Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003627.1 Hibiscus syriacus cultivar Beakdansim tig00007673_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: 99670
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4200 original size:132 final size:129
Alignment explanation
Indices: 3973--4235 Score: 330
Period size: 132 Copynumber: 2.0 Consensus size: 129
3963 ATTGTTATGT
* * * ** * *
3973 TGTGTTGAATCCATTGGTTCCTGTTTCTTACCTTGCTCATTTTCCTTCGTTTCCAAGCACTCCTT
1 TGTGCTGAATCCATTGATTCCTGTTTCTTACCATGCTCATGGTCCTCCGTTGCCAAGCACTCCTT
* *
4038 TATCGTCGTTGTTGCTGGTAACGGGGATGGTGATCCTGGCGCCGCTTGTTCACTTTCTTTATCA
66 TATCGTCGTTGTTCCTGGTAACAGGGATGGTGATCCTGGCGCCGCTTGTTCACTTTCTTTATCA
* * *
4102 TGTGCTGAATCCGTTGATTCTTGTTTCTTACCATGCTCATGGTCCTCCGTTGCCGAGCAGTACTC
1 TGTGCTGAATCCATTGATTCCTGTTTCTTACCATGCTCATGGTCCTCCGTTGCC-A--AGCACTC
* * * * *
4167 CTTTATTGTCGTTGTTTCCT-GTATCAGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTCTTTA
63 CTTTATCGTCGTTG-TTCCTGGTAACAGGGATGGTGATCCTGGCGCCGCTTGTTCACTTTCTTTA
4231 TCA
127 TCA
4234 TG
1 TG
4236 GTCTTTATGT
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
129 45 0.40
130 1 0.01
132 63 0.56
133 4 0.04
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (129 bp):
TGTGCTGAATCCATTGATTCCTGTTTCTTACCATGCTCATGGTCCTCCGTTGCCAAGCACTCCTT
TATCGTCGTTGTTCCTGGTAACAGGGATGGTGATCCTGGCGCCGCTTGTTCACTTTCTTTATCA
Found at i:4482 original size:153 final size:153
Alignment explanation
Indices: 4098--4824 Score: 808
Period size: 153 Copynumber: 4.7 Consensus size: 153
4088 CACTTTCTTT
* * * * * * * *
4098 ATCATGTGCTGAATCCGTTGATTCTTGTTTCTTACCATGCTCATGGTCCTCCGTTGCCGAGCAGT
1 ATCATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCC-A--AGC
* * * *
4163 ACTCCTTTATTGTCGTTGTTTCCT-GTATCAGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTC
63 ACTCCTTTATTGTCGTTG-TTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTC
*
4227 TTTATCATGGTCTTTATGTTCCTTGTA
127 TTTATCATGATCTTTATGTTCCTTGTA
4254 AT-ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACT
1 ATCATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACT
*
4318 CCTTTATCGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTA
66 CCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTA
*
4383 TCATGGTCTTTATGTTCCTTGTA
131 TCATGATCTTTATGTTCCTTGTA
4406 AT-ATTGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCAC
1 ATCA-TGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCAC
*
4470 TCCTTTATCGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTT
65 TCCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTT
* * * *
4535 ATCATCATCTTTATGCTCCTTTTC
130 ATCATGATCTTTATGTTCCTTGTA
* * *
4559 ATGATGTGTTGAATCCATTGGTTCCT-TTATCTTA-CTT-TT-ATCGGAATCCTCCATTTCTGAA
1 ATCATGTGTTGAATCCGTTGGTTCCTGTT-TCTTACCTTGTTCAT-GG--TCCTCCATTTC-CAA
* * * * * *
4620 -CATTCCATTGTTGTCATTGTTGCTGGTAACGATGATGGTGATCCTGATGGTCTGGGTGCGGGCT
61 GCACTCCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGAT-C-------CT-GGTGCGGGTT
*
4684 GTTCGCTTTCTTTATCATGATCTTTATGTTCCTTGTA
117 GTTCACTTTCTTTATCATGATCTTTATGTTCCTTGTA
* * * * * * *
4721 ATCATGTTTTGAATCCGTAGGTTCCTTTTTCTCACCTTGATCA-GAATCCTCCATTTCTGAA-CA
1 ATCATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATG-GTCCTCCATTTC-CAAGCA
* * * * * *
4784 TTTCATTGTTGTCATTGTTGCTGGCAACGGTGATGGTGATC
64 CTCCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATC
4825 TTGATGGTCC
Statistics
Matches: 507, Mismatches: 42, Indels: 39
0.86 0.07 0.07
Matches are distributed among these distances:
150 2 0.00
151 8 0.02
152 91 0.18
153 219 0.43
154 5 0.01
155 48 0.09
156 2 0.00
161 3 0.01
162 121 0.24
163 6 0.01
164 1 0.00
165 1 0.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (153 bp):
ATCATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACT
CCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTA
TCATGATCTTTATGTTCCTTGTA
Found at i:4746 original size:162 final size:152
