Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007917.1 Hibiscus syriacus cultivar Beakdansim tig00110320_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: 409361
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:196871 original size:17 final size:18
Alignment explanation
Indices: 196838--196884 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
196828 AATTGTCAAT
* *
196838 ATATATATATATATATTA
1 ATATATATATTTTTATTA
*
196856 CTATA-ATATTTTTATTA
1 ATATATATATTTTTATTA
196873 ATATATATATTT
1 ATATATATATTT
196885 AAAGACAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATATATATTTTTATTA
Found at i:203902 original size:16 final size:16
Alignment explanation
Indices: 203881--203911 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
203871 GTTATGACCC
*
203881 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
203897 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
203912 ATAGAAATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:218528 original size:16 final size:16
Alignment explanation
Indices: 218482--218530 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
218472 TCAACGTTTT
*
218482 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
218498 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
218514 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
218530 T
1 T
218531 TTATTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.08, C:0.10, G:0.22, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:222636 original size:27 final size:27
Alignment explanation
Indices: 222606--222659 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
222596 TGCCGCCTAA
222606 AATACTGTTTTTTCAGATGAACCCCTT
1 AATACTGTTTTTTCAGATGAACCCCTT
222633 AATACTGTTTTTTCAGATGAACCCCTT
1 AATACTGTTTTTTCAGATGAACCCCTT
222660 CACTCAAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (27 bp):
AATACTGTTTTTTCAGATGAACCCCTT
Found at i:227786 original size:30 final size:30
Alignment explanation
Indices: 227731--229086 Score: 1070
Period size: 30 Copynumber: 46.3 Consensus size: 30
227721 ATCACTACCT
* * * *
227731 CCTCCTTACAAGTATGAGTCTCCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
227761 CCCCCATATAAGTACAAGTCACCACCACC-
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
227790 TCTCCGTACAAGTACGAGTCACCACCTCCACCTCCA
1 CCTCCATACAAGTACGAGTCACCA---CCA---CCA
* * *
227826 CCTCCGTACAAGTACGAGTCTCCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
227856 CCTCCATACAAATACAAGTCACCA-CACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
227885 CCT-CGTACAAGTATGAGTCACCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * * * *
227914 CCTCCTTACAAATATGGGTCACCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
227944 CCTCCATACAAGTATGAGTCACCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
227974 CCTCCGTACAAGTATGAGTCTCCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228004 CCTCCGTACAAGTATGAGTC-CC-CC-CTCA
1 CCTCCATACAAGTACGAGTCACCACCAC-CA
* *
228032 CCTCCGTACAAGTACAAGT---CACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228059 CCTCCATACAAGTATGAGTCACCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228089 CCTCCGTACAAGTATGAGTCACCACCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228119 CCTCC--ACAAATACAAGTCACCACCACCG
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228147 CCTCCATACAAGTACAAGT---CTCCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228174 CCTCCATACAAGTATGAGT--CCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228202 CATCCATACAAATACAAGT---CACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228229 CCTCCTTATAAGTACGAGTCACCACCACCG
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228259 CCTCCATACAAGTACGAGT--CCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228287 GCTCCATACAAGTACAAGTCACCACCA-C-
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228315 CCTCCATACAAGTATGAGTCACCACCACCACCA
1 CCTCCATACAAGTACGAGT---CACCACCACCA
* * *
228348 CCTCCGTACAAGTATGAGTCACCACCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228378 CCTCCGTACAAGTATGAGT---CACCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228405 CCTCCATACAAGTACAAGTCACCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228435 CCTCCCTACAAGTACAAGTCA-CACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228464 CCTCCCTACAAGTATGAGTCACCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228494 CCTCCGTACAAGTACGAGTCACCACCA-CA
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228523 CCTCCGTACAAGTACGAGTCACCACCA-CA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228552 CCTCCGTACAAGTACGAGTCACCGCCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
228582 CCTCC-TACAAGTACGAGTCACCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
*
228611 CCTCCCTACAAGTACGAGTCACCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228641 CCTCCCTACAAGTACGAGTCACCACCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* ** * * *
228671 CCT-TAT-GTA-TACAAATCACC-CCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* *
228697 CCTCCATACAAGTACGAATCACCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
*** * *
228727 CCTCCATATGTGTACAAGTCACCCCCACC-
1 CCTCCATACAAGTACGAGTCACCACCACCA
** * * * * *
228756 TTTCCATACAAATATGAATCACCA-CTCCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228785 CCTCCATACAAATACGAATCACCACCTCCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
*** * * *
228815 CC-CCATATGTGTACAAGTCACCTCCA-CT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * * *
228843 CCTCCATACAAATATGAATCACCACCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * *
228873 CCTCCATACAAGTACGAATCACCACC-TCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
** * * *
228902 CCTCCATAGTA-TACAAGTCACCTCCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * * * * *
228931 CCACCATACAAATATGAATCACCACCTCCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
* **** *
228961 TCTCCATATGTCTACAAGTCACCACCACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * * *
228991 CCT-TATACAAATATGAGTCACCACAACCA
1 CCTCCATACAAGTACGAGTCACCACCACCA
* * * *
229020 CCTCCCATATAAGTATGAATCACC-CCTCCA
1 CCT-CCATACAAGTACGAGTCACCACCACCA
*** * *
229050 CCTCCATATGTGTACAAGTCACC-CCACCT
1 CCTCCATACAAGTACGAGTCACCACCACCA
229079 CCTCCATA
1 CCTCCATA
229087 TGTTTACAAG
Statistics
Matches: 1088, Mismatches: 192, Indels: 93
0.79 0.14 0.07
Matches are distributed among these distances:
26 10 0.01
27 100 0.09
28 142 0.13
29 291 0.27
30 474 0.44
31 23 0.02
32 4 0.00
33 20 0.02
35 2 0.00
36 22 0.02
ACGTcount: A:0.30, C:0.41, G:0.09, T:0.19
Consensus pattern (30 bp):
CCTCCATACAAGTACGAGTCACCACCACCA
Found at i:227833 original size:36 final size:36
Alignment explanation
Indices: 227791--227861 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
227781 ACCACCACCT
227791 CTCCGTACAAGTACGAGTCACCACCTCCACCTCCAC
1 CTCCGTACAAGTACGAGTCACCACCTCCACCTCCAC
*
227827 CTCCGTACAAGTACGAGTCTCCACCTCCACCTCCA
1 CTCCGTACAAGTACGAGTCACCACCTCCACCTCCA
227862 TACAAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.46, G:0.11, T:0.18
Consensus pattern (36 bp):
CTCCGTACAAGTACGAGTCACCACCTCCACCTCCAC
Found at i:227872 original size:36 final size:35
Alignment explanation
Indices: 227796--227874 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 35
227786 CACCTCTCCG
**
227796 TACAAGTACGAGTCACCACCTCCACCTCCACCTCCG
1 TACAAGTACGAGTCACCACCTCCACCTCCA-CTCAA
*
227832 TACAAGTACGAGTCTCCACCTCCACCTCCA-TACAAA
1 TACAAGTACGAGTCACCACCTCCACCTCCACT-C-AA
227868 TACAAGT
1 TACAAGT
227875 CACCACACCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.03
35 1 0.03
36 36 0.95
ACGTcount: A:0.30, C:0.41, G:0.10, T:0.19
Consensus pattern (35 bp):
TACAAGTACGAGTCACCACCTCCACCTCCACTCAA
Found at i:227966 original size:88 final size:90
Alignment explanation
Indices: 227731--228956 Score: 1126
Period size: 88 Copynumber: 14.0 Consensus size: 90
227721 ATCACTACCT
* * * *
227731 CCTCCTTACAAGTATGAGTCTCCACCTCCACCCCCATATAAGTACAAGTCACCACCACCT-CTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
*
227795 GTACAAGTACGAGTCACCACCTCCACCTCCA
66 ATACAAGTACGAGTCACCA---CCA---CCA
* * *
227826 CCTCCGTACAAGTACGAGTCTCCACCTCCACCTCCATACAAATACAAGTCACCA-CACCTCCT-C
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* * *
227889 GTACAAGTATGAGTCACCACCTCCA
66 ATACAAGTACGAGTCACCACCACCA
* * * ** * *
227914 CCTCCTTACAAATATGGGTCACCACCTCCACCTCCATACAAGTATGAGTCACCACCTCCACCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* * *
227979 GTACAAGTATGAGTCTCCACCACCA
66 ATACAAGTACGAGTCACCACCACCA
* *
228004 CCTCCGTACAAGTATGAGTC-CCCCCT-CACCTCCGTACAAGTACAAGTCACCACCA---CCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
*
228064 ATACAAGTATGAGTCACCACCACCA
66 ATACAAGTACGAGTCACCACCACCA
* * * *
228089 CCTCCGTACAAGTATGAGTCACCACCACCTCCTCC--ACAAATACAAGTCACCACCACCGCCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* *
228152 ATACAAGTACAAGT---CTCCACCA
66 ATACAAGTACGAGTCACCACCACCA
* * *
228174 CCTCCATACAAGTATGAGT--CCACCTCCACATCCATACAAATACAAGTCACCACCACCTCCT--
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* *
228235 -TATAAGTACGAGTCACCACCACCG
66 ATACAAGTACGAGTCACCACCACCA
* * *
228259 CCTCCATACAAGTACGAGT--CCACCTCCAGCTCCATACAAGTACAAGTCACCACCA-C-CCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
*
228320 ATACAAGTATGAGTCACCACCACCACCA
66 ATACAAGTACGAGT---CACCACCACCA
* * * **
228348 CCTCCGTACAAGTATGAGTCACCACCACCTCCTCCGTACAAGTATGAGT---CACCACCTCCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
*
228410 ATACAAGTACAAGTCACCACCACCA
66 ATACAAGTACGAGTCACCACCACCA
* ** * * ** *
228435 CCTCCCTACAAGTACAAGTCA-CACCACCACCTCCCTACAAGTATGAGTCACCACCACCACCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
*
228499 GTACAAGTACGAGTCACCACCA-CA
66 ATACAAGTACGAGTCACCACCACCA
* * * * * * *
228523 CCTCCGTACAAGTACGAGTCACCACC-ACACCTCCGTACAAGTACGAGTCACCGCCTCCACCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
228587 -TACAAGTACGAGTCACCACCACCA
66 ATACAAGTACGAGTCACCACCACCA
* * * * * *
228611 CCTCCCTACAAGTACGAGTCACCACCACCACCTCCCTACAAGTACGAGTCACCACCACCTCCT-T
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
** * * *
228675 AT-GTA-TACAAATCACC-CCACCT
66 ATACAAGTACGAGTCACCACCACCA
* * * *** * *
228697 CCTCCATACAAGTACGAATCACCACCTCCACCTCCATATGTGTACAAGTCACCCCCACCT-TTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* * * * *
228761 ATACAAATATGAATCACCA-CTCCT
66 ATACAAGTACGAGTCACCACCACCA
* * * * *** *
228785 CCTCCATACAAATACGAATCACCACCTCCACC-CCATATGTGTACAAGTCACCTCCA-CTCCTCC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* * * *
228848 ATACAAATATGAATCACCACCACCT
66 ATACAAGTACGAGTCACCACCACCA
* * * * ** * *
228873 CCTCCATACAAGTACGAATCACCACCT-CTCCTCCATAGTA-TACAAGTCACCTCCACCTCCACC
1 CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
* * *
228936 ATACAAATATGAATCACCACC
66 ATACAAGTACGAGTCACCACC
228957 TCCTTCTCCA
Statistics
Matches: 978, Mismatches: 115, Indels: 83
0.83 0.10 0.07
Matches are distributed among these distances:
82 11 0.01
83 14 0.01
84 1 0.00
85 175 0.18
86 100 0.10
87 129 0.13
88 284 0.29
89 107 0.11
90 58 0.06
91 24 0.02
94 24 0.02
95 51 0.05
ACGTcount: A:0.31, C:0.41, G:0.10, T:0.19
Consensus pattern (90 bp):
CCTCCGTACAAGTATGAGTCACCACCTCCACCTCCATACAAGTACAAGTCACCACCACCTCCTCC
ATACAAGTACGAGTCACCACCACCA
Found at i:228743 original size:59 final size:60
Alignment explanation
Indices: 227731--229057 Score: 909
Period size: 58 Copynumber: 22.6 Consensus size: 60
227721 ATCACTACCT
* ** * * * *
227731 CCTCCTTACAAGTATGAGTCTCCACCTCCACCCCCATATAAGTAC-AAGTCACCACCACC-
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAA-TCACCACCACCA
* * * * * * *
227790 TCTCCGTACAAGTACGAGTCACCACCTCCACCTCCACCTCCGTACAAGTACGAGTCTCCACCTCC
1 CCTCCATACAAGTACAAGTCACCA---CCA---CCACCTCCATACAAGTACGAATCACCACCACC
227855 A
60 A
* * * * * *
227856 CCTCCATACAAATACAAGTCACCA-CACCTCCT-CGTACAAGTATGAGTCACCACCTCCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * *** * * * *
227914 CCTCCTTACAAATATGGGTCACCACCTCCACCTCCATACAAGTATGAGTCACCACCTCCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* ** * * * *
227974 CCTCCGTACAAGTATGAGTCTCCACCACCACCTCCGTACAAGTATGAGTC-CC-CC-CTCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCAC-CA
* * *
228032 CCTCCGTACAAGTACAAGT---CACCACCACCTCCATACAAGTATGAGTCACCACCACCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* ** * * *
228089 CCTCCGTACAAGTATGAGTCACCACCACCTCCTCC--ACAAATAC-AAGTCACCACCACCG
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAA-TCACCACCACCA
* * * *
228147 CCTCCATACAAGTACAAGT---CTCCACCACCTCCATACAAGTATGAGT--CCACCTCCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * * * * *
228202 CATCCATACAAATACAAGT---CACCACCACCTCCTTATAAGTACGAGTCACCACCACCG
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * *
228259 CCTCCATACAAGTACGAGT--CCACCTCCAGCTCCATACAAGTAC-AAGTCACCACCA-C-
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAA-TCACCACCACCA
** * * * *
228315 CCTCCATACAAGTATGAGTCACCACCACCACCACCTCCGTACAAGTATGAGTCACCACCACCT
1 CCTCCATACAAGTACAAGT---CACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* ** *
228378 CCTCCGTACAAGTATGAGT---CACCACCTCCTCCATACAAGTAC-AAGTCACCACCACCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAA-TCACCACCACCA
* * * *
228435 CCTCCCTACAAGTACAAGTCA-CACCACCACCTCCCTACAAGTATGAGTCACCACCACCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * * *
228494 CCTCCGTACAAGTACGAGTCACCACCA-CACCTCCGTACAAGTACGAGTCACCACCA-CA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * * * *
228552 CCTCCGTACAAGTACGAGTCACCGCCTCCACCTCC-TACAAGTACGAGTCACCACCACCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * * * *
228611 CCTCCCTACAAGTACGAGTCACCACCACCACCTCCCTACAAGTACGAGTCACCACCACCT
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* ** * * *
228671 CCT-TAT-GTA-TACAAATCACC-CCACCTCCTCCATACAAGTACGAATCACCACCTCCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
*** * ** * * * *
228727 CCTCCATATGTGTACAAGTCACCCCCACC-TTTCCATACAAATATGAATCACCA-CTCCT
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * *** * *
228785 CCTCCATACAAATACGAA-TCACCACCTCCACC-CCATATGTGTAC-AAGTCACCTCCA-CT
1 CCTCCATACAAGTAC-AAGTCACCACCACCACCTCCATACAAGTACGAA-TCACCACCACCA
* * * * *
228843 CCTCCATACAAATATGAA-TCACCACCACCTCCTCCATACAAGTACGAATCACCACC-TCT
1 CCTCCATACAAGTA-CAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
** * * * * * * *
228902 CCTCCATAGTA-TACAAGTCACCTCCACCTCCACCATACAAATATGAATCACCACCTCCT
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* **** * * * * *
228961 TCTCCATATGTCTACAAGTCACCACCACCACCT-TATACAAATATGAGTCACCACAACCA
1 CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
* * *
229020 CCTCCCATATAAGTATGAA-TCACC-CCTCCACCTCCATA
1 CCT-CCATACAAGTA-CAAGTCACCACCACCACCTCCATA
229058 TGTGTACAAG
Statistics
Matches: 1043, Mismatches: 166, Indels: 117
0.79 0.13 0.09
Matches are distributed among these distances:
55 85 0.08
56 55 0.05
57 117 0.11
58 279 0.27
59 253 0.24
60 154 0.15
61 31 0.03
62 6 0.01
63 18 0.02
65 24 0.02
66 21 0.02
ACGTcount: A:0.31, C:0.41, G:0.09, T:0.19
Consensus pattern (60 bp):
CCTCCATACAAGTACAAGTCACCACCACCACCTCCATACAAGTACGAATCACCACCACCA
Found at i:229117 original size:30 final size:29
Alignment explanation
Indices: 228662--229110 Score: 114
Period size: 29 Copynumber: 15.3 Consensus size: 29
228652 GTACGAGTCA
* * * *
228662 CCACCACCTCCTTATGTATACAAATCACC
1 CCACCTCCTCCATATGTGTACAAGTCACC
***
228691 CCACCTCCTCCATACAAGTACGAA-TCACC
1 CCACCTCCTCCATATGTGTAC-AAGTCACC
* *
228720 ACCTCCACCTCCATATGTGTACAAGTCACCC
1 -CCACCTCCTCCATATGTGTACAAGTCA-CC
* **** *
228751 CCACCT-TTCCATACAAATATGAA-TCACC
