Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 16
Found at i:3333861 original size:201 final size:207
Alignment explanation
Indices: 3333585--3334031 Score: 651
Period size: 201 Copynumber: 2.2 Consensus size: 207
3333575 TTCAACAAAT
* * *
3333585 GGGTTCGCTCCCTATTTCTCTAGGGAGTATGAAACTCAGACATATTCTTCAACGGGTTCGCTCCT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACACATTCTTCAACGGGTTCGCTCCT
3333650 TCCCTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGA
66 TCCCTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGA
* *
3333715 GTATAGAACTCGAACATC-TCAAATGGGTTCGCT-CC-CTTTCTTTAGGGAGTATAGAACTC-GA
131 GTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAG-
3333776 ACATCTCTTC-AC
195 ACATCTCTTCAAC
*
3333788 -GGTTCGCCTCCCTCTTTCTCTAGGGAGTATGGGACTC-GA-ACA-TCTTCAACTGGGTTCGCTC
1 GGGTTCG-CTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACACATTCTTCAAC-GGGTTCGCTC
* *
3333849 CTTCCCTCTTTAAGGAGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCTTCTTTCTTTAAG
64 CTTCCCTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
* * * *
3333914 GAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
129 GAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCA
3333979 GACATCTCTTCAAAC
194 GACATCTCTTC-AAC
* * * *
3333994 GGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACTCA
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCA
3334032 AATAATCTTC
Statistics
Matches: 217, Mismatches: 17, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
200 8 0.04
201 93 0.43
202 21 0.10
203 29 0.13
204 32 0.15
205 1 0.00
206 28 0.13
207 5 0.02
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (207 bp):
GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGACACATTCTTCAACGGGTTCGCTCCT
TCCCTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGA
GTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAGA
CATCTCTTCAAC
Found at i:3333882 original size:102 final size:102
Alignment explanation
Indices: 3333585--3334030 Score: 498
Period size: 102 Copynumber: 4.4 Consensus size: 102
3333575 TTCAACAAAT
* * * * * *
3333585 GGGTTCGCTCCCTATTTCTCTAGGGAGTATGAAACTCAGACATATTCTTCAACGGGTTCGCTCCT
1 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTC-GA-ACA-TCTTCAACGGGTTCGCTCCT
3333650 TCCCTCTTTAAGGAGTATAGAACTCGAACA--TCTTCAAAC
63 TCCCTCTTTAAGGAGTATAGAACTCGAACATCTCTTC-AAC
* *
3333689 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATC-TCAAATGGGTTCGCTCCCTT
1 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC-AACGGGTTCGCT-CCTT
*
3333753 ---TCTTTAGGGAGTATAGAACTCGAACATCTCTTC-AC
64 CCCTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAAC
* * * *
3333788 -GGTTCGCCTCCCTCTTTCTCTAGGGAGTATGGGACTCGAACATCTTCAACTGGGTTCGCTCCTT
1 GGGTTCG-CTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAC-GGGTTCGCTCCTT
* *
3333852 CCCTCTTTAAGGAGTATGGAACTCGAACATCT-TTAAAC
64 CCCTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAAC
* * * *
3333890 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCGCTCCCTC
1 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCA-ACGGGTTCGCTCCTTC
** * * *
3333955 TTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAAC
65 CCTCTTTAAGGAGTATAGAACTCGA-ACATCTCTTC-AAC
*
3333994 GGGTTCACTCCTTCTTTCTTTAAGGAGTATGGAACTC
1 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTC
3334031 AAATAATCTT
Statistics
Matches: 293, Mismatches: 33, Indels: 32
0.82 0.09 0.09
Matches are distributed among these distances:
98 6 0.02
99 65 0.22
100 13 0.04
101 21 0.07
102 107 0.37
103 12 0.04
104 69 0.24
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (102 bp):
GGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAACGGGTTCGCTCCTTCC
CTCTTTAAGGAGTATAGAACTCGAACATCTCTTCAAC
Found at i:3334471 original size:36 final size:36
Alignment explanation
Indices: 3334405--3334666 Score: 312
Period size: 36 Copynumber: 7.3 Consensus size: 36
3334395 ACTCTTCTGA
* * * **
3334405 GAAGGCTTAAAATGGATCTGCTTCACTACTCTTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTATTCTCCGGT
* * * *
3334442 GAAGACTTAAGATGGTTTACTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
3334478 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
3334514 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
3334550 GAAGGCTTCAGATGGTTAGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
3334586 GAAGGCTTAGGATGG-TTGCTTCACTATTCTCCAGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
3334621 GAAGGCTTCAGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
3334657 GAAGGCTTAA
1 GAAGGCTTAA
3334667 AATTAACTTT
Statistics
Matches: 197, Mismatches: 26, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
35 32 0.16
36 152 0.77
37 13 0.07
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:3338859 original size:6 final size:6
Alignment explanation
Indices: 3338848--3338872 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3338838 TGCAATGCGA
3338848 AAATGC AAATGC AAATGC AAATGC A
1 AAATGC AAATGC AAATGC AAATGC A
3338873 CGAGGGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:3343345 original size:28 final size:28
Alignment explanation
Indices: 3343313--3343385 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
3343303 ATGGTAAGCC
3343313 CGGGTTGGAAATGGTGAAGGCACTGGCA
1 CGGGTTGGAAATGGTGAAGGCACTGGCA
3343341 CGGGTTGGAAATGGTGAAGGCACTGGCA
1 CGGGTTGGAAATGGTGAAGGCACTGGCA
3343369 CGGGTTGGAAATGGTGA
1 CGGGTTGGAAATGGTGA
3343386 GCTCACGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.25, C:0.12, G:0.44, T:0.19
Consensus pattern (28 bp):
CGGGTTGGAAATGGTGAAGGCACTGGCA
Found at i:3350029 original size:3 final size:3
Alignment explanation
Indices: 3350021--3350064 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
3350011 TTTATTTTGT
**
3350021 TTA TTA TTA TCG TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3350065 CATTATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3350069 original size:26 final size:26
Alignment explanation
Indices: 3350021--3350070 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
3350011 TTTATTTTGT
* **
3350021 TTATTATTATCGTTATTTTATTATTA
1 TTATTATTATCATTATTACATTATTA
*
3350047 TTATTATTATTATTATTACATTAT
1 TTATTATTATCATTATTACATTAT
3350071 AATTTTTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (26 bp):
TTATTATTATCATTATTACATTATTA
Found at i:3350541 original size:28 final size:26
Alignment explanation
Indices: 3350504--3350558 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
3350494 ATAGAGGACC
3350504 ATTCGAGTTTTGCAGAAAAAAAGGAGAG
1 ATTCGAG-TTTG-AGAAAAAAAGGAGAG
* * *
3350532 ATTCGGGTTTGATAAAAAAAGGGGAG
1 ATTCGAGTTTGAGAAAAAAAGGAGAG
3350558 A
1 A
3350559 GATAAACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.58
27 4 0.17
28 6 0.25
ACGTcount: A:0.42, C:0.05, G:0.31, T:0.22
Consensus pattern (26 bp):
ATTCGAGTTTGAGAAAAAAAGGAGAG
Found at i:3352573 original size:155 final size:155
Alignment explanation
Indices: 3352291--3352601 Score: 550
Period size: 155 Copynumber: 2.0 Consensus size: 155
3352281 GGCGCTGTGG
* * *
3352291 GGGTGTTTATCATTCTCCACGCGTAACCGACTCCCGAACCGTTTTTAATCGAATCTTTGGTAAAC
1 GGGTGCTTATCATTCTCCACGCGTAACCGACTCCCGAACCATTTTTAATCGAATCTTCGGTAAAC
3352356 GCATACCATTTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTAAAAGACGTTTTAGGTATT
66 GCATACCATTTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTAAAAGACGTTTTAGGTATT
*
3352421 CAACCTACCTTACCCAAAGGTTGAT
131 CAACCTACCTTACCCAAAAGTTGAT
* *
3352446 GGGTGCTTATCCTTCTCCACGCGTAACCGACTCTCGAACCATTTTTAATCGAATCTTCGGTAAAC
1 GGGTGCTTATCATTCTCCACGCGTAACCGACTCCCGAACCATTTTTAATCGAATCTTCGGTAAAC
*
3352511 GCATACCATTTTTGTCTTAAAAAATGTTTTTTCTTAAAATTGTTTTAAAAGACGTTTTAGGTATT
66 GCATACCATTTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTAAAAGACGTTTTAGGTATT
*
3352576 CTACCTACCTTACCCAAAAGTTGAT
131 CAACCTACCTTACCCAAAAGTTGAT
3352601 G
1 G
3352602 ACGACTCATT
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
155 148 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (155 bp):
GGGTGCTTATCATTCTCCACGCGTAACCGACTCCCGAACCATTTTTAATCGAATCTTCGGTAAAC
GCATACCATTTTTGTCTTAAAAAATGATTTTTCTTAAAATTGTTTTAAAAGACGTTTTAGGTATT
CAACCTACCTTACCCAAAAGTTGAT
Found at i:3354955 original size:84 final size:84
Alignment explanation
Indices: 3354814--3354981 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
3354804 ATATGAGGAG
3354814 TGATGAAAACTTCCGAAAATATGTATAACGATGGAGGGATGTTACATCTCAAGTGTACCCACCGA
1 TGATGAAAACTTCCGAAAATATGTATAACGATGGAGGGATGTTACATCTCAAGTGTACCCACCGA
3354879 TGACTGAAAGAGAGTTCAT
66 TGACTGAAAGAGAGTTCAT
3354898 TGATGAAAACTTCCGAAAATATGTATAACGATGGAGGGATGTTACATCTCAAGTGTACCCACCGA
1 TGATGAAAACTTCCGAAAATATGTATAACGATGGAGGGATGTTACATCTCAAGTGTACCCACCGA
3354963 TGACTGAAAGAGAGTTCAT
66 TGACTGAAAGAGAGTTCAT
3354982 CACCCTATTC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (84 bp):
TGATGAAAACTTCCGAAAATATGTATAACGATGGAGGGATGTTACATCTCAAGTGTACCCACCGA
TGACTGAAAGAGAGTTCAT
Found at i:3357569 original size:36 final size:36
Alignment explanation
Indices: 3357515--3357649 Score: 164
Period size: 36 Copynumber: 3.8 Consensus size: 36
3357505 TGAGAATTTT
3357515 AAAACAAATGTTTGTCTCGCTTGAGACAATTTCTCTC
1 AAAACAAAT-TTTGTCTCGCTTGAGACAATTTCTCTC
* *
3357552 AAAACAAATTTTGTCTCGCTTGAGAC-ATTTTTCTA
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTC
* * * * *
3357587 AAAATAATTTTTGTCTCGTTTGAGATAATTTCTTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTC
* * *
3357623 AAAACAAATTTCGTCTAGTTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
3357650 TTTTTTCCTT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
35 29 0.35
36 45 0.54
37 9 0.11
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTCTC
Found at i:3357589 original size:71 final size:71
Alignment explanation
Indices: 3357521--3357654 Score: 205
Period size: 71 Copynumber: 1.9 Consensus size: 71
3357511 TTTTAAAACA
* *
3357521 AATGTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTTGTCTCGCTTGAGACATTTTTCT
1 AATGTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTAGCTTGAGACATTTTTCT
3357586 AAAAAT
66 AAAAAT
* * * * *
3357592 AATTTTTGTCTCGTTTGAGATAATTTCTTTCAAAACAAATTTCGTCTAGTTTGAGACATTTTT
1 AATGTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTAGCTTGAGACATTTTT
3357655 TCCTTTGAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 56 1.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (71 bp):
AATGTTTGTCTCGCTTGAGACAATTTCTCTCAAAACAAATTTCGTCTAGCTTGAGACATTTTTCT
AAAAAT
Found at i:3357766 original size:36 final size:35
Alignment explanation
Indices: 3357720--3357829 Score: 141
Period size: 36 Copynumber: 3.1 Consensus size: 35
3357710 TTAAGATCGT
3357720 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
* * *
3357755 TTTCTCTAAAAACAATTTTTGTCTTGTTTGAGACAA
1 TTTCTCTAAAAACAA-ATTTGTCTCGCTTGAGACAA
* *
3357791 TTTATCTAAAAACAAATGTTGTCTCACTTGAGACAA
1 TTTCTCTAAAAACAAAT-TTGTCTCGCTTGAGACAA
3357827 TTT
1 TTT
3357830 TCCAAATTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
35 7 0.11
36 57 0.89
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:3357907 original size:30 final size:31
Alignment explanation
Indices: 3357867--3357924 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3357857 AACAAACATC
*
3357867 ATCTTGGAGTC-GTTTCTTTTGAAACAAGGG
1 ATCTTGGAGTCTATTTCTTTTGAAACAAGGG
*
3357897 ATCTTTGAGTCTATTTCTTTTGAAACAA
1 ATCTTGGAGTCTATTTCTTTTGAAACAA
3357925 AACTTTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (31 bp):
ATCTTGGAGTCTATTTCTTTTGAAACAAGGG
Found at i:3358146 original size:38 final size:37
Alignment explanation
Indices: 3358054--3358160 Score: 119
Period size: 36 Copynumber: 2.9 Consensus size: 37
3358044 TTTTTTAAGA
***
3358054 AAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTAC
1 AAAATCTTTGAGTATGTTTCTTT-GAAACAAAACAAAC
* *
3358092 --CATCTTTGAGTTTGTTTCCTTTGAAACAAAACAAAC
1 AAAATCTTTGAGTATGTTT-CTTTGAAACAAAACAAAC
*
3358128 AAAATCTTTGAGTATGTTTTTCTTGAAACAAAA
1 AAAATCTTTGAGTATGTTTCT-TTGAAACAAAA
3358161 ACATATTTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
36 26 0.46
37 5 0.09
38 26 0.46
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.38
Consensus pattern (37 bp):
AAAATCTTTGAGTATGTTTCTTTGAAACAAAACAAAC
Found at i:3358173 original size:32 final size:32
Alignment explanation
Indices: 3358120--3358210 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
3358110 CTTTGAAACA
*
3358120 AAACAAACAAAATCTTTGAGTATGTTTTTCTTG
1 AAACAAA-AACATCTTTGAGTATGTTTTTCTTG
*
3358153 AAACAAAAACATATTTGAGTATGTTTTTCTTG
1 AAACAAAAACATCTTTGAGTATGTTTTTCTTG
*
3358185 AAACAAAAACATCTTTGAGTTTGTTT
1 AAACAAAAACATCTTTGAGTATGTTT
3358211 CTCCCGAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 47 0.87
33 7 0.13
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (32 bp):
AAACAAAAACATCTTTGAGTATGTTTTTCTTG
Found at i:3364210 original size:25 final size:25
Alignment explanation
Indices: 3364162--3364210 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3364152 GAAGTTATAT
* *
3364162 TAAAATTTTAAGGTTCACATAATTG
1 TAAAATTTTAAGATTCACAAAATTG
3364187 TAAAATTTTAAGATGT-ACAAAATT
1 TAAAATTTTAAGAT-TCACAAAATT
3364211 AAATAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (25 bp):
TAAAATTTTAAGATTCACAAAATTG
Found at i:3365489 original size:23 final size:23
Alignment explanation
Indices: 3365454--3365510 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
3365444 AGACGAATTA
* * *
3365454 AAGAAGGACAAATGGGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
3365477 AAGAAGAAGAAATGAGTTTATGG
1 AAGAAGAAGAAATGAGTTTATGG
3365500 AAGAAGAAGAA
1 AAGAAGAAGAA
3365511 GAAGAAGAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.49, C:0.02, G:0.32, T:0.18
Consensus pattern (23 bp):
AAGAAGAAGAAATGAGTTTATGG
Found at i:3365505 original size:26 final size:26
Alignment explanation
Indices: 3365476--3365639 Score: 108
Period size: 26 Copynumber: 6.2 Consensus size: 26
3365466 TGGGTTTATG
3365476 GAAGAAGAAGAAATGAGTTTATGGAA
1 GAAGAAGAAGAAATGAGTTTATGGAA
* *** *
3365502 GAAGAAGAAGAAGAAGAGGAAATGAGTTTATG
1 GAAGAAGAAGAA-ATGAGTTTATG-G---A-A
*
3365534 GAAGAAGAAGAATAAACGAGTTTATGGAA
1 GAAGAAGAAG---AAATGAGTTTATGGAA
* *
3365563 GAAGAAGAATAAACGAGTTTATGGAA
1 GAAGAAGAAGAAATGAGTTTATGGAA
* *
3365589 G-A-AA-AAGCAGTGAGTTTATGGAA
1 GAAGAAGAAGAAATGAGTTTATGGAA
3365612 GAAGAAG-A-AAAT--GTTTATGGAA
1 GAAGAAGAAGAAATGAGTTTATGGAA
3365634 GAAGAA
1 GAAGAA
3365640 TAAACGTTTT
Statistics
Matches: 109, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
22 16 0.15
23 16 0.15
24 5 0.05
25 4 0.04
26 29 0.27
27 7 0.06
28 1 0.01
29 9 0.08
30 1 0.01
31 1 0.01
32 10 0.09
33 1 0.01
34 7 0.06
35 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.30, T:0.18
Consensus pattern (26 bp):
GAAGAAGAAGAAATGAGTTTATGGAA
Found at i:3365524 original size:35 final size:35
Alignment explanation
Indices: 3365476--3365545 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
3365466 TGGGTTTATG
3365476 GAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAA
1 GAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAA
*
3365511 GAAGAAGAGGAAATGAGTTTATGGAAGAAGAAGAA
1 GAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAA
3365546 TAAACGAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.14
Consensus pattern (35 bp):
GAAGAAGAAGAAATGAGTTTATGGAAGAAGAAGAA
Found at i:3365539 original size:23 final size:23
Alignment explanation
Indices: 3365511--3365662 Score: 146
Period size: 26 Copynumber: 6.4 Consensus size: 23
3365501 AGAAGAAGAA
* *
3365511 GAAGAAGAGGAAATGAGTTTATG
1 GAAGAAGAAGAAACGAGTTTATG
3365534 GAAGAAGAAGAATAAACGAGTTTATG
1 GAAGAAGAAG---AAACGAGTTTATG
3365560 GAAGAAGAAGAATAAACGAGTTTATG
1 GAAGAAGAAG---AAACGAGTTTATG
* * **
3365586 GAAGAAAAAGCAGTGAGTTTATG
1 GAAGAAGAAGAAACGAGTTTATG
3365609 GAAGAAGAAGAAA--ATGTTTATG
1 GAAGAAGAAGAAACGA-GTTTATG
* **
3365631 GAAGAAGAATAAACGTTTTTATG
1 GAAGAAGAAGAAACGAGTTTATG
3365654 GAAGAAGAA
1 GAAGAAGAA
3365663 AAATGATTCA
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.01
22 19 0.17
23 44 0.40
26 47 0.42
ACGTcount: A:0.48, C:0.03, G:0.28, T:0.21
Consensus pattern (23 bp):
GAAGAAGAAGAAACGAGTTTATG
Found at i:3393809 original size:15 final size:15
Alignment explanation
Indices: 3393789--3393818 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3393779 AATATTGACA
3393789 TTAATTTTCTATATT
1 TTAATTTTCTATATT
3393804 TTAATTTTCTATATT
1 TTAATTTTCTATATT
3393819 ATTTTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAATTTTCTATATT
Found at i:3409327 original size:3 final size:3
Alignment explanation
Indices: 3409319--3409343 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3409309 ATGATAAATG
3409319 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3409344 TAAAAAGAAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3415785 original size:15 final size:15
Alignment explanation
Indices: 3415767--3415796 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3415757 CCACGGTGCT
3415767 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
3415782 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
3415797 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:3421333 original size:18 final size:19
Alignment explanation
Indices: 3421304--3421348 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3421294 GATAAATTTA
*
3421304 TATTTT-ATTTATTTAT-T
1 TATTTTAATTTATATATAT
3421321 TATTTTAATTTATATATAT
1 TATTTTAATTTATATATAT
3421340 TA-TTTAATT
1 TATTTTAATT
3421349 GATTAGGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTAATTTATATATAT
Found at i:3421626 original size:11 final size:11
Alignment explanation
Indices: 3421612--3421647 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3421602 CTCTTAAAAC
3421612 TAAATAATATA
1 TAAATAATATA
3421623 TAAATAATATA
1 TAAATAATATA
3421634 T-AAT-ATAT-
1 TAAATAATATA
3421642 TAAATA
1 TAAATA
3421648 TTTAGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 7 0.30
10 3 0.13
11 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATAATATA
Found at i:3436831 original size:15 final size:16
Alignment explanation
Indices: 3436801--3436833 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3436791 AAATTTGATC
*
3436801 TAAATTAATCTATCAA
1 TAAATTAATATATCAA
3436817 TAAATTAA-ATATCAA
1 TAAATTAATATATCAA
3436832 TA
1 TA
3436834 GTTAGTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATTAATATATCAA
Found at i:3440540 original size:229 final size:229
Alignment explanation
Indices: 3440139--3440595 Score: 808
Period size: 229 Copynumber: 2.0 Consensus size: 229
3440129 TCGTATCTCT
*
3440139 AGAAAATCTATTGACCAAATAACACCTGAATTCCATTCAAAAAGTAGTTGCAAGTTTGTTGTTGT
1 AGAAAATCTATTGACCAAATAACACCTGAATTCCATTCAAAAAGTAGTTGCAAGTCTGTTGTTGT
3440204 TTTGAGCTTCTTTTCTAAGGCTTTGAGGTATGGATCAATTGGAAGATTTTATCCATCTTCCTTTG
66 TTTGAGCTTCTTTTCTAAGGCTTTGAGGTATGGATCAATTGGAAGATTTTATCCATCTTCCTTTG
3440269 ATGTGAGTCTTGTGATGCATATATCACATGCCAAGCTAGTAAACTAATAAGTGTCAAGGGCAGAG
131 ATGTGAGTCTTGTGATGCATATATCACATGCCAAGCTAGTAAACTAATAAGTGTCAAGGGCAGAG
* *
3440334 ACAAATGTACTAAGCCCCTTAG-GAGAGCAAGTGG
196 ACAAATGCACCAAGCCCCTTAGAG-GAGCAAGTGG
* * *
3440368 AGAAAATCTATTGACCAAATAACACCTGAATTCTATTCAAAGAGTCGTTGCAAGTCTGTTGTTGT
1 AGAAAATCTATTGACCAAATAACACCTGAATTCCATTCAAAAAGTAGTTGCAAGTCTGTTGTTGT
* *
3440433 TTTGAGTTTCTTTTCTAAGGCTTTGAGGTGTGGATCAATTGGAAGATTTTATCCATCTTCCTTTG
66 TTTGAGCTTCTTTTCTAAGGCTTTGAGGTATGGATCAATTGGAAGATTTTATCCATCTTCCTTTG
* *
3440498 ATGTGAGTCTTGTTATGCATATATCACATGCCATGCTAGTAAACTAATAAGTGTCAAGGGCAGAG
131 ATGTGAGTCTTGTGATGCATATATCACATGCCAAGCTAGTAAACTAATAAGTGTCAAGGGCAGAG
3440563 ACAAATGCACCAAGCCCCTTAGAGGAGCAAGTG
196 ACAAATGCACCAAGCCCCTTAGAGGAGCAAGTG
3440596 CATACTTATT
Statistics
Matches: 217, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
229 216 1.00
230 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (229 bp):
AGAAAATCTATTGACCAAATAACACCTGAATTCCATTCAAAAAGTAGTTGCAAGTCTGTTGTTGT
TTTGAGCTTCTTTTCTAAGGCTTTGAGGTATGGATCAATTGGAAGATTTTATCCATCTTCCTTTG
ATGTGAGTCTTGTGATGCATATATCACATGCCAAGCTAGTAAACTAATAAGTGTCAAGGGCAGAG
ACAAATGCACCAAGCCCCTTAGAGGAGCAAGTGG
Found at i:3443714 original size:22 final size:21
Alignment explanation
Indices: 3443670--3443738 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 21
3443660 TAAAATATTA
* *
3443670 AATTATAAAGTACTAAAAGTCT
1 AATTATAAATTATTAAAA-TCT
3443692 AATTATAAATTAGTTAAAATCT
1 AATTATAAATTA-TTAAAATCT
* *
3443714 AAATT-TAATTTAATTAAAATAT
1 -AATTATAAATT-ATTAAAATCT
3443736 AAT
1 AAT
3443739 ATTTATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 3 0.08
22 27 0.68
23 10 0.25
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (21 bp):
AATTATAAATTATTAAAATCT
Found at i:3445159 original size:19 final size:19
Alignment explanation
Indices: 3445135--3445179 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3445125 TTTTTTTATA
3445135 AACAATAATATAC-GATATG
1 AACAATAATATACTG-TATG
*
3445154 AACAATATTATACTGTATG
1 AACAATAATATACTGTATG
3445173 AACAATA
1 AACAATA
3445180 CTGTGAACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (19 bp):
AACAATAATATACTGTATG
Found at i:3446041 original size:31 final size:31
Alignment explanation
Indices: 3446003--3446139 Score: 125
Period size: 37 Copynumber: 4.0 Consensus size: 31
3445993 CCCGAAGGAC
3446003 CAGTCCATA-GATCCCGAAGAATC-TAGGTAAT
1 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAT
3446034 CAGTCCATATGTCCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
3446065 CTATAACTGTCCATATGTCCCGAAGAACATAGGTAAT
1 C----A--GTCCATATGTCCCGAAGAACATAGGTAAT
*
3446102 CTATAACTGTCCATATGTCCCAAAGAACATAGGTAAT
1 C----A--GTCCATATGTCCCGAAGAACATAGGTAAT
3446139 C
1 C
3446140 TGTAATTGTC
Statistics
Matches: 97, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
30 1 0.01
31 28 0.29
32 1 0.01
35 1 0.01
37 66 0.68
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:3446078 original size:37 final size:37
Alignment explanation
Indices: 3446036--3446174 Score: 224
Period size: 37 Copynumber: 3.8 Consensus size: 37
3446026 TAGGTAATCA
3446036 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
3446073 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
* * *
3446110 GTCCATATGTCCCAAAGAACATAGGTAATCTGTAATT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
* * *
3446147 GTCTATATGTTCTGAAGAACATAGGTAA
1 GTCCATATGTCCCGAAGAACATAGGTAA
3446175 CCCTCGACTC
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 95 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (37 bp):
GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
Found at i:3448141 original size:2 final size:2
Alignment explanation
Indices: 3448134--3448160 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3448124 AAATAAATAA
3448134 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 A
3448161 CTTCTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3448472 original size:2 final size:2
Alignment explanation
Indices: 3448465--3448506 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3448455 TATTATTACT
3448465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3448507 CTTCTATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3453720 original size:226 final size:225
Alignment explanation
Indices: 3453327--3453789 Score: 806
Period size: 226 Copynumber: 2.1 Consensus size: 225
3453317 CTTTTGTATT
3453327 TTTAAAATTTAATTCATGTCCAATAACATTATATTCTTAATATAAACTAAAACAAATTTTATGTT
1 TTTAAAATTTAATTCATGTCCAATAACATTATATTCTTAATATAAACTAAAACAAATTTTATGTT
* *
3453392 ATGATTTTTTTATTGCCCTCCCGGTTCCAAGGCTTCGCCTTTATTAATCTGGACCGACCTGCGTC
66 ATGATTTTTTTATTGCCCTCCCGGTTCCAAGGCTTCGCCTTTACTAATCCGGACCGACCTGCGTC
3453457 GCATACGTTATAGAATTTCATGTCAACTTTATTGTTTTATAGTTACATAACTCACATGTTAAATT
131 GCATACGTTATAGAATTTCATGTCAACTTTATTGTTTTATAGTTACATAACTCACATGTTAAATT
3453522 AATGTAATAGAATTTATTT-AATAATTATAG
196 AATGTAATAGAATTT-TTTAAATAATTATAG
*
3453552 TTTAAAATTTAATTGATGTCCAATAACATTATATTCTTAATATAAACTAAAACAAATTTTATGTT
1 TTTAAAATTTAATTCATGTCCAATAACATTATATTCTTAATATAAACTAAAACAAATTTTATGTT
* * *
3453617 GTGAATTTTTTTATTGCCCTCCCGGTTCCAAGGCTTCTCCTTTACTAATCCGGACTGACCTGCGT
66 ATG-ATTTTTTTATTGCCCTCCCGGTTCCAAGGCTTCGCCTTTACTAATCCGGACCGACCTGCGT
* *
3453682 CGCATACGTTATAGAATTTCATGTCAACTTTATTGTTTTATATTTGCATAACTCACATGTTAAAT
130 CGCATACGTTATAGAATTTCATGTCAACTTTATTGTTTTATAGTTACATAACTCACATGTTAAAT
*
3453747 TAATGTAATGGAATTTTTTAAATAATTATAG
195 TAATGTAATAGAATTTTTTAAATAATTATAG
3453778 TTT--AATTTAATT
1 TTTAAAATTTAATT
3453790 TTTTTAATAA
Statistics
Matches: 227, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
224 9 0.04
225 69 0.30
226 149 0.66
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (225 bp):
TTTAAAATTTAATTCATGTCCAATAACATTATATTCTTAATATAAACTAAAACAAATTTTATGTT
ATGATTTTTTTATTGCCCTCCCGGTTCCAAGGCTTCGCCTTTACTAATCCGGACCGACCTGCGTC
GCATACGTTATAGAATTTCATGTCAACTTTATTGTTTTATAGTTACATAACTCACATGTTAAATT
AATGTAATAGAATTTTTTAAATAATTATAG
Found at i:3454438 original size:60 final size:59
Alignment explanation
Indices: 3454348--3454517 Score: 159
Period size: 60 Copynumber: 2.9 Consensus size: 59
3454338 CTAAACTATA
* * * *
3454348 ACTCTCATTTTAAATT-GATCTTTAAGCTTTTAAATATTTCAATTTCATCCTCAAACTACG
1 ACTCTCATTTCAAATTAG-TCCTTAAACTTTTGAATATTTCAATTTCATCC-CAAACTACG
* *
3454408 ACTCTCATTTCAAATTAGTCCTTAAACTTTTGAACA-TTCTAATTTCATCCCTAAACTATG
1 ACTCTCATTTCAAATTAGTCCTTAAACTTTTGAATATTTC-AATTTCATCCC-AAACTACG
* * ** * *
3454468 AC-C-CCTTTCTAAATTAATCCCCAAACTTTTGAATATTCCAATTTTATCCC
1 ACTCTCATTTC-AAATTAGTCCTTAAACTTTTGAATATTTCAATTTCATCCC
3454518 CAAATTCATC
Statistics
Matches: 92, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
58 5 0.05
59 36 0.39
60 50 0.54
61 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (59 bp):
ACTCTCATTTCAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCATCCCAAACTACG
Found at i:3454462 original size:29 final size:29
Alignment explanation
Indices: 3454430--3454517 Score: 70
Period size: 30 Copynumber: 3.0 Consensus size: 29
3454420 AATTAGTCCT
*
3454430 TAAACTTTTGAACATTCTAATTTCATCCC
1 TAAACTTTTGAACATTCTAATTTAATCCC
* * * *
3454459 TAAAC-TATGACCCCTTTCTAAATTAATCCC
1 TAAACTTTTGA--ACATTCTAATTTAATCCC
* * * *
3454489 CAAACTTTTGAATATTCCAATTTTATCCC
1 TAAACTTTTGAACATTCTAATTTAATCCC
3454518 CAAATTCATC
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
28 4 0.09
29 17 0.40
30 18 0.42
31 4 0.09
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (29 bp):
TAAACTTTTGAACATTCTAATTTAATCCC
Found at i:3454499 original size:59 final size:61
Alignment explanation
Indices: 3454387--3454521 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 61
3454377 TTAAATATTT
* **
3454387 CAATTTCAT-CCTCAAACTACGACTCTCATTTCAAATTAGTCCTTAAACTTTTGAACATTC
1 CAATTTCATCCCTCAAACTACGACTCTCATTTCAAATTAATCCCCAAACTTTTGAACATTC
* * * *
3454447 TAATTTCATCCCT-AAACTATGAC-C-CCTTTCTAAATTAATCCCCAAACTTTTGAATATTC
1 CAATTTCATCCCTCAAACTACGACTCTCATTTC-AAATTAATCCCCAAACTTTTGAACATTC
*
3454506 CAATTTTATCCC-CAAA
1 CAATTTCATCCCTCAAA
3454522 TTCATCTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 5 0.08
59 38 0.60
60 17 0.27
61 3 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (61 bp):
CAATTTCATCCCTCAAACTACGACTCTCATTTCAAATTAATCCCCAAACTTTTGAACATTC
Found at i:3454720 original size:60 final size:59
Alignment explanation
Indices: 3454639--3454778 Score: 160
