Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003854.1 Hibiscus syriacus cultivar Beakdansim tig00008285_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: 151844
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:111865 original size:2 final size:2
Alignment explanation
Indices: 111858--111888 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
111848 CCCATTTATG
111858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
111889 ACATGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113145 original size:21 final size:19
Alignment explanation
Indices: 113095--113145 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
113085 ACTATGATTG
*
113095 TATATGATTAT-ATAAAAT
1 TATATTATTATGATAAAAT
* *
113113 TATAATAATATGATATAAAT
1 TATATTATTATGATA-AAAT
113133 TAATATTATTATG
1 T-ATATTATTATG
113146 GGTAAATATG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 8 0.32
19 3 0.12
20 5 0.20
21 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
TATATTATTATGATAAAAT
Found at i:121161 original size:19 final size:19
Alignment explanation
Indices: 121137--121186 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
121127 TTGTATTAAT
*
121137 AATTAAAATGAGGGTAAAA
1 AATTAAAATAAGGGTAAAA
* * *
121156 AATTAAGAATAATGGTCACA
1 AATTAA-AATAAGGGTAAAA
121176 AATTAAAATAA
1 AATTAAAATAA
121187 AATAACACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.58, C:0.04, G:0.14, T:0.24
Consensus pattern (19 bp):
AATTAAAATAAGGGTAAAA
Found at i:129600 original size:20 final size:22
Alignment explanation
Indices: 129575--129630 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
129565 AGAATAATTA
129575 TGTCTTTGTGACATG-T-TCTC
1 TGTCTTTGTGACATGTTATCTC
* *
129595 TGTCTTTATGGCATGTTTATCTC
1 TGTCTTTGTGACATG-TTATCTC
129618 TGTCTTTGTGACA
1 TGTCTTTGTGACA
129631 CATTTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.45
22 1 0.03
23 15 0.52
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.50
Consensus pattern (22 bp):
TGTCTTTGTGACATGTTATCTC
Found at i:130184 original size:16 final size:18
Alignment explanation
Indices: 130163--130196 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
130153 TTGTAAAATT
130163 ATTTAAAT-TAA-TATTC
1 ATTTAAATATAATTATTC
130179 ATTTAAATATAATTATTC
1 ATTTAAATATAATTATTC
130197 TATTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTAAATATAATTATTC
Found at i:130245 original size:7 final size:7
Alignment explanation
Indices: 130232--130261 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
130222 TGTATCTATA
130232 ATTAAAC
1 ATTAAAC
*
130239 GTTAAAC
1 ATTAAAC
130246 ATTAAAC
1 ATTAAAC
130253 ATTAAAC
1 ATTAAAC
130260 AT
1 AT
130262 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (7 bp):
ATTAAAC
Found at i:131949 original size:20 final size:19
Alignment explanation
Indices: 131901--131947 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
131891 AACGATTTTC
* * *
131901 TTTTAAAAGCAAAATTAGA
1 TTTTAAAATCAAAATAAAA
131920 TTTTGAAAATCAAAATAAAA
1 TTTT-AAAATCAAAATAAAA
131940 TTTTAAAA
1 TTTTAAAA
131948 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (19 bp):
TTTTAAAATCAAAATAAAA
Found at i:133667 original size:21 final size:21
Alignment explanation
Indices: 133609--133673 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 21
133599 GTAAGTTTTA
* *
133609 GATCGGTCCCTTTAT-AAAAG
1 GATCGATCCCTCTATGAAAAG
* * * *
133629 GATAGAT-CCTCAAGGAAAAT
1 GATCGATCCCTCTATGAAAAG
133649 GATCGATCCCTCTATGAAAAG
1 GATCGATCCCTCTATGAAAAG
133670 GATC
1 GATC
133674 AATCTTTTTC
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
19 4 0.12
20 15 0.45
21 14 0.42
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
GATCGATCCCTCTATGAAAAG
Found at i:134951 original size:14 final size:16
Alignment explanation
Indices: 134910--134954 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
134900 CTTATTTTAT
134910 AATTATACCTAATACA
1 AATTATACCTAATACA
* *
134926 ATTTATAACTAA-A-A
1 AATTATACCTAATACA
134940 AATTATACCTAATAC
1 AATTATACCTAATAC
134955 GAAAAGTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTATACCTAATACA
Found at i:135332 original size:2 final size:2
Alignment explanation
Indices: 135325--135349 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
135315 ATCCTAACTC
135325 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
135350 ATTAGATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:135719 original size:6 final size:6
Alignment explanation
Indices: 135710--135786 Score: 127
Period size: 6 Copynumber: 12.8 Consensus size: 6
135700 TAAACACTGA
* * *
135710 GCTGGA GCTGGG GCTGGA GCTGGG GCTGGG GCTGGA GCTGGG GCTGGG
1 GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG GCTGGG
135758 GCTGGG GCTGGG GCTGGG GCTGGG GCTGG
1 GCTGGG GCTGGG GCTGGG GCTGGG GCTGG
135787 TTATAGAGGT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.04, C:0.17, G:0.62, T:0.17
Consensus pattern (6 bp):
GCTGGG
Found at i:142265 original size:19 final size:19
Alignment explanation
Indices: 142241--142278 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
142231 AGATGCTAAG
142241 TTACATATCAAATAACAAA
1 TTACATATCAAATAACAAA
142260 TTACATATCAAATAACAAA
1 TTACATATCAAATAACAAA
142279 GAAGATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (19 bp):
TTACATATCAAATAACAAA
Found at i:142286 original size:19 final size:19
Alignment explanation
Indices: 142243--142286 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
142233 ATGCTAAGTT
**
142243 ACATATCAAATAACAAATT
1 ACATATCAAATAACAAAGA
142262 ACATATCAAATAACAAAGA
1 ACATATCAAATAACAAAGA
*
142281 AGATAT
1 ACATAT
142287 AACACATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.23
