Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 74 of 193
Found at i:23747085 original size:3 final size:3
Alignment explanation
Indices: 23747079--23747140 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
23747069 TATCCGTAGT
* * * * * *
23747079 AGC AGC ACC AGT AGC AGC AGC AGC AGC TGC AGG AGC ATC AGC AGT AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC AGC
* *
23747127 AGT AGC AGC CGC AG
1 AGC AGC AGC AGC AG
23747141 GTATCTAGTC
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.31, C:0.29, G:0.32, T:0.08
Consensus pattern (3 bp):
AGC
Found at i:23748271 original size:16 final size:15
Alignment explanation
Indices: 23748235--23748270 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
23748225 TCAAACTAAT
23748235 ATTTTTAAAACATCC
1 ATTTTTAAAACATCC
* *
23748250 ATTTTTAAAATATTC
1 ATTTTTAAAACATCC
23748265 ATTTTT
1 ATTTTT
23748271 TCTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTAAAACATCC
Found at i:23749996 original size:21 final size:21
Alignment explanation
Indices: 23749945--23749985 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
23749935 AGCCTAGACC
*
23749945 ATGTGGTTACTCCACACGCCG
1 ATGTGGCTACTCCACACGCCG
23749966 ATGTGGCTACTCCACACGCC
1 ATGTGGCTACTCCACACGCC
23749986 CGTGTGTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.37, G:0.22, T:0.22
Consensus pattern (21 bp):
ATGTGGCTACTCCACACGCCG
Found at i:23751885 original size:3 final size:3
Alignment explanation
Indices: 23751877--23751937 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
23751867 AAGCAAAACG
23751877 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23751925 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
23751938 ATCATTAACG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:23752873 original size:45 final size:45
Alignment explanation
Indices: 23752822--23752963 Score: 212
Period size: 45 Copynumber: 3.2 Consensus size: 45
23752812 AGCGAAATGT
* * *
23752822 ATATCATGTATGTAGTATAGCATAATAAATCAAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATAAATCAAATAATATTTACC
* *
23752867 ATATCATACATATCGTATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATAAATCAAATAATATTTACC
* * *
23752912 ATATCATGCATATCGTATAGCATACTTAATCAAATAATATTTATC
1 ATATCATGCATATCGTATAGCATAATAAATCAAATAATATTTACC
23752957 ATATCAT
1 ATATCAT
23752964 AATTAATCAA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (45 bp):
ATATCATGCATATCGTATAGCATAATAAATCAAATAATATTTACC
Found at i:23752964 original size:29 final size:29
Alignment explanation
Indices: 23752932--23752992 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
23752922 TATCGTATAG
* * *
23752932 CATACTTAATCAAATAATATTTATCATAT
1 CATAATTAATCAAATAATACTTACCATAT
*
23752961 CATAATTAATCAAATAGTACTTACCATAT
1 CATAATTAATCAAATAATACTTACCATAT
23752990 CAT
1 CAT
23752993 GCATATCGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (29 bp):
CATAATTAATCAAATAATACTTACCATAT
Found at i:23752975 original size:74 final size:74
Alignment explanation
Indices: 23752887--23753038 Score: 232
Period size: 74 Copynumber: 2.1 Consensus size: 74
23752877 TATCGTATAG
* * *
23752887 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGCATACTTAATCAAATAATAT
1 CATAATCAATCAAATAATACTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
*
23752952 TTATCATAT
66 TTACCATAT
* * * *
23752961 CATAATTAATCAAATAGTACTTACCATATCATGCATATCGTATTGTATAATCAATCAAATAATAT
1 CATAATCAATCAAATAATACTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
23753026 TTACCATAT
66 TTACCATAT
23753035 CATA
1 CATA
23753039 TATATCGTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (74 bp):
CATAATCAATCAAATAATACTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
TTACCATAT
Found at i:23753017 original size:45 final size:45
Alignment explanation
Indices: 23752961--23753612 Score: 841
Period size: 45 Copynumber: 14.8 Consensus size: 45
23752951 TTTATCATAT
* * * *
23752961 CATAATTAATCAAATAGTACTTACCATATCATGCATATCGTATTG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* ** *
23753006 TATAATCAATCAAATAATATTTACCATATCATATATATCGTATAA
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* * ** *
23753051 CATAATCAATCAATTAATATTTATCATATCATTTATATCGTATAA
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* * * * *
23753096 CATACTTAATCAAATAATATTTACCATATCATGCACACCTTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* * *
23753141 CATAATCAATCGAATAA-AATTATCATATCATGCATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
23753185 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
23753230 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* *
23753275 CATAATCAATCAAATAATATTTA-C-TAT-AT-CA-A--GCATAT
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
23753313 CAT-AT-AAT--AAT-A--TTTACCATATCATGCATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* *
23753351 CATAATCAATCAAATAATATTTACCATATCATGCATACCGTATAA
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* * *
23753396 CATAGTCAATCAAATAATATTTACCATATCATGAATATCGTATAT
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
* *
23753441 CATAATTAATCAAATAATATTTACCATATCATGCATGTCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
** *
23753486 TGTAATCAATCAAATAATATTTACCATATCATGAATATCGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
*
23753531 CATAATCAATCAAATAATATTTACCATATCATGAATA-CTGTATAG
1 CATAATCAATCAAATAATATTTACCATATCATGCATATC-GTATAG
* * * *
23753576 TAGAGTCAATCAAATAATATTTATCATATCATGCATA
1 CATAATCAATCAAATAATATTTACCATATCATGCATA
23753613 CCATTAAGGG
Statistics
Matches: 531, Mismatches: 60, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
31 4 0.01
32 1 0.00
33 4 0.01
34 5 0.01
35 2 0.00
36 4 0.01
37 2 0.00
38 14 0.03
39 2 0.00
40 4 0.01
41 2 0.00
42 5 0.01
43 4 0.01
44 40 0.08
45 438 0.82
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (45 bp):
CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
Found at i:23753325 original size:31 final size:31
Alignment explanation
Indices: 23753287--23753349 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
23753277 TAATCAATCA
*
23753287 AATAATATTTACTATATCAAGCATATCATAT
1 AATAATATTTACCATATCAAGCATATCATAT
* *
23753318 AATAATATTTACCATATCATGCATATCGTAT
1 AATAATATTTACCATATCAAGCATATCATAT
23753349 A
1 A
23753350 GCATAATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (31 bp):
AATAATATTTACCATATCAAGCATATCATAT
Found at i:23753333 original size:76 final size:76
Alignment explanation
Indices: 23753242--23753387 Score: 274
Period size: 76 Copynumber: 1.9 Consensus size: 76
23753232 TAATCAATCA
*
23753242 AATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACTATATCAA
1 AATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCAA
23753307 GCATATCATAT
66 GCATATCATAT
*
23753318 AATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCAT
1 AATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCAA
23753383 GCATA
66 GCATA
23753388 CCGTATAACA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (76 bp):
AATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCAA
GCATATCATAT
Found at i:23758868 original size:45 final size:45
Alignment explanation
Indices: 23758797--23758912 Score: 182
Period size: 45 Copynumber: 2.6 Consensus size: 45
23758787 CAATTCGATG
23758797 TCAATCAAATAATATTTACCATATCATGCATA-CTGTATAGCATAA
1 TCAATCAAATAATATTTACCATATCATGCATATC-GTATAGCATAA
* *
23758842 TTAATCCAATAATATTTATCC-TATCATGCATATCGTATAGCATAA
1 TCAATCAAATAATATTTA-CCATATCATGCATATCGTATAGCATAA
23758887 TCAATCAAATAATATTTACCATATCA
1 TCAATCAAATAATATTTACCATATCA
23758913 CCGGTTTGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
44 2 0.03
45 59 0.92
46 3 0.05
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.35
Consensus pattern (45 bp):
TCAATCAAATAATATTTACCATATCATGCATATCGTATAGCATAA
Found at i:23759853 original size:29 final size:29
Alignment explanation
Indices: 23759736--23759855 Score: 89
Period size: 29 Copynumber: 4.0 Consensus size: 29
23759726 TAAATATTTG
* * *
23759736 GAGCATTATTGTAGTTTTTCCAAAGTTTTGA
1 GAGCATTATTGTAATTTTACTAAAG--TTGA
* **
23759767 GGGTTTTATTGTAATTTTACTAAAGTTGA
1 GAGCATTATTGTAATTTTACTAAAGTTGA
* ** * *
23759796 GGGTGTTTACTATAATTTTAC-AAATGTTGA
1 GAG-CATTATTGTAATTTTACTAAA-GTTGA
*
23759826 GAGCATTATTGTAATTTTGCTAAAGTTGA
1 GAGCATTATTGTAATTTTACTAAAGTTGA
23759855 G
1 G
23759856 GGTGTTTTTG
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
29 28 0.39
30 24 0.34
31 19 0.27
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (29 bp):
GAGCATTATTGTAATTTTACTAAAGTTGA
Found at i:23759870 original size:29 final size:30
Alignment explanation
Indices: 23759763--23759870 Score: 116
Period size: 29 Copynumber: 3.7 Consensus size: 30
23759753 TTCCAAAGTT
23759763 TTGAGGGT-TTTATTGTAATTTTACTAAAG
1 TTGAGGGTGTTTATTGTAATTTTACTAAAG
* *
23759792 TTGAGGGTGTTTACTATAATTTTAC-AAATG
1 TTGAGGGTGTTTATTGTAATTTTACTAAA-G
* ** *
23759822 TTGAGAG-CATTATTGTAATTTTGCTAAAG
1 TTGAGGGTGTTTATTGTAATTTTACTAAAG
*
23759851 TTGAGGGTGTTT-TTGCAATT
1 TTGAGGGTGTTTATTGTAATT
23759871 AAACCATTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
29 37 0.59
30 26 0.41
ACGTcount: A:0.27, C:0.06, G:0.22, T:0.45
Consensus pattern (30 bp):
TTGAGGGTGTTTATTGTAATTTTACTAAAG
Found at i:23767170 original size:15 final size:15
Alignment explanation
Indices: 23767150--23767184 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
23767140 TATTTTGTTC
23767150 GAAAAAAATTGAAAA
1 GAAAAAAATTGAAAA
23767165 GAAAAAAATTGAAAA
1 GAAAAAAATTGAAAA
23767180 -AAAAA
1 GAAAAA
23767185 TTGAATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (15 bp):
GAAAAAAATTGAAAA
Found at i:23767182 original size:11 final size:12
Alignment explanation
Indices: 23767151--23767189 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
23767141 ATTTTGTTCG
23767151 AAAAAAATTGAAAA
1 AAAAAAATTG--AA
23767165 GAAAAAAATTGAA
1 -AAAAAAATTGAA
23767178 AAAAAAATTGAA
1 AAAAAAATTGAA
23767190 TTGAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
15 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:23767196 original size:15 final size:13
Alignment explanation
Indices: 23767150--23767199 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 13
23767140 TATTTTGTTC
23767150 GAAAAAAATTGAAAA
1 GAAAAAAATTG--AA
23767165 GAAAAAAATTGAA
1 GAAAAAAATTGAA
23767178 -AAAAAAATTGAA
1 GAAAAAAATTGAA
23767190 TTGAAAAAAA
1 --GAAAAAAA
23767200 CGAAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.38
13 2 0.06
15 18 0.56
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
GAAAAAAATTGAA
Found at i:23767209 original size:27 final size:27
Alignment explanation
Indices: 23767151--23767210 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
23767141 ATTTTGTTCG
*
23767151 AAAAAAATTGAAAAGAAAAAAATTGAA
1 AAAAAAATTGAAAAGAAAAAAATCGAA
**
23767178 AAAAAAATTGAATTGAAAAAAA-CGAA
1 AAAAAAATTGAAAAGAAAAAAATCGAA
*
23767204 AGAAAAA
1 AAAAAAA
23767211 GAAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 9 0.31
27 20 0.69
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (27 bp):
AAAAAAATTGAAAAGAAAAAAATCGAA
Found at i:23774164 original size:31 final size:32
Alignment explanation
Indices: 23774121--23774199 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
23774111 CCTAAATTTT
* * *
23774121 TATATTATTTTTAACTTTTTATTTATA-AAATA
1 TATATTATTTTTAA-TTATTAATTACATAAATA
*
23774153 T-TATTAATTTTAATTATTAATTACATAAATA
1 TATATTATTTTTAATTATTAATTACATAAATA
23774184 TATATTATTTTTAATT
1 TATATTATTTTTAATT
23774200 TATAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 9 0.22
31 17 0.43
32 14 0.35
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (32 bp):
TATATTATTTTTAATTATTAATTACATAAATA
Found at i:23774840 original size:198 final size:200
Alignment explanation
Indices: 23774497--23775020 Score: 1007
Period size: 198 Copynumber: 2.6 Consensus size: 200
23774487 AACAATAAAA
*
23774497 TAAAAACCTAATGTGTAACAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
1 TAAAGACCTAATGTGTAACAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
23774562 AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTACACTC
66 AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTACACTC
23774627 TTATTTTTCTAAGTTGTTCACTTATTGTCTTCATCCTCTTAA-T-TTATGAAAAAAATTGAAAAC
131 TTATTTTTCTAAGTTGTTCACTTATTGTCTTCATCCTCTTAATTATTATGAAAAAAATTGAAAAC
23774690 TAACC
196 TAACC
*
23774695 TAAAGACCTAATGTGTAATAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
1 TAAAGACCTAATGTGTAACAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
23774760 AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTACACTC
66 AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTACACTC
23774825 TTATTTTTCTAAGTTGTTCACTTATTGTCTTCATCCTCTTAATTTATTATGAAAAAAATTGAAAA
131 TTATTTTTCTAAGTTGTTCACTTATTGTCTTCATCCTCTTAA-TTATTATGAAAAAAATTGAAAA
23774890 CTAACC
195 CTAACC
23774896 TAAAGACCTAATGTGTAACAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
1 TAAAGACCTAATGTGTAACAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
23774961 AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTA
66 AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTA
23775021 TTGAAGTTTG
Statistics
Matches: 320, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
198 170 0.53
200 1 0.00
201 149 0.47
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (200 bp):
TAAAGACCTAATGTGTAACAGCCCGATTTTCAAAGATTGTCGAAAACAGTGATTTTGGGATCACA
AATCTAGCGAGTTGTTGTTAATTTATTTATTTTAATATTTATGCTGTTATATGCATTGTACACTC
TTATTTTTCTAAGTTGTTCACTTATTGTCTTCATCCTCTTAATTATTATGAAAAAAATTGAAAAC
TAACC
Found at i:23786409 original size:27 final size:27
Alignment explanation
Indices: 23786379--23786437 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
23786369 TAATAGGCAT
*
23786379 TTCATACTTAGTATTTATATTTTCTAA
1 TTCATACTTACTATTTATATTTTCTAA
23786406 TTCATACTTACTATTTATATTTTCTAA
1 TTCATACTTACTATTTATATTTTCTAA
*
23786433 CTCAT
1 TTCAT
23786438 TGTTGTTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.02, T:0.54
Consensus pattern (27 bp):
TTCATACTTACTATTTATATTTTCTAA
Found at i:23791814 original size:15 final size:16
Alignment explanation
Indices: 23791796--23791834 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
23791786 CTAAAGTATT
*
23791796 CTAAATTAAATTA-AA
1 CTAAATTAAACTATAA
*
23791811 CTAAATTAAACTATGA
1 CTAAATTAAACTATAA
23791827 CTAAATTA
1 CTAAATTA
23791835 TATTCCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (16 bp):
CTAAATTAAACTATAA
Found at i:23797064 original size:18 final size:18
Alignment explanation
Indices: 23797043--23797112 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
23797033 TCAATCTCCA
23797043 CAAGATCTTCTTCTTCCT
1 CAAGATCTTCTTCTTCCT
* * *
23797061 CAAGATCCTCGTCTTCTT
1 CAAGATCTTCTTCTTCCT
* *
23797079 CAGGATCTTCTTCTTTCT
1 CAAGATCTTCTTCTTCCT
* *
23797097 CAGGCTCTTCTTCTTC
1 CAAGATCTTCTTCTTC
23797113 TTTAGCTTGC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.44
Consensus pattern (18 bp):
CAAGATCTTCTTCTTCCT
Found at i:23815287 original size:19 final size:19
Alignment explanation
Indices: 23815243--23815289 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
23815233 GTTTTCATGA
*
23815243 ATTTTTATTTTGTCATGGC
1 ATTTTTGTTTTGTCATGGC
*
23815262 ATTTTTGTTTTGTCATTGC
1 ATTTTTGTTTTGTCATGGC
23815281 ATTTTTGTT
1 ATTTTTGTT
23815290 AAGTTAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.09, G:0.15, T:0.64
Consensus pattern (19 bp):
ATTTTTGTTTTGTCATGGC
Found at i:23815892 original size:16 final size:16
Alignment explanation
Indices: 23815863--23815905 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 16
23815853 TCACTCGAAA
23815863 AAGAAAAATGAGAAAAAGG
1 AAGAAAAA-GA-AAAAA-G
23815882 AAGAAAAAGAAAAAAG
1 AAGAAAAAGAAAAAAG
23815898 AAGAAAAA
1 AAGAAAAA
23815906 AATTATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 2 0.08
19 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
AAGAAAAAGAAAAAAG
Found at i:23816429 original size:16 final size:16
Alignment explanation
Indices: 23816400--23816442 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 16
23816390 TCACTCGAAA
23816400 AAGAAAAATGAGAAAAAGG
1 AAGAAAAA-GA-AAAAA-G
23816419 AAGAAAAAGAAAAAAG
1 AAGAAAAAGAAAAAAG
23816435 AAGAAAAA
1 AAGAAAAA
23816443 AATTATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 2 0.08
19 8 0.33
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
AAGAAAAAGAAAAAAG
Found at i:23816450 original size:537 final size:537
Alignment explanation
Indices: 23815437--23816513 Score: 2127
Period size: 537 Copynumber: 2.0 Consensus size: 537
23815427 TGTTTCTTGT
23815437 GTTAATGAAAATATGCAGAATTTAAAAAATGTGTCCACAATTTTTATTTTTATGCGTAAATCTTG
1 GTTAATGAAAATATGCAGAATTTAAAAAATGTGTCCACAATTTTTATTTTTATGCGTAAATCTTG
23815502 ATTTGCTTGGAATGCTGATGTGTAAATTAGATGAATGTGAATGAATAGTGAGTCTTCTATTTTTA
66 ATTTGCTTGGAATGCTGATGTGTAAATTAGATGAATGTGAATGAATAGTGAGTCTTCTATTTTTA
*
23815567 AATGAATGATTAGAATTGCTTTAGTAATGAATGGATAGTATGAATGTTTGAATCTTGAACTAACT
131 AATGAATGATTAGAATTGCTTCAGTAATGAATGGATAGTATGAATGTTTGAATCTTGAACTAACT
23815632 GTCCAGTTGCAGTAAAATTGTATGAATAAAAGACACTCCAATGTGAGTGCATTTTGACTTTTCAA
196 GTCCAGTTGCAGTAAAATTGTATGAATAAAAGACACTCCAATGTGAGTGCATTTTGACTTTTCAA
23815697 GGGAGAACACTCCACTTTAGGTTTAGAAAATCATCTGGCCAAAAGCCGTCACTACAAGAGTGTGT
261 GGGAGAACACTCCACTTTAGGTTTAGAAAATCATCTGGCCAAAAGCCGTCACTACAAGAGTGTGT
23815762 GTTGGCACAATTACATACCTCCTAGGGGTTTGTTGCACCCCACCGTTATTGCCCAGGAATAAAGG
326 GTTGGCACAATTACATACCTCCTAGGGGTTTGTTGCACCCCACCGTTATTGCCCAGGAATAAAGG
23815827 TAGAGTAATGTAATTACATCTCTAAGTCACTCGAAAAAGAAAAATGAGAAAAAGGAAGAAAAAGA
391 TAGAGTAATGTAATTACATCTCTAAGTCACTCGAAAAAGAAAAATGAGAAAAAGGAAGAAAAAGA
23815892 AAAAAGAAGAAAAAAATTATGATAAATGTTGTATTGGTTCAAGGAAGATTAGGATTCAATTCATG
456 AAAAAGAAGAAAAAAATTATGATAAATGTTGTATTGGTTCAAGGAAGATTAGGATTCAATTCATG
23815957 ATACTAACATTTATGAA
521 ATACTAACATTTATGAA
23815974 GTTAATGAAAATATGCAGAATTTAAAAAATGTGTCCACAATTTTTATTTTTATGCGTAAATCTTG
1 GTTAATGAAAATATGCAGAATTTAAAAAATGTGTCCACAATTTTTATTTTTATGCGTAAATCTTG
*
23816039 ATTTGCTTGGAATGCTGATGTGTAAATTAGATGAATGTGAATGGATAGTGAGTCTTCTATTTTTA
66 ATTTGCTTGGAATGCTGATGTGTAAATTAGATGAATGTGAATGAATAGTGAGTCTTCTATTTTTA
23816104 AATGAATGATTAGAATTGCTTCAGTAATGAATGGATAGTATGAATGTTTGAATCTTGAACTAACT
131 AATGAATGATTAGAATTGCTTCAGTAATGAATGGATAGTATGAATGTTTGAATCTTGAACTAACT
23816169 GTCCAGTTGCAGTAAAATTGTATGAATAAAAGACACTCCAATGTGAGTGCATTTTGACTTTTCAA
196 GTCCAGTTGCAGTAAAATTGTATGAATAAAAGACACTCCAATGTGAGTGCATTTTGACTTTTCAA
*
23816234 GGGAGAACACTCCACTTTAGGTTTAGAAAATCATCTGGCCAAAAGCTGTCACTACAAGAGTGTGT
261 GGGAGAACACTCCACTTTAGGTTTAGAAAATCATCTGGCCAAAAGCCGTCACTACAAGAGTGTGT
23816299 GTTGGCACAATTACATACCTCCTAGGGGTTTGTTGCACCCCACCGTTATTGCCCAGGAATAAAGG
326 GTTGGCACAATTACATACCTCCTAGGGGTTTGTTGCACCCCACCGTTATTGCCCAGGAATAAAGG
23816364 TAGAGTAATGTAATTACATCTCTAAGTCACTCGAAAAAGAAAAATGAGAAAAAGGAAGAAAAAGA
391 TAGAGTAATGTAATTACATCTCTAAGTCACTCGAAAAAGAAAAATGAGAAAAAGGAAGAAAAAGA
23816429 AAAAAGAAGAAAAAAATTATGATAAATGTTGTATTGGTTCAAGGAAGATTAGGATTCAATTCATG
456 AAAAAGAAGAAAAAAATTATGATAAATGTTGTATTGGTTCAAGGAAGATTAGGATTCAATTCATG
23816494 ATACTAACATTTATGAA
521 ATACTAACATTTATGAA
23816511 GTT
1 GTT
23816514 GCAGTTTTTA
Statistics
Matches: 537, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
537 537 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (537 bp):
GTTAATGAAAATATGCAGAATTTAAAAAATGTGTCCACAATTTTTATTTTTATGCGTAAATCTTG
ATTTGCTTGGAATGCTGATGTGTAAATTAGATGAATGTGAATGAATAGTGAGTCTTCTATTTTTA
AATGAATGATTAGAATTGCTTCAGTAATGAATGGATAGTATGAATGTTTGAATCTTGAACTAACT
GTCCAGTTGCAGTAAAATTGTATGAATAAAAGACACTCCAATGTGAGTGCATTTTGACTTTTCAA
GGGAGAACACTCCACTTTAGGTTTAGAAAATCATCTGGCCAAAAGCCGTCACTACAAGAGTGTGT
GTTGGCACAATTACATACCTCCTAGGGGTTTGTTGCACCCCACCGTTATTGCCCAGGAATAAAGG
TAGAGTAATGTAATTACATCTCTAAGTCACTCGAAAAAGAAAAATGAGAAAAAGGAAGAAAAAGA
AAAAAGAAGAAAAAAATTATGATAAATGTTGTATTGGTTCAAGGAAGATTAGGATTCAATTCATG
ATACTAACATTTATGAA
Found at i:23827153 original size:9 final size:9
Alignment explanation
Indices: 23827121--23827151 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
23827111 CACGTTTGGA
23827121 GAAGATGAT
1 GAAGATGAT
23827130 GAAGATGAT
1 GAAGATGAT
*
23827139 GAAGGTGAT
1 GAAGATGAT
23827148 GAAG
1 GAAG
23827152 GTTTTCGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (9 bp):
GAAGATGAT
Found at i:23828539 original size:28 final size:28
Alignment explanation
Indices: 23828499--23828552 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
23828489 ACATGTATGC
23828499 GACCCCCCACAAGTAAGTATATATATAT
1 GACCCCCCACAAGTAAGTATATATATAT
*
23828527 GACCCCCTACAAGTAAGTATATATAT
1 GACCCCCCACAAGTAAGTATATATAT
23828553 GCAAACCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (28 bp):
GACCCCCCACAAGTAAGTATATATATAT
Found at i:23828998 original size:30 final size:29
Alignment explanation
Indices: 23828944--23829046 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
23828934 AGCCTGTGTG
23828944 AACCCCTTGTTTGTGAGAGCCCATGTGCA
1 AACCCCTTGTTTGTGAGAGCCCATGTGCA
* *
23828973 AACCCTCTTGTGTATGTGA-AG-CCATGTACG
1 AACCC-CTTGT-T-TGTGAGAGCCCATGTGCA
* * * *
23829003 AACACCTTG-TAGATGCGAGCCCATGTGTA
1 AACCCCTTGTTTG-TGAGAGCCCATGTGCA
* *
23829032 AACCTCTTGTATGTG
1 AACCCCTTGTTTGTG
23829047 TGAATCTGTA
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
26 1 0.02
27 3 0.05
28 2 0.04
29 24 0.44
30 17 0.31
31 3 0.05
32 5 0.09
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (29 bp):
AACCCCTTGTTTGTGAGAGCCCATGTGCA
Found at i:23832114 original size:26 final size:28
Alignment explanation
Indices: 23832085--23832143 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 28
23832075 TACGAACCTA
* *
23832085 TGTGCGAGCCCTTTGA-GCAAACCCT-T
1 TGTGCGAGCCCTTTAATGAAAACCCTGT
* *
23832111 TGTGTGAGTCCTTTAATGAAAACCCTGT
1 TGTGCGAGCCCTTTAATGAAAACCCTGT
23832139 TGTGC
1 TGTGC
23832144 ACGATGTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 13 0.50
27 8 0.31
28 5 0.19
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
TGTGCGAGCCCTTTAATGAAAACCCTGT
Found at i:23833810 original size:69 final size:69
Alignment explanation
Indices: 23833722--23833858 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 69
23833712 GTCTTACATA
* * *
23833722 TATACACTACCATGGTCCAACCAT-GGTATTACATTTGAACAACA-GCCATAGCCTCACCATGGT
1 TATACACTACCATGGTCCAACCATGGGT-TTACATTCGAACAA-ATGCCATAGCCCCAACATGGT
23833785 CTTACG
64 CTTACG
* * * *
23833791 TATACATTGCCATGGTCCAACCATGGGTTTATATTCGAACAAATGCCATAGCCCCAATATGGTCT
1 TATACACTACCATGGTCCAACCATGGGTTTACATTCGAACAAATGCCATAGCCCCAACATGGTCT
23833856 TAC
66 TAC
23833859 TTTTATAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 1 0.02
69 55 0.93
70 3 0.05
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (69 bp):
TATACACTACCATGGTCCAACCATGGGTTTACATTCGAACAAATGCCATAGCCCCAACATGGTCT
TACG
Found at i:23835553 original size:23 final size:24
Alignment explanation
Indices: 23835514--23835575 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
23835504 AGCCTTTAGG
* *
23835514 ATAAT-CAAGCGAGCCTAAATTGT
1 ATAATACATGCGAACCTAAATTGT
23835537 -TAATACATGCGAACCTAAATTGT
1 ATAATACATGCGAACCTAAATTGT
* *
23835560 ATATTGCATGCGAACC
1 ATAATACATGCGAACC
23835576 CTAGGTGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 4 0.12
23 16 0.48
24 13 0.39
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (24 bp):
ATAATACATGCGAACCTAAATTGT
Found at i:23844617 original size:21 final size:22
Alignment explanation
Indices: 23844585--23844625 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23844575 TAAGAAAATG
23844585 TATCATGCAAA-TAAATAAAAA
1 TATCATGCAAATTAAATAAAAA
23844606 TATCAATG-AAATTAAATAAA
1 TATC-ATGCAAATTAAATAAA
23844626 GATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (22 bp):
TATCATGCAAATTAAATAAAAA
Found at i:23846597 original size:98 final size:98
Alignment explanation
Indices: 23846485--23846942 Score: 370
Period size: 97 Copynumber: 4.7 Consensus size: 98
23846475 GTCATCGTGG
* * * *
23846485 CTTCAATCTATCCCTCTTCAGTTTTAAGGTATTAGGTTCGCCATCACAACTTCAACCTATTCCTC
1 CTTCAATCTTTCCCTCTTCAGTTTTAAGGTATTAGGTCCGTCATCACAACTTCAACCTATCCCTC
*
23846550 TTATGTTTTAAGGTGTAAGATCCGTCGTTGTGA
66 TTATGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* ** * * ** *
23846583 CTTTAATCTTTCCCTCTTTGGTTTTTAGGGTGTTAGGTCCGTCATTGCGACTTCAACCTATCCCT
1 CTTCAATCTTTCCCTCTTCAG-TTTTAAGGTATTAGGTCCGTCATCACAACTTCAACCTATCCCT
* * * * *
23846648 CTTTTATTTTAAGGTCTAAGGTCCGTCGTTGCGG
65 CTTATGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* * * * ** * * *
23846682 CTTCAACCTTT-CCTCCTT-GGTTTTAGGGTGTTAGGTCCGTTGTTACGACTTCAACATATCCCT
1 CTTCAATCTTTCCCT-CTTCAGTTTTAAGGTATTAGGTCCGTCATCACAACTTCAACCTATCCCT
* **
23846745 CTTCA-GTTTTAAGGTGTTAGATTTGTCGTTGCGA
65 CTT-ATGTTTTAAGGTGTAAGATCCGTCGTTGCGA
* ** * * * *
23846779 CTTCAATCTTTCCCTCTTCAGCTTTAAGACATTAGATCCGTCATCGCAGCTTCAACCTATTCCTC
1 CTTCAATCTTTCCCTCTTCAGTTTTAAGGTATTAGGTCCGTCATCACAACTTCAACCTATCCCTC
* * * *
23846844 TT-TGATTTTAAGGTGTAAGGTCTGCCGTTAC-A
66 TTATG-TTTTAAGGTGTAAGATCCGTCGTTGCGA
* ** * * * * ** *
23846876 GCTTCAA-CCTTCCCTCTTTGGTTTTAGGGTGTTAGGTCCATCGTTGCAACTTCAATCTATCCCT
1 -CTTCAATCTTTCCCTCTTCAGTTTTAAGGTATTAGGTCCGTCATCACAACTTCAACCTATCCCT
23846940 CTT
65 CTT
23846943 CAAACTCTAT
Statistics
Matches: 284, Mismatches: 68, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
97 124 0.44
98 85 0.30
99 75 0.26
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.40
Consensus pattern (98 bp):
CTTCAATCTTTCCCTCTTCAGTTTTAAGGTATTAGGTCCGTCATCACAACTTCAACCTATCCCTC
TTATGTTTTAAGGTGTAAGATCCGTCGTTGCGA
Found at i:23846599 original size:49 final size:48
Alignment explanation
Indices: 23846427--23846942 Score: 315
Period size: 49 Copynumber: 10.5 Consensus size: 48
23846417 TAAAATTCAC
* * * * *
23846427 CGTTGCGACTTCAATCTGTTCCCACTTTGATTTCAAGGTGTTAGATCTGT
1 CGTTGCGACTTCAACCT-TTCCCTCTTTG-TTTTAAGGTGTTAGGTCCGT
* * * * * * * * * *
23846477 CATCGTGGCTTCAATCTATCCCTCTTCAGTTTTAAGGTATTAGGTTCGC
1 CGTTGCGACTTCAACCTTTCCCTCTT-TGTTTTAAGGTGTTAGGTCCGT
* ** * * *
23846526 CATCACAACTTCAACCTATT-CCTCTTATGTTTTAAGGTGTAAGATCCGT
1 CGTTGCGACTTCAACCT-TTCCCTCTT-TGTTTTAAGGTGTTAGGTCCGT
* * * *
23846575 CGTTGTGACTTTAATCTTTCCCTCTTTGGTTTTTAGGGTGTTAGGTCCGT
1 CGTTGCGACTTCAACCTTTCCCTCTTT-G-TTTTAAGGTGTTAGGTCCGT
* * * * *
23846625 CATTGCGACTTCAACCTATCCCTCTTTTATTTTAAGGTCTAAGGTCCGT
1 CGTTGCGACTTCAACCTTTCCCTC-TTTGTTTTAAGGTGTTAGGTCCGT
* * *
23846674 CGTTGCGGCTTCAACCTTT-CCTCCTTGGTTTTAGGGTGTTAGGTCCGT
1 CGTTGCGACTTCAACCTTTCCCT-CTTTGTTTTAAGGTGTTAGGTCCGT
* * * * * * **
23846722 TGTTACGACTTCAACATATCCCTCTTCAGTTTTAAGGTGTTAGATTTGT
1 CGTTGCGACTTCAACCTTTCCCTCTT-TGTTTTAAGGTGTTAGGTCCGT
* * * *** *
23846771 CGTTGCGACTTCAATCTTTCCCTCTTCAGCTTTAAGACATTAGATCCGT
1 CGTTGCGACTTCAACCTTTCCCTCTT-TGTTTTAAGGTGTTAGGTCCGT
* * * * *
23846820 CATCGC-AGCTTCAACCTATT-CCTCTTTGATTTTAAGGTGTAAGGTCTGC
1 CGTTGCGA-CTTCAACCT-TTCCCTCTTTG-TTTTAAGGTGTTAGGTCCGT
* * *
23846869 CGTTAC-AGCTTCAACC-TTCCCTCTTTGGTTTTAGGGTGTTAGGTCCAT
1 CGTTGCGA-CTTCAACCTTTCCCTCTTT-GTTTTAAGGTGTTAGGTCCGT
* * *
23846917 CGTTGCAACTTCAATCTATCCCTCTT
1 CGTTGCGACTTCAACCTTTCCCTCTT
23846943 CAAACTCTAT
Statistics
Matches: 353, Mismatches: 97, Indels: 33
0.73 0.20 0.07
Matches are distributed among these distances:
47 2 0.01
48 78 0.22
49 217 0.61
50 53 0.15
51 3 0.01
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (48 bp):
CGTTGCGACTTCAACCTTTCCCTCTTTGTTTTAAGGTGTTAGGTCCGT
Found at i:23846819 original size:146 final size:146
Alignment explanation
Indices: 23846485--23846944 Score: 374
Period size: 146 Copynumber: 3.1 Consensus size: 146
23846475 GTCATCGTGG
* ** * * * * *
23846485 CTTCAATCTATCCCTCTTCAGTTTTAAGGTATTAGGTTCGCCATCACAACTTCAACCTATTCCTC
1 CTTCAATCTATCCCTCTTCAGCTTTAAGACATTAGATCCGTCATCGCAGCTTCAACCTATTCCTC
* * * ** * * ** *
23846550 TTATG-TTTTAAGGTGTAAGATCCGTCGTT-GTGACTTTAATCTTTCCCTCTTTGGTTTTTAGGG
66 CT-TGATTTTAAGGTGTAAGGTCCGCCGTTACAG-CTTCAA-CATTCCCTCTTCAG-TTTTAAGG
* * * *
23846613 TGTTAGGTCCGTCATTGCGA
127 TGTTAGATCCATCGTTGCAA
* * * * * * * * *
23846633 CTTCAACCTATCCCTCTTTTA-TTTTAAGGTC-TAAGGTCCGTCGTTGCGGCTTCAACCT-TTCC
1 CTTCAATCTATCCCTC-TTCAGCTTTAA-GACATTAGATCCGTCATCGCAGCTTCAACCTATTCC
* * * **
23846695 TCCTTGGTTTTAGGGTGTTAGGTCCGTTGTTAC-GACTTCAACATATCCCTCTTCAGTTTTAAGG
64 TCCTTGATTTTAAGGTGTAAGGTCCGCCGTTACAG-CTTCAACAT-TCCCTCTTCAGTTTTAAGG
*** *
23846759 TGTTAGATTTGTCGTTGCGA
127 TGTTAGATCCATCGTTGCAA
*
23846779 CTTCAATCTTTCCCTCTTCAGCTTTAAGACATTAGATCCGTCATCGCAGCTTCAACCTATTCCTC
1 CTTCAATCTATCCCTCTTCAGCTTTAAGACATTAGATCCGTCATCGCAGCTTCAACCTATTCCTC
* * * ** *
23846844 TTTGATTTTAAGGTGTAAGGTCTGCCGTTACAGCTTCAACCTTCCCTCTTTGGTTTTAGGGTGTT
66 CTTGATTTTAAGGTGTAAGGTCCGCCGTTACAGCTTCAACATTCCCTCTTCAGTTTTAAGGTGTT
*
23846909 AGGTCCATCGTTGCAA
131 AGATCCATCGTTGCAA
23846925 CTTCAATCTATCCCTCTTCA
1 CTTCAATCTATCCCTCTTCA
23846945 AACTCTATGA
Statistics
Matches: 249, Mismatches: 54, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
145 5 0.02
146 118 0.47
147 81 0.33
148 41 0.16
149 4 0.02
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (146 bp):
CTTCAATCTATCCCTCTTCAGCTTTAAGACATTAGATCCGTCATCGCAGCTTCAACCTATTCCTC
CTTGATTTTAAGGTGTAAGGTCCGCCGTTACAGCTTCAACATTCCCTCTTCAGTTTTAAGGTGTT
AGATCCATCGTTGCAA
Found at i:23846882 original size:195 final size:196
Alignment explanation
Indices: 23846530--23846944 Score: 514
Period size: 195 Copynumber: 2.1 Consensus size: 196
23846520 GTTCGCCATC
* * *
23846530 ACAACTTCAACCTATTCCTCTT-ATGTTTTAAGGTGTAAGATCCGTCGTTGTGACTTTAATCTTT
1 ACAACTTCAA-CTATCCCTCTTCATGTTTTAAGGTGTAAGATCCGTCGTTGCGACTTCAATCTTT
** * * *** * * *
23846594 CCCTCTTTGGTTTTTAGGGTGTTAGGTCCGTCATTGCGACTTCAACCTATCCCTCTTTTATTTTA
65 CCCTCTTCAGTCTTTAAGACATTAGATCCGTCATCGCGACTTCAACCTATCCCTCTTTGATTTTA
* * * * * *
23846659 AGGTCTAAGGTCCGTCGTTGCGGCTTCAACCTTTCCTCCTTGGTTTTAGGGTGTTAGGTCCGTTG
130 AGGTCTAAGGTCCGCCGTTACAGCTTCAACCTTCCCTCCTTGGTTTTAGGGTGTTAGGTCCATCG
23846724 TT
195 TT
* * **
23846726 ACGACTTCAACATATCCCTCTTCA-GTTTTAAGGTGTTAGATTTGTCGTTGCGACTTCAATCTTT
1 ACAACTTCAAC-TATCCCTCTTCATGTTTTAAGGTGTAAGATCCGTCGTTGCGACTTCAATCTTT
*
23846790 CCCTCTTCAG-CTTTAAGACATTAGATCCGTCATCGC-AGCTTCAACCTATTCCTCTTTGATTTT
65 CCCTCTTCAGTCTTTAAGACATTAGATCCGTCATCGCGA-CTTCAACCTATCCCTCTTTGATTTT
* * *
23846853 AAGGTGTAAGGTCTGCCGTTACAGCTTCAACCTTCCCTCTTTGGTTTTAGGGTGTTAGGTCCATC
129 AAGGTCTAAGGTCCGCCGTTACAGCTTCAACCTTCCCTCCTTGGTTTTAGGGTGTTAGGTCCATC
23846918 GTT
194 GTT
*
23846921 GCAACTTCAATCTATCCCTCTTCA
1 ACAACTTCAA-CTATCCCTCTTCA
23846945 AACTCTATGA
Statistics
Matches: 186, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
194 1 0.01
195 122 0.66
196 62 0.33
197 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (196 bp):
ACAACTTCAACTATCCCTCTTCATGTTTTAAGGTGTAAGATCCGTCGTTGCGACTTCAATCTTTC
CCTCTTCAGTCTTTAAGACATTAGATCCGTCATCGCGACTTCAACCTATCCCTCTTTGATTTTAA
GGTCTAAGGTCCGCCGTTACAGCTTCAACCTTCCCTCCTTGGTTTTAGGGTGTTAGGTCCATCGT
T
Found at i:23854613 original size:26 final size:26
Alignment explanation
Indices: 23854557--23854618 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
23854547 ATACATAACA
* * *
23854557 AAAATAAAATGCAAAGTAACATATAT
1 AAAATAAAATACAAAGTAACACAAAT
23854583 AAAATAAAATACAAAG-AATCACAAAT
1 AAAATAAAATACAAAGTAA-CACAAAT
* *
23854609 TAAATTAAAT
1 AAAATAAAAT
23854619 CGAATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 2 0.07
26 28 0.93
ACGTcount: A:0.65, C:0.08, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAATAAAATACAAAGTAACACAAAT
Found at i:23855561 original size:21 final size:22
Alignment explanation
Indices: 23855529--23855569 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23855519 TAAGAAAATG
23855529 TATCATGCAAA-TAAATAAAAA
1 TATCATGCAAATTAAATAAAAA
23855550 TATCAATG-AAATTAAATAAA
1 TATC-ATGCAAATTAAATAAA
23855570 GACAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (22 bp):
TATCATGCAAATTAAATAAAAA
Found at i:23857026 original size:87 final size:87
Alignment explanation
Indices: 23856934--23857118 Score: 370
Period size: 87 Copynumber: 2.1 Consensus size: 87
23856924 GGTTGTAAAC
23856934 AAATGGGTTTTATTTTTGTAATTTTTTATTTGATTGAGTTAATAAAAGGAAAATGGGTTTAAATG
1 AAATGGGTTTTATTTTTGTAATTTTTTATTTGATTGAGTTAATAAAAGGAAAATGGGTTTAAATG
23856999 GTAATTGTAGGAGCCTGGATAA
66 GTAATTGTAGGAGCCTGGATAA
23857021 AAATGGGTTTTATTTTTGTAATTTTTTATTTGATTGAGTTAATAAAAGGAAAATGGGTTTAAATG
1 AAATGGGTTTTATTTTTGTAATTTTTTATTTGATTGAGTTAATAAAAGGAAAATGGGTTTAAATG
23857086 GTAATTGTAGGAGCCTGGATAA
66 GTAATTGTAGGAGCCTGGATAA
23857108 AAATGGGTTTT
1 AAATGGGTTTT
23857119 TACAACGGTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 98 1.00
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (87 bp):
AAATGGGTTTTATTTTTGTAATTTTTTATTTGATTGAGTTAATAAAAGGAAAATGGGTTTAAATG
GTAATTGTAGGAGCCTGGATAA
Found at i:23877707 original size:33 final size:34
Alignment explanation
Indices: 23877650--23877726 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
23877640 TATTTTTCTG
* * * *
23877650 TTATATTATGCTTGCAAGTTTTGTTAAGGGATTAC
1 TTATATT-TACTTGAAAGTTTTGTTAAAGGACTAC
*
23877685 TTATGTTTACTTGAAAG-TTTGTTAAAGGACTAC
1 TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
23877718 TTATATTTA
1 TTATATTTA
23877727 TATTAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 22 0.61
34 8 0.22
35 6 0.17
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (34 bp):
TTATATTTACTTGAAAGTTTTGTTAAAGGACTAC
Found at i:23882644 original size:17 final size:16
Alignment explanation
Indices: 23882624--23882681 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
23882614 CCCTTGACCT
23882624 TTAATCTTCCATCTTCC
1 TTAA-CTTCCATCTTCC
* *
23882641 TTAACCTCCAT-TGACC
1 TTAACTTCCATCT-TCC
23882657 TTTAACCTTCCATCTTCC
1 -TTAA-CTTCCATCTTCC
23882675 TTAACTT
1 TTAACTT
23882682 TTCATATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
15 1 0.03
16 11 0.33
17 12 0.36
18 8 0.24
19 1 0.03
ACGTcount: A:0.21, C:0.34, G:0.02, T:0.43
Consensus pattern (16 bp):
TTAACTTCCATCTTCC
Found at i:23882660 original size:34 final size:34
Alignment explanation
Indices: 23882612--23882679 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
23882602 AACCTTTCAT
* *
23882612 CTCCCTTGACCTTTAATCTTCCATCTTCCTTAAC
1 CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
23882646 CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
1 CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
23882680 TTTTCATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.19, C:0.38, G:0.03, T:0.40
Consensus pattern (34 bp):
CTCCATTGACCTTTAACCTTCCATCTTCCTTAAC
Found at i:23882864 original size:19 final size:19
Alignment explanation
Indices: 23882840--23882878 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23882830 TCTTGTGTTC
*
23882840 TTTATATCAT-TATTATTAT
1 TTTATAACATATATT-TTAT
23882859 TTTATAACATATATTTTAT
1 TTTATAACATATATTTTAT
23882878 T
1 T
23882879 CTCCACATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATAACATATATTTTAT
Found at i:23883393 original size:21 final size:22
Alignment explanation
Indices: 23883366--23883433 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
23883356 TCAAACCTCA
23883366 AAACCCTTAAACCTTAAA-TTT
1 AAACCCTTAAACCTTAAACTTT
* *
23883387 GAACCCTAAAACC-TAAACTTTT
1 AAACCCTTAAACCTTAAAC-TTT
*
23883409 AAACCC-TAAA-CTTAAACCTT
1 AAACCCTTAAACCTTAAACTTT
23883429 AAACC
1 AAACC
23883434 TAAAACTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.31
21 19 0.49
22 8 0.21
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.26
Consensus pattern (22 bp):
AAACCCTTAAACCTTAAACTTT
Found at i:23883439 original size:20 final size:22
Alignment explanation
Indices: 23883366--23883440 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 22
23883356 TCAAACCTCA
*
23883366 AAACCCTTAAACCTTAAA-T-TT
1 AAACCC-TAAAACTTAAACTCTT
* * *
23883387 GAACCCTAAAACCTAAACTTTT
1 AAACCCTAAAACTTAAACTCTT
23883409 AAACCCT-AAACTTAAAC-CTT
1 AAACCCTAAAACTTAAACTCTT
23883429 AAA-CCTAAAACT
1 AAACCCTAAAACT
23883441 CAAAACTCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 3 0.07
20 19 0.42
21 15 0.33
22 8 0.18
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (22 bp):
AAACCCTAAAACTTAAACTCTT
Found at i:23883440 original size:35 final size:36
Alignment explanation
Indices: 23883358--23883441 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 36
23883348 TCATAAGCTC
* * * *
23883358 AAACCTCAAAACCCTTAAACCTTAAATTTGAACCCTA
1 AAACCT-AAAACTCTTAAACCCTAAACTTGAAACCTA
* *
23883395 AAACCT-AAACTTTTAAACCCTAAACTT-AAACCTT
1 AAACCTAAAACTCTTAAACCCTAAACTTGAAACCTA
23883429 AAACCTAAAACTC
1 AAACCTAAAACTC
23883442 AAAACTCGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
34 11 0.28
35 22 0.56
37 6 0.15
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (36 bp):
AAACCTAAAACTCTTAAACCCTAAACTTGAAACCTA
Found at i:23883462 original size:27 final size:26
Alignment explanation
Indices: 23883436--23883497 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
23883426 CTTAAACCTA
23883436 AAACTCAAAACTCGAACTCAAATCCT
1 AAACTCAAAACTCGAACTCAAATCCT
* **
23883462 AAACTTTAAATTTCGAACTCAAATCCT
1 AAAC-TCAAAACTCGAACTCAAATCCT
*
23883489 GAATCTCAA
1 -AAACTCAA
23883498 GATTTGAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.14
27 22 0.76
28 3 0.10
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (26 bp):
AAACTCAAAACTCGAACTCAAATCCT
Found at i:23883669 original size:21 final size:19
Alignment explanation
Indices: 23883630--23883678 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
23883620 GCACAAAAAA
23883630 ATAAAAAATATTAACTTAT
1 ATAAAAAATATTAACTTAT
*
23883649 GA-AAAAAATATTAAAATTTAT
1 -ATAAAAAATATT--AACTTAT
23883670 ATAAAAAAT
1 ATAAAAAAT
23883679 GTTTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAAAAATATTAACTTAT
Found at i:23896515 original size:10 final size:10
Alignment explanation
Indices: 23896475--23896530 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
23896465 TATGAAATCG
23896475 TAAAAGAATTA
1 TAAAA-AATTA
23896486 T-AAAAATTA
1 TAAAAAATTA
***
23896495 TAAACTTTTA
1 TAAAAAATTA
23896505 TAAAAAATTA
1 TAAAAAATTA
23896515 TAAAAAAATTA
1 T-AAAAAATTA
23896526 TAAAA
1 TAAAA
23896531 TGCATAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
9 6 0.16
10 20 0.54
11 11 0.30
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:23896522 original size:11 final size:11
Alignment explanation
Indices: 23896502--23896530 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23896492 TTATAAACTT
23896502 TTAT-AAAAAA
1 TTATAAAAAAA
23896512 TTATAAAAAAA
1 TTATAAAAAAA
23896523 TTATAAAA
1 TTATAAAA
23896531 TGCATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TTATAAAAAAA
Found at i:23901144 original size:15 final size:15
Alignment explanation
Indices: 23901126--23901161 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
23901116 TAAAAATAAT
23901126 ATAAAAAATTAACAA-
1 ATAAAAAATTAA-AAG
23901141 ATAAAAAATTAAAAG
1 ATAAAAAATTAAAAG
23901156 ATAAAA
1 ATAAAA
23901162 TTATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (15 bp):
ATAAAAAATTAAAAG
Found at i:23902025 original size:10 final size:9
Alignment explanation
Indices: 23901991--23902028 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
23901981 TGCGGCTGCG
23901991 AAAAAT-TA
1 AAAAATATA
23901999 AAAAA-ATA
1 AAAAATATA
23902007 AAAAATATA
1 AAAAATATA
23902016 AAAAATTATA
1 AAAAA-TATA
23902026 AAA
1 AAA
23902029 TGCTTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 12 0.44
9 8 0.30
10 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAATATA
Found at i:23902070 original size:20 final size:20
Alignment explanation
Indices: 23902047--23902103 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
23902037 TTAGTACAGT
*
23902047 TTTTATAATTTTTTTATGA-A
1 TTTTATAATTTTTTTA-CATA
* *
23902067 TTTTAT-ATTTCTTTACATT
1 TTTTATAATTTTTTTACATA
23902086 TTTTATAATTTTTTTACA
1 TTTTATAATTTTTTTACA
23902104 ACCTTATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 16 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATAATTTTTTTACATA
Found at i:23902142 original size:21 final size:19
Alignment explanation
Indices: 23902114--23902226 Score: 65
Period size: 20 Copynumber: 5.9 Consensus size: 19
23902104 ACCTTATAAA
23902114 ATTTTATA-ATTTTTTTAT
1 ATTTTATATATTTTTTTAT
*
23902132 ATTTCTATATATTTTATTAT
1 ATTT-TATATATTTTTTTAT
*
23902152 -TTTTGTATGATTTTTTATAAT
1 ATTTTATAT-ATTTTTT-T-AT
* * **
23902173 ATTTAATA-ATATTTAAAT
1 ATTTTATATATTTTTTTAT
*
23902191 ATTTT-TATAGTTTTTATTAA
1 ATTTTATATA-TTTTT-TTAT
*
23902211 AATTTA-ATATTTTTTT
1 ATTTTATATATTTTTTT
23902227 TTTTTTATTT
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
17 2 0.03
18 17 0.24
19 22 0.31
20 23 0.32
21 2 0.03
22 5 0.07
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTATATATTTTTTTAT
Found at i:23902145 original size:28 final size:31
Alignment explanation
Indices: 23902108--23902182 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 31
23902098 TTTACAACCT
* *
23902108 TATAAAATTTTATAATTTTTTTAT-A-TTTC
1 TATAATATTTTATAATTTTTGTATGATTTTC
* *
23902137 TAT-ATATTTTATTATTTTTGTATGATTTTT
1 TATAATATTTTATAATTTTTGTATGATTTTC
*
23902167 TATAATATTTAATAAT
1 TATAATATTTTATAAT
23902183 ATTTAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 17 0.46
29 4 0.11
30 6 0.16
31 10 0.27
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (31 bp):
TATAATATTTTATAATTTTTGTATGATTTTC
Found at i:23902205 original size:39 final size:40
Alignment explanation
Indices: 23902115--23902220 Score: 96
Period size: 41 Copynumber: 2.7 Consensus size: 40
23902105 CCTTATAAAA
* * * *
23902115 TTTTATAATTTTTT-T-ATATTT-CTATATATTTTATTAT
1 TTTTATAGTTTTTTATAATATTTAATATATATTTAAATAT
*
23902152 TTTTGTATGATTTTTTATAATATTTAATA-ATATTTAAATAT
1 TTTTATA-G-TTTTTTATAATATTTAATATATATTTAAATAT
*
23902193 TTTTATAG-TTTTTATTAAAATTTAATAT
1 TTTTATAGTTTTTTA-TAATATTTAATAT
23902221 TTTTTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
37 6 0.11
38 6 0.11
39 17 0.31
40 2 0.04
41 22 0.40
42 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (40 bp):
TTTTATAGTTTTTTATAATATTTAATATATATTTAAATAT
Found at i:23902232 original size:28 final size:29
Alignment explanation
Indices: 23902163--23902224 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
23902153 TTTGTATGAT
* * *
23902163 TTTTTATAATATTTAATAATATTTAAATA
1 TTTTTATAGTTTTTAATAAAATTTAAATA
*
23902192 TTTTTATAGTTTTTATTAAAATTT-AATA
1 TTTTTATAGTTTTTAATAAAATTTAAATA
23902220 TTTTT
1 TTTTT
23902225 TTTTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTTATAGTTTTTAATAAAATTTAAATA
Found at i:23902462 original size:90 final size:90
Alignment explanation
Indices: 23902356--23902557 Score: 282
Period size: 90 Copynumber: 2.2 Consensus size: 90
23902346 TTAATTGTTT
* * *
23902356 TTTTTTTTAAAAAGTTTGAGTACCTTTTTGATGCATTTTGA-AAGTTTAAATACCCAATTGAGTG
1 TTTTTTTAAAAAAGTTTGAGGACATTTTTGATGCATTTTGATAA-TTTAAATACCCAATTGAGTG
*
23902420 CAAAAAAAA-TGTAGGGGCTTAATTG
65 CAAAAAAAATTGTAAGGGCTTAATTG
* * *
23902445 CTTTTTTTGAAAAAGTTTGAGGATATTTTTGATGCATTTTGATAATTTAAATATCCAATTGAGTG
1 -TTTTTTTAAAAAAGTTTGAGGACATTTTTGATGCATTTTGATAATTTAAATACCCAATTGAGTG
*
23902510 CAAAAAAAATTGTAAGGGTTTAATTG
65 CAAAAAAAATTGTAAGGGCTTAATTG
*
23902536 TATTTTTTAAAAAAATTTGAGG
1 T-TTTTTTAAAAAAGTTTGAGG
23902558 GTTTTTTACA
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
90 66 0.66
91 34 0.34
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.41
Consensus pattern (90 bp):
TTTTTTTAAAAAAGTTTGAGGACATTTTTGATGCATTTTGATAATTTAAATACCCAATTGAGTGC
AAAAAAAATTGTAAGGGCTTAATTG
Found at i:23918519 original size:23 final size:23
Alignment explanation
Indices: 23918493--23918536 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
23918483 GTTTCTAAAG
23918493 ATAACCTTGTGGATCCGTTTACT
1 ATAACCTTGTGGATCCGTTTACT
23918516 ATAACCTTGTGGATCCGTTTA
1 ATAACCTTGTGGATCCGTTTA
23918537 TTAAGAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (23 bp):
ATAACCTTGTGGATCCGTTTACT
Found at i:23918785 original size:229 final size:229
Alignment explanation
Indices: 23918377--23918974 Score: 1016
Period size: 229 Copynumber: 2.6 Consensus size: 229
23918367 CTACAATAGC
*
23918377 TAATACCAAGGAAATGAGAAGTCACAAGAGGACGAAACACATTGATTGAAAGTATCACTTGATAC
1 TAATACCAAGGAAATGAGAAGTCACAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
* *
23918442 GAGAGGCAATTGCCGAAGGAATTGTCAATGTGATGAAACTAGTTTCTAAAGATAACCTTGTGGAT
66 GAGAGGCAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
*
23918507 CCGTTTACTATAACCTTGTGGATCCGTTTATTAAGAATCTTATAACTAGGAGTTTTAACAAACAC
131 CCGTTTACTATAACCTTGTGGATCCGTTTACTAAGAATCTTATAACTAGGAGTTTTAACAAACAC
* ** * **
23918572 GTCCAGGATATGGGAATGCGAAATGTGACACATT
196 ATCCAGGATAACGGAATGCAAAACATGACACATT
* *
23918606 TAATACTAAGGAAATAAGAAGTCACAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
1 TAATACCAAGGAAATGAGAAGTCACAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
*
23918671 GAGAGGTAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
66 GAGAGGCAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
* * * * *
23918736 TCGTTTATTATAACCTTGTGGATCTGTTTACTAGGAATCTTGTAACTAGGAGTTTTAACAAACAC
131 CCGTTTACTATAACCTTGTGGATCCGTTTACTAAGAATCTTATAACTAGGAGTTTTAACAAACAC
*
23918801 ATCCAGGATAACGGAATGCAAAACATGATACATT
196 ATCCAGGATAACGGAATGCAAAACATGACACATT
*
23918835 TAATACCAAGGAAATGAGAAGTCATAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
1 TAATACCAAGGAAATGAGAAGTCACAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
23918900 GAGAGGCAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
66 GAGAGGCAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
23918965 CCGTTTACTA
131 CCGTTTACTA
23918975 AGAATCTTGT
Statistics
Matches: 344, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
229 344 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (229 bp):
TAATACCAAGGAAATGAGAAGTCACAAGAGGATGAAACACATTGATTGAAAGTATCACTTGATAC
GAGAGGCAATTACCGAAGGAATTGTCAATGTGATGAAAGTAGTTTCTAAAGATAACCTTGTGGAT
CCGTTTACTATAACCTTGTGGATCCGTTTACTAAGAATCTTATAACTAGGAGTTTTAACAAACAC
ATCCAGGATAACGGAATGCAAAACATGACACATT
Found at i:23921000 original size:16 final size:16
Alignment explanation
Indices: 23920979--23921010 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23920969 AGTAATTTTT
*
23920979 ATGTTAAAGGAGTAAA
1 ATGTTAAAGGAATAAA
23920995 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
23921011 TTTGTAAGGA
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:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:23922651 original size:21 final size:24
Alignment explanation
Indices: 23922598--23922651 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 24
23922588 GTTTATGAGA
23922598 TATCGGTAGTTCTGTACATAATAG
1 TATCGGTAGTTCTGTACATAATAG
* * *
23922622 TATCAGTAG-TCTG-A-ATACTTG
1 TATCGGTAGTTCTGTACATAATAG
23922643 TATCGGTAG
1 TATCGGTAG
23922652 AAGCTACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 13 0.50
22 1 0.04
23 4 0.15
24 8 0.31
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (24 bp):
TATCGGTAGTTCTGTACATAATAG
Found at i:23932124 original size:30 final size:30
Alignment explanation
Indices: 23932063--23932380 Score: 245
Period size: 29 Copynumber: 10.9 Consensus size: 30
23932053 GTTCAAGGTT
* *
23932063 AAAATGTAA-TTTTGGAAACTT-TAGGGGTA
1 AAAATGTAATTTTTGGAAAGTTCGA-GGGTA
* *
23932092 AAAATGTAATTTTAGGAAAGTTCGAGGTTA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
* * *
23932122 AAAA-GTGATTTTT-GAGAAGTTC-TGGATA
1 AAAATGTAATTTTTGGA-AAGTTCGAGGGTA
* * *
23932150 AAAATGTGATTTTTAG-AAGTTCGGGGGTA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
*
23932179 AAAATGTAATTTTT-GAAAGTTTGA-GG--
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
*
23932205 AAAATATAATTTTT-GAGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGA-AAGTTCGAGGGTA
* *
23932235 AAAATGTGATTTTTGG-AAGATCGAGGGTA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGTA
* *
23932264 AAAATGTGATTTTTGGAAA-TTCG-GAGGCA
1 AAAATGTAATTTTTGGAAAGTTCGAG-GGTA
* * * *
23932293 AAAATATAATTTTTGGAAAATTTTG-GGGTT
1 AAAATGTAATTTTTGG-AAAGTTCGAGGGTA
* * *
23932323 AAAATGTGATTTTTGAGAAAGTTTGA-GGTT
1 AAAATGTAATTTTTG-GAAAGTTCGAGGGTA
* *
23932353 AAAATGTAATTTTTGAAAAGTTCAAGGG
1 AAAATGTAATTTTTGGAAAGTTCGAGGG
23932381 CCTCTTTAGC
Statistics
Matches: 238, Mismatches: 32, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
26 15 0.06
27 7 0.03
28 22 0.09
29 109 0.46
30 78 0.33
31 7 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTCGAGGGTA
Found at i:23932152 original size:58 final size:59
Alignment explanation
Indices: 23932090--23932375 Score: 200
Period size: 59 Copynumber: 4.9 Consensus size: 59
23932080 ACTTTAGGGG
* *
23932090 TAAAAATGTAATTTTAGGAAAGTTCGAGGTTAAAAA-GTGATTTTTGAGAAGTTCTGGA
1 TAAAAATGTAATTTTAGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCTGGA
* *
23932148 TAAAAATGTGATTTTTA-G-AAGTTCGGGGGTAAAAATGTAATTTTTGA-AAGTT-T-GA
1 TAAAAATGT-AATTTTAGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCTGGA
** * * * * * *
23932203 GGAAAATATAATTTT-TGAGAAGTTCGAGGGTAAAAATGTGATTTTTG-GAAGATCGAGGG
1 TAAAAATGTAATTTTAGGA-AAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTC-TGGA
* * * * * * *
23932262 TAAAAATGTGATTTTTGGAAA-TTCG-GAGGCAAAAATATAATTTTTG-GAAAATTTTGGGG
1 TAAAAATGTAATTTTAGGAAAGTTCGAG-GGTAAAAATGTAATTTTTGAG-AAGTTCT-GGA
* * * * * *
23932321 TTAAAATGTGATTTTTGAGAAAGTTTGA-GGTTAAAATGTAATTTTTGAAAAGTTC
1 TAAAAATGTAATTTTAG-GAAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTC
23932376 AAGGGCCTCT
Statistics
Matches: 178, Mismatches: 33, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
54 6 0.03
55 8 0.04
56 31 0.17
57 21 0.12
58 41 0.23
59 42 0.24
60 26 0.15
61 3 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (59 bp):
TAAAAATGTAATTTTAGGAAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCTGGA
Found at i:23934446 original size:100 final size:99
Alignment explanation
Indices: 23934268--23934994 Score: 334
Period size: 99 Copynumber: 7.3 Consensus size: 99
23934258 TGAGGTGCTA
* * * *
23934268 GGTTAGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTAATGGTATCGGATTCGCCGTTGCGAC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCACATCTTAATGGTATCGGATTCGCCGTTGCGAC
*
23934333 CTCAATCCTTCCCATCGTATCTTCTAAGGTACCG
66 CTCAATCCTTCCCATCGCATCTTCTAAGGTACCG
* ** *
23934367 GGTTCGCCGTTCCGGCCTCAACCTTTCCCGTCACATCTTCTTAGGTATCAGG-TTCGCCGTTGTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCACATCTTAAT-GGTATC-GGATTCGCCGTTGCG
* *
23934431 GCCTCAA-CCTTTCCCATCGCATCTTCTTAGGTACCG
64 ACCTCAATCC-TTCCCATCGCATCTTCTAAGGTACCG
* * * ** * * * **
23934467 GGTTCGCCGTTGTGGCCTCAACCTTTCTCTTCGTATCTTCATGGTA-CTGGGTTCACAATTGC-A
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCACATCTTAATGGTATC-GGATTCGCCGTTGCGA
* * * * *
23934530 GTCTC-ATCCTTTCTCATCACATCTTTTTAGGTACCG
65 -CCTCAATCC-TTCCCATCