Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 26
Found at i:3529934 original size:23 final size:22
Alignment explanation
Indices: 3529907--3529972 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
3529897 TAGGATATTT
3529907 ATTAAATTTGAATATGATTTTA
1 ATTAAATTTGAATATGATTTTA
* *
3529929 TGTTAAGGTATTT-TATAT--TTTTA
1 -ATTAA---ATTTGAATATGATTTTA
3529952 ATTAAATTTGAATATGATTTT
1 ATTAAATTTGAATATGATTTT
3529973 TACGTATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 13
0.66 0.08 0.26
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
22 8 0.24
23 9 0.27
25 4 0.12
26 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (22 bp):
ATTAAATTTGAATATGATTTTA
Found at i:3533804 original size:131 final size:131
Alignment explanation
Indices: 3533639--3533995 Score: 471
Period size: 131 Copynumber: 2.7 Consensus size: 131
3533629 CGATATTGAG
* *** * * * * * *
3533639 AATAGTAATATCTTTTCATTTTGGTCGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
1 AATAGTAATATCTTTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCATGAAAGGTCATT
* * * * * *
3533704 TATTCTTGATTGGAAATAATTTGATATTGTCGTTTTCTCTCGAATTAATACCGATTTTTAAGACA
66 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATACCGAATTTTAAGACA
3533769 A
131 A
* *
3533770 AATAGTAATATCTTTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCACGAAAGATCATT
1 AATAGTAATATCTTTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCATGAAAGGTCATT
* * * * ** **
3533835 TATTCTCGATTGGAGATCATTAGATATTATCATTTTCACTTGAATTGATATTGAATTTTAAGATG
66 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATACCGAATTTTAAGACA
3533900 A
131 A
*
3533901 AATAGTAATATCTCTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCATGAAAGGTCATT
1 AATAGTAATATCTTTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCATGAAAGGTCATT
3533966 TATTCTCGATTGGAAATAATTAGATATTAT
66 TATTCTCGATTGGAAATAATTAGATATTAT
3533996 AGTTTTGACT
Statistics
Matches: 195, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
131 195 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (131 bp):
AATAGTAATATCTTTTTATTTCAATTGGGGTAATAAATGACTGTTTTAATGCATGAAAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATACCGAATTTTAAGACA
A
Found at i:3538717 original size:2 final size:2
Alignment explanation
Indices: 3538706--3538736 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3538696 TAAAGGCGAT
3538706 TA TA -A 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
3538737 CATTAAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3540804 original size:134 final size:134
Alignment explanation
Indices: 3540421--3541268 Score: 766
Period size: 134 Copynumber: 6.3 Consensus size: 134
3540411 GCAAATCAAA
* * * * *
3540421 CTCGATTTAATCTTCCCTGAGTGATAG-GGAAATGAATTAACGTCCCCAGATCTGATCTTT-CCT
1 CTCGATTCAATCTTCCCTGAGTGACAGTGG-AATGAATCAACATTCCCAGATCTGAT-TTTCCCT
** * * * * * * **
3540484 CTTGAATAAGGAGAAAAAATCCCTCTCTTTCATGATTTGGTATTCCCTAAGTAATGGTGGAACAA
64 CAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAA
3540549 GTCTGC
129 GTCTGC
* * * * * * * * *
3540555 ATAGGTTCAATCTTCCCTGAGTGATAGTGGGATGAATCAAC-GTCTCTAGATATGA-TTTCCATC
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTC-CCAGATCTGATTTTCCCTC
** * ** *
3540618 AAGAAGAAGCAGGGCAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAG
65 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
3540683 TTTGC
130 TCTGC
* * * * *
3540688 CTCGATTCAATCTTCCCTGAGTGACAGTAGAATGAGTCAACATTGCCATATCTGATTTTCCCTAA
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTCA
* * * *
3540753 AGAAGAAGTAGAACAGATCCCTCGCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAAGT
66 AGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
3540818 CTGC
131 CTGC
** * * * * *
3540822 CTTAATTCAATCTTCCCTGAATGATAGTGGAATGATTCAACA-TCCTCAGATCTGATCTTCTCTC
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCC-CAGATCTGATTTTCCCTC
* * ** * * *
3540886 CATAAGAAGTGGAACAAATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAG
65 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
3540951 TCTGC
130 TCTGC
* * * *
3540956 CTCGATTCAATCTTTCCTGAG-GACAGTGGAATAAATCAACA-TCCCTACACCTGATCTTT-CCT
1 CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCCC-AGATCTGAT-TTTCCCT
* * * * * *
3541018 CCAGAAGAAGCATAACAAATCCCTCTCTTTCAAAATTTAATATTCCCAGAGTGACAGTGGAGA-A
64 CAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGA-ACA
*
3541082 AGTCTTC
128 AGTCTGC
* * * * *
3541089 CTTGATTCAATCTT-CCTCGAGTAACAGTGGAATGAATCAACGTCCCCAGATTTGATTTTCCCTC
1 CTCGATTCAATCTTCCCT-GAGTGACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTC
* * * ** *
3541153 AAGAATAAGC-GAAACAAATCCTTCTTTTTCAAGATTTGATATTTTCGTTGAGTAATAGTGGAAC
65 AAGAAGAAGCAG-AACAAATCCCTCTCTTTCAAGATTTGATA--TTCCCTGAGTAACAGTGGAAC
*
3541217 AAGTCTAC
127 AAGTCTGC
* * * * *
3541225 CCCGATTCAATCTTCCCTAAAG-AACAATGGAATGAGTCAACATT
1 CTCGATTCAATCTTCCCT-GAGTGACAGTGGAATGAATCAACATT
3541269 TCTCGATTTG
Statistics
Matches: 577, Mismatches: 119, Indels: 34
0.79 0.16 0.05
Matches are distributed among these distances:
132 7 0.01
133 209 0.36
134 299 0.52
135 6 0.01
136 51 0.09
137 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATTCCCAGATCTGATTTTCCCTCA
AGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
CTGC
Found at i:3540997 original size:267 final size:266
Alignment explanation
Indices: 3540421--3541242 Score: 791
Period size: 267 Copynumber: 3.1 Consensus size: 266
3540411 GCAAATCAAA
* * * * * * * * * *
3540421 CTCGATTTAATCTTCCCTGAGTGATAG-GGAAATGAATTAACGTCCCCAGATCTGATCTTTCCTC
1 CTCGATTCAATCTTCCCTGAGTGACAGTAG-AATAAATCAACATCCCTACACCTGATCTTTCCTA
** * * * * * * * **
3540485 TTGAATAAGGAGAAAAAATCCCTCTCTTTCATGATTTGGTATTCCCTAAGTAATGGTGGAACAAG
65 AAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAAG
* * *
3540550 TCTG-CATAGGTTCAATCTTCCCTGAGTGATAGTGGGATGAATCAACGT-CTCTAGATATGATTT
130 TCTGCCTTA-ATTCAATCTTCCCTGAGTGATAGTGGAATGAATCAACGTCCTC-AGATATGATTT
* * * * *
3540613 CCATCAAGAAGAAGCAGG-GCAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGG
193 CC-TCAAGAAGAAG-AGGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGG
*
3540677 AACAAGTTTGC
256 AACAAGTCTGC
* * * * *
3540688 CTCGATTCAATCTTCCCTGAGTGACAGTAGAATGAGTCAACATTGCC-ATATCTGAT-TTTCCCT
1 CTCGATTCAATCTTCCCTGAGTGACAGTAGAATAAATCAACA-TCCCTACACCTGATCTTT-CCT
* * *
3540751 AAAGAAGAAGTAGAACAGATCCCTCGCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAA
64 AAAGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAA
* * * *
3540816 GTCTGCCTTAATTCAATCTTCCCTGAATGATAGTGGAATGATTCAACATCCTCAGATCTGATCTT
129 GTCTGCCTTAATTCAATCTTCCCTGAGTGATAGTGGAATGAATCAACGTCCTCAGATATGAT-TT
* * * * * *
3540881 CTCTCCATAAGAAGTGGAACAAATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTGATAGTGGA
193 C-CTCAAGAAGAAGAGGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGA
3540946 ACAAGTCTGC
257 ACAAGTCTGC
* * **
3540956 CTCGATTCAATCTTTCCTGAG-GACAGTGGAATAAATCAACATCCCTACACCTGATCTTTCCTCC
1 CTCGATTCAATCTTCCCTGAGTGACAGTAGAATAAATCAACATCCCTACACCTGATCTTTCCTAA
* * * *
3541020 AGAAGAAGCATAACAAATCCCTCTCTTTCAAAATTTAATATTCCCA-GAGTGACAGTGGAGA-AA
66 AGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATT-CCATGAGTAACAGTGGA-ACAA
* * * * * *
3541083 GTCTTCCTTGATTCAATCTT-CCTCGAGTAACAGTGGAATGAATCAACGTCCCCAGATTTGATTT
129 GTCTGCCTTAATTCAATCTTCCCT-GAGTGATAGTGGAATGAATCAACGTCCTCAGATATGA-TT
* * * * * **
3541147 TCCCTCAAGAATAAGCGAAACAAATCCTTCTTTTTCAAGATTTGATATTTTCGTTGAGTAATAGT
192 T-CCTCAAGAAGAAGAGGAACAAATCCATCTCTTTCAAGATTTGATA--TTCCCTGAGTAATAGT
*
3541212 GGAACAAGTCTAC
254 GGAACAAGTCTGC
*
3541225 CCCGATTCAATCTTCCCT
1 CTCGATTCAATCTTCCCT
3541243 AAAGAACAAT
Statistics
Matches: 458, Mismatches: 80, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
266 9 0.02
267 308 0.67
268 99 0.22
269 42 0.09
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (266 bp):
CTCGATTCAATCTTCCCTGAGTGACAGTAGAATAAATCAACATCCCTACACCTGATCTTTCCTAA
AGAAGAAGCAGAACAAATCCCTCTCTTTCAAGATTTGATATTCCATGAGTAACAGTGGAACAAGT
CTGCCTTAATTCAATCTTCCCTGAGTGATAGTGGAATGAATCAACGTCCTCAGATATGATTTCCT
CAAGAAGAAGAGGAACAAATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAA
GTCTGC
Found at i:3541185 original size:401 final size:402
Alignment explanation
Indices: 3540429--3541242 Score: 907
Period size: 401 Copynumber: 2.0 Consensus size: 402
3540419 AACTCGATTT
* * * *
3540429 AATCTTCCCTGAGTGATAGGGAAATGAATTAACGTCCCCAGATCTGATCTTTCCTCTTGAATAAG
1 AATCTTCCCTGAATGATAGGGAAATGAATTAACATCCCCAGATCTGATCTTTCCTCATGAAGAAG
* * * *
3540494 GAGAAAAAATCCCTCTCTTTCATGATTTGGTATTCCCTAAGTAATGGTGGAACAAGTCTGCATAG
66 GAGAAAAAATCCCTCTCTTCCAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGTCTGCATAG
* * * * * * * *
3540559 GTTCAATCTTCCCTGAGTGATAGTGGGATGAATCAACGTCTCTAGATATGATTTCCATCAAGAAG
131 ATTCAATCTTCCCTGAGTGACAGTGGAATAAATCAACATCCCTACACATGATTTCCATCAAGAAG
** * * *
3540624 AAGCAGGGCAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAGTGGAACAAGTTTGCC
196 AAGCAGAACAAATCAATCTCTTTCAAAATTTAATATTCCCTAAGTAACAGTGGAACAAGTTTGCC
* * ** *
3540689 TCGATTCAATCTTCCCTGAGTGACAGTAGAATGAGTCAACATTGCCATATCTGATTTTCCCTAAA
261 TCGATTCAATCTTCCCTGAGTAACAGTAGAATGAATCAACATCCCCAGATCTGATTTTCCCTAAA
* *
3540754 GAAGAAGTAGAACAGATCCCTCGCTTTCAAGATTTGATA-TTCCATGAGTAACAGTGGAACAAGT
326 GAAGAAGGAGAACAAATCCCTCGCTTTCAAGATTTGATATTTCCATGAGTAACAGTGGAACAAGT
* **
3540818 CTGCCTTAATTC
391 CTACCCCAATTC
*
3540830 AATCTTCCCTGAATGATAGTGG-AATG-ATTCAACATCCTCAGATCTGATC-TTCTCTCCAT-AA
1 AATCTTCCCTGAATGATAG-GGAAATGAATT-AACATCCCCAGATCTGATCTTTC-CT-CATGAA
* * *
3540891 GAAGTG-GAACAAATCCCTCTCTTCCAAGATTTGATATTCCCTGAGTGATAGTGGAACAAGTCTG
62 GAAG-GAGAAAAAATCCCTCTCTTCCAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGTCTG
* * * *
3540955 CCTCGATTCAATCTTTCCTGAG-GACAGTGGAATAAATCAACATCCCTACACCTGATCTTTCC-T
126 CATAGATTCAATCTTCCCTGAGTGACAGTGGAATAAATCAACATCCCTACACATGA--TTTCCAT
* * ** *
3541018 CCAGAAGAAGCATAACAAATCCCTCTCTTTCAAAATTTAATATTCCC-AGAGTGACAGTGGAGA-
189 CAAGAAGAAGCAGAACAAATCAATCTCTTTCAAAATTTAATATTCCCTA-AGTAACAGTGGA-AC
* * * *
3541081 AAGTCTT-CCTTGATTCAATCTT-CCTCGAGTAACAGTGGAATGAATCAACGTCCCCAGATTTGA
252 AAGT-TTGCCTCGATTCAATCTTCCCT-GAGTAACAGTAGAATGAATCAACATCCCCAGATCTGA
* * * ** **
3541144 TTTTCCCTCAAGAATAAGCGA-AACAAATCCTTCTTTTTCAAGATTTGATATTTTCGTTGAGTAA
315 TTTTCCCTAAAGAAGAAG-GAGAACAAATCCCTCGCTTTCAAGATTTGATA-TTTCCATGAGTAA
* *
3541208 TAGTGGAACAAGTCTACCCCGATTC
378 CAGTGGAACAAGTCTACCCCAATTC
3541233 AATCTTCCCT
1 AATCTTCCCT
3541243 AAAGAACAAT
Statistics
Matches: 342, Mismatches: 57, Indels: 26
0.80 0.13 0.06
Matches are distributed among these distances:
400 35 0.10
401 253 0.74
402 14 0.04
403 40 0.12
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (402 bp):
AATCTTCCCTGAATGATAGGGAAATGAATTAACATCCCCAGATCTGATCTTTCCTCATGAAGAAG
GAGAAAAAATCCCTCTCTTCCAAGATTTGATATTCCCTAAGTAATAGTGGAACAAGTCTGCATAG
ATTCAATCTTCCCTGAGTGACAGTGGAATAAATCAACATCCCTACACATGATTTCCATCAAGAAG
AAGCAGAACAAATCAATCTCTTTCAAAATTTAATATTCCCTAAGTAACAGTGGAACAAGTTTGCC
TCGATTCAATCTTCCCTGAGTAACAGTAGAATGAATCAACATCCCCAGATCTGATTTTCCCTAAA
GAAGAAGGAGAACAAATCCCTCGCTTTCAAGATTTGATATTTCCATGAGTAACAGTGGAACAAGT
CTACCCCAATTC
Found at i:3541443 original size:3 final size:3
Alignment explanation
Indices: 3541437--3541491 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
3541427 TTCCTCCTGC
* * * *
3541437 TAT TAT TA- TAT TAT TAT TTT TAT TAT TAA TGT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3541484 TAT TAT TA
1 TAT TAT TA
3541492 ATAAATACAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3543752 original size:130 final size:130
Alignment explanation
Indices: 3543569--3543905 Score: 442
Period size: 130 Copynumber: 2.6 Consensus size: 130
3543559 TAGGTCGGAG
** * * * * * *
3543569 TAATAAATGACTACTTTAAGGCATGAGAGGTCTTTTATTATCGATTGGAAATAATTTA-ATATTG
1 TAATAAATGA-TTTTTTAATGCACGAAAGGTCATTTATTCTCGATTGGAAATAA-TTAGATATTA
* * * **
3543633 TCGTTTTCTCTCGAATTAATACCGATTTTTGTGACAAAATAGTAATATATCTTTATTTCAATTGG
64 TCGTTTTCACTCGAATCAATACCGAATTTTAAGACAAAATAGTAATATATCTTTATTTCAATTGG
3543698 GA
129 GA
*
3543700 TAATAAATGATTTTTTAATGCACGAAAGGTCATTTATTCTCGATCGGAAATAATTAGATATTATC
1 TAATAAATGATTTTTTAATGCACGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
* * ** * * *
3543765 ATTTTCACTTGAATCAATATTGAATTTTAAGACGAAATAGTAATATCTCTTTATTTCAATTGGGG
66 GTTTTCACTCGAATCAATACCGAATTTTAAGACAAAATAGTAATATATCTTTATTTCAATTGGGA
*
3543830 TAATAAATTATTGTTTTAATGCACGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
1 TAATAAATGATT-TTTTAATGCACGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTAT
3543895 CGTTTTCACTC
65 CGTTTTCACTC
3543906 TTAAAATTAT
Statistics
Matches: 179, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
129 3 0.02
130 106 0.59
131 70 0.39
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (130 bp):
TAATAAATGATTTTTTAATGCACGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATC
GTTTTCACTCGAATCAATACCGAATTTTAAGACAAAATAGTAATATATCTTTATTTCAATTGGGA
Found at i:3555004 original size:54 final size:54
Alignment explanation
Indices: 3554916--3555353 Score: 583
Period size: 54 Copynumber: 8.1 Consensus size: 54
3554906 TTGCCCCTAC
* * *
3554916 AGTGTCGAAACAGGTTATTCATCTACATAGGATGAATTCCGTGAAATGCACACTT
1 AGTGCCGAAAC-GATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* * * * * *
3554971 AGTACAGAAACGATTATTTATCCACAAAGGATGAACTCCGTGAAATGCACACTC
1 AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* * * *
3555025 AGTGCCGAAATGATTATTCATCCACATAGGATGAATTCTGTGAAATACACGCTT
1 AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
*
3555079 AGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
1 AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* **
3555133 AGTGCCGAAACGATTATTCAT-CTCATAGGATGAATTCAATGAAATGCACACTT
1 AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* ** *
3555186 AGTGCCGAAA-TAGTTATTCATCCACATAGGATGAATTATGCGAAATGCACACTT
1 AGTGCCGAAACGA-TTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* * *
3555240 AGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTTAAATGCACATTT
1 AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
* * * * *
3555294 AGTGCCGAAACGGTTATTCATCCACTTAGGATGAATTCCGTGAGATACACTCTT
1 AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
3555348 AGTGCC
1 AGTGCC
3555354 TATTTGGTAA
Statistics
Matches: 333, Mismatches: 47, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
52 1 0.00
53 47 0.14
54 277 0.83
55 8 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (54 bp):
AGTGCCGAAACGATTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTT
Found at i:3555312 original size:215 final size:217
Alignment explanation
Indices: 3554916--3555353 Score: 621
Period size: 215 Copynumber: 2.0 Consensus size: 217
3554906 TTGCCCCTAC
* * **
3554916 AGTGTCGAAACAGGTTATTCATCTACATAGGATGAATTCCGTGAAATGCACACTTAGTACAGAAA
1 AGTGCCGAAACAGATTATTCATCTACATAGGATGAATTCAATGAAATGCACACTTAGTACAGAAA
* * * * *
3554981 CGATTATTTATCCACAAAGGATGAACTCCGTGAAATGCACACTCAGTGCCGAAATGATTATTCAT
66 AGATTATTCATCCACAAAGGATGAACTACGCGAAATGCACACTCAGTGCCGAAACGATTATTCAT
* *
3555046 CCACATAGGATGAATTCTGTGAAATACACGCTTAGTGCCGAAACGGTTATTCATCCACATAGGAT
131 CCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGGAT
*
3555111 GAATTCCGTGAAATGCACACTT
196 GAATTCCGTGAAATACACACTT
* *
3555133 AGTGCCGAAAC-GATTATTCATCT-CATAGGATGAATTCAATGAAATGCACACTTAGTGCCGAAA
1 AGTGCCGAAACAGATTATTCATCTACATAGGATGAATTCAATGAAATGCACACTTAGTACAGAAA
* * * * *
3555196 TAG-TTATTCATCCACATAGGATGAATTATGCGAAATGCACACTTAGTGCCGAAACGGTTATTCA
66 -AGATTATTCATCCACAAAGGATGAACTACGCGAAATGCACACTCAGTGCCGAAACGATTATTCA
* * * *
3555260 TCCACATAGGATGAATTCCGTTAAATGCACATTTAGTGCCGAAACGGTTATTCATCCACTTAGGA
130 TCCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGGA
* *
3555325 TGAATTCCGTGAGATACACTCTT
195 TGAATTCCGTGAAATACACACTT
3555348 AGTGCC
1 AGTGCC
3555354 TATTTGGTAA
Statistics
Matches: 195, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
215 173 0.89
216 12 0.06
217 10 0.05
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (217 bp):
AGTGCCGAAACAGATTATTCATCTACATAGGATGAATTCAATGAAATGCACACTTAGTACAGAAA
AGATTATTCATCCACAAAGGATGAACTACGCGAAATGCACACTCAGTGCCGAAACGATTATTCAT
CCACATAGGATGAATTCCGTGAAATACACACTTAGTGCCGAAACGGTTATTCATCCACATAGGAT
GAATTCCGTGAAATACACACTT
Found at i:3555322 original size:27 final size:27
Alignment explanation
Indices: 3555235--3555322 Score: 65
Period size: 27 Copynumber: 3.3 Consensus size: 27
3555225 GCGAAATGCA
3555235 CACTTAGTGCCGAAACGGTTATTCATC
1 CACTTAGTGCCGAAACGGTTATTCATC
* ** * * *
3555262 CACATAG-GATGAATTCCGTTA--AATGC
1 CACTTAGTGCCGAA-ACGGTTATTCAT-C
*
3555288 ACATTTAGTGCCGAAACGGTTATTCATC
1 -CACTTAGTGCCGAAACGGTTATTCATC
3555316 CACTTAG
1 CACTTAG
3555323 GATGAATTCC
Statistics
Matches: 41, Mismatches: 14, Indels: 12
0.61 0.21 0.18
Matches are distributed among these distances:
25 2 0.05
26 5 0.12
27 27 0.66
28 5 0.12
29 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (27 bp):
CACTTAGTGCCGAAACGGTTATTCATC
Found at i:3561624 original size:17 final size:18
Alignment explanation
Indices: 3561603--3561648 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3561593 TTAAAAATGT
3561603 AAAAATAAAAT-AAATAC-
1 AAAAATAAAATGAAA-ACA
*
3561620 CAAAATAAAATGAAAACA
1 AAAAATAAAATGAAAACA
3561638 AAAAATAAAAT
1 AAAAATAAAAT
3561649 TATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATGAAAACA
Found at i:3564064 original size:20 final size:19
Alignment explanation
Indices: 3564035--3564079 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3564025 ACTATGCTGA
* *
3564035 AAATTAATGTTTGAGTGTTG
1 AAATTAATGTTAGAATG-TG
*
3564055 AAATTGATGTTAGAATGTG
1 AAATTAATGTTAGAATGTG
3564074 AAATTA
1 AAATTA
3564080 GAATATTTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (19 bp):
AAATTAATGTTAGAATGTG
Found at i:3565517 original size:30 final size:31
Alignment explanation
Indices: 3565443--3565561 Score: 143
Period size: 30 Copynumber: 3.8 Consensus size: 31
3565433 TCAAATTAGC
*
3565443 ACTATAGTGTGTAAGGACACTTAGTGCATATCGT
1 ACTATAGTGTGTAAGGACACTTAGTACA-A--GT
*
3565477 ACTATGGTGTGTAAGGACACTTAGTACAA-T
1 ACTATAGTGTGTAAGGACACTTAGTACAAGT
* *
3565507 ACTATAGTGTGTAAGGACACTTAGCA-AAGC
1 ACTATAGTGTGTAAGGACACTTAGTACAAGT
* *
3565537 ACTGTAGTATGTAAGGACACTTAGT
1 ACTATAGTGTGTAAGGACACTTAGT
3565562 GTAGGACTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
29 2 0.03
30 47 0.62
33 1 0.01
34 26 0.34
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (31 bp):
ACTATAGTGTGTAAGGACACTTAGTACAAGT
Found at i:3565571 original size:30 final size:30
Alignment explanation
Indices: 3565439--3565587 Score: 118
Period size: 30 Copynumber: 4.8 Consensus size: 30
3565429 ATAATCAAAT
* *
3565439 TAGCACTATAGTGTGTAAGGACACTTAGTGCA
1 TAGCACTGTAGTATGTAAGGACACTTAGT--A
* * * *
3565471 TATCGTACTATGGTGTGTAAGGACACTTAGTA
1 TA--GCACTGTAGTATGTAAGGACACTTAGTA
* ** * * *
3565503 CAATACTATAGTGTGTAAGGACACTTAGCA
1 TAGCACTGTAGTATGTAAGGACACTTAGTA
* *
3565533 AAGCACTGTAGTATGTAAGGACACTTAGTG
1 TAGCACTGTAGTATGTAAGGACACTTAGTA
* *
3565563 TAGGACTGTGGTATGTAAGGACACT
1 TAGCACTGTAGTATGTAAGGACACT
3565588 CAGTGTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
30 70 0.71
32 4 0.04
34 25 0.25
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGCACTGTAGTATGTAAGGACACTTAGTA
Found at i:3565593 original size:30 final size:30
Alignment explanation
Indices: 3565537--3565594 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
3565527 TTAGCAAAGC
*
3565537 ACTGTAGTATGTAAGGACACTTAGTGTAGG
1 ACTGTAGTATGTAAGGACACTCAGTGTAGG
*
3565567 ACTGTGGTATGTAAGGACACTCAGTGTA
1 ACTGTAGTATGTAAGGACACTCAGTGTA
3565595 TATGGTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (30 bp):
ACTGTAGTATGTAAGGACACTCAGTGTAGG
Found at i:3566098 original size:17 final size:19
Alignment explanation
Indices: 3566070--3566116 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
3566060 TTATTATAGT
3566070 CAGTATTAAATAAAT-TTA
1 CAGTATTAAATAAATATTA
3566088 CAGTA-TAAATAAATATTA
1 CAGTATTAAATAAATATTA
3566106 CTA-TATTAAAT
1 C-AGTATTAAAT
3566117 TATATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.35
18 11 0.42
19 6 0.23
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (19 bp):
CAGTATTAAATAAATATTA
Found at i:3574967 original size:30 final size:30
Alignment explanation
Indices: 3574893--3575037 Score: 137
Period size: 30 Copynumber: 4.7 Consensus size: 30
3574883 TCGGATTGGC
* *
3574893 ACTATAGTGTGTAAGTACACTTAGTACGTATGGT
1 ACTATAGTGTGTAAGGACACTTAGTAC--A--AT
*
3574927 ACTATGGTGTGTAAGGACACTTAGTACAAT
1 ACTATAGTGTGTAAGGACACTTAGTACAAT
* *
3574957 ACTATAGTGTGTAAGGATACTTAGTACAAA
1 ACTATAGTGTGTAAGGACACTTAGTACAAT
* * * * *
3574987 AATGTAGTGTGTAAGGACACTCAGTGCAAC
1 ACTATAGTGTGTAAGGACACTTAGTACAAT
* * *
3575017 ACTGTGGTGTTTAAGGACACT
1 ACTATAGTGTGTAAGGACACT
3575038 CAATGTATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
30 70 0.73
32 1 0.01
34 25 0.26
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.30
Consensus pattern (30 bp):
ACTATAGTGTGTAAGGACACTTAGTACAAT
Found at i:3577354 original size:150 final size:150
Alignment explanation
Indices: 3577083--3577362 Score: 488
Period size: 150 Copynumber: 1.9 Consensus size: 150
3577073 TAAGCGAACA
*
3577083 TTTCGAATGGGCAAGTAAAATTCACCTTCTCCTTATCTACTAGCGCCACCATAATTTGGAAAAAC
1 TTTCGAATGGGCAAGTAAAATTCACCTTCTCCTGATCTACTAGCGCCACCATAATTTGGAAAAAC
* * * *
3577148 CTTAAAATCCATTAAGGTAATAGTAATGAGTTTTTCTGCTAAGCGTTTGATTATTTGGTCTATAA
66 CTGAAAATCCATCAAGGTAATAATAATGAATTTTTCTGCTAAGCGTTTGATTATTTGGTCTATAA
3577213 ATGGAAGAGGGGAATAATCT
131 ATGGAAGAGGGGAATAATCT
* *
3577233 TTTCGAGTGGGCATGTAAAATTCACCTTCTCCTGATCTACTAGCGCCACCATAATTTGGAAAAAC
1 TTTCGAATGGGCAAGTAAAATTCACCTTCTCCTGATCTACTAGCGCCACCATAATTTGGAAAAAC
*
3577298 CTGAAAATCCATCAAGGTTATAATAATGAATTTTTCTGCTAAGCGTTTGATTATTTGGTCTATAA
66 CTGAAAATCCATCAAGGTAATAATAATGAATTTTTCTGCTAAGCGTTTGATTATTTGGTCTATAA
3577363 TACATGCTTC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
150 122 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (150 bp):
TTTCGAATGGGCAAGTAAAATTCACCTTCTCCTGATCTACTAGCGCCACCATAATTTGGAAAAAC
CTGAAAATCCATCAAGGTAATAATAATGAATTTTTCTGCTAAGCGTTTGATTATTTGGTCTATAA
ATGGAAGAGGGGAATAATCT
Found at i:3578335 original size:21 final size:21
Alignment explanation
Indices: 3578288--3578335 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
3578278 AAGGGAGATC
3578288 TTTTGATTTCTTGGTTATCTTA
1 TTTT-ATTTCTTGGTTATCTTA
* * * *
3578310 CTTTATTTTTTGTTTATCTTG
1 TTTTATTTCTTGGTTATCTTA
3578331 TTTTA
1 TTTTA
3578336 ATCTTTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.12, C:0.08, G:0.10, T:0.69
Consensus pattern (21 bp):
TTTTATTTCTTGGTTATCTTA
Found at i:3578733 original size:27 final size:26
Alignment explanation
Indices: 3578677--3578726 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
3578667 TTATTTTTCT
*
3578677 ATTTAAAAAAACAAAAAAAAATTAAA
1 ATTTAAAAAAACAAAAAAAAATGAAA
* *
3578703 ATTTCAAAAAA-AAAAGAAAATGAA
1 ATTTAAAAAAACAAAAAAAAATGAA
3578727 GGAATTTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (26 bp):
ATTTAAAAAAACAAAAAAAAATGAAA
Found at i:3582972 original size:22 final size:22
Alignment explanation
Indices: 3582939--3582980 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3582929 CAATTTCTTT
*
3582939 ATCTTTTGTTTATCTTGTTTTA
1 ATCTTTTGTTTACCTTGTTTTA
3582961 ATCTTGTT-TTTACCTTGTTT
1 ATCTT-TTGTTTACCTTGTTT
3582981 CCAGCATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.67
Consensus pattern (22 bp):
ATCTTTTGTTTACCTTGTTTTA
Found at i:3587390 original size:17 final size:17
Alignment explanation
Indices: 3587368--3587400 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3587358 CCATGTACAT
*
3587368 GCCTTGTGACTAGCCAA
1 GCCTTGTGACCAGCCAA
3587385 GCCTTGTGACCAGCCA
1 GCCTTGTGACCAGCCA
3587401 GGCCATGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.33, G:0.24, T:0.21
Consensus pattern (17 bp):
GCCTTGTGACCAGCCAA
Found at i:3588272 original size:14 final size:14
Alignment explanation
Indices: 3588253--3588304 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
3588243 CAAGCACTCC
3588253 AAAAGAAGAAAATA
1 AAAAGAAGAAAATA
3588267 AAAAGAAGAAAA-A
1 AAAAGAAGAAAATA
*
3588280 AAAA-AAGCAAAT-
1 AAAAGAAGAAAATA
3588292 AAAAGAAAGAAAA
1 AAAAG-AAGAAAA
3588305 AATGAAGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 10 0.30
13 5 0.15
14 18 0.55
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAAGAAGAAAATA
Found at i:3588291 original size:26 final size:26
Alignment explanation
Indices: 3588253--3588306 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3588243 CAAGCACTCC
*
3588253 AAAAGAAGAAAATAAAA-AGAAGAAAA
1 AAAAAAAGAAAATAAAAGA-AAGAAAA
*
3588279 AAAAAAAGCAAATAAAAGAAAGAAAA
1 AAAAAAAGAAAATAAAAGAAAGAAAA
3588305 AA
1 AA
3588307 TGAAGCACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (26 bp):
AAAAAAAGAAAATAAAAGAAAGAAAA
Found at i:3588665 original size:22 final size:22
Alignment explanation
Indices: 3588639--3588688 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
3588629 CACGAGCATA
3588639 TTGAGTGATATTCAAGTTTTCT
1 TTGAGTGATATTCAAGTTTTCT
3588661 TTGAGTGATATTCAAGTTTTCT
1 TTGAGTGATATTCAAGTTTTCT
*
3588683 TGGAGT
1 TTGAGT
3588689 AAACTCGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.48
Consensus pattern (22 bp):
TTGAGTGATATTCAAGTTTTCT
Found at i:3590133 original size:21 final size:21
Alignment explanation
Indices: 3590108--3590149 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3590098 ATATAATTAT
3590108 TTTTATAGATAGTTTTCATGA
1 TTTTATAGATAGTTTTCATGA
*
3590129 TTTTATAGATATTTTTCATGA
1 TTTTATAGATAGTTTTCATGA
3590150 ATAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTTATAGATAGTTTTCATGA
Found at i:3590272 original size:18 final size:18
Alignment explanation
Indices: 3590249--3590284 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3590239 CTCTTAAGTT
3590249 TAAGTTAAGTAAAAAAAA
1 TAAGTTAAGTAAAAAAAA
3590267 TAAGTTAAGTAAAAAAAA
1 TAAGTTAAGTAAAAAAAA
3590285 AGGTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (18 bp):
TAAGTTAAGTAAAAAAAA
Found at i:3597261 original size:31 final size:31
Alignment explanation
Indices: 3597226--3597287 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3597216 CTCCTGTTAT
* * **
3597226 TTACTCGGGCTGAGCAGTACTTACTGAATCA
1 TTACTCGGACTGAGAAACACTTACTGAATCA
3597257 TTACTCGGACTGAGAAACACTTACTGAATCA
1 TTACTCGGACTGAGAAACACTTACTGAATCA
3597288 GAGCAGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (31 bp):
TTACTCGGACTGAGAAACACTTACTGAATCA
Found at i:3597842 original size:29 final size:29
Alignment explanation
Indices: 3597788--3597844 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3597778 GCCAGGGTTA
**
3597788 CTAAACGATCTGGGTTTTCCTGGGATAAT
1 CTAAACGATCTGGGTTCACCTGGGATAAT
*
3597817 CTAAACGGATCTGGGTTCACGT-GGATAA
1 CTAAAC-GATCTGGGTTCACCTGGGATAA
3597845 GATAAATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (29 bp):
CTAAACGATCTGGGTTCACCTGGGATAAT
Found at i:3601871 original size:31 final size:30
Alignment explanation
Indices: 3601831--3601906 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 30
3601821 TGAGGCGACC
* * *
3601831 CTTGCGTAGGCTCTGTGGCCCTGAGAGTTTT
1 CTTGGGTAGGCTCT-TGGCCCCGAGAATTTT
3601862 CTTGGGTAGGCCTCCTTGGCCCCGAGAATTTT
1 CTTGGGTAGG-CT-CTTGGCCCCGAGAATTTT
3601894 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
3601907 ACAGGCCCCG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 1 0.03
31 11 0.28
32 26 0.65
33 2 0.05
ACGTcount: A:0.11, C:0.25, G:0.32, T:0.33
Consensus pattern (30 bp):
CTTGGGTAGGCTCTTGGCCCCGAGAATTTT
Found at i:3601917 original size:31 final size:32
Alignment explanation
Indices: 3601847--3601918 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
3601837 TAGGCTCTGT
* * *
3601847 GGCCCTGAGAGTTTTCTTGGGTAGGCCTCCTT
1 GGCCCCGAGAATTTTCTTGGGTAGGCCTCCTA
3601879 GGCCCCGAGAATTTTCTTGGGTAGG-CTCAC-A
1 GGCCCCGAGAATTTTCTTGGGTAGGCCTC-CTA
3601910 GGCCCCGAG
1 GGCCCCGAG
3601919 GTACTCCCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.14, C:0.28, G:0.32, T:0.26
Consensus pattern (32 bp):
GGCCCCGAGAATTTTCTTGGGTAGGCCTCCTA
Found at i:3602618 original size:31 final size:31
Alignment explanation
Indices: 3602580--3602652 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
3602570 TAAGGCGACC
* * * *
3602580 CTTGGGTAGGCTCTGCG-GCCCTGATATTTTT
1 CTTGGGTAGGC-CTCCGACCCCTGAGAATTTT
3602611 CTTGGGTAGGCCTCCGTACCCCTGAGAATTTT
1 CTTGGGTAGGCCTCCG-ACCCCTGAGAATTTT
3602643 CTTGGGTAGG
1 CTTGGGTAGG
3602653 TTCGTAGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 4 0.11
31 11 0.31
32 21 0.58
ACGTcount: A:0.12, C:0.23, G:0.30, T:0.34
Consensus pattern (31 bp):
CTTGGGTAGGCCTCCGACCCCTGAGAATTTT
Found at i:3606590 original size:2 final size:2
Alignment explanation
Indices: 3606585--3606627 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
3606575 TGCACAACAA
*
3606585 AT AT AT -T AGT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3606627 A
1 A
3606628 CTCTGTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3608565 original size:2 final size:2
Alignment explanation
Indices: 3608554--3608585 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3608544 TCATCGACTC
3608554 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3608586 TATTAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3614407 original size:17 final size:20
Alignment explanation
Indices: 3614385--3614432 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
3614375 GTTGTCATCT
3614385 AAAATATTTAA-A-A-ATAA
1 AAAATATTTAATACATATAA
*
3614402 AAAATATTAAATACATATAA
1 AAAATATTTAATACATATAA
*
3614422 AAAATAATTAA
1 AAAATATTTAA
3614433 GTTAATCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 1 0.04
19 1 0.04
20 13 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATATTTAATACATATAA
Found at i:3615523 original size:15 final size:16
Alignment explanation
Indices: 3615493--3615528 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
3615483 AAAAAGGGAG
3615493 AACAAGAAGAAGAGAAGA
1 AACAAGAA-AAGA-AAGA
3615511 AACAAGAAAAGAAAGA
1 AACAAGAAAAGAAAGA
3615527 AA
1 AA
3615529 AATGTGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (16 bp):
AACAAGAAAAGAAAGA
Found at i:3619578 original size:18 final size:18
Alignment explanation
Indices: 3619555--3619594 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3619545 GAGAGAAGTA
3619555 AAAATAAAGAAATAAAAT
1 AAAATAAAGAAATAAAAT
*
3619573 AAAATAAAGGAATAAAAT
1 AAAATAAAGAAATAAAAT
3619591 AAAA
1 AAAA
3619595 AGAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAATAAAGAAATAAAAT
Found at i:3623360 original size:31 final size:29
Alignment explanation
Indices: 3623301--3623386 Score: 109
Period size: 31 Copynumber: 2.9 Consensus size: 29
3623291 AAAATTTAGA
3623301 TAGTGACCAAAATAGAAATTTTAAAAGTT
1 TAGTGACCAAAATAGAAATTTTAAAAGTT
* * *
3623330 TAGTGACTAAAGTATAAACTTTTGAAAAGTT
1 TAGTGACCAAAATAGAAA-TTTT-AAAAGTT
* *
3623361 TAGGGACCAAAATAGTAATTTTAAAA
1 TAGTGACCAAAATAGAAATTTTAAAA
3623387 AGTTACATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 19 0.40
30 8 0.17
31 20 0.43
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (29 bp):
TAGTGACCAAAATAGAAATTTTAAAAGTT
Found at i:3623789 original size:30 final size:31
Alignment explanation
Indices: 3623740--3623800 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
3623730 TTTGACTTAG
3623740 GGAAGATGATAAGGGTTAGGTGTCTTGGTTT
1 GGAAGATGATAAGGGTTAGGTGTCTTGGTTT
3623771 GGAAGATGATAA-GGTTAGGTGTCTTGGTTT
1 GGAAGATGATAAGGGTTAGGTGTCTTGGTTT
3623801 AATGGTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.36
Consensus pattern (31 bp):
GGAAGATGATAAGGGTTAGGTGTCTTGGTTT
Found at i:3625116 original size:24 final size:24
Alignment explanation
Indices: 3625069--3625117 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3625059 TGCATGACAT
* *
3625069 TGTACATAGATGTTTTATAGATCA
1 TGTACATAGATGTTTTAAACATCA
3625093 TGTACATAGATGTTTTAAACATCA
1 TGTACATAGATGTTTTAAACATCA
3625117 T
1 T
3625118 CTGGAATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (24 bp):
TGTACATAGATGTTTTAAACATCA
Found at i:3627577 original size:93 final size:94
Alignment explanation
Indices: 3627465--3627660 Score: 211
Period size: 94 Copynumber: 2.1 Consensus size: 94
3627455 ATACAATTAT
* ** * * *
3627465 TATCGATACTATGAGGAAA-GTACCAATACCATTGATTCAGAATGTAGAAATGGTATCGATACTG
1 TATCGATACTAAGAGGAAAGGTACCAATACCAAGGATCCAGAATGTAAAAATAGTATCGATAC--
* *
3627529 TAACA-G-AGTATCGGTACCATAGTATAGAAG
64 TAA-AGGAAGTATCAGTACCAAAGTATAGAAG
* * * * *
3627559 TATCGGTACTAAGA-GAAAGGTATCGATACCAAGGATCCATAATGTAAAAATATTATCGATACTA
1 TATCGATACTAAGAGGAAAGGTACCAATACCAAGGATCCAGAATGTAAAAATAGTATCGATACTA
3627623 AAGGAAGTATCAGTACCAAAGTATAGAAG
66 AAGGAAGTATCAGTACCAAAGTATAGAAG
*
3627652 TATTGATAC
1 TATCGATAC
3627661 CATGGTAGGG
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
91 1 0.01
92 4 0.05
93 33 0.39
94 46 0.55
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (94 bp):
TATCGATACTAAGAGGAAAGGTACCAATACCAAGGATCCAGAATGTAAAAATAGTATCGATACTA
AAGGAAGTATCAGTACCAAAGTATAGAAG
Found at i:3628053 original size:54 final size:54
Alignment explanation
Indices: 3627989--3628394 Score: 609
Period size: 54 Copynumber: 7.5 Consensus size: 54
3627979 TAAGTATTAC
* *
3627989 AATTACCGTATTGGCACTATGTATGCAA-TATAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACT-TAAGAAATTCATAATGAGTTTATG
* *
3628043 AATTTCCGTATTGGCACTATGTGTGCAAATTAAGAAATTCATAAAGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * *
3628097 AATTTTCGTATTGACACTATTTGTGCAACTTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * *
3628151 AATTTCAGTATTGGTACTATGTGTGCAACTTAAGAAAATCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
*
3628205 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTACG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
*
3628259 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGATTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
* * * * *
3628313 AATTTTCGTATTAGCACTATATGTGCAATTTAAGAAATTCATAATAAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
**
3628367 AATTTTTGTATTGGCAC-ATGGTGTGCAA
1 AATTTCCGTATTGGCACTAT-GTGTGCAA
3628395 ACTACTTAAT
Statistics
Matches: 321, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
53 2 0.01
54 318 0.99
55 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (54 bp):
AATTTCCGTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATG
Found at i:3633769 original size:19 final size:21
Alignment explanation
Indices: 3633745--3633815 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 21
3633735 TGTAGAAATG
3633745 GTATCGATACTATA-ATAG-A
1 GTATCGATACTATAGATAGAA
*
3633764 GTATCGATACCATAGTATAGAA
1 GTATCGATACTATAG-ATAGAA
* *
3633786 GTATCGGTACTA-AGAGA-AA
1 GTATCGATACTATAGATAGAA
3633805 GGTATCGATAC
1 -GTATCGATAC
3633816 CAAGGATCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 15 0.35
20 11 0.26
21 6 0.14
22 11 0.26
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (21 bp):
GTATCGATACTATAGATAGAA
Found at i:3634284 original size:54 final size:53
Alignment explanation
Indices: 3634225--3634613 Score: 589
Period size: 54 Copynumber: 7.2 Consensus size: 53
3634215 TGTAATTACC
* *
3634225 GTATTGGCACTTTGTGTGCAACTTAAGAAATTTATAATGAGTTTATGAATTTCT
1 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTT-T
3634279 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
1 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
* * *
3634332 CGTATTGACACTATTTGTGCAACTTAAGAAATTCATAATGCGTTTATGAATTTT
1 -GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
* *
3634386 AGTATTGGCACTATGTGTGCAACTTAAGAAAATCATAATGAGTTTATGAATTTCC
1 -GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTT-T
*
3634441 GTATTGGCACTATGTGTGCAACTTAAAAAATTCATAATGAGTTTATGAATTTCT
1 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTT-T
* *
3634495 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGATTTTATAAATTTT
1 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
* * * *
3634548 CGTATTAGCACTATATGTACAACTTAAGAAATTCATAATAAGTTTATGAATTTTT
1 -GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAA-TTTT
3634603 GTATTGGCACT
1 GTATTGGCACT
3634614 GGGTGAGAAA
Statistics
Matches: 307, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
53 2 0.01
54 301 0.98
55 4 0.01
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (53 bp):
GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTT
Found at i:3640223 original size:22 final size:23
Alignment explanation
Indices: 3640180--3640224 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3640170 TAAGGTTTCA
**
3640180 TTTGGTTAGTTTTTCGTTTCATT
1 TTTGGTTAGTTTTTCGAATCATT
*
3640203 TTTGGTTGGTTTTT-GAATCATT
1 TTTGGTTAGTTTTTCGAATCATT
3640225 GAGTATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.11, C:0.07, G:0.20, T:0.62
Consensus pattern (23 bp):
TTTGGTTAGTTTTTCGAATCATT
Found at i:3641365 original size:54 final size:54
Alignment explanation
Indices: 3641219--3641615 Score: 609
Period size: 54 Copynumber: 7.4 Consensus size: 54
3641209 GCAATTACCT
* *
3641219 TATTGGCACTATGTGTGCAACATAAGAAATTTATAATGAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
3641273 TATTGGCACTA-GTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
** *
3641326 TATTGATACTATTTGTGCAACTTAAGAAATTCATAATGAGTTTATGAA-TTTCAG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTC-G
* *
3641380 TATTGGCACTATGTGTGCCACTTAAGAAAATCATAATGAGTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
* *
3641434 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAATTTATGAATTTCCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
*
3641488 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGATTTTATGAATTTTCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
* * * * * *
3641542 TATTAGCACTATATGTGCAACATAAGAAATTCATAATAAGCTTATGAATTTTTG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
**
3641596 TATTGGCACTGGGTGTGCAA
1 TATTGGCACTATGTGTGCAA
3641616 ACTACTTAAT
Statistics
Matches: 313, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
53 53 0.17
54 256 0.82
55 4 0.01
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (54 bp):
TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
Found at i:3643929 original size:158 final size:153
Alignment explanation
Indices: 3643685--3643993 Score: 478
Period size: 158 Copynumber: 2.0 Consensus size: 153
3643675 ATGAATTTCT
* *
3643685 GTATTGCCACTATGTGCGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGGCACT
1 GTATTGCCACTATGTGCGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGCACT
3643750 ATGTGTGCAACTTAAGAAATTCATAATAAGTTTATTATATGAATTTCAGTATTGGCACTATGTGT
66 ATGTGTGCAACTTAAGAAATTCATAATAAG----TT-TATGAATTTCAGTATTGGCACTATGTGT
*
3643815 -ACAACTTAATAAATTCATAATGAGTTCC
126 GA-AACTTAATAAATTCATAATAAGTTCC
* *
3643843 GTATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAA-TTTCTATATTGGCAC
1 GTATTGCCACTATGTGCGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTC-ATATTGGCAC
* *
3643907 TATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATTGGCACTATGTGTGAAA
65 TATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCAGTATTGGCACTATGTGTGAAA
3643972 CTTAATAAATTCATAATAAGTT
130 CTTAATAAATTCATAATAAGTT
3643994 TATGAATTTT
Statistics
Matches: 142, Mismatches: 7, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
153 50 0.35
154 3 0.02
157 4 0.03
158 85 0.60
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (153 bp):
GTATTGCCACTATGTGCGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGCACT
ATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCAGTATTGGCACTATGTGTGAAAC
TTAATAAATTCATAATAAGTTCC
Found at i:3644022 original size:54 final size:54
Alignment explanation
Indices: 3643632--3644015 Score: 491
Period size: 54 Copynumber: 7.2 Consensus size: 54
3643622 ACAATTACCA
* * * * *
3643632 TATTGGCATTGTGTGTGCAACGTAAGAAATTCATAATGAGTTAATGAATTTCTG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTG
* * *
3643686 TATTGCCACTATGTGCGCAACTTAAGAAATTCATAATGAGTTTATGAATTT-TCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCT-G
*
3643740 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATTATATGAATTTCAG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAG----TT-TATGAATTTCTG
* * *
3643799 TATTGGCACTATGTGTACAACTTAATAAATTCATAAT--G---A-G---TTCCG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTG
*
3643844 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTA
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTG
*
3643898 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTG
* * *
3643952 TATTGGCACTATGTGTGAAACTTAATAAATTCATAATAAGTTTATGAATTTTTG
1 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTG
3644006 TATTGGCACT
1 TATTGGCACT
3644016 GGGTGTGCTA
Statistics
Matches: 291, Mismatches: 23, Indels: 32
0.84 0.07 0.09
Matches are distributed among these distances:
45 39 0.13
47 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
53 1 0.00
54 198 0.68
57 1 0.00
58 2 0.01
59 45 0.15
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (54 bp):
TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTG
Found at i:3644055 original size:108 final size:108
Alignment explanation
Indices: 3643632--3644066 Score: 410
Period size: 108 Copynumber: 4.1 Consensus size: 108
3643622 ACAATTACCA
* * * * * * * *
3643632 TATTGGCATTGTGTGTGCAACGTAAGAAATTCATAATGAGTTAATGAATTTCTGTATTGCCACTA
1 TATTGGCACTATGTGTGAAACTTAAGAAATTCATAATAAGTTTATGAATTTCTATATTGGCACTA
* * * * *
3643697 TGTGCGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTCG
66 GGTGTGCAACTTAAGAAATTCATAATAAATTTATGAATTTACG
*
3643740 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATTATATGAATTTC-AGTATTG
1 TATTGGCACTATGTGTGAAACTTAAGAAATTCATAATAAG----TT-TATGAATTTCTA-TATTG
* * * * *
3643804 GCACTATGTGTACAACTTAATAAATTC---AT--A---ATG-AGTTCCG
60 GCACTAGGTGTGCAACTTAAGAAATTCATAATAAATTTATGAATTTACG
*
3643844 TATTGGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTATATTGGCACTA
1 TATTGGCACTATGTGTGAAACTTAAGAAATTCATAATAAGTTTATGAATTTCTATATTGGCACTA
* * *
3643909 TGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTT-CTG
66 GGTGTGCAACTTAAGAAATTCATAATAAATTTATGAATTTAC-G
* * * *
3643952 TATTGGCACTATGTGTGAAACTTAATAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACTG
1 TATTGGCACTATGTGTGAAACTTAAGAAATTCATAATAAGTTTATGAATTTCTATATTGGCACTA
*** * *
3644017 GGTGTGCTAAC-TACTTAATTTATAGTAAATTTGA-GAATTTACG
66 GGTGTGC-AACTTAAGAAATTCATAATAAATTT-ATGAATTTACG
3644060 TATTGGC
1 TATTGGC
3644067 CCTACTGGTG
Statistics
Matches: 277, Mismatches: 30, Indels: 40
0.80 0.09 0.12
Matches are distributed among these distances:
99 40 0.14
100 3 0.01
102 2 0.01
104 45 0.16
105 3 0.01
107 4 0.01
108 134 0.48
109 5 0.02
110 2 0.01
112 2 0.01
113 37 0.13
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (108 bp):
TATTGGCACTATGTGTGAAACTTAAGAAATTCATAATAAGTTTATGAATTTCTATATTGGCACTA
GGTGTGCAACTTAAGAAATTCATAATAAATTTATGAATTTACG
Found at i:3644915 original size:81 final size:81
Alignment explanation
Indices: 3644777--3645172 Score: 589
Period size: 81 Copynumber: 4.9 Consensus size: 81
3644767 ACAGCTAGGC
* ** * *
3644777 ATTTAGCCTTTCATCTAACTACCATAATTGATA-CTTATCTGTCAAATGCACAACTAGGCAATTA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTT-TCTGTCAAATGCACAGCTAGGCAATTA
3644841 ATCTTTTACTCAAAGGT
65 ATCTTTTACTCAAAGGT
* * *
3644858 ATTTAACCTTTCATCTAAGTGGCATAATTGACGCCTTTCTGTCAAATGCACAGCTAGGCAATTCA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
3644923 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
3644939 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
* *
3645004 ACTTTTACTCAAAGTT
66 TCTTTTACTCAAAGGT
* *
3645020 ATTTAACCTTTCATCTAAATGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGG-ATATTA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCA-ATTA
3645084 ATCTTTTACTCAAAGGT
65 ATCTTTTACTCAAAGGT
* * * * * * *
3645101 ATTTAACCTTTCATCTAACTGGAATAATTGATACATTTCTATTAAATTCATAGCTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
3645166 TCTTTTA
66 TCTTTTA
3645173 TTTAAAACAG
Statistics
Matches: 287, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.00
81 282 0.98
82 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
TCTTTTACTCAAAGGT
Found at i:3651901 original size:81 final size:81
Alignment explanation
Indices: 3651565--3651895 Score: 475
Period size: 81 Copynumber: 4.1 Consensus size: 81
3651555 AAGCATTTAG
* * * * *
3651565 TCTTTTACTCTAA-GTCATTTAGCATTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGT-ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATG
* *
3651629 CACAGCTAAGCATTTAA
65 CACAGCTAGGCAATTAA
* * *
3651646 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
* *
3651711 ACAGTTAGGCTATTAA
66 ACAGCTAGGCAATTAA
* * *
3651727 ACTTTTACTCAAAGATATTTAATCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
3651792 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* **
3651808 TCTTTTACTTAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
*
3651873 ACAGCTAGGTAATTAA
66 ACAGCTAGGCAATTAA
3651889 TCTTTTA
1 TCTTTTA
3651896 TTTAAAATAG
Statistics
Matches: 224, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
81 223 1.00
82 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:3659864 original size:20 final size:20
Alignment explanation
Indices: 3659839--3659885 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3659829 AGGTAAAATG
*
3659839 TCTGTAGTCTGCGGATTATA
1 TCTGTAGTCTGCGGATTACA
3659859 TCTGTAGTCTGCGGATTACA
1 TCTGTAGTCTGCGGATTACA
3659879 TCTGTAG
1 TCTGTAG
3659886 GTATCTGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TCTGTAGTCTGCGGATTACA
Found at i:3660055 original size:31 final size:31
Alignment explanation
Indices: 3660014--3660072 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3660004 AACTTAAAAG
*
3660014 AATTTAACAATACTGAAATTTAAATAATTTT
1 AATTTAACAATACTAAAATTTAAATAATTTT
*
3660045 AATTTTACAATACTAAAATTTAAATAAT
1 AATTTAACAATACTAAAATTTAAATAAT
3660073 CTATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.41
Consensus pattern (31 bp):
AATTTAACAATACTAAAATTTAAATAATTTT
Found at i:3660843 original size:2 final size:2
Alignment explanation
Indices: 3660838--3660863 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3660828 AAATTACTTA
3660838 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
3660864 TTTAAAATTT
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:3661817 original size:2 final size:2
Alignment explanation
Indices: 3661812--3661891 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
3661802 ACACACACAC
*
3661812 AT AT AT AT AT AT AC 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
3661854 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
3661892 TAAATTATTG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3666110 original size:16 final size:16
Alignment explanation
Indices: 3666089--3666141 Score: 70
Period size: 16 Copynumber: 3.1 Consensus size: 16
3666079 CTAAATTGAA
3666089 AATAATAAAAAATATT
1 AATAATAAAAAATATT
3666105 AATAATAAAAAATATAT
1 AATAATAAAAAATAT-T
3666122 AATATATAATATAAATATT
1 AATA-ATAA-A-AAATATT
3666141 A
1 A
3666142 TATGCATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 15 0.45
17 5 0.15
18 4 0.12
19 3 0.09
20 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAATAAAAAATATT
Found at i:3666250 original size:42 final size:42
Alignment explanation
Indices: 3666122--3666259 Score: 99
Period size: 42 Copynumber: 3.4 Consensus size: 42
3666112 AAAAATATAT
* * * *
3666122 AATATATAATATA-AATAT-TATATGCATACTATATAT-TCTAC
1 AATATATATTATATAATATATATATACATA-TACATATAT-TAA
* * * * *
3666163 TATATATATAATACT-ATATATATATATATATATATATATTCA
1 AATATATATTATA-TAATATATATATACATATACATATATTAA
* * *
3666205 AATATATATTATATAATTTATATATACATATACATTTTTTAA
1 AATATATATTATATAATATATATATACATATACATATATTAA
3666247 AATA-ATA-TATATA
1 AATATATATTATATA
3666260 CTAAAACATT
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
40 6 0.08
41 14 0.18
42 48 0.62
43 9 0.12
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.46
Consensus pattern (42 bp):
AATATATATTATATAATATATATATACATATACATATATTAA
Found at i:3666256 original size:2 final size:2
Alignment explanation
Indices: 3666116--3666236 Score: 87
Period size: 2 Copynumber: 62.5 Consensus size: 2
3666106 ATAATAAAAA
* **
3666116 AT AT AT A- AT AT AT A- AT AT AA AT AT -T AT AT GC AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
3666156 AT -T CT ACT AT AT AT AT A- AT ACT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * *
3666198 AT AT -T CAA AT AT AT AT -T AT AT A- AT TT AT AT AT AC AT AT A
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3666237 CATTTTTTAA
Statistics
Matches: 94, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
1 8 0.09
2 80 0.85
3 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3666305 original size:28 final size:28
Alignment explanation
Indices: 3666248--3666306 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3666238 ATTTTTTAAA
* *
3666248 ATAATATATATACTAAAACATTAACCAT
1 ATAATATATATACTAAAACATAAACAAT
* *
3666276 ATAATATATATTA-TAAAATATAAATAAT
1 ATAATATATA-TACTAAAACATAAACAAT
3666304 ATA
1 ATA
3666307 TAAAATACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAATATATATACTAAAACATAAACAAT
Found at i:3671099 original size:118 final size:127
Alignment explanation
Indices: 3670896--3671129 Score: 369
Period size: 118 Copynumber: 1.9 Consensus size: 127
3670886 GTCTAGTAAG
3670896 AAATAGGTAAATCAGACCAAATAGAAATTTCGGGAAAAATTGAAGGATAATAAATTAGGCTTCAA
1 AAATAGGTAAAT-AGACCAAATAGAAATTTCGGGAAAAATTGAAGGATAATAAATTAGGCTTC--
3670961 AATATTATTTCCACATTTTAAAATGATCGAAAATAATAGAAACCATTGGATAGAGGGTTAATTAG
63 -ATATTATTTCCACATTTTAAAATGATCGAAAATAATAGAAACCATTGGATAGAGGGTTAATTAG
3671026 T
127 T
3671027 AAATAGGTAAAT-GA-CAAATAGAAATTTCGGG-AAAA-TGAA-GATAAT-AATTAGGCTTC-T-
1 AAATAGGTAAATAGACCAAATAGAAATTTCGGGAAAAATTGAAGGATAATAAATTAGGCTTCATA
3671084 TT-TTTCCACATTTTAAAATGATCGAAAATAATAGAAACCATTGGAT
66 TTATTTCCACATTTTAAAATGATCGAAAATAATAGAAACCATTGGAT
3671130 TTGAGGATTT
Statistics
Matches: 103, Mismatches: 0, Indels: 13
0.89 0.00 0.11
Matches are distributed among these distances:
118 44 0.43
119 2 0.02
120 1 0.01
124 11 0.11
125 6 0.06
126 4 0.04
127 4 0.04
128 17 0.17
129 2 0.02
131 12 0.12
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.29
Consensus pattern (127 bp):
AAATAGGTAAATAGACCAAATAGAAATTTCGGGAAAAATTGAAGGATAATAAATTAGGCTTCATA
TTATTTCCACATTTTAAAATGATCGAAAATAATAGAAACCATTGGATAGAGGGTTAATTAGT
Found at i:3679643 original size:21 final size:21
Alignment explanation
Indices: 3679613--3679663 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3679603 GGCGTGTATT
*
3679613 AATACCTTA-TTAATGTTTTA
1 AATACCTTATTTAATGCTTTA
*
3679633 AATACGCTTATTTATTGCTTTA
1 AATAC-CTTATTTAATGCTTTA
*
3679655 AATAACTTA
1 AATACCTTA
3679664 GTTTGTCGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 8 0.31
22 13 0.50
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (21 bp):
AATACCTTATTTAATGCTTTA
Found at i:3691196 original size:20 final size:20
Alignment explanation
Indices: 3691168--3691210 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3691158 TGAAAAATGG
3691168 TAAAAAAAAT-AAATAAAAGA
1 TAAAAAAAATGAAA-AAAAGA
* *
3691188 TAAATAAAATGAAAAGAAGA
1 TAAAAAAAATGAAAAAAAGA
3691208 TAA
1 TAA
3691211 TCCTCACGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAAAAATGAAAAAAAGA
Found at i:3700039 original size:21 final size:21
Alignment explanation
Indices: 3699987--3700041 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
3699977 TATTCGAGAA
*
3699987 AGTATAGATACTCTCATATAG
1 AGTATTGATACTCTCATATAG
3700008 AGGT-TTCGATACT-TCATATAGG
1 A-GTATT-GATACTCTCATATA-G
3700030 AGTATTGATACT
1 AGTATTGATACT
3700042 AATGGAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (21 bp):
AGTATTGATACTCTCATATAG
Found at i:3703312 original size:45 final size:44
Alignment explanation
Indices: 3703143--3703440 Score: 443
Period size: 44 Copynumber: 6.7 Consensus size: 44
3703133 GTATATGATA
* *
3703143 ACGAGCTTATCGAATAATGGTAAGTATATGGGTAAAATAAGCTT
1 ACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTT
3703187 ACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTT
1 ACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTT
* *
3703231 ATGAGCTTATGGAATAATGGTAAGTATATTGATAAAATAAGCTT
1 ACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTT
* * *
3703275 TCGAGCTTAGGGATTTAATGGTAAGTATATTGGTAAAATAAGCTT
1 ACGAGCTTATGGA-ATAATGGTAAGTATATTGGTAAAATAAGCTT
**
3703320 ACGAGCTTATGGAATAATGGTAAGTATATTAATAAAATAAGCTT
1 ACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTT
* *
3703364 ACGAGCTTAGGGATTTAATGGTAAGTATATTGGTAAAATAAGCTT
1 ACGAGCTTATGGA-ATAATGGTAAGTATATTGGTAAAATAAGCTT
* * *
3703409 ACGAGCTTATGGATTAAATGATATGTATATTG
1 ACGAGCTTATGGAAT-AATGGTAAGTATATTG
3703441 ATAAGAAATT
Statistics
Matches: 230, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
44 136 0.59
45 94 0.41
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
ACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTT
Found at i:3703328 original size:89 final size:89
Alignment explanation
Indices: 3703143--3703444 Score: 489
Period size: 89 Copynumber: 3.4 Consensus size: 89
3703133 GTATATGATA
* * * * *
3703143 ACGAGCTTATCGAATAATGGTAAGTATATGGGTAAAATAAGCTTACGAGCTTATGGA-ATAATGG
1 ACGAGCTTATGGAATAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATGG
3703207 TAAGTATATTGGTAAAATAAGCTT
66 TAAGTATATTGGTAAAATAAGCTT
* *
3703231 ATGAGCTTATGGAATAATGGTAAGTATATTGATAAAATAAGCTTTCGAGCTTAGGGATTTAATGG
1 ACGAGCTTATGGAATAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATGG
3703296 TAAGTATATTGGTAAAATAAGCTT
66 TAAGTATATTGGTAAAATAAGCTT
*
3703320 ACGAGCTTATGGAATAATGGTAAGTATATTAATAAAATAAGCTTACGAGCTTAGGGATTTAATGG
1 ACGAGCTTATGGAATAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATGG
3703385 TAAGTATATTGGTAAAATAAGCTT
66 TAAGTATATTGGTAAAATAAGCTT
* * *
3703409 ACGAGCTTATGGATTAAATGATATGTATATTGATAA
1 ACGAGCTTATGGAAT-AATGGTAAGTATATTGATAA
3703445 GAAATTTTAT
Statistics
Matches: 198, Mismatches: 14, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
88 51 0.26
89 130 0.66
90 17 0.09
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (89 bp):
ACGAGCTTATGGAATAATGGTAAGTATATTGATAAAATAAGCTTACGAGCTTAGGGATTTAATGG
TAAGTATATTGGTAAAATAAGCTT
Found at i:3709750 original size:23 final size:23
Alignment explanation
Indices: 3709724--3709797 Score: 139
Period size: 23 Copynumber: 3.2 Consensus size: 23
3709714 GATGTAATCA
3709724 GTTAGTTGTGTAGTTAGGAAGCT
1 GTTAGTTGTGTAGTTAGGAAGCT
3709747 GTTAGTTGTGTAGTTAGGAAGCT
1 GTTAGTTGTGTAGTTAGGAAGCT
*
3709770 GTTAGTTGTGTAGTGAGGAAGCT
1 GTTAGTTGTGTAGTTAGGAAGCT
3709793 GTTAG
1 GTTAG
3709798 GAGCAATTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.22, C:0.04, G:0.36, T:0.38
Consensus pattern (23 bp):
GTTAGTTGTGTAGTTAGGAAGCT
Found at i:3713581 original size:19 final size:18
Alignment explanation
Indices: 3713557--3713596 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
3713547 GTTTAAGTAC
3713557 TTAGTTTATTTCCTTAATG
1 TTAGTTTATTTCCTT-ATG
3713576 TTAGTTTATTTCCTTATG
1 TTAGTTTATTTCCTTATG
3713594 TTA
1 TTA
3713597 TGTATATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (18 bp):
TTAGTTTATTTCCTTATG
Found at i:3714755 original size:22 final size:21
Alignment explanation
Indices: 3714725--3714765 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3714715 CATGTCCATT
*
3714725 TCATCATCAATACCATCAACA
1 TCATCATCAAGACCATCAACA
3714746 TCATCCATCAAGACCATCAA
1 TCAT-CATCAAGACCATCAA
3714766 TTACGTAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.22
Consensus pattern (21 bp):
TCATCATCAAGACCATCAACA
Found at i:3715057 original size:5 final size:5
Alignment explanation
Indices: 3715049--3715076 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3715039 AAGAAATTCA
3715049 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
3715077 GACTCCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3718024 original size:2 final size:2
Alignment explanation
Indices: 3718017--3718045 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3718007 AGTTATTTTC
3718017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3718046 GTTATTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3721202 original size:31 final size:33
Alignment explanation
Indices: 3721158--3721248 Score: 114
Period size: 32 Copynumber: 2.7 Consensus size: 33
3721148 ACATAAATAG
*
3721158 AAAAATAATAAATAGAAAAACCAAACATTCATT
1 AAAAACAATAAATAGAAAAACCAAACATTCATT
*
3721191 -AAAA-AATAAATAGAAAAACCCAATCATTCATT
1 AAAAACAATAAATAGAAAAA-CCAAACATTCATT
3721223 CAAAAAACAATAAATAGGAAAAACCA
1 --AAAAACAATAAATA-GAAAAACCA
3721249 TTACACTCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
31 14 0.27
32 16 0.31
35 4 0.08
36 11 0.22
37 6 0.12
ACGTcount: A:0.64, C:0.14, G:0.04, T:0.18
Consensus pattern (33 bp):
AAAAACAATAAATAGAAAAACCAAACATTCATT
Found at i:3725255 original size:18 final size:17
Alignment explanation
Indices: 3725232--3725269 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3725222 AAAACAAGCA
3725232 TCTCTTCATGA-TCTTCAT
1 TCTCTTCA-GATTCTTC-T
3725250 TCTCTTCAGATTCTTCT
1 TCTCTTCAGATTCTTCT
3725267 TCT
1 TCT
3725270 TGTATTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.13, C:0.29, G:0.05, T:0.53
Consensus pattern (17 bp):
TCTCTTCAGATTCTTCT
Found at i:3726840 original size:23 final size:22
Alignment explanation
Indices: 3726828--3726874 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
3726818 GCTTTGTTCT
3726828 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTC-ATTTCTTC
3726851 TTTTGAGTGCTTT-ATTTC-TC
1 TTTTGAGTGCTTTCATTTCTTC
3726871 TTTT
1 TTTT
3726875 CTGGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.25
21 5 0.21
23 13 0.54
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.62
Consensus pattern (22 bp):
TTTTGAGTGCTTTCATTTCTTC
Found at i:3731476 original size:14 final size:15
Alignment explanation
Indices: 3731457--3731497 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
3731447 CGGATCGATG
3731457 TCAGTTCAGGT-AAA
1 TCAGTTCAGGTCAAA
3731471 TCAGTTCAGGTCAAA
1 TCAGTTCAGGTCAAA
*
3731486 ACAGTTCAGGTC
1 TCAGTTCAGGTC
3731498 CGGAGCAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (15 bp):
TCAGTTCAGGTCAAA
Found at i:3732276 original size:11 final size:11
Alignment explanation
Indices: 3732248--3732294 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
3732238 TACATAGTTT
3732248 ATTA-ATATAA
1 ATTATATATAA
3732258 ATTATATAGT--
1 ATTATATA-TAA
3732268 -TTATATATAA
1 ATTATATATAA
3732278 ATTATATATAA
1 ATTATATATAA
3732289 ATTATA
1 ATTATA
3732295 CAATCTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.03
9 7 0.22
10 4 0.12
11 19 0.59
12 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
ATTATATATAA
Found at i:3732277 original size:20 final size:20
Alignment explanation
Indices: 3732227--3732285 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 20
3732217 ACTATTGAAC
* *
3732227 TATATATAAACTACATAGTT
1 TATATATAAATTATATAGTT
3732247 TATTAATATAAATTATATAGTT
1 TA-T-ATATAAATTATATAGTT
3732269 TATATATAAATTATATA
1 TATATATAAATTATATA
3732286 TAAATTATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 17 0.49
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATAAATTATATAGTT
Found at i:3732294 original size:20 final size:20
Alignment explanation
Indices: 3732252--3732304 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
3732242 TAGTTTATTA
**
3732252 ATATAAATTATATAGTTTAT
1 ATATAAATTATATAGTAAAT
3732272 ATATAAATTATATA-TAAAT
1 ATATAAATTATATAGTAAAT
3732291 -TATACAATCTATAT
1 ATATA-AAT-TATAT
3732305 TTATATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.14
19 6 0.21
20 19 0.66
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATAAATTATATAGTAAAT
Found at i:3732335 original size:26 final size:25
Alignment explanation
Indices: 3732306--3732355 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
3732296 AATCTATATT
* *
3732306 TATATATTATGTATAATTATAAATAA
1 TATATACTATGTATAAAT-TAAATAA
3732332 TATATACTATGTATAAATTAAATA
1 TATATACTATGTATAAATTAAATA
3732356 GTTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
TATATACTATGTATAAATTAAATAA
Found at i:3732378 original size:9 final size:9
Alignment explanation
Indices: 3732364--3732395 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3732354 TAGTTTATTA
3732364 ATATAAACT
1 ATATAAACT
3732373 ATATAAACT
1 ATATAAACT
*
3732382 ATGTAAACT
1 ATATAAACT
3732391 ATATA
1 ATATA
3732396 GTTTACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (9 bp):
ATATAAACT
Found at i:3732410 original size:20 final size:20
Alignment explanation
Indices: 3732387--3732583 Score: 91
Period size: 20 Copynumber: 9.4 Consensus size: 20
3732377 AAACTATGTA
3732387 AACTATATAGTTTACATATG
1 AACTATATAGTTTACATATG
3732407 AACTATATATATAGTTTAC-TAGTG
1 AAC----TATATAGTTTACATA-TG
*** **
3732431 AACTATATAAAATATTTAT-
1 AACTATATAGTTTACATATG
* * *
3732450 ATAGTATATA-TTATATATATA
1 A-ACTATATAGTT-TACATATG
*
3732471 AACTATATAGTTTATATATG
1 AACTATATAGTTTACATATG
*
3732491 AAC--TATAGTTTACATATA
1 AACTATATAGTTTACATATG
* *
3732509 AAATATAATTGATATTTACATATG
1 AACTAT-A-T-A-GTTTACATATG
* * *
3732533 AACTATAT-GTATAAATTATTTA
1 AACTATATAGTTTACA-TA--TG
3732555 AACTATATAGTTTACATATG
1 AACTATATAGTTTACATATG
3732575 AACTATATA
1 AACTATATA
3732584 TATAGTTTAT
Statistics
Matches: 134, Mismatches: 23, Indels: 40
0.68 0.12 0.20
Matches are distributed among these distances:
18 15 0.11
19 5 0.04
20 55 0.41
21 6 0.04
22 13 0.10
23 9 0.07
24 31 0.23
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (20 bp):
AACTATATAGTTTACATATG
Found at i:3732422 original size:24 final size:24
Alignment explanation
Indices: 3732390--3732439 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3732380 CTATGTAAAC
3732390 TATATAGTTTACATA-TGAACTATA
1 TATATAGTTTAC-TAGTGAACTATA
3732414 TATATAGTTTACTAGTGAACTATA
1 TATATAGTTTACTAGTGAACTATA
3732438 TA
1 TA
3732440 AAATATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (24 bp):
TATATAGTTTACTAGTGAACTATA
Found at i:3732452 original size:84 final size:83
Alignment explanation
Indices: 3732359--3732643 Score: 243
Period size: 84 Copynumber: 3.4 Consensus size: 83
3732349 TTAAATAGTT
* *
3732359 TATTAATATAAACTATATAAACTATGTAAACTATATAGTTTACATATGAACTATATATATAGTTT
1 TATTTATATAAACTATATAAA-TATATAAACTATATAGTTTACATATGAACTATATATATAGTTT
3732424 ACTAGTGAACTATATAAAA
65 ACTAGTGAACTATATAAAA
* * *
3732443 TATTTATATAGTA-TATATTATATATATAAACTATATAGTTTATATATGAAC------TATAGTT
1 TATTTATATA-AACTATA-TAAATATATAAACTATATAGTTTACATATGAACTATATATATAGTT
* *
3732501 TACATA-T-AA-AATATAATTGA
64 TAC-TAGTGAACTATATAA--AA
* *
3732521 TATTTACATATGAACTATATGTATAAATTATTTAAACTATATAGTTTACATATGAACTATATATA
1 TATTT--ATATAAAC--TA--TATAAA-TATATAAACTATATAGTTTACATATGAACTATATATA
* *
3732586 TAGTTTATTAGTGAACTATATAAAC
59 TAGTTTACTAGTGAACTATATAAAA
* *
3732611 TATTTATAT--AGTATATACTATATATAAACTATA
1 TATTTATATAAACTATATA-AATATATAAACTATA
3732644 GTTTATATTT
Statistics
Matches: 159, Mismatches: 19, Indels: 48
0.70 0.08 0.21
Matches are distributed among these distances:
76 6 0.04
77 2 0.01
78 17 0.11
79 3 0.02
80 4 0.03
82 18 0.11
83 4 0.03
84 71 0.45
85 4 0.03
86 1 0.01
88 4 0.03
89 2 0.01
90 15 0.09
91 2 0.01
92 6 0.04
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.42
Consensus pattern (83 bp):
TATTTATATAAACTATATAAATATATAAACTATATAGTTTACATATGAACTATATATATAGTTTA
CTAGTGAACTATATAAAA
Found at i:3732594 original size:42 final size:41
Alignment explanation
Indices: 3732385--3732607 Score: 150
Period size: 42 Copynumber: 5.3 Consensus size: 41
3732375 ATAAACTATG
3732385 TAAACTATATAGTTTACATATGAACTATATATATAGTTTACTA
1 TAAACTATATAGTTTACATATGAACTATATATATA-TTTA-TA
* *** ** * *
3732428 GTGAACTATATAAAATATTTAT-ATAGTATATAT-TATATATA
1 -TAAACTATATAGTTTACATATGA-ACTATATATATATTTATA
* * * * *
3732469 TAAACTATATAGTTTATATATGAACTATAGTTTACATATAAAA
1 TAAACTATATAGTTTACATATGAACTATA-TATATAT-TTATA
* * *
3732512 TATAA-T-TGATA-TTTACATATGAACTATATGTATAAATTATT
1 TA-AACTAT-ATAGTTTACATATGAACTATATATAT-ATTTATA
3732553 TAAACTATATAGTTTACATATGAACTATATATATAGTTTATTA
1 TAAACTATATAGTTTACATATGAACTATATATATA-TTTA-TA
*
3732596 GTGAACTATATA
1 -TAAACTATATA
3732608 AACTATTTAT
Statistics
Matches: 135, Mismatches: 30, Indels: 28
0.70 0.16 0.15
Matches are distributed among these distances:
40 23 0.17
41 17 0.13
42 48 0.36
43 12 0.09
44 35 0.26
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (41 bp):
TAAACTATATAGTTTACATATGAACTATATATATATTTATA
Found at i:3732616 original size:24 final size:25
Alignment explanation
Indices: 3732561--3732622 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
3732551 TTTAAACTAT
* *
3732561 ATAGTTTACATA-TGAACTATATAT
1 ATAGTTTATATAGTGAACTATATAA
3732585 ATAGTTTAT-TAGTGAACTATATAA
1 ATAGTTTATATAGTGAACTATATAA
3732609 ACTA-TTTATATAGT
1 A-TAGTTTATATAGT
3732623 ATATACTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 2 0.06
24 25 0.76
25 6 0.18
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (25 bp):
ATAGTTTATATAGTGAACTATATAA
Found at i:3732627 original size:9 final size:9
Alignment explanation
Indices: 3732600--3732721 Score: 56
Period size: 9 Copynumber: 12.9 Consensus size: 9
3732590 TTATTAGTGA
*
3732600 ACTATATAA
1 ACTATATAT
*
3732609 ACTATTTAT
1 ACTATATAT
3732618 A-TAGTATAT
1 ACTA-TATAT
3732627 ACTATATAT
1 ACTATATAT
*
3732636 AAACTATAGTTT
1 --ACTATA-TAT
*
3732648 A-TATTTAT
1 ACTATATAT
*
3732656 A-TACTACAT
1 ACTA-TATAT
3732665 ACTATAGTTGAT
1 ACTATA--T-AT
*
3732677 A-TTTATAT
1 ACTATATAT
3732685 ACTATATATT
1 ACTATATA-T
3732695 A-TATATAT
1 ACTATATAT
3732703 AAACTATATAT
1 --ACTATATAT
3732714 ACTATATA
1 ACTATATA
3732722 GTATAATTTA
Statistics
Matches: 87, Mismatches: 11, Indels: 30
0.68 0.09 0.23
Matches are distributed among these distances:
8 11 0.13
9 47 0.54
10 8 0.09
11 16 0.18
12 5 0.06
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (9 bp):
ACTATATAT
Found at i:3732671 original size:27 final size:27
Alignment explanation
Indices: 3732638--3732697 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
3732628 CTATATATAA
*
3732638 ACTATAGTTTATATTTATATACTACAT
1 ACTATAGTTGATATTTATATACTACAT
*
3732665 ACTATAGTTGATATTTATATACTATAT
1 ACTATAGTTGATATTTATATACTACAT
*
3732692 ATTATA
1 ACTATA
3732698 TATATAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.48
Consensus pattern (27 bp):
ACTATAGTTGATATTTATATACTACAT
Found at i:3732703 original size:20 final size:20
Alignment explanation
Indices: 3732615--3732726 Score: 70
Period size: 20 Copynumber: 5.3 Consensus size: 20
3732605 ATAAACTATT
* *
3732615 TATATAGTATATACTATATA
1 TATATACTATATATTATATA
3732635 TA-A-ACTATAGT-TTATATTTA
1 TATATACTATA-TATTATA--TA
*
3732655 TATACTACATACTATAGTTGATATT
1 TATA-TAC-TA-TATA-TT-ATATA
3732680 TATATACTATATATTATATA
1 TATATACTATATATTATATA
*
3732700 TATAAACTATATA-TACTATA
1 TATATACTATATATTA-TATA
3732720 TAGTATA
1 TA-TATA
3732727 ATTTACATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
18 9 0.12
19 4 0.05
20 28 0.38
21 6 0.08
22 4 0.05
23 4 0.05
24 6 0.08
25 7 0.10
26 2 0.03
27 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (20 bp):
TATATACTATATATTATATA
Found at i:3732710 original size:27 final size:27
Alignment explanation
Indices: 3732680--3732847 Score: 76
Period size: 27 Copynumber: 6.5 Consensus size: 27
3732670 AGTTGATATT
3732680 TATATACTATATATTATATATATAAAC
1 TATATACTATATATTATATATATAAAC
* *
3732707 TATATA-TA-CTA-TATA-GTAT-AA-
1 TATATACTATATATTATATATATAAAC
* *
3732728 T-T-TAC-ATATGAACTATATATAAAAAC
1 TATATACTATAT--ATTATATATATAAAC
*
3732754 TATATAAACTATA-GTT-TATATATAAAC
1 TATAT--ACTATATATTATATATATAAAC
* * * *
3732781 TATATACTATAGT-TGATATTTATATAG
1 TATATACTATA-TATTATATATATAAAC
*
3732808 TATATACTATA-ATT-TATACTTATAAAA
1 TATATACTATATATTATATA--TATAAAC
*
3732835 TTTATACTATATA
1 TATATACTATATA
3732848 AATTCAGAGT
Statistics
Matches: 104, Mismatches: 17, Indels: 39
0.65 0.11 0.24
Matches are distributed among these distances:
19 3 0.03
20 2 0.02
21 1 0.01
22 3 0.03
23 7 0.07
24 6 0.06
25 13 0.12
26 5 0.05
27 56 0.54
28 3 0.03
30 2 0.02
31 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (27 bp):
TATATACTATATATTATATATATAAAC
Found at i:3732743 original size:34 final size:36
Alignment explanation
Indices: 3732680--3732748 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
3732670 AGTTGATATT
*
3732680 TATATACTATATATTATATATATAAACTATATATAC
1 TATATACTATATATTATACATATAAACTATATATAC
* *
3732716 TATATAGTATA-ATT-TACATATGAACTATATATA
1 TATATACTATATATTATACATATAAACTATATATA
3732749 AAAACTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATACTATATATTATACATATAAACTATATATAC
Found at i:3732789 original size:25 final size:25
Alignment explanation
Indices: 3732743--3732845 Score: 89
Period size: 27 Copynumber: 3.9 Consensus size: 25
3732733 ATATGAACTA
*
3732743 TATATAAAAACTATATAAACTATAGTT
1 TATATATAAACTATAT--ACTATAGTT
3732770 TATATATAAACTATATACTATAGTT
1 TATATATAAACTATATACTATAGTT
* * * *
3732795 GATATTTATATAGTATATACTATAATT
1 --TATATATAAACTATATACTATAGTT
* *
3732822 TATACTTATAAAATTTATACTATA
1 TATA--TATAAACTATATACTATA
3732846 TAAATTCAGA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
25 12 0.19
27 51 0.81
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (25 bp):
TATATATAAACTATATACTATAGTT
Found at i:3732790 original size:47 final size:47
Alignment explanation
Indices: 3732665--3732791 Score: 125
Period size: 47 Copynumber: 2.7 Consensus size: 47
3732655 TATACTACAT
* * * *
3732665 ACTATAGTTGATATTTATATACTATATATTATATATATAAACTATATAT
1 ACTATAGTT--TATATATATACTATATACTATATATAAAAACTATATAA
* *
3732714 ACTATA-TAGTATA-ATTTAC-ATATGAACTATATATAAAAACTATATAA
1 ACTATAGT-TTATATATATACTATAT--ACTATATATAAAAACTATATAA
*
3732761 ACTATAGTTTATATATAAACTATATACTATA
1 ACTATAGTTTATATATATACTATATACTATA
3732792 GTTGATATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
45 4 0.06
46 5 0.08
47 38 0.60
48 6 0.10
49 10 0.16
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (47 bp):
ACTATAGTTTATATATATACTATATACTATATATAAAAACTATATAA
Found at i:3732838 original size:15 final size:16
Alignment explanation
Indices: 3732818--3732849 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3732808 TATATACTAT
3732818 AATTTATACT-TATAA
1 AATTTATACTATATAA
3732833 AATTTATACTATATAA
1 AATTTATACTATATAA
3732849 A
1 A
3732850 TTCAGAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTATACTATATAA
Found at i:3732960 original size:20 final size:18
Alignment explanation
Indices: 3732916--3732970 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 18
3732906 ACTATTTATA
3732916 TATATACTACGTATATAGTT
1 TATATA-TAC-TATATAGTT
3732936 TATATATACTATATAGTT
1 TATATATACTATATAGTT
*
3732954 TACATATGAACTATATA
1 TATATAT--ACTATATA
3732971 TAAAAACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 15 0.47
19 3 0.09
20 14 0.44
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (18 bp):
TATATATACTATATAGTT
Found at i:3732980 original size:13 final size:14
Alignment explanation
Indices: 3732962--3732990 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3732952 TTTACATATG
3732962 AACTATATATA-AA
1 AACTATATATATAA
3732975 AACTATATATATAA
1 AACTATATATATAA
3732989 AA
1 AA
3732991 ATTATATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
AACTATATATATAA
Found at i:3732996 original size:13 final size:15
Alignment explanation
Indices: 3732965--3733017 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
3732955 ACATATGAAC
3732965 TATATATAAAAACTA
1 TATATATAAAAACTA
*
3732980 TATATATAAAAATTA
1 TATATATAAAAACTA
*
3732995 TATGGTATATACAAACTA
1 TA---TATATAAAAACTA
3733013 TATAT
1 TATAT
3733018 TATATAGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 19 0.59
18 13 0.41
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (15 bp):
TATATATAAAAACTA
Found at i:3733005 original size:18 final size:18
Alignment explanation
Indices: 3732967--3733079 Score: 94
Period size: 18 Copynumber: 6.6 Consensus size: 18
3732957 ATATGAACTA
3732967 TATATAAAAAC--TATA-
1 TATATAAAAACTATATAG
* *
3732982 TATATAAAAATTATATGG
1 TATATAAAAACTATATAG
* *
3733000 TATATACAAACTATATAT
1 TATATAAAAACTATATAG
***
3733018 TATAT-AGTTC-AT-TAG
1 TATATAAAAACTATATAG
*
3733033 TATATATAAACTATATAG
1 TATATAAAAACTATATAG
*
3733051 TATATAAAAACTATATGG
1 TATATAAAAACTATATAG
*
3733069 TATATATAAAC
1 TATATAAAAAC
3733080 CATACATTAT
Statistics
Matches: 74, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
15 17 0.23
16 3 0.04
17 6 0.08
18 48 0.65
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
TATATAAAAACTATATAG
Found at i:3733089 original size:69 final size:68
Alignment explanation
Indices: 3732965--3733119 Score: 231
Period size: 69 Copynumber: 2.3 Consensus size: 68
3732955 ACATATGAAC
* * * *
3732965 TATATATAAA-AACTATATATATAAAAATTATATGGTATATACAAACTATATATTATATAGTTCA
1 TATATATAAACTA-TATATATATAAAAACTATATGGTATATACAAACCATACATTATATAGTTCA
3733029 TTAG
65 TTAG
*
3733033 TATATATAAACTATATAGTATATAAAAACTATATGGTATATATAAACCATACATTATATAGTTCA
1 TATATATAAACTATATA-TATATAAAAACTATATGGTATATACAAACCATACATTATATAGTTCA
3733098 TTAG
65 TTAG
*
3733102 TATATATAACCTATATAT
1 TATATATAAACTATATAT
3733120 TAATTTATTA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
68 15 0.19
69 64 0.81
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (68 bp):
TATATATAAACTATATATATATAAAAACTATATGGTATATACAAACCATACATTATATAGTTCAT
TAG
Found at i:3733252 original size:61 final size:61
Alignment explanation
Indices: 3733178--3733319 Score: 221
Period size: 61 Copynumber: 2.3 Consensus size: 61
3733168 TCTAAGGATC
* *
3733178 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGTAACATTAAATTTGGGCT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
* * *
3733239 AAATTGAAGAAATTTTAAATATGAAGCTTAAATTAATATATTGCATCATTAAATTTGGACT
1 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
* *
3733300 AAATTGAATAAATTTAAAAT
1 AAATTGAACAAATTTTAAAT
3733320 TAGGAGACAA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 74 1.00
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.37
Consensus pattern (61 bp):
AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGCAACATTAAATTTGGACT
Found at i:3733851 original size:102 final size:101
Alignment explanation
Indices: 3733543--3733872 Score: 400
Period size: 103 Copynumber: 3.3 Consensus size: 101
3733533 TTCATAATTT
*
3733543 TTCATCCGTGTTCATCCCAAAAACCCTCATTTGATCTTCACTAACACCAAAACCCAAACCATTTC
1 TTCATCCGTGTTCATCCCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCA-TTC
* * * * *
3733608 GTGTTTTTTCGATCAAACACTCATAATTTCAACCCTTG
65 TTGTTTTTTCGATCAAACACCCAAAAATTC-ATCCTTG
* * *
3733646 TTCATTCGTGTTCATCCCAAAAACCCTCATTTGATCTTCAGAAACACCAAAACCCAAACTATT-T
1 TTCATCCGTGTTCATCCCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCATTCT
** *
3733710 CCTTTTTT--ATCAAACACCCAAAAATTCATCTCGTG
66 TGTTTTTTCGATCAAACACCCAAAAATTCATC-CTTG
* * * * *
3733745 TTCATCCATGTTCATCCC-AAAACCATTATTTGATCTCCACAAACACCAAAACCTAAACCCATTC
1 TTCATCCGTGTTCATCCCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAA-CCATTC
*
3733809 TTGTTTTTTCGATCAAACACCCAAAAGTTCATCCATTG
65 TTGTTTTTTCGATCAAACACCCAAAAATTCATCC-TTG
* *
3733847 TTCATCCGTGTTCTTCCC-CAAACCCT
1 TTCATCCGTGTTCATCCCAAAAACCCT
3733873 TACAAACACC
Statistics
Matches: 193, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
98 36 0.19
99 39 0.20
100 7 0.04
101 7 0.04
102 47 0.24
103 57 0.30
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.32
Consensus pattern (101 bp):
TTCATCCGTGTTCATCCCAAAAACCCTCATTTGATCTTCACAAACACCAAAACCCAAACCATTCT
TGTTTTTTCGATCAAACACCCAAAAATTCATCCTTG
Found at i:3734069 original size:12 final size:12
Alignment explanation
Indices: 3734054--3734155 Score: 62
Period size: 12 Copynumber: 8.6 Consensus size: 12
3734044 CCCTAACCCT
3734054 AACCCAAACCTG
1 AACCCAAACCTG
**
3734066 AACCCAAACCCA
1 AACCCAAACCTG
* * *
3734078 AACTCGAACATG
1 AACCCAAACCTG
* **
3734090 AAACCAAACCCC
1 AACCCAAACCTG
*
3734102 AACCCAAAACTG
1 AACCCAAACCTG
* *
3734114 AACCCAAAACTA
1 AACCCAAACCTG
* *
3734126 AACCCGAACC-C
1 AACCCAAACCTG
* *
3734137 AATCCAAACCCG
1 AACCCAAACCTG
3734149 AACCCAA
1 AACCCAA
3734156 TCCAAACCCG
Statistics
Matches: 64, Mismatches: 25, Indels: 2
0.70 0.27 0.02
Matches are distributed among these distances:
11 8 0.12
12 56 0.88
ACGTcount: A:0.47, C:0.41, G:0.06, T:0.06
Consensus pattern (12 bp):
AACCCAAACCTG
Found at i:3734077 original size:6 final size:6
Alignment explanation
Indices: 3734048--3734164 Score: 51
Period size: 6 Copynumber: 19.8 Consensus size: 6
3734038 TCTAACCCCT
* ** * * **
3734048 AACCCT AACCCA AACCTG AACCCA AACCCA AACTCG AACATGA AA-CCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AAC-CCA AACCCA
* * ** * * * *
3734096 AACCCC AACCCA AAACTG AACCCA AAACTA AACCCG AACCC- AATCCA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* *
3734143 AACCCG AACCC- AATCCA AACCC
1 AACCCA AACCCA AACCCA AACCC
3734165 GAATCTGAAT
Statistics
Matches: 78, Mismatches: 29, Indels: 8
0.68 0.25 0.07
Matches are distributed among these distances:
5 11 0.14
6 64 0.82
7 3 0.04
ACGTcount: A:0.45, C:0.43, G:0.05, T:0.07
Consensus pattern (6 bp):
AACCCA
Found at i:3734129 original size:30 final size:31
Alignment explanation
Indices: 3734054--3734138 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 31
3734044 CCCTAACCCT
* *
3734054 AACCCAAACCTGAACCCAAACCC-AAACTCG
1 AACCCAAAACTAAACCCAAACCCAAAACTCG
*** * *
3734084 AACATGAAACCAAACCCCAACCCAAAACT-G
1 AACCCAAAACTAAACCCAAACCCAAAACTCG
*
3734114 AACCCAAAACTAAACCCGAACCCAA
1 AACCCAAAACTAAACCCAAACCCAA
3734139 TCCAAACCCG
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
30 37 0.88
31 5 0.12
ACGTcount: A:0.48, C:0.40, G:0.06, T:0.06
Consensus pattern (31 bp):
AACCCAAAACTAAACCCAAACCCAAAACTCG
Found at i:3734145 original size:17 final size:17
Alignment explanation
Indices: 3734125--3734167 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
3734115 ACCCAAAACT
3734125 AAACCCGAACCCAATCC
1 AAACCCGAACCCAATCC
3734142 AAACCCGAACCCAATCC
1 AAACCCGAACCCAATCC
3734159 AAACCCGAA
1 AAACCCGAA
3734168 TCTGAATCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.44, C:0.44, G:0.07, T:0.05
Consensus pattern (17 bp):
AAACCCGAACCCAATCC
Found at i:3736364 original size:20 final size:20
Alignment explanation
Indices: 3736323--3736367 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
3736313 ATTCTGTTTT
*
3736323 ATATTGTTTGCTTCTGTATG
1 ATATTGTTTGCTTCTCTATG
3736343 ATATTGTTTGCTTCTACT-TG
1 ATATTGTTTGCTTCT-CTATG
3736363 ATATT
1 ATATT
3736368 TGTAAAGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.56
Consensus pattern (20 bp):
ATATTGTTTGCTTCTCTATG
Found at i:3742514 original size:16 final size:16
Alignment explanation
Indices: 3742482--3742516 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3742472 TATAATATTG
**
3742482 AAACTTGAACTCGAAA
1 AAACTTGAACTAAAAA
3742498 AAACTTGAACTAAAAA
1 AAACTTGAACTAAAAA
3742514 AAA
1 AAA
3742517 TTTAGAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.17
Consensus pattern (16 bp):
AAACTTGAACTAAAAA
Found at i:3744277 original size:20 final size:20
Alignment explanation
Indices: 3744251--3744303 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3744241 TGATTCAAGT
3744251 GGTATCGATACCAAGAGG-G
1 GGTATCGATACCAAGAGGAG
* * *
3744270 GAGTATCGATACTATGAGGAT
1 G-GTATCGATACCAAGAGGAG
3744291 GGTATCGATACCA
1 GGTATCGATACCA
3744304 TTGTTAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (20 bp):
GGTATCGATACCAAGAGGAG
Found at i:3745108 original size:81 final size:81
Alignment explanation
Indices: 3744972--3745273 Score: 432
Period size: 81 Copynumber: 3.8 Consensus size: 81
3744962 TTCCAAAAGA
* *
3744972 AAAAGATTAATGGCCTAG-TCGTGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAACG
1 AAAAGATTAATGGCCTAGCT-GTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
3745036 GTTAAATATCATTAAGT
65 GTTAAATATCGTTAAGT
*
3745053 AAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGA
1 AAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGG
3745118 TTAAATATCGTTAAGT
66 TTAAATATCGTTAAGT
* * *
3745134 AAAAGAGTAATGGCCTAGCTGTGCATTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGG
*
3745199 TTAAATATCGTTGAGT
66 TTAAATATCGTTAAGT
** * * * * *
3745215 AAAAGA-T--TGGCCTAGCTGCACATTTGACAGAAAAGTTTCAATTATGCAAGTTATATGAA
1 AAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
3745274 AGGCTCCATG
Statistics
Matches: 202, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
78 43 0.21
80 1 0.00
81 157 0.78
82 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (81 bp):
AAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGG
TTAAATATCGTTAAGT
Found at i:3745388 original size:45 final size:45
Alignment explanation
Indices: 3745332--3745679 Score: 500
Period size: 45 Copynumber: 7.7 Consensus size: 45
3745322 GATATAAACG
*
3745332 GTATATAAAGGCATGAAAGGATGTCATAAATGAAATGTATAATAGT
1 GTATA-AAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
3745378 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
*
3745423 GTATAAAAGGCATGAAAGGGTGCCATAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
*
3745468 GTATAAAAGGCATGAAAGGATGCCAAAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
* *
3745513 GTATAAAAGGCATGAAAAGATGCCAAAAATGAAATGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
* *
3745558 GTATAAAAGGCATGAAAAGATGCCATAAATGAAAAGTATAATAGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
* * ** * * *
3745603 GCATTATCGGCATGAAAGGATGCCATAATTGAAATGCAT-ATGGT
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
* * ** * *
3745647 GCATTATTGGCATAAAAGGATGCCAGAAATGAA
1 GTATAAAAGGCATGAAAGGATGCCATAAATGAA
3745680 TATGCGTGCA
Statistics
Matches: 282, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
44 33 0.12
45 244 0.87
46 5 0.02
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (45 bp):
GTATAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGT
Found at i:3745451 original size:22 final size:22
Alignment explanation
Indices: 3745380--3745451 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
3745370 ATAATAGTGT
*
3745380 ATAAAAGGCATGAAAGGATGCC
1 ATAAAAGGCATGAAAGGGTGCC
* ** ** *
3745402 ATAAATGAAATGTATAATAGTG-T
1 ATAAAAGGCATG-A-AAGGGTGCC
3745425 ATAAAAGGCATGAAAGGGTGCC
1 ATAAAAGGCATGAAAGGGTGCC
3745447 ATAAA
1 ATAAA
3745452 TGAAATGTAT
Statistics
Matches: 34, Mismatches: 13, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
21 5 0.15
22 15 0.44
23 10 0.29
24 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (22 bp):
ATAAAAGGCATGAAAGGGTGCC
Found at i:3745709 original size:84 final size:86
Alignment explanation
Indices: 3745601--3745829 Score: 273
Period size: 84 Copynumber: 2.6 Consensus size: 86
3745591 AAGTATAATA
* *
3745601 GTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATGGTGCATTATTGGCATAAAAGG
1 GTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATGGTGCATTATCGACATAAAAGG
*
3745666 ATGCC-A-GAAATGAATATGC
66 ATACCAATGAAATGAATATGC
** * *
3745685 GTGCATTATCACCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATCGACATGAAAG
1 GTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATAT-GGTGCATTATCGACATAAAAG
* *
3745750 GATACCATAATTGAAATGCATATGG
65 GATACC--AA-TGAAATGAATATGC
* ** *
3745775 GTGCATTATCGGCATGAAAGGATGCCAAAAATAAAAATGCATAAGGGTGCATTAT
1 GTGCATTATCGGCATGAAAGGATGCC-ATAATTGAAATGCAT-ATGGTGCATTAT
3745830 AAACATGAAT
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
84 40 0.33
85 23 0.19
88 1 0.01
90 35 0.29
91 21 0.17
92 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.26
Consensus pattern (86 bp):
GTGCATTATCGGCATGAAAGGATGCCATAATTGAAATGCATATGGTGCATTATCGACATAAAAGG
ATACCAATGAAATGAATATGC
Found at i:3745723 original size:45 final size:45
Alignment explanation
Indices: 3745341--3745829 Score: 300
Period size: 45 Copynumber: 11.0 Consensus size: 45
3745331 GGTATATAAA
* * * * * * **
3745341 GGCATGAAAGGATGTCATAAATGAAATGTATAAT-AGTGTATAAAA
1 GGCATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATC
* * * * * **
3745386 GGCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTATAAAA
1 GGCATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATC
* * * * * * **
3745431 GGCATGAAAGGGTGCCATAAATGAAATGTATAAT-AGTGTATAAAA
1 GGCATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATC
* * * * * * **
3745476 GGCATGAAAGGATGCCAAAAATGAAATGTATAAT-AGTGTATAAAA
1 GGCATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATC
* * * * * * * **
3745521 GGCATGAAAAGATGCCAAAAATGAAATGTATAAT-AGTGTATAAAA
1 GGCATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATC
* * * * *
3745566 GGCATGAAAAGATGCCATAAATGAAAAGTATAAT-AGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATC
* *
3745611 GGCATGAAAGGATGCCATAATTGAAATGCATAT-GGTGCATTATT
1 GGCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATC
* *
3745655 GGCATAAAAGGATGCC---A--GAAATGAATATGCGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATC
**
3745695 ACCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATC
* * *
3745740 GACATGAAAGGATACCATAATTGAAATGCATATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATC
* ** * *
3745785 GGCATGAAAGGATGCCAAAAATAAAAATGCATAAGGGTGCATTAT
1 GGCATGAAAGGATGCC-ATAATTGAAATGAATATGGGTGCATTAT
3745830 AAACATGAAT
Statistics
Matches: 402, Mismatches: 35, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
39 10 0.02
40 22 0.05
41 1 0.00
43 1 0.00
44 26 0.06
45 318 0.79
46 24 0.06
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGAATATGGGTGCATTATC
Found at i:3745736 original size:129 final size:130
Alignment explanation
Indices: 3745568--3745806 Score: 365
Period size: 129 Copynumber: 1.8 Consensus size: 130
3745558 GTATAAAAGG
* * *
3745568 CATGAAAAGATGCCATAAATGAAAAGTATAATAGTGCATTATCGGCATGAAAGGATGCCATAATT
1 CATGAAAAGATGCCATAAATGAAAAGAATAATAGTGCATTATCGACATGAAAGGATACCATAATT
* *
3745633 GAAATGCATAT-GGTGCATTATTGGCATAAAAGGATGCCAGAAATGAATATGCGTGCATTATCAC
66 GAAATGCATATGGGTGCATTATCGGCATAAAAGGATGCCAAAAATGAATATGCGTGCATTATCAC
* * * *
3745697 CATGAAAGGATGCCATAATTGAAATGAAT-ATGGGTGCATTATCGACATGAAAGGATACCATAAT
1 CATGAAAAGATGCCATAAATGAAAAGAATAAT-AGTGCATTATCGACATGAAAGGATACCATAAT
*
3745761 TGAAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCAAAAAT
65 TGAAATGCATATGGGTGCATTATCGGCATAAAAGGATGCCAAAAAT
3745807 AAAAATGCAT
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
128 2 0.02
129 66 0.67
130 30 0.31
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (130 bp):
CATGAAAAGATGCCATAAATGAAAAGAATAATAGTGCATTATCGACATGAAAGGATACCATAATT
GAAATGCATATGGGTGCATTATCGGCATAAAAGGATGCCAAAAATGAATATGCGTGCATTATCAC
Found at i:3750766 original size:17 final size:19
Alignment explanation
Indices: 3750713--3750765 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
3750703 TATTCGAATA
3750713 TTTGAATCGAATATATAAT
1 TTTGAATCGAATATATAAT
3750732 TTTGAATCGAATATATAAT
1 TTTGAATCGAATATATAAT
3750751 TTTGAATCGAATATA
1 TTTGAATCGAATATA
3750766 AAATCTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (19 bp):
TTTGAATCGAATATATAAT
Found at i:3751215 original size:13 final size:13
Alignment explanation
Indices: 3751187--3751232 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3751177 TTCAAACAAA
*
3751187 CCAAAATCAAACAT
1 CCAAAA-CAAATAT
3751201 CCAAAACAAATAT
1 CCAAAACAAATAT
*
3751214 CCAAACCAAATAT
1 CCAAAACAAATAT
*
3751227 TCAAAA
1 CCAAAA
3751233 TCCATCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (13 bp):
CCAAAACAAATAT
Found at i:3752602 original size:13 final size:14
Alignment explanation
Indices: 3752577--3752614 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3752567 TCTAATAGGC
3752577 AATTTTG-AAAACT
1 AATTTTGAAAAACT
3752590 -ATTTTGAAAAACT
1 AATTTTGAAAAACT
*
3752603 AAGTTTGAAAAA
1 AATTTTGAAAAA
3752615 TTATAATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 6 0.27
13 6 0.27
14 10 0.45
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (14 bp):
AATTTTGAAAAACT
Found at i:3775259 original size:10 final size:10
Alignment explanation
Indices: 3775246--3775273 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3775236 GCATCTCATG
3775246 TAGCTACATT
1 TAGCTACATT
3775256 TAGCTACATT
1 TAGCTACATT
3775266 TAGCTACA
1 TAGCTACA
3775274 CTTGATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (10 bp):
TAGCTACATT
Found at i:3785744 original size:2 final size:2
Alignment explanation
Indices: 3785737--3785763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3785727 TACCGAAAAT
3785737 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3785764 GATTGAATCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3795287 original size:20 final size:20
Alignment explanation
Indices: 3795262--3795302 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3795252 CCATCTTTCG
3795262 CTTCCATCTCTCATTTTAAA
1 CTTCCATCTCTCATTTTAAA
3795282 CTTCCATCTCTCATTTTAAA
1 CTTCCATCTCTCATTTTAAA
3795302 C
1 C
3795303 AACCCACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (20 bp):
CTTCCATCTCTCATTTTAAA
Found at i:3799511 original size:23 final size:24
Alignment explanation
Indices: 3799485--3799531 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3799475 AAAAAAAGAA
*
3799485 AAGAAA-TTAAAGCACTCCAAAAG
1 AAGAAAGTTAAAGCACTCAAAAAG
**
3799508 AAGAAAGTTCCAGCACTCAAAAAG
1 AAGAAAGTTAAAGCACTCAAAAAG
3799532 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.13
Consensus pattern (24 bp):
AAGAAAGTTAAAGCACTCAAAAAG
Done.