Alignment explanation
Indices: 4101--5082 Score: 784
Period size: 153 Copynumber: 6.2 Consensus size: 152
4091 TTTCTTTATC
* * * * * * * *
4101 ATGTGCTGAATCCGTTGATTCTTGTTTCTTACCATGCTCATGGTCCTCCGTTGCCGAGCAGTACT
1 ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCC-A--AGCACT
* * * * * * *
4166 CCTTTATTGTCGTTGTTTCCT-GTATCAGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTCTTT
63 CCATTATCGTCATTG-TTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTT
*
4230 ATCATGGTCTTTATGTTCCTTGTAAT
127 ATCATGATCTTTATGTTCCTTGTAAT
*
4256 ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACTCCT
1 ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACTCCA
*
4321 TTATCGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTATCA
66 TTATCGTCATTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTATCA
*
4386 TGGTCTTTATGTTCCTTGTAAT
131 TGATCTTTATGTTCCTTGTAAT
4408 ATTGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACTCC
1 A-TGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACTCC
* *
4473 TTTATCGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTATC
65 ATTATCGTCATTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTATC
* * * *
4538 ATCATCTTTATGCTCCTTTTCAT
130 ATGATCTTTATGTTCCTTGTAAT
* *
4561 GATGTGTTGAATCCATTGGTTCCT-TTATCTTA-CTT-TT-ATCGGAATCCTCCATTTCTGAA-C
1 -ATGTGTTGAATCCGTTGGTTCCTGTT-TCTTACCTTGTTCAT-GG--TCCTCCATTTC-CAAGC
* * * * *
4621 ATTCCATTGTTGTCATTGTTGCTGGTAACGATGATGGTGATCCTGATGGTCTGGGTGCGGGCTGT
60 ACTCCATTATCGTCATTGTTGCTGGTAACGGTGATGGTGAT-C-------CT-GGTGCGGGTTGT
*
4686 TCGCTTTCTTTATCATGATCTTTATGTTCCTTGTAAT
116 TCACTTTCTTTATCATGATCTTTATGTTCCTTGTAAT
* * * * * * * *
4723 CATGTTTTGAATCCGTAGGTTCCTTTTTCTCACCTTGATCA-GAATCCTCCATTTCTGAA-CATT
1 -ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATG-GTCCTCCATTTC-CAAGCACT
* * * * * * *
4786 TCATTGTTGTCATTGTTGCTGGCAACGGTGATGGTGATCTTGATGGTCCGGG-TGCATATTATTT
63 CCATTATCGTCATTGTTGCTGGTAACGGTGATGGTGATC---CTGGTGCGGGTTG--T-TCA---
* * *
4850 GCTTTCTTTATCAT-ATTTTTACGTTCCTTGTCAT
119 -CTTTCTTTATCATGATCTTTATGTTCCTTGTAAT
* ** * * * ** *
4884 GATGCGTCGTTGAATCCATTGGTTTTTGTTTCTTACCATGCTCGTTATCCTCCATTTCCGAGCA-
1 -AT--GT-GTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCAC
* * ** * *
4948 -CAACT-TCGTCATTGTTGCTGGTAATACTGGTGTTGATCTTGATGGCCTTGGTGCAGATTGTTC
62 TCCATTATCGTCATTGTTGCTGGT-A-AC--G-G-TGATGGTGAT--CC-TGGTGCGGGTTGTTC
* * *
5011 GCTTTCTTTATCATGATCATTATGTTCCTTGTCAT
118 ACTTTCTTTATCATGATCTTTATGTTCCTTGTAAT
* * ** *
5046 GATGTGTTGAATTCATTGGTTTTTGCTTCTTACCTTG
1 -ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTG
5083 CTGAGAATCC
Statistics
Matches: 697, Mismatches: 85, Indels: 86
0.80 0.10 0.10
Matches are distributed among these distances:
150 2 0.00
151 8 0.01
152 91 0.13
153 219 0.31
154 5 0.01
155 50 0.07
156 7 0.01
157 2 0.00
158 1 0.00
159 29 0.04
160 2 0.00
161 50 0.07
162 157 0.23
163 11 0.02
164 41 0.06
165 3 0.00
166 2 0.00
167 14 0.02
168 2 0.00
169 1 0.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (152 bp):
ATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTCCAAGCACTCCA
TTATCGTCATTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCTTTATCA
TGATCTTTATGTTCCTTGTAAT
Found at i:4776 original size:315 final size:305
Alignment explanation
Indices: 4163--4824 Score: 784
Period size: 315 Copynumber: 2.1 Consensus size: 305
4153 GCCGAGCAGT
* * *
4163 ACTCCTTTATTGTCGTTGTTTCCT-GTATCAGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTC
1 ACTCCTTTATTGTCGTTG-TTGCTGGTAACGGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTC
** * *
4227 TTTATCATGGTCTTTATGTTCCTTGTAATATGTGTTGAATCCGTTGGTTCCTGTTTCTTACCTTG
65 TTTATCATCATCTTTATGCTCCTTGTAATATGTGTTGAATCCATTGGTTCCTGTTTCTTACCTTG
* * *
4292 TTCATGGTCCTCCATTTCCAAGCACTCCTTTATCGTCGTTGTTGCTGGTAACGGTGATGGTGATC
130 TTCATGGTCCTCCATTTCCAAGCACTCCATTATCGTCATTGTTGCTGGTAACGATGATGGTGATC
* *