Period size: 60 Copynumber: 2.3 Consensus size: 59
3454629 GTATATATGT
*
3454639 ATAGTTTGGGATGAATTTTG-AATGTTCAAAAATATTGGGGACCAATTTAGAATGA-AGATC
1 ATAGTTTGGGATGAA-TTTGAAATGTTCAAAAAT-TTGAGGACCAATTTAGAATGATAG-TC
* *
3454699 ATAGTTTGGGGATGACA-TTGAAATTTTCAAAAATTTGAGGACTAATTTAGAATGATAGTC
1 ATAGTTT-GGGATGA-ATTTGAAATGTTCAAAAATTTGAGGACCAATTTAGAATGATAGTC
* *
3454759 ATATTTTAGGGATCAATTTG
1 ATAGTTT-GGGATGAATTTG
3454779 GAATATTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
59 1 0.01
60 46 0.67
61 21 0.30
62 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (59 bp):
ATAGTTTGGGATGAATTTGAAATGTTCAAAAATTTGAGGACCAATTTAGAATGATAGTC
Found at i:3456092 original size:21 final size:21
Alignment explanation
Indices: 3456040--3456096 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
3456030 ACAAACAATA
3456040 AAAAATAAAATAAGATAATAAAC
1 AAAAAT-AAATAA-ATAATAAAC
*
3456063 AAATA-AAATAAA-AATAAAC
1 AAAAATAAATAAATAATAAAC
3456082 AAGAAATAAATAAAT
1 AA-AAATAAATAAAT
3456097 TAGAAAAACC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 13 0.45
23 4 0.14
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAAATAAATAAATAATAAAC
Found at i:3456092 original size:26 final size:26
Alignment explanation
Indices: 3456032--3456095 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
3456022 AAGATAAAAC
* * *
3456032 AAACAATAAAAAATAAAATAAGATAAT
1 AAACAA-ATAAAATAAAATAAGACAAG
3456059 AAACAAATAAAATAAAAATAA-ACAAG
1 AAACAAATAAAAT-AAAATAAGACAAG
*
3456085 AAATAAATAAA
1 AAACAAATAAA
3456096 TTAGAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.16
Consensus pattern (26 bp):
AAACAAATAAAATAAAATAAGACAAG
Found at i:3456456 original size:26 final size:26
Alignment explanation
Indices: 3456427--3456476 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3456417 AAATAATAAG
*
3456427 TAAAATAT-ATACATAAATAAAATACC
1 TAAAATATGATAAATAAA-AAAATACC
3456453 TAAAATATGATAAATAAAAAAATA
1 TAAAATATGATAAATAAAAAAATA
3456477 ACATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (26 bp):
TAAAATATGATAAATAAAAAAATACC
Found at i:3456517 original size:15 final size:15
Alignment explanation
Indices: 3456497--3456529 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3456487 AATAATAAAT
3456497 AAAGAAAA-AGAATAA
1 AAAGAAAACA-AATAA
3456512 AAAGAAAACAAATAA
1 AAAGAAAACAAATAA
3456527 AAA
1 AAA
3456530 AATTATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAGAAAACAAATAA
Found at i:3456620 original size:9 final size:9
Alignment explanation
Indices: 3456606--3456662 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
3456596 AAAATTGTAG
3456606 TAATAAAAA
1 TAATAAAAA
*
3456615 TAATAAAGA
1 TAATAAAAA
3456624 TAATATAAAGAA
1 T-A-ATAAA-AA
3456636 TAATAATAAA
1 TAATAA-AAA
*
3456646 AAATAAAAA
1 TAATAAAAA
*
3456655 TAGTAAAA
1 TAATAAAA
3456663 GGGTATAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
9 18 0.46
10 12 0.31
11 7 0.18
12 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (9 bp):
TAATAAAAA
Found at i:3456706 original size:18 final size:19
Alignment explanation
Indices: 3456685--3456728 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
3456675 AAATAAGTAT
3456685 ATATATATAATAATA-ATA
1 ATATATATAATAATACATA
*
3456703 ATATATATAATAATACGTA
1 ATATATATAATAATACATA
3456722 ATATATA
1 ATATATA
3456729 AAAAAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
ATATATATAATAATACATA
Found at i:3456726 original size:15 final size:15
Alignment explanation
Indices: 3456687--3456717 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
3456677 ATAAGTATAT
3456687 ATATATAATAATAATA
1 ATATAT-ATAATAATA
3456703 ATATATATAATAATA
1 ATATATATAATAATA
3456718 CGTAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATATATAATAATA
Found at i:3457200 original size:5 final size:5
Alignment explanation
Indices: 3457190--3457226 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
3457180 AAAAAGCTTT
3457190 TCCTC TCCTC TCCTC TCCTC TCCTC TCCTC TCCTC TC
1 TCCTC TCCTC TCCTC TCCTC TCCTC TCCTC TCCTC TC
3457227 TACGAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
TCCTC
Found at i:3457834 original size:2 final size:2
Alignment explanation
Indices: 3457827--3457898 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
3457817 TAATAATACC
3457827 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
3457869 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3457899 CGATGTACAC
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3458908 original size:100 final size:100
Alignment explanation
Indices: 3458772--3458952 Score: 265
Period size: 100 Copynumber: 1.8 Consensus size: 100
3458762 GGAAATTGTT
* * *
3458772 TGTTGACAGTCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCATT
1 TGTTGACAATCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGCCTCGAGTCCAATATCATT
3458837 CGTTGTGAAGTTGAAATTGACTCTGAATAAAATTG
66 CGTTGTGAAGTTGAAATTGACTCTGAATAAAATTG
* * * * * *
3458872 TGTTGACAATCAGCTGCCCCTTC-GTCGTGAAGTTGAGCTTGTGTTGCCTTGGGTCCAATATCCT
1 TGTTGACAATCAGCCGCCCATTCACT-GTGAAGTTGAGCTTGTGTTGCCTCGAGTCCAATATCAT
3458936 TCGTTGTGAAGTTGAAA
65 TCGTTGTGAAGTTGAAA
3458953 ATGGCTATGA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 1 0.01
100 70 0.99
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (100 bp):
TGTTGACAATCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGCCTCGAGTCCAATATCATT
CGTTGTGAAGTTGAAATTGACTCTGAATAAAATTG
Found at i:3465254 original size:12 final size:11
Alignment explanation
Indices: 3465239--3465310 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 11
3465229 AAATATGAAG
3465239 TAAAAAAAAAGA
1 TAAAAAAAAA-A
*
3465251 TAAAACAAACAA
1 TAAAA-AAAAAA
3465263 TAAAAAATAAAA
1 TAAAAAA-AAAA
* *
3465275 TAAGATAAGATAA
1 TAA-A-AAAAAAA
3465288 TAAACAAATAAAA
1 TAAA-AAA-AAAA
3465301 TAAAAAAAAA
1 TAAAAAAAAA
3465311 CAAGAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
11 5 0.10
12 23 0.48
13 18 0.38
14 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:3465322 original size:26 final size:25
Alignment explanation
Indices: 3465239--3465334 Score: 79
Period size: 26 Copynumber: 3.8 Consensus size: 25
3465229 AAATATGAAG
*
3465239 TAAAAAA-AAAGAT-AAAACAAACAA
1 TAAAAAATAAA-ATAAAAAAAAACAA
* * * *
3465263 TAAAAAATAAAATAAGATAAGATAA
1 TAAAAAATAAAATAAAAAAAAACAA
3465288 TAAACAAATAAAATAAAAAAAAACAA
1 TAAA-AAATAAAATAAAAAAAAACAA
* * *
3465314 GAAATAAATAAATTAGAAAAA
1 TAAA-AAATAAAATAAAAAAA
3465335 CCAAATGAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 9 0.16
25 13 0.23
26 34 0.61
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (25 bp):
TAAAAAATAAAATAAAAAAAAACAA
Found at i:3465615 original size:2 final size:2
Alignment explanation
Indices: 3465608--3465643 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3465598 ACTATGTATG
3465608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3465644 TGGTTAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3465729 original size:21 final size:21
Alignment explanation
Indices: 3465679--3465737 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
3465669 AAATATATAC
* *
3465679 ATAAATAAAATACCTAAAATATG
1 ATAAATAAAA-A-ATAACATATG
3465702 ATAAATAAAAAATAACATAT-
1 ATAAATAAAAAATAACATATG
*
3465722 ATATAATAATAAATAA
1 ATA-AATAAAAAATAA
3465738 ATAAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 1 0.03
23 10 0.31
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
ATAAATAAAAAATAACATATG
Found at i:3465764 original size:15 final size:14
Alignment explanation
Indices: 3465732--3465770 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
3465722 ATATAATAAT
*
3465732 AAATAAATAAAAAG
1 AAATAAAAAAAAAG
3465746 -AATAAAAAGAAAAG
1 AAATAAAAA-AAAAG
3465760 AAATAAAAAAA
1 AAATAAAAAAA
3465771 TTATAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 7 0.32
14 7 0.32
15 8 0.36
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (14 bp):
AAATAAAAAAAAAG
Found at i:3465966 original size:27 final size:28
Alignment explanation
Indices: 3465915--3465984 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
3465905 TATAAAAAGA
3465915 AATAAGTAAATATATATATACATATAAT
1 AATAAGTAAATATATATATACATATAAT
* *
3465943 AATAA-TATATATATATATATATATAAT
1 AATAAGTAAATATATATATACATATAAT
*
3465970 AATACGT-AATATATA
1 AATAAGTAAATATATA
3465985 AAAAAGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 31 0.84
28 6 0.16
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (28 bp):
AATAAGTAAATATATATATACATATAAT
Found at i:3465984 original size:2 final size:2
Alignment explanation
Indices: 3465924--3465967 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
3465914 AAATAAGTAA
*
3465924 AT AT AT AT AT AC AT AT A- AT A- AT A- 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
3465963 AT AT A
1 AT AT A
3465968 ATAATACGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3466269 original size:26 final size:28
Alignment explanation
Indices: 3466240--3466307 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 28
3466230 TTTTATTTCT
3466240 CATTTTCCT-TC-CTCTCAAGCCAAAGC
1 CATTTTCCTCTCTCTCTCAAGCCAAAGC
3466266 CA--TTCCTCTCTCTCTCAAGCCAAAGC
1 CATTTTCCTCTCTCTCTCAAGCCAAAGC
3466292 CA--TTCCTCTCTCTCTC
1 CATTTTCCTCTCTCTCTC
3466308 TCTCTCTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 5 0.12
25 2 0.05
26 33 0.82
ACGTcount: A:0.19, C:0.43, G:0.06, T:0.32
Consensus pattern (28 bp):
CATTTTCCTCTCTCTCTCAAGCCAAAGC
Found at i:3466304 original size:2 final size:2
Alignment explanation
Indices: 3466297--3466321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3466287 AAAGCCATTC
3466297 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3466322 GTTTCCTCTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3469002 original size:60 final size:60
Alignment explanation
Indices: 3468929--3469075 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
3468919 ATTTATGGGT
* * *
3468929 AAAG-TACACAAATGAT-CTCTTGACTATA-AGATATTATTTTACTGAGT-CATCCAAGTATTA
1 AAAGTTACA-AAATGATCCTC-TGACTATAGA-ACATTATTTTACTGAGTCCCT-CAACTATTA
* * **
3468989 AAAGTTACAAAATGATCCTCTGATTATAGAACATTGTTTTGTTGAGTCCCTCAACTATTA
1 AAAGTTACAAAATGATCCTCTGACTATAGAACATTATTTTACTGAGTCCCTCAACTATTA
*
3469049 AAAGTTACAAAATGGTCACTC-GACTAT
1 AAAGTTACAAAATGATC-CTCTGACTAT
3469076 TCCTTATGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
60 60 0.82
61 13 0.18
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (60 bp):
AAAGTTACAAAATGATCCTCTGACTATAGAACATTATTTTACTGAGTCCCTCAACTATTA
Found at i:3469349 original size:60 final size:60
Alignment explanation
Indices: 3469283--3469403 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
3469273 GTCAGGTGAT
** * * * *
3469283 CATTTTGTAACTTTT-AATAGTCGAGGGACTCAACAAAATAACATCTTATAGTTGGGGGAC
1 CATTTTGTAACTTTTGAA-AGTCGAAAGACTCAACAAAACAACACCTTATAATTAGGGGAC
* *
3469343 CATTTTGTAACTTTTGAAAGTTGAAAGACTCAGCAAAACAACACCTTATAATTAGGGGAC
1 CATTTTGTAACTTTTGAAAGTCGAAAGACTCAACAAAACAACACCTTATAATTAGGGGAC
3469403 C
1 C
3469404 GTTAGTGTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 50 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (60 bp):
CATTTTGTAACTTTTGAAAGTCGAAAGACTCAACAAAACAACACCTTATAATTAGGGGAC
Found at i:3475308 original size:41 final size:41
Alignment explanation
Indices: 3475262--3475386 Score: 198
Period size: 41 Copynumber: 3.0 Consensus size: 41
3475252 CCAGAAATCT
3475262 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTTTTC
** *
3475303 CGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTTTT-C
3475345 CGTGTTTGTTTCACGTAATTCGTTTT-TCGGAAAATGTTTTC
1 CGTGTTTGTTTCACGTAATTCGTTTTCT-GGAAAATGTTTTC
3475386 C
1 C
3475387 AGTATTTGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 39 0.51
42 37 0.49
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (41 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTTTTC
Found at i:3475361 original size:42 final size:42
Alignment explanation
Indices: 3475262--3475386 Score: 207
Period size: 42 Copynumber: 3.0 Consensus size: 42
3475252 CCAGAAATCT
*
3475262 CGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTTTT-C
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
* *
3475303 CGTGTTTGTTTCACGTAATTCGTTTTCCAGAAAATATTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
*
3475345 CGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
3475387 AGTATTTGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 37 0.48
42 40 0.52
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
Found at i:3475641 original size:21 final size:22
Alignment explanation
Indices: 3475608--3475665 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
3475598 TAATTATTAA
*
3475608 AATATTTAAAATATATTT-AT-T
1 AATATTT-TAATATATTTAATAT
3475629 AATATTTCTAATA-ATTTAATAT
1 AATATTT-TAATATATTTAATAT
*
3475651 TATATTTTAATATAT
1 AATATTTTAATATAT
3475666 AAATAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 18 0.58
22 9 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTTAATATATTTAATAT
Found at i:3475678 original size:26 final size:26
Alignment explanation
Indices: 3475649--3475730 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
3475639 ATAATTTAAT
3475649 ATTATATTTTAATATATAAATAAATA
1 ATTATATTTTAATATATAAATAAATA
* * *
3475675 ATTATATTATAATATA-AGATATTATA
1 ATTATATTTTAATATATAAATA-AATA
* * *
3475701 TTTTTATTTTAATA-ATATAATAAATT
1 ATTATATTTTAATATATA-AATAAATA
3475727 ATTA
1 ATTA
3475731 ATAAAATTTA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
25 5 0.12
26 34 0.81
27 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
ATTATATTTTAATATATAAATAAATA
Found at i:3475698 original size:20 final size:19
Alignment explanation
Indices: 3475663--3475702 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3475653 TATTTTAATA
3475663 TATAAATAAATAATTATAT
1 TATAAATAAATAATTATAT
3475682 TATAATATAAGAT-ATTATAT
1 TATAA-ATAA-ATAATTATAT
3475702 T
1 T
3475703 TTTATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
TATAAATAAATAATTATAT
Found at i:3475862 original size:23 final size:23
Alignment explanation
Indices: 3475836--3475880 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3475826 AATAATATTT
3475836 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3475859 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3475881 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3475959 original size:33 final size:29
Alignment explanation
Indices: 3475920--3475990 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
3475910 AATATAATTT
*
3475920 ATAATATTTTTATTTCAATAAAATATATCAATA
1 ATAATATTTTTA-TT-AATAAAAT-TAT-AAAA
*
3475953 TTAATATTTTTATTAATAAAATTATAAAA
1 ATAATATTTTTATTAATAAAATTATAAAA
3475982 ATAATATTT
1 ATAATATTT
3475991 AATAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 3 0.09
31 8 0.23
32 2 0.06
33 11 0.31
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATAAAA
Found at i:3476004 original size:91 final size:89
Alignment explanation
Indices: 3475849--3476012 Score: 199
Period size: 91 Copynumber: 1.8 Consensus size: 89
3475839 TAAAGATATT
* * * * * *
3475849 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAAT-
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
3475913 ATAATTTATAATATTTTTATTTCAA
66 AT-ATTTATAATATTTTTATTTCAA
*
3475938 TAAAATATATCAATATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
3476001 AATAATATTTAT
62 AATAATATTTAT
3476013 TGTATGTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
89 9 0.14
90 2 0.03
91 28 0.44
92 14 0.22
93 10 0.16
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (89 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
ATATTTATAATATTTTTATTTCAA
Found at i:3476214 original size:15 final size:15
Alignment explanation
Indices: 3476194--3476236 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
3476184 CATTTTTTAA
*
3476194 AATTCAAATTTCAGT
1 AATTCAATTTTCAGT
*
3476209 AATTCATTTTTCA-T
1 AATTCAATTTTCAGT
3476223 AATTCAATTTTCAG
1 AATTCAATTTTCAG
3476237 AAAACCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (15 bp):
AATTCAATTTTCAGT
Found at i:3476226 original size:29 final size:29
Alignment explanation
Indices: 3476178--3476236 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3476168 TTTTAGAAAT
*
3476178 GTAATTCATTTTTTAAAATTCAAATTTCA
1 GTAATTCATTTTTCAAAATTCAAATTTCA
* *
3476207 GTAATTCATTTTTCATAATTCAATTTTCA
1 GTAATTCATTTTTCAAAATTCAAATTTCA
3476236 G
1 G
3476237 AAAACCAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (29 bp):
GTAATTCATTTTTCAAAATTCAAATTTCA
Found at i:3476227 original size:14 final size:14
Alignment explanation
Indices: 3476179--3476235 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
3476169 TTTAGAAATG
* *
3476179 TAATTCATTTTTTA
1 TAATTCAATTTTCA
* *
3476193 AAATTCAAATTTCA
1 TAATTCAATTTTCA
*
3476207 GTAATTCATTTTTCA
1 -TAATTCAATTTTCA
3476222 TAATTCAATTTTCA
1 TAATTCAATTTTCA
3476236 GAAAACCAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (14 bp):
TAATTCAATTTTCA
Found at i:3485581 original size:3 final size:3
Alignment explanation
Indices: 3485573--3485602 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3485563 TAATTACTAT
3485573 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3485603 AAAAGCTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3491226 original size:6 final size:7
Alignment explanation
Indices: 3491209--3491234 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3491199 CACATGAATT
3491209 TTTTTTA
1 TTTTTTA
3491216 TTTTTTA
1 TTTTTTA
3491223 TTTTTTA
1 TTTTTTA
3491230 TTTTT
1 TTTTT
3491235 GAATAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:3493409 original size:57 final size:59
Alignment explanation
Indices: 3493327--3493454 Score: 147
Period size: 57 Copynumber: 2.2 Consensus size: 59
3493317 TTTATAGGGC
* * * *
3493327 AAATTAT-AAATGATCTCTTAGTTATAGA-ATATTATTTAATTTAATTTTT-ATTATTAA
1 AAATTATAAAATAATCTCTTAATTATA-ATATATTATTTAATTGAATTTTTAAATATTAA
* * * *
3493384 AAGTTATAAAATAATCT-TTAATTATAATGTGTTATTTTATTGAATTTTTAAATATTAA
1 AAATTATAAAATAATCTCTTAATTATAATATATTATTTAATTGAATTTTTAAATATTAA
3493442 AAATTATAAAATA
1 AAATTATAAAATA
3493455 GTTATTTAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
56 1 0.02
57 31 0.53
