Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002135.1 Hibiscus syriacus cultivar Beakdansim tig00004368_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: 145433
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1201 original size:19 final size:20
Alignment explanation
Indices: 1173--1220 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
1163 ACAGTCATAC
*
1173 CAAGGACGAAGACTATTCAT
1 CAAGGACGAAGACAATTCAT
*
1193 CAA-GACGAAGACAATTCGT
1 CAAGGACGAAGACAATTCAT
1212 CAAGGACGA
1 CAAGGACGA
1221 GAAGACCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.15
Consensus pattern (20 bp):
CAAGGACGAAGACAATTCAT
Found at i:5621 original size:7 final size:7
Alignment explanation
Indices: 5599--5694 Score: 54
Period size: 7 Copynumber: 13.6 Consensus size: 7
5589 CATCATAAAG
*
5599 AGAAAGA
1 AGAAAAA
5606 AGAAAAA
1 AGAAAAA
*
5613 A-ATAGAA
1 AGA-AAAA
*
5620 A-AAAAT
1 AGAAAAA
5626 AGAAAAA
1 AGAAAAA
* *
5633 AGATAGA
1 AGAAAAA
5640 AGAAAAA
1 AGAAAAA
*
5647 AGAGAAA
1 AGAAAAA
*
5654 AGAAAAT
1 AGAAAAA
* *
5661 TGAAAATG
1 AGAAAA-A
5669 AGAAAAA
1 AGAAAAA
5676 ATGAAAATA
1 A-GAAAA-A
5685 A-AAAAA
1 AGAAAAA
5691 AGAA
1 AGAA
5695 GGAAAGAAGA
Statistics
Matches: 67, Mismatches: 16, Indels: 12
0.71 0.17 0.13
Matches are distributed among these distances:
6 6 0.09
7 49 0.73
8 10 0.15
9 2 0.03
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (7 bp):
AGAAAAA
Found at i:5621 original size:10 final size:10
Alignment explanation
Indices: 5606--5646 Score: 64
Period size: 10 Copynumber: 3.9 Consensus size: 10
5596 AAGAGAAAGA
5606 AGAAAAAAAT
1 AGAAAAAAAT
5616 AGAAAAAAAT
1 AGAAAAAAAT
5626 AGAAAAAAGAT
1 AGAAAAAA-AT
5637 AGAAGAAAAA
1 AGAA-AAAAA
5647 AGAGAAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 18 0.62
11 7 0.24
12 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (10 bp):
AGAAAAAAAT
Found at i:7969 original size:36 final size:36
Alignment explanation
Indices: 7881--8061 Score: 258
Period size: 36 Copynumber: 5.0 Consensus size: 36
7871 GATTGGGGCA
*
7881 AGTCAATCTTAAGCCTTCACCGGAGAGTAGTGAAGC
1 AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
* *
7917 GGTC-ATCTTAAGCCTTCACCGAAGAGGAGTGAAGC
1 AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
*
7952 AGTCATTCTTAAGCCTTCACCGAAGAAG-AGTGAAGC
1 AGTCAATCTTAAGCCTTCACCGAAG-AGTAGTGAAGC
* *
7988 AGTTAATCTTAAGCCTTCACCAAAGAGTAGTGAAGC
1 AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
* *
8024 AACTCAATCTTAAGCCTTAACCGAAGAGTAGTGAAGC
1 -AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
8061 A
1 A
8062 AATCCATCCG
Statistics
Matches: 129, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
35 34 0.26
36 61 0.47
37 34 0.26
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (36 bp):
AGTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC
Found at i:8454 original size:42 final size:41
Alignment explanation
Indices: 8387--8488 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
8377 TTCACAATTT
* * * *
8387 ATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
* * *
8428 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
*
8470 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
8489 CATAAAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
Found at i:8491 original size:205 final size:205
Alignment explanation
Indices: 8065--9763 Score: 2573
Period size: 205 Copynumber: 8.2 Consensus size: 205
8055 TGAAGCAAAT
* * *
8065 CCATCCGTAAGACCTTCGGGTAGGATGTTTTCA-TTGAATTTGAAAAT-AAGAAAATGATGATTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAA-AAAATGATG---T
*
8128 AAGATGATGAAATTTTTGAAAACGAAGAATGCGGGTTTCAAAATTTCACAATTTATAAGTCCTTC
62 ----TG--G-AATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTC
* *
8193 GGGCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCCTCGGGTCATCTGTAAGTCTTTAGAG
120 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAG
*
8258 CAAGATGATAAGTCCTCCGGG
185 CAAGATGATAAGTCCTTCGGG
* * *
8279 ACATCCATAAAACCCTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTGGA
* *
8344 ATTTTTGAAAATGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTTGGGCCATCAGT
66 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
8409 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
131 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
8474 GTCCTTCGGG
196 GTCCTTCGGG
*