4357 CTGGTGCGGGTTGTTCACTTTCTTTATCATGGTCTTTATGTTCCTTGTAATATTGTGTTGAATCC
195 CTGGTGCGGGCTGTTCACTTTCTTTATCATGATCTTTATGTTCCTTGTAATATTGTGTTGAATCC
* * * *
4422 GTTGGTTCCTGTTTCTTACCTTGTTCATGGTCCTCCATTTC-CAAGC
260 GTAGGTTCCTGTTTCTCACCTTGATCATGATCCTCCATTTCTCAA-C
* *
4468 ACTCCTTTATCGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGTGCGGGTTGTTCACTTTCT
1 ACTCCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTCT
* *
4533 TTATCATCATCTTTATGCTCCTTTTCATGATGTGTTGAATCCATTGGTTCCT-TTATCTTA-CTT
66 TTATCATCATCTTTATGCTCCTTGTAAT-ATGTGTTGAATCCATTGGTTCCTGTT-TCTTACCTT
* * * *
4596 -TT-ATCGGAATCCTCCATTTCTGAA-CATTCCATTGTTGTCATTGTTGCTGGTAACGATGATGG
129 GTTCAT-GG--TCCTCCATTTC-CAAGCACTCCATTATCGTCATTGTTGCTGGTAACGATGATGG
*
4658 TGATCCTGATGGTCTGGGTGCGGGCTGTTCGCTTTCTTTATCATGATCTTTATGTTCCTTGTAAT
190 TGAT-C-------CT-GGTGCGGGCTGTTCACTTTCTTTATCATGATCTTTATGTTCCTTGTAAT
* * *
4723 CA-TGTTTTGAATCCGTAGGTTCCTTTTTCTCACCTTGATCA-GAATCCTCCATTTCTGAAC
246 -ATTGTGTTGAATCCGTAGGTTCCTGTTTCTCACCTTGATCATG-ATCCTCCATTTCTCAAC
* * * * * *
4783 ATTTCATTGTTGTCATTGTTGCTGGCAACGGTGATGGTGATC
1 ACTCCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATC
4825 TTGATGGTCC
Statistics
Matches: 303, Mismatches: 35, Indels: 28
0.83 0.10 0.08
Matches are distributed among these distances:
303 2 0.01
304 8 0.03
305 83 0.27
306 74 0.24
307 3 0.01
314 3 0.01
315 127 0.42
316 3 0.01
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (305 bp):
ACTCCTTTATTGTCGTTGTTGCTGGTAACGGTGATGGTGATCCTGGCGCGGGTTGTTCACTTTCT
TTATCATCATCTTTATGCTCCTTGTAATATGTGTTGAATCCATTGGTTCCTGTTTCTTACCTTGT
TCATGGTCCTCCATTTCCAAGCACTCCATTATCGTCATTGTTGCTGGTAACGATGATGGTGATCC
TGGTGCGGGCTGTTCACTTTCTTTATCATGATCTTTATGTTCCTTGTAATATTGTGTTGAATCCG
TAGGTTCCTGTTTCTCACCTTGATCATGATCCTCCATTTCTCAAC
Found at i:4987 original size:161 final size:159
Alignment explanation
Indices: 4527--5113 Score: 422
Period size: 162 Copynumber: 3.6 Consensus size: 159
4517 GGGTTGTTCA
* * * * * *
4527 CTTTCTTTATCATCATCTTTATGCTCCTTTTCATGATGTGTTGAATCCATTGGTTCCTTTATCTT
1 CTTTCTTTATCATGATCATTACGTTCCTTGTCATGATGTGTTGAATCCATTGGTT--TTT-GCTT
** * * * * * *
4592 ACTT-TTAT-C-G-GAATCCTCCATTTCTGAACATTCCATTGTTGTCATTGTTGCTGGTAACGA-
63 -CTTACCATGCTGAGAATCCTCCATTTCAGAGCA--CAACT-TCGTCATTGTTGCTGGTAA-TAC
* * * * * ** *
4652 TGATGGTGATCCTGATGGTCTGGGTGCGGGCTGTTCG
123 TGGTGTTGATCTTGATGGCCTGGGTGCAGATTATTCG
* * * * * * *
4689 CTTTCTTTATCATGATCTTTATGTTCCTTGTAATCATGTTTTGAATCCGTAGGTTCCTTT--TTC
1 CTTTCTTTATCATGATCATTACGTTCCTTGTCATGATGTGTTGAATCCATTGGTT--TTTGCTTC
* * * * * * * * * ***
4752 TCACCTTGATCAGAATCCTCCATTTCTGAACATTTC-ATTGTTGTCATTGTTGCTGGCAACGGTG
64 TTACCATGCTGAGAATCCTCCATTTCAGAGCA---CAACT-TCGTCATTGTTGCTGGTAATACTG
* * * *
4816 ATGGTGATCTTGATGGTCC-GGGTGCATATTATTTG
125 GTGTTGATCTTGATGG-CCTGGGTGCAGATTATTCG
** *
4851 CTTTCTTTATCAT-ATTTTTACGTTCCTTGTCATGATGCGTCGTTGAATCCATTGGTTTTTGTTT
1 CTTTCTTTATCATGATCATTACGTTCCTTGTCATGAT--GT-GTTGAATCCATTGGTTTTTGCTT
** *
4915 CTTACCATGCTCG-TTATCCTCCATTTCCGAGCACAACTTCGTCATTGTTGCTGGTAATACTGGT
63 CTTACCATGCT-GAGAATCCTCCATTTCAGAGCACAACTTCGTCATTGTTGCTGGTAATACTGGT
* *
4979 GTTGATCTTGATGGCCTTGGTGCAGATTGTTCG
127 GTTGATCTTGATGGCCTGGGTGCAGATTATTCG
* *
5012 CTTTCTTTATCATGATCATTATGTTCCTTGTCATGATGTGTTGAATTCATTGGTTTTTGCTTCTT
1 CTTTCTTTATCATGATCATTACGTTCCTTGTCATGATGTGTTGAATCCATTGGTTTTTGCTTCTT
*
5077 ACCTTGCTGAGAATCCTCCATTTCAGAGCACAACTTC
66 ACCATGCTGAGAATCCTCCATTTCAGAGCACAACTTC
5114 AAATTTGTCA
Statistics
Matches: 347, Mismatches: 61, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
158 3 0.01
159 58 0.17
160 4 0.01
161 78 0.22
162 159 0.46
163 6 0.02
164 39 0.11
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (159 bp):
CTTTCTTTATCATGATCATTACGTTCCTTGTCATGATGTGTTGAATCCATTGGTTTTTGCTTCTT
ACCATGCTGAGAATCCTCCATTTCAGAGCACAACTTCGTCATTGTTGCTGGTAATACTGGTGTTG
ATCTTGATGGCCTGGGTGCAGATTATTCG
Found at i:5565 original size:137 final size:139
Alignment explanation
