Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005336.1 Hibiscus syriacus cultivar Beakdansim tig00012084_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: 90696
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8783 original size:59 final size:59
Alignment explanation
Indices: 8709--9009 Score: 451
Period size: 59 Copynumber: 5.1 Consensus size: 59
8699 ATACACTATT
* * *
8709 TTTCAACTAACTTGCATTAGTGGCACCTTTATTCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACC
* * * * *
8768 TTTCATTTAACTTGCATTATTGGAACCTTTCTGCCAAATGAATAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACC
8827 TTTCATCTAACTTGCATTATTGGCACCTTTCTGT-CAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCT-TCCAAATGCACAGTTAGGCATTTAACC
* * **
8886 TTTCATCTAACTTGCATTATTGGAACCTTTTTTCCAAACACACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACC
* * *
8945 TTTCATCTAACTTGCATTATTGACACGTTTCTGCCAAATGCACAGTTAGGCATTTAACC
1 TTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACC
9004 TTTCAT
1 TTTCAT
9010 TTTAGAGAAA
Statistics
Matches: 216, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
58 1 0.00
59 215 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (59 bp):
TTTCATCTAACTTGCATTATTGGCACCTTTCTTCCAAATGCACAGTTAGGCATTTAACC
Found at i:10363 original size:2 final size:2
Alignment explanation
Indices: 10351--10427 Score: 122
Period size: 2 Copynumber: 39.0 Consensus size: 2
10341 TAACATATTC
10351 AT AT A- 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
*
10392 AT AT AT AT AT AT AT AT AT AT AGT AT A- AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
10428 TCATAGTATT
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 2 0.03
2 66 0.94
3 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15932 original size:2 final size:2
Alignment explanation
Indices: 15925--15952 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15915 TTGTAGAGTA
15925 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
15953 TGTGAAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20111 original size:112 final size:112
Alignment explanation
Indices: 19788--20120 Score: 352
Period size: 113 Copynumber: 2.9 Consensus size: 112
19778 ATCAAATTAC
* * * * *
19788 ACTCAGCAACCGATAACATCGAAT-TCTTCAGATGTTTCATTACTGCTTATCTACCAAGTATCAA
1 ACTCTGCAAACGATAA-ATCGAATCT-TTC-GATGTTTCATTACT-CATATCTAACAACTATCAA
* * * * *
19852 GCAAGGTAGAGTATCTGAAGAATTCAAAGTTAACATAAATGCAAAATAACA
62 GCAAGATAGAGTATCTGAAGAATTCGAAGATACCATAGATGCAAAATAACA
* * *
19903 ACTCTGCAATCGATAAATCGAATCTTTCAATGTTTCA-CAGCTACATATCTAACAACTATCAAGC
1 ACTCTGCAAACGATAAATCGAATCTTTCGATGTTTCATTA-CT-CATATCTAACAACTATCAAGC
* * *
19967 AAGCTAGAGTATCTGAAGAATTTGAAGCTACCATAGATGCAAAATAACA
64 AAGATAGAGTATCTGAAGAATTCGAAGATACCATAGATGCAAAATAACA
* * * *
20016 ACTCTGCAAAC-AGTAAAATCGAATCTTTTGATGTTTCATTACT-ATATATAGCAACTATCAAGA
1 ACTCTGCAAACGA-T-AAATCGAATCTTTCGATGTTTCATTACTCATATCTAACAACTATCAAGC
* *
20079 AAGATCGAGTATCAGAAGAATTCGAAGATACCAT-GAGTGCAA
64 AAGATAGAGTATCTGAAGAATTCGAAGATACCATAGA-TGCAA
20121 CTATACATTC
Statistics
Matches: 186, Mismatches: 26, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
111 2 0.01
112 53 0.28
113 82 0.44
114 33 0.18
115 16 0.09
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (112 bp):
ACTCTGCAAACGATAAATCGAATCTTTCGATGTTTCATTACTCATATCTAACAACTATCAAGCAA
GATAGAGTATCTGAAGAATTCGAAGATACCATAGATGCAAAATAACA
Found at i:22960 original size:2 final size:2
Alignment explanation
Indices: 22948--23883 Score: 96
Period size: 2 Copynumber: 463.0 Consensus size: 2
22938 ATTAAGTATG
* * * *
22948 TA TA CTA TA TA TA TA AA CTA TA TA GTT TA TA TA TG TA GTT TA TA
1 TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * *
22992 TA TA GTA TA TA TA GTT TA T- TA -A TA TA AA T- TA TA CA -A TT TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
23032 TA TA TA AA T- TA TA TA TA AA CTA TA CA -A T- TA TA TT TA CA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
23072 T- TA TA TA TA -A T- TA TA AA T- TA TA TA TA CTA TA TA AA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
23110 TA TA TT TA T- TA -A TA TA AA CTA TA TA TA TA TA TA T- TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A
* ** * * * * *