8484 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTGGA
8549 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
66 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
* * *
8614 AAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGTCATCTGTAAGTATTTAGAGCAATATGATAA
131 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
8679 GTCCTTCGGG
196 GTCCTTCGGG
*
8689 CCATCCATAAAACCTTCGGGTAGGAT-TTTTCA-TTGAATTTGAAAATAAGAAAATAATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAT--GAAAA-AA-----T-
* *
8752 AGATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCG
57 -GATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCG
* * * **
8817 GGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGCAAGTCTTCCGAGC
121 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC
* *
8882 ATGATGATTAAGTCCTTCGAG
186 AAGATGA-TAAGTCCTTCGGG
* * * *
8903 CCATCCATAAAACTTTCGGGTATGATGTTTTCACATGAATTTGAAAATAAAAAAATGATGATGGA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTGGA
*
8968 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGAGCCATCAGT
66 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
9033 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
131 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
9098 GTCCTTCGGG
196 GTCCTTCGGG
*
9108 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAGAATGAAAAAATGATGTTGGA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTGGA
* *
9173 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAAGTTCACAATTTATAAGTCATTCGGGCCATCAGT
66 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
9238 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
131 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
9303 GTCCTTCGGG
196 GTCCTTCGGG
* *
9313 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGTTGATGGA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTGGA
*
9378 ATTTTTGAAAATGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
66 ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
*
9443 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAA
131 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
9508 GTCCTTCGGG
196 GTCCTTCGGG
* * * *
9518 CCATCCGTAAGACCTTCGGGTAAGATGTTTTCA-TTGAATTTGAAAAT-AAGAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAA-AAAATGATG--TT
9581 AAGATGATAAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTC
63 --G--G----AATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTC
* * * *
9646 GGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAG
120 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAG
* * *
9711 CATGATGCTTAAATCCTTCGGG
185 CAAGATG-ATAAGTCCTTCGGG
* ** *
9733 TCATCCATAAGGCCTTCGGGCAGGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTT
9764 TCACCAAGAT
Statistics
Matches: 1377, Mismatches: 81, Indels: 53
0.91 0.05 0.04
Matches are distributed among these distances:
203 14 0.01
204 27 0.02
205 801 0.58
206 132 0.10
208 4 0.00
210 1 0.00
211 1 0.00
212 1 0.00
213 127 0.09
214 189 0.14
215 65 0.05
216 15 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (205 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAATGATGTTGGA
ATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGT
AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAA
GTCCTTCGGG
Found at i:8873 original size:42 final size:42
Alignment explanation
Indices: 8810--8907 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
8800 AATTTATAAG
* * *
8810 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAACAAGTCTTCCGAGCATGATGATTAAA
* * *
8852 TCCTTCGGGTCATCAGCAAGTCTTCCGAGCATGATGATTAAG
1 TCCTTCGGGCCATCAACAAGTCTTCCGAGCATGATGATTAAA
*
8894 TCCTTCGAGCCATC
1 TCCTTCGGGCCATC
8908 CATAAAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (42 bp):
TCCTTCGGGCCATCAACAAGTCTTCCGAGCATGATGATTAAA
Found at i:9077 original size:42 final size:41
Alignment explanation
Indices: 9011--9112 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
9001 TTCACAATTT
* * * *
9011 ATAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
* * *
9052 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
*
9094 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
9113 CATAAAACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG
Found at i:9265 original size:624 final size:623
Alignment explanation
Indices: 8065--9763 Score: 2745
Period size: 624 Copynumber: 2.7 Consensus size: 623
8055 TGAAGCAAAT
* * *
8065 CCATCCGTAAGACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATGATGATTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATAATG-TTTAA
*
8130 GATGATGAAATTTTTGAAAACGAAGAATGCGGGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
65 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* *
8195 GCCATCAGTAAGTCTTTCGAACATGATGCTTAAATCCCTCGGGTCATCTGTAAGTCTTTAGAGCA
130 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
* * * * *
8260 AGATGATAAGTCCTCCGGGACATCCATAAAACCCTCGGGTAGGATGTTTTCACATGAATTTGAGA
195 AGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAA
* * *
8325 ATGAAAAAATGATGTTGGAATTTTTGAAAATGAAGAATGCGAGTTTCAAAATTTCACAATTTATA
260 ATAAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATA
*
8390 AGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGT
325 AGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGT
8455 CTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACAT
390 CTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACAT
*
8520 GAATTTGAGAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTC
455 GAATTTGAGAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAAGTTC
*
8585 ACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGTC
520 ACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGTC
*
8650 ATCTGTAAGTATTTAGAGCAATATGATAAGTCCTTCGGG
585 ATCTGTAAGTATTTAGAGCAAGATGATAAGTCCTTCGGG
8689 CCATCCATAAAACCTTCGGGTAGGAT-TTTTCATTGAATTTGAAAATAAGAAAATAATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATAATG-TTTAA
8753 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
65 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
* * * **
8818 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCAGCAAGTCTTCCGAGCA
130 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
* * * *
8883 TGATGATTAAGTCCTTCGAGCCATCCATAAAACTTTCGGGTATGATGTTTTCACATGAATTTGAA
195 AGATGA-TAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAAGATGTTTTCACATGAATTTGAA
8948 AATAAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
259 AATAAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTAT
*
9013 AAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
324 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
9078 TCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACA
389 TCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACA
9143 TGAATTTGAGAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAAGTT
454 TGAATTTGAGAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAAGTT
*
9208 CACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
519 CACAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGT
*
9273 CATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGG
584 CATCTGTAAGTATTTAGAGCAAGATGATAAGTCCTTCGGG
*
9313 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAAT--GAAAA-AATG-TT--
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCA-TTGAATTTGAAAATAAGAAAATAATGTTTAA
*
9372 GATG--G-AATTTTTGAAAATGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
65 GATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGG
*
9434 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
130 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
* * *
9499 AGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCGGGTAAGATGTTTTCA-TTGAATTTGAAA
195 AGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAA
**
9563 ATAAGAAAATGATGTTTTAAGATGATAAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTC
260 ATAA-AAAA--A-----T--GATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTC
* *
9628 ACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGCC
315 ACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTC
* * * * * * ** *
9693 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCCATAAGGCCTTCGGGCAGGA
380 ATCTGTAAGTCTTTAGAGCAAGATG-ATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGA
9758 TGTTTT
444 TGTTTT
9764 TCACCAAGAT
Statistics
Matches: 1002, Mismatches: 59, Indels: 27
0.92 0.05 0.02
Matches are distributed among these distances:
614 15 0.01
615 45 0.04
616 120 0.12
617 2 0.00
619 4 0.00
621 2 0.00
622 1 0.00
623 167 0.17
624 588 0.59
625 45 0.04
626 13 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (623 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCATTGAATTTGAAAATAAGAAAATAATGTTTAAG
ATGATGAAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAA
GATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAAGATGTTTTCACATGAATTTGAAAA
TAAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAATTTCACAATTTATAA
GTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTC
TTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATG
AATTTGAGAATGAAAAAATGATGTTGGAATTTTTGAAAACGAAGAATGCGAGTTTCAAAAGTTCA
CAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCGTAAATCCTTCGGGTCA
TCTGTAAGTATTTAGAGCAAGATGATAAGTCCTTCGGG
Found at i:9283 original size:42 final size:41
Alignment explanation
Indices: 9224--9317 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 41
9214 TTATAAGTCA
* * *
9224 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCC
1 TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG-ATAAATCC
* * *
9266 TTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCC
1 TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAATCC
9307 TTCGGGCCATC
1 TTCGGGCCATC
9318 CATAAAACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (41 bp):
TTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAATCC
Found at i:9528 original size:41 final size:42
Alignment explanation
Indices: 9421--9533 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
9411 TTCACAATTT
* * *
9421 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
* * * *
9463 TTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATG-
1 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
*
9504 ATAAGTCCTTCGGGCCATCCGTAAGACCTT
1 ATAAGTCCTTCGGGCCATCAGTAAG-CCTT
9534 CGGGTAAGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 21 0.36
42 38 0.64
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (42 bp):
ATAAGTCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGC
Found at i:9661 original size:20 final size:20
Alignment explanation
Indices: 9636--9708 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
9626 TCACAATTTA
9636 TAAGTCCTTCGGGCCATCAG
1 TAAGTCCTTCGGGCCATCAG
* * * *
9656 TAAGTCTTTTGAG-CATGATG
1 TAAGTCCTTCGGGCCATCA-G
*
9676 CTTAAATCCTTCGGGCCATCAG
1 --TAAGTCCTTCGGGCCATCAG
*
9698 TAAGTCTTTCG
1 TAAGTCCTTCG
9709 AGCATGATGC
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
19 4 0.11
20 20 0.53
22 10 0.26
23 4 0.11
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCAG
Found at i:9699 original size:42 final size:42
Alignment explanation
Indices: 9640--9737 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
9630 AATTTATAAG
*
9640 TCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
9682 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
*
9724 TCCTTCGGGTCATC
1 TCCTTCGGGCCATC
9738 CATAAGGCCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
Found at i:15847 original size:56 final size:58
Alignment explanation
Indices: 15721--15886 Score: 221
Period size: 57 Copynumber: 2.9 Consensus size: 58
15711 AGGTTGTTCC
* * * ** * * *
15721 TTGTGTGCTAGATTTGCGTATAATTGCGTCATGATAAATTTGGCTCTG-TTTTTTTGG
1 TTGTGTGCTAGATATGTGTATAACTATGACATGATAAATTTAGCTCTGATTTTTTTGA
15778 TTGTGTGCTAGATATGTGTATAACTATGACATGATAAA-TTAGCTCTGATTTTTTT-A
1 TTGTGTGCTAGATATGTGTATAACTATGACATGATAAATTTAGCTCTGATTTTTTTGA
* *
15834 TTGTGTGCTAGATATGTGCATAACTATGACATGATAAATTTAGCTTTGATTTT
1 TTGTGTGCTAGATATGTGTATAACTATGACATGATAAATTTAGCTCTGATTTT
15887 AGGGCCACAT
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
56 45 0.46
57 52 0.54
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (58 bp):
TTGTGTGCTAGATATGTGTATAACTATGACATGATAAATTTAGCTCTGATTTTTTTGA
Found at i:21197 original size:23 final size:24
Alignment explanation
Indices: 21167--21215 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
21157 ATGTGTGTAC
21167 GTAA-TTTTTTTTAACATTTTAGG
1 GTAATTTTTTTTTAACATTTTAGG
21190 GTAATTTTTTTTTAACATTTTAGG
1 GTAATTTTTTTTTAACATTTTAGG
21214 GT
1 GT
21216 GATTACAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.24, C:0.04, G:0.14, T:0.57
Consensus pattern (24 bp):
GTAATTTTTTTTTAACATTTTAGG
Found at i:23728 original size:2 final size:2
Alignment explanation
Indices: 23721--23783 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
23711 CATAATTTTG
23721 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
23763 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