Indices: 5279--5531 Score: 332
Period size: 137 Copynumber: 1.8 Consensus size: 139
5269 CGTCGGTATT
* * * *
5279 GGTGATGGCGGTCTTTTTGGTCCTAGTGTGGGATGTTCGGCTTCTTTATCATAATCATTATGTTC
1 GGTGATGGTGGTCTTTTTGG--CTAGTGTGGGATGTTCGCCTTCGTGATCATAATCATTATGTTC
* * *
5344 CTTACCCTGTTCAGAATTCTCCATTTCAGGGTACTGCCTCATAGTTAACAACGCAGCCCTCCTCG
64 CATACCCTGTTCAGAATTCTCCAATTCAGAGTACTGCCTCATAGTTAACAACGCAGCCCTCCTCG
5409 CAACCGGTAAA
129 CAACCGGTAAA
*
5420 GGTGATGGTGGTC-TTTTGG-TAGTGTGGGATGTTCGCCTTCGTGATCATGATCATTATGTTCCA
1 GGTGATGGTGGTCTTTTTGGCTAGTGTGGGATGTTCGCCTTCGTGATCATAATCATTATGTTCCA
* * * * * *
5483 TACCGT-TCTCGGAATTCTCGAATTCCGAGTGCTGCCTCATCGTTAACAA
66 TACCCTGT-TCAGAATTCTCCAATTCAGAGTACTGCCTCATAGTTAACAA
5532 TGCGGTCCTC
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
136 1 0.01
137 78 0.80
140 6 0.06
141 12 0.12
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (139 bp):
GGTGATGGTGGTCTTTTTGGCTAGTGTGGGATGTTCGCCTTCGTGATCATAATCATTATGTTCCA
TACCCTGTTCAGAATTCTCCAATTCAGAGTACTGCCTCATAGTTAACAACGCAGCCCTCCTCGCA
ACCGGTAAA
Found at i:8842 original size:22 final size:22
Alignment explanation
Indices: 8814--8855 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
8804 ATTGATATAA
8814 TTATACATTT-ATTCCTAATTAT
1 TTATACATTTGA-TCCTAATTAT
8836 TTATACATTTGATCCTAATT
1 TTATACATTTGATCCTAATT
8856 TAAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATACATTTGATCCTAATTAT
Found at i:13971 original size:15 final size:15
Alignment explanation
Indices: 13951--13981 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13941 TATGCTTGCA
13951 TTACACTTTACATCC
1 TTACACTTTACATCC
13966 TTACACTTTACATCC
1 TTACACTTTACATCC
13981 T
1 T
13982 CTTTCGTATC
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:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (15 bp):
TTACACTTTACATCC
Found at i:16784 original size:2 final size:2
Alignment explanation
Indices: 16777--16804 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16767 CTGTATGTGA
16777 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
16805 TCACCTTGAA
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:20263 original size:6 final size:6
Alignment explanation
Indices: 20252--20293 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
20242 GACACGTATT
20252 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCA-G ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
20294 CGAGACGGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 13 0.38
6 21 0.62
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:20941 original size:21 final size:19
Alignment explanation
Indices: 20890--20944 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
20880 TAATTTACTA
*
20890 TAGACTATCGCAACGAATT
1 TAGACTATCGCAACGAATG
* **
20909 TGGAAAATCGCAACGACACTG
1 TAGACTATCGCAACGA-A-TG
20930 TAGACTATCGCAACG
1 TAGACTATCGCAACG
20945 CGAAATGGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 13 0.48
20 1 0.04
21 13 0.48
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (19 bp):
TAGACTATCGCAACGAATG
Found at i:20964 original size:41 final size:41
Alignment explanation
Indices: 20886--21029 Score: 184
Period size: 41 Copynumber: 3.5 Consensus size: 41
20876 TTTTTAATTT
* *
20886 ACTATAGACTATCGCAA--CGAATTTGGAAAATCGCAACGAC
1 ACTATACACTATCGCAACGCGAA-ATGGAAAATCGCAACGAC
* *
20926 ACTGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGAC
1 ACTATACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
** * *
20967 ACTATACACTATCGCAATACGAGATGGAAAATCGCAATGAC
1 ACTATACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
*
21008 ACTTTACACTATCGCAACGCGA
1 ACTATACACTATCGCAACGCGA
21030 TTTTCAACTA
Statistics
Matches: 91, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 16 0.18
41 71 0.78
42 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
ACTATACACTATCGCAACGCGAAATGGAAAATCGCAACGAC
Found at i:21022 original size:62 final size:62
