Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008558.1 Hibiscus syriacus cultivar Beakdansim tig00111463_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: 2950132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:498331 original size:22 final size:22
Alignment explanation
Indices: 498225--498949 Score: 241
Period size: 22 Copynumber: 31.6 Consensus size: 22
498215 ATCTTTTATT
* * *
498225 TATATATTATGTATACTATAAAT
1 TATATA-TATATATAATATAAAG
*
498248 TATATATACTATGTATAAATTATATAG
1 TATATATA-TA--TAT-AA-TATAAAG
* *
498275 TTTATATAGT-TAAAATATAAAG
1 TATATATA-TATATAATATAAAG
*
498297 TATCTA-AGTATATAATATAAAG
1 TATATATA-TATATAATATAAAG
* *
498319 TATATATACATATAAAATATAAG
1 TATATATATATATAATATA-AAG
* * *
498342 TATGTATATATACATATATATA-
1 TATATATATATATA-ATATAAAG
* * * *
498364 TATATATAAATTTTAGTACAAAG
1 TATATATATA-TATAATATAAAG
*
498387 TATATA-AGTATATAATATAAAA
1 TATATATA-TATATAATATAAAG
*
498409 TATATA-AGA-ATTAAATATAAAG
1 TATATATATATA-T-AATATAAAG
*
498431 TATATATATACATATAATATATATATATA
1 TATATATAT--ATAT-A-ATATA-A-A-G
498460 TATATATATATATAATATAAAG
1 TATATATATATATAATATAAAG
*
498482 TATATA-AGTAT-TAAATACAAAG
1 TATATATA-TATAT-AATATAAAG
*
498504 TATATAAAGTATAATTATAAAGACTAAAG
1 TATAT--A-TAT-A-TAT-AATA-TAAAG
498533 TATATA-AGTATATAATATAAAG
1 TATATATA-TATATAATATAAAG
*
498555 TATATATACATATAA-AGTATAAG
1 TATATATATATATAATA-TA-AAG
* * * * * *
498578 TATGTATGTATGTATGTATGTATG
1 TATATATATATATA-ATAT-AAAG
*
498602 TATCTATATATATATATATAAAGG
1 TATATATATATATA-ATATAAA-G
* * *
498626 T-T-TAGTATAAAGT-GTATATA-
1 TATATA-TATATA-TAATATAAAG
498646 TATATATATATATAATATAAAG
1 TATATATATATATAATATAAAG
* *
498668 TATA-AT-TATATTATATATA-
1 TATATATATATATAATATAAAG
* **
498687 TATATATATA-AAAAGT-TTTAG
1 TATATATATATATAA-TATAAAG
* * *
498708 AATAAAGTATATATACATAGATAA-
1 TATATA-TATATATA-ATATA-AAG
498732 -ATATATATATATAATATAAAG
1 TATATATATATATAATATAAAG
*
498753 TATA-AT-TATA-AAGATTAAAG
1 TATATATATATATAATA-TAAAG
* * *
498773 TATATA-AGGATCTAATGTAAAG
1 TATATATA-TATATAATATAAAG
* *
498795 TATACA-AGTAT-TAAATATAAAT
1 TATATATA-TATAT-AATATAAAG
*
498817 TATATATACATATAATATATATA-
1 TATATATATATATAATATA-A-AG
498840 TATATATGTATATAATAATATAAAG
1 TATATA--TATAT-ATAATATAAAG
*
498865 TATATA-AGTATAT-ATATAAAC
1 TATATATA-TATATAATATAAAG
* *
498886 TATAATGTATGTATATATATAAAG
1 TAT-ATATATATATA-ATATAAAG
*
498910 TATAAGTAAATATATAAACTATAAAG
1 TAT-A-TATATATAT-AA-TATAAAG
*
498936 TATAAATATATATA
1 TATATATATATATA
498950 CTTTATATTA
Statistics
Matches: 529, Mismatches: 94, Indels: 158
0.68 0.12 0.20
Matches are distributed among these distances:
19 7 0.01
20 36 0.07
21 46 0.09
22 193 0.36
23 83 0.16
24 54 0.10
25 36 0.07
26 30 0.06
27 20 0.04
28 6 0.01
29 18 0.03
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (22 bp):
TATATATATATATAATATAAAG
Found at i:498439 original size:73 final size:73
Alignment explanation
Indices: 498358--498560 Score: 222
Period size: 73 Copynumber: 2.8 Consensus size: 73
498348 TATATACATA
*
498358 TATATATATATATAAATTTTAGTACAAAGTATATAAGTATATAATATAAAATATATAAGAATTAA
1 TATATATATATATAAATTTTAGTACAAAGTATATAAGTATATAATATAAAGTATATAAGAATTAA
*
498423 ATATAAAG
66 ATACAAAG
* * * * *
498431 TATATATATACATATAATATATA-TATATA-TATATATA-TATATAATATAAAGTATATAAGTAT
1 TATATATATATATA-AAT-TTTAGTACAAAGTATATA-AGTATATAATATAAAGTATATAAGAAT
498493 TAAATACAAAG
63 TAAATACAAAG
*
498504 TATATA-A-AGTAT-AATTATAAAG-ACTAAAGTATATAAGTATATAATATAAAGTATATA
1 TATATATATA-TATAAATT-T-TAGTAC-AAAGTATATAAGTATATAATATAAAGTATATA
498561 TACATATAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
69 1 0.01
70 3 0.03
71 3 0.03
72 6 0.06
73 84 0.78
74 8 0.07
75 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.37
Consensus pattern (73 bp):
TATATATATATATAAATTTTAGTACAAAGTATATAAGTATATAATATAAAGTATATAAGAATTAA
ATACAAAG
Found at i:498517 original size:29 final size:29
Alignment explanation
Indices: 498474--498580 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 29
498464 TATATATATA
*
498474 ATATAAAGTATATAAGTATTAAATAC-AAAGT
1 ATATAAAG--TATAAGTA-TAAAGACTAAAGT
*
498505 ATATAAAGTATAATTATAAAGACTAAAGT
1 ATATAAAGTATAAGTATAAAGACTAAAGT
* *
498534 ATAT-AAGTATATAATATAAAGTA-TATATA-C
1 ATATAAAGTATA-AGTATAAAG-ACTA-A-AGT
498564 ATATAAAGTATAAGTAT
1 ATATAAAGTATAAGTAT
498581 GTATGTATGT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
28 13 0.20
29 26 0.40
30 10 0.15
31 16 0.25
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (29 bp):
ATATAAAGTATAAGTATAAAGACTAAAGT
Found at i:498713 original size:77 final size:81
Alignment explanation
Indices: 498606--498762 Score: 214
Period size: 85 Copynumber: 1.9 Consensus size: 81
498596 TGTATGTATC
* * *
498606 TATATATATATATATAAAGGTTTAGTATAAAG-TGTAT-AT-AT-ATATATATATATAATATAAA
1 TATATATATATATAAAAAGGTTTAGAATAAAGATATATAATAATAATATATATATATAATATAAA
498667 GTATAATTATATTATA
66 GTATAATTATATTATA
*
498683 TATATATATATATAAAAAGTTTTAGAATAAAGTATATATACATAGATAAATATATATATATAATA
1 TATATATATATATAAAAAGGTTTAGAATAAAG-ATATATA-ATA-AT-AATATATATATATAATA
498748 TAAAGTATAATTATA
62 TAAAGTATAATTATA
498763 AAGATTAAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
77 29 0.43
79 4 0.06
81 2 0.03
83 2 0.03
85 31 0.46
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (81 bp):
TATATATATATATAAAAAGGTTTAGAATAAAGATATATAATAATAATATATATATATAATATAAA
GTATAATTATATTATA
Found at i:498831 original size:17 final size:16
Alignment explanation
Indices: 498808--498870 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
498798 ACAAGTATTA
498808 AATATAAATTATATAT
1 AATATAAATTATATAT
498824 ACATAT-AA-TATATAT
1 A-ATATAAATTATATAT
*
498839 -ATATATATGTATATAAT
1 AATATAAAT-TATAT-AT
*
498856 AATATAAAGTATATA
1 AATATAAATTATATA
498871 AGTATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
13 4 0.11
14 1 0.03
15 7 0.18
16 9 0.24
17 11 0.29
18 6 0.16
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATAAATTATATAT
Found at i:498871 original size:17 final size:16
Alignment explanation
Indices: 498305--498913 Score: 107
Period size: 15 Copynumber: 38.1 Consensus size: 16
498295 AGTATCTAAG
498305 TATATAATATAAAGTA
1 TATATAATATAAAGTA
*
498321 TATATACATATAAAATA
1 TATATA-ATATAAAGTA
498338 TAAGTATGTATATATACATA-TA
1 T-A-TA--TA-ATATA-A-AGTA
498360 TATATATATATAAA-T-
1 TATATA-ATATAAAGTA
* *
498375 T-T-TAGTACAAAGTA
1 TATATAATATAAAGTA
*
498389 TATA-AGTATATAA-TA
1 TATATAATATA-AAGTA
*
498404 TA-A-AATATATAAGAA
1 TATATAATATA-AAGTA
498419 T-TA-AATATAAAGTATA
1 TATATAATATAAAG--TA
498435 TATATACATATAATA-TA
1 TATATA-ATATAA-AGTA
*
498452 TATATATATATATA-TA
1 TATATA-ATATAAAGTA
498468 TATATAATATAAAGTA
1 TATATAATATAAAGTA
*
498484 TATA-AGTATTAAA-TA
1 TATATAATA-TAAAGTA
* *
498499 CAAAGT-ATATAAAGTA
1 TATA-TAATATAAAGTA
498515 TA-AT--TATAAAG-A
1 TATATAATATAAAGTA
*
498527 CTA-A-AGTATATAAG--
1 -TATATAATATA-AAGTA
498541 TATATAATATAAAGTA
1 TATATAATATAAAGTA
498557 TATATACATATAAAGTA
1 TATATA-ATATAAAGTA
* * *
498574 TA-AGTATGTATGTATGTA
1 TATA-TA-ATAT-AAAGTA
* * **
498592 TGTATGTATGTATCTA-TA
1 --TATATA-ATATAAAGTA
*
498610 TATATATATATAAAG-G
1 TATATA-ATATAAAGTA
* *
498626 T-T-TAGTATAAAGTG
1 TATATAATATAAAGTA
*
498640 TATAT-ATATATA-TA
1 TATATAATATAAAGTA
498654 TATATAATATAAAGTA
1 TATATAATATAAAGTA
* *
498670 TAATTATATTATATA-TA
1 T-A-TATAATATAAAGTA
*
498687 TATATATATAAAAAGT-
1 TATATA-ATATAAAGTA
498703 T-T-TAGA-ATAAAGTA
1 TATATA-ATATAAAGTA
498717 TATATACATAGATAAA-TA
1 TATATA-AT--ATAAAGTA
498735 TATAT-ATATAATA-TA
1 TATATAATATAA-AGTA
*
498750 AAGTATAATTATAAAG-A
1 TA-TATAA-TATAAAGTA
*
498767 T-TA-AAGTATATAAGGATC
1 TATATAA-TATA-AA-G-TA
*
498785 TAATGTAAAGTATACAAGTA
1 T-ATAT-AA-TATA-AAGTA
*
498805 T-TA-AATATAAATTA
1 TATATAATATAAAGTA
498819 TATATACATAT-AA-TA
1 TATATA-ATATAAAGTA
*
498834 TATAT-ATATATATGTA
1 TATATAATATA-AAGTA
498850 TATAATAATATAAAGTA
1 TAT-ATAATATAAAGTA
*
498867 TATA-AGTAT--A-TA
1 TATATAATATAAAGTA
*
498879 TATA-AACTATAATGTA
1 TATATAA-TATAAAGTA
*
498895 TGTATATATATAAAGTA
1 TATATA-ATATAAAGTA
498912 TA
1 TA
498914 AGTAAATATA
Statistics
Matches: 451, Mismatches: 60, Indels: 163
0.67 0.09 0.24
Matches are distributed among these distances:
12 13 0.03
13 36 0.08
14 52 0.12
15 91 0.20
16 89 0.20
17 74 0.16
18 45 0.10
19 13 0.03
20 15 0.03
21 9 0.02
22 13 0.03
23 1 0.00
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (16 bp):
TATATAATATAAAGTA
Found at i:499029 original size:15 final size:14
Alignment explanation
Indices: 498941--499601 Score: 93
Period size: 13 Copynumber: 48.1 Consensus size: 14
498931 TAAAGTATAA
498941 ATATA-TATACTTT
1 ATATATTATACTTT
498954 ATAT-TATATAC-TT
1 ATATAT-TATACTTT
498967 ATATACTT-TAGTCTTT
1 ATATA-TTATA--CTTT
*
498983 ATA-ATTATACTCT
1 ATATATTATACTTT
*
498996 ATATATATATA-TATA
1 ATATAT-TATACT-TT
499011 ATATACTTATACTTT
1 ATATA-TTATACTTT
499026 ATATTATTATA-TATT
1 ATA-TATTATACT-TT
499041 -TATA-TATACTTT
1 ATATATTATACTTT
* * * *
499053 AT-TCTAAAAATTT
1 ATATATTATACTTT
*
499066 ATATGTATATACTTT
1 ATATAT-TATACTTT
*
499081 ATAT-TTAATAGTTT
1 ATATATT-ATACTTT
499095 ATATA-TATA--TT
1 ATATATTATACTTT
*
499106 ATATTATTATA-TAT
1 ATA-TATTATACTTT
*
499120 GTATA-TATACTTT
1 ATATATTATACTTT
*
499133 ATACTA--AAACTTT
1 ATA-TATTATACTTT
*
499146 ATATA-TATA-TAT
1 ATATATTATACTTT
* *
499158 ATACACTTTATAGTTT
1 ATATA--TTATACTTT
499174 ATATA-TATAC-TT
1 ATATATTATACTTT
499186 ATATACTT-TAGTCTTT
1 ATATA-TTATA--CTTT
* *
499202 TTA-ATTATAATTT
1 ATATATTATACTTT
* *
499215 TTATA-TATA--TA
1 ATATATTATACTTT
499226 ATATATTTATAC-TT
1 ATATA-TTATACTTT
*
499240 ATA-CTTATACTTT
1 ATATATTATACTTT
* *
499253 ATATTATTGTA-TAT
1 ATA-TATTATACTTT
*
499267 CTATA-TATACTTT
1 ATATATTATACTTT
*
499280 ATACTA--AAACTTTT
1 ATA-TATTATAC-TTT
* *
499294 TTATATATATA-ATT
1 ATATAT-TATACTTT
*
499308 ATACT-TTATAGTTT
1 ATA-TATTATACTTT
* *
499322 ATATGTATATA-TAT
1 ATATAT-TATACTTT
*
499336 ATATACTTGTACTTT
1 ATATA-TTATACTTT
499351 ATATGTATATATACTTT
1 ATA--TAT-TATACTTT
*
499368 AGATACTTATA---T
1 ATATA-TTATACTTT
*
499380 A-CT-TTAGT-CTTT
1 ATATATTA-TACTTT
499392 ATA-ATTATACTTT
1 ATATATTATACTTT
499405 ATATA-TATA-TTT
1 ATATATTATACTTT
* *
499417 ATATATATAAAGTTT
1 ATATAT-TATACTTT
* * *
499432 -TAGTATAAT-GTAT
1 ATA-TATTATACTTT
*
499445 ATATACTTTATAGTTT
1 ATATA--TTATACTTT
*
499461 ATATATATACACACTTT
1 ATATAT-T--ATACTTT
* * * *
499478 ATGCT-TTAAAGTAT
1 AT-ATATTATACTTT
**
499492 ATATAACTTATGGTTT
1 ATAT-A-TTATACTTT
* *
499508 TTATA-TATA-TAT
1 ATATATTATACTTT
*
499520 ATATATATATA-TAT
1 ATATAT-TATACTTT
499534 ATATATTATACTTT
1 ATATATTATACTTT
*
499548 ATAGT-TTACACTTT
1 ATA-TATTATACTTT
499562 ATATA-TATAC-TT
1 ATATATTATACTTT
*
499574 ATA-CTTATACTTT
1 ATATATTATACTTT
499587 ATATATATATA-TTT
1 ATATAT-TATACTTT
499601 A
1 A
499602 AAAAAGTGTA
Statistics
Matches: 479, Mismatches: 76, Indels: 185
0.65 0.10 0.25
Matches are distributed among these distances:
9 3 0.01
10 1 0.00
11 11 0.02
12 66 0.14
13 132 0.28
14 122 0.25
15 83 0.17
16 41 0.09
17 19 0.04
18 1 0.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (14 bp):
ATATATTATACTTT
Found at i:499130 original size:80 final size:80
Alignment explanation
Indices: 499018--499189 Score: 249
Period size: 80 Copynumber: 2.1 Consensus size: 80
499008 ATAATATACT
* * * * *
499018 TATACTTTATATTATTATATATTTATATATACTTTATTCTAAAAATTTATATGTATATACTTTAT
1 TATAC-TTATATTATTATATATGTATATATACTTTATACTAAAAATTTATATATATATA-TATAC
499083 A-TTTAATAGTTTATATA
64 ACTTT-ATAGTTTATATA
*
499100 TATA-TTATATTATTATATATGTATATATACTTTATACTAAAACTTTATATATATATATATACAC
1 TATACTTATATTATTATATATGTATATATACTTTATACTAAAAATTTATATATATATATATACAC
499164 TTTATAGTTTATATA
66 TTTATAGTTTATATA
499179 TATACTTATAT
1 TATACTTATAT
499190 ACTTTAGTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
79 20 0.24
80 58 0.71
82 4 0.05
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (80 bp):
TATACTTATATTATTATATATGTATATATACTTTATACTAAAAATTTATATATATATATATACAC
TTTATAGTTTATATA
Found at i:499178 original size:20 final size:21
Alignment explanation
Indices: 499123--499195 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 21
499113 TATATATGTA
*
499123 TATATACTTTATACTA-AAACTT
1 TATATACTTTATA-TATACAC-T
*
499145 TATATA-TATATATATACACT
1 TATATACTTTATATATACACT
* *
499165 T-TATAGTTTATATATATACT
1 TATATACTTTATATATACACT
499185 TATATACTTTA
1 TATATACTTTA
499196 GTCTTTTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.09
20 17 0.40
21 16 0.37
22 6 0.14
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (21 bp):
TATATACTTTATATATACACT
Found at i:499180 original size:2 final size:2
Alignment explanation
Indices: 497903--499160 Score: 175
Period size: 2 Copynumber: 639.0 Consensus size: 2
497893 CAATATAGTT
* * *
497903 TA TA TT TA TA T- TA T- TA TA TA CTA TA TA TA AA CTA TA TA -A TT
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* *
497944 TA TA TT TA TA -A TA T- TA TA TA CTA TA TA TA AA CTA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA
* * * *
497985 TA TG TA TA AA CTA TA TA GTT TA T- TA -A TA TA AA CTA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
**
498026 -A GC TA TA TA GTA TA TA TA TA TA TA TA TA -A TA TA T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
498066 TA TA AA CTA TG TA TA TA AA CTA TA TA CA T- TT TA TT TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
498108 T- TA TA TA CTA TA TA TA AA CTA TA TA TA T- TA TG TA TA AA CTA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
498149 TA T- TT TA T- TA -A TA TA AA T- TA TA TA T- TT TA TA TG TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
498186 T- TA TA TA -A GA -A T- TA TA TT TA AA TA TA TA CA TC T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
498223 TT TA TA TA T- TA TG TA TA CTA TA AA T- TA TA TA TA CTA TG TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
498265 AA T- TA TA TA GTT TA TA TA GT- TA -A AA TA TA AA GTA TC TA -A
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * *
498304 GTA TA TA -A TA TA AA GTA TA TA TA CA TA TA -A AA TA TA -A GTA
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * * *
498344 TG TA TA TA TA CA TA TA TA TA TA TA TA TA AA T- TT TA GTA CA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
498386 GTA TA TA -A GTA TA TA -A TA TA -A AA TA TA TA -A GA -A T- TA AA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
498424 TA TA AA GTA TA TA TA TA CA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
498466 TA TA TA TA -A TA TA AA GTA TA TA -A GTA T- TA AA TA CA AA GTA
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
498506 TA TA AA GTA TA -A T- TA TA AA GA CTA AA GTA TA TA -A GTA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA -TA TA TA
* * * * *
498547 -A TA TA AA GTA TA TA TA CA TA TA AA GTA TA -A GTA TG TA TG TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA
* * * * * * ** *
498588 TG TA TG TA TG TA TG TA TC TA TA TA TA TA TA TA TA AA GG TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
498630 GTA TA AA GTG TA TA TA TA TA TA TA TA TA TA -A TA TA AA GTA TA
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
498672 -A T- TA TA T- TA TA TA TA TA TA TA TA TA AA AA GT- TT TA GA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
498710 TA AA GTA TA TA TA CA TA GA TA AA TA TA TA TA TA TA -A TA TA AA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
498752 GTA TA -A T- TA TA AA GA T- TA AA GTA TA TA -A GGA TC TA -A TG
1 -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * * * *
498790 TA AA GTA TA CA -A GTA T- TA AA TA TA AA T- TA TA TA TA CA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
498831 -A TA TA TA TA TA TA TA TG TA TA TA -A TA -A TA TA AA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
498871 -A GTA TA TA TA TA AA CTA TA -A TG TA TG TA TA TA TA TA AA GTA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
498912 TA -A GTA AA TA TA TA AA CTA TA AA GTA TA AA TA TA TA TA CTT TA
1 TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
498955 TA T- TA TA TA CT- TA TA TA CTT TA GTC TT TA TA -A T- TA TA CTC
1 TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA TA TA TA -TA
*
498995 TA TA TA TA TA TA TA TA -A TA TA CT- TA TA CTT TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * * * * * *
499035 TA TA TT TA TA TA TA CTT TA T- TC TA AA AA TT TA TA TG TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
499077 CTT TA TA TT TA -A TA GTT TA TA TA TA TA T- TA TA T- TA T- TA TA
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
499117 TA TG TA TA TA TA CTT TA TA CTA -A AA CTT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
499159 TA
1 TA
499161 CACTTTATAG
Statistics
Matches: 879, Mismatches: 227, Indels: 300
0.63 0.16 0.21
Matches are distributed among these distances:
1 85 0.10
2 723 0.82
3 71 0.08
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:499243 original size:114 final size:107
Alignment explanation
Indices: 498946--499282 Score: 275
Period size: 114 Copynumber: 3.1 Consensus size: 107
498936 TATAAATATA
* * *
498946 TATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTCTATATATATATATATA
1 TATACTTTATA-TATATACTTATATACTTTAGTCTTTATAATTATAATTTTTATATATATATATA
* *
499011 -ATATACTTATACTTTATA-TTATTATATATTTATATATACTT
65 TATATACTTATACTTTATACTAATTATATATTTATATACACTT
* ** * * * * *
499052 TATTCTAAAAATTTATA-TGTATATACTTTA-TATTTAATAGTTTATATATATATTATAT-TAT-
1 TATACTTTATATATATACT-TATATACTTTAGTCTTT-ATA-ATTATA-AT-TTTTATATATATA
*
499113 TATATATGTA-TATATACTTTATACTAAAACTTTATATATATATATATACACTT
61 TATATATATACT-TATACTTTATACT--AA--TTATATAT-T-TATATACACTT
* *
499166 TATAGTTTATATATATACTTATATACTTTAGTCTTTTTAATTATAATTTTTATATATATAATATA
1 TATACTTTATATATATACTTATATACTTTAGTCTTTATAATTATAATTTTTATATATAT-ATATA
* *
499231 TTTATACTTATAC-TTATACT--TTATATTATTGTATAT-CTA-TA
65 TATATACTTATACTTTATACTAATTATA-TATT-TATATAC-ACTT
499272 TATACTTTATA
1 TATACTTTATA
499283 CTAAAACTTT
Statistics
Matches: 180, Mismatches: 29, Indels: 44
0.71 0.11 0.17
Matches are distributed among these distances:
104 5 0.03
105 19 0.11
106 29 0.16
107 31 0.17
108 9 0.05
110 1 0.01
111 7 0.04
112 13 0.07
113 13 0.07
114 47 0.26
115 6 0.03
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (107 bp):
TATACTTTATATATATACTTATATACTTTAGTCTTTATAATTATAATTTTTATATATATATATAT
ATATACTTATACTTTATACTAATTATATATTTATATACACTT
Found at i:499514 original size:2 final size:2
Alignment explanation
Indices: 499509--499543 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
499499 TTATGGTTTT
499509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
499544 CTTTATAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:499711 original size:2 final size:2
Alignment explanation
Indices: 499704--499743 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
499694 TAAAATTCGT
499704 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
499744 ATTTTTCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:500208 original size:21 final size:22
Alignment explanation
Indices: 500168--500234 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
500158 TTGTACTTTA
500168 TATACATATATAAAGTATAAAG
1 TATACATATATAAAGTATAAAG
* *
500190 TATACGTATAT-ATGTATAAAG
1 TATACATATATAAAGTATAAAG
500211 TATA-AT-TATAAAG-ACTAAAG
1 TATACATATATAAAGTA-TAAAG
500231 TATA
1 TATA
500235 TAAGCATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.10
20 12 0.31
21 13 0.33
22 10 0.26
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.34
Consensus pattern (22 bp):
TATACATATATAAAGTATAAAG
Found at i:500251 original size:22 final size:22
Alignment explanation
Indices: 500226--500437 Score: 195
Period size: 22 Copynumber: 9.5 Consensus size: 22
500216 TTATAAAGAC
*
500226 TAAAGTATATAAGCATATAATA
1 TAAAGTATATAAGTATATAATA
*
500248 TAAAATATATAAGTAT-TAA-A
1 TAAAGTATATAAGTATATAATA
500268 CTTAAAGTATATATATGTATATAATAATA
1 --TAAAGTATATA-A-G--TAT-ATAATA
*
500297 TAAAGTATATAATTATATAATA
1 TAAAGTATATAAGTATATAATA
* * *
500319 CATAGTATATAAGTATATTATA
1 TAAAGTATATAAGTATATAATA
* *
500341 TAAAGTATATAAGTGTTTAATA
1 TAAAGTATATAAGTATATAATA
500363 T-AAGTATATAAGTAT-TAATTA
1 TAAAGTATATAAGTATATAA-TA
500384 TAAAGTATATAAGTATAT-ATA
1 TAAAGTATATAAGTATATAATA
* *
500405 TAAACTATA-ATGTATATATATA
1 TAAAGTATATAAGTATATA-ATA
*
500427 TATA-TATATAA
1 TAAAGTATATAA
500438 AATATACTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 30
0.77 0.09 0.15
Matches are distributed among these distances:
20 11 0.07
21 33 0.21
22 88 0.56
23 5 0.03
24 1 0.01
26 4 0.03
27 11 0.07
28 3 0.02
29 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (22 bp):
TAAAGTATATAAGTATATAATA
Found at i:500301 original size:71 final size:67
Alignment explanation
Indices: 500226--500413 Score: 192
Period size: 71 Copynumber: 2.8 Consensus size: 67
500216 TTATAAAGAC
* *
500226 TAAAGTATATAAGCATATAATATAAAATATATAAGTATTA-AACT-TAAAGTATATATATGTATA
1 TAAAGTATATAAGTATATAATATAAAGTATATAAGTATTATAA-TATAAAGTATATA-A-GTAT-
500289 TAATAATA
62 T--TAATA
* * * * *
500297 TAAAGTATATAATTATATAATACATAGTATATAAGTA-TATTATATAAAGTATATAAGTGTTTAA
1 TAAAGTATATAAGTATATAATATAAAGTATATAAGTATTATAATATAAAGTATATAAGTATTTAA
500361 TA
66 TA
*
500363 T-AAGTATATAAGTAT-TAATTATAAAGTATATAAGTA-TAT-ATATAAACTATA
1 TAAAGTATATAAGTATATAA-TATAAAGTATATAAGTATTATAATATAAAGTATA
500414 ATGTATATAT
Statistics
Matches: 103, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
64 14 0.14
65 31 0.30
66 6 0.06
68 1 0.01
69 3 0.03
70 4 0.04
71 44 0.43
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (67 bp):
TAAAGTATATAAGTATATAATATAAAGTATATAAGTATTATAATATAAAGTATATAAGTATTTAA
TA
Found at i:500306 original size:17 final size:15
Alignment explanation
Indices: 500228--500443 Score: 103
Period size: 14 Copynumber: 15.1 Consensus size: 15
500218 ATAAAGACTA
*
500228 AAGTATATAAGCATAT
1 AAGTATATAA-TATAT
*
500244 AA-TATAAAATATAT
1 AAGTATATAATATAT
500258 AAGTAT-TAA-ACT-T
1 AAGTATATAATA-TAT
*
500271 AAAGTATAT-ATATGT
1 -AAGTATATAATATAT
500286 -A-TATAATAATATA-
1 AAGTAT-ATAATATAT
500299 AAGTATATAATTATAT
1 AAGTATATAA-TATAT
* *
500315 AA-TACATAGTATAT
1 AAGTATATAATATAT
*
500329 AAGTATATTATATA-
1 AAGTATATAATATAT
* *
500343 AAGTATATAAGTGTTT
1 AAGTATATAA-TATAT
*
500359 AA-TATA-AGTATAT
1 AAGTATATAATATAT
500372 AAGTAT-TAAT-TAT
1 AAGTATATAATATAT
500385 AAAGTATATAAGTATAT
1 -AAGTATATAA-TATAT
500402 -A-TATA-AACTATA-
1 AAGTATATAA-TATAT
*
500414 ATGTATAT-ATATAT
1 AAGTATATAATATAT
*
500428 ATA-TATATAAAATAT
1 A-AGTATATAATATAT
500443 A
1 A
500444 CTTATACTTT
Statistics
Matches: 153, Mismatches: 20, Indels: 55
0.67 0.09 0.24
Matches are distributed among these distances:
12 3 0.02
13 23 0.15
14 69 0.45
15 48 0.31
16 7 0.05
17 3 0.02
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (15 bp):
AAGTATATAATATAT
Found at i:500306 original size:49 final size:45
Alignment explanation
Indices: 500190--500437 Score: 193
Period size: 43 Copynumber: 5.6 Consensus size: 45
500180 AAGTATAAAG
* * * *
500190 TATACGTATAT-ATGTATAAAG--TATAATTATAAAGACTAAAGTA
1 TATAAGTATATAATATATAAAGTATATAAGTATTAA-ACTAAAGTA
*
500233 TATAAGCATATAATATA-AAA-TATATAAGTATTAAACTTAAAGTA
1 TATAAGTATATAATATATAAAGTATATAAGTATTAAAC-TAAAGTA
* *
500277 TATATATGTATATAATAATATAAAGTATATAATTATATAATAC-ATAGTA
1 TATA-A-GTATATAAT-ATATAAAGTATATAAGTAT-TAA-ACTAAAGTA
* *
500326 TATAAGTATAT--TATATAAAGTATATAAGTGTTTAA-TATAAGTA
1 TATAAGTATATAATATATAAAGTATATAAGTATTAAACTA-AAGTA
* *
500369 TATAAGTAT-TAAT-TATAAAGTATATAAGTATATATA-TAAACTA
1 TATAAGTATATAATATATAAAGTATATAAGTAT-TAAACTAAAGTA
* *
500412 TA-ATGTATAT-ATATATATA-TATATAA
1 TATAAGTATATAATATATAAAGTATATAA
500438 AATATACTTA
Statistics
Matches: 169, Mismatches: 18, Indels: 37
0.75 0.08 0.17
Matches are distributed among these distances:
42 17 0.10
43 58 0.34
44 47 0.28
45 2 0.01
46 8 0.05
47 9 0.05
48 4 0.02
49 19 0.11
50 3 0.02
51 2 0.01
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.39
Consensus pattern (45 bp):
TATAAGTATATAATATATAAAGTATATAAGTATTAAACTAAAGTA
Found at i:500327 original size:93 final size:88
Alignment explanation
Indices: 500204--500443 Score: 231
Period size: 93 Copynumber: 2.6 Consensus size: 88
500194 CGTATATATG
500204 TATAAAG--TATAATTATA-AAGACTAAAGTATATAAGCATATAATATAAAATATATAAGTATTA
1 TATAAAGTATATAATTATATAAGACTAAAGTATATAAGCATATAATATAAAATATATAAGTATTA
500266 AACT-TAAAGTATATATATGTATATAAT
66 AA-TAT-AAGTATATA-A-GTAT-TAAT
* * * * * *
500293 AATATAAAGTATATAATTATATAATAC-ATAGTATATAAGTATATTATATAAAGTATATAAGTGT
1 --TATAAAGTATATAATTATATAAGACTAAAGTATATAAGCATATAATATAAAATATATAAGTAT
*
500357 TTAATATAAGTATATAAGTATTAAT
64 TAAATATAAGTATATAAGTATTAAT
* *
500382 TATAAAGTATATAAGTATATATATAAACTATAATGTATATATA-TATATATATATAAAATATA
1 TATAAAGTATATAA-T-TATATA-AGACTA-AA-GTATATA-AGCATATA-ATATAAAATATA
500444 CTTATACTTT
Statistics
Matches: 126, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
87 14 0.11
88 1 0.01
89 10 0.08
90 7 0.06
91 9 0.07
92 11 0.09
93 58 0.46
94 16 0.13
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (88 bp):
TATAAAGTATATAATTATATAAGACTAAAGTATATAAGCATATAATATAAAATATATAAGTATTA
AATATAAGTATATAAGTATTAAT
Found at i:500333 original size:8 final size:8
Alignment explanation
Indices: 500228--500402 Score: 119
Period size: 8 Copynumber: 23.1 Consensus size: 8
500218 ATAAAGACTA
500228 AAGTATAT
1 AAGTATAT
*
500236 AAGCATAT
1 AAGTATAT
500244 AA-TATA-
1 AAGTATAT
*
500250 AAATATAT
1 AAGTATAT
500258 AAGTAT-T
1 AAGTATAT
*
500265 AAACT-TA-
1 -AAGTATAT
500272 AAGTATAT
1 AAGTATAT
500280 ATATGTATAT
1 A-A-GTATAT
500290 AA-TAATAT
1 AAGT-ATAT
500298 AAAGTATAT
1 -AAGTATAT
*
500307 AATTATAT
1 AAGTATAT
*
500315 AA-TACAT
1 AAGTATAT
500322 -AGTATAT
1 AAGTATAT
500329 AAGTATAT
1 AAGTATAT
*
500337 TA-TATA-
1 AAGTATAT
500343 AAGTATAT
1 AAGTATAT
*
500351 AAGTGT-T
1 AAGTATAT
*
500358 TA--ATAT
1 AAGTATAT
500364 AAGTATAT
1 AAGTATAT
500372 AAGTAT-T
1 AAGTATAT
*
500379 AATTATA-
1 AAGTATAT
500386 AAGTATAT
1 AAGTATAT
500394 AAGTATAT
1 AAGTATAT
500402 A
1 A
500403 TATAAACTAT
Statistics
Matches: 131, Mismatches: 16, Indels: 40
0.70 0.09 0.21
Matches are distributed among these distances:
5 1 0.01
6 9 0.07
7 42 0.32
8 63 0.48
9 8 0.06
10 8 0.06
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.39
Consensus pattern (8 bp):
AAGTATAT
Found at i:500400 original size:28 final size:29
Alignment explanation
Indices: 500360--500443 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
500350 TAAGTGTTTA
* *
500360 ATATAAG-TATATAAGTATTAATTATAAAGT
1 ATATAAGATATAT-A-TATAAACTATAAAGT
*
500390 ATATAAG-TATATATATAAACTATAATGT
1 ATATAAGATATATATATAAACTATAAAGT
* *
500418 ATATATATATATATATATAAAATATA
1 ATATA-AGATATATATATAAACTATA
500444 CTTATACTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 17 0.36
29 2 0.04
30 28 0.60
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.40
Consensus pattern (29 bp):
ATATAAGATATATATATAAACTATAAAGT
Found at i:500456 original size:26 final size:28
Alignment explanation
Indices: 500425--500633 Score: 124
Period size: 28 Copynumber: 7.7 Consensus size: 28
500415 TGTATATATA
*
500425 TATA-TATATATAAAATATACTTATACTT
1 TATAGTATATAT-ATATATACTTATACTT
*
500453 TATATTAT-TATATA-AGTA-TATATACTT
1 TATAGTATATATATATA-TACT-TATACTT
* * *
500480 TATACTAAAATTATATATATAC--ACACTT
1 TATAGT-ATA-TATATATATACTTATACTT
500508 TATAGT-T-TATATATATACTTATACTT
1 TATAGTATATATATATATACTTATACTT
* *
500534 TATAGTTTATATATATATACTTGTACTT
1 TATAGTATATATATATATACTTATACTT
*
500562 TATATGTATACATACT-T-TA--TATAC-T
1 TATA-GTATATATA-TATATACTTATACTT
* * * *
500587 TATA-TACTTTAGTCTTTATAATTATACTT
1 TATAGTA-TATA-TATATATACTTATACTT
500616 TATA-TATATATATATATA
1 TATAGTATATATATATATA
500634 TATATAAGTA
Statistics
Matches: 143, Mismatches: 17, Indels: 43
0.70 0.08 0.21
Matches are distributed among these distances:
23 2 0.01
24 14 0.10
25 7 0.05
26 19 0.13
27 23 0.16
28 50 0.35
29 18 0.13
30 9 0.06
31 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (28 bp):
TATAGTATATATATATATACTTATACTT
Found at i:500456 original size:28 final size:28
Alignment explanation
Indices: 500397--500571 Score: 84
Period size: 28 Copynumber: 6.3 Consensus size: 28
500387 AGTATATAAG
* *
500397 TATATATATAAACTATAATGTATA-TATATA
1 TATATATATAAAATATACT-TATACT-T-TA
500427 TATATATATAAAATATACTTATACTTTA
1 TATATATATAAAATATACTTATACTTTA
*
500455 TAT-TATTATATAAGTATA--TATACTTTA
1 TATATA-TATA-AAATATACTTATACTTTA
* * *
500482 TACTA-AAATTATATATATAC--ACACTTTA
1 TA-TATATA-TA-AAATATACTTATACTTTA
*
500510 TAGT-T-TAT-ATATATACTTATACTTTA
1 TA-TATATATAAAATATACTTATACTTTA
* * *
500536 TAGTTTATAT-ATATATACTTGTACTTTA
1 TA-TATATATAAAATATACTTATACTTTA
*
500564 TATGTATA
1 TATATATA
500572 CATACTTTAT
Statistics
Matches: 121, Mismatches: 12, Indels: 27
0.76 0.08 0.17
Matches are distributed among these distances:
24 8 0.07
26 12 0.10
27 21 0.17
28 51 0.42
29 11 0.09
30 18 0.15
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (28 bp):
TATATATATAAAATATACTTATACTTTA
Found at i:500499 original size:34 final size:31
Alignment explanation
Indices: 500427--500500 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 31
500417 TATATATATA
* *
500427 TATATATATAAAATATACTTATACTTTATAT
1 TATATATATAAAATATACTTATACTTAAAAT
500458 TAT-TATATAAGTATATATACTTTATAC-TAAAAT
1 TATATATATAA--A-ATATAC-TTATACTTAAAAT
500491 TATATATATA
1 TATATATATA
500501 CACACTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
30 7 0.19
31 3 0.08
32 1 0.03
33 13 0.36
34 12 0.33
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (31 bp):
TATATATATAAAATATACTTATACTTAAAAT
Found at i:500517 original size:24 final size:25
Alignment explanation
Indices: 500490--500550 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
500480 TATACTAAAA
500490 TTATATATATAC-ACACTTTATAGT
1 TTATATATATACTACACTTTATAGT
*
500514 TTATATATATACTTATACTTTATAGT
1 TTATATATATAC-TACACTTTATAGT
500540 TTATATATATA
1 TTATATATATA
500551 TACTTGTACT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
24 12 0.35
26 22 0.65
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (25 bp):
TTATATATATACTACACTTTATAGT
Found at i:500623 original size:2 final size:2
Alignment explanation
Indices: 500616--500708 Score: 61
Period size: 2 Copynumber: 46.0 Consensus size: 2
500606 AATTATACTT
500616 TA TA TA TA TA TA TA TA TA TA TA TA -A GTA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * * *
500657 AA GT- TT TA GTA TA -A TGA -A TA AA TA CTT TA TA GTA TA TA TA TA
1 TA -TA TA TA -TA TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA
500699 TA TA TA TA TA
1 TA TA TA TA TA
500709 CACTTTATAG
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
1 5 0.07
2 61 0.84
3 7 0.10
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:500669 original size:17 final size:19
Alignment explanation
Indices: 500622--500660 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
500612 ACTTTATATA
500622 TATATATATATATATATAAG
1 TATATA-ATATATATATAAG
500642 TATATAATATATATA-AAG
1 TATATAATATATATATAAG
500660 T
1 T
500661 TTTAGTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TATATAATATATATATAAG
Found at i:501411 original size:18 final size:20
Alignment explanation
Indices: 501353--501425 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 20
501343 ATATATAAAG
501353 TATATTAATTATCATAATTAA
1 TATATTAATTATCATAATT-A
*
501374 TATATTAAGTAT-AT--TTA
1 TATATTAATTATCATAATTA
*
501391 TTATTTTAATTATCATAATTA
1 -TATATTAATTATCATAATTA
501412 -ATATT--TTATCATAA
1 TATATTAATTATCATAA
501426 CATTTAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 10 0.23
18 12 0.27
19 6 0.14
20 2 0.05
21 14 0.32
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (20 bp):
TATATTAATTATCATAATTA
Found at i:501418 original size:21 final size:21
Alignment explanation
Indices: 501357--501419 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
501347 ATAAAGTATA
*
501357 TTAATTATCATAATTAATATA
1 TTAATTATCATAATTAATATT
* *
501378 TTAAGTAT-AT--TTATTATT
1 TTAATTATCATAATTAATATT
501396 TTAATTATCATAATTAATATT
1 TTAATTATCATAATTAATATT
501417 TTA
1 TTA
501420 TCATAACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 13 0.38
19 2 0.06
20 2 0.06
21 17 0.50
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAATTATCATAATTAATATT
Found at i:504008 original size:45 final size:45
Alignment explanation
Indices: 503886--504137 Score: 285
Period size: 46 Copynumber: 5.8 Consensus size: 45
503876 ATAAAATTAT
*
503886 GAGCTTATAGAAT-AATGGCAAGTATA-TGGATAAAATAAGCTTAC
1 GAGCTTATAGAATAAATGGTAAGTATATTGG-TAAAATAAGCTTAC
* * *
503930 AAGCTTATGAAAATAAATGGTAAGTATACTGGTAAAATAAGCTTAC
1 GAGCTTAT-AGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
* *
503976 GAGTTTATAGAATAAATGGTAAGTATGTTGGTAAAATAAGCTTAC
1 GAGCTTATAGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
* *
504021 GAGCTTATTGGAATAAATGGTAAGTATTTTGGTAAAATAAGCTT-C
1 GAGCTTA-TAGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
504066 TG-G---AT----TAAATGGTAAGTATATTGGTAAAATAAGCTTAC
1 -GAGCTTATAGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
* *
504104 GAGCTTATAGGATAAATGATATA-TATATTGGTAA
1 GAGCTTATAGAATAAATGGTA-AGTATATTGGTAA
504138 GAAAGTTGTA
Statistics
Matches: 180, Mismatches: 13, Indels: 29
0.81 0.06 0.13
Matches are distributed among these distances:
37 31 0.17
38 2 0.01
41 3 0.02
42 1 0.01
44 7 0.04
45 65 0.36
46 68 0.38
47 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (45 bp):
GAGCTTATAGAATAAATGGTAAGTATATTGGTAAAATAAGCTTAC
Found at i:504013 original size:91 final size:87
Alignment explanation
Indices: 503890--504111 Score: 262
Period size: 91 Copynumber: 2.6 Consensus size: 87
503880 AATTATGAGC
* * *
503890 TTATAGAAT-AATGGCAAGTATATGGATAAAATAAGCTTACAAGCTTATGAAAATAAATGGTAAG
1 TTATAGAATAAATGGTAAGTATTTGG-TAAAATAAGCTTACGAGCTTATG-AAATAAATGGTAAG
503954 TATACTGGTAAAATAAGCTTAC-GAG
64 TATACTGGTAAAATAAGCTT-CTG-G
*
503979 TTTATAGAATAAATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATTGGAATAAATGGTAA
1 -TTATAGAATAAATGGTAAGTAT-TTGGTAAAATAAGCTTACGAGCTTA-TGAAATAAATGGTAA
**
504044 GTATTTTGGTAAAATAAGCTTCTGG
63 GTATACTGGTAAAATAAGCTTCTGG
504069 --AT----TAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 TTATAGAATAAATGGTAAGTAT-TTGGTAAAATAAGCTTACGAGCTTAT
504112 AGGATAAATG
Statistics
Matches: 121, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
82 1 0.01
83 39 0.32
87 2 0.02
90 11 0.09
91 63 0.52
92 5 0.04
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (87 bp):
TTATAGAATAAATGGTAAGTATTTGGTAAAATAAGCTTACGAGCTTATGAAATAAATGGTAAGTA
TACTGGTAAAATAAGCTTCTGG
Found at i:504076 original size:37 final size:37
Alignment explanation
Indices: 504029--504101 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
504019 ACGAGCTTAT
*
504029 TGGAATAAATGGTAAGTATTTTGGTAAAATAAGCTTC
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTC
*
504066 TGGATTAAATGGTAAGTATATTGGTAAAATAAGCTT
1 TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTT
504102 ACGAGCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (37 bp):
TGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTC
Found at i:511712 original size:46 final size:45
Alignment explanation
Indices: 511616--511887 Score: 341
Period size: 45 Copynumber: 6.0 Consensus size: 45
511606 GTAACCAGGC
* * * *
511616 AAATAAGCTTATGAGCTTTTGGAAT-AATTGAAAGTATA-TGGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGG-TA
*
511660 AAATAAGCTTACGAGCTTATGAAAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATATTGGTA
* *
511706 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * * *
511751 AAATAAGCATATGAGCTTATAGGAATAAATGGTAAGTATTTTTGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
* * * *
511797 AAATGAGCTTATGAGCTTATGGATTAAATAGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
** *
511842 AAATAAGCTTACGAGCTTATGGAATAAATTATATGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
511887 A
1 A
511888 GAAAGTTTTA
Statistics
Matches: 199, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
44 19 0.10
45 104 0.52
46 73 0.37
47 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:511769 original size:91 final size:90
Alignment explanation
Indices: 511616--511887 Score: 334
Period size: 91 Copynumber: 3.0 Consensus size: 90
511606 GTAACCAGGC
* * * *
511616 AAATAAGCTTATGAGCTTTTGGAAT-AATTGAAAGTATATGGATAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTATGAGCTTATGGAATAAATAGTAAGTATTTGG-TAAAATAAGCTTACGAGCTTAT
*
511680 GAAAATAAATGGTAAGTATATTGGTA
65 GAGAATAAATGGTAAGTATATTGGTA
* * * * *
511706 AAATAAGCTTACGAGCTTATAGAATAAATGGTAAGTATGTTGGTAAAATAAGCATATGAGCTTAT
1 AAATAAGCTTATGAGCTTATGGAATAAATAGTAAGTAT-TTGGTAAAATAAGCTTACGAGCTTAT
* *
511771 -AGGAATAAATGGTAAGTATTTTTGTA
65 GA-GAATAAATGGTAAGTATATTGGTA
* *
511797 AAATGAGCTTATGAGCTTATGGATTAAATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTATGAGCTTATGGAATAAATAGTAAGTAT-TTGGTAAAATAAGCTTACGAGCTTAT
** *
511862 G-GAATAAATTATATGTATATTGGTA
65 GAGAATAAATGGTAAGTATATTGGTA
511887 A
1 A
511888 GAAAGTTTTA
Statistics
Matches: 154, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
90 43 0.28
91 108 0.70
92 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (90 bp):
AAATAAGCTTATGAGCTTATGGAATAAATAGTAAGTATTTGGTAAAATAAGCTTACGAGCTTATG
AGAATAAATGGTAAGTATATTGGTA
Found at i:512305 original size:20 final size:20
Alignment explanation
Indices: 512275--512412 Score: 96
Period size: 20 Copynumber: 7.2 Consensus size: 20
512265 GTTCGAGTTC
*
512275 ATATTAACTATATATATTAT
1 ATATAAACTATATATATTAT
*
512295 GTATAAACTATATAGT-TTAT
1 ATATAAACTATATA-TATTAT
* * *
512315 ACATAAAGTATATAAATTAT
1 ATATAAACTATATATATTAT
512335 ATAT--A-TA-A-ACTA-TAT
1 ATATAAACTATATA-TATTAT
*
512350 ATATAAACTATATATATAAT
1 ATATAAACTATATATATTAT
* *
512370 GTATAAACTATATTTTATTA-
1 ATATAAACTATA-TATATTAT
*
512390 ATATAAATTATATAGT-TTAT
1 ATATAAACTATATA-TATTAT
512410 ATA
1 ATA
512413 GTTTAAATAT
Statistics
Matches: 91, Mismatches: 15, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
15 8 0.09
16 2 0.02
17 3 0.03
18 3 0.03
19 7 0.08
20 62 0.68
21 6 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATAAACTATATATATTAT
Found at i:512339 original size:13 final size:13
Alignment explanation
Indices: 512323--512403 Score: 76
Period size: 13 Copynumber: 6.2 Consensus size: 13
512313 ATACATAAAG
512323 TATATAAATTATA
1 TATATAAATTATA
*
512336 TATATAAACTATA
1 TATATAAATTATA
*
512349 TATATAAACTATA
1 TATATAAATTATA
512362 TATAT-AATGTATA
1 TATATAAAT-TATA
* **
512375 AACTATATTTTAT-
1 TA-TATAAATTATA
512388 TAATATAAATTATA
1 T-ATATAAATTATA
512402 TA
1 TA
512404 GTTTATATAG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
12 2 0.04
13 44 0.80
14 8 0.15
15 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (13 bp):
TATATAAATTATA
Found at i:512374 original size:26 final size:26
Alignment explanation
Indices: 512296--512368 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
512286 ATATATTATG
* * *
512296 TATAAACTATATAGTTTATACATAAAGTA
1 TATAAACTATATA-TATAAAC-TATA-TA
*
512325 TATAAATTATATATATAAACTATATA
1 TATAAACTATATATATAAACTATATA
512351 TATAAACTATATATATAA
1 TATAAACTATATATATAA
512369 TGTATAAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 19 0.49
27 3 0.08
28 5 0.13
29 12 0.31
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (26 bp):
TATAAACTATATATATAAACTATATA
Found at i:512479 original size:84 final size:77
Alignment explanation
Indices: 512390--512600 Score: 173
Period size: 84 Copynumber: 2.6 Consensus size: 77
512380 TATTTTATTA
*
512390 ATATAAATTATATAGTTTATATAGTTTAAATATAAAGTATATATACATATAAAGTATAAGTATGT
1 ATATAAAATATATAG-TTATATAGTTTAAATATAAAGTATATATACATATAAAGTAT-A-TA--T
* *
512455 ATATATATATAA-AGTTTT
61 ACATATATATAATA--TGT
* * * *
512473 AGTATAAAGTATATAAG-TATATAATATAAAATATATAAG-A-AT-TAAATATAAAGTATATATA
1 A-TATAAAATATAT-AGTTATATAGT-TTAAATATA-AAGTATATATACATATAAAGTATATATA
512534 CATATATATAATATGT
62 CATATATATAATATGT
* *
512550 ATATAATAATATAAAG-TATATAAGTATATAATATAAAGTATATATACATAT
1 ATATAA-AATATATAGTTATAT-AGTTTA-AATATAAAGTATATATACATAT
512601 TGTAACCACC
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
76 16 0.15
77 17 0.16
78 14 0.13
79 7 0.07
80 2 0.02
81 1 0.01
82 13 0.12
83 10 0.10
84 20 0.19
85 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (77 bp):
ATATAAAATATATAGTTATATAGTTTAAATATAAAGTATATATACATATAAAGTATATATACATA
TATATAATATGT
Found at i:512488 original size:22 final size:23
Alignment explanation
Indices: 512459--512593 Score: 85
Period size: 22 Copynumber: 6.3 Consensus size: 23
512449 GTATGTATAT
* *
512459 ATATATAAAGT-TTTAGTATAAA
1 ATATATAAAGTATATAATATAAA
*
512481 GTATAT-AAGTATATAATATAAA
1 ATATATAAAGTATATAATATAAA
*
512503 ATATAT-AAGAAT-TAAATATAAA
1 ATATATAAAGTATAT-AATATAAA
* * *
512525 GTATAT--A-TACAT-ATATATA
1 ATATATAAAGTATATAATATAAA
* *
512544 ATATGTATA-TA-ATAATATAAA
1 ATATATAAAGTATATAATATAAA
*
512565 GTATAT-AAGTATATAATATAAA
1 ATATATAAAGTATATAATATAAA
*
512587 GTATATA
1 ATATATA
512594 TACATATTGT
Statistics
Matches: 89, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
19 10 0.11
20 4 0.04
21 22 0.25
22 53 0.60
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATATAAAGTATATAATATAAA
Found at i:512535 original size:99 final size:98
Alignment explanation
Indices: 512415--512593 Score: 260
Period size: 99 Copynumber: 1.8 Consensus size: 98
512405 TTTATATAGT
*
512415 TTAAATATAAAGTATATATACATATAAAGTATAAGTATGTATAT-AT-ATATAAAGT-T-TTAGT
1 TTAAATATAAAGTATATATACATAT--A-TATAA-TATGTATATAATAATATAAAGTATATAAGT
512476 ATA-AAGTATATAAGTATATAATATAAAATATATAAGAA
62 ATATAA-TATA-AAGTATATAATATAAAATATATAAGAA
512514 TTAAATATAAAGTATATATACATATATATAATATGTATATAATAATATAAAGTATATAAGTATAT
1 TTAAATATAAAGTATATATACATATATATAATATGTATATAATAATATAAAGTATATAAGTATAT
512579 AATATAAAGTATATA
66 AATATAAAGTATATA
512594 TACATATTGT
Statistics
Matches: 74, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
95 9 0.12
96 7 0.09
97 10 0.14
98 10 0.14
99 36 0.49
100 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (98 bp):
TTAAATATAAAGTATATATACATATATATAATATGTATATAATAATATAAAGTATATAAGTATAT
AATATAAAGTATATAATATAAAATATATAAGAA
Found at i:512600 original size:22 final size:21
Alignment explanation
Indices: 512475--512593 Score: 113
Period size: 22 Copynumber: 5.6 Consensus size: 21
512465 AAAGTTTTAG
512475 TATAAAGTATATAAGTATATAA
1 TATAAAGTATATAA-TATATAA
* *
512497 TATAAAATATATAAGA-ATTAAA
1 TATAAAGTATATAATATA-T-AA
*
512519 TATAAAGTATAT-ATACAT-A
1 TATAAAGTATATAATATATAA
*
512538 TATATAA-TATGT-ATATAATAA
1 TATA-AAGTATATAATAT-ATAA
512559 TATAAAGTATATAAGTATATAA
1 TATAAAGTATATAA-TATATAA
512581 TATAAAGTATATA
1 TATAAAGTATATA
512594 TACATATTGT
Statistics
Matches: 81, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
19 12 0.15
20 7 0.09
21 14 0.17
22 45 0.56
23 3 0.04
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (21 bp):
TATAAAGTATATAATATATAA
Found at i:524665 original size:6 final size:6
Alignment explanation
Indices: 524654--524722 Score: 69
Period size: 6 Copynumber: 12.5 Consensus size: 6
524644 CCTGAGAAGG
* *
524654 AAAAGA AAAAGA ACAAGA AAAA-T AAAAG- AAAA-A AAAA-A AAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
524697 AAAAGA AATAG- AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
524723 TGAGAGGTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
5 26 0.49
6 27 0.51
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:524682 original size:11 final size:11
Alignment explanation
Indices: 524653--524722 Score: 99
Period size: 11 Copynumber: 6.5 Consensus size: 11
524643 GCCTGAGAAG
524653 GAAAAGAAAAA
1 GAAAAGAAAAA
524664 GAACAAGAAAAA
1 GAA-AAGAAAAA
*
524676 TAAAAGAAAAA
1 GAAAAGAAAAA
524687 -AAAA-AAAAA
1 GAAAAGAAAAA
*
524696 GAAAAGAAATA
1 GAAAAGAAAAA
524707 GAAAAGAAAAA
1 GAAAAGAAAAA
524718 GAAAA
1 GAAAA
524723 TGAGAGGTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
9 5 0.09
10 8 0.15
11 30 0.57
12 10 0.19
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.03
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:528943 original size:4 final size:4
Alignment explanation
Indices: 528936--528964 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
528926 ATGTATGTAT
528936 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
528965 AACTTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:529012 original size:22 final size:22
Alignment explanation
Indices: 528984--529486 Score: 237
Period size: 22 Copynumber: 23.3 Consensus size: 22
528974 TTTATATGTG
*
528984 TATATATATAAACTATAAAGTA
1 TATATATATAAAGTATAAAGTA
*
529006 TATATATAAAAAGTAT-AA-T-
1 TATATATATAAAGTATAAAGTA
* * **
529025 TATAAAGACTAAAGTATATAAACA
1 TATATATA-TAAAGTATA-AAGTA
529049 TATA-ATATAAAGTATATAAGTA
1 TATATATATAAAGTATA-AAGTA
*
529071 TATA-ATATAAAATATACAAGTA
1 TATATATATAAAGTATA-AAGTA
* *
529093 T-TAAATATAAAGTAT-ATGTA
1 TATATATATAAAGTATAAAGTA
* *
529113 CGTATATA-ATATA-TAT-ATGTA
1 --TATATATATAAAGTATAAAGTA
529134 TATAATAATATAAAGTAT--A-TA
1 TAT-AT-ATATAAAGTATAAAGTA
** *
529155 TATATAGT-TTTAGTATAAACTA
1 TATATA-TATAAAGTATAAAGTA
*
529177 TATATACATATATAA-TA-AAAATA
1 TATAT--ATATA-AAGTATAAAGTA
* *
529200 TATAT-TATATA-TATATA-TA
1 TATATATATAAAGTATAAAGTA
529219 TATATATATATAAGTAT-AA-T-
1 TATATATATA-AAGTATAAAGTA
* * *
529239 TATAAAGACTAAAGTATATAAGCA
1 TATATATA-TAAAGTATA-AAGTA
529263 TATA-ATATAAAGTATATAAGTA
1 TATATATATAAAGTATA-AAGTA
* * *
529285 T-TAAATATTAAGTATATA-TA
1 TATATATATAAAGTATAAAGTA
* * *
529305 CATATA-ATATA-TAT-ATGTA
1 TATATATATAAAGTATAAAGTA
529324 TATAATAATATAAAGTATATAAGTA
1 TAT-AT-ATATAAAGTATA-AAGTA
529349 TATAT-TATAAAGTATATAAGTA
1 TATATATATAAAGTATA-AAGTA
*
529371 TATA-ATATAAAGTATATAAGTT
1 TATATATATAAAGTATA-AAGTA
* *
529393 TTTA-ATAT-AAGTATTTAAGTA
1 TATATATATAAAGTA-TAAAGTA
* *
529414 T-TAAATATAAAGTATATAAGTG
1 TATATATATAAAGTATA-AAGTA
* *
529436 TATATATATAAACTATAATGTATA
1 TATATATATAAAGTATAAAG--TA
529460 TATATATATAAAGTAT-AAGTA
1 TATATATATAAAGTATAAAGTA
*
529481 AATATA
1 TATATA
529487 CATACTTTAT
Statistics
Matches: 379, Mismatches: 55, Indels: 95
0.72 0.10 0.18
Matches are distributed among these distances:
19 33 0.09
20 48 0.13
21 53 0.14
22 168 0.44
23 39 0.10
24 30 0.08
25 8 0.02
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
TATATATATAAAGTATAAAGTA
Found at i:529121 original size:19 final size:18
Alignment explanation
Indices: 529097--529236 Score: 59
Period size: 17 Copynumber: 8.2 Consensus size: 18
529087 CAAGTATTAA
*
529097 ATATAAAGTATATGTACGT
1 ATATAAA-TATATATACGT
*
529116 ATAT-AATATATATATGT
1 ATATAAATATATATACGT
*
529133 ATAT-AATA-ATATAAAGT
1 ATATAAATATATAT-ACGT
* *
529150 ATATATATATAGTTTTA-GT
1 ATATAAATATA--TATACGT
* *
529169 ATA-AACTATATATACAT
1 ATATAAATATATATACGT
* *
529186 ATAT-AATAAAAATA--T
1 ATATAAATATATATACGT
*
529201 ATAT-TATATATATA--T
1 ATATAAATATATATACGT
* *
529216 ATATATATATATATAAGT
1 ATATAAATATATATACGT
529234 ATA
1 ATA
529237 ATTATAAAGA
Statistics
Matches: 96, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
15 17 0.18
16 17 0.18
17 35 0.36
18 14 0.15
19 10 0.10
20 1 0.01
21 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (18 bp):
ATATAAATATATATACGT
Found at i:529126 original size:2 final size:2
Alignment explanation
Indices: 529115--529230 Score: 91
Period size: 2 Copynumber: 59.0 Consensus size: 2
529105 TATATGTACG
* *
529115 TA TA TA -A TA TA TA TA TG TA TA TA -A TA -A TA TA AA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
529155 TA TA TA GT- TT TA GTA TA AA CTA TA TA TA CA TA TA TA -A TA AA
1 TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
529196 AA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
529231 AGTATAATTA
Statistics
Matches: 93, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
1 6 0.06
2 82 0.88
3 5 0.05
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:529399 original size:86 final size:87
Alignment explanation
Indices: 528989--529476 Score: 277
Period size: 86 Copynumber: 5.6 Consensus size: 87
528979 ATGTGTATAT
* * * * *
528989 ATATAAACTATA-AAGTATATA-TATAAA-AAGTATAATTATA-AAGACTAAAGTATATAAACAT
1 ATATAAAGTATATAAGTATATATTATAAAGTA-TATAAGTATATAATA-TAAAGTATATATACAT
*
529050 ATAATATAAAGTATATAAGT-ATATA
64 ATAATAT-AAGTATGTAAGTAATA-A
* * * * * * *
529075 ATATAAAATATACAAGTAT-TAAATATAAAGTATATGTACGTATATAATATATA-TATGTATATA
1 ATATAAAGTATATAAGTATAT-ATTATAAAGTATA--TAAGTATATAATATAAAGTATATATACA
*
529138 -ATAATATAAAGTATAT-A-T-ATATA
63 TATAATAT-AAGTATGTAAGTAATA-A
* ** * * * * * * * *
529161 GT-TTTAGTATA-AACTATATATACATATA-TAATAAAAATATATATTATATA-TATATATATAT
1 ATATAAAGTATATAAGTATATAT-TATAAAGT-ATATAAGTATATAATATAAAGTATATATACAT
*
529222 ATATATATAAGTA--TAA-TTATAA
64 ATA-ATATAAGTATGTAAGTAATAA
* * * *
529244 AGACTAAAGTATATAAGCATATAATATAAAGTATATAAGTAT-TAAATATTAAGTATATATACAT
1 ATA-TAAAGTATATAAGTATATATTATAAAGTATATAAGTATAT-AATATAAAGTATATATACAT
529308 ATAATATATA-TATGTATA-TAAT-A
64 ATAATATA-AGTATGTA-AGTAATAA
** *
529331 ATATAAAGTATATAAGTATATATTATAAAGTATATAAGTATATAATATAAAGTATATA-AGTTTT
1 ATATAAAGTATATAAGTATATATTATAAAGTATATAAGTATATAATATAAAGTATATATA-CATA
* *
529395 TAATATAAGTATTTAAGTATTAA
65 TAATATAAGTATGTAAGTAATAA
* * *
529418 ATATAAAGTATATAAGTGTATATATATAAACTATA-ATGTATATATATATATAAAGTATA
1 ATATAAAGTATATAAGTATATAT-TATAAAGTATATAAG--TATATA-ATATAAAGTATA
529477 AGTAAATATA
Statistics
Matches: 319, Mismatches: 50, Indels: 62
0.74 0.12 0.14
Matches are distributed among these distances:
82 1 0.00
83 25 0.08
84 19 0.06
85 52 0.16
86 107 0.34
87 39 0.12
88 38 0.12
89 14 0.04
90 21 0.07
91 3 0.01
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (87 bp):
ATATAAAGTATATAAGTATATATTATAAAGTATATAAGTATATAATATAAAGTATATATACATAT
AATATAAGTATGTAAGTAATAA
Found at i:529413 original size:43 final size:44
Alignment explanation
Indices: 528983--529476 Score: 274
Period size: 44 Copynumber: 10.9 Consensus size: 44
528973 CTTTATATGT
* *
528983 GTATAT-ATATAAACTATA-AAGTATAT-ATATAAA-AAGTATAA
1 GTATATAATATAAAGTATATAAGTATATAATATAAAGTA-TATAA
* * **
529024 TTATA-AAGACTAAAGTATATAAACATATAATATAAAGTATATAA
1 GTATATAATA-TAAAGTATATAAGTATATAATATAAAGTATATAA
* * *
529068 GTATATAATATAAAATATACAAGTAT-TAAATATAAAGTATATGTAC
1 GTATATAATATAAAGTATATAAGTATAT-AATATAAAGTATA--TAA
*
529114 GTATATAATATATATATGTATATAA-TAATATAA-AGTATA-TATATATA
1 GTATATAATATA-A-A-GTATATAAGT-ATATAATA-TAAAGTATATA-A
* * * * *
529161 GT-TTTAGTATAAACTATATATACATATATAATA-AAAATATATATTA
1 GTATATAATATAAAGTATATA-A-GTATATAATATAAAGTATATA--A
* *
529207 -TATATATATATATATATATATATAAGTATA-ATTATAAAGACTAAAGTATATAA
1 GTATATA-ATATA-A-A-GTATATAAGTATATAATATAAAG--T--A-T--ATAA
* *
529260 GCATATAATATAAAGTATATAAGTAT-TAAATATTAAGTATATATA
1 GTATATAATATAAAGTATATAAGTATAT-AATATAAAGTATATA-A
* * *
529305 -CATATAATATATA-TATGT-A-TATAATAATATAAAGTATATAA
1 GTATATAATATAAAGTATATAAGTAT-ATAATATAAAGTATATAA
*
529346 GTATATATTATAAAGTATATAAGTATATAATATAAAGTATATAA
1 GTATATAATATAAAGTATATAAGTATATAATATAAAGTATATAA
* * *
529390 GTTTTTAATAT-AAGTATTTAAGTAT-TAAATATAAAGTATATAA
1 GTATATAATATAAAGTATATAAGTATAT-AATATAAAGTATATAA
* * *
529433 GTGTATATATATAAACTATA-ATGTATATATATATATAAAGTATA
1 GTATATA-ATATAAAGTATATAAG--TATATA-ATATAAAGTATA
529477 AGTAAATATA
Statistics
Matches: 354, Mismatches: 47, Indels: 98
0.71 0.09 0.20
Matches are distributed among these distances:
41 10 0.03
42 34 0.10
43 56 0.16
44 93 0.26
45 27 0.08
46 35 0.10
47 24 0.07
48 15 0.04
49 16 0.05
50 19 0.05
51 8 0.02
52 2 0.01
53 7 0.02
54 5 0.01
55 3 0.01
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (44 bp):
GTATATAATATAAAGTATATAAGTATATAATATAAAGTATATAA
Found at i:529453 original size:30 final size:28
Alignment explanation
Indices: 529020--529470 Score: 177
Period size: 30 Copynumber: 16.0 Consensus size: 28
529010 TATAAAAAGT
* *
529020 ATAATTATAAAG-ACTA-AAGTATATAAAC
1 ATAAATATAAAGTA-TATAAGTATAT-AAT
529048 ATATAATATAAAGTATATAAGTATATAAT
1 ATA-AATATAAAGTATATAAGTATATAAT
529077 ATAAAATATACAAGTAT-TAA--ATATAA-
1 AT-AAATATA-AAGTATATAAGTATATAAT
* * *
529103 AGTATATGT-ACGTATATAA-TATAT-AT
1 A-TAAATATAAAGTATATAAGTATATAAT
** *
529129 ATGTATATAATAATATA-AAGTATAT-AT
1 ATAAATATAA-AGTATATAAGTATATAAT
* ** *
529156 ATATAGT-TTTAGTATA-AACTATATATACAT
1 ATA-AATATAAAGTATATAA--GTATATA-AT
* *
529186 ATATAATA-AAAATATAT-ATTATATATAT
1 ATA-AATATAAAGTATATAAGTATATA-AT
* * *
529214 ATATATATATA-TATATAAGTATA-ATT
1 ATAAATATAAAGTATATAAGTATATAAT
* *
529240 ATAAAGACTAAAGTATATAAGCATATAAT
1 ATAAATA-TAAAGTATATAAGTATATAAT
*
529269 ATAAAGTATATAAGTAT-TAAATATTAAGTATAT
1 ATAAA-TATA-AAGTATATAAGTA-T-A-TA-AT
* *
529302 ATACATATAATA-TATATATGTATAT-A-
1 ATAAATATAA-AGTATATAAGTATATAAT
529328 AT-AATATAAAGTATATAAG--TAT-AT
1 ATAAATATAAAGTATATAAGTATATAAT
529352 AT---TATAAAGTATATAAGTATATAAT
1 ATAAATATAAAGTATATAAGTATATAAT
*
529377 ATAAAGTATATAAGTTTTTAATATAAGTATTTAAGT
1 ATAAA-TATA-AAG----T-ATATAAGTATATAA-T
*
529413 ATTAAATATAAAGTATATAAGTGTATATAT
1 A-TAAATATAAAGTATATAAGTATATA-AT
*
529443 ATAAACTATAATGTATATATA-TATATAA
1 ATAAA-TATAAAGTATATA-AGTATATAA
529471 AGTATAAGTA
Statistics
Matches: 327, Mismatches: 44, Indels: 103
0.69 0.09 0.22
Matches are distributed among these distances:
22 15 0.05
23 4 0.01
24 11 0.03
25 26 0.08
26 28 0.09
27 34 0.10
28 38 0.12
29 46 0.14
30 72 0.22
31 9 0.03
32 11 0.03
33 6 0.02
34 1 0.00
35 16 0.05
36 6 0.02
37 4 0.01
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (28 bp):
ATAAATATAAAGTATATAAGTATATAAT
Found at i:529483 original size:64 final size:63
Alignment explanation
Indices: 529262--529486 Score: 189
Period size: 65 Copynumber: 3.4 Consensus size: 63
529252 GTATATAAGC
*
529262 ATATAATATAAAGTAT-A-TAAGTATTAAA-TAT-TAAGTATATATACATATAATATATATATGT
1 ATATAATATAAAGTATAAGTAAATA-TAAAGTATATAAGTATATAT--ATATAA-ATATATATGT
529323 AT
62 AT
529325 ATAATAATATAAAGTATATAAGTATATATTATAAAGTATATAAGTATATA-ATATAAAGTATATA
1 AT-ATAATATAAAG--TATAAGTA-A-A-TATAAAGTATATAAGTATATATATATAAA-TATATA
*
529389 AGT-T
59 TGTAT
* *
529393 -TTTAATAT-AAGTATTTAAGTATTAAATATAAAGTATATAAGTGTATATATATAAACTATA-AT
1 ATATAATATAAAGTA--TAAG---TAAATATAAAGTATATAAGTATATATATATAAA-TATATAT
529455 GTAT
60 GTAT
529459 ATATATATATAAAGTATAAGTAAATATA
1 ATATA-ATATAAAGTATAAGTAAATATA
529487 CATACTTTAT
Statistics
Matches: 134, Mismatches: 7, Indels: 41
0.74 0.04 0.23
Matches are distributed among these distances:
63 4 0.03
64 19 0.14
65 30 0.22
66 22 0.16
67 10 0.07
68 10 0.07
69 20 0.15
70 4 0.03
71 5 0.04
72 10 0.07
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (63 bp):
ATATAATATAAAGTATAAGTAAATATAAAGTATATAAGTATATATATATAAATATATATGTAT
Found at i:529514 original size:8 final size:7
Alignment explanation
Indices: 529488--529673 Score: 51
Period size: 7 Copynumber: 27.4 Consensus size: 7
529478 GTAAATATAC
529488 ATACTTT
1 ATACTTT
529495 ATA-TTAT
1 ATACTT-T
529502 ATACTTGT
1 ATACTT-T
529510 ATACTTT
1 ATACTTT
529517 AGT-CTTT
1 A-TACTTT
*
529524 ATA-ATT
1 ATACTTT
529530 ATACTCTAT
1 ATACT-T-T
*
529539 ATA-TAT
1 ATACTTT
*
529545 ATA-TAT
1 ATACTTT
529551 ATAC-TT
1 ATACTTT
529557 ATACTTT
1 ATACTTT
*
529564 ATATTATT
1 ATACT-TT
529572 ATA-TATT
1 ATACT-TT
*
529579 -TA-TAT
1 ATACTTT
529584 ATACTTT
1 ATACTTT
*
529591 ATAC-TA
1 ATACTTT
* *
529597 AAACTAT
1 ATACTTT
*
529604 ATA-TAT
1 ATACTTT
*
529610 ATA-TAT
1 ATACTTT
*
529616 AGACTTT
1 ATACTTT
*
529623 ATAGTTT
1 ATACTTT
*
529630 ATA-TAT
1 ATACTTT
529636 ATACTTAT
1 ATACTT-T
*
529644 AAACTTT
1 ATACTTT
529651 AGT-CTTT
1 A-TACTTT
*
529658 ATA-ATT
1 ATACTTT
529664 ATACTTT
1 ATACTTT
529671 ATA
1 ATA
529674 TATATAATAT
Statistics
Matches: 137, Mismatches: 23, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
5 1 0.01
6 54 0.39
7 55 0.40
8 23 0.17
9 4 0.03
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.51
Consensus pattern (7 bp):
ATACTTT
Found at i:529553 original size:27 final size:25
Alignment explanation
Indices: 529523--529577 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
529513 CTTTAGTCTT
529523 TATAATTATACTCTATATATATATATA
1 TATAATTATACTCTATAT-TAT-TATA
* *
529550 TATACTTATACTTTATATTATTATA
1 TATAATTATACTCTATATTATTATA
529575 TAT
1 TAT
529578 TTATATATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 7 0.27
26 3 0.12
27 16 0.62
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (25 bp):
TATAATTATACTCTATATTATTATA
Found at i:529586 original size:27 final size:26
Alignment explanation
Indices: 529529--529841 Score: 92
Period size: 27 Copynumber: 12.0 Consensus size: 26
529519 TCTTTATAAT
*
529529 TATACTCTATATATATATATATATAC
1 TATACTTTATATATATATATATATAC
*
529555 TTATACTTTATATTATTATATATTTATA-
1 -TATACTTTATA-TA-TATATATATATAC
529583 TATACTTTATACTAAAACTATATATATATA-
1 TATACTTTATA-T---A-TATATATATATAC
529613 TATAGACTTTATAGT-T-TATATATATAC
1 TAT--ACTTTATA-TATATATATATATAC
* *
529640 TTATAAACTTTA-GTCT-T-TATA-AT--
1 -TAT--ACTTTATATATATATATATATAC
*
529663 TATACTTTATATATATA-ATATA-CC
1 TATACTTTATATATATATATATATAC
* **
529687 TATATTTTATAT-TAT-TATATATGTT
1 TATACTTTATATATATATATATAT-AC
* * * * *
529712 TGTA-TGTATGTATGTATAATTTATAC
1 TATACTTTATATATATAT-ATATATAC
*
529738 TAAAACTTTATATATATATATATATAC
1 T-ATACTTTATATATATATATATATAC
*
529765 T-TA-TTTACT-TATATACT-TATAT-T
1 TATACTTTA-TATATATA-TATATATAC
* * * *
529788 TAATAC-TTATATACTTTAGTCTTTATAAT
1 T-ATACTTTATATA-TATA-TATATAT-AC
*
529817 TATACTTTATATATATATACATATA
1 TATACTTTATATATATATATATATA
529842 AGTATATAAT
Statistics
Matches: 216, Mismatches: 35, Indels: 71
0.67 0.11 0.22
Matches are distributed among these distances:
20 6 0.03
21 2 0.01
22 7 0.03
23 10 0.05
24 32 0.15
25 17 0.08
26 22 0.10
27 47 0.22
28 29 0.13
29 20 0.09
30 15 0.07
32 9 0.04
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (26 bp):
TATACTTTATATATATATATATATAC
Found at i:529636 original size:2 final size:2
Alignment explanation
Indices: 529536--529616 Score: 53
Period size: 2 Copynumber: 40.0 Consensus size: 2
529526 AATTATACTC
*
529536 TA TA TA TA TA TA TA TA TA CT- TA TA CTT TA TA T- TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
529577 TT TA TA TA TA CTT TA TA CTA -A AA CTA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
529617 GACTTTATAG
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
1 4 0.06
2 53 0.84
3 6 0.10
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:529658 original size:28 final size:28
Alignment explanation
Indices: 529544--529669 Score: 79
Period size: 28 Copynumber: 4.5 Consensus size: 28
529534 TCTATATATA
529544 TATATATATACTTAT--ACTTTATA--T
1 TATATATATACTTATAAACTTTATACTT
* *
529568 TAT-TATATATTTATATATACTTTATACTAAAAC
1 TATATATATACTTATA-A-ACTTTATACT----T
* *
529601 TATATATATA-TATATAGACTTTATAGTT
1 TATATATATACT-TATAAACTTTATACTT
529629 TATATATATACTTATAAACTTTAGT-CTT
1 TATATATATACTTATAAACTTTA-TACTT
529657 TATA-ATTATACTT
1 TATATA-TATACTT
529670 TATATATATA
Statistics
Matches: 80, Mismatches: 7, Indels: 26
0.71 0.06 0.23
Matches are distributed among these distances:
23 10 0.12
24 3 0.04
27 9 0.11
28 33 0.41
29 2 0.03
32 9 0.11
33 4 0.05
34 10 0.12
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (28 bp):
TATATATATACTTATAAACTTTATACTT
Found at i:529690 original size:24 final size:23
Alignment explanation
Indices: 529663--529707 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
529653 TCTTTATAAT
529663 TATACTTTATATATATAATATACC
1 TATACTTTATAT-TATAATATACC
* *
529687 TATATTTTATATTATTATATA
1 TATACTTTATATTATAATATA
529708 TGTTTGTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
TATACTTTATATTATAATATACC
Found at i:529773 original size:8 final size:8
Alignment explanation
Indices: 529758--529803 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 8
529748 TATATATATA
529758 TATATACT
1 TATATACT
*
529766 TATTTACT
1 TATATACT
529774 TATATACT
1 TATATACT
529782 TATAT--T
1 TATATACT
529788 TA-ATACT
1 TATATACT
529795 TATATACT
1 TATATACT
529803 T
1 T
529804 TAGTCTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 3 0.09
8 25 0.76
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (8 bp):
TATATACT
Found at i:529834 original size:35 final size:36
Alignment explanation
Indices: 529745--529836 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
529735 TACTAAAACT
* * *
529745 TTATATATATATATATATACTTATTTACTTATATAC
1 TTATATTTATATATATATACTTATGTACTTATATAA
529781 TTATATTTA-ATACTTATATACTT-TAGT-CTT-TATAA
1 TTATATTTATATA--TATATACTTAT-GTACTTATATAA
529816 TTATACTTTATATATATATAC
1 TTATA-TTTATATATATATAC
529837 ATATAAGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
35 19 0.40
36 16 0.33
37 13 0.27
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (36 bp):
TTATATTTATATATATATACTTATGTACTTATATAA
Found at i:529847 original size:12 final size:14
Alignment explanation
Indices: 529830--529868 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
529820 ACTTTATATA
529830 TATATACATAT-AAG
1 TATATA-ATATAAAG
529844 TATATAATATAAAG
1 TATATAATATAAAG
529858 TATATAATATA
1 TATATAATATA
529869 TATAAAGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (14 bp):
TATATAATATAAAG
Found at i:529849 original size:16 final size:16
Alignment explanation
Indices: 529828--529873 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
529818 ATACTTTATA
*
529828 TATATATACATATAAG
1 TATATATATATATAAG
529844 TATATA-ATATA-AAG
1 TATATATATATATAAG
529858 TATATAATATATATAA
1 TATAT-ATATATATAA
529874 AGTTTTAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.31
15 5 0.19
16 11 0.42
17 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (16 bp):
TATATATATATATAAG
Found at i:530042 original size:2 final size:2
Alignment explanation
Indices: 530035--530076 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
530025 TTATACATAC
530035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
530077 GATAATTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:530515 original size:7 final size:7
Alignment explanation
Indices: 530503--530528 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
530493 TATATACATA
530503 TATAAAC
1 TATAAAC
530510 TATAAAC
1 TATAAAC
530517 TATAAAC
1 TATAAAC
530524 TATAA
1 TATAA
530529 GTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (7 bp):
TATAAAC
Found at i:530573 original size:2 final size:2
Alignment explanation
Indices: 530530--530563 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
530520 AAACTATAAG
530530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
530564 AAAGTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:530626 original size:22 final size:22
Alignment explanation
Indices: 530601--530650 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
530591 GTTTGGATAT
530601 AAATAT-TAAATATAAAGTATTA
1 AAATATATAAATAT-AAGTATTA
*
530623 AAATATATTAATATAAGTATT-
1 AAATATATAAATATAAGTATTA
530644 AAATATA
1 AAATATA
530651 AAGTATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.27
22 13 0.50
23 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATATATAAATATAAGTATTA
Found at i:530628 original size:15 final size:13
Alignment explanation
Indices: 530597--530652 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
530587 AAGTGTTTGG
530597 ATATAAATATTAA
1 ATATAAATATTAA
530610 ATATAAAGTATTAA
1 ATATAAA-TATTAA
530624 A-AT--ATATT-A
1 ATATAAATATTAA
*
530633 ATATAAGTATTAA
1 ATATAAATATTAA
530646 ATATAAA
1 ATATAAA
530653 GTATATTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
9 2 0.06
10 6 0.17
11 1 0.03
12 4 0.11
13 16 0.44
14 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:530786 original size:18 final size:19
Alignment explanation
Indices: 530752--530787 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
530742 TTATAAAATC
530752 AAAATCTCATAATTTTATT
1 AAAATCTCATAATTTTATT
*
530771 AAAATCTTAT-ATTTTAT
1 AAAATCTCATAATTTTAT
530788 CAATGGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATCTCATAATTTTATT
Found at i:548708 original size:419 final size:416
Alignment explanation
Indices: 547931--548719 Score: 1276
Period size: 418 Copynumber: 1.9 Consensus size: 416
547921 CCCTTAGAAT
* * *
547931 GGATTTGTAAGGCTGGGTCTTTCCTCTTTATAGCACAGGTTCTTCCTTGGTCATTTCTAGGATAC
1 GGATTTGTAAGGCTGGGTCTTTCCTCTCTATAGCACAGGTTCTTCCTTAGTCATTTATAGGATAC
* *
547996 TATCAAAGTCCTTGTTTACCACCCCCTAAAAAACCATTATAAAGTTTGGGTCTTTGTTTTTTTTA
66 TATCAAAGTCCTTGTTTACCACCCCCTAAAAAACAATTAT-AAGTTTGGGCCTTTGTTTTTTTTA
* * *
548061 ACATTAGTTCTTCTTTGAGTATTCTTTGAGATACTATCCTCATCAACTTTCCCTTATTTCGTTAA
130 ACATTAGTTCTTCTTTGAGAATTCTTTGAGATACTATACTCATCAACTTTCCCTTATTTCATTAA
**
548126 CCATATCATATTTACAACCAAACATCTTCCACTACCATCTCTCATAATTAAACGACCATTTACCA
195 CCATATCATATCCACAACCAAACATCTTCCACTACCATCTCTCATAATTAAACGACCATTTACCA
* *
548191 TCACGATTACCACTTTAGCACATCCATTTATACCATTATCTTATATAGGTTATTTTACTTTCTTC
260 TCACGATTACCACTTTAGCACATCCATTTATACCATTATCTTATACAGGTTATTTTACTTCCTTC
* *
548256 CTAGATCCACAATCAATCGATAAGGCTACCATATGATGTAATAAGGCGTTTCTACCTTTTATTAT
325 CTAGAACCACAATCAATCGATAAGGCCACCATATGATGTAATAAGGCGTTTCTACCTTTTATTAT
548321 GATACTTCTGGTTCATATCTATAGCAC
390 GATACTTCTGGTTCATATCTATAGCAC
*
548348 GGATTTGTAAGGCTGGGTCTTTGCTCTCTATAGCACTA-GTTCTTCCTTAGTCATTTATAGGATA
1 GGATTTGTAAGGCTGGGTCTTTCCTCTCTATAGCAC-AGGTTCTTCCTTAGTCATTTATAGGATA
* * *
548412 CTATCAAATTCCTTGTTTACCACCCCTTAAAGAAGCAATTGAT-AGTTTGGGCCTTTGTTTTTTT
65 CTATCAAAGTCCTTGTTTACCACCCCCTAAA-AAACAATT-ATAAGTTTGGGCCTTTG-TTTTTT
* *
548476 TTAACATTGGTTCTTCTTTGAGAATTCTTTGAGATACTCTACTCATCAACTTTCCCTTATTTCAT
127 TTAACATTAGTTCTTCTTTGAGAATTCTTTGAGATACTATACTCATCAACTTTCCCTTATTTCAT
* * *
548541 TAACCATATCATATCCACAACCGAACATCTTCCGCTACTATCTCTCATAATTAAACCGACCATTT
192 TAACCATATCATATCCACAACCAAACATCTTCCACTACCATCTCTCATAATTAAA-CGACCATTT
* *
548606 ACCATCACGATTACCACTTTAGCCCATCCATTTATACCATTATCTTATACAGGTTATTTTTCTTC
256 ACCATCACGATTACCACTTTAGCACATCCATTTATACCATTATCTTATACAGGTTATTTTACTTC
*
548671 CTTCCTAGAACCAGAATCAATCGATAAGGCCACCATATGATGTAATAAG
321 CTTCCTAGAACCACAATCAATCGATAAGGCCACCATATGATGTAATAAG
548720 TCGTATTACA
Statistics
Matches: 341, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
417 100 0.29
418 123 0.36
419 118 0.35
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38
Consensus pattern (416 bp):
GGATTTGTAAGGCTGGGTCTTTCCTCTCTATAGCACAGGTTCTTCCTTAGTCATTTATAGGATAC
TATCAAAGTCCTTGTTTACCACCCCCTAAAAAACAATTATAAGTTTGGGCCTTTGTTTTTTTTAA
CATTAGTTCTTCTTTGAGAATTCTTTGAGATACTATACTCATCAACTTTCCCTTATTTCATTAAC
CATATCATATCCACAACCAAACATCTTCCACTACCATCTCTCATAATTAAACGACCATTTACCAT
CACGATTACCACTTTAGCACATCCATTTATACCATTATCTTATACAGGTTATTTTACTTCCTTCC
TAGAACCACAATCAATCGATAAGGCCACCATATGATGTAATAAGGCGTTTCTACCTTTTATTATG
ATACTTCTGGTTCATATCTATAGCAC
Found at i:553572 original size:19 final size:19
Alignment explanation
Indices: 553547--553589 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
553537 TCTACCTTAT
* *
553547 CAGTAAAATATGGTATGAA
1 CAGTAAAAAACGGTATGAA
*
553566 TAGTAAAAAACGGTATGAA
1 CAGTAAAAAACGGTATGAA
553585 CAGTA
1 CAGTA
553590 CCATGATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (19 bp):
CAGTAAAAAACGGTATGAA
Found at i:554970 original size:2 final size:2
Alignment explanation
Indices: 554965--555007 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
554955 ACACACACAC
554965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
555007 A
1 A
555008 AATTTCACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:555086 original size:30 final size:33
Alignment explanation
Indices: 555010--555086 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 33
555000 TATATATAAA
555010 TTTCACATATCACA-TTTAATCATGTAGTTCAC
1 TTTCACATATCACATTTTAATCATGTAGTTCAC
** * * *
555042 TCACACCTAACACATTTTCAT-ATG-A-TTCAC
1 TTTCACATATCACATTTTAATCATGTAGTTCAC
555072 TTTCACATATCACAT
1 TTTCACATATCACAT
555087 ATTCCTTTTC
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
30 16 0.46
31 1 0.03
32 13 0.37
33 5 0.14
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (33 bp):
TTTCACATATCACATTTTAATCATGTAGTTCAC
Found at i:556826 original size:17 final size:17
Alignment explanation
Indices: 556801--556834 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
556791 TGATTGGAAT
*
556801 AAATAAATTGAAATTTA
1 AAATAAATTAAAATTTA
*
556818 AAATGAATTAAAATTTA
1 AAATAAATTAAAATTTA
556835 CGAGTTTTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
AAATAAATTAAAATTTA
Found at i:563256 original size:17 final size:17
Alignment explanation
Indices: 563236--563268 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
563226 GATGAATGGA
563236 AAATGATTCTGATTTGG
1 AAATGATTCTGATTTGG
*
563253 AAATGATTTTGATTTG
1 AAATGATTCTGATTTG
563269 AATTGCATGA
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:0.30, C:0.03, G:0.21, T:0.45
Consensus pattern (17 bp):
AAATGATTCTGATTTGG
Found at i:564260 original size:18 final size:18
Alignment explanation
Indices: 564237--564272 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
564227 TGATTGAAAT
*
564237 AAATAAATTAAAATTTTA
1 AAATAAATCAAAATTTTA
564255 AAATAAATCAAAATTTTA
1 AAATAAATCAAAATTTTA
564273 CGAGTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAAATCAAAATTTTA
Found at i:566887 original size:11 final size:11
Alignment explanation
Indices: 566868--566915 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
566858 ACCTATGAGG
566868 AAGAACTAATA
1 AAGAACTAATA
*
566879 AAGATCTAATA
1 AAGAACTAATA
566890 AAGAACTAATA
1 AAGAACTAATA
*
566901 AGGAACTAATA
1 AAGAACTAATA
566912 AAGA
1 AAGA
566916 TCTCAGCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 33 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.19
Consensus pattern (11 bp):
AAGAACTAATA
Found at i:568981 original size:24 final size:24
Alignment explanation
Indices: 568939--568990 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
568929 GTATTAGTGC
* *
568939 ATTAGTGCATTCGTACAC-TCCTAT
1 ATTAATGCATTCATACACTTCC-AT
*
568963 ATTAATGCATTCATGCACTTCCAT
1 ATTAATGCATTCATACACTTCCAT
568987 ATTA
1 ATTA
568991 GTAACATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (24 bp):
ATTAATGCATTCATACACTTCCAT
Found at i:569788 original size:54 final size:54
Alignment explanation
Indices: 569726--570395 Score: 871
Period size: 54 Copynumber: 12.4 Consensus size: 54
569716 ACAACTACAA
* * *
569726 TAATAAATTATTTAAAATAAATGAATCTATATTTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
569780 TATTAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
569834 TAATAAATTATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** **
569891 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* *
569946 -AACTACA--A--T--AATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
569994 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
570048 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
570102 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
570156 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
570210 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
570268 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * **
570322 TAATAAATTATTTAAAAATAAATCAATCCATATTTTATAATAAAT-TAT-TTTA-
1 TAATAAATTATTT-AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
570374 AAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
570396 TATTTTATAA
Statistics
Matches: 550, Mismatches: 44, Indels: 47
0.86 0.07 0.07
Matches are distributed among these distances:
48 30 0.05
49 4 0.01
50 6 0.01
51 10 0.02
52 13 0.02
53 3 0.01
54 355 0.65
55 40 0.07
56 5 0.01
57 17 0.03
58 67 0.12
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:569816 original size:22 final size:22
Alignment explanation
Indices: 569790--569832 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
569780 TATTAAATTA
569790 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
569812 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
569833 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:569841 original size:22 final size:22
Alignment explanation
Indices: 569792--569840 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
569782 TTAAATTATT
**
569792 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
569814 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
569837 TAAA
1 TAAA
569841 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:569895 original size:80 final size:79
Alignment explanation
Indices: 569795--570353 Score: 548
Period size: 80 Copynumber: 6.9 Consensus size: 79
569785 AATTATTTAA
569795 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* * *
569860 TCATACAACTACAAT
66 CCATA-AATTAAAAT
569875 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* *
569940 CCATACAACTACAAT
66 CCATA-AATTAAAAT
*
569955 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
**
570020 CCATATTTTAAAAT
66 CCATAAATTAAAAT
* * * ** *
570034 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATC
1 -AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
* * *
570093 AATCCATACTAATAAATTATTTAA-
59 AATCAAT-C-CATAAATTA--AAAT
570117 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
**
570182 CCATATTTTAAAAT
66 CCATAAATTAAAAT
* * * *
570196 AAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-AAA
1 -AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-TA-AATTATTTAAAA
* * * *
570257 TCAATCCATACTAATAAATTATTTAA-
57 TAAATCAAT-C-CATAAATTA--AAAT
570283 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT-AAAATAAATCAA
570348 TCCATA
65 TCCATA
570354 TTTTATAATA
Statistics
Matches: 397, Mismatches: 46, Indels: 71
0.77 0.09 0.14
Matches are distributed among these distances:
76 21 0.05
77 6 0.02
78 3 0.01
79 8 0.02
80 210 0.53
81 13 0.03
82 31 0.08
83 11 0.03
84 16 0.04
85 12 0.03
86 62 0.16
87 2 0.01
88 2 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (79 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATAAATTAAAAT
Found at i:569921 original size:22 final size:22
Alignment explanation
Indices: 569846--569920 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 22
569836 ATAAATTATT
* *
569846 TAAAATAAATCAATTCATACAA
1 TAAAATAAATCAATCCATATAA
**
569868 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
569894 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
569917 TAAA
1 TAAA
569921 TTATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 16 0.38
23 8 0.19
25 3 0.07
26 15 0.36
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:570001 original size:22 final size:23
Alignment explanation
Indices: 569926--570000 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
569916 ATAAATTATT
569926 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
* **
569948 CTACAATAATAAATCAATTCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
569974 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
569997 TAAA
1 TAAA
570001 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:570030 original size:22 final size:22
Alignment explanation
Indices: 570004--570046 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
569994 TAATAAATTA
570004 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
570026 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
570047 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:570055 original size:22 final size:22
Alignment explanation
Indices: 570006--570054 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
569996 ATAAATTATT
**
570006 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
570028 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
570051 TAAA
1 TAAA
570055 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:570084 original size:22 final size:22
Alignment explanation
Indices: 570058--570100 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
570048 TAATAAATTA
570058 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
570080 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
570101 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:570109 original size:22 final size:22
Alignment explanation
Indices: 570060--570108 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
570050 ATAAATTATT
**
570060 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
570082 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
570105 TAAA
1 TAAA
570109 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:570138 original size:22 final size:22
Alignment explanation
Indices: 570112--570154 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
570102 TAATAAATTA
570112 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
570134 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
570155 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:570163 original size:22 final size:22
Alignment explanation
Indices: 570114--570162 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
570104 ATAAATTATT
**
570114 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
570136 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
570159 TAAA
1 TAAA
570163 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:570217 original size:22 final size:22
Alignment explanation
Indices: 570168--570216 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
570158 ATAAATTATT
**
570168 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
570190 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
570213 TAAA
1 TAAA
570217 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:570304 original size:22 final size:22
Alignment explanation
Indices: 570278--570320 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
570268 TAATAAATTA
570278 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
570300 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
570321 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:570329 original size:22 final size:22
Alignment explanation
Indices: 570280--570328 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
570270 ATAAATTATT
**
570280 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
570302 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
570325 TAAA
1 TAAA
570329 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:570372 original size:15 final size:15
Alignment explanation
Indices: 570352--570470 Score: 179
Period size: 15 Copynumber: 8.0 Consensus size: 15
570342 AATCAATCCA
*
570352 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
570367 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
570382 TA-TTTAAAATAAAT
1 TATTTTAAAATAAAT
*
570396 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
*
570411 TATTTTATAATAAA-
1 TATTTTAAAATAAAT
570425 TATTTTTAAAATAAAT
1 TA-TTTTAAAATAAAT
*
570441 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
570456 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
570471 AACCTTATTA
Statistics
Matches: 96, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
14 16 0.17
15 78 0.81
16 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:570377 original size:37 final size:33
Alignment explanation
Indices: 570297--570470 Score: 127
Period size: 30 Copynumber: 5.5 Consensus size: 33
570287 AATCAATCCA
*
570297 TATTTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
*
570330 TATTTAAAAATAAATCAATCCATATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAAT
* *
570367 TATTTTAAAATAAAT-TAT--TTAA-AATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
* * * *
570396 TATTTTATAATAAAT-TAT--TTTATAATAAA-
1 TATTTTAAAATAAATCAATCCATAATAATAAAT
* * *
570425 TATTTTTAAAATAAAT-TAT--TTTATAATAAAT
1 TA-TTTTAAAATAAATCAATCCATAATAATAAAT
570456 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
570471 AACCTTATTA
Statistics
Matches: 126, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
29 29 0.23
30 46 0.37
31 2 0.02
33 23 0.18
34 2 0.02
36 2 0.02
37 22 0.17
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (33 bp):
TATTTTAAAATAAATCAATCCATAATAATAAAT
Found at i:570386 original size:30 final size:30
Alignment explanation
Indices: 570352--570470 Score: 197
Period size: 30 Copynumber: 4.0 Consensus size: 30
570342 AATCAATCCA
570352 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
* *
570382 TA-TTTAAAATAAATTATTTTATAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
570411 TATTTTATAATAAA-TATTTTTAAAATAAAT
1 TATTTTATAATAAATTA-TTTTAAAATAAAT
570441 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
570471 AACCTTATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
29 29 0.35
30 51 0.62
31 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:570448 original size:45 final size:45
Alignment explanation
Indices: 570352--570471 Score: 215
Period size: 45 Copynumber: 2.7 Consensus size: 45
570342 AATCAATCCA
570352 TATTTTATAATAAATTATTTTAAAATAAAT-TATTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAATATATTTAAAATAAAT
* *
570396 TATTTTATAATAAATTATTTTATAATAAATATTTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAATATATTTAAAATAAAT
570441 TATTTTATAATAAATTATTTTAAAATAAATA
1 TATTTTATAATAAATTATTTTAAAATAAATA
570472 ACCTTATTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 29 0.40
45 43 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (45 bp):
TATTTTATAATAAATTATTTTAAAATAAATATATTTAAAATAAAT
Found at i:570455 original size:166 final size:165
Alignment explanation
Indices: 569763--570395 Score: 750
Period size: 166 Copynumber: 3.9 Consensus size: 165
569753 TATATTTTAA
* * *
569763 AATAAATCAATACATACTATTAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAAT-AATCCATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
* *** * * * *
569828 CCATACTAATAAATTATTTAAAATAAATCAATTCATACAACTACAAT-AATAAATCAAT-C-CAT
65 CCATACTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACAAAT
* *
569890 --A-T-TTTAAAATAAATCAATCCATACTAA-TAAATTATTT
129 AAATTATTTAAAATAAATCAATCCATA-AAACTACA--A--T
* * *
569927 AAAATAAATCAATCCATACAACTACA--A--T--AATAAATCAATTCATATTTTAAAATAAATCA
1 --AATAAAT-AATCCATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCA
* *
569986 ATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA
63 ATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAA
* **
570051 TAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-
128 TAAATTATTTAAAATAAATCAATCCATAAAACTACAAT
*
570085 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAAT-AATCCATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
*
570150 CCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATA
65 CCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATA
*
570215 AATTATTTAAAATAAATCAATCCATACAACTACAAT
130 AATTATTTAAAATAAATCAATCCATAAAACTACAAT
*
570251 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAAT-AATCCATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
* * *
570316 CCATACTAATAAATTATTTAAAAATAAATCAATCCATATTTTATAATAAAT-TAT-TTTA-AAAT
65 CCATACTAATAAATTATTT-AAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAAT
570378 AAATTATTTAAAATAAAT
129 AAATTATTTAAAATAAAT
570396 TATTTTATAA
Statistics
Matches: 421, Mismatches: 27, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
156 21 0.05
158 1 0.00
159 5 0.01
160 78 0.19
161 2 0.00
162 125 0.30
163 2 0.00
164 23 0.05
165 8 0.02
166 126 0.30
167 30 0.07
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (165 bp):
AATAAATAATCCATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATC
CATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACAAATAA
ATTATTTAAAATAAATCAATCCATAAAACTACAAT
Found at i:571708 original size:13 final size:13
Alignment explanation
Indices: 571686--571745 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
571676 TAACCAATAC
*
571686 TTTCACATTT-CA
1 TTTCATATTTGCA
571698 TGTTCATATTTTGCA
1 T-TTCATA-TTTGCA
*
571713 TTTCATATTTGTA
1 TTTCATATTTGCA
571726 TTTCATATTT-CA
1 TTTCATATTTGCA
571738 TATTCATA
1 T-TTCATA
571746 CCCCAATGTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 3 0.07
13 26 0.63
14 9 0.22
15 3 0.07
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (13 bp):
TTTCATATTTGCA
Found at i:573594 original size:45 final size:45
Alignment explanation
Indices: 573530--573634 Score: 192
Period size: 45 Copynumber: 2.3 Consensus size: 45
573520 AGTGCACTTA
573530 GGGTGTATCGATACACTAATTACATTCGATGTTTTTCTGAGCCAG
1 GGGTGTATCGATACACTAATTACATTCGATGTTTTTCTGAGCCAG
*
573575 GGGTGTATCGATACACTAATTACATTTGATGTTTTTCTGAGCCAG
1 GGGTGTATCGATACACTAATTACATTCGATGTTTTTCTGAGCCAG
*
573620 GGGTGTATCGGTACA
1 GGGTGTATCGATACA
573635 TCAGACAGTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (45 bp):
GGGTGTATCGATACACTAATTACATTCGATGTTTTTCTGAGCCAG
Found at i:573690 original size:55 final size:55
Alignment explanation
Indices: 573619--573759 Score: 219
Period size: 55 Copynumber: 2.6 Consensus size: 55
573609 TTCTGAGCCA
* * * ** *
573619 GGGGTGTATCGGTACATCAGACAGTGTATTGATACATAAAATGCATTCGATGTTG
1 GGGGTGTATCGATACATCAAAGAGTGTATCAATACACAAAATGCATTCGATGTTG
*
573674 GGGGTGTATCGATACATCAAAGAGTGTATCAATACACAAAATGCATTTGATGTTG
1 GGGGTGTATCGATACATCAAAGAGTGTATCAATACACAAAATGCATTCGATGTTG
573729 GGGGTGTATCGATACATCAAAGAGTGTATCA
1 GGGGTGTATCGATACATCAAAGAGTGTATCA
573760 GTATCTCTCT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (55 bp):
GGGGTGTATCGATACATCAAAGAGTGTATCAATACACAAAATGCATTCGATGTTG
Found at i:574102 original size:21 final size:22
Alignment explanation
Indices: 574078--574120 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
574068 ATAATTTTTG
574078 AAATCAA-ATTGAAAATTATTC
1 AAATCAATATTGAAAATTATTC
*
574099 AAATCAATTTTGAAAATTATTC
1 AAATCAATATTGAAAATTATTC
574121 CCCCTTACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (22 bp):
AAATCAATATTGAAAATTATTC
Found at i:575887 original size:13 final size:12
Alignment explanation
Indices: 575858--575891 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
575848 AATGGGCAAT
*
575858 TTTTGAAAACTA
1 TTTTGAAAACAA
575870 TTTTGAAAACAA
1 TTTTGAAAACAA
575882 TGTTTGAAAA
1 T-TTTGAAAA
575892 ATCATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (12 bp):
TTTTGAAAACAA
Found at i:580394 original size:116 final size:116
Alignment explanation
Indices: 580238--580453 Score: 315
Period size: 116 Copynumber: 1.9 Consensus size: 116
580228 AAGCTTAACT
* *
580238 TTTAAATCAAAATTTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAGAGCTCTAAATCCTTCTT
1 TTTAAATCAAAAATTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTT
* *
580303 CAATATTTCATTTTGATTTTCAAAATCCATTTTAGTTCTTAGAAGAAGATG
66 CAACATTACATTTTGATTTTCAAAATCCATTTTAGTTCTTAGAAGAAGATG
* * * * * *
580354 TTTAATTCAAAAATTTCTTTTTTAAAGTTTTCAGATTTCATTTTTGAAAGCTCTAACTCCTTTTT
1 TTTAAATCAAAAATTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTT
* * *
580419 CAACATTACATTTTGATTTTCCAAGTCTATTTTAG
66 CAACATTACATTTTGATTTTCAAAATCCATTTTAG
580454 CTTTCAAAAG
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
116 87 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.48
Consensus pattern (116 bp):
TTTAAATCAAAAATTTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTT
CAACATTACATTTTGATTTTCAAAATCCATTTTAGTTCTTAGAAGAAGATG
Found at i:581922 original size:55 final size:55
Alignment explanation
Indices: 581826--581970 Score: 184
Period size: 55 Copynumber: 2.6 Consensus size: 55
581816 TCCTAAGCCA
* * *
581826 GGGGTGTATC-AGTACATCAGACAGTGTATCGATACACAAAATGCATTCGATATTG
1 GGGGTGTATCGA-TACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATATTG
* * * * * *
581881 GGGGTGTATCGATACATCAAAGATTGTATTGGTACATAAAATGGATTCGTTGTTG
1 GGGGTGTATCGATACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATATTG
*
581936 GGGGTATATCGATACATCAAAGAGTGTATCGGTAC
1 GGGGTGTATCGATACATCAAAGAGTGTATCGGTAC
581971 CTCTCTTTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 76 0.99
56 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (55 bp):
GGGGTGTATCGATACATCAAAGAGTGTATCGGTACACAAAATGCATTCGATATTG
Found at i:587132 original size:16 final size:17
Alignment explanation
Indices: 587109--587147 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
587099 TGTGAAAGTT
*
587109 ATGAAAAGAATCTGAAA
1 ATGAAAAGAATATGAAA
587126 A-GAAAAGAATATGAAA
1 ATGAAAAGAATATGAAA
587142 ATGAAA
1 ATGAAA
587148 TATGAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.64, C:0.03, G:0.18, T:0.15
Consensus pattern (17 bp):
ATGAAAAGAATATGAAA
Found at i:587665 original size:2 final size:2
Alignment explanation
Indices: 587658--587692 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
587648 GAATGGATCG
587658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
587693 TATGTTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:601400 original size:17 final size:18
Alignment explanation
Indices: 601358--601405 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
601348 ATCTTAAGGG
*
601358 AGTGTATCGATACACTACC
1 AGTGCATCGATACACTA-C
*
601377 TGTGCATCGATACACT-C
1 AGTGCATCGATACACTAC
601394 AGTGCATTCGAT
1 AGTGCA-TCGAT
601406 GTTTATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 14 0.56
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (18 bp):
AGTGCATCGATACACTAC
Found at i:614367 original size:46 final size:45
Alignment explanation
Indices: 614232--614452 Score: 304
Period size: 45 Copynumber: 4.9 Consensus size: 45
614222 GTAAACATAC
* * * *
614232 AAATAAGCTTATGCGCTTATGGATT-AAT-GAAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
*
614275 AAATAAACTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* *
614320 AAATAAGCCTACGAGCTTATGTGATTAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATG-GATTAAATGGTAAGTATATTGGTA
*
614366 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
* * *
614411 AAATAAGCTTACAAGCTTATGGGA-TAAATGGAAATTATATTG
1 AAATAAGCTTACGAGCTTAT-GGATTAAATGGTAAGTATATTG
614453 ATAAGAAATT
Statistics
Matches: 160, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
43 22 0.14
44 3 0.02
45 89 0.56
46 46 0.29
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
Found at i:614379 original size:91 final size:90
Alignment explanation
Indices: 614232--614451 Score: 311
Period size: 91 Copynumber: 2.5 Consensus size: 90
614222 GTAAACATAC
* * *
614232 AAATAAGCTTATGCGCTTATGGATT-AAT-GAAAATATATTGGTAAAATAAACTTACGAGCTTAT
1 AAATAAGCTTACGAGCTTATGGATTAAATGGAAAATATATTAGTAAAATAAACTTACGAGCTTAT
*
614295 GGATTAAATGGTAAGTATATTGGTA
66 GGAATAAATGGTAAGTATATTGGTA
* * * *
614320 AAATAAGCCTACGAGCTTATGTGATTAAATGGTAAGTATATTAGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATG-GATTAAATGGAAAATATATTAGTAAAATAAACTTACGAGCTTA
614385 TGGAATAAATGGTAAGTATATTGGTA
65 TGGAATAAATGGTAAGTATATTGGTA
* *
614411 AAATAAGCTTACAAGCTTATGGGA-TAAATGGAAATTATATT
1 AAATAAGCTTACGAGCTTAT-GGATTAAATGGAAAATATATT
614452 GATAAGAAAT
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
88 18 0.16
89 4 0.03
90 18 0.16
91 75 0.65
92 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGATTAAATGGAAAATATATTAGTAAAATAAACTTACGAGCTTAT
GGAATAAATGGTAAGTATATTGGTA
Found at i:619765 original size:10 final size:9
Alignment explanation
Indices: 619741--619809 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
619731 TCAAAATGTT
*
619741 ATAAGAAAA
1 ATAAAAAAA
619750 ATAAAAAAA
1 ATAAAAAAA
619759 CAT-AAAAAA
1 -ATAAAAAAA
*
619768 GTAAATAAAA
1 ATAAA-AAAA
619778 AT-AAAAAA
1 ATAAAAAAA
*
619786 GTAAAAAATA
1 ATAAAAAA-A
* *
619796 ATAATAATA
1 ATAAAAAAA
619805 ATAAA
1 ATAAA
619810 TCACAAGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 6 0.13
9 28 0.60
10 13 0.28
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:619772 original size:18 final size:17
Alignment explanation
Indices: 619746--619799 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 17
619736 ATGTTATAAG
619746 AAAAA-TAAAAAAACATA
1 AAAAAGTAAAAAAA-ATA
619763 AAAAAGTAAATAAAAATA
1 AAAAAGTAAA-AAAAATA
619781 AAAAAGTAAAAAATAATA
1 AAAAAGTAAAAAA-AATA
619799 A
1 A
619800 TAATAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.24
18 22 0.65
19 4 0.12
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.15
Consensus pattern (17 bp):
AAAAAGTAAAAAAAATA
Found at i:619801 original size:27 final size:26
Alignment explanation
Indices: 619740--619809 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
619730 GTCAAAATGT
* *
619740 TATAAGAAAAATAAAAAAACATAAAAAA
1 TATAATAAAAAT-AAAAAA-GTAAAAAA
619768 GTA-AATAAAAATAAAAAAGTAAAAAA
1 -TATAATAAAAATAAAAAAGTAAAAAA
*
619794 TAATAATAATAATAAA
1 T-ATAATAAAAATAAA
619810 TCACAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 1 0.03
26 8 0.22
27 17 0.47
28 8 0.22
29 2 0.06
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (26 bp):
TATAATAAAAATAAAAAAGTAAAAAA
Found at i:619830 original size:34 final size:34
Alignment explanation
Indices: 619789--619914 Score: 95
Period size: 34 Copynumber: 3.7 Consensus size: 34
619779 TAAAAAAGTA
619789 AAAAATAATAATAATAATAAATCACAAGAAATTT
1 AAAAATAATAATAATAATAAATCACAAGAAATTT
*
619823 AAAAAT-A-AATAAATAAATAAA--ACTAGTAAATTT
1 AAAAATAATAAT-AAT-AATAAATCACAAG-AAATTT
**
619856 AAATAAATAAATAATAATTAATAAATCA-AAGAAAAAT
1 -AA-AAAT-AATAATAA-TAATAAATCACAAGAAATTT
* *
619893 AAAAAAAAT-ATTA-AATAAATCA
1 AAAAATAATAATAATAATAAATCA
619915 AAGGTAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
31 9 0.12
32 7 0.09
33 13 0.17
34 17 0.23
35 7 0.09
36 2 0.03
37 13 0.17
38 6 0.08
39 1 0.01
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.25
Consensus pattern (34 bp):
AAAAATAATAATAATAATAAATCACAAGAAATTT
Found at i:619912 original size:31 final size:33
Alignment explanation
Indices: 619856--619917 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 33
619846 TAGTAAATTT
619856 AAATAAATAAATAATAATTAATAAATCAAAGAA
1 AAATAAATAAATAATAATTAATAAATCAAAGAA
619889 AAATAAA-AAA-AAT-ATTAAATAAATCAAAG
1 AAATAAATAAATAATAATT-AATAAATCAAAG
619918 GTAAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 3 0.11
31 15 0.54
32 3 0.11
33 7 0.25
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (33 bp):
AAATAAATAAATAATAATTAATAAATCAAAGAA
Found at i:621653 original size:85 final size:85
Alignment explanation
Indices: 621555--622843 Score: 434
Period size: 85 Copynumber: 15.3 Consensus size: 85
621545 TGACAGTTCC
*** *
621555 TTGTTGATAGATAGTTTTTCTCGA-CTTAAGCTAAGCTGTAAATTTAGTATGT-TCTTGAGCTAA
1 TTGTTGATAGATAGCCCTTCTC-ACCTTAAGCTAAGCTGTAAATTTAATATGTCT-TTGAGCTAA
*
621618 ATGGAATCGAACTCAAAGGTAT
64 ATGGAATCAAACTCAAAGGTAT
* * *
621640 TTGTTGATAGATAGCCCTTCTCACCTTAAGTTATGCTGTAAATTTAATATGTCTTTGAGCTGAAT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* ** *
621705 GTAATCAAACTTGAAGGTCT
66 GGAATCAAACTCAAAGGTAT
* * * * * * * * * * * * * *
621725 TTATGGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATATGCCTTTGAGTTGAGT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* * * *
621790 GTACTCAAACTCGAAGGTCT
66 GGAATCAAACTCAAAGGTAT
* * * * * * ** * *
621810 TAGTT-ACCAGATAGCCCTTCTCGCCTTGAGCTATGTTGTAAATTCGATATGCCTTTGAGCTGAA
1 TTGTTGA-TAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAA
* * ** *
621874 TGTAATCGAACTCGTA-GTCT
65 TGGAATCAAACTCAAAGGTAT
* * * * * * *
621894 TTGTTGATAGATAGCCGTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGAAT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* *
621959 GTAATCAAACTCGAAGGT-T
66 GGAATCAAACTCAAAGGTAT
* * * * * * * *
621978 TTGGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAAATTTGATGTGCCTTTGAGCTAAG
1 TT-GTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAA
* * *
622043 TGTAATCAAACTCGAAGGTCT
65 TGGAATCAAACTCAAAGGTAT
* * * * * * * ** * *
622064 TGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAAT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* * *
622129 GTAATCAAACTCGAAGGTCTT
66 GGAATCAAACTCAAAGGT-AT
* * * * * * * * * ** * *
622150 TTGCTAACAGATTGCCCTTCTC-CCTTGAGCTATGCTATAAATTTAATGTGCCTTTGAATTGAGT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* * * *
622214 GTAATCAAACTCGAAGTTCT
66 GGAATCAAACTCAAAGGTAT
* * * * * * * * * * * * * *
622234 TGGTTGACAGATAACCCTTCTCGCTTTGAGTTATGCTATAAATTTGATATGCCTTT--TCGAACT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* *
622297 TGAAT----GTC-----T-T
66 GGAATCAAACTCAAAGGTAT
* * * * * * * * * *
622307 TTGTTAACAGATATCCCTTCTCGCCTTGAGCTACGCTGTAAAGTTAATGT-TCCTTTGAGCTGAG
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGT-CTTTGAGCTAAA
* * * *
622371 TGTAATCGAACTCAATGGTCT
65 TGGAATCAAACTCAAAGGTAT
* * ** ** ** * * * * * *
622392 TAGTTGACAGATAATCCTTCTTGCCTTGTGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* * *
622457 -GTATCCGAACTCGAAGGCCT-T
66 GGAAT-CAAACTCAAAGG--TAT
* * * * * * *
622478 TTGTTGACAGATAGCCCTTATCGCCTTAAGCTATGCTGTAAATTTGATGTGTCTTTGAGCTAAGT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* * * *
622543 GTAA-CTGAACTCGAAGGTCT
66 GGAATC-AAACTCAAAGGTAT
* *** * * * * * * * * *
622563 TGGTTGATAGATAATACTTCTTACCTTGAGTTATGTTGT--A-CTAGATAAGCCTTTGAGCTGAA
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTA-ATATGTCTTTGAGCTAAA
* * *
622625 TGTAATCGAACTCAAAGGTCTT
65 TGGAATCAAACTCAAAGGT-AT
* * * * * * * * * * * * *
622647 TTATTGACATATAACCATTCTCACATTGAGCTATGCTGTAAATATCATGT-TACTTTGAGCTGAG
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGT-CTTTGAGCTAAA
* * * *
622711 TGTAATCGAACTCGAAGGTCT
65 TGGAATCAAACTCAAAGGTAT
* * * * * * * * ***
622732 TGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGGGT
1 TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
* * *
622797 GTAATCAAACTCGAAGGTCT
66 GGAATCAAACTCAAAGGTAT
* * * *
622817 TGGTTGACAGATAACCCTTCTCGCCTT
1 TTGTTGATAGATAGCCCTTCTCACCTT
622844 GAGTTATACT
Statistics
Matches: 971, Mismatches: 196, Indels: 74
0.78 0.16 0.06
Matches are distributed among these distances:
73 45 0.05
74 1 0.00
75 6 0.01
79 4 0.00
82 1 0.00
83 35 0.04
84 130 0.13
85 627 0.65
86 119 0.12
87 3 0.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (85 bp):
TTGTTGATAGATAGCCCTTCTCACCTTAAGCTAAGCTGTAAATTTAATATGTCTTTGAGCTAAAT
GGAATCAAACTCAAAGGTAT
Found at i:621954 original size:254 final size:254
Alignment explanation
Indices: 621572--622856 Score: 1333
Period size: 254 Copynumber: 5.1 Consensus size: 254
621562 TAGATAGTTT
* * * * * * *
621572 TTCTCGACTTAAGCTAAGCTGTAAATTTAGTATG-TTCTTGAGCTAAATGGAATCGAACTCAAAG
1 TTCTCGCCTTGAGCTATGCTGTAAATTGA-TATGCCT-TTGAGCTGAATGTAATCGAACTCAAAG
* * * * * *
621636 GTATTTGTTGATAGATAGCCCTTCTCACCTTAAGTTATGCTGTAAATTTAATATGTCTTTGAGCT
64 GTCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCT
* * * * * *
621701 GAATGTAATCAAACTTGAAGGTCTTTATGGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAA
129 GAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAA
* * *
621766 ATTTGATATGCCTTTGAGTTGAGTGTACTCAAACTCGAAGGTCTTAGTT-ACCAGATAGCCC
194 ATTTGATATGCCTTTGAGCTGAGTGTACTCAAACTCGAAGGTCTTGGTTGA-CAGATAACCC
* **
621827 TTCTCGCCTTGAGCTATGTTGTAAATTCGATATGCCTTTGAGCTGAATGTAATCGAACTCGTA-G
1 TTCTCGCCTTGAGCTATGCTGTAAATT-GATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGG
* * *
621891 TCTTTGTTGATAGATAGCCGTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTG
65 TCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTG
* * * *
621956 AATGTAATCAAACTCGAAGGT-TTTGGTTGACAGATAGCCCTTCTCACCTTGAGCTATGTTGTAA
130 AGTGTAATCAAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAA
* * *
622020 ATTTGATGTGCCTTTGAGCTAAGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCC
194 ATTTGATATGCCTTTGAGCTGAGTGTACTCAAACTCGAAGGTCTTGGTTGACAGATAACCC
* * *
622081 TTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATT-GATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGG
* * * * *
622146 TCTTTTGCTAACAGATTGCCCTTCTC-CCTTGAGCTATGCTATAAATTT-A-ATGTGCCTTTGAA
65 TC-TTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGT-CC-TTGAG
* * * * * *
622208 TTGAGTGTAATCAAACTCGAAGTTCTTGGTTGACAGATAACCCTTCTCGCTTTGAGTTATGCTAT
127 CTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
* * * * *
622273 AAATTTGATATGCCTTT--TC-GA----ACT-----T-GAATGTCTTTTGTTAACAGATATCCC
192 AAATTTGATATGCCTTTGAGCTGAGTGTACTCAAACTCGAAGGTC-TTGGTTGACAGATAACCC
* * * * * *
622324 TTCTCGCCTTGAGCTACGCTGTAAAGTTAATGTTCCTTTGAGCTGAGTGTAATCGAACTCAATGG
1 TTCTCGCCTTGAGCTATGCTGTAAA-TTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGG
* ** ** * *
622389 TCTTAGTTGACAGATAATCCTTCTTGCCTTGTGTTATGCTGTAAATTTGATATG-CCTTTGAGCT
65 TCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGTCC-TTGAGCT
* * * * *
622453 GAGTGT-ATCCGAACTCGAAGGCCTTTTGTTGACAGATAGCCCTTATCGCCTTAAGCTATGCTGT
129 GAGTGTAAT-CAAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
* * * * * **
622517 AAATTTGATGTGTCTTTGAGCTAAGTGTAACT-GAACTCGAAGGTCTTGGTTGATAGATAATAC
192 AAATTTGATATGCCTTTGAGCTGAGTGT-ACTCAAACTCGAAGGTCTTGGTTGACAGATAACCC
** * * * * *
622580 TTCTTACCTTGAGTTATGTTGT-ACTAGATAAGCCTTTGAGCTGAATGTAATCGAACTCAAAGGT
1 TTCTCGCCTTGAGCTATGCTGTAAATTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGT
* * * * * * * * *
622644 CTTTTATTGACATATAACCATTCTCACATTGAGCTATGCTGTAAATATCATGT-TACTTTGAGCT
66 C-TTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGT-CCTTGAGCT
* *
622708 GAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAA
129 GAGTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAA
* *
622773 ATTTGATATGCCTTTGAGCTGGGTGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCC
194 ATTTGATATGCCTTTGAGCTGAGTGTACTCAAACTCGAAGGTCTTGGTTGACAGATAACCC
* *
622834 TTCTCGCCTTGAGTTATACTGTA
1 TTCTCGCCTTGAGCTATGCTGTA
622857 CTGGATTCAT
Statistics
Matches: 847, Mismatches: 148, Indels: 70
0.80 0.14 0.07
Matches are distributed among these distances:
242 24 0.03
243 115 0.14
244 51 0.06
245 3 0.00
246 1 0.00
247 1 0.00
248 2 0.00
252 4 0.00
253 10 0.01
254 364 0.43
255 211 0.25
256 55 0.06
257 6 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (254 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGT
CTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTGA
GTGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
TTGATATGCCTTTGAGCTGAGTGTACTCAAACTCGAAGGTCTTGGTTGACAGATAACCC
Found at i:622844 original size:85 final size:85
Alignment explanation
Indices: 622290--622856 Score: 595
Period size: 85 Copynumber: 6.7 Consensus size: 85
622280 ATATGCCTTT
* * * * * * * *
622290 TCGAACTTGAATGTCTTTTGTTAACAGATATCCCTTCTCGCCTTGAGCTACGCTGTAAAGTTAAT
1 TCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
* *
622355 GTTCCTTTGAGCTGAGTGTAA
65 ATGCCTTTGAGCTGAGTGTAA
* * * * *
622376 TCGAACTC-AATGGTCTTAGTTGACAGATAATCCTTCTTGCCTTGTGTTATGCTGTAAATTTGAT
1 TCGAACTCGAA-GGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
622440 ATGCCTTTGAGCTGAGTGT-A
65 ATGCCTTTGAGCTGAGTGTAA
* * * * *
622460 TCCGAACTCGAAGGCCTTTTGTTGACAGATAGCCCTTATCGCCTTAAGCTATGCTGTAAATTTGA
1 T-CGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* * *
622525 TGTGTCTTTGAGCTAAGTGTAA
64 TATGCCTTTGAGCTGAGTGTAA
* ** ** * * * *
622547 -CTGAACTCGAAGGTCTTGGTTGATAGATAATACTTCTTACCTTGAGTTATGTTGT--ACTAGAT
1 TC-GAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
* *
622609 AAGCCTTTGAGCTGAATGTAA
65 ATGCCTTTGAGCTGAGTGTAA
* ** * * * * * *
622630 TCGAACTCAAAGGTCTTTTATTGACATATAACCATTCTCACATTGAGCTATGCTGTAAATATCAT
1 TCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
* **
622695 GTTACTTTGAGCTGAGTGTAA
65 ATGCCTTTGAGCTGAGTGTAA
622716 TCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATA
1 TCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATA
*
622781 TGCCTTTGAGCTGGGTGTAA
66 TGCCTTTGAGCTGAGTGTAA
* * *
622801 TCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATACTGTA
1 TCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTA
622857 CTGGATTCAT
Statistics
Matches: 389, Mismatches: 82, Indels: 21
0.79 0.17 0.04
Matches are distributed among these distances:
83 33 0.08
84 32 0.08
85 209 0.54
86 114 0.29
87 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (85 bp):
TCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATA
TGCCTTTGAGCTGAGTGTAA
Found at i:624008 original size:99 final size:99
Alignment explanation
Indices: 623844--624034 Score: 274
Period size: 99 Copynumber: 1.9 Consensus size: 99
623834 ATATATAAAT
* * * *
623844 ACCTTTATGAGGTTAGTTGAATCTTATCCATAAAACTGGGGTATTTAACAAATTACCTTACAGGG
1 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAACAGGGGCATTTAACAAATTACCTTACAGGG
* * *
623909 ACAGCTCAAGCTTTATTGTATAGATATTATAATC
66 ACAACTAAAACTTTATTGTATAGATATTATAATC
* * * *
623943 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCAGGGGCATTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAACAGGGGCATTTAACAAATTACCTTACAGGG
*
624008 ACAACTAAAACTTTATTGTATATATAT
66 ACAACTAAAACTTTATTGTATAGATAT
624035 AATGTTATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (99 bp):
ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAACAGGGGCATTTAACAAATTACCTTACAGGG
ACAACTAAAACTTTATTGTATAGATATTATAATC
Found at i:626545 original size:15 final size:15
Alignment explanation
Indices: 626525--626568 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
626515 GAAAATAATA
626525 AAAATAAATAAAAAT
1 AAAATAAATAAAAAT
626540 AAAATAAA-AAATAAT
1 AAAATAAATAAA-AAT
*
626555 AAAGTAAATAAAAA
1 AAAATAAATAAAAA
626569 AATCAAAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (15 bp):
AAAATAAATAAAAAT
Found at i:626569 original size:21 final size:19
Alignment explanation
Indices: 626516--626570 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
626506 AAGAACAAAG
626516 AAAAT-AATAAAAATAAATA
1 AAAATAAATAAAAA-AAATA
626535 AAAATAAAATAAAAAATAAT-
1 AAAAT-AAATAAAAAA-AATA
*
626555 AAAGTAAATAAAAAAA
1 AAAATAAATAAAAAAA
626571 TCAAAGGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.03
19 15 0.47
20 5 0.16
21 11 0.34
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAATAAATAAAAAAAATA
Found at i:626603 original size:10 final size:10
Alignment explanation
Indices: 626516--626568 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
626506 AAGAACAAAG
626516 AAAAT-AATA
1 AAAATAAATA
626525 AAAATAAATA
1 AAAATAAATA
626535 AAAATAAAATA
1 AAAAT-AAATA
626546 AAAA-ATAAT-
1 AAAATA-AATA
*
626555 AAAGTAAATA
1 AAAATAAATA
626565 AAAA
1 AAAA
626569 AATCAAAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 12 0.32
10 16 0.43
11 9 0.24
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
AAAATAAATA
Done.