1 CCACCTCCTCCATATGTGTA-CAAGTCACC
* * ****
228779 ACTCCTCCTCCATACAAATACGAA-TCACC
1 CCACCTCCTCCATATGTGTAC-AAGTCACC
* *
228808 ACCTCCACC-CCATATGTGTACAAGTCACC
1 -CCACCTCCTCCATATGTGTACAAGTCACC
**** *
228837 TCCA-CTCCTCCATACAAATATGAA-TCACC
1 -CCACCTCCTCCATATGTGTA-CAAGTCACC
***
228866 ACCACCTCCTCCATACAAGTACGAA-TCACC
1 -CCACCTCCTCCATATGTGTAC-AAGTCACC
* *
228896 ACC-TCTCCTCCATA-GTATACAAGTCACC
1 -CCACCTCCTCCATATGTGTACAAGTCACC
* **** *
228924 TCCACCTCCACCATACAAATATGAA-TCACC
1 -CCACCTCCTCCATATGTGTA-CAAGTCACC
* * *
228954 ACCTCCTTCTCCATATGTCTACAAGTCACC
1 -CCACCTCCTCCATATGTGTACAAGTCACC
* * **** **
228984 ACCACCACCT-TATACAAATATGAGTCACC
1 -CCACCTCCTCCATATGTGTACAAGTCACC
* * ** *
229013 ACAACCACCTCCCATATAAGTATGAA-TCACC
1 -CCACCTCCT-CCATATGTGTA-CAAGTCACC
* *
229044 CCTCCACCTCCATATGTGTACAAGTCACC
1 CCACCTCCTCCATATGTGTACAAGTCACC
*
229073 CCACCTCCTCCATATGTTTACAAGTCACC
1 CCACCTCCTCCATATGTGTACAAGTCACC
229102 TCCACCTCC
1 -CCACCTCC
229111 CACATATTAC
Statistics
Matches: 314, Mismatches: 83, Indels: 45
0.71 0.19 0.10
Matches are distributed among these distances:
27 2 0.01
28 23 0.07
29 164 0.52
30 108 0.34
31 16 0.05
32 1 0.00
ACGTcount: A:0.31, C:0.41, G:0.06, T:0.22
Consensus pattern (29 bp):
CCACCTCCTCCATATGTGTACAAGTCACC
Found at i:229120 original size:27 final size:27
Alignment explanation
Indices: 229044--229124 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 27
229034 ATGAATCACC
* *
229044 CCTCCACCT-CCATATGTGTACAAGTCA
1 CCTCCACCTCCCACATAT-TACAAGTCA
229071 CC-CCACCTCCTC-CATATGTTTACAAGTCA
1 CCTCCACCTCC-CACATA---TTACAAGTCA
229100 CCTCCACCTCCCACATATTACAAGT
1 CCTCCACCTCCCACATATTACAAGT
229125 AAACTTCGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
26 6 0.13
27 13 0.29
28 1 0.02
29 12 0.27
30 13 0.29
ACGTcount: A:0.26, C:0.41, G:0.07, T:0.26
Consensus pattern (27 bp):
CCTCCACCTCCCACATATTACAAGTCA
Found at i:231047 original size:20 final size:20
Alignment explanation
Indices: 231024--231078 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
231014 CACGGAATGT
*
231024 AAGATTATCAGTGAG-AATAA
1 AAGATTACCAG-GAGAAATAA
*
231044 AAGATTACCAGGGGAAATAA
1 AAGATTACCAGGAGAAATAA
231064 AAGATTACCA-GAGAA
1 AAGATTACCAGGAGAA
231079 TATGATTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.18
Consensus pattern (20 bp):
AAGATTACCAGGAGAAATAA
Found at i:231314 original size:44 final size:45
Alignment explanation
Indices: 231259--231351 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 45
231249 TTTAAAATTT
231259 AAATTCATAAAATTTATATAA-TTTTTTACAAAATTAAAAAGATA
1 AAATTCATAAAATTTATATAATTTTTTTACAAAATTAAAAAGATA
231303 AAATTCATAAAATTTATATAATTTTTTTTTACAAAATTAAAAAGATA
1 AAATTCATAAAATTTATATAA--TTTTTTTACAAAATTAAAAAGATA
231350 AA
1 AA
231352 TATGTTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
44 21 0.46
47 25 0.54
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (45 bp):
AAATTCATAAAATTTATATAATTTTTTTACAAAATTAAAAAGATA
Found at i:233916 original size:9 final size:10
Alignment explanation
Indices: 233881--233919 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
233871 GAAATTTATT
*
233881 ATTTTTTAAT
1 ATTTTTTAAG
*
233891 AGTGTTTTAAG
1 A-TTTTTTAAG
233902 ATTTTTTAAG
1 ATTTTTTAAG
233912 ATTTTTTA
1 ATTTTTTA
233920 TTTTTAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (10 bp):
ATTTTTTAAG
Found at i:235475 original size:53 final size:53
Alignment explanation
Indices: 235418--235523 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
235408 GAGAAAGTGG
235418 CTGATAGGGTTTGGTTTAGGCTGAGAGTGAAATAAATGAGTTAGGGTTAGAAT
1 CTGATAGGGTTTGGTTTAGGCTGAGAGTGAAATAAATGAGTTAGGGTTAGAAT
235471 CTGATAGGGTTTGGTTTAGGCTGAGAGTGAAATAAATGAGTTAGGGTTAGAAT
1 CTGATAGGGTTTGGTTTAGGCTGAGAGTGAAATAAATGAGTTAGGGTTAGAAT
235524 ATTTACCCTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (53 bp):
CTGATAGGGTTTGGTTTAGGCTGAGAGTGAAATAAATGAGTTAGGGTTAGAAT
Found at i:250708 original size:2 final size:2
Alignment explanation
Indices: 250701--250731 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
250691 AATATAAACC
250701 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 T
250732 TTCTATTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:252622 original size:15 final size:16
Alignment explanation
Indices: 252602--252631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
252592 GATTATCAGT
252602 GGGAAT-AAATTACTA
1 GGGAATAAAATTACTA
252617 GGGAATAAAATTACT
1 GGGAATAAAATTACT
252632 GAAAATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (16 bp):
GGGAATAAAATTACTA
Found at i:252807 original size:35 final size:35
Alignment explanation
Indices: 252760--252832 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
252750 ATAATATTAC
252760 AAATTATAAATA-TTATACATTTTCTTTAAAAAATT
1 AAATTATAAATATTTATACATTTT-TTTAAAAAATT
* *
252795 AAATTCAT-AATATTTATATATTTTTTTACAAAATT
1 AAATT-ATAAATATTTATACATTTTTTTAAAAAATT
252830 AAA
1 AAA
252833 AATATAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 22 0.65
36 12 0.35
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (35 bp):
AAATTATAAATATTTATACATTTTTTTAAAAAATT
Found at i:253779 original size:141 final size:138
Alignment explanation
Indices: 253517--253804 Score: 310
Period size: 141 Copynumber: 2.0 Consensus size: 138
253507 TTCTAAGAAG
* ** *
253517 AATAGTATTAAATACGTCATTTATAAAAACATATCAATTTATTGTTACATCATTTTGAAAAAAAA
1 AATAATATTAAATAAATCATTTATAAAAACATACCAATTTATTGTTACATCATTTTGAAAAAAAA
* * *
253582 ATACATTTGAAACAACTGGATACACAATACGTAGATAAATTCATATTTTCAATTTCAAACATATA
66 ATACATCTGAAAAAACTGGATACACAATACGTAGAGAAATTCATA-TTT--ATTTCAAACATATA
253647 TTTATTAATTT
128 TTTATTAATTT
* *
253658 AATAATATTAAATAAATCATTTATAAATACTATACCAA-TTATT-TCTACATCCTTTTGAAAAAA
1 AATAATATTAAATAAATCATTTATAAAAAC-ATACCAATTTATTGT-TACATCATTTTG----AA
* * *
253721 AAAATAAATACATCTGAAAAAACTTGATACACGATACTTAGAGAAATTCATATTTTTCAATTTCA
60 AAAA-AAATACATCTGAAAAAACTGGATACACAATACGTAGAGAAATTCATA--TTT--ATTTCA
* *
253786 AGCATATATTTGTTAATTT
120 AACATATATTTATTAATTT
253805 GATTCAAAGA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
140 1 0.01
141 42 0.34
142 6 0.05
145 6 0.05
146 41 0.33
147 29 0.23
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.38
Consensus pattern (138 bp):
AATAATATTAAATAAATCATTTATAAAAACATACCAATTTATTGTTACATCATTTTGAAAAAAAA
ATACATCTGAAAAAACTGGATACACAATACGTAGAGAAATTCATATTTATTTCAAACATATATTT
ATTAATTT
Found at i:260954 original size:20 final size:21
Alignment explanation
Indices: 260904--260955 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
260894 ATTATGACTA
*
260904 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTCCCAATT
**
260925 TCGCGTTGCGATTTCCCAA-T
1 TCGCAATGCGATTTCCCAATT
260945 TCGCAATGCGA
1 TCGCAATGCGA
260956 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTCCCAATT
Found at i:260968 original size:20 final size:20
Alignment explanation
Indices: 260945--261053 Score: 103
Period size: 21 Copynumber: 5.3 Consensus size: 20
260935 ATTTCCCAAT
* *
260945 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATTAGAAAA
* **
260965 TCGCAATGCGATACT-GACTA
1 TCGCAATGCGA-ATTAGAAAA
*
260985 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TTAGAAAA
*
261006 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TTAGAAAA
*
261027 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TTAGAAAA
261048 TCGCAA
1 TCGCAA
261054 CGCGGTACTG
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 25 0.32
21 52 0.67
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATTAGAAAA
Found at i:261010 original size:21 final size:21
Alignment explanation
Indices: 260984--261053 Score: 140
Period size: 21 Copynumber: 3.3 Consensus size: 21
260974 GATACTGACT
260984 ATCGCAATGCGAATTTGGAAA
1 ATCGCAATGCGAATTTGGAAA
261005 ATCGCAATGCGAATTTGGAAA
1 ATCGCAATGCGAATTTGGAAA
261026 ATCGCAATGCGAATTTGGAAA