58 27 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (59 bp):
AAATTATAAAATAATCTCTTAATTATAATATATTATTTAATTGAATTTTTAAATATTAA
Found at i:3493791 original size:2 final size:2
Alignment explanation
Indices: 3493784--3493809 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3493774 ATCGGGGATC
3493784 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
3493810 TTACTCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3494074 original size:55 final size:55
Alignment explanation
Indices: 3493987--3494097 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
3493977 TTAATATCTT
* * * *
3493987 CGTCCTTCTCGTGTCTCTGCCCCCATTAATCCCTTGTTTACTCTTTCAAGCTAAA
1 CGTCCTTCTCATGTCTCTACCCCCATTAATCCCTTGCTTACTCTTTCAAGCAAAA
* *
3494042 CGTCCTTCTCATGTCTCTACCCCCATTGATCCCTTGCTTATTCTTTCAAGCAAAA
1 CGTCCTTCTCATGTCTCTACCCCCATTAATCCCTTGCTTACTCTTTCAAGCAAAA
3494097 C
1 C
3494098 ATGTTTGTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.18, C:0.35, G:0.10, T:0.37
Consensus pattern (55 bp):
CGTCCTTCTCATGTCTCTACCCCCATTAATCCCTTGCTTACTCTTTCAAGCAAAA
Found at i:3494716 original size:17 final size:18
Alignment explanation
Indices: 3494680--3494723 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3494670 TAAAATTCAA
*
3494680 AATATAAAAATATTTAAAT
1 AATA-AAAAATATCTAAAT
3494699 AATAAAAAATATCT-AAT
1 AATAAAAAATATCTAAAT
3494716 -ATAAAAAA
1 AATAAAAAA
3494724 GGACTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 3 0.12
18 9 0.38
19 4 0.17
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAAAATATCTAAAT
Found at i:3494719 original size:16 final size:17
Alignment explanation
Indices: 3494679--3494723 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
3494669 TTAAAATTCA
*
3494679 AAATAT-AAAAATATTT
1 AAATATAAAAAATATCT
3494695 AAATAATAAAAAATATCT
1 AAAT-ATAAAAAATATCT
3494713 -AATATAAAAAA
1 AAATATAAAAAA
3494724 GGACTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 12 0.46
17 5 0.19
18 9 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATAAAAAATATCT
Found at i:3494746 original size:15 final size:15
Alignment explanation
Indices: 3494726--3494765 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3494716 ATAAAAAAGG
*
3494726 ACTAAAAATTAAATT
1 ACTAAAAATTAAAAT
*
3494741 ACTAAAAATAAAAAT
1 ACTAAAAATTAAAAT
*
3494756 ACTAACAATT
1 ACTAAAAATT
3494766 CTAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
ACTAAAAATTAAAAT
Found at i:3496613 original size:15 final size:15
Alignment explanation
Indices: 3496589--3496645 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
3496579 TTCTAGTAAG
3496589 TAAT-TTTTTATTTT
1 TAATATTTTTATTTT
*
3496603 TAATATTTTTATATT
1 TAATATTTTTATTTT
*
3496618 TAA-ACTTTTTGTTTT
1 TAATA-TTTTTATTTT
*
3496633 TGGATATTTTTAT
1 T-AATATTTTTAT
3496646 ATCTTAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 5 0.15
15 21 0.62
16 7 0.21
17 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (15 bp):
TAATATTTTTATTTT
Found at i:3496690 original size:20 final size:20
Alignment explanation
Indices: 3496654--3496692 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3496644 ATATCTTAAA
*
3496654 TTTTAAAATAAATATTATTT
1 TTTTAAAATAAAAATTATTT
3496674 TTTTAAAA-AATAAATTATT
1 TTTTAAAATAA-AAATTATT
3496693 GAACTTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATAAAAATTATTT
Found at i:3496997 original size:27 final size:27
Alignment explanation
Indices: 3496966--3497017 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3496956 GTAGTTTTTT
* * *
3496966 ATAATTTTATAAATTTTTTTTAAATTA
1 ATAATATTATAAAGTTTTTTAAAATTA
*
3496993 ATAATATTATTAAGTTTTTTAAAAT
1 ATAATATTATAAAGTTTTTTAAAAT
3497018 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATAATATTATAAAGTTTTTTAAAATTA
Found at i:3500891 original size:26 final size:26
Alignment explanation
Indices: 3500855--3500906 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3500845 TTACCTTAGG
3500855 TATCAATACCAAAAAGGGCATCAATA
1 TATCAATACCAAAAAGGGCATCAATA
*
3500881 TATCGATACCAAAAAGGGCATCAATA
1 TATCAATACCAAAAAGGGCATCAATA
3500907 CTCATCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (26 bp):
TATCAATACCAAAAAGGGCATCAATA
Found at i:3506623 original size:43 final size:43
Alignment explanation
Indices: 3506534--3506741 Score: 197
Period size: 43 Copynumber: 4.8 Consensus size: 43
3506524 TTTAAAAAAA
* * * * *
3506534 AATTATAAAAGTAAAAAATGAGATTTAAAAAATTAGGGGGCCTC
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTA-GGGTCTTC
*
3506578 AATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAAGGGTC-TC
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATT-AGGGTCTTC
* * *
3506621 AATTATACAA-GTAAAAAGTGCGGTTGAAAAAAAAATTAGGGACTTC
1 AATTATA-AAGGTAAAAAGTGAGATTG---AAAAAATTAGGGTCTTC
** ** *
3506667 AATTATAAATATAAAAAGTGAGATTGAAAAAATTAGACTCTTT
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGTCTTC
**
3506710 AATTATAAAGGTAAAAA-CAAGATTGAAAAAAT
1 AATTATAAAGGTAAAAAGTGAGATTGAAAAAAT
3506742 ATGTACTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
42 13 0.09
43 50 0.36
44 36 0.26
45 8 0.06
46 30 0.22
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (43 bp):
AATTATAAAGGTAAAAAGTGAGATTGAAAAAATTAGGGTCTTC
Found at i:3506670 original size:46 final size:46
Alignment explanation
Indices: 3506560--3506698 Score: 135
Period size: 46 Copynumber: 3.1 Consensus size: 46
3506550 AATGAGATTT
* * ** *
3506560 AAAAAATTAGGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTG---
1 AAAAAATTA-AGGGACTCAATTATAAATATAAAAAGTGAGATTGAAA
* * * *
3506604 AAAAAATTAAGGGTCTCAATTATACAA-GTAAAAAGTGCGGTTGAAA
1 AAAAAATTAAGGGACTCAATTATA-AATATAAAAAGTGAGATTGAAA
3506650 AAAAAATT-AGGGACTTCAATTATAAATATAAAAAGTGAGATTGAAA
1 AAAAAATTAAGGGAC-TCAATTATAAATATAAAAAGTGAGATTGAAA
3506696 AAA
1 AAA
3506699 TTAGACTCTT
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
43 26 0.32
44 11 0.14
45 7 0.09
46 36 0.45
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (46 bp):
AAAAAATTAAGGGACTCAATTATAAATATAAAAAGTGAGATTGAAA
Found at i:3506714 original size:89 final size:90
Alignment explanation
Indices: 3506560--3506726 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 90
3506550 AATGAGATTT
* * * **
3506560 AAAAAATTAGGGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAAGGGTCTCAATT
1 AAAAAATTAGGGGACCTCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAAGACTCTCAATT
3506625 ATACAA-GTAAAAAGTGCGGTTGAAA
66 ATA-AAGGTAAAAAGTGCGGTTGAAA
* * *
3506650 AAAAAATTA-GGGACTTCAATTATAAATATAAAAAGTGAGATTGAAAAAATT-AGACTCTTTAAT
1 AAAAAATTAGGGGACCTCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAAGACTC-TCAAT
3506713 TATAAAGGTAAAAA
65 TATAAAGGTAAAAA
3506727 CAAGATTGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 6 0.09
89 52 0.78
90 9 0.13
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.26
Consensus pattern (90 bp):
AAAAAATTAGGGGACCTCAATTATAAAGATAAAAAGTGAGATTGAAAAAATTAAGACTCTCAATT
ATAAAGGTAAAAAGTGCGGTTGAAA
Found at i:3516439 original size:31 final size:31
Alignment explanation
Indices: 3516401--3516461 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3516391 ATTGTCAATG
3516401 ACGTGGTAAATCTTATATGTCTAAAGTGATT
1 ACGTGGTAAATCTTATATGTCTAAAGTGATT
*
3516432 ACGTGGTAAATCTTATGTGTCTAAAGTGAT
1 ACGTGGTAAATCTTATATGTCTAAAGTGAT
3516462 GACATGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (31 bp):
ACGTGGTAAATCTTATATGTCTAAAGTGATT
Found at i:3516479 original size:31 final size:31
Alignment explanation
Indices: 3516407--3516501 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
3516397 AATGACGTGG
* * * *
3516407 TAAATCTTATATGTCTAAAGTGATTACGTGG
1 TAAATCTTATGTGTCTAAAGTGATAACATGA
*
3516438 TAAATCTTATGTGTCTAAAGTGATGACATGA
1 TAAATCTTATGTGTCTAAAGTGATAACATGA
* *
3516469 TATATGTTATGTGT-TCAAAGTGATAACATGA
1 TAAATCTTATGTGTCT-AAAGTGATAACATGA
3516500 TA
1 TA
3516502 CATATCTCTT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (31 bp):
TAAATCTTATGTGTCTAAAGTGATAACATGA
Found at i:3518004 original size:17 final size:18
Alignment explanation
Indices: 3517984--3518018 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3517974 TTATTTTAGA
*
3517984 TCAAT-TATTAAATAAAT
1 TCAATATATTAAAGAAAT
3518001 TCAATATATTAAAGAAAT
1 TCAATATATTAAAGAAAT
3518019 ATAAAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (18 bp):
TCAATATATTAAAGAAAT
Found at i:3529429 original size:183 final size:183
Alignment explanation
Indices: 3529121--3529488 Score: 736
Period size: 183 Copynumber: 2.0 Consensus size: 183
3529111 GTTTTTGCTG
3529121 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
1 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
3529186 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
66 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
3529251 CTTAAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
131 CTTAAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
3529304 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
1 CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
3529369 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
66 CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
3529434 CTTAAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
131 CTTAAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
3529487 CT
1 CT
3529489 AAACAGTCAG
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 185 1.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (183 bp):
CTTCATATGTAGACCAGCAGATTGCAGCAGCAGGAGCATGGAAAAGCATTCGGGGAATCCATCCC
CTCATGAGGCCCTTGTAGCCGTCCTTTCGCACAATTGTTTCAACCACATCCCCAATAGAACTACT
CTTAAATCTATCACACCCGCATACACCCTGTTATACAATTTTTAATAACAATA
Found at i:3537163 original size:179 final size:178
Alignment explanation
Indices: 3536863--3537220 Score: 682
Period size: 179 Copynumber: 2.0 Consensus size: 178
3536853 TCGTTGATTA
3536863 CCTCATATGTTTAATCGATCTTGTCTTGGTGGATCACTGGCATTGTCGAATTGATTCATTCTATT
1 CCTCATATGTTTAATCGATCTTGTCTTGGTGGATCACTGGCATTGTCGAATTGATTCATTC-ATT
3536928 GTTCATGGCGGCCATTTGTTTGAATTCCAACAACTGTAGCTGTTAGTGTGGCTAATGTGTTTGCC
65 GTTCATGGCGGCCATTTGTTTGAATTCCAACAACTGTAGCTGTTAGTGTGGCTAATGTGTTTGCC
3536993 ATGTTTTCAGGTTTTACCAGTTGAATCTCCAGTTCTTTGTTCTTGTCTT
130 ATGTTTTCAGGTTTTACCAGTTGAATCTCCAGTTCTTTGTTCTTGTCTT
3537042 CCTCATATGTTTAATCGATCTTGTCTTGGTGGATCACTGGCATTGTCGAATTGATTCATTC-TTG
1 CCTCATATGTTTAATCGATCTTGTCTTGGTGGATCACTGGCATTGTCGAATTGATTCATTCATTG
3537106 TTCATGGCGGCCATTTGTTGTTGAATTCCAACAACTGTAGCTGTTAGTGTGGCTAATGTGTTTGC
66 TTCATGGCGGCCATTTG-T-TTGAATTCCAACAACTGTAGCTGTTAGTGTGGCTAATGTGTTTGC
3537171 CATGTTTTCAGGTTTTACCAGTTGAATCTCCAGTTCTTTGTTCTTGTCTT
129 CATGTTTTCAGGTTTTACCAGTTGAATCTCCAGTTCTTTGTTCTTGTCTT
3537221 TTGTGAAAAT
Statistics
Matches: 177, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
177 20 0.11
178 1 0.01
179 156 0.88
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (178 bp):
CCTCATATGTTTAATCGATCTTGTCTTGGTGGATCACTGGCATTGTCGAATTGATTCATTCATTG
TTCATGGCGGCCATTTGTTTGAATTCCAACAACTGTAGCTGTTAGTGTGGCTAATGTGTTTGCCA
TGTTTTCAGGTTTTACCAGTTGAATCTCCAGTTCTTTGTTCTTGTCTT
Found at i:3540778 original size:21 final size:20
Alignment explanation
Indices: 3540752--3540850 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
3540742 ATCAGTTTCC
3540752 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
3540773 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
3540792 ACAAATTCGCATTGCGATTTTCCA
1 A-AAA-TCGCAACGCGATTTT--G
* *
3540816 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
3540836 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3540851 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 27 0.44
22 11 0.18
23 3 0.05
24 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:3540879 original size:20 final size:20
Alignment explanation
Indices: 3540817--3541008 Score: 191
Period size: 20 Copynumber: 9.8 Consensus size: 20
3540807 GATTTTCCAA
* ** *
3540817 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
3540837 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
3540857 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3540877 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
3540897 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
3540917 AAATCTGCAA----TATCCGT
1 AAATC-GCAACGCGTATCCGT
*
3540934 ATATCGC-ACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
3540953 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
3540973 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
3540993 AAATCGCAACGCGTAT
1 AAATCGCAACGCGTAT
3541009 TTAAAGCGCC
Statistics
Matches: 142, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
15 1 0.01
16 2 0.01
17 9 0.06
19 15 0.11
20 109 0.77
21 6 0.04
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:3540975 original size:56 final size:56
Alignment explanation
Indices: 3540870--3541008 Score: 156
Period size: 56 Copynumber: 2.4 Consensus size: 56
3540860 TCGCAACGCG
* * **
3540870 TATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCTGCAA
1 TATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCATATCCGTAAATC-GCAA
*
3540927 TATCCGTATATCGC-ACGCGTATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAACGA
1 TATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCAT-ATCCGTAAATCGC-A--A
*
3540985 GAATCCGTAAATCGCAACGCGTAT
1 -TATCCGTAAATCGCAACGCGTAT
3541009 TTAAAGCGCC
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
55 3 0.04
56 32 0.46
57 13 0.19
58 1 0.01
59 12 0.17
60 8 0.12
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (56 bp):
TATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCATATCCGTAAATCGCAA
Found at i:3540995 original size:76 final size:76
Alignment explanation
Indices: 3540859--3541001 Score: 209
Period size: 76 Copynumber: 1.9 Consensus size: 76
3540849 GAACACATAA
* * * **
3540859 ATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCTG
1 ATCGCAACGCGTATCCGTAAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATC-G
3540924 CAATATCCGTAT
65 CAATATCCGTAT
3540936 ATCGC-ACGCGTATCCGTAAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCCGTAAATCG
1 ATCGCAACGCGTATCCGTAAATCGCAACG-TGAATCCGTAAATCGCAACGAGAATCCGTAAATCG
3540999 CAA
65 CAA
3541002 CGCGTATTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
75 4 0.07
76 50 0.83
77 6 0.10
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (76 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGTGAATCCGTAAATCGCAACGAGAATCCGTAAATCGC
AATATCCGTAT
Found at i:3541415 original size:33 final size:33
Alignment explanation
Indices: 3541376--3541446 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
3541366 TTCACTTAGA
*
3541376 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
3541409 TTTCATTTCGTGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3541442 TTTCA
1 TTTCA
3541447 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3541564 original size:19 final size:20
Alignment explanation
Indices: 3541519--3541627 Score: 99
Period size: 19 Copynumber: 5.8 Consensus size: 20
3541509 TTTGCAGAAG
* *
3541519 TCGCAACGAGATAAATTAAAA
1 TCGCAACGAGA-GAATGAAAA
**
3541540 TCGCAACGAGAGAATG-ATG
1 TCGCAACGAGAGAATGAAAA
3541559 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
3541580 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
3541594 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
3541613 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
3541628 CGCAACGCGA
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
14 9 0.12
16 4 0.06
17 2 0.03
19 28 0.39
20 10 0.14
21 19 0.26
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:3541580 original size:40 final size:38
Alignment explanation
Indices: 3541517--3541627 Score: 142
Period size: 40 Copynumber: 3.0 Consensus size: 38
3541507 AATTTGCAGA
* *
3541517 AGTCGCAACGAGATAAATTAAAATCGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
3541555 GATGTCGCAACGAGAGAAATGAAAATCGCAACGAGAG-A-
1 -A-GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
*
3541593 A-TCGCAAC--GCGAAATGAAAATCGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
3541628 CGCAACGCGA
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
33 23 0.35
34 1 0.02
35 7 0.11
37 1 0.02
39 2 0.03
40 32 0.48
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (38 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
Found at i:3541591 original size:21 final size:21
Alignment explanation
Indices: 3541519--3541593 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3541509 TTTGCAGAAG
* *
3541519 TCGCAACGAGATAAATTAAAA
1 TCGCAACGAGAGAAATGAAAA
**
3541540 TCGCAACGAGAG-AATG-ATG
1 TCGCAACGAGAGAAATGAAAA
3541559 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
3541580 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
3541594 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 13 0.28
20 7 0.15
21 26 0.57
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:3541597 original size:14 final size:14
Alignment explanation
Indices: 3541578--3541634 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3541568 GAGAAATGAA
3541578 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3541592 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3541611 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3541625 AATCGCAACG
1 AATCGCAACG
3541635 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3541610 original size:33 final size:33
Alignment explanation
Indices: 3541570--3541650 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3541560 CGCAACGAGA
3541570 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3541603 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3541636 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
3541651 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3541668 original size:19 final size:19
Alignment explanation
Indices: 3541646--3541718 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
3541636 GAAACCAAAA
*
3541646 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3541665 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* *
3541679 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
3541698 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3541717 TC
1 TC
3541719 AACCAAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.23
16 2 0.05
17 3 0.07
19 29 0.66
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3552312 original size:17 final size:17
Alignment explanation
Indices: 3552290--3552328 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3552280 ACAAGAATCT
*
3552290 TCTTCCGCCTTACTGCC
1 TCTTCCGCCTAACTGCC
3552307 TCTTCCGCCTAACTGCC
1 TCTTCCGCCTAACTGCC
3552324 TCTTC
1 TCTTC
3552329 TCGCTCGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.08, C:0.46, G:0.10, T:0.36
Consensus pattern (17 bp):
TCTTCCGCCTAACTGCC
Found at i:3554885 original size:36 final size:38
Alignment explanation
Indices: 3554830--3554920 Score: 105
Period size: 40 Copynumber: 2.4 Consensus size: 38
3554820 GAAAAATTAT
*
3554830 TAACTTTATTTACACCTGTGTGAG-A-CTTTTTTCCCTC
1 TAAC-TTATTTACACCTGTGTGAGAAGCCTTTTTCCCTC
* * *
3554867 TAACTTATTTATAGCTGTGTGAGATAGTCCTTTTTCCCTT
1 TAACTTATTTACACCTGTGTGAGA-AG-CCTTTTTCCCTC
3554907 TAACTTATTTACAC
1 TAACTTATTTACAC
3554921 TGGTGTAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 17 0.39
37 4 0.09
38 1 0.02
40 22 0.50
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (38 bp):
TAACTTATTTACACCTGTGTGAGAAGCCTTTTTCCCTC
Found at i:3559615 original size:42 final size:42
Alignment explanation
Indices: 3559556--3559671 Score: 223
Period size: 42 Copynumber: 2.8 Consensus size: 42
3559546 CCCGAATTCT
*
3559556 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
3559598 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
3559640 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
3559672 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
Found at i:3559901 original size:28 final size:30
Alignment explanation
Indices: 3559869--3559942 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 30
3559859 AAATATTTAA
3559869 AATATATTATTAATATT-TATAATAAT-AT-
1 AATATATTATTAATATTATATAA-AATAATC
*
3559897 AATATATTTTTAATATTATATAAAATAATC
1 AATATATTATTAATATTATATAAAATAATC
3559927 AATTATATTA-TAATAT
1 AA-TATATTATTAATAT
3559943 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
28 19 0.47
29 7 0.17
30 8 0.20
31 6 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
AATATATTATTAATATTATATAAAATAATC
Found at i:3559970 original size:29 final size:28
Alignment explanation
Indices: 3559936--3560028 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
3559926 CAATTATATT
3559936 ATAATATAAGATATTATATTTT-TAT-TTTA
1 ATAATATAAGA-ATT-T-TTTTATATATTTA
*
3559965 ATAATATAATAATTTTTTTATATATTTA
1 ATAATATAAGAATTTTTTTATATATTTA
* * *
3559993 ATAAT-GAATAATATTATTTATATATTTCA
1 ATAATATAAGAAT-TTTTTTATATATTT-A
3560022 ATAATAT
1 ATAATAT
3560029 TTTAGTAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.07
27 10 0.18
28 25 0.45
29 16 0.29
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATAATATAAGAATTTTTTTATATATTTA
Found at i:3560012 original size:28 final size:28
Alignment explanation
Indices: 3559952--3560027 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 28
3559942 TAAGATATTA
* *
3559952 TATTTTTAT-TTTAATAATATAATAATT
1 TATTTATATATTTAATAATAGAATAATT
*
3559979 TTTTTATATATTTAATAAT-GAATAATAT
1 TATTTATATATTTAATAATAGAATAAT-T
3560007 TATTTATATATTTCAATAATA
1 TATTTATATATTT-AATAATA
3560028 TTTTAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 13 0.32
28 22 0.54
29 6 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TATTTATATATTTAATAATAGAATAATT
Found at i:3560272 original size:20 final size:20
Alignment explanation
Indices: 3560194--3560263 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
3560184 TTTCCAGATG
3560194 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3560214 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
3560234 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3560254 TTTTCCAGAA
1 TTTTCCAGAA
3560264 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:3560272 original size:40 final size:40
Alignment explanation
Indices: 3560194--3560272 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
3560184 TTTCCAGATG
* **
3560194 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
3560234 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
3560273 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:3560282 original size:15 final size:15
Alignment explanation
Indices: 3560246--3560327 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
3560236 TTACAGAAAT
**
3560246 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
3560261 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
3560275 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
3560290 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
3560305 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
3560320 GTAATTCA
1 GTAATTCA
3560328 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:3560298 original size:30 final size:30
Alignment explanation
Indices: 3560246--3560327 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
3560236 TTACAGAAAT
3560246 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
3560275 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
3560305 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
3560328 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:3560320 original size:45 final size:44
Alignment explanation
Indices: 3560246--3560332 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
3560236 TTACAGAAAT
**
3560246 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
3560290 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
3560333 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:3563535 original size:29 final size:29
Alignment explanation
Indices: 3563453--3563535 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
3563443 TTATTAAAGT
* *
3563453 ATATTTTATTATATTTAATATTTTT--TTA
1 ATATTTTATT-TAATTAATTTTTTTGCTTA
* * *
3563481 GTAATTTATTTAATT-ATTTTAATTGCTTA
1 ATATTTTATTTAATTAATTTT-TTTGCTTA
3563510 ATATTTTATTTAATTAATTTTTTTGC
1 ATATTTTATTTAATTAATTTTTTTGC
3563536 AGATATAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
26 4 0.09
27 6 0.14
28 8 0.19
29 20 0.47
30 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (29 bp):
ATATTTTATTTAATTAATTTTTTTGCTTA
Found at i:3564821 original size:19 final size:19
Alignment explanation
Indices: 3564797--3564839 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
3564787 CGTGCTCCGG
3564797 CAATTTGGTTGTTTTCAAC
1 CAATTTGGTTGTTTTCAAC
3564816 CAATTTGGTTGTTTTCAAC
1 CAATTTGGTTGTTTTCAAC
3564835 CAATT
1 CAATT
3564840 CCGGAAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (19 bp):
CAATTTGGTTGTTTTCAAC
Found at i:3569991 original size:21 final size:22
Alignment explanation
Indices: 3569961--3570013 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
3569951 ACTTTATCCT
* *
3569961 ATTAATATTATACT-AAATAAA
1 ATTATTATTATAATCAAATAAA
3569982 A-TATTAATTA-AATCAAATAAA
1 ATTATT-ATTATAATCAAATAAA
3570003 ATTATTATTAT
1 ATTATTATTAT
3570014 TTCAACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 5 0.19
21 17 0.65
22 4 0.15
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATTATTATAATCAAATAAA
Found at i:3571789 original size:61 final size:61
Alignment explanation
Indices: 3571694--3571824 Score: 244
Period size: 61 Copynumber: 2.1 Consensus size: 61
3571684 TTAATCATAC
*
3571694 ACCCTTTTAATAGCATGATTCATAATTAAATATGGATGTGCTTCTTGATTATATCAATAGT
1 ACCCTTTTAATAGCATGATTCATAATTAAATATGGACGTGCTTCTTGATTATATCAATAGT
*
3571755 ACCCTTTTAATAGCATGATTCATAATTAAATATGGACGTGCTTCTTGATTATATCAATATT
1 ACCCTTTTAATAGCATGATTCATAATTAAATATGGACGTGCTTCTTGATTATATCAATAGT
3571816 ACCCTTTTA
1 ACCCTTTTA
3571825 TTAGAATTTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (61 bp):
ACCCTTTTAATAGCATGATTCATAATTAAATATGGACGTGCTTCTTGATTATATCAATAGT
Found at i:3573737 original size:4 final size:4
Alignment explanation
Indices: 3573728--3573753 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3573718 AAAATGTGGC
3573728 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3573754 TCTAGGGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:3575905 original size:32 final size:33
Alignment explanation
Indices: 3575864--3575941 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
3575854 TTTAAATAGT
* *
3575864 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
3575896 TATTATTTTTTATTAAAATAATATTTATATAAA
1 TATTATTTTTTATTAAAATAATATTTATATAAA
3575929 TATTATTTATTTA
1 TATTATTT-TTTA
3575942 GAATTATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 15 0.37
33 22 0.54
34 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:3576104 original size:17 final size:17
Alignment explanation
Indices: 3576082--3576135 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3576072 AATGTTAATA
3576082 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
3576099 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
3576116 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
3576133 TTT
1 TTT
3576136 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Done.