Alignment explanation
Indices: 20956--21091 Score: 159
Period size: 62 Copynumber: 2.2 Consensus size: 62
20946 GAAATGGAAA
* * * * *
20956 ATCGCAACGAC-ACTATAC-ACTATCGCAATACGAGATGGAAAATCGCAATGACACTTTACACT
1 ATCGCAACG-CGA-TATACAACTATCGCAACACGAAATGGAAAATCACAACGACACTGTACACT
* * * *
21018 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAGACT
1 ATCGCAACGCGATATACAACTATCGCAACACGAAATGGAAAATCACAACGACACTGTACACT
21080 ATCGCAACGCGA
1 ATCGCAACGCGA
21092 AATGCAACGC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
61 4 0.06
62 59 0.94
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (62 bp):
ATCGCAACGCGATATACAACTATCGCAACACGAAATGGAAAATCACAACGACACTGTACACT
Found at i:30854 original size:14 final size:13
Alignment explanation
Indices: 30817--30864 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
30807 AATTGATTTA
*
30817 AATTTAAAATTAAT
1 AATTTTAAA-TAAT
30831 CAATTTTAAATAAT
1 -AATTTTAAATAAT
30845 AATTTGTAAATAAT
1 AATTT-TAAATAAT
*
30859 TATTTT
1 AATTTT
30865 TATTGTCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 6 0.20
14 16 0.53
15 8 0.27
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (13 bp):
AATTTTAAATAAT
Found at i:33204 original size:36 final size:36
Alignment explanation
Indices: 33163--33265 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
33153 AGTTGAGTAT
33163 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
33199 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCC
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
33235 TATCATCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
33266 CCAGCACCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:39473 original size:7 final size:7
Alignment explanation
Indices: 39461--39511 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
39451 ATAGGTTATT
39461 ATATATG
1 ATATATG
39468 ATATATG
1 ATATATG
39475 ATATGAT-
1 ATAT-ATG
*
39482 ATACATG
1 ATATATG
39489 ATTATATG
1 A-TATATG
*
39497 CATATGTG
1 -ATATATG
39505 ATATATG
1 ATATATG
39512 TTATGAGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.06
7 21 0.58
8 12 0.33
9 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (7 bp):
ATATATG
Found at i:40483 original size:37 final size:37
Alignment explanation
Indices: 40410--40483 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
40400 TTATATTTTA
*
40410 AATTTTGTAAAAAAAATTATATAAATATTATGAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTATCAATTT
* * *
40447 AATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 AATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
40484 GTAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.41
37 19 0.59
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
AATTTTGTAAAAAAAATTATATAAATATTATCAATTT
Found at i:42346 original size:25 final size:26
Alignment explanation
Indices: 42328--42382 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
42318 AAAATTATTA
42328 AGAATAA-AAAATAAAAAAAATATAC
1 AGAATAATAAAATAAAAAAAATATAC
** *
42353 ATTATAATAAAATAAAAAAAA-ATAA
1 AGAATAATAAAATAAAAAAAATATAC
42378 AGAAT
1 AGAAT
42383 TTCAACGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.20
Consensus pattern (26 bp):
AGAATAATAAAATAAAAAAAATATAC
Found at i:45362 original size:34 final size:34
Alignment explanation
Indices: 45319--45420 Score: 195
Period size: 34 Copynumber: 3.0 Consensus size: 34
45309 CACGCACTAC
*
45319 ATTTAGTATATTAATGTAAGTTGGAATCATCTAT
1 ATTTAGTATATTAATATAAGTTGGAATCATCTAT
45353 ATTTAGTATATTAATATAAGTTGGAATCATCTAT
1 ATTTAGTATATTAATATAAGTTGGAATCATCTAT
45387 ATTTAGTATATTAATATAAGTTGGAATCATCTAT
1 ATTTAGTATATTAATATAAGTTGGAATCATCTAT
45421 GGAGTTGACT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 67 1.00
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (34 bp):
ATTTAGTATATTAATATAAGTTGGAATCATCTAT
Found at i:49979 original size:29 final size:29
Alignment explanation
Indices: 49917--50012 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 29
49907 ATTTTATAGA
* * * *
49917 AATAGCACCCCTTTTCAAATTAATTACCAA
1 AATAGCACCCATTTT-GAATTAATTCCCAT
49947 AATAGCACCCATTTTGAATTAATTCCCAT
1 AATAGCACCCATTTTGAATTAATTCCCAT
* ** * *
49976 AATAGCACCAAAATCGAATAAATTCCCAT
1 AATAGCACCCATTTTGAATTAATTCCCAT
50005 AATAGCAC
1 AATAGCAC
50013 TGATCAACGG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
29 43 0.75
30 14 0.25
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (29 bp):
AATAGCACCCATTTTGAATTAATTCCCAT
Found at i:57183 original size:29 final size:30
Alignment explanation
Indices: 57141--57197 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
57131 TAACACATCT
57141 TTTTCGAATTAATTACCAAAATAACACCCA
1 TTTTCGAATTAATTACCAAAATAACACCCA
* * *
57171 TTTT-GAATTAATTCCCATAATATCACC
1 TTTTCGAATTAATTACCAAAATAACACC
57198 AAAATCGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
TTTTCGAATTAATTACCAAAATAACACCCA
Found at i:57262 original size:18 final size:18
Alignment explanation
Indices: 57234--57286 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
57224 ACCGGTCAAC
*
57234 GGTCAAC-GGTCGGTTCG
1 GGTCAACGGGTCGGGTCG
57251 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
57269 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCG
57287 TGACCGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:67199 original size:30 final size:30
Alignment explanation
Indices: 67163--67289 Score: 245
Period size: 30 Copynumber: 4.2 Consensus size: 30
67153 CCCGCAGGAC
67163 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
67193 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
67223 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
67253 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
67283 CTGTCCA
1 CTATCCA
67290 TACGTTCTGT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 96 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:72821 original size:30 final size:30
Alignment explanation
Indices: 72785--72911 Score: 245
Period size: 30 Copynumber: 4.2 Consensus size: 30
72775 CCCACAGGAC
72785 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
72815 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
72845 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
72875 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
72905 CTGTCCA
1 CTATCCA
72912 TACGTTCCGT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 96 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:73038 original size:21 final size:21
Alignment explanation
Indices: 73013--73066 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
73003 ATCCTTTTAC
*
73013 ATATTCATGTAACCATATCAT
1 ATATTCATATAACCATATCAT
73034 ATATTCATATAACCATATCAT
1 ATATTCATATAACCATATCAT
73055 ATATTCATATAA
1 ATATTCATATAA
73067 GCTCATGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.39
Consensus pattern (21 bp):
ATATTCATATAACCATATCAT
Found at i:80304 original size:17 final size:17
Alignment explanation
Indices: 80282--80334 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
80272 AAAGTCTTAT
80282 TATTATTGTGATTAAAG
1 TATTATTGTGATTAAAG
*
80299 TATTATTGTTATT--A-
1 TATTATTGTGATTAAAG
80313 -A-TATTGTGATTAAAG
1 TATTATTGTGATTAAAG
80328 TATTATT
1 TATTATT
80335 AGGGATGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 9 0.31
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 16 0.55
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (17 bp):
TATTATTGTGATTAAAG
Found at i:80320 original size:29 final size:29
Alignment explanation
Indices: 80278--80334 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
80268 ACGGAAAGTC
*
80278 TTATTATTATTGTGATTAAAGTATTATTG
1 TTATTAATATTGTGATTAAAGTATTATTG
80307 TTATTAATATTGTGATTAAAGTATTATT
1 TTATTAATATTGTGATTAAAGTATTATT
80335 AGGGATGGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (29 bp):
TTATTAATATTGTGATTAAAGTATTATTG
