Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006578.1 Hibiscus syriacus cultivar Beakdansim tig00016122_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: 51274
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2844 original size:41 final size:39
Alignment explanation
Indices: 2787--2962 Score: 226
Period size: 41 Copynumber: 4.3 Consensus size: 39
2777 CTATCACAAA
*
2787 TTCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAAT--CGTTGCGATTTTCCAT
*** *
2828 TTCGCGTTGCGATAGTTGAAAATCGTTGCGATAGTTAAAAA
1 TTCGCGTTGCGATAGTTGAAAATCGTTGCGAT--TTTCCAT
* *
2869 ATCGCGTTGCGATAGTTAAAAAATCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTT-GAAAATCGTTGCGATTTTCCAT
2909 TTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCG--TTGCGATTTTCCAT
2950 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
2963 TTTCCATTTC
Statistics
Matches: 117, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 16 0.14
40 19 0.16
41 68 0.58
42 14 0.12
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (39 bp):
TTCGCGTTGCGATAGTTGAAAATCGTTGCGATTTTCCAT
Found at i:2879 original size:22 final size:20
Alignment explanation
Indices: 2832--2901 Score: 106
Period size: 22 Copynumber: 3.5 Consensus size: 20
2822 TTCCATTTCG
*
2832 CGTTGCGATAGTT-GAAAAT
1 CGTTGCGATAGTTAAAAAAT
2851 CGTTGCGATAGTTAAAAAAT
1 CGTTGCGATAGTTAAAAAAT
2871 CGCGTTGCGATAGTTAAAAAAT
1 --CGTTGCGATAGTTAAAAAAT
2893 CGTTGCGAT
1 CGTTGCGAT
2902 TTTCCATTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
19 13 0.28
20 14 0.30
22 20 0.43
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTTAAAAAAT
Found at i:2916 original size:20 final size:20
Alignment explanation
Indices: 2893--2982 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
2883 GTTAAAAAAT
2893 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* ** **
2913 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
*
2934 CATTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
2954 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
2974 CGTTGCGAT
1 CGTTGCGAT
2983 AGTCTACAGT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:2924 original size:81 final size:82
Alignment explanation
Indices: 2788--2942 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 82
2778 TATCACAAAT
*
2788 TCGCGTTGCAATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCAATAGTTAAAAATC-CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
2853 -TTGCGATAGTTAAAAAA
65 ATTGCGATAGTTAAAAAA
*
2870 TCGCGTTGCGATAGTTAAAAAAT-CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
1 TCGCGTTGCAATAGTT-AAAAATCCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCG
2934 CATTGCGAT
65 -ATTGCGAT
2943 TTTCCATTTC
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
81 41 0.60
82 15 0.22
83 12 0.18
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (82 bp):
TCGCGTTGCAATAGTTAAAAATCCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGA
TTGCGATAGTTAAAAAA
Found at i:2931 original size:61 final size:61
Alignment explanation
Indices: 2851--2985 Score: 166
Period size: 61 Copynumber: 2.2 Consensus size: 61
2841 AGTTGAAAAT
*
2851 CGTTGCGATAGTTAAAAAATCGCGTTGCGATAGTTAAAAAAT-CGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTTAAAAAATCGCATTGCGAT--TTAAAAAATCCGTTGCGATTTTCCATTTCG
* *** **
2913 CGTTGCGATAGTT-GAAAATCGCATTGCGATTTTCCATTTCGCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTTAAAAAATCGCATTGCGATTTAAAAAATC-CGTTGCGATTTTCCATTTCG
2974 CGTTGCGATAGT
1 CGTTGCGATAGT
2986 CTACAGTTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 4 0.06
61 47 0.73
62 13 0.20
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (61 bp):
CGTTGCGATAGTTAAAAAATCGCATTGCGATTTAAAAAATCCGTTGCGATTTTCCATTTCG
Found at i:3002 original size:22 final size:22
Alignment explanation
Indices: 2974--3026 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
2964 TTCCATTTCG
2974 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
2996 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
3018 CGTTGCGAT
1 CGTTGCGAT
3027 TTTCCAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:3156 original size:5 final size:5
Alignment explanation
Indices: 3128--3202 Score: 89
Period size: 5 Copynumber: 14.6 Consensus size: 5
3118 CGTATTACCA
3128 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGA-C
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC
* **
3175 CGACC CGACA CGACC CGAGA CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGA
3203 GACGAGACGA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
4 4 0.06
5 41 0.66
6 17 0.27
ACGTcount: A:0.27, C:0.52, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:3179 original size:29 final size:31
Alignment explanation
Indices: 3129--3207 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
3119 GTATTACCAC
3129 GACCACGACCACGACCACGACCCGACCCGACCC
1 GACCACGACC-CGA-CACGACCCGACCCGACCC
*
3162 GACC-CGACCCGAC-CGACCCGACACGACCC
1 GACCACGACCCGACACGACCCGACCCGACCC
* *
3191 GA-GACGACCCGAGACGA
1 GACCACGACCCGACACGA
3208 GACGAGACGG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 25 0.61
30 4 0.10
31 3 0.07
32 5 0.12
33 4 0.10
ACGTcount: A:0.28, C:0.49, G:0.23, T:0.00
Consensus pattern (31 bp):
GACCACGACCCGACACGACCCGACCCGACCC
Found at i:3213 original size:20 final size:20
Alignment explanation
Indices: 3133--3216 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
3123 TACCACGACC
* *
3133 ACGACCACGACCACGACCCGAC
1 ACGACC-CGA-CACGACACGAG
* * *
3155 CCGACCCGACCCGACCCGA-
1 ACGACCCGACACGACACGAG
* *
3174 CCGACCCGACACGACCCGAG
1 ACGACCCGACACGACACGAG
* *
3194 ACGACCCGAGACGAGACGAG
1 ACGACCCGACACGACACGAG
3214 ACG
1 ACG
3217 GACGGCGGCG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 18 0.33
20 28 0.52
21 3 0.06
22 5 0.09
ACGTcount: A:0.29, C:0.46, G:0.25, T:0.00
Consensus pattern (20 bp):
ACGACCCGACACGACACGAG
Found at i:3854 original size:19 final size:19
Alignment explanation
Indices: 3830--3868 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3820 AAATTTTCGC
3830 AATTTGGAAAATCGCAACG
1 AATTTGGAAAATCGCAACG
3849 AATTTGGAAAATCGCAACG
1 AATTTGGAAAATCGCAACG
3868 A
1 A
3869 CAACTGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (19 bp):
AATTTGGAAAATCGCAACG
Found at i:3927 original size:21 final size:21
Alignment explanation
Indices: 3901--3954 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
3891 GAACTGGAAA
3901 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
3922 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
3943 ATCGCAACGCGA
1 ATCGCAACGCGA
3955 AATGGAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:3961 original size:62 final size:62
Alignment explanation
Indices: 3878--4080 Score: 226
Period size: 62 Copynumber: 3.4 Consensus size: 62
3868 ACAACTGTAG
* *
3878 ACTATCGCAACGTGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
** * * * ** **
3940 ACTATCGCAACGCGAAATGGAAAAT--C-A---G--TTGAAAATCTCGCAACGCAAACTGGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
* *
3994 A-AATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
4055 ACTATCGCAACGCGAAATGGAAAATC
1 ACTATCGCAACGCGAAATGGAAAATC
4081 AGTTATCGCA
Statistics
Matches: 109, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
53 22 0.20
54 18 0.17
56 2 0.02
59 2 0.02
60 1 0.01
61 18 0.17
62 46 0.42
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
Found at i:3998 original size:22 final size:22
Alignment explanation
Indices: 3970--4018 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 22
3960 AAAATCAGTT
3970 GAAAATCTCGCAACGC-AAACTG
1 GAAAATCTCGCAACGCGAAA-TG
3992 GAAAA--TCGCAACGCGAAATG
1 GAAAATCTCGCAACGCGAAATG
4012 GAAAATC
1 GAAAATC
4019 GTAACGCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 16 0.67
21 3 0.12
22 5 0.21
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (22 bp):
GAAAATCTCGCAACGCGAAATG
Found at i:4002 original size:20 final size:20
Alignment explanation
Indices: 3977--4027 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
3967 GTTGAAAATC
3977 TCGCAACGC-AAACTGGAAAA
1 TCGCAACGCGAAA-TGGAAAA
3997 TCGCAACGCGAAATGGAAAA
1 TCGCAACGCGAAATGGAAAA
*
4017 TCGTAACGCGA
1 TCGCAACGCGA
4028 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAATGGAAAA
Found at i:4014 original size:115 final size:109
Alignment explanation
Indices: 3881--4158 Score: 403
Period size: 115 Copynumber: 2.5 Consensus size: 109
3871 ACTGTAGACT
* *
3881 ATCGCAACGTGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
3946 GCAACGCGAAATGGAAAATCAGTTGAAAATCTCGCAACGCAAACTGGAAA
66 GCAACGCGAAATGGAAAATCAGTT----A--TCGCAACGCAAACTGGAAA
*
3996 ATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
*
4061 GCAACGCGAAATGGAAAATCAGTTATCGCAACGCGAACTGGAAA
66 GCAACGCGAAATGGAAAATCAGTTATCGCAACGCAAACTGGAAA
** ** * *
4105 ATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATTATCGCAACGCGA
1 ATCGCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGA
4159 AATGCAACGC
Statistics
Matches: 151, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
109 33 0.22
110 31 0.21
111 1 0.01
115 86 0.57
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (109 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
GCAACGCGAAATGGAAAATCAGTTATCGCAACGCAAACTGGAAA
Found at i:4045 original size:21 final size:21
Alignment explanation
Indices: 4016--4158 Score: 126
Period size: 21 Copynumber: 6.6 Consensus size: 21
4006 GAAATGGAAA
*
4016 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
4037 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** **
4058 ATCGCAACGCGAAATGGAAAATCAGTT
1 ATCGCAACGCG--AT----TTTCAACT
** ** *
4085 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
4105 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
4126 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
4147 ATCGCAACGCGA
1 ATCGCAACGCGA
4159 AATGCAACGC
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
20 15 0.15
21 64 0.66
23 2 0.02
25 1 0.01
27 15 0.15
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:4114 original size:89 final size:89
Alignment explanation
Indices: 3996--4162 Score: 307
Period size: 89 Copynumber: 1.9 Consensus size: 89
3986 AAACTGGAAA
*
3996 ATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
4061 GCAACGCGAAATGGAAAATCAGTT
66 GCAACGCGAAATGGAAAATCAGTT
* *
4085 ATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATTATC
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
4150 GCAACGCGAAATG
66 GCAACGCGAAATG
4163 CAACGCGAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 75 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (89 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATC
GCAACGCGAAATGGAAAATCAGTT
Found at i:6718 original size:25 final size:27
Alignment explanation
Indices: 6690--6751 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 27
6680 TTATGTTCTC
* *
6690 AAATTTATTACTATA-ATTTTTAAG-A
1 AAATTTATTAATATATATTTATAAGTA
* *
6715 AAATCTATTAATTTATATTTATAAGTA
1 AAATTTATTAATATATATTTATAAGTA
6742 AATATTTATT
1 AA-ATTTATT
6752 TATTTAGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 12 0.41
26 8 0.28
27 3 0.10
28 6 0.21
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (27 bp):
AAATTTATTAATATATATTTATAAGTA
Found at i:6942 original size:120 final size:116
Alignment explanation
Indices: 6724--6950 Score: 275
Period size: 122 Copynumber: 1.9 Consensus size: 116
6714 AAAATCTATT
*
6724 AATTTATATTTATAAGTAAATATTTATTTATTTAGAAATATCAGAAAGGGCTTCTAGGTATCTTA
1 AATTTATATTTATAAGTAAATATTTATTTATTTAAAAATATCAGAAAGGGCTTCTAGGTATCTTA
* * *
6789 AGACAACTCTTTTCTTGATATTAAAAATAAATAAATAACTAAAACATTTAAAA
66 AGACAACTCTTTCCTTAACATT-AAAATAAAT-AATAACTAAAACATTTAAAA
*
6842 AATTTAT-TTTAATATAGTAAGATATTTATTTATTTAAAAATATTTAGAAAAGGGCTTCTA-GT-
1 AATTTATATTT-ATA-AGTAA-ATATTTATTTATTTAAAAATA-TCAG-AAAGGGCTTCTAGGTA
*
6904 TGCTTTAAGACAGCTCTTTCCTTCAACATT-AAA-AAATAATAACTAAA
61 T-C-TTAAGACAACTCTTTCCTT-AACATTAAAATAAATAATAACTAAA
6951 GTATTTTCTT
Statistics
Matches: 95, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
117 3 0.03
118 10 0.11
119 15 0.16
120 25 0.26
121 9 0.09
122 29 0.31
123 4 0.04
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (116 bp):
AATTTATATTTATAAGTAAATATTTATTTATTTAAAAATATCAGAAAGGGCTTCTAGGTATCTTA
AGACAACTCTTTCCTTAACATTAAAATAAATAATAACTAAAACATTTAAAA
Found at i:8816 original size:3 final size:3
Alignment explanation
Indices: 8808--8849 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
8798 AAATATTTAT
8808 TAA TAA TAAA TAA TAA TAA TAA TAA TAA T-A TAA TAAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
8850 TTCAAATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.78
4 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12129 original size:20 final size:20
Alignment explanation
Indices: 12106--12160 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
12096 TGGAATATTC
*
12106 TGGAGATGTGTGGAACCTTG
1 TGGAGATGTGTGGAACCTTA
*
12126 TGGAG-TAGTGTGGATCCTTA
1 TGGAGAT-GTGTGGAACCTTA
12146 TGGAAGA-GTGTGGAA
1 TGG-AGATGTGTGGAA
12161 GAATATGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.24, C:0.07, G:0.40, T:0.29
Consensus pattern (20 bp):
TGGAGATGTGTGGAACCTTA
Found at i:13457 original size:25 final size:25
Alignment explanation
Indices: 13423--13481 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
13413 CTTTGGATTA
*
13423 TCTCATTTGCTATGATTTTCCATGG
1 TCTCTTTTGCTATGATTTTCCATGG
*
13448 TCTCTTTTGCTATGATTTTCCATTG
1 TCTCTTTTGCTATGATTTTCCATGG
13473 TCTCATTTT
1 TCTC-TTTT
13482 TCTCTCTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (25 bp):
TCTCTTTTGCTATGATTTTCCATGG
Found at i:27332 original size:2 final size:2
Alignment explanation
Indices: 27325--27362 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
27315 CATAAAAGCA
27325 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
27363 TAGATTGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31520 original size:24 final size:24
Alignment explanation
Indices: 31488--31599 Score: 179
Period size: 24 Copynumber: 4.7 Consensus size: 24
31478 ATTTATTATA
*
31488 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
31512 ATACTTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
31536 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* * *
31560 ATACTTGACCTGGATTTTGCTCTG
1 ATACTTGACCTGGATTCTGATCGG
31584 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
31600 ATGTTATGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:31756 original size:18 final size:19
Alignment explanation
Indices: 31725--31761 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
31715 ACGGTGGGTG
31725 TAGTTCTGGGGAACCTACA
1 TAGTTCTGGGGAACCTACA
31744 TAGTTCT-GGGAACCTACA
1 TAGTTCTGGGGAACCTACA
31762 CATTTGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (19 bp):
TAGTTCTGGGGAACCTACA
Found at i:32685 original size:21 final size:23
Alignment explanation
Indices: 32645--32689 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
32635 GGAGGTTATT
*
32645 TTTTAAATAGTAATTTAAATAAA
1 TTTTAAATAGTAATTCAAATAAA
32668 TTTTAAA-A-TAATTCAAATAAA
1 TTTTAAATAGTAATTCAAATAAA
32689 T
1 T
32690 AAATTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 1 0.05
23 7 0.33
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTTAAATAGTAATTCAAATAAA
Found at i:33852 original size:16 final size:17
Alignment explanation
Indices: 33822--33911 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 17
33812 AAAAAATACA
*
33822 ATATT-CCCAGTAATC-
1 ATATTCCCCGGTAATCT
33837 ATATTCCCCGGTAATCTT
1 ATATTCCCCGGTAATC-T
*
33855 TTATTCCCCGGTAATCTT
1 ATATTCCCCGGTAATC-T
*
33873 TTATTCCTCCCGGTAATCTT
1 ATATT-C-CCCGGTAATC-T
*
33893 TTATTCCTCCTGGTAATCT
1 ATATTCC-CC-GGTAATCT
33912 TACATTCTGT
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
15 5 0.08
16 9 0.14
18 23 0.35
19 5 0.08
20 24 0.36
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (17 bp):
ATATTCCCCGGTAATCT
Found at i:33918 original size:20 final size:19
Alignment explanation
Indices: 33838--33912 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 19
33828 CCAGTAATCA
33838 TATTCC-CCGGTAATCTTT
1 TATTCCTCCGGTAATCTTT
33856 TATTCC-CCGGTAATCTTT
1 TATTCCTCCGGTAATCTTT
33874 TATTCCTCCCGGTAATCTTT
1 TATTCCT-CCGGTAATCTTT
33894 TATTCCTCCTGGTAATCTT
1 TATTCCTCC-GGTAATCTT
33913 ACATTCTGTG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
18 24 0.44
19 2 0.04
20 28 0.52
ACGTcount: A:0.16, C:0.28, G:0.11, T:0.45
Consensus pattern (19 bp):
TATTCCTCCGGTAATCTTT
Found at i:34717 original size:21 final size:21
Alignment explanation
Indices: 34692--34753 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
34682 GTTTCCAGAT
** *
34692 TCGCAATGCGATTTTGGATTA
1 TCGCAATGCGAACTTGGACTA
34713 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
34734 TCGCAATGCGAACTTGGACT
1 TCGCAATGCGAACTTGGACT
34754 CGACTATCGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:35446 original size:6 final size:6
Alignment explanation
Indices: 35415--35473 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
35405 TCTCGATTCG
35415 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
35459 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
35474 AATACGTGTC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:35615 original size:20 final size:21
Alignment explanation
Indices: 35566--35617 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
35556 TGCGATTTTG
*
35566 GACTATCGCAATGCGAACTTC
1 GACTATCGCAATGCGAACTCC
*
35587 GACTATCGCAATGCGATCTCC
1 GACTATCGCAATGCGAACTCC
*
35608 G-GTATCGCAA
1 GACTATCGCAA
35618 ATCAGTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (21 bp):
GACTATCGCAATGCGAACTCC
Found at i:37754 original size:41 final size:41
Alignment explanation
Indices: 37666--37758 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 41
37656 ATTGATACTT
* * * **
37666 TAGCGGCGTTTTTTGTAAAAACGCCGCAATAGTGTGGTTTA
1 TAGCGGCGTTTGTTGAAAAAACGCCGCAATAGTATGGTAAA
*
37707 TTGCGGCGTTTGTT-AAAAAACGCCGCAATA-TATCGGTAAAA
1 TAGCGGCGTTTGTTGAAAAAACGCCGCAATAGTAT-GGT-AAA
37748 TAGCGGCGTTT
1 TAGCGGCGTTT
37759 ATACCACAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.05
40 18 0.42
41 23 0.53
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (41 bp):
TAGCGGCGTTTGTTGAAAAAACGCCGCAATAGTATGGTAAA
Found at i:37820 original size:41 final size:39
Alignment explanation
Indices: 37746--37922 Score: 237
Period size: 39 Copynumber: 4.4 Consensus size: 39
37736 ATATCGGTAA
* * *
37746 AATAGCGGCGTTTATACCACAAACGCCATAATAGTGTTAATC
1 AATAGTGGCGTTTTTA--ACAAACGCCACAATAGTG-TAATC
* *
37788 AATAGTGGCGTTTTTAGATAAACGCCACAATAGTTTTAATC
1 AATAGTGGCGTTTTTA-ACAAACGCCACAATAG-TGTAATC
*
37829 AGTAGTGGCGTTTTTTAACAAACGCCACAATAGTGTAATC
1 AATAGTGGCG-TTTTTAACAAACGCCACAATAGTGTAATC
37869 AATAGTGGCGTTTTTAACAAACGCCACAATAGTGTAATC
1 AATAGTGGCGTTTTTAACAAACGCCACAATAGTGTAATC
*
37908 AATAGTGGCATTTTT
1 AATAGTGGCGTTTTT
37923 TTGTATAAAC
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 43 0.35
40 15 0.12
41 43 0.35
42 21 0.17
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (39 bp):
AATAGTGGCGTTTTTAACAAACGCCACAATAGTGTAATC
Found at i:37935 original size:81 final size:82
Alignment explanation
Indices: 37764--37923 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 82
37754 CGTTTATACC
* * *
37764 ACAAACGCCATAATAGTGTTAATCAATAGTGGCGTTTTTAGATAAACGCCACAATAGTTTTAATC
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCACAATAGTTGTAATC
*
37829 AGTAGTGGCGTTTTTTA
66 AATAGTGGCGTTTTTTA
37846 ACAAACGCCACAATAGTG-TAATCAATAGTGGCGTTTTTA-ACAAACGCCACAATAG-TGTAATC
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCACAATAGTTGTAATC
*
37908 AATAGTGGCATTTTTT
66 AATAGTGGCGTTTTTT
37924 TGTATAAACG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
79 20 0.27
80 15 0.21
81 21 0.29
82 17 0.23
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (82 bp):
ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCACAATAGTTGTAATC
AATAGTGGCGTTTTTTA
Found at i:39384 original size:24 final size:24
Alignment explanation
Indices: 39357--39414 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
39347 CATTTTCGTA
39357 ATAAACGCCGTAATAGTTTTTAAT
1 ATAAACGCCGTAATAGTTTTTAAT
39381 ATAAACGCCGTAATAGTTTTTAAT
1 ATAAACGCCGTAATAGTTTTTAAT
39405 ATAAACGCCG
1 ATAAACGCCG
39415 CAATTGTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (24 bp):
ATAAACGCCGTAATAGTTTTTAAT
Found at i:44027 original size:21 final size:21
Alignment explanation
Indices: 43951--44020 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
43941 ATGAAGCAAG
*
43951 GGAAGCAGA-GAGAGCAGCAGT
1 GGAAGCA-ACGAGAGCAGCAGC
*
43972 GGAAGCAACTAGAGCAGCAGC
1 GGAAGCAACGAGAGCAGCAGC
*
43993 GGAAGCAACTAGAGCAGCAGC
1 GGAAGCAACGAGAGCAGCAGC
44014 GGAAGCA
1 GGAAGCA
44021 GAGAGAGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 1 0.02
21 45 0.98
ACGTcount: A:0.39, C:0.20, G:0.37, T:0.04
Consensus pattern (21 bp):
GGAAGCAACGAGAGCAGCAGC
Found at i:44035 original size:21 final size:20
Alignment explanation
Indices: 43951--44072 Score: 82
Period size: 21 Copynumber: 5.8 Consensus size: 20
43941 ATGAAGCAAG
* *
43951 GGAAGCAGAGAGAGCAGCAGT
1 GGAAGCA-AGAGAGAAGCAGC
* *
43972 GGAAGCAACTAGAGCAGCAGC
1 GGAAGCAA-GAGAGAAGCAGC
* *
43993 GGAAGCAACTAGAGCAGCAGC
1 GGAAGCAA-GAGAGAAGCAGC
*
44014 GGAAGCAGAGAGAGAAGTAGC
1 GGAAGCA-AGAGAGAAGCAGC
* * *
44035 GGCAGCACATAGAGAGGCAGC
1 GGAAGCA-AGAGAGAAGCAGC
* *
44056 GGCAGAACAGAGAGAAG
1 GGAAGCA-AGAGAGAAG
44073 TAATATATCA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 84 0.98
22 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.39, T:0.04
Consensus pattern (20 bp):
GGAAGCAAGAGAGAAGCAGC
Found at i:44036 original size:42 final size:41
Alignment explanation
Indices: 43951--44074 Score: 108
Period size: 42 Copynumber: 3.0 Consensus size: 41
43941 ATGAAGCAAG
* * * * * *
43951 GGAAGCAGAGAGAGCAGCAGTGGAAGCAACTAGAGCAGCAGC
1 GGAAGCACATAGAGCAGCAGCGGAAGCAA-GAGAGAAGTAGC
43993 GGAAGCA-ACTAGAGCAGCAGCGGAAGCAGAGAGAGAAGTAGC
1 GGAAGCACA-TAGAGCAGCAGCGGAAGCA-AGAGAGAAGTAGC
* * *
44035 GGCAGCACATAGAG-AGGCAGCGGCAGAACAGAGAGAAGTA
1 GGAAGCACATAGAGCA-GCAGCGGAAGCA-AGAGAGAAGTA
44075 ATATATCAGC
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
41 2 0.03
42 65 0.94
43 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.38, T:0.05
Consensus pattern (41 bp):
GGAAGCACATAGAGCAGCAGCGGAAGCAAGAGAGAAGTAGC
Found at i:44620 original size:43 final size:43
Alignment explanation
Indices: 44428--44682 Score: 185
Period size: 43 Copynumber: 5.9 Consensus size: 43
44418 TTTGTGATAA
* * * * *
44428 AAACGCCGCGAAATCTCAACACATATTGCGGCGTTT-T-CGACGA
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATG-C-C
* * * * * **
44471 AAATGCCGCTAAATCTCAAGACATATTCTGCGGCGTTTGTAGGAA
1 AAACGCCGCTAAATATCAACACCTA-T-TGCGGCGTTTGTATGCC
* * * * * * * *
44516 AAACGCTGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAG-A
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-ATGCC
* *
44559 AAACGCCGCTAAACATCAACGA-CTATTGCGGCGTTTGTCTGCC
1 AAACGCCGCTAAATATCAAC-ACCTATTGCGGCGTTTGTATGCC
* * *
44602 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTTTTATGCC
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGCC
* *
44645 AAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT
44683 TGAACAATTG
Statistics
Matches: 170, Mismatches: 34, Indels: 16
0.77 0.15 0.07
Matches are distributed among these distances:
42 2 0.01
43 135 0.79
44 4 0.02
45 27 0.16
46 1 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGCC
Found at i:44695 original size:86 final size:86
Alignment explanation
Indices: 44559--44725 Score: 203
Period size: 86 Copynumber: 1.9 Consensus size: 86
44549 TTTGTGAAGA
* *
44559 AAACGCCGCTAAACATCAACGACTATTGCGGCGTTTGTCTGCCAAATGCCGTTAAATATCAACAC
1 AAACGCCGCTAAACATCAACGACTATTGCGGCGTTTGTCTGACAAATGCCGCTAAATATCAACAC
44624 CTATTGCGGCGTTTTTATGCC
66 CTATTGCGGCGTTTTTATGCC
* * * * * * ***
44645 AAACGCCGCTAAATATCAA-TACCTTTTGCGGCGTTTGT-TGAACAATTGCCGCTATATGTTGTC
1 AAACGCCGCTAAACATCAACGA-CTATTGCGGCGTTTGTCTG-ACAAATGCCGCTAAATATCAAC
44708 ACCTATTGCGGCGTTTTT
64 ACCTATTGCGGCGTTTTT
44726 TTGTTGAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 3 0.04
86 65 0.96
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (86 bp):
AAACGCCGCTAAACATCAACGACTATTGCGGCGTTTGTCTGACAAATGCCGCTAAATATCAACAC
CTATTGCGGCGTTTTTATGCC
Found at i:44696 original size:43 final size:43
Alignment explanation
Indices: 44432--44723 Score: 171
Period size: 43 Copynumber: 6.7 Consensus size: 43
44422 TGATAAAAAC
* * * * *
44432 GCCGCGAAATCTCAACACATATTGCGGCGTTT-T-CGACGAAAAT
1 GCCGCTAAATATCAACACCTATTGCGGCGTTTGTATG-C-CAAAT
* * * * ** *
44475 GCCGCTAAATCTCAAGACATATTCTGCGGCGTTTGTAGGAAAAAC
1 GCCGCTAAATATCAACACCTA-T-TGCGGCGTTTGTATGCCAAAT
* * * * * * * * *
44520 GCTGGTAAAAATAAACATCTACTGCGGCGTTTGTGAAG-AAAAC
1 GCCGCTAAATATCAACACCTATTGCGGCGTTTGT-ATGCCAAAT
* *
44563 GCCGCTAAACATCAACGA-CTATTGCGGCGTTTGTCTGCCAAAT
1 GCCGCTAAATATCAAC-ACCTATTGCGGCGTTTGTATGCCAAAT
* * *
44606 GCCGTTAAATATCAACACCTATTGCGGCGTTTTTATGCCAAAC
1 GCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGCCAAAT
* * * *
44649 GCCGCTAAATATCAATACCTTTTGCGGCGTTTGT-TGAACAATT
1 GCCGCTAAATATCAACACCTATTGCGGCGTTTGTATG-CCAAAT
* * ***
44692 GCCGCTATATGTTGTCACCTATTGCGGCGTTT
1 GCCGCTAAATATCAACACCTATTGCGGCGTTT
44724 TTTTGTTGAA
Statistics
Matches: 197, Mismatches: 43, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
42 4 0.02
43 160 0.81
44 4 0.02
45 27 0.14
46 1 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (43 bp):
GCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGCCAAAT
Found at i:47635 original size:32 final size:34
Alignment explanation
Indices: 47576--47640 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 34
47566 TACAATCAAT
** * *
47576 CGAATTTTTTTTTTCTTTAACTTTTAA-CTGAAC
1 CGAATTTTTTTTTTCTGAAAATATTAACCTGAAC
47609 CGAATTTTTTTTTT-TGAAAATATTAACCTGAA
1 CGAATTTTTTTTTTCTGAAAATATTAACCTGAA
47641 TAAATTTCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 8 0.30
33 19 0.70
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (34 bp):
CGAATTTTTTTTTTCTGAAAATATTAACCTGAAC
Found at i:50926 original size:2 final size:2
Alignment explanation
Indices: 50921--50956 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50911 CACAAATCTA
50921 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
50957 TACCTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.