Consensus pattern (19 bp):
ACATATCAAATAACAAAGA
Found at i:143143 original size:20 final size:21
Alignment explanation
Indices: 143118--143169 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
143108 TTTTCCCAAT
*
143118 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
143138 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
143159 TCGCAATGCGA
1 TCGCAATGCGA
143170 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:143183 original size:20 final size:20
Alignment explanation
Indices: 143158--143251 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
143148 AATTGGGAAA
143158 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
143178 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
143198 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
143219 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
143239 TTCGCAACGCGAT
1 ATCGCAATGCGAT
143252 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:143846 original size:19 final size:19
Alignment explanation
Indices: 143824--143988 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
143814 GAAACCAAAA
*
143824 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
143843 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
143862 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
143881 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
143895 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
143914 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
143928 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
143947 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
143967 ATCTCGTTGTGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
143987 TC
1 TC
143989 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 24
0.74 0.11 0.15
Matches are distributed among these distances:
14 19 0.16
16 4 0.03
17 5 0.04
19 58 0.50
20 30 0.26
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:143884 original size:38 final size:33
Alignment explanation
Indices: 143829--143963 Score: 153
Period size: 33 Copynumber: 3.9 Consensus size: 33
143819 CAAAATCGCA
*
143829 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
*
143867 TTGTGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
143900 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
143933 TTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
143964 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 15 0.17
36 3 0.03
38 24 0.27
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:143918 original size:33 final size:33
Alignment explanation
Indices: 143876--143963 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
143866 GTTGTGATTT
143876 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
143909 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
143942 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
143964 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:146157 original size:21 final size:21
Alignment explanation
Indices: 146133--146283 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
146123 TCATTCCTCG
146133 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
146154 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
146175 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
146196 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
146217 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
146238 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
146259 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
146280 AGAG
1 AGAG
146284 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:146158 original size:42 final size:42
Alignment explanation
Indices: 146106--146283 Score: 198
Period size: 42 Copynumber: 4.2 Consensus size: 42
146096 TCACTCCTAT
* *
146106 CGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCAC
* * * * * *
146148 CGTTCAAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTAT
1 CGTTCAAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCAC
* *
146190 CGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCAC
* * *
146232 CGTTCAAGAGGCCACTGTCA-TCGTTGAAGAGGT-CCCTCCCAC
1 CGTTCAAGAGGCCACTATCATTCCTCG-AGA-GTCCCCTCCCAC
*
146274 CATTCAAGAG
1 CGTTCAAGAG
146284 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 4 0.04
42 106 0.95
43 2 0.02
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATTCCTCGAGAGTCCCCTCCCAC
Found at i:146262 original size:84 final size:84
Alignment explanation
Indices: 146078--146253 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
146068 CCCGACTCGC
*
146078 CTGTCATCCCTCAAGAGTTCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
146143 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
146162 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
146227 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
146246 CTGTCATC
1 CTGTCATC
146254 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:146283 original size:84 final size:84
Alignment explanation
Indices: 146078--146283 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
146068 CCCGACTCGC
* * * * *
146078 CTGTCATCCCTCAAGAGTTCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
146143 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
146162 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
146227 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
146246 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
146284 CCCGATTCAC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
84 109 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:147648 original size:14 final size:14