Found at i:80523 original size:15 final size:15
Alignment explanation
Indices: 80503--80537 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
80493 GCCCCACATT
* *
80503 CGCCCCGCATCTGCC
1 CGCCCCACATCGGCC
80518 CGCCCCACATCGGCC
1 CGCCCCACATCGGCC
80533 CGCCC
1 CGCCC
80538 AGCTAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.63, G:0.20, T:0.09
Consensus pattern (15 bp):
CGCCCCACATCGGCC
Found at i:80985 original size:154 final size:157
Alignment explanation
Indices: 80705--81017 Score: 596
Period size: 154 Copynumber: 2.0 Consensus size: 157
80695 CATCAAAATC
80705 TGTATTCAGTATAGGTGGAAGAGTAATTGGTCCTTATCGTAGGCGACTACTTCTGAAGACGATTG
1 TGTATTCAGTATAGGTGGAAGAGTAATTGGTCCTTATCGTAGGCGACTACTTCTGAAGACGATTG
80770 AAGCATTAATGTATGCTCAAAATTGGCTTTGGGCCGATATTAAAGGTAATATTATTATTTAATTT
66 AAGCATTAATGTATGCTCAAAATTGGCTTTGGGCCGATATTAAAGGTAATATTATTATTTAATTT
80835 ATA-T-TTGTTAAA-TGTGCTTAATTA
131 ATATTATTGTTAAATTGTGCTTAATTA
80859 TGTATTCAGTATAGGTGGAAGAGTAATTGGTCCTTATCGTAGGCGACTACTTCTGAAGACGATTG
1 TGTATTCAGTATAGGTGGAAGAGTAATTGGTCCTTATCGTAGGCGACTACTTCTGAAGACGATTG
80924 AAGCATTAATGTATGCTCAAAATTGGCTTTGGGCCGATATTAAAGGTAATATTATTATTTAATTT
66 AAGCATTAATGTATGCTCAAAATTGGCTTTGGGCCGATATTAAAGGTAATATTATTATTTAATTT
80989 ATATTAGTTGTTAAATTGTGCTTAATTA
131 ATATTA-TTGTTAAATTGTGCTTAATTA
81017 T
1 T
81018 CTTATTAAAG
Statistics
Matches: 155, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
154 133 0.86
155 1 0.01
157 8 0.05
158 13 0.08
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (157 bp):
TGTATTCAGTATAGGTGGAAGAGTAATTGGTCCTTATCGTAGGCGACTACTTCTGAAGACGATTG
AAGCATTAATGTATGCTCAAAATTGGCTTTGGGCCGATATTAAAGGTAATATTATTATTTAATTT
ATATTATTGTTAAATTGTGCTTAATTA
Found at i:84973 original size:22 final size:22
Alignment explanation
Indices: 84948--84989 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
84938 CTGAATGATT
*
84948 CAGTGCTGACTGATTCAACAAA
1 CAGTGCTGAATGATTCAACAAA
84970 CAGTGCTGAATGATTCAACA
1 CAGTGCTGAATGATTCAACA
84990 CAGAAGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (22 bp):
CAGTGCTGAATGATTCAACAAA
Found at i:87052 original size:2 final size:2
Alignment explanation
Indices: 87045--87105 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
87035 TTTGAATCTA
87045 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
87087 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
87106 ACGATGACAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:87598 original size:25 final size:25
Alignment explanation
Indices: 87570--87621 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
87560 GTATCATGTT
87570 TTTTTATTATAAATAGAGATGTAAC
1 TTTTTATTATAAATAGAGATGTAAC
*
87595 TTTTTATTATAAATATAGATGTAAC
1 TTTTTATTATAAATAGAGATGTAAC
87620 TT
1 TT
87622 AAACCTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (25 bp):
TTTTTATTATAAATAGAGATGTAAC
Found at i:89261 original size:14 final size:14
Alignment explanation
Indices: 89234--89273 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
89224 TAAAAAAAAT
89234 TATAATTATTAATAA
1 TATAATT-TTAATAA
* *
89249 TTTATTTTTAATAA
1 TATAATTTTAATAA
89263 TATAATTTTAA
1 TATAATTTTAA
89274 AAAATCTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATAATTTTAATAA
Found at i:89710 original size:87 final size:87
Alignment explanation
Indices: 89564--89826 Score: 508
Period size: 87 Copynumber: 3.0 Consensus size: 87
89554 CTACAAACAA
*
89564 TTCACGGATTGAAATCATTGAATTATTTGTGTGCCTTGCAAATTTTATTTAAGTAGGTGAGTACA
1 TTCACGGATTGAAATCATTGAATCATTTGTGTGCCTTGCAAATTTTATTTAAGTAGGTGAGTACA
89629 CTATTAGATTCAACAATAAGGT
66 CTATTAGATTCAACAATAAGGT
*
89651 TTCACGGATTGAAATCATTGAATCATTTGTGTGCCTTGCAAATTTTATTCAAGTAGGTGAGTACA
1 TTCACGGATTGAAATCATTGAATCATTTGTGTGCCTTGCAAATTTTATTTAAGTAGGTGAGTACA
89716 CTATTAGATTCAACAATAAGGT
66 CTATTAGATTCAACAATAAGGT
89738 TTCACGGATTGAAATCATTGAATCATTTGTGTGCCTTGCAAATTTTATTTAAGTAGGTGAGTACA
