Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 17
Found at i:4297873 original size:22 final size:21
Alignment explanation
Indices: 4297777--4297898 Score: 102
Period size: 22 Copynumber: 5.5 Consensus size: 21
4297767 AAGAGAGAAA
*
4297777 AAAAGAAAAAAGAGAAAAAAAGG
1 AAAAGAAAAAAGAG-AAAAGA-G
* *
4297800 AAAA-AAGAAAGAGAAAAGAA
1 AAAAGAAAAAAGAGAAAAGAG
*
4297820 AGAAAGAAAAAGATAGAAAAAGAG
1 A-AAAGAAAAA-AGAG-AAAAGAG
* *
4297844 AAAAGAGAAAAGAGAAAAGAA
1 AAAAGAAAAAAGAGAAAAGAG
* *
4297865 AAAAGGAGAAAAGAGAAAAGAA
1 AAAA-GAAAAAAGAGAAAAGAG
4297887 AAGAAGAAAAAA
1 AA-AAGAAAAAA
4297899 AAATTGAATC
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.01
21 18 0.22
22 40 0.48
23 17 0.20
24 7 0.08
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (21 bp):
AAAAGAAAAAAGAGAAAAGAG
Found at i:4298927 original size:51 final size:51
Alignment explanation
Indices: 4298862--4299052 Score: 278
Period size: 51 Copynumber: 3.7 Consensus size: 51
4298852 CATATTATCC
*
4298862 ATGT-GGGTATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCT
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCT
* * *
4298912 ATGTGTGGCATCTTGAAGGCTCACATCAGCATAAAAAAGATAGAAGTAATCC
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCAT-GAAAAGATAGAAGTAATCT
* *
4298964 ATATGGGGCATCTTGAAGGCTCCCATCAGCATGAAAAGATAGAAGTAAT-T
1 ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCT
* *
4299014 CATGTGGGGTATCTTGAAGGCTCACACCAGCATGAAAAG
1 -ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAG
4299053 GTTGGGATAT
Statistics
Matches: 125, Mismatches: 13, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
50 4 0.03
51 75 0.60
52 46 0.37
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (51 bp):
ATGTGGGGCATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCT
Found at i:4300938 original size:177 final size:177
Alignment explanation
Indices: 4300639--4301169 Score: 845
Period size: 177 Copynumber: 3.0 Consensus size: 177
4300629 TATTTCCCGA
* * * *
4300639 ATTTGTAAGTCTTTCGGGCCATCCATAATACCTTCAATGCAGGATGTTTTCAAATGAGATTTTAG
1 ATTTGTAAGTCATACGGGCCATCCATAACACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
*
4300704 AAACTAAGCCTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
66 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
* *
4300769 AAGGGGTTCCTTAACAACTAAGAAACTAAGCCTTCGGGGGTTTATTG
131 AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
* *
4300816 ATTTGTAAGTCATACGGGCCATCCATAAGATCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
1 ATTTGTAAGTCATACGGGCCATCCATAACACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
* * * *
4300881 AAACTAAGTCTTTGGGGGTTTCCTAATTATCTCAAAAGAGTTATTAAAGGGAGCTAAGCCTAACA
66 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
*
4300946 AAGGGGCTCCTTGACAACTAAGAAACTAAGCC-TC-GGGGTTTCTTG
131 AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
* * *
4300991 ATTTGTAAGTCCTACAGGCCATCCAT--CACCTTCAGTGCAGGATGTTTTTAAATGAGATTTTAG
1 ATTTGTAAGTCATACGGGCCATCCATAACACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
* * *
4301054 AAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACA
66 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
*
4301119 AAGGGGTTCCTTGACAACTAAGAAACTAAGCTTTCGGGGGTTTCTTG
131 AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
4301166 ATTT
1 ATTT
4301170 ATAGAATTCG
Statistics
Matches: 325, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
173 122 0.38
174 2 0.01
175 49 0.15
176 2 0.01
177 150 0.46
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (177 bp):
ATTTGTAAGTCATACGGGCCATCCATAACACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
Found at i:4301413 original size:124 final size:124
Alignment explanation
Indices: 4301187--4301479 Score: 462
Period size: 124 Copynumber: 2.4 Consensus size: 124
4301177 TCGTAATAAA
* * *
4301187 AAGAACTCATCTGAACAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGT
1 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGA
** * * *
4301252 CTCTATCGTAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATCTG
66 CTCTATCACAGAAGGAGATAGAGCAACAGAGCCATTTCCATAAAGGAGTTCATAATCTG
*
4301311 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTGCTTGA
1 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGA
* * *
4301376 CTCTATCACAGAAGGAGATGGTGCAACAGATCCATTTCCATAAAGGAGTTCATAATCTG
66 CTCTATCACAGAAGGAGATAGAGCAACAGAGCCATTTCCATAAAGGAGTTCATAATCTG
*
4301435 AAGAACTCGTCTGAAGAGG-AGAAGAAGTTCATAATCTGAAGAACT
1 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACT
4301480 CGTCTGAAGA
Statistics
Matches: 156, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
123 25 0.16
124 131 0.84
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (124 bp):
AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGA
CTCTATCACAGAAGGAGATAGAGCAACAGAGCCATTTCCATAAAGGAGTTCATAATCTG
Found at i:4301508 original size:39 final size:38
Alignment explanation
Indices: 4301422--4301556 Score: 198
Period size: 39 Copynumber: 3.5 Consensus size: 38
4301412 TCCATAAAGG
*
4301422 AGTTCATAATCTGAAGAACTCGTCTGAAGAGGAGAAGA
1 AGTTCATAATCTGAAGAACTCGTCTGAAGAGAAGAAGA
4301460 AGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGA
1 AGTTCATAATCTGAAGAACTCGTCTGAAGA-GAAGAAGA
* * *
4301499 AGTTCATAATCTGAAGAACTCATTTGAAGAGAAAGAATA
1 AGTTCATAATCTGAAGAACTCGTCTGAAGAG-AAGAAGA
* *
4301538 AGTTAATAATATGAAGAAC
1 AGTTCATAATCTGAAGAAC
4301557 GTATTTAACT
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
38 31 0.35
39 58 0.65
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (38 bp):
AGTTCATAATCTGAAGAACTCGTCTGAAGAGAAGAAGA
Found at i:4301515 original size:20 final size:20
Alignment explanation
Indices: 4301454--4301516 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
4301444 TCTGAAGAGG
4301454 AGAAGAAGTTCATAATCTGA
1 AGAAGAAGTTCATAATCTGA
*** **
4301474 AGAACTCG-TC-TGAAGATGA
1 AGAAGAAGTTCAT-AATCTGA
4301493 AGAAGAAGTTCATAATCTGA
1 AGAAGAAGTTCATAATCTGA
4301513 AGAA
1 AGAA
4301517 CTCATTTGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 16 0.53
21 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (20 bp):
AGAAGAAGTTCATAATCTGA
Found at i:4301591 original size:201 final size:200
Alignment explanation
Indices: 4301298--4301679 Score: 509
Period size: 201 Copynumber: 1.9 Consensus size: 200
4301288 TCCATACAGG
* * * * * *
4301298 AGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCA
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCA
* *
4301363 ACCTTTTGCTTGACTCTATCACAGAAGGAGATGGTGCAACAGATC-CATTTCCATAAAGGAGTTC
66 ACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAAC--ATCACATTTCCAT-AAGGAGTTC
** * *
4301427 ATAATCTGAAGAACTCGTCTGAAG-AGGAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAT
128 ATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAT
4301491 GAAGAAGA
193 GAAGAAGA
* * *
4301499 AGTTCATAATCTGAAGAACTCATTTGAAGAGAAAGAATAAGTTAATAATATGAAGAACGTATTTA
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCA
* * * * *
4301564 ACTTTTTG-TTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCATAAGGAGTTCG
66 ACCTTTTGCTT-GACTCTATCACAGAAGGAGATAGAGCAACATC-ACATTTCCATAAGGAGTTCA
*
4301628 TAATAAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAAC
129 TAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAAC
4301680 ATATTCAACA
Statistics
Matches: 156, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
199 3 0.02
200 30 0.19
201 123 0.79
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (200 bp):
AGTTCATAATCTGAAGAACTCATCTGAAGAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCA
ACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAACATCACATTTCCATAAGGAGTTCATA
ATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAA
GAAGA
Found at i:4301658 original size:123 final size:123
Alignment explanation
Indices: 4301493--4302063 Score: 721
Period size: 123 Copynumber: 4.6 Consensus size: 123
4301483 CTGAAGATGA
* * ** * * * *
4301493 AGAAGAAGTTCATAATCTGAAGAACTCATTTGAAG-AGAAAGAATAAGTTAATAATATGAAGAAC
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCATAATCTGAAGAAC
* * * *
4301557 GTATTTAACTTTTTGTTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
65 ATATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* *
4301616 ATAAGGAGTTCGTAATAAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* * * * *
4301681 TATTCAACATTTTTGCTCGATTCTATCGTAGAATGAGATATAGCAGCATTAACATTTCC
66 TATTCAAC-CTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* * * *
4301740 AGAAAGAGTTCGTAATAAGAAGAACTCGTCTGAAGAGGAAGAAAAAGTTCATAATCTGAAGAACA
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* * * * *
4301805 TATTCAACCTTTTGCTCGATTATATCGCATAAGGAGATAGAGCAGTATCAACGTTTCT
66 TATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* * *
4301863 AGAAGGAGTTCGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACG
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* * * * *
4301928 TATTCAACCTTTTGCTTGACTGTATCGCAAAAGGAGATAGAGCAGCATCAACGTTTCC
66 TATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* * * ** *
4301986 AGAAGGAGTTCGTAATAAAAAGAACTCATATGAAGAAGAAGAAGAAGTTTATAATAAGAAGAACT
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* *
4302051 TGTTCAACATTTT
66 TATTCAACCTTTT
4302064 CATCTTAATC
Statistics
Matches: 393, Mismatches: 53, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
123 279 0.71
124 114 0.29
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (123 bp):
AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
TATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
Found at i:4301790 original size:325 final size:325
Alignment explanation
Indices: 4301187--4301803 Score: 775
Period size: 325 Copynumber: 1.9 Consensus size: 325
4301177 TCGTAATAAA
* * * * *
4301187 AAGAACTCATCTGAACAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGT
1 AAGAACTCATCTGAACAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCAACCTTTTACTTGT
* **
4301252 CTCTATCGTAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATCTGAAGAAC
66 CTCTATCGCAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATAAGAAGAAC
* * * * *
4301317 TCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTGCTTGACTCTAT
131 TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTCGACTCTAT
* * * **
4301382 CACAGAAGGAGATGGTGCAACAGATCCATTTCCATAAAGGAGTTCATAATCTGAAGAACTCGTCT
196 CACAGAAGGAGATGATGCAACAGATACATTTCCAGAAAGGAGTTCATAATAAGAAGAACTCGTCT
*
4301447 GAAGAGGAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGAAGTTCATAATCTG
261 GAAGAGGAGAAAAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGAAGTTCATAATCTG
* * * * **
4301512 AAGAACTCATTTGAAGAGAAAGAATAAGTTAATAATATGAAGAACGTATTTAA-CTTTTTGTTCG
1 AAGAACTCATCTGAACAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCAACCTTTTACTT-G
*
4301576 AT-TCTATCGCAGAAGGAGATAGAGCAGCATCA-A-C-ATTTCCATA-AGGAGTTCGTAATAAGA
65 -TCTCTATCGCAGAAGGAGATAGAGCA--AT-AGAGCTATTTCCATACAGGAGTTCATAATAAGA
* *
4301636 AGAATTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACATTTTTGCTCGA
126 AGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAAC-CTTTTGCTCGA
* ** * * * *
4301701 TTCTATCGTAGAATGAGAT-ATAGCAGCA-TTAACATTTCCAGAAA-GAGTTCGTAATAAGAAGA
190 CTCTATCACAGAAGGAGATGAT-GCAACAGAT-ACATTTCCAGAAAGGAGTTCATAATAAGAAGA
4301763 ACTCGTCTGAAGAGGAAGAAAAAGTTCATAATCTGAAGAAC
253 ACTCGTCTGAAGAGG-AGAAAAAGTTCATAATCTGAAGAAC
4301804 ATATTCAACC
Statistics
Matches: 248, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
324 101 0.41
325 141 0.57
326 2 0.01
327 3 0.01
328 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (325 bp):
AAGAACTCATCTGAACAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCAACCTTTTACTTGT
CTCTATCGCAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATAAGAAGAAC
TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTCGACTCTAT
CACAGAAGGAGATGATGCAACAGATACATTTCCAGAAAGGAGTTCATAATAAGAAGAACTCGTCT
GAAGAGGAGAAAAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGAAGTTCATAATCTG
Found at i:4301875 original size:247 final size:246
Alignment explanation
Indices: 4301511--4302063 Score: 737
Period size: 247 Copynumber: 2.2 Consensus size: 246
4301501 TTCATAATCT
* * * * * * *
4301511 GAAGAACTCATTTGAAGAGAAAGAATAAGTTAATAATATGAAGAACGTATTTAACTTTTTGTTCG
1 GAAGAACTCATATGAAGAGGAAGAAAAAGTTAATAATATGAAGAACATATTCAACATTTTGCTCG
* * *
4301576 ATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCATAAGGAGTTCGTAATAAGAAGAAT
66 ATTATATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAAC
* *
4301641 TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACATTTTTGCTCGATTCTA
131 TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAAC-CTTTTGCTCGACTCTA
* * * * *
4301706 TCGTAGAATGAGATATAGCAGCATTAACATTTCCAGAAAGAGTTCGTAATAA
195 TCGCAAAAGGAGATAGAGCAGCATCAACATTTCCAGAAAGAGTTCGTAATAA
* * * * *
4301758 GAAGAACTCGTCTGAAGAGGAAGAAAAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTCG
1 GAAGAACTCATATGAAGAGGAAGAAAAAGTTAATAATATGAAGAACATATTCAACATTTTGCTCG
* * * *
4301823 ATTATATCGCATAAGGAGATAGAGCAGTATCAACGTTTCTAGAAGGAGTTCGTAATAAGAAGAAC
66 ATTATATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAAC
* * * * *
4301888 TCATTTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACGTATTCAACCTTTTGCTTGACTGTAT
131 TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTCGACTCTAT
* *
4301953 CGCAAAAGGAGATAGAGCAGCATCAACGTTTCCAGAAGGAGTTCGTAATAA
196 CGCAAAAGGAGATAGAGCAGCATCAACATTTCCAGAAAGAGTTCGTAATAA
* * * * * * *
4302004 AAAGAACTCATATGAAGAAGAAGAAGAAGTTTATAATAAGAAGAACTTGTTCAACATTTT
1 GAAGAACTCATATGAAGAGGAAGAAAAAGTTAATAATATGAAGAACATATTCAACATTTT
4302064 CATCTTAATC
Statistics
Matches: 264, Mismatches: 42, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
246 106 0.40
247 158 0.60
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (246 bp):
GAAGAACTCATATGAAGAGGAAGAAAAAGTTAATAATATGAAGAACATATTCAACATTTTGCTCG
ATTATATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCAGAAGGAGTTCGTAATAAGAAGAAC
TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTCGACTCTAT
CGCAAAAGGAGATAGAGCAGCATCAACATTTCCAGAAAGAGTTCGTAATAA
Found at i:4302192 original size:3 final size:3
Alignment explanation
Indices: 4302184--4302244 Score: 99
Period size: 3 Copynumber: 21.0 Consensus size: 3
4302174 TTTCTCCCAT
*
4302184 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4302231 TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
4302245 AGTGATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4302217 original size:23 final size:23
Alignment explanation
Indices: 4302188--4302244 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
4302178 TCCCATTTAT
*
4302188 TATTATTATTATTATTATTATTA
1 TATTATTATTATTATTATCATTA
*
4302211 TATTATTATTATTATTATCATTT
1 TATTATTATTATTATTATCATTA
4302234 TATTATTATTA
1 TATTATTATTA
4302245 AGTGATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTATTATTATTATCATTA
Found at i:4303805 original size:2 final size:2
Alignment explanation
Indices: 4303798--4303824 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4303788 AAAACCTTAA
4303798 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
4303825 CTTTAGTTTT
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:4304826 original size:3 final size:3
Alignment explanation
Indices: 4304818--4304886 Score: 54
Period size: 3 Copynumber: 22.7 Consensus size: 3
4304808 AATTTTTTCA
* *
4304818 TAT TAT TAT TTT TCA- TAT TAT TAT TAT TAT TAT ATAT TAT AAT T-T
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
4304863 ATAT TAT TAT AAAT T-T TAT TAT TA
1 -TAT TAT TAT -TAT TAT TAT TAT TA
4304887 ATAATAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 4 0.08
3 43 0.81
4 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:4304873 original size:15 final size:15
Alignment explanation
Indices: 4304817--4304891 Score: 66
Period size: 15 Copynumber: 4.9 Consensus size: 15
4304807 TAATTTTTTC
*
4304817 ATATTATTAT-TTTT
1 ATATTATTATAATTT
*
4304831 CATATTATTATTA-TT
1 -ATATTATTATAATTT
4304846 ATTATATATTATAATTT
1 A-TAT-TATTATAATTT
4304863 ATATTATTATAAATTT
1 ATATTATTAT-AATTT
4304879 -TATTATTAATAAT
1 ATATTATT-ATAAT
4304892 AAATAAATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.02
15 31 0.60
16 17 0.33
17 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTATTATAATTT
Found at i:4304891 original size:31 final size:31
Alignment explanation
Indices: 4304832--4304891 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
4304822 ATTATTTTTC
*
4304832 ATATTATTATTATTATTATATATTATAATTT
1 ATATTATTATAATTATTATATATTATAATTT
4304863 ATATTATTATAAATT-TTAT-TATTAATAAT
1 ATATTATTAT-AATTATTATATATT-ATAAT
4304892 AAATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 19 0.73
32 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
ATATTATTATAATTATTATATATTATAATTT
Found at i:4305129 original size:24 final size:24
Alignment explanation
Indices: 4305102--4305154 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4305092 CGTTCATTTA
4305102 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
4305126 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
4305150 CGTTC
1 CGTTC
4305155 ATTTATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.47
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:4305154 original size:14 final size:14
Alignment explanation
Indices: 4305112--4305143 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4305102 CGTTCGTGAA
4305112 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
4305126 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
4305140 CGTT
1 CGTT
4305144 TATGTTCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:4305160 original size:24 final size:24
Alignment explanation
Indices: 4305113--4305163 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4305103 GTTCGTGAAC
*
4305113 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* *
4305137 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
4305161 GTT
1 GTT
4305164 TAACCCAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.24, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:4306352 original size:10 final size:10
Alignment explanation
Indices: 4306337--4306411 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
4306327 GGGTCTCCAA
4306337 CGTTTATGTT
1 CGTTTATGTT
4306347 CGTTTATGTT
1 CGTTTATGTT
4306357 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
4306368 ATGTTCGTGTT
1 -CGTTTATGTT
4306379 CGTTTATGTT
1 CGTTTATGTT
4306389 CG----TGTT
1 CGTTTATGTT
4306395 CGTTTATGTT
1 CGTTTATGTT
*
4306405 CTTTTAT
1 CGTTTAT
4306412 TTATTAAACG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.66
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.20, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:4306368 original size:16 final size:16
Alignment explanation
Indices: 4306343--4306405 Score: 117
Period size: 16 Copynumber: 3.9 Consensus size: 16
4306333 CCAACGTTTA
4306343 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
4306359 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
4306375 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4306391 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
4306406 TTTTATTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.13, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4306498 original size:16 final size:16
Alignment explanation
Indices: 4306477--4306509 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4306467 AAAAAAACTT
4306477 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4306493 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
4306509 T
1 T
4306510 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4308017 original size:12 final size:12
Alignment explanation
Indices: 4307997--4308046 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
4307987 TTATTTGCAA
4307997 TATTATTTT-AT
1 TATTATTTTAAT
*
4308008 TATTACTTTTGA-
1 TATTA-TTTTAAT
4308020 TA-TATTTTAAT
1 TATTATTTTAAT
*
4308031 TATTACTTTAAT
1 TATTATTTTAAT
4308043 TATT
1 TATT
4308047 TTATTATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 9 0.27
12 18 0.55
13 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTATTTTAAT
Found at i:4308098 original size:18 final size:20
Alignment explanation
Indices: 4308064--4308103 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
4308054 CTTAGTCATA
*
4308064 TAAATATATATATATTTGTT
1 TAAATATATATATATTTATT
4308084 TAAATA-ATA-ATATTTATT
1 TAAATATATATATATTTATT
4308102 TA
1 TA
4308104 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TAAATATATATATATTTATT
Found at i:4308868 original size:26 final size:27
Alignment explanation
Indices: 4308839--4308894 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
4308829 ACTTATAATA
*
4308839 TTTATTATATTTTTA-TTATTAATGTT
1 TTTATTATATTTTTAGATATTAATGTT
* *
4308865 TTTATTTTATTTTTAGATATTAATTTT
1 TTTATTATATTTTTAGATATTAATGTT
4308892 TTT
1 TTT
4308895 GTAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (27 bp):
TTTATTATATTTTTAGATATTAATGTT
Found at i:4311209 original size:7 final size:7
Alignment explanation
Indices: 4311193--4311232 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
4311183 TTTTCATACA
4311193 TGCA-TT
1 TGCATTT
4311199 TGCATTT
1 TGCATTT
4311206 TGCATCTT
1 TGCAT-TT
4311214 TGCATTT
1 TGCATTT
4311221 T-CATTT
1 TGCATTT
4311227 TGCATT
1 TGCATT
4311233 CATACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.32
7 14 0.45
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:4318406 original size:54 final size:54
Alignment explanation
Indices: 4318258--4318409 Score: 196
Period size: 54 Copynumber: 2.8 Consensus size: 54
4318248 ATAGAGGCAA
** * * * * * **
4318258 AAACCACATTAAAGGATGAATGTATTGTCAAATGCTTTACAAAAATCTGGGCAG
1 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
4318312 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
1 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
* * *
4318366 AAGCCACAGGAAATGATGAATGTGTTGTCAAGTGTTTTACGAAC
1 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
4318410 CAGCGATTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (54 bp):
AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
Found at i:4319586 original size:45 final size:45
Alignment explanation
Indices: 4319535--4319642 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
4319525 TTTTTGATAT
* * * *
4319535 TTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGC
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAAGATGC
* * *
4319580 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGTAAGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAAGATGC
4319625 TTTCAAACAGCCTTCGGG
1 TTTCAAA-A-CCTTCGGG
4319643 AGCTTTTTGA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 45 0.83
46 1 0.02
47 8 0.15
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAAGATGC
Found at i:4319629 original size:121 final size:121
Alignment explanation
Indices: 4319476--4320073 Score: 928
Period size: 121 Copynumber: 4.9 Consensus size: 121
4319466 CTATTTCCCA
* *
4319476 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
4319541 AACCTTCGGGTCATCTATAAGCCCTTCAATGCATGATGCTTTCAAAACCTTCGGGT
66 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * *
4319597 CATCCATAAGACCTGCAGTGTAAGATGTTTTCAAACAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
4319662 AACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCAGGT
66 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
**
4319718 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTAAGGAGC-TTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* * * * *
4319782 AGCCTTTGGGTAATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGC
66 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTC-AAAACCTTCGGGT
4319839 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATGTTTCA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAT-TTTCA
* *
4319904 AAGCCTTCGGGTCATCTGTAAGCCCTTCAGTACATGATGCTTTCAAAACCTTCGGGT
65 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* *
4319961 CATCCATAAGACCTGTAGTGCAGGATGTTTTCAAAAGAAAGCCTTCAGGAGCTTTTTGATATTTT
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTC--AA-AAAGCCTTCGGGAGCTTTTTGATATTTT
* * * *
4320026 CAAAACCTTCGGGTCATTTCTAAGCCCTTCAGTGAATGATGTTTTCAA
63 CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAA
4320074 CATTTCCATC
Statistics
Matches: 436, Mismatches: 35, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
120 54 0.12
121 214 0.49
122 52 0.12
123 45 0.10
124 47 0.11
125 24 0.06
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (121 bp):
CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
Found at i:4319707 original size:45 final size:45
Alignment explanation
Indices: 4319656--4319753 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
4319646 TTTTTGATAT
* * ** * * *
4319656 TTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCAGGATGC
*
4319701 TTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCAGGATGT
1 TTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCAGGATGC
4319746 TTTCAAAA
1 TTTCAAAA
4319754 AGCCTTAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (45 bp):
TTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGTGCAGGATGC
Found at i:4319826 original size:45 final size:45
Alignment explanation
Indices: 4319770--4319884 Score: 113
Period size: 46 Copynumber: 2.5 Consensus size: 45
4319760 AAGGAGCTTT
* * * * ** * *
4319770 TGATATTTTCAAAGCCTTTGGGTAATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGCAATCCATAAGACCTGCAGTGCA
*
4319815 TGATGTTTTCAAAAACCTTCGGGCCATCCATAAGACCTGCAGTGCA
1 TGATGTTTTC-AAAACCTTCGGGCAATCCATAAGACCTGCAGTGCA
*
4319861 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
4319885 AGCTTTTTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 9 0.16
46 41 0.71
47 8 0.14
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGCAATCCATAAGACCTGCAGTGCA
Found at i:4319993 original size:45 final size:45
Alignment explanation
Indices: 4319899--4319996 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
4319889 TTTTGATATG
* ** * *
4319899 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTACATGATGC
1 TTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTACAGGATGC
* *
4319944 TTTCAAAACCTTCGGGTCATCCATAAGACCTGT-AGTGCAGGATGT
1 TTTCAAAACCTTCGGGTCATCCATAAGACCT-TCAGTACAGGATGC
4319989 TTTCAAAA
1 TTTCAAAA
4319997 GAAAGCCTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCATAAGACCTTCAGTACAGGATGC
Found at i:4320200 original size:3 final size:3
Alignment explanation
Indices: 4320194--4320239 Score: 58
Period size: 3 Copynumber: 14.7 Consensus size: 3
4320184 AATTTTTTTA
4320194 TAT TAT TAT ATAT TAT TAT T-T ATAT TAT TAT ATAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TA
4320240 AATAAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 1 0.03
3 31 0.79
4 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4320207 original size:10 final size:10
Alignment explanation
Indices: 4320192--4320239 Score: 71
Period size: 10 Copynumber: 4.7 Consensus size: 10
4320182 CTAATTTTTT
4320192 TATATTATTA
1 TATATTATTA
4320202 TATATTATTA
1 TATATTATTA
4320212 TTTATATTATTA
1 --TATATTATTA
4320224 TATATTATTA
1 TATATTATTA
4320234 T-TATTA
1 TATATTA
4320240 AATAAATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.14
10 21 0.58
12 10 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTATTA
Found at i:4320218 original size:22 final size:22
Alignment explanation
Indices: 4320190--4320235 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4320180 CACTAATTTT
4320190 TTTATATTATTATATATTATTA
1 TTTATATTATTATATATTATTA
4320212 TTTATATTATTATATATTATTA
1 TTTATATTATTATATATTATTA
4320234 TT
1 TT
4320236 ATTAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATATTATTATATATTATTA
Found at i:4321554 original size:30 final size:29
Alignment explanation
Indices: 4321482--4321554 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
4321472 ATTAATTGCT
*
4321482 TATATTTTATAATTTTATCATTAAGTTTTA
1 TATATTTTA-AATTTTACCATTAAGTTTTA
*
4321512 TATAATTT-AATTTTAACCA-TAAGTTTTA
1 TATATTTTAAATTTT-ACCATTAAGTTTTA
4321540 TATATTTTACAATTT
1 TATATTTTA-AATTT
4321555 AATTTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 22 0.59
29 3 0.08
30 12 0.32
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (29 bp):
TATATTTTAAATTTTACCATTAAGTTTTA
Found at i:4321680 original size:2 final size:2
Alignment explanation
Indices: 4321667--4321702 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4321657 TATCTTAGTC
*
4321667 AT AT AA 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
4321703 CTGTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4321961 original size:132 final size:133
Alignment explanation
Indices: 4321722--4321962 Score: 303
Period size: 132 Copynumber: 1.8 Consensus size: 133
4321712 TAATAATATT
4321722 TATTAATTTTTTAATATCAAAGAAAAGGGTTGTCTTAAAGCAACTAAAAATCCTTTTCTGATATT
1 TATTAATTTTTTAATATCAAAGAAAAGGGTTGTCTTAAAGCAACTAAAAATCCTTTTCTGATATT
* * *
4321787 CTTAAACAAAATAAATATCATACTTTTATTGATTATATATTAATTTATTTAAAAAAATGTTTTAT
66 CTTAAACAAAATAAATATCATACTTATATTGATTACAAATTAATTTATTTAAAAAAATGTTTTAT
4321852 TAA
131 TAA
* * ** * * *
4321855 TATTTATTTTTTAATAT-TAAGAAATTGGTTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATT
1 TATTAATTTTTTAATATCAAAGAAAAGGGTTGTCTTAAAGCAACTAAAAATCCTTTTCTGATATT
* *
4321919 -TCTAAA-TAAATAAATATCTTA-TTCATATAT-ATATACAAATTAAT
66 CT-TAAACAAAATAAATATCATACTT-ATAT-TGAT-TACAAATTAAT
4321963 AGATTTTCTT
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
130 2 0.02
131 19 0.21
132 55 0.60
133 16 0.17
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (133 bp):
TATTAATTTTTTAATATCAAAGAAAAGGGTTGTCTTAAAGCAACTAAAAATCCTTTTCTGATATT
CTTAAACAAAATAAATATCATACTTATATTGATTACAAATTAATTTATTTAAAAAAATGTTTTAT
TAA
Found at i:4330163 original size:17 final size:17
Alignment explanation
Indices: 4330126--4330165 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4330116 TAGTCAACTG
* * *
4330126 TTGACTGTTGACCTGCG
1 TTGACCGTTGACCGGCA
4330143 TTGACCGTTGACCGGCA
1 TTGACCGTTGACCGGCA
4330160 TTGACC
1 TTGACC
4330166 ACTGTTGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (17 bp):
TTGACCGTTGACCGGCA
Found at i:4332750 original size:12 final size:12
Alignment explanation
Indices: 4332732--4332793 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
4332722 ACCTGAATTC
4332732 TGTTCTGATTTT
1 TGTTCTGATTTT
* *
4332744 TGATCTGGA-TTC
1 TGTTCT-GATTTT
* * *
4332756 TGTTTTGATATC
1 TGTTCTGATTTT
4332768 TGTTCTGATTTT
1 TGTTCTGATTTT
*
4332780 TGTTTTGATTTT
1 TGTTCTGATTTT
4332792 TG
1 TG
4332794 ATATTTCCGT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTTCTGATTTT
Found at i:4332755 original size:24 final size:23
Alignment explanation
Indices: 4332728--4332795 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
4332718 CATGACCTGA
*
4332728 ATTCTGTTCTGATTTTTGATCTGG
1 ATTCTGTTTTGATTTTTGATCT-G
* * *
4332752 ATTCTGTTTTGATATCTGTTCTG
1 ATTCTGTTTTGATTTTTGATCTG
*
4332775 ATTTTTGTTTTGATTTTTGAT
1 A-TTCTGTTTTGATTTTTGAT
4332796 ATTTCCGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.13, C:0.09, G:0.18, T:0.60
Consensus pattern (23 bp):
ATTCTGTTTTGATTTTTGATCTG
Found at i:4344866 original size:18 final size:18
Alignment explanation
Indices: 4344843--4344877 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4344833 TTGTCACCTT
4344843 ATATTTATTTAGTTTAAC
1 ATATTTATTTAGTTTAAC
* *
4344861 ATATTTTTTTATTTTAA
1 ATATTTATTTAGTTTAA
4344878 TGCATAGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
ATATTTATTTAGTTTAAC
Found at i:4346411 original size:20 final size:21
Alignment explanation
Indices: 4346376--4346416 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
4346366 CAAATGATAA
4346376 TGATGTGGCAAAATGGAATGAC
1 TGATGTGG-AAAATGGAATGAC
4346398 TGATGTGG-AAATGGAATGA
1 TGATGTGGAAAATGGAATGA
4346417 TGGTGGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.34, T:0.24
Consensus pattern (21 bp):
TGATGTGGAAAATGGAATGAC
Found at i:4352910 original size:17 final size:17
Alignment explanation
Indices: 4352888--4352927 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
4352878 GTCCTAGAAT
4352888 AATGCCTTATCTACCTC
1 AATGCCTTATCTACCTC
4352905 AATGCCTTATCTACCTC
1 AATGCCTTATCTACCTC
4352922 AATGCC
1 AATGCC
4352928 CTTTGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.35, G:0.07, T:0.33
Consensus pattern (17 bp):
AATGCCTTATCTACCTC
Found at i:4362354 original size:104 final size:103
Alignment explanation
Indices: 4362148--4362373 Score: 256
Period size: 104 Copynumber: 2.2 Consensus size: 103
4362138 TGATCATCTA
*
4362148 TTCGACACAATTATCAATACAAATTGTGATGAATTTTTCGACACTAAAAAAATATTTTGTGACCA
1 TTCGACACAATTATCAATACAAATTGTGATAAATTTTTCGACACTAAAAAAATATTTTGTGACCA
* *
4362213 TCAATATTGTTACACCAAGTATTTTTAGTGACCAAATG
66 CCAATATTGATACACCAAGTATTTTTAGTGACCAAATG
* * * * * * *
4362251 TTCGATACTATTATCAATAGAAATTGTGATAAATTTATTTGATACTGAAAATATATTTTGTGACC
1 TTCGACACAATTATCAATACAAATTGTGATAAATTT-TTCGACACTAAAAAAATATTTTGTGACC
* * ** * *
4362316 ACCAATGTT-ATCCTAGTAAGTGTTTTTAGTGACGAAATG
65 ACCAATATTGATAC-ACCAAGTATTTTTAGTGACCAAATG
* * *
4362355 TTTGACACCATTAACAATA
1 TTCGACACAATTATCAATA
4362374 ACTCCGTCAC
Statistics
Matches: 101, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
103 34 0.34
104 67 0.66
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (103 bp):
TTCGACACAATTATCAATACAAATTGTGATAAATTTTTCGACACTAAAAAAATATTTTGTGACCA
CCAATATTGATACACCAAGTATTTTTAGTGACCAAATG
Found at i:4363405 original size:3 final size:3
Alignment explanation
Indices: 4363397--4363471 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
4363387 CCGAAGACCG
4363397 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
4363443 TTA TTA TTA TTA TTA TTA TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4363472 TCTTCAAGCC
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.