Alignment explanation
Indices: 147629--147664 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
147619 ATTGTTTAAT
147629 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
147643 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
147657 TGATTTGT
1 TGATTTGT
147665 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:147832 original size:19 final size:19
Alignment explanation
Indices: 147771--147823 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
147761 AAAAAGTACT
147771 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
147790 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
147809 ATCGCAATGCGAAAT
1 ATCGCAATGCGAAAT
147824 TAAATTCGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:147850 original size:19 final size:19
Alignment explanation
Indices: 147828--147976 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
147818 CGAAATTAAA
147828 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
147847 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
147862 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
147880 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
147894 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
147913 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
147928 -T--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
147944 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
147963 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
147977 AGACATTAAG
Statistics
Matches: 93, Mismatches: 19, Indels: 35
0.63 0.13 0.24
Matches are distributed among these distances:
12 7 0.08
14 23 0.25
16 3 0.03
17 7 0.08
19 43 0.46
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:147874 original size:33 final size:31
Alignment explanation
Indices: 147827--147956 Score: 197
Period size: 33 Copynumber: 4.1 Consensus size: 31
147817 GCGAAATTAA
*
147827 ATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
147858 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT--CTCGTTGCGATTTTCATTTCGCATTGCG
**
147891 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 --ATTCTCGTTGCGATTTTCATTTCGCATTGCG
147924 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTCTCGTTGCGATTTTCATTTCGCATTGCG
147955 AT
1 AT
147957 AGTAATTTCC
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 34 0.38
33 53 0.59
35 3 0.03
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.42
Consensus pattern (31 bp):
ATTCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:147921 original size:66 final size:64
Alignment explanation
Indices: 147825--147955 Score: 235
Period size: 66 Copynumber: 2.0 Consensus size: 64
147815 ATGCGAAATT
*
147825 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATT--CTCGTTGCGATTTTCATTTCGCATTGC
147890 G
64 G
147891 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCG
147955 A
1 A
147956 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 29 0.45
66 35 0.55
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (64 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:150269 original size:12 final size:12
Alignment explanation
Indices: 150254--150278 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
150244 TTTTCGGGGA
150254 CTTTTTCTTCTT
1 CTTTTTCTTCTT
150266 CTTTTTCTTCTT
1 CTTTTTCTTCTT
150278 C
1 C
150279 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:150484 original size:24 final size:24
Alignment explanation
Indices: 150450--150503 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
150440 CTGAAACATC
*
150450 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
150474 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
150498 ATCAAA
1 ATCAAA
150504 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:151333 original size:33 final size:33
Alignment explanation
Indices: 151291--151418 Score: 157
Period size: 33 Copynumber: 3.8 Consensus size: 33
151281 TCATTTGACC
* * *
151291 ATCGTAATGCGAAATGCAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
151324 ATCACAATGCGAAATGAAAAAGGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
151357 ATCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
151390 ATCGCAAAGCGAAAATTAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
151419 CGATTTTAGT
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 65 0.81
34 15 0.19
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:151465 original size:33 final size:34
Alignment explanation
Indices: 151418--151532 Score: 137
Period size: 33 Copynumber: 3.5 Consensus size: 34
151408 AAATCGCAAC
* * *
151418 GCGATTTT-AGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
*
151451 GCGATTTTCA-TTTCGCATTGTGATTCTATCGTT
1 GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
* *
151484 GCGATTTTC-TTTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
**
151517 GCGATAGTCAGTTTCG
1 GCGATTTTCAGTTTCG
151533 TGTTGCGACA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 64 0.91
34 6 0.09
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (34 bp):
GCGATTTTCAGTTTCGCATTGCGATTCTATCGTT
Found at i:151506 original size:19 final size:18
Alignment explanation
Indices: 151449--151508 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
151439 GATTTTGTCG
151449 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTC-TTTCGCA
* *
151468 TTGTGA--TTCTATCG--
1 TTGCGATTTTCTTTCGCA
151482 TTGCGATTTTCTTTTCGCA
1 TTGCGATTTTC-TTTCGCA
151501 TTGCGATT
1 TTGCGATT
151509 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.22
17 7 0.22
19 13 0.41
ACGTcount: A:0.13, C:0.18, G:0.18, T:0.50
Consensus pattern (18 bp):
TTGCGATTTTCTTTCGCA
Done.