1 TTCACGGATTGAAATCATTGAATCATTTGTGTGCCTTGCAAATTTTATTTAAGTAGGTGAGTACA
89803 CTATTAGATTCAACAATAAGGT
66 CTATTAGATTCAACAATAAGGT
89825 TT
1 TT
89827 TTAAAGTAAT
Statistics
Matches: 173, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 173 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (87 bp):
TTCACGGATTGAAATCATTGAATCATTTGTGTGCCTTGCAAATTTTATTTAAGTAGGTGAGTACA
CTATTAGATTCAACAATAAGGT
Found at i:91157 original size:184 final size:183
Alignment explanation
Indices: 90947--91331 Score: 593
Period size: 184 Copynumber: 2.1 Consensus size: 183
90937 ATTAAATTTT
*
90947 AAATATTAA-ATA-TATATATAACATATGGGTTCAGCCCAAACCATTTAAAACCCAATTAATAAT
1 AAATATTAATATATTATATATAACATATGGGTTAAGCCCAAACCATTTAAAACCCAATTAATAAT
* * *
91010 TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAA-TTATA-T-AAAATT
66 TTAAAATACAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTA-ACTGAAAA-T
* *
91072 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
*
91128 AAATATTAAATATATTATATATAACATATGGGTTAAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATT-AATATATTATATATAACATATGGGTTAAGCCCAAACCATTTAAAACCCAATTAATAA
*
91193 TTTAAAATATAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAACTGAAAATT
65 TTTAAAATACAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAACTGAAAATT
91258 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
91312 AAACATTTAAT-TTTTATATA
1 AAATA-TTAATATATTATATA
91332 AATTAAATTT
Statistics
Matches: 187, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
181 7 0.04
182 2 0.01
183 11 0.06
184 116 0.62
185 47 0.25
186 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (183 bp):
AAATATTAATATATTATATATAACATATGGGTTAAGCCCAAACCATTTAAAACCCAATTAATAAT
TTAAAATACAATAACATTTAAACCTAAATCAATATTAATTAATTAAAAAATTTAACTGAAAATTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:91970 original size:17 final size:17
Alignment explanation
Indices: 91927--91978 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
91917 ATTACAGTAG
*
91927 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
91944 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
91959 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
91976 AAA
1 AAA
91979 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:92669 original size:24 final size:24
Alignment explanation
Indices: 92618--92682 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 24
92608 AAAATAAAAT
*
92618 ATATTTTCATTTATGTTCGTTTAC
1 ATATGTTCATTTATGTTCGTTTAC
92642 ----GTTCATTTATGTTCGTTTAC
1 ATATGTTCATTTATGTTCGTTTAC
*
92662 ATATGTTCGTTTATGTTCGTT
1 ATATGTTCATTTATGTTCGTT
92683 CATTTGTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 19 0.54
24 16 0.46
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.57
Consensus pattern (24 bp):
ATATGTTCATTTATGTTCGTTTAC
Found at i:92676 original size:10 final size:10
Alignment explanation
Indices: 92627--92682 Score: 58
Period size: 10 Copynumber: 5.2 Consensus size: 10
92617 TATATTTTCA
92627 TTTATGTTCG
1 TTTATGTTCG
* *
92637 TTTACGTTCA
1 TTTATGTTCG
92647 TTTATGTTCG
1 TTTATGTTCG
92657 TTTACATATGTTCG
1 -TT---TATGTTCG
92671 TTTATGTTCG
1 TTTATGTTCG
92681 TT
1 TT
92683 CATTTGTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 26 0.68
11 2 0.05
13 2 0.05
14 8 0.21
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.57
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:92699 original size:24 final size:24
Alignment explanation
Indices: 92618--92684 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
92608 AAAATAAAAT
*
92618 ATATTTTCATTTATGTTCGTT---
1 ATATGTTCATTTATGTTCGTTCAC
* *
92639 -TACGTTCATTTATGTTCGTTTAC
1 ATATGTTCATTTATGTTCGTTCAC
*
92662 ATATGTTCGTTTATGTTCGTTCA
1 ATATGTTCATTTATGTTCGTTCA
92685 TTTGTGTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 18 0.49
24 19 0.51
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.55
Consensus pattern (24 bp):
ATATGTTCATTTATGTTCGTTCAC
Done.