23784 GTTTAAATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24055 original size:16 final size:16
Alignment explanation
Indices: 24034--24068 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
24024 ATTCATTGTA
*
24034 TTCAAAACTTATCATT
1 TTCAAAACTCATCATT
24050 TTCAAAACTCATCATT
1 TTCAAAACTCATCATT
24066 TTC
1 TTC
24069 TATTAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (16 bp):
TTCAAAACTCATCATT
Found at i:26783 original size:17 final size:20
Alignment explanation
Indices: 26746--26785 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
26736 AATTTAATTA
26746 TTTTTATTTGTTTATAATAT
1 TTTTTATTTGTTTATAATAT
26766 TTTTTA-TT-TTTA-AATAT
1 TTTTTATTTGTTTATAATAT
26783 TTT
1 TTT
26786 AGGTTGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
19 2 0.10
20 6 0.30
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTATTTGTTTATAATAT
Found at i:28321 original size:64 final size:64
Alignment explanation
Indices: 28175--28321 Score: 140
Period size: 64 Copynumber: 2.3 Consensus size: 64
28165 GAAGGTGTAT
* * * ** * *
28175 CGATACACAGGTAGTGCATCGATGCACTCTTTTAAAATAAAAAGATCGAATGCAATTAGTGCAT
1 CGATGCACAAGTAGTGCATCAATGCACTCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
* * *
28239 CGATGCATAAGGCA-TGCATCAATGCA-TCCCATTAATAAT-AAAACATCGAATGCATTTTA-TG
1 CGATGCACAA-GTAGTGCATCAATGCACT-CCATTAA-AATAAAAACATCGAATGCA-ATTAGTG
28300 CAC
62 CAC
28303 CGATGCACAAGTAGTGCAT
1 CGATGCACAAGTAGTGCAT
28322 TGATGCATAC
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
63 3 0.05
64 55 0.83
65 8 0.12
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
CGATGCACAAGTAGTGCATCAATGCACTCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
Found at i:28745 original size:29 final size:29
Alignment explanation
Indices: 28706--28786 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
28696 TATGTGATAT
28706 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
* *
28736 GAGAAATGACATAAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
28765 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
28787 ACATATAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
28 7 0.15
29 35 0.74
30 5 0.11
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:32852 original size:29 final size:29
Alignment explanation
Indices: 32813--32951 Score: 235
Period size: 29 Copynumber: 4.8 Consensus size: 29
32803 TATGTGATAT
32813 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
32843 GAGAAATGACATGAGTTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
32872 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
* *
32901 GAGAAATGACATGAACTACAGGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
32930 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
32952 ACATATAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 6 0.06
29 92 0.89
30 5 0.05
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:34802 original size:105 final size:104
Alignment explanation
Indices: 34624--34817 Score: 334
Period size: 105 Copynumber: 1.9 Consensus size: 104
34614 CAAAAAATTA
*
34624 AACCATGAGAACTTAGTGAGGCCTCTTTAAATGCATATGGAGACCAAGGAACCAAGTAAGCCCTT
1 AACCATGAGAACTTAGTGAGGCCTCTTTAAATGCAGATGGAGACCAAGGAACCAAGTAAGCCCTT
*
34689 CCATGAGCAATAAATTCATAACCTAGGGCCGAAAAAACCG
66 CCAAGAGCAAT-AATTCATAACCTAGGGCCGAAAAAACCG
**
34729 AACCATGAGAACTTAGTGAGGCCTCTTTAAATGCAGATGGAGACCAAGGGCCCAAGTAAGCCCTT
1 AACCATGAGAACTTAGTGAGGCCTCTTTAAATGCAGATGGAGACCAAGGAACCAAGTAAGCCCTT
*
34794 CCAAGAGCAATAGTTCATAACCTA
66 CCAAGAGCAATAATTCATAACCTA
34818 ATGCTTTCAA
Statistics
Matches: 84, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 12 0.14
105 72 0.86
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (104 bp):
AACCATGAGAACTTAGTGAGGCCTCTTTAAATGCAGATGGAGACCAAGGAACCAAGTAAGCCCTT
CCAAGAGCAATAATTCATAACCTAGGGCCGAAAAAACCG
Found at i:47455 original size:30 final size:30
Alignment explanation
Indices: 47407--47481 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 30
47397 CCCGGGGACG
*
47407 AACTTAAAC-TAT-AAAATTCTAAGTGGTA
1 AACTTAAACTTATAAAAATTCTAAGGGGTA
47435 AACTTAAACTTATAAAAATTCTAAGGGGTA
1 AACTTAAACTTATAAAAATTCTAAGGGGTA
47465 AACTTAAACTTATAAAA
1 AACTTAAACTTATAAAA
47482 TTATAGTGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 9 0.20
29 3 0.07
30 32 0.73
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (30 bp):
AACTTAAACTTATAAAAATTCTAAGGGGTA
Found at i:48261 original size:25 final size:25
Alignment explanation
Indices: 48227--48276 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
48217 AATGTGACAT
48227 GAAATGAATTTATTTCTTCTGTATC
1 GAAATGAATTTATTTCTTCTGTATC
48252 GAAATGAATTTATTTCTTCTGTATC
1 GAAATGAATTTATTTCTTCTGTATC
48277 ATAATTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (25 bp):
GAAATGAATTTATTTCTTCTGTATC
Found at i:51156 original size:2 final size:2
Alignment explanation
Indices: 51151--51187 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51141 TTTAAAATTA
51151 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51188 AAGTATTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54170 original size:3 final size:3
Alignment explanation
Indices: 54162--54186 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54152 TCCCACCGCC
54162 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
54187 AGTTCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:54295 original size:11 final size:11
Alignment explanation
Indices: 54279--54308 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
54269 TGAAAAAGCT
*
54279 TGCTTCATTGC
1 TGCTTCATTAC
54290 TGCTTCATTAC
1 TGCTTCATTAC
54301 TGCTTCAT
1 TGCTTCAT
54309 GTTTCCCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (11 bp):
TGCTTCATTAC
Found at i:58325 original size:11 final size:11
Alignment explanation
Indices: 58309--58333 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58299 TAAGACATAA
58309 TGCCAGTATAC
1 TGCCAGTATAC
58320 TGCCAGTATAC
1 TGCCAGTATAC
58331 TGC
1 TGC
58334 TGAAAAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (11 bp):
TGCCAGTATAC
Found at i:59791 original size:5 final size:5
Alignment explanation
Indices: 59783--59823 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
59773 ATTTGCCACT
* * *
59783 CCTCT CCTCT CCTCT CCTCA CCTCA CCTCA CCTCA CCTCA C
1 CCTCA CCTCA CCTCA CCTCA CCTCA CCTCA CCTCA CCTCA C
59824 TATGTTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.12, C:0.61, G:0.00, T:0.27
Consensus pattern (5 bp):
CCTCA
Found at i:66083 original size:16 final size:17
Alignment explanation
Indices: 66042--66090 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
66032 TTACAAAGTA
*
66042 TATATAATAAAAAATTT
1 TATATAATAAAATATTT
*
66059 TCT-TAATAAAATATTT
1 TATATAATAAAATATTT
66075 TATAT-ATAAAAATATT
1 TATATAAT-AAAATATT
66091 ATTAATGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATAATAAAATATTT
Found at i:82080 original size:20 final size:20
Alignment explanation
Indices: 82057--82096 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
82047 AGTGAGAAAC
82057 AGTATAGTTTACCCTTATTT
1 AGTATAGTTTACCCTTATTT
82077 AGTATAGTTTACCCTTATTT
1 AGTATAGTTTACCCTTATTT
82097 TAAAAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (20 bp):
AGTATAGTTTACCCTTATTT
Found at i:82498 original size:21 final size:20
Alignment explanation
Indices: 82464--82509 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
82454 CGAACGGATT
*
82464 ATTTTATTATTATTTTAATA
1 ATTTTATAATTATTTTAATA
*
82484 ATTTTAATAATTATTTTATTA
1 ATTTT-ATAATTATTTTAATA
82505 ATTTT
1 ATTTT
82510 TTAAACTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTATAATTATTTTAATA
Found at i:82499 original size:12 final size:12
Alignment explanation
Indices: 82461--82513 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
82451 TATCGAACGG
*
82461 ATTATTTT-ATT
1 ATTATTTTAATA
82472 ATTATTTTAAT-
1 ATTATTTTAATA
82483 A--ATTTTAATA
1 ATTATTTTAATA
*
82493 ATTATTTTATTA
1 ATTATTTTAATA
82505 ATT-TTTTAA
1 ATTATTTTAA
82514 ACTTTAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 14 0.39
12 13 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTTTAATA
Found at i:101027 original size:15 final size:15
Alignment explanation
Indices: 101003--101035 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
100993 AATGGAGGTA
101003 GCTGAAATGATGGTT
1 GCTGAAATGATGGTT
101018 GCTGAAATGATGGTT
1 GCTGAAATGATGGTT
101033 GCT
1 GCT
101036 TACCTGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (15 bp):
GCTGAAATGATGGTT
Found at i:101237 original size:2 final size:2
Alignment explanation
Indices: 101230--101266 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
101220 TGATATAATT
101230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101267 TTCTTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:102717 original size:33 final size:33