23151 TT TA GGG T- TA -A TT TA TG TA -A T- TA TA TG TA CTT TA TA TA CA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
23191 TA TA TA AA CTA TA TA AA CTA TA TA GTT TA TA TA TA -A AA TA TG
1 TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
23233 TA TA CA -A T- TA TA TA TA TA TA TA TA TA TA AA CTA CA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
23273 TA -A T- TGA TA TT TA TA TA CTA TA TA AA CTA TA GTT TA TA T- TA
1 TA TA TA T-A TA TA TA TA TA -TA TA TA TA -TA TA -TA TA TA TA TA
*
23314 TA TA CTA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA T- 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
* * * *
23357 TA AA T- TA TA TA TA CA -A TA TA T- TT TA CA TA TGA -A CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA
* * * * *
23397 TA AA AA CTA TA TA TA TA AA CTA TA TA AA CTA TA GTG 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
* *
23441 AA CTA TA TA CTA TA GT- TGA TA TT TA TA TA -A TA TA TA CTA TA -A
1 TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA TA TA TA TA -TA TA TA
* *
23483 T- TGA TA TT TA TA TA CTA TA -A TA TA TA -A TT TA TA CTA TA TA
1 TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
23523 AA T- TCA AA GTA TA TA T- TA TA TG TA AA TA CTA TA TA -A T- TA
1 TA TA T-A TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
23562 AA TA AA TA AA T- TA -A TA AA T- TA TT TA TA TA -A TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
23601 CA TA TA TA TA CTA TA TA TA CTA TA TA GTT TA CA TA TGA -A CTA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA T-A TA -TA TA
* * * * * *
23645 TA TA AA AA CTA TA TA CTA CA GT- TGA AA TT TA TA TA CTC TA TA -A
1 TA TA TA TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA
* * * * *
23688 TA TA TA TA -A TT TA CA TA TA AA CTA TA TA -A TT TA CA TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA
* * * * *
23729 CTG TA CA TA TA GTT TA T- TA -A TGA -A CTA TA TA AA CTA TT TA TA
1 -TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA TA TA -TA TA TA TA
* *
23771 TA GTA TA TA CTA TA TA TA TA AA CTA TA TA TA CTA TA TA -A TT TA
1 TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
* ** * *
23814 CA TA TGA GC TA TA TA AA AA CTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
*
23858 TA TA TA TA TA TA AA CTA TA TA T- TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA
23884 GTTGAGTTCT
Statistics
Matches: 651, Mismatches: 159, Indels: 248
0.62 0.15 0.23
Matches are distributed among these distances:
1 57 0.09
2 512 0.79
3 82 0.13
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:22980 original size:11 final size:11
Alignment explanation
Indices: 22966--23010 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 11
22956 ATATATAAAC
22966 TATATAGTTTA
1 TATATAGTTTA
22977 TATATGTAGTTTA
1 TATA--TAGTTTA
22990 TATATAG--TA
1 TATATAGTTTA
22999 TATATAGTTTA
1 TATATAGTTTA
23010 T
1 T
23011 TAATATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.30
11 10 0.33
13 11 0.37
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:23077 original size:30 final size:30
Alignment explanation
Indices: 23008--23103 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 30
22998 ATATATAGTT
*
23008 TATTAATATAAATTATACAATTTATATATAAA
1 TATT-ATATAAATTATACAA-TTATATATACA
* *
23040 T-TATATATAAACTATACAATTATATTTACA
1 TAT-TATATAAATTATACAATTATATATACA
23070 TATTATATATAATTATA-AATTATATATACTA
1 TATTATATA-AATTATACAATTATATATAC-A
23101 TAT
1 TAT
23104 AAATTATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
30 27 0.49
31 26 0.47
32 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
TATTATATAAATTATACAATTATATATACA
Found at i:23080 original size:17 final size:17
Alignment explanation
Indices: 23060--23114 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
23050 ACTATACAAT
* *
23060 TATATTTACATATTATA
1 TATAATTACAAATTATA
*
23077 TATAATTATAAATTATA
1 TATAATTACAAATTATA
* *
23094 TATACTATATAAATTATA
1 TATAAT-TACAAATTATA
23112 TAT
1 TAT
23115 TTATTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATTACAAATTATA
Found at i:23147 original size:11 final size:11
Alignment explanation
Indices: 22948--23369 Score: 87
Period size: 11 Copynumber: 36.2 Consensus size: 11
22938 ATTAAGTATG
*
22948 TATACTATATA
1 TATATTATATA
*
22959 TATA-AACTATA
1 TATATTA-TATA
22970 TAGT-TTATATA
1 TA-TATTATATA
*
22981 TGTAGTT-TATA
1 TATA-TTATATA
*
22992 TATAGTATATA
1 TATATTATATA
23003 TAGT-TTATTAATA
1 TA-TATTA-T-ATA
* *
23016 TAAATTATACA
1 TATATTATATA
23027 -AT-TTATATA
1 TATATTATATA
*
23036 TAAATTATATA
1 TATATTATATA
* * *
23047 TAAACTATACA
1 TATATTATATA
*
23058 -AT-TATATTTA
1 TATAT-TATATA
*
23068 CATATTATATA
1 TATATTATATA
*
23079 TA-ATTATAAA
1 TATATTATATA
23089 TTATATATACTATA
1 -TATAT-TA-TATA
*
23103 TAAATTATATA
1 TATATTATATA
*
23114 TTTATTAATATA
1 TATATT-ATATA
*
23126 AACTATATATATA
1 TA-TAT-TATATA
23139 TATATTATATGA
1 TATATTATAT-A
* *
23151 TTTAGGGTTAATTTA
1 TATA---TT-ATATA
* *
23166 TGTAATTATATG
1 TAT-ATTATATA
23178 TACT-TTATATA
1 TA-TATTATATA
* *
23189 CATA-TATAAA
1 TATATTATATA
*
23199 CTATA-TAAACTA
1 -TATATTATA-TA
23211 TATAGTTTATATA
1 TATA--TTATATA
* * *
23224 TAAAATATGTA
1 TATATTATATA
*
23235 TACAATTATATA
1 TA-TATTATATA
23247 TATATATATATA
1 TATAT-TATATA
* * *
23259 TAAACTACATAA
1 TATATTATAT-A
*
23271 TATAATTGATATT
1 TAT-ATT-ATATA
23284 TATA-TACTATA
1 TATATTA-TATA
* * *
23295 TAAACTATAGTT
1 TATATTATA-TA
23307 TATATTATATA
1 TATATTATATA
*
23318 CTATACTATAGTTGA
1 -TATATTATA--T-A
*
23333 TATTTATATACTA
1 TATAT-TATA-TA
23346 TATATTATATA
1 TATATTATATA
*
23357 TAAATTATATA
1 TATATTATATA
23368 TA
1 TA
23370 CAATATATTT
Statistics
Matches: 298, Mismatches: 65, Indels: 96
0.65 0.14 0.21
Matches are distributed among these distances:
9 6 0.02
10 24 0.08
11 125 0.42
12 73 0.24
13 41 0.14
14 15 0.05
15 10 0.03
16 4 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (11 bp):
TATATTATATA
Found at i:23227 original size:29 final size:30
Alignment explanation
Indices: 23190--23303 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 30
23180 CTTTATATAC
23190 ATATATAAACTATATAAACTATATAGTT-T
1 ATATATAAACTATATAAACTATATAGTTAT
* * *
23219 ATATATAAAATATGTATACAATTATATATATATAT
1 ATATATAAACTA--TATA-AACTATATA-GT-TAT
*
23254 ATATATAAACTACAT-AA-TATA-A-TTGAT
1 ATATATAAACTATATAAACTATATAGTT-AT
* *
23281 ATTTATATACTATATAAACTATA
1 ATATATAAACTATATAAACTATA
23304 GTTTATATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
26 1 0.01
27 15 0.22
28 2 0.03
29 16 0.24
30 4 0.06
31 6 0.09
32 8 0.12
33 3 0.04
34 1 0.01
35 12 0.18
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
ATATATAAACTATATAAACTATATAGTTAT
Found at i:23296 original size:9 final size:9
Alignment explanation
Indices: 23284--23449 Score: 53
Period size: 9 Copynumber: 18.4 Consensus size: 9
23274 AATTGATATT
23284 TATATACTA
1 TATATACTA
*
23293 TATAAACTA
1 TATATACTA
*
23302 TAGTTTA-TA
1 TA-TATACTA
23311 TTATATACTA
1 -TATATACTA
*
23321 TACTATAGT-
1 TA-TATACTA
23330 TGATAT--T-
1 T-ATATACTA
23337 TATATACTA
1 TATATACTA
23346 TATATTA-TA
1 TATA-TACTA
* *
23355 TATAAATTA
1 TATATACTA
*
23364 TATATACAA
1 TATATACTA
**
23373 TATATTTTA
1 TATATACTA
*
23382 CATATGAACTA
1 TATAT--ACTA
*
23393 TATATA-AA
1 TATATACTA
*
23401 AACTATA-TA
1 TA-TATACTA
*
23410 TATAAACTA
1 TATATACTA
*
23419 TATAAACTA
1 TATATACTA
*
23428 TAGTGTA-TA
1 TA-TATACTA
*
23437 TATAAACTA
1 TATATACTA
23446 TATA
1 TATA
23450 CTATAGTTGA
Statistics
Matches: 116, Mismatches: 25, Indels: 32
0.67 0.14 0.18
Matches are distributed among these distances:
6 4 0.03
7 2 0.02
8 9 0.08
9 79 0.68
10 16 0.14
11 6 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (9 bp):
TATATACTA
Found at i:23317 original size:7 final size:7
Alignment explanation
Indices: 23239--23368 Score: 51
Period size: 7 Copynumber: 18.3 Consensus size: 7
23229 TATGTATACA
23239 ATTATAT
1 ATTATAT
23246 ATATATAT
1 AT-TATAT
*
23254 ATATATAA
1 AT-TATAT
* *
23262 ACTACAT
1 ATTATAT
*
23269 AATATA-
1 ATTATAT
23275 ATTGATAT
1 ATT-ATAT
23283 -TTATAT
1 ATTATAT
*
23289 ACTATAT
1 ATTATAT
*
23296 A-AACTAT
1 ATTA-TAT
23303 AGTT-TAT
1 A-TTATAT
23310 ATTATAT
1 ATTATAT
23317 ACTATACTAT
1 A-T-TA-TAT
23327 AGTTGATAT
1 A-TT-ATAT
23336 -TTATAT
1 ATTATAT
*
23342 ACTATAT
1 ATTATAT
23349 ATTATAT
1 ATTATAT
23356 A-TA-A-
1 ATTATAT
23360 ATTATAT
1 ATTATAT
23367 AT
1 AT
23369 ACAATATATT
Statistics
Matches: 94, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
4 1 0.01
5 3 0.03
6 16 0.17
7 48 0.51
8 14 0.15
9 6 0.06
10 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (7 bp):
ATTATAT
Found at i:23467 original size:27 final size:27
Alignment explanation
Indices: 23405--23524 Score: 113
Period size: 27 Copynumber: 4.4 Consensus size: 27
23395 TATAAAAACT
23405 ATATATATAAACTATATAAACTATAG-TG
1 ATATATATAAACTATAT--ACTATAGTTG
23433 -TATATATAAACTATATACTATAGTTG
1 ATATATATAAACTATATACTATAGTTG
* *
23459 ATATTTATATAA-TATATACTATAATTG
1 ATATATATA-AACTATATACTATAGTTG
* * * *
23486 ATATTTATATACTATAATA-TATAATTT
1 ATATATATAAACTAT-ATACTATAGTTG
23513 ATACTATATAAA
1 ATA-TATATAAA
23525 TTCAAAGTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.09
26 3 0.04
27 59 0.74
28 11 0.14
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (27 bp):
ATATATATAAACTATATACTATAGTTG
Found at i:23615 original size:9 final size:9
Alignment explanation
Indices: 23585--23626 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
23575 ATAAATTATT
*
23585 TATATAATA
1 TATATACTA
23594 TATACTACATA
1 TATA-TAC-TA
23605 TATATACTA
1 TATATACTA
23614 TATATACTA
1 TATATACTA
23623 TATA
1 TATA
23627 GTTTACATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 19 0.63
10 5 0.17
11 6 0.20
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (9 bp):
TATATACTA
Found at i:24758 original size:19 final size:19
Alignment explanation
Indices: 24736--24774 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
24726 AGAGGGTGCT
*
24736 GACCGGCTGAACTGGTCTG
1 GACCGACTGAACTGGTCTG
*
24755 GACCGACTGGACTGGTCTG
1 GACCGACTGAACTGGTCTG
24774 G
1 G
24775 TCTGGTCTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (19 bp):
GACCGACTGAACTGGTCTG
Found at i:24872 original size:29 final size:29
Alignment explanation
Indices: 24830--24895 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
24820 ATTGACCTAG
24830 TCGTTGACCGTTGACCAGGCGTTGATCGA
1 TCGTTGACCGTTGACCAGGCGTTGATCGA
*
24859 TCGTTGACCGTTGACCAGGCGTTGATCGG
1 TCGTTGACCGTTGACCAGGCGTTGATCGA
*
24888 CCGTTGAC
1 TCGTTGAC
24896 TTTTTTTGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (29 bp):
TCGTTGACCGTTGACCAGGCGTTGATCGA
Found at i:30639 original size:24 final size:23
Alignment explanation
Indices: 30594--30671 Score: 56
Period size: 24 Copynumber: 3.4 Consensus size: 23
30584 ACACTTAACA
* *
30594 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATACAT-CATTTGAAT
*
30618 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATACATCAT-TTGAAT
* *
30640 -TGCACCGATACA-CACCTTGAAT
1 GTGCATCGATACATCA-TTTGAAT
30662 GTGCATCGAT
1 GTGCATCGAT
30672 GCACATGGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
20 5 0.12
21 11 0.26
23 11 0.26
24 16 0.37
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (23 bp):
GTGCATCGATACATCATTTGAAT
Found at i:31077 original size:27 final size:27
Alignment explanation
Indices: 31047--31103 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
31037 AAAAACAAAC
31047 AATTTTTCAAAAAAAAATTA-ATTTCGA
1 AATTTTT-AAAAAAAAATTAGATTTCGA
**
31074 AATTTTTTTAAAAAAATTATGATTTCGA
1 AATTTTTAAAAAAAAATTA-GATTTCGA
31102 AA
1 AA
31104 ATCAGTAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 7 0.27
28 9 0.35
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (27 bp):
AATTTTTAAAAAAAAATTAGATTTCGA
Found at i:33360 original size:65 final size:63
Alignment explanation
Indices: 33241--33450 Score: 194
Period size: 65 Copynumber: 3.3 Consensus size: 63
33231 TTTGTCAGAG
* * *
33241 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGC
33303 ATT
61 ATT
* * *
33306 TCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCAAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCAT
33370 T
63 T
* * * * * *
33371 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGTACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
*
33435 TGATACATCGATGCAC
1 TGATGCATCGATGCAC
33451 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 44 0.36
65 68 0.56
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:38892 original size:14 final size:14
Alignment explanation
Indices: 38869--38909 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
38859 TGCTTTAAAC
38869 TTTTCTTTCTTTTCT-
1 TTTTC-TTCTTTT-TG
38884 TTTTCTTCTTTTTG
1 TTTTCTTCTTTTTG
38898 TTTTCTTCTTTT
1 TTTTCTTCTTTT
38910 GAGTGCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 19 0.76
15 5 0.20
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTTCTTCTTTTTG
Found at i:42892 original size:14 final size:14
Alignment explanation
Indices: 42860--42893 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
42850 TTGAAGATTT
*
42860 ATAACATAAGAATC
1 ATAATATAAGAATC
42874 ATAATATAAGAATC
1 ATAATATAAGAATC
42888 ATAATA
1 ATAATA
42894 AATATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (14 bp):
ATAATATAAGAATC
Found at i:44467 original size:5 final size:5
Alignment explanation
Indices: 44446--44484 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
44436 AGACACGTAT
44446 GACCAC GACCAC GACCC GACCC GACCC GACCC GACCC GA
1 GACC-C GACC-C GACCC GACCC GACCC GACCC GACCC GA
44485 GACGAGACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.70
6 10 0.30
ACGTcount: A:0.26, C:0.54, G:0.21, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:45007 original size:6 final size:6
Alignment explanation
Indices: 44989--45021 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
44979 TCGTCTCGTC
*
44989 TCGT-G TCGGGG TCGTGG TCGTGG TCGTGG TCGT
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
45022 CCGCGCGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 3 0.12
6 22 0.88
ACGTcount: A:0.00, C:0.18, G:0.48, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:45143 original size:42 final size:41
Alignment explanation
Indices: 45096--45188 Score: 118
Period size: 41 Copynumber: 2.2 Consensus size: 41
45086 ACAACGAATT
*
45096 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAATGCGAAC
1 TGGAAAATCGCAACG-CGAA-TGTCA-ACTATCGCAACGCGAAC
* *
45138 TGGAAAATCGCAACGCGGATTTCAACTATCGCAACGCGAAC
1 TGGAAAATCGCAACGCGAATGTCAACTATCGCAACGCGAAC
45179 TGGAAAATCG
1 TGGAAAATCG
45189 TTACGATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 29 0.63
42 17 0.37
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGAATGTCAACTATCGCAACGCGAAC
Found at i:45149 original size:20 final size:20
Alignment explanation
Indices: 45096--45188 Score: 71
Period size: 20 Copynumber: 4.5 Consensus size: 20
45086 ACAACGAATT
45096 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
** *
45116 TGTAGACTATCGCAATGCGAAC
1 TG--GAAAATCGCAACGCGAAC
* *
45138 TGGAAAATCGCAACGCGGAT
1 TGGAAAATCGCAACGCGAAC
** *
45158 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAC
45179 TGGAAAATCG
1 TGGAAAATCG
45189 TTACGATTTT
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
20 22 0.42
21 16 0.30
22 15 0.28
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.17
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:45215 original size:39 final size:40
Alignment explanation
Indices: 45121--45215 Score: 122
Period size: 41 Copynumber: 2.4 Consensus size: 40
45111 ACAACTGTAG
*
45121 ACTATCGCAATGCGAACTGGAAAATCGCAACGCGGATTTCA
1 ACTATCGCAACGCGAACTGGAAAATCGCAAC-CGGATTTCA
** *
45162 ACTATCGCAACGCGAACTGGAAAATCGTTA-C-GATTTTTA
1 ACTATCGCAACGCGAACTGGAAAATCGCAACCGGA-TTTCA
45201 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
45216 TTTTCAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
38 2 0.04
39 20 0.41
41 27 0.55
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (40 bp):
ACTATCGCAACGCGAACTGGAAAATCGCAACCGGATTTCA
Found at i:45216 original size:21 final size:21
Alignment explanation
Indices: 45192--45236 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
45182 AAAATCGTTA
*
45192 CGATTTTTAACTATCGCAACG
1 CGATTTTCAACTATCGCAACG
*
45213 CGATTTTCAATTATCGCAACG
1 CGATTTTCAACTATCGCAACG
45234 CGA
1 CGA
45237 AATGCAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (21 bp):
CGATTTTCAACTATCGCAACG
Found at i:51129 original size:21 final size:19
Alignment explanation
Indices: 51105--51154 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
51095 GTTGAATACA
51105 AATATTTTAATATTTAATTTG
1 AATATTTTAA-ATTTAA-TTG
*
51126 AATAATTTTAACTTTAATTG
1 AAT-ATTTTAAATTTAATTG
*
51146 AATTTTTTA
1 AATATTTTA
51155 TTTGTTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 6 0.23
21 8 0.31
22 7 0.27
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
AATATTTTAAATTTAATTG
Found at i:51133 original size:22 final size:20
Alignment explanation
Indices: 51108--51148 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
51098 GAATACAAAT
51108 ATTTTAATATTTAATTTGAATA
1 ATTTTAA-ATTTAA-TTGAATA
