1 0.03
37 2 0.06
38 2 0.06
39 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (35 bp):
TTTTATTTAATAATAATAATAATTAAAATAATATA
Found at i:106665 original size:14 final size:15
Alignment explanation
Indices: 106641--106699 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 15
106631 TCAAATTTCA
106641 TATATAAATAAATAT
1 TATATAAATAAATAT
106656 TATA-AAATAAATAT
1 TATATAAATAAATAT
106670 TATTAATAAAATAAATAAT
1 TA-T-AT-AAATAAAT-AT
106689 TA-ATAAA-AAAT
1 TATATAAATAAAT
106700 TAAACTCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.41
15 8 0.21
16 3 0.08
18 8 0.21
19 4 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATATAAATAAATAT
Found at i:106667 original size:18 final size:18
Alignment explanation
Indices: 106644--106730 Score: 79
Period size: 18 Copynumber: 4.7 Consensus size: 18
106634 AATTTCATAT
*
106644 ATAAATAAATATTATAAA
1 ATAAATAATTATTATAAA
106662 ATAAAT-ATTATTAATAAA
1 ATAAATAATTATT-ATAAA
* *
106680 ATAAATAATTAATAAAAA
1 ATAAATAATTATTATAAA
* *
106698 ATTAAACTCAA-AATTTTAAA
1 A-TAAA-T-AATTATTATAAA
106718 ATAAATAATTATT
1 ATAAATAATTATT
106731 CACCTTAAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
17 7 0.13
18 26 0.47
19 13 0.24
20 7 0.13
21 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAATAATTATTATAAA
Found at i:107597 original size:3 final size:3
Alignment explanation
Indices: 107589--107686 Score: 196
Period size: 3 Copynumber: 32.7 Consensus size: 3
107579 TAGTGCATAA
107589 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
107637 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
107685 AT
1 AT
107687 ATGTACTTCT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:109522 original size:2 final size:2
Alignment explanation
Indices: 109515--109568 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
109505 TTTGAGCTTA
109515 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
*
109557 AT AT AT AA AT AT
1 AT AT AT AT AT AT
109569 TTTAGTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:123618 original size:11 final size:11
Alignment explanation
Indices: 123602--123659 Score: 73
Period size: 11 Copynumber: 5.3 Consensus size: 11
123592 TATTTTTTTC
123602 AAAAAAAA-CA
1 AAAAAAAAGCA
*
123612 AAAAAAAAGTA
1 AAAAAAAAGCA
*
123623 AAAAAAAGGCA
1 AAAAAAAAGCA
*
123634 CAAAAAAAGCA
1 AAAAAAAAGCA
123645 AAAAAAAAGCCA
1 AAAAAAAAG-CA
123657 AAA
1 AAA
123660 TTTCAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
10 8 0.20
11 27 0.68
12 5 0.12
ACGTcount: A:0.79, C:0.10, G:0.09, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGCA
Found at i:123638 original size:12 final size:12
Alignment explanation
Indices: 123602--123659 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 12
123592 TATTTTTTTC
123602 AAAAAAAA--CA
1 AAAAAAAAGGCA
*
123612 AAAAAAAA-G-T
1 AAAAAAAAGGCA
123622 AAAAAAAAGGCA
1 AAAAAAAAGGCA
*
123634 CAAAAAAA-GCA
1 AAAAAAAAGGCA
*
123645 AAAAAAAAGCCA
1 AAAAAAAAGGCA
123657 AAA
1 AAA
123660 TTTCAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 16 0.41
11 11 0.28
12 12 0.31
ACGTcount: A:0.79, C:0.10, G:0.09, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGGCA
Found at i:127674 original size:10 final size:10
Alignment explanation
Indices: 127659--127702 Score: 65
Period size: 9 Copynumber: 4.6 Consensus size: 10
127649 AACGCTGAAA
127659 ACCGGTTTTG
1 ACCGGTTTTG
*
127669 ACCGG-TTTA
1 ACCGGTTTTG
127678 ACCGGTTTTG
1 ACCGGTTTTG
127688 ACCGG-TTTG
1 ACCGGTTTTG
127697 ACCGGT
1 ACCGGT
127703 CACGACCCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 17 0.57
10 13 0.43
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:127682 original size:19 final size:19
Alignment explanation
Indices: 127658--127702 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
127648 GAACGCTGAA
127658 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
127677 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
*
127696 GACCGGT
1 AACCGGT
127703 CACGACCCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:127709 original size:19 final size:19
Alignment explanation
Indices: 127668--127715 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
127658 AACCGGTTTT
***
127668 GACCGGTTTAACCGGTTTT
1 GACCGGTTTAACCGGTCAC
*
127687 GACCGGTTTGACCGGTCAC
1 GACCGGTTTAACCGGTCAC
*
127706 GACCCGTTTA
1 GACCGGTTTA
127716 CCTGACCCGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (19 bp):
GACCGGTTTAACCGGTCAC
Found at i:127744 original size:17 final size:18
Alignment explanation
Indices: 127719--127765 Score: 87
Period size: 17 Copynumber: 2.7 Consensus size: 18
127709 CCGTTTACCT
127719 GACCCGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
127737 GA-CCGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
127754 GACCCGTTGACC
1 GACCCGTTGACC
127766 GTTGACCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.61
18 11 0.39
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (18 bp):
GACCCGTTGACCCGACCC
Found at i:127835 original size:29 final size:29
Alignment explanation
Indices: 127773--127848 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
127763 ACCGTTGACC
*** *
127773 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
127802 TGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
127831 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
127849 TTTTAAAAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:127923 original size:10 final size:10
Alignment explanation
Indices: 127898--127931 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
127888 TGTTGACCTC
127898 CTTTGACCAG
1 CTTTGACCAG
127908 AACTTTGACCAG
1 --CTTTGACCAG
127920 CTTTGACCAG
1 CTTTGACCAG
127930 CT
1 CT
127932 ATTAAACGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (10 bp):
CTTTGACCAG
Found at i:134979 original size:18 final size:18
Alignment explanation
Indices: 134958--134992 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
134948 CTGACCCGTT
134958 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
134976 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
134993 GTTGACCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:134992 original size:13 final size:13
Alignment explanation
Indices: 134938--134981 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
134928 CGACCCGTTT
*
134938 ACCCGTTGACCTG
1 ACCCGTTGACCCG
134951 ACCCGTTGACCCG
1 ACCCGTTGACCCG
134964 ACCCGTTGACCCG
1 ACCCGTTGACCCG
134977 ACCCG
1 ACCCG
134982 ACCCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:134992 original size:26 final size:26
Alignment explanation
Indices: 134928--134999 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
134918 TGACCGGTCA
* *
134928 CGACCCGTTTACCCGTTGACCTGACC
1 CGACCCGTTGACCCGTTGACCCGACC
134954 CGTTGACCC---GACCCGTTGACCCGACC
1 C---GACCCGTTGACCCGTTGACCCGACC
134980 CGACCCGTTGA-CCGTTGACC
1 CGACCCGTTGACCCGTTGACC
135000 GGTGCTATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
23 5 0.13
25 9 0.24
26 19 0.50
29 5 0.13
ACGTcount: A:0.15, C:0.43, G:0.22, T:0.19
Consensus pattern (26 bp):
CGACCCGTTGACCCGTTGACCCGACC
Found at i:135075 original size:29 final size:29
Alignment explanation
Indices: 135000--135075 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
134990 ACCGTTGACC
* ** *
135000 GGTGCTATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTCTGGAAATTAATTCGAAATG
* *
135029 TGTGCTAGTCTGGAAATTAATTCGAAATG
1 GGTGCTATTCTGGAAATTAATTCGAAATG
* *
135058 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGAAATT
135076 TTTTTAAAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGAAATTAATTCGAAATG
Found at i:141646 original size:34 final size:34
Alignment explanation
Indices: 141603--141670 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
141593 GAATTCCATT
* *
141603 TTGAATTATTATTGATGTTAGAACCTGGTGCAAC
1 TTGAATTATTAATGATGTTAAAACCTGGTGCAAC
141637 TTGAATTATTAATGATGTTAAAACCTGGTGCAAC
1 TTGAATTATTAATGATGTTAAAACCTGGTGCAAC
141671 AACAAAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (34 bp):
TTGAATTATTAATGATGTTAAAACCTGGTGCAAC
Done.