Alignment explanation
Indices: 102677--102741 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
102667 CATTTTTTAT
102677 ATAGCTAATTCATATTGAAATAAACACTCACAC
1 ATAGCTAATTCATATTGAAATAAACACTCACAC
*
102710 ATAGCTAATTCATATTGAAATAAACATTCACA
1 ATAGCTAATTCATATTGAAATAAACACTCACA
102742 AATATAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.29
Consensus pattern (33 bp):
ATAGCTAATTCATATTGAAATAAACACTCACAC
Found at i:107365 original size:18 final size:18
Alignment explanation
Indices: 107337--107381 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
107327 TATTTATCAG
* *
107337 AAATAATATTTCTTATGT
1 AAATGATATTTCTGATGT
*
107355 AGATGATATTTCTGATGT
1 AAATGATATTTCTGATGT
107373 AAATGATAT
1 AAATGATAT
107382 GCTTAAGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (18 bp):
AAATGATATTTCTGATGT
Found at i:112743 original size:24 final size:24
Alignment explanation
Indices: 112716--112765 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
112706 ATAAAGAACC
112716 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
112740 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
112764 AA
1 AA
112766 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:116977 original size:21 final size:21
Alignment explanation
Indices: 116951--116990 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
116941 CAGAACCCCA
*
116951 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
116972 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
116991 TCAATGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:123538 original size:17 final size:18
Alignment explanation
Indices: 123518--123559 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
123508 TTATTACACA
* *
123518 TTTTTTTC-TTTTTTTCT
1 TTTTTTTCACTTTTTCCT
123535 TTTTTTTCACTTTTTCCT
1 TTTTTTTCACTTTTTCCT
123553 TTTTTTT
1 TTTTTTT
123560 TACGCTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTCACTTTTTCCT
Found at i:124745 original size:15 final size:15
Alignment explanation
Indices: 124712--124754 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
124702 AAAATAATAT
* *
124712 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
124727 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
124741 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
124755 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:127956 original size:24 final size:24
Alignment explanation
Indices: 127929--127978 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
127919 ATAAAGAACC
127929 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
127953 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
127977 AA
1 AA
127979 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:131278 original size:2 final size:2
Alignment explanation
Indices: 131271--131319 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
131261 ATACAGAATG
131271 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
131313 AT AT AT A
1 AT AT AT A
131320 AAGTTTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:132903 original size:30 final size:30
Alignment explanation
Indices: 132863--132924 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
132853 AATTCGACAT
**
132863 GACTCAAATTTTATAAACTTGACTCAACTC
1 GACTCAAATTTTATAAACACGACTCAACTC
*
132893 GACTCGAATTTTATAAACACGACTCAACTC
1 GACTCAAATTTTATAAACACGACTCAACTC
132923 GA
1 GA
132925 AAAAATTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (30 bp):
GACTCAAATTTTATAAACACGACTCAACTC
Found at i:145431 original size:71 final size:71
Alignment explanation
Indices: 145289--145431 Score: 157
Period size: 71 Copynumber: 2.0 Consensus size: 71
145279 TATTGGGCAA
* * * *
145289 ACACAAATAAAATTTCAAAGTGGACAACTTTTAATAAAAACAACTAATATAAAAAATTGAATTAC
1 ACACAAATAAAATTTCAAAGTGAACAACCTTCAATAAAAACAACTAATATAAAAAAAT-AATTAC
*
145354 AGGGTGG
65 AAGGTGG
* *
145361 ACAC-AATAAAATTTTAAAGTGAAC-ACCTTCAATAAAATGAACAATTAATATAAAAAAAT-ATT
1 ACACAAATAAAATTTCAAAGTGAACAACCTTCAAT-AAA--AACAACTAATATAAAAAAATAATT
*
145423 ATAAGGTGG
63 ACAAGGTGG
145432 GC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
70 7 0.12
71 31 0.52
72 4 0.07
73 18 0.30
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.26
Consensus pattern (71 bp):
ACACAAATAAAATTTCAAAGTGAACAACCTTCAATAAAAACAACTAATATAAAAAAATAATTACA
AGGTGG
Done.