*
51130 ATTTTAACTTTAATTGAAT
1 ATTTTAAATTTAATTGAAT
51149 TTTTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTAAATTTAATTGAATA
Found at i:53039 original size:28 final size:28
Alignment explanation
Indices: 52976--53060 Score: 120
Period size: 28 Copynumber: 3.1 Consensus size: 28
52966 GCTTGGATTT
* * * *
52976 GAAGTTAAATAGCAATGGA-C-CATTTT
1 GAAGTTAAATGGCAAGGGACCACAATTA
53002 GAAGTTAAATGGCAAGGGACCACAATTA
1 GAAGTTAAATGGCAAGGGACCACAATTA
53030 GAAGTTAAATGGCAAGGGACCACAATTA
1 GAAGTTAAATGGCAAGGGACCACAATTA
53058 GAA
1 GAA
53061 ATATGACTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
26 17 0.32
27 1 0.02
28 35 0.66
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (28 bp):
GAAGTTAAATGGCAAGGGACCACAATTA
Found at i:59968 original size:3 final size:3
Alignment explanation
Indices: 59949--59992 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
59939 CAAAAACATG
* *
59949 TAA TAC TAA TAAA TAA TAA TAA TAA TAAA TAT TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
59993 CCCAGACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:59974 original size:16 final size:16
Alignment explanation
Indices: 59949--59992 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
59939 CAAAAACATG
*
59949 TAATACTAATAAATAA
1 TAATAATAATAAATAA
*
59965 TAATAATAATAAATAT
1 TAATAATAATAAATAA
59981 TAATAATAATAA
1 TAATAATAATAA
59993 CCCAGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:60676 original size:258 final size:261
Alignment explanation
Indices: 60115--60694 Score: 644
Period size: 258 Copynumber: 2.2 Consensus size: 261
60105 CAAGTGAAAG
* * * * * ** * * *
60115 TGACAGATAACCCGAAGGATTTAATTATCATGCTCAAAAGACTTGTTGATGGTCCGAAGGACTT-
1 TGACAGATGACCTGAAGCATTTAATCACCATGCTCAAAAGACTTACTAACGGCCCGAAGGACTTA
* * * * *
60179 ---ATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATTGTTTTCTTACTTTTCAAAAATT
66 CAAATTTAGGGAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATT
* *
60241 TCATTTTATAAAAAAATTAAATGAAAAGCTTTGAAAATTGCTTTTCTCATTTTTCAAAAACATCA
131 TCATTTTATAAAAAAATTAAATGAAAAGATTTGAAAATTACTTTTCTCATTTTTCAAAAACATCA
* * * *
60306 TATGAAAGCATCTTGCCCAAAGGTCTTATTGATGGCCCAAAGGACTTATCATCTCGCTCGAAAGA
196 TATGAAAACATCTTACCCAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTAGCTCGAAAGA
60371 C
261 C
* * * * * * *
60372 TGATAGATGACCTGAAGCATTTAATCATCATTCTCAAAAGACTTACTGATGGCCCGGATGACTTA
1 TGACAGATGACCTGAAGCATTTAATCACCATGCTCAAAAGACTTACTAACGGCCCGAAGGACTTA
* * *
60437 CAAATTTAGGGAATAGTCTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTATTTTTC-TAAA-T
66 CAAATTTAGGGAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATT
* * *
60500 TCTATTTTCTGAAAATATTAAATGAGAAA-ATTTGAAAATTACTTTTCTCATTTTTC-AAAA-AT
131 TC-ATTTTATAAAAAAATTAAATGA-AAAGATTTGAAAATTACTTTTCTCATTTTTCAAAAACAT
* * * * *
60562 CATGTGAAAACAT-TCTACCCGAATGTCTTATAGATGGCTCAAATGACTTATTC-TCTAGCTCGA
194 CATATGAAAACATCT-TACCCAAAGGTCTTATAGATGGCCCAAAGGACTTA-TCATCTAGCTCGA
*
60625 AAGAT
257 AAGAC
* * *
60630 TGACAGATGATCC-GAAGGATTTAATCACCATGCTCGAAATACTTACTAACGGCCCGAAGGACTT
1 TGACAGATGA-CCTGAAGCATTTAATCACCATGCTCAAAAGACTTACTAACGGCCCGAAGGACTT
60694 A
65 A
60695 TCATCTTGCT
Statistics
Matches: 270, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
257 54 0.20
258 107 0.40
259 11 0.04
260 47 0.17
261 51 0.19
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (261 bp):
TGACAGATGACCTGAAGCATTTAATCACCATGCTCAAAAGACTTACTAACGGCCCGAAGGACTTA
CAAATTTAGGGAATAGTCTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATT
TCATTTTATAAAAAAATTAAATGAAAAGATTTGAAAATTACTTTTCTCATTTTTCAAAAACATCA
TATGAAAACATCTTACCCAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTAGCTCGAAAGA
C
Found at i:60739 original size:41 final size:42
Alignment explanation
Indices: 60619--60754 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 42
60609 TTATTCTCTA
* * * *
60619 GCTCGAAAGATTGACAGATGATCCGAAGGATTTAATCACCAT
1 GCTCGAAAGACTAACAGATGACCCGAAGGATTTAATCATCAT
* * * * * *
60661 GCTCGAAATACTTACTA-ACGGCCCGAAGGACTT-ATCATCTT
1 GCTCGAAAGACTAAC-AGATGACCCGAAGGATTTAATCATCAT
* *
60702 GCTCGAGAGACTAACAGATGACCCGAA-GATTTAATCATCAA
1 GCTCGAAAGACTAACAGATGACCCGAAGGATTTAATCATCAT
60743 GCTCGAAAGACT
1 GCTCGAAAGACT
60755 TATTGATGGC
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
40 5 0.07
41 43 0.59
42 24 0.33
43 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (42 bp):
GCTCGAAAGACTAACAGATGACCCGAAGGATTTAATCATCAT
Found at i:64605 original size:2 final size:2
Alignment explanation
Indices: 64598--64633 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
64588 ACCATCAAAT
64598 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
64634 GAGTGAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:72161 original size:18 final size:18
Alignment explanation
Indices: 72140--72180 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
72130 TAATAGTGAG
72140 TTATTATAAAATATAT-TT
1 TTATTAT-AAATATATCTT
*
72158 TTATTATAATTATATCTT
1 TTATTATAAATATATCTT
72176 TTATT
1 TTATT
72181 TATATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTATAAATATATCTT
Found at i:72202 original size:19 final size:18
Alignment explanation
Indices: 72140--72203 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
72130 TAATAGTGAG
*
72140 TTATTATAAAATATAT-TT
1 TTATTAT-AATTATATCTT
72158 TTATTATAATTATATCTT
1 TTATTATAATTATATCTT
* * *
72176 TTATTTATATTTTTATGTCT
1 TTA-TTATAATTATATCT-T
72196 TTATTATA
1 TTATTATA
72204 GTTTAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 7 0.18
18 12 0.31
19 16 0.41
20 4 0.10
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (18 bp):
TTATTATAATTATATCTT
Found at i:72261 original size:13 final size:13
Alignment explanation
Indices: 72226--72267 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
72216 ATGTTTTATA
72226 TATAATGATATTTTT
1 TATAAT-AT-TTTTT
72241 TA-AA-ATTTTTT
1 TATAATATTTTTT
72252 TATAATATTTTTT
1 TATAATATTTTTT
72265 TAT
1 TAT
72268 TTTTGAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.28
12 4 0.16
13 10 0.40
14 2 0.08
15 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
TATAATATTTTTT
Found at i:77924 original size:44 final size:44
Alignment explanation
Indices: 77849--77935 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
77839 GTTATATGAT
77849 ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGAC
1 ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGAC
* * *** *
77893 ATGATCTATGTGATTATTTGTCTATGTGATATAAGCTATGTGA
1 ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGA
77936 AATATGTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (44 bp):
ATGATCTACGTGATTATATGAAAATGAGATATAAGCTATGTGAC
Found at i:77933 original size:14 final size:14
Alignment explanation
Indices: 77876--77935 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
77866 ATGAAAATGA
77876 GATATAAGCTATGT
1 GATATAAGCTATGT
* * *
77890 GACATGATCTATGT
1 GATATAAGCTATGT
**
77904 GATTATTTGTCTATGT
1 GA-TATAAG-CTATGT
77920 GATATAAGCTATGT
1 GATATAAGCTATGT
77934 GA
1 GA
77936 AATATGTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 21 0.60
15 6 0.17
16 8 0.23
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (14 bp):
GATATAAGCTATGT
Found at i:78040 original size:23 final size:23
Alignment explanation
Indices: 78014--78099 Score: 68
Period size: 23 Copynumber: 3.7 Consensus size: 23
78004 TCAAGGATTC
*
78014 TACGCGGTCATTCGGGATAATTA
1 TACGCGGTCCTTCGGGATAATTA
** * * *
78037 TACGTAGTCCTTCGGGACATTTT
1 TACGCGGTCCTTCGGGATAATTA
*
78060 TACGCGGTCCTTCAGGATATATCTA
1 TACGCGGTCCTTCGGGATA-AT-TA
*
78085 T--GTGGTCCTTCGGGA
1 TACGCGGTCCTTCGGGA
78100 CATTTCTATG
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
23 44 0.94
24 1 0.02
25 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.34
Consensus pattern (23 bp):
TACGCGGTCCTTCGGGATAATTA
Found at i:78066 original size:46 final size:46
Alignment explanation
Indices: 78014--78104 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
78004 TCAAGGATTC
*
78014 TACGCGGTCATTCGGGATA-AT-TATACGTAGTCCTTCGGGACATTTT
1 TACGCGGTCATTCAGGATATATCTAT--GTAGTCCTTCGGGACATTTT
* *
78060 TACGCGGTCCTTCAGGATATATCTATGTGGTCCTTCGGGACATTT
1 TACGCGGTCATTCAGGATATATCTATGTAGTCCTTCGGGACATTT
78105 CTATGTGGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 35 0.88
47 2 0.05
48 3 0.08
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (46 bp):
TACGCGGTCATTCAGGATATATCTATGTAGTCCTTCGGGACATTTT
Found at i:78107 original size:23 final size:23
Alignment explanation
Indices: 78043--78112 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
78033 ATTATACGTA
* * *
78043 GTCCTTCGGGACATTTTTACGCG
1 GTCCTTCGGGACATTTCTATGTG
* * *
78066 GTCCTTCAGGATATATCTATGTG
1 GTCCTTCGGGACATTTCTATGTG
78089 GTCCTTCGGGACATTTCTATGTG
1 GTCCTTCGGGACATTTCTATGTG
78112 G
1 G
78113 CACTTTGGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (23 bp):
GTCCTTCGGGACATTTCTATGTG
Found at i:78138 original size:24 final size:24
Alignment explanation
Indices: 78103--78148 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
78093 TTCGGGACAT
* *
78103 TTCTATGTGGCACTTTGGTGCATA
1 TTCTATGCGGCACTTCGGTGCATA
78127 TTCTATGCGGCACTTCGGTGCA
1 TTCTATGCGGCACTTCGGTGCA
78149 ATTTATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (24 bp):
TTCTATGCGGCACTTCGGTGCATA
Found at i:78293 original size:2 final size:2
Alignment explanation
Indices: 78281--78311 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
78271 GATGATGATG
78281 AT AT AT GAT 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
78312 GATTTTGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78767 original size:16 final size:16
Alignment explanation
Indices: 78743--78774 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
78733 GATTTCAAAC
*
78743 AAATCTTTTTAAAAGT
1 AAATATTTTTAAAAGT
78759 AAATATTTTTAAAAGT
1 AAATATTTTTAAAAGT
78775 CAATGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
AAATATTTTTAAAAGT
Found at i:81047 original size:17 final size:17
Alignment explanation
Indices: 81025--81066 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
81015 AATTAAAGGG
81025 AGATTCGATATTCTCCA
1 AGATTCGATATTCTCCA
81042 AGATTCGATATTCTCCA
1 AGATTCGATATTCTCCA
81059 AGA-TCGAT
1 AGATTCGAT
81067 TTACGTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (17 bp):
AGATTCGATATTCTCCA
Found at i:84986 original size:44 final size:44
Alignment explanation
Indices: 84893--84989 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
84883 TTTATTCCAT
* *
84893 GCTATATGATATGATCTATGTGATTATATGAAAATGAGATATAA
1 GCTATGTGACATGATCTATGTGATTATATGAAAATGAGATATAA
* * *** *
84937 ACTATGTGACATGATCTATGTGATTATTTGTCTATGTGATATAA
1 GCTATGTGACATGATCTATGTGATTATATGAAAATGAGATATAA
84981 GCTATGTGA
1 GCTATGTGA
84990 AATATATAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (44 bp):
GCTATGTGACATGATCTATGTGATTATATGAAAATGAGATATAA
Found at i:85220 original size:23 final size:23
Alignment explanation
Indices: 85065--85213 Score: 183
Period size: 23 Copynumber: 6.4 Consensus size: 23
85055 GAGTCAAGGG
* *
85065 TTCTATGTGGTCCTTCGGGAAAA
1 TTCTATGTGGTCCTTCGGGACAT
85088 TTCTATGTGGTTCCTTCGGGACAT
1 TTCTATGTGG-TCCTTCGGGACAT
* * *
85112 TTCTACGCT-GTCATTCGAGACAT
1 TTCTATG-TGGTCCTTCGGGACAT
*
85135 ATCTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* *
85158 TTCTACGCGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* *
85181 ATCTATGTGGTCTTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
85204 TTCTATGTGG
1 TTCTATGTGG
85214 AACTTCGTTG
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
22 1 0.01
23 86 0.81
24 18 0.17
25 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAT
Found at i:85242 original size:24 final size:24
Alignment explanation
Indices: 85215--85273 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
85205 TCTATGTGGA
* *
85215 ACTTCGTTGCATATTCTACGCGGC
1 ACTTCGGTGCATATTCTACACGGC
85239 ACTTCGGTGCATATTCTACACGGC
1 ACTTCGGTGCATATTCTACACGGC
85263 ACTTCGGTGCA
1 ACTTCGGTGCA
85274 ATTTATACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.31
Consensus pattern (24 bp):
ACTTCGGTGCATATTCTACACGGC
Found at i:85406 original size:2 final size:2
Alignment explanation
Indices: 85399--85432 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
85389 TGATGATGAG
* *
85399 AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85433 GCTTTTGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:86939 original size:20 final size:20
Alignment explanation
Indices: 86884--86951 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
86874 GCCGATTTAG
*
86884 GTTGACTCAATTCGGTTCGA
1 GTTGACTCAATTCGATTCGA
* * *** *
86904 GCTGATTCAGGCCGATTCGT
1 GTTGACTCAATTCGATTCGA
*
86924 GTTGACTCAATTCGATTTGA
1 GTTGACTCAATTCGATTCGA
86944 GTTGACTC
1 GTTGACTC
86952 GAATCGGTTC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGACTCAATTCGATTCGA
Done.