1 ATCGCAATGCGAATTTGGAAA
261047 ATCGCAA
1 ATCGCAA
261054 CGCGGTACTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAATTTGGAAA
Found at i:261016 original size:41 final size:41
Alignment explanation
Indices: 260945--261114 Score: 166
Period size: 41 Copynumber: 4.1 Consensus size: 41
260935 ATTTCCCAAT
* * *
260945 TCGCAATGCGAA-TAAGTAAATCGCAATGCGATACTGACTA
1 TCGCAATGCGAATTTAGAAAATCGCAACGCGATACTGACTA
* * * **
260985 TCGCAATGCGAATTTGGAAAATCGCAATGCGA-ATTTGGAAAA
1 TCGCAATGCGAATTTAGAAAATCGCAACGCGATA-CT-GACTA
* *
261027 TCGCAATGCGAATTTGGAAAATCGCAACGCGGTACTGACTA
1 TCGCAATGCGAATTTAGAAAATCGCAACGCGATACTGACTA
* * * *
261068 TCGCAACGCG-ATAATACAAAATCGCAACGCGATACTGACTT
1 TCGCAATGCGAAT-TTAGAAAATCGCAACGCGATACTGACTA
261109 TCGCAA
1 TCGCAA
261115 CTCGATACTT
Statistics
Matches: 108, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
40 15 0.14
41 58 0.54
42 34 0.31
43 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (41 bp):
TCGCAATGCGAATTTAGAAAATCGCAACGCGATACTGACTA
Found at i:261072 original size:20 final size:20
Alignment explanation
Indices: 261047--261161 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
261037 AATTTGGAAA
*
261047 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGATACTGACT
* *
261067 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
261088 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
261108 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* ***
261128 TTCGCAACTAAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
261148 TTCGCAACGAGATA
1 ATCGCAACGCGATA
261162 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.75
21 15 0.19
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:261089 original size:83 final size:82
Alignment explanation
Indices: 260945--261099 Score: 195
Period size: 83 Copynumber: 1.9 Consensus size: 82
260935 ATTTCCCAAT
* * * * **
260945 TCGCAATGCGAATAAGTAAATCGCAATGCGATACTGACTATCGCAATGCGAATTTGGAAAATCGC
1 TCGCAATGCGAATAAGAAAATCGCAACGCGATACTGACTATCGCAACGCGAATATACAAAATCGC
*
261010 AATGCGAATTTGGAAAA
66 AACGCGAATTTGGAAAA
** *
261027 TCGCAATGCGAATTTGGAAAATCGCAACGCGGTACTGACTATCGCAACGCG-ATAATACAAAATC
1 TCGCAATGCGAA-TAAGAAAATCGCAACGCGATACTGACTATCGCAACGCGAAT-ATACAAAATC
261091 GCAACGCGA
64 GCAACGCGA
261100 TACTGACTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
82 14 0.23
83 47 0.77
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (82 bp):
TCGCAATGCGAATAAGAAAATCGCAACGCGATACTGACTATCGCAACGCGAATATACAAAATCGC
AACGCGAATTTGGAAAA
Found at i:261115 original size:41 final size:41
Alignment explanation
Indices: 261044--261181 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
261034 GCGAATTTGG
* *
261044 AAAATCGCAACGCGGTACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
261085 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
** *** *
261125 AATTTCGCAACTAAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
261166 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
261182 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:261376 original size:22 final size:22
Alignment explanation
Indices: 261348--261391 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
261338 CACTCTCTCA
261348 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
261370 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
261392 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:261694 original size:20 final size:20
Alignment explanation
Indices: 261640--261713 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
261630 AAATCGCAAC
* *
261640 GCGATTTT-ATTCTCTCGTT
1 GCGATTTTCATTTTCGCGTT
** **
261659 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
261679 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
261699 GCGATTTTCATTTTC
1 GCGATTTTCATTTTC
261714 AGAAACTATT
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 6 0.14
20 37 0.86
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.47
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:262431 original size:25 final size:24
Alignment explanation
Indices: 262377--262431 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
262367 TGTTTATTAT
* *
262377 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
262401 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
262427 TGTTT
1 TGTTT
262432 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:262671 original size:527 final size:527
Alignment explanation
Indices: 261678--262727 Score: 2055
Period size: 527 Copynumber: 2.0 Consensus size: 527
261668 AAATTCGCGT
261678 TGCGATTTTCATTTTCGTGTTGCGATTTTCATTTTCAGAAACTATTCTTCTTCTGCAAATTGAAA
1 TGCGATTTTCATTTTCGTGTTGCGATTTTCATTTTCAGAAACTATTCTTCTTCTGCAAATTGAAA
261743 CTTGAATGAATTGCATTACTTCAACCAAAAAACAAAGACAAATAAGTAATTCACAGTGTTGCAAA
66 CTTGAATGAATTGCATTACTTCAACCAAAAAACAAAGACAAATAAGTAATTCACAGTGTTGCAAA
261808 ATTAAGTTTGAAGAATAAACTACTACTCTTTATGTTTATTATTGTTTTTGGTATATCTTCACAGT
131 ATTAAGTTTGAAGAATAAACTACTACTCTTTATGTTTATTATTGTTTTTGGTATATCTTCACAGT
261873 GTAGTTTTTGGTATATCTAACTTAGGATGTTTATTGTTTTTGTAGAACTTTTATTCGGCTCAATT
196 GTAGTTTTTGGTATATCTAACTTAGGATGTTTATTGTTTTTGTAGAACTTTTATTCGGCTCAATT
261938 GACCTTAAGAAATAAAGTCAGCCTGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAA
261 GACCTTAAGAAATAAAGTCAGCCTGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAA
* *
262003 AAATGTTTGAGGATACTTGCTTTGGGCCATGGCTGGAAGTATAATATCCCGGTGGAGATGCGATG
326 AAATGTTTGAGGATACTTGCTTTGGGCCATGGCTGAAAGTACAATATCCCGGTGGAGATGCGATG
262068 TTGACACACCTGTTTCTTCAAACCATGACTAGGGATCTACCAGATACTATACAACGTCGTGATGA
391 TTGACACACCTGTTTCTTCAAACCATGACTAGGGATCTACCAGATACTATACAACGTCGTGATGA
*
262133 AGAGATATGGTTTGATTTTCCACCGGCGTATATGTGTTTTGGGCGGGAGAAGTTTTGCTTAATCA
456 AGAGATATGGTTTGATTTTCCACCGGCGTATATGTGTTTTGGGCAGGAGAAGTTTTGCTTAATCA
262198 CCGTATA
521 CCGTATA
262205 TGCGATTTTCATTTTCGTGTTGCGATTTTCATTTTCAGAAACTATTCTTCTTCTGCAAATTGAAA
1 TGCGATTTTCATTTTCGTGTTGCGATTTTCATTTTCAGAAACTATTCTTCTTCTGCAAATTGAAA
262270 CTTGAATGAATTGCATTACTTCAACCAAAAAACAAAGACAAATAAGTAATTCACAGTGTTGCAAA
66 CTTGAATGAATTGCATTACTTCAACCAAAAAACAAAGACAAATAAGTAATTCACAGTGTTGCAAA
*
262335 TTTAAGTTTGAAGAATAAACTACTACTCTTTATGTTTATTATTGTTTTTGGTATATCTTCACAGT
131 ATTAAGTTTGAAGAATAAACTACTACTCTTTATGTTTATTATTGTTTTTGGTATATCTTCACAGT
*
262400 GTAGTTTTTGGTATATCTAACTTAGTATGTTTATTGTTTTTGTAGAACTTTTATTCGGCTCAATT
196 GTAGTTTTTGGTATATCTAACTTAGGATGTTTATTGTTTTTGTAGAACTTTTATTCGGCTCAATT
262465 GACCTTAAGAAATAAAGTCAGCCTGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAA
261 GACCTTAAGAAATAAAGTCAGCCTGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAA
262530 AAATGTTTGAGGATACTTGCTTTGGGCCATGGCTGAAAGTACAATATCCCGGTGGAGATGCGATG
326 AAATGTTTGAGGATACTTGCTTTGGGCCATGGCTGAAAGTACAATATCCCGGTGGAGATGCGATG
262595 TTGACACACCTGTTTCTTCAAACCATGACTAGGGATCTACCAGATACTATACAACGTCGTGATGA
391 TTGACACACCTGTTTCTTCAAACCATGACTAGGGATCTACCAGATACTATACAACGTCGTGATGA
262660 AGAGATATGGTTTGATTTTCCACCGGCGTATATGTGTTTTGGGCAGGAGAAGTTTTGCTTAATCA
456 AGAGATATGGTTTGATTTTCCACCGGCGTATATGTGTTTTGGGCAGGAGAAGTTTTGCTTAATCA
262725 CCG
521 CCG
262728 GTCTACGCTT
Statistics
Matches: 518, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
527 518 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (527 bp):
TGCGATTTTCATTTTCGTGTTGCGATTTTCATTTTCAGAAACTATTCTTCTTCTGCAAATTGAAA
CTTGAATGAATTGCATTACTTCAACCAAAAAACAAAGACAAATAAGTAATTCACAGTGTTGCAAA
ATTAAGTTTGAAGAATAAACTACTACTCTTTATGTTTATTATTGTTTTTGGTATATCTTCACAGT
GTAGTTTTTGGTATATCTAACTTAGGATGTTTATTGTTTTTGTAGAACTTTTATTCGGCTCAATT
GACCTTAAGAAATAAAGTCAGCCTGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAA
AAATGTTTGAGGATACTTGCTTTGGGCCATGGCTGAAAGTACAATATCCCGGTGGAGATGCGATG
TTGACACACCTGTTTCTTCAAACCATGACTAGGGATCTACCAGATACTATACAACGTCGTGATGA
AGAGATATGGTTTGATTTTCCACCGGCGTATATGTGTTTTGGGCAGGAGAAGTTTTGCTTAATCA
CCGTATA
Found at i:263478 original size:18 final size:18
Alignment explanation
Indices: 263452--263499 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
263442 TCCACTTCGG
263452 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
263470 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
263488 GAGCCATCACCT
1 GAGCCATCACCT
263500 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:264138 original size:20 final size:19
Alignment explanation
Indices: 264087--264138 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
264077 GCGATTTGTG
***
264087 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGCCA
*
264106 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGCCA
264125 TTTCCGCGTTGCGA
1 TTT-CGCGTTGCGA
264139 AAGTAAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.38
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:264593 original size:41 final size:42
Alignment explanation
Indices: 264503--264593 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 42
264493 CCCGACTCAC
* * *
264503 CTGTCATTCCTCAACAGTCCCCTCCAATCATTCAAGAGGCCC
1 CTGTCATCCCTCAACAGTCCCCTCCAACCATTCAAGAGGCCA
* * * *
264545 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAACAGTCCCCTCCAACCATTCAAGAGGCCA
264586 CTGTCATC
1 CTGTCATC
264594 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 22 0.54
42 19 0.46
ACGTcount: A:0.23, C:0.42, G:0.13, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAACAGTCCCCTCCAACCATTCAAGAGGCCA
Found at i:264602 original size:41 final size:42
Alignment explanation
Indices: 264531--264623 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 42
264521 CCCCTCCAAT
*
264531 CATTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCCCCAC
1 CATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCCCCCAC
* * ** * *
264572 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCCCCCAC
*
264614 CATTCCAGAG
1 CATTCAAGAG
264624 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 24 0.57
42 18 0.43
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.19
Consensus pattern (42 bp):
CATTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCCCCCAC
Found at i:266135 original size:20 final size:20
Alignment explanation
Indices: 266110--266148 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
266100 ATGTTGAAGG
266110 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
266130 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
266149 GAGAAAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:266175 original size:19 final size:19
Alignment explanation
Indices: 266151--266218 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
266141 ATCGCAACGA
*
266151 GAAAATCGCAATTCGAAAT
1 GAAAATCGCAATGCGAAAT
266170 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
266189 GAAAATTGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
266203 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
266219 TTTTCTAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:266304 original size:40 final size:41
Alignment explanation
Indices: 266218--266313 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 41
266208 TCGCAATGCG
* * ***
266218 ATTTTCTAGTTGCAATAGCCATTTTCGCGTTGCGATTTTTC
1 ATTTTCAAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
*
266259 A-TTTCAAATTGCGATAGCCATTTTCGCGTTGCGA-TAGCC
1 ATTTTCAAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
*
266298 ATTTTCACGTTGCGAT
1 ATTTTCAAGTTGCGAT
266314 TTCCCCGTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.07
40 42 0.91
41 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (41 bp):
ATTTTCAAGTTGCGATAGCCATTTTCGCGTTGCGATTAGCC
Found at i:266311 original size:20 final size:20
Alignment explanation
Indices: 266226--266313 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
266216 CGATTTTCTA
* *
266226 GTTGCAATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCAC
*** *
266246 GTTGCGATTTTTCA-TTTCAA
1 GTTGCGA-TAGCCATTTTCAC
* *
266266 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCAC
266286 GTTGCGATAGCCATTTTCAC
1 GTTGCGATAGCCATTTTCAC
266306 GTTGCGAT
1 GTTGCGAT
266314 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 3 0.06
20 46 0.88
21 3 0.06
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCAC
Found at i:266552 original size:20 final size:20
Alignment explanation
Indices: 266527--266576 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
266517 TTGAAGATGA
266527 TTGCGATTTTCAGAATCT-CG
1 TTGCGATTTTCAGAAT-TGCG
***
266547 TTGCGAAAGTCAGAATTGCG
1 TTGCGATTTTCAGAATTGCG
266567 TTGCGATTTT
1 TTGCGATTTT
266577 GTATTATCTC
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATTGCG
Found at i:266647 original size:20 final size:21
Alignment explanation
Indices: 266603--266651 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
266593 ATAGTCAGTA
*
266603 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
266624 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
266644 TCGCATTG
1 TCGCATTG
266652 AGAATTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:267444 original size:24 final size:24
Alignment explanation
Indices: 267417--267470 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
267407 GTATTCAAAA
*
267417 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
267441 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
267465 TTTGAT
1 TTTGAT
267471 GATGTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:267662 original size:12 final size:12
Alignment explanation
Indices: 267645--267669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
267635 ATATAATCCT
267645 GAAGAAGAAAAA
1 GAAGAAGAAAAA
267657 GAAGAAGAAAAA
1 GAAGAAGAAAAA
267669 G
1 G
267670 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:270095 original size:14 final size:14
Alignment explanation
Indices: 270076--270112 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
270066 CATCAATTAA
270076 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
270090 ACAAATCACCTTTT
1 ACAAATCAACTTTT
270104 ACAAATCAA
1 ACAAATCAA
270113 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:271546 original size:42 final size:42
Alignment explanation
Indices: 271500--271579 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
271490 CGATGACAGT
* *
271500 GGCCTCTTGAACGGTAGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
271542 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
271580 CAGGCGAGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:271860 original size:17 final size:17
Alignment explanation
Indices: 271838--271870 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
271828 ATACTAACTT
271838 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
271855 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
271871 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:271981 original size:91 final size:90
Alignment explanation
Indices: 271801--271985 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
271791 ATTTCCAACT
*
271801 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAAC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAAC
*
271866 AGAATTGGCAGCAACTGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
271894 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAACA
*
271958 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
271985 T
1 T
271986 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAACAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:272230 original size:63 final size:63
Alignment explanation
Indices: 272155--272282 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
272145 AGTAGACACA
*
272155 TCCATACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGACC
1 TCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGACC
*
272218 TCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGGCC
1 TCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGACC
272281 TC
1 TC
272283 ATCACGTAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.22
Consensus pattern (63 bp):
TCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGACC
Found at i:273764 original size:20 final size:19
Alignment explanation
Indices: 273733--273793 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
273723 TATTTTGGTT
273733 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
273752 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
273773 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
273792 GA
1 GA
273794 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:273815 original size:33 final size:33
Alignment explanation
Indices: 273758--273854 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
273748 ACGAGATAAT
273758 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
273792 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* * **
273825 TAGAATCGCAACGCAAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
273855 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:274446 original size:20 final size:20
Alignment explanation
Indices: 274421--274532 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
274411 GCTATGTAAA
274421 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
274441 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
274461 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* ** *
274482 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATGTAAGTAT
* * *
274502 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
274522 TCGCATTGCGA
1 TCGCATTGCGA
274533 ATTATGAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:274545 original size:41 final size:41
Alignment explanation
Indices: 274413--274670 Score: 154
Period size: 41 Copynumber: 6.3 Consensus size: 41
274403 CGAATGGCGC
* * * *
274413 TATGTAAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGAT-TTACGTATTCGCATTGCGAAT
* * * * * *
274454 TACG-TATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* *
274495 TACT--TAATCGCGTTGCGATTTACGTATTCGCATTGCGAAT
1 TA-TGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
* * * *
274535 TATGAAAATCGCATCGCGA-ATACGTAAATCGCAATGCGAAT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* * *
274576 TAGGAAAATTGCATTGCGATAGT-CAGTA-TCGCATTGCG-AT
1 TATGAAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * * * *
274616 TTTCCAAATTCTCATTGCGATTTACTTATTCACATTGCGAAT
1 TAT-GAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
**
274658 TGGGAAAATCGCA
1 TATGAAAATCGCA
274671 ACGCGAAATT
Statistics
Matches: 166, Mismatches: 38, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
39 2 0.01
40 40 0.24
41 116 0.70
42 5 0.03
43 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
Found at i:274548 original size:21 final size:21
Alignment explanation
Indices: 274441--274594 Score: 91
Period size: 20 Copynumber: 7.5 Consensus size: 21
274431 ATAGTAAGAT
* * *
274441 TCGCATTGCGATTTACG-TAT
1 TCGCATTGCGAATTACGAAAA
* * ** *
274461 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGAATTACGAAAA
* **
274482 TCGCATTGCGATTTAC-TTAA
1 TCGCATTGCGAATTACGAAAA
* * * *
274502 TCGCGTTGCGATTTACG-TAT
1 TCGCATTGCGAATTACGAAAA
*
274522 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTACGAAAA
* *
274543 TCGCATCGCGAA-TACGTAAA
1 TCGCATTGCGAATTACGAAAA
* *
274563 TCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATTACGAAAA
*
274584 TTGCATTGCGA
1 TCGCATTGCGA
274595 TAGTCAGTAT
Statistics
Matches: 108, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
20 64 0.59
21 44 0.41
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGAATTACGAAAA
Found at i:274565 original size:61 final size:60
Alignment explanation
Indices: 274413--274573 Score: 175
Period size: 61 Copynumber: 2.6 Consensus size: 60
274403 CGAATGGCGC
274413 TATGTAAATCGCATTGCG-ATA-GTAAGATTCGCATTGCGATTTACGTATTCGCATTGCGAT
1 TATGTAAATCGCATTGCGAATACGTAA-A-TCGCATTGCGATTTACGTATTCGCATTGCGAT
* * * * * *
274473 TTTCCTAATTCGCATTGCGATTTAC-TTAATCGCGTTGCGATTTACGTATTCGCATTGCGAAT
1 TAT-GTAAATCGCATTGCGA-ATACGTAAATCGCATTGCGATTTACGTATTCGCATTGCG-AT
* * *
274535 TATGAAAATCGCATCGCGAATACGTAAATCGCAATGCGA
1 TATGTAAATCGCATTGCGAATACGTAAATCGCATTGCGA
274574 ATTAGGAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 11
0.75 0.14 0.10
Matches are distributed among these distances:
60 5 0.06
61 66 0.82
62 5 0.06
63 4 0.05
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (60 bp):
TATGTAAATCGCATTGCGAATACGTAAATCGCATTGCGATTTACGTATTCGCATTGCGAT
Found at i:274697 original size:21 final size:22
Alignment explanation
Indices: 274645--274697 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
274635 ATTTACTTAT
274645 TCACATTGCG-AATTGGGAAAA
1 TCACATTGCGAAATTGGGAAAA
* **
274666 TCGCAACGCGAAATT-GGAAAA
1 TCACATTGCGAAATTGGGAAAA
274687 TCACATTGCGA
1 TCACATTGCGA
274698 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
TCACATTGCGAAATTGGGAAAA
Found at i:283394 original size:23 final size:23
Alignment explanation
Indices: 283368--283436 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
283358 CACCACAGCT
*
283368 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
283391 CGTAGAATTGCACCGGAA-TGCCG
1 CGTAGAATTGCACC-GAAGTGCCA
*
283414 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
283437 TATAATAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.05
23 35 0.88
24 3 0.08
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:283623 original size:103 final size:103
Alignment explanation
Indices: 283452--283875 Score: 803
Period size: 103 Copynumber: 4.1 Consensus size: 103
283442 TAATGTCCAT
* * *
283452 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
283517 GACTTCACACATGTTCCAAAGAATGCATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
283555 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
283620 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
283658 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
283723 GACTTCACACATGTTCTAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
283761 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
283826 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
283864 AAGGACCACATA
1 AAGGACCACATA
283876 GACCCTCGAC
Statistics
Matches: 315, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 315 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:285240 original size:21 final size:21
Alignment explanation
Indices: 285215--285260 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
285205 TTCTGGTTCG
* * *
285215 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
285236 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
285257 CTTG
1 CTTG
285261 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:294328 original size:40 final size:41
Alignment explanation
Indices: 294243--294486 Score: 246
Period size: 41 Copynumber: 6.0 Consensus size: 41
294233 TTTCAAAAAT
* * * * **
294243 GCCGCTACAGGCTCATACTTTAGTAGCTTTTTTTTACAATA-
1 GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAA-AC
*
294284 GCCGCTATAGACCCATACTTTAGT-GCCTTTTTAAACAAAC
1 GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAAAC
* * *
294324 GCCGCTACAGAACCATACTATAGTGGCGTTTTTAAACAAAC
1 GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAAAC
** * * * *
294365 GCCTTTAAATACTCATCCTTTAGTGGCCTTTTTAAACAATA-
1 GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAA-AC
* *
294406 GCCGCTATAGACCCATACTTTAGT-GACTTTTTAAACAAAC
1 GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAAAC
* * *
294446 GCCGCTACAGAACCATACTTTAGTGG-CATTTTAGACAAAC
1 GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAAAC
294486 G
1 G
294487 TCGTTAAATA
Statistics
Matches: 168, Mismatches: 30, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
39 2 0.01
40 80 0.48
41 85 0.51
42 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (41 bp):
GCCGCTACAGACCCATACTTTAGTGGCCTTTTTAAACAAAC
Found at i:294407 original size:122 final size:121
Alignment explanation
Indices: 294254--294511 Score: 392
Period size: 122 Copynumber: 2.1 Consensus size: 121
294244 CCGCTACAGG
* * ** *
294254 CTCATACTTTAGTAGCTTTTTTTTACAATAGCCGCTATAGACCCATACTTTAGTGCCTTTTTAAA
1 CTCATACTTTAGTGGCCTTTTTAAACAATAGCCGCTATAGACCCATACTTTAGTGACTTTTTAAA
* *
294319 CAAACGCCGCTACAGAACCATACTATAGTGGCGTTTTTAAACAAACGCCTTTAAATA
66 CAAACGCCGCTACAGAACCATACTATAGTGGC-ATTTTAAACAAACGCCGTTAAATA
*
294376 CTCATCCTTTAGTGGCCTTTTTAAACAATAGCCGCTATAGACCCATACTTTAGTGACTTTTTAAA
1 CTCATACTTTAGTGGCCTTTTTAAACAATAGCCGCTATAGACCCATACTTTAGTGACTTTTTAAA
* * *
294441 CAAACGCCGCTACAGAACCATACTTTAGTGGCATTTTAGACAAACGTCGTTAAATA
66 CAAACGCCGCTACAGAACCATACTATAGTGGCATTTTAAACAAACGCCGTTAAATA
294497 -TGCATACTTTAGTGG
1 CT-CATACTTTAGTGG
294512 TATTTTCTAA
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
120 1 0.01
121 32 0.26
122 90 0.73
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (121 bp):
CTCATACTTTAGTGGCCTTTTTAAACAATAGCCGCTATAGACCCATACTTTAGTGACTTTTTAAA
CAAACGCCGCTACAGAACCATACTATAGTGGCATTTTAAACAAACGCCGTTAAATA
Found at i:296717 original size:41 final size:41
Alignment explanation
Indices: 296658--296778 Score: 109
Period size: 41 Copynumber: 3.0 Consensus size: 41
296648 AATTTTATTT
* * * *
296658 AAACGCCACTAAAGACTCGTACTTTAGTGATATTTTTATAT
1 AAACGCCATTAAAAACTCGTACTTTAGTGACATTTTTATAC
* * * * * *
296699 AAAC-CCTATTATATACTCGTATTTTAATGGCGTTTTTATAC
1 AAACGCC-ATTAAAAACTCGTACTTTAGTGACATTTTTATAC
* * *
296740 AAACGCCGTTAAAAACTCGTACTTTAGTGGCGTTTTTAT
1 AAACGCCATTAAAAACTCGTACTTTAGTGACATTTTTAT
296779 GCCGTAATAG
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 2 0.03
41 60 0.94
42 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (41 bp):
AAACGCCATTAAAAACTCGTACTTTAGTGACATTTTTATAC
Found at i:306542 original size:18 final size:18
Alignment explanation
Indices: 306519--306553 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
306509 TTCCATCCGG
*
306519 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
306537 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
306554 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:307482 original size:149 final size:149
Alignment explanation
Indices: 307232--307546 Score: 603
Period size: 149 Copynumber: 2.1 Consensus size: 149
307222 TATAATTGCA
* *
307232 CCGAAGTACCACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
307297 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
307362 CACAGAATATATATATATC
131 CACAGAATATATATATATC
307381 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
307446 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
*
307511 CATAGAATATATATATATC
131 CACAGAATATATATATATC
307530 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
307547 CCCTCTACCC
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 163 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:308108 original size:63 final size:63
Alignment explanation
Indices: 308002--308160 Score: 212
Period size: 63 Copynumber: 2.5 Consensus size: 63
307992 TAATGGAGGC
* * * *
308002 ATGCATCGATGCACTTCTGATGCATCGATGCACTGAGGGCATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTTCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
* ** **
308065 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTTCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
*
308128 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTTCTTATGCATCGATGCAC
308161 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 80 0.95
64 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTTCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:308152 original size:19 final size:20
Alignment explanation
Indices: 308128--308165 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
308118 ATTTAAATTA
308128 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
308147 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
308166 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:314301 original size:23 final size:23
Alignment explanation
Indices: 314275--314320 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
314265 CACCACAGCT
*
314275 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
314298 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
314321 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:314537 original size:149 final size:149
Alignment explanation
Indices: 314300--314601 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 149
314290 AAGTGCCACG
314300 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
314365 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
314430 TATATCCCGAAAGACCGCA
131 TATATCCCGAAAGACCGCA
*
314449 TAGAATTGCACTGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
314514 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
* *
314579 TATATCCCGAAGGACCGCG
131 TATATCCCGAAAGACCGCA
314598 TAGA
1 TAGA
314602 CCCTCTACCC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
TATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
TATATCCCGAAAGACCGCA
Found at i:315143 original size:63 final size:63
Alignment explanation
Indices: 315057--315215 Score: 212
Period size: 63 Copynumber: 2.5 Consensus size: 63
315047 TAATGGAGGC
* * * * *
315057 ATGCATCGATGTACTTCTGATGCATCGATGCACTGAGGGCATTCGATGTTCAT-TTTATTATAA
1 ATGCATCGATGCACTTCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AATAA
* ** *
315120 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTTCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAATAA
*
315183 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTTCTTATGCATCGATGCAC
315216 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 80 0.95
64 4 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTTCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAATAA
Found at i:315207 original size:19 final size:20
Alignment explanation
Indices: 315183--315220 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
315173 ATTTAAATTA
315183 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
315202 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
315221 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:317241 original size:18 final size:18
Alignment explanation
Indices: 317218--317255 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
317208 CAATGGTCAA
317218 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
317236 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
317254 CG
1 CG
317256 TGACCGGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.50, T:0.16
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:319175 original size:21 final size:18
Alignment explanation
Indices: 319128--319180 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 18
319118 TCAAAGTTTT
319128 GGTCAACAGTGGTCAACGGC
1 GGTCAAC-G-GGTCAACGGC
319148 GGTCAACGGGTCAACGGTTC
1 GGTCAACGGGTCAACGG--C
319168 GAGTCAACGGGTC
1 G-GTCAACGGGTC
319181 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.30
19 1 0.03
20 9 0.30
21 11 0.37
ACGTcount: A:0.23, C:0.25, G:0.36, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCAACGGC
Found at i:319203 original size:13 final size:13
Alignment explanation
Indices: 319154--319204 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
319144 CGGCGGTCAA
*
319154 CGGGTCAACGGTT
1 CGGGTCAACGGGT
*
319167 CGAGTCAACGGGT
1 CGGGTCAACGGGT
319180 CGGGT---CGGGT
1 CGGGTCAACGGGT
*
319190 CGGGTAAACGGGT
1 CGGGTCAACGGGT
319203 CG
1 CG
319205 AGTCGGGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 10 0.31
13 22 0.69
ACGTcount: A:0.16, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:320305 original size:21 final size:18
Alignment explanation
Indices: 320258--320310 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 18
320248 TCAAAGTTTT
320258 GGTCAACAGTGGTCAACAGC
1 GGTCAAC-G-GGTCAACAGC
320278 GGTCAACGGGTCAACGAGTC
1 GGTCAACGGGTCAAC-AG-C
320298 GAGTCAACGGGTC
1 G-GTCAACGGGTC
320311 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 9 0.30
21 11 0.37
ACGTcount: A:0.26, C:0.25, G:0.34, T:0.15
Consensus pattern (18 bp):
GGTCAACGGGTCAACAGC
Found at i:320333 original size:13 final size:13
Alignment explanation
Indices: 320284--320334 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
320274 CAGCGGTCAA
*
320284 CGGGTCAACGAGT
1 CGGGTCAACGGGT
*
320297 CGAGTCAACGGGT
1 CGGGTCAACGGGT
320310 CGGGT---CGGGT
1 CGGGTCAACGGGT
*
320320 CGGGTAAACGGGT
1 CGGGTCAACGGGT
320333 CG
1 CG
320335 AGTCGGGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 10 0.31
13 22 0.69
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:321914 original size:58 final size:53
Alignment explanation
Indices: 321851--321960 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 53
321841 TTTTTGTCCC
*
321851 ATAATTTGTCTTTCATATTGATTATATATACACATAATTTTAAGAGATATATTTAACA
1 ATAATTTGTCTCTCATATTG---A-ATATACACATAA-TTTAAGAGATATATTTAACA
* * *
321909 ATAATTTGTGTCTCATATTGACTATACACATAATTTAGGAGATATATTTAAC
1 ATAATTTGTCTCTCATATTGAATATACACATAATTTAAGAGATATATTTAAC
321961 TAAAGAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 18 0.38
54 11 0.23
55 1 0.02
58 18 0.38
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (53 bp):
ATAATTTGTCTCTCATATTGAATATACACATAATTTAAGAGATATATTTAACA
Found at i:323758 original size:19 final size:19
Alignment explanation
Indices: 323722--323763 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
323712 TTATTAAAAC
323722 TTAA-AAAATATTTAAATT
1 TTAATAAAATATTTAAATT
323740 TTAATAAAA-ATTTACAATT
1 TTAATAAAATATTTA-AATT
*
323759 ATAAT
1 TTAAT
323764 CGTAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATAAAATATTTAAATT
Found at i:324583 original size:19 final size:19
Alignment explanation
Indices: 324526--324583 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
324516 AATTAATTTT
*
324526 TTAAAATTTAAAAACTATAA
1 TTAAAATATAAAAACTA-AA
*
324546 --AATAATATAAATA-TCAAA
1 TTAA-AATATAAAAACT-AAA
324564 TTAAAATATAAAAACTAAA
1 TTAAAATATAAAAACTAAA
324583 T
1 T
324584 CTAATTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 11
0.68 0.07 0.25
Matches are distributed among these distances:
18 5 0.17
19 22 0.73
20 3 0.10
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAAAATATAAAAACTAAA
Found at i:329355 original size:9 final size:9
Alignment explanation
Indices: 329323--329401 Score: 86
Period size: 9 Copynumber: 8.3 Consensus size: 9
329313 CTGCTGGAAA
329323 ACCGGTTTG
1 ACCGGTTTG
*
329332 ACCAGTTTTG
1 ACC-GGTTTG
329342 AACCGGTTTG
1 -ACCGGTTTG
*
329352 ACCGGTTCG
1 ACCGGTTTG
329361 AACCGGTTTG
1 -ACCGGTTTG
*
329371 ACCGGTCTG
1 ACCGGTTTG
329380 AACCGGTTTG
1 -ACCGGTTTG
*
329390 ACCGGTCTG
1 ACCGGTTTG
329399 ACC
1 ACC
329402 CGACCCGACT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 30 0.51
10 26 0.44
11 3 0.05
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:329396 original size:19 final size:19
Alignment explanation
Indices: 329322--329399 Score: 113
Period size: 19 Copynumber: 4.1 Consensus size: 19
329312 GCTGCTGGAA
* *
329322 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
329342 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
329361 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
329380 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
329399 A
1 A
329400 CCCGACCCGA
Statistics
Matches: 55, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
18 1 0.02
19 40 0.73
20 14 0.25
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:329419 original size:17 final size:17
Alignment explanation
Indices: 329397--329435 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
329387 TTGACCGGTC
*
329397 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
*
329414 TGACCCGACTCGACCGT
1 TGACCCGACCCGACCGT
329431 TGACC
1 TGACC
329436 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:333570 original size:43 final size:43
Alignment explanation
Indices: 333509--333594 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
333499 CAGTGGAGGA
*
333509 AACTGGGTGGCATCTTCTGGTGAAATTGAGTGTTATAAAGTTC
1 AACTGGGTGGCATCTTCTGGTGAAATTGAGCGTTATAAAGTTC
*
333552 AACTGGGTGGCATCTTCTGGTTAAATTGAGCGTTATAAAGTTC
1 AACTGGGTGGCATCTTCTGGTGAAATTGAGCGTTATAAAGTTC
333595 GCTTGGTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.35
Consensus pattern (43 bp):
AACTGGGTGGCATCTTCTGGTGAAATTGAGCGTTATAAAGTTC
Found at i:345688 original size:22 final size:22
Alignment explanation
Indices: 345646--345688 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
345636 AATCTAAATC
* *
345646 TATTTGAATGTGAAATCATTTA
1 TATTTGAATGTCAAATAATTTA
345668 TATTTGAATG-CATAATAATTT
1 TATTTGAATGTCA-AATAATTT
345689 TTAAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (22 bp):
TATTTGAATGTCAAATAATTTA
Found at i:363118 original size:2 final size:2
Alignment explanation
Indices: 363111--363140 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
363101 AACTCACATC
363111 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
363141 ACAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:366567 original size:22 final size:23
Alignment explanation
Indices: 366529--366573 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
366519 TAAAATATCT
*
366529 AAATTAATTAAATTTC-ATAAAA
1 AAATTAATCAAATTTCAATAAAA
366551 AAATTAAATCAAA-TTCAATAAAA
1 AAATT-AATCAAATTTCAATAAAA
366574 GAATATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATTAATCAAATTTCAATAAAA
Found at i:378369 original size:15 final size:16
Alignment explanation
Indices: 378341--378373 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
378331 AAAATCTTTC
378341 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
378357 TTTCCCG-TCTAGATT
1 TTTCCCGTTCTAGATT
378372 TT
1 TT
378374 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.24, G:0.12, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:379150 original size:16 final size:17
Alignment explanation
Indices: 379123--379157 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
379113 TATCGCCGAC
379123 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
379140 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
379156 CG
1 CG
379158 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:387836 original size:29 final size:29
Alignment explanation
Indices: 387801--387882 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
387791 AAACTAAATT
*
387801 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
387830 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
387859 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
387883 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:392607 original size:29 final size:29
Alignment explanation
Indices: 392572--392653 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
392562 AAACTAAATT
*
392572 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
392601 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
392630 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
392654 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:403156 original size:2 final size:2
Alignment explanation
Indices: 403149--403182 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
403139 TACTGGCATA
403149 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
403183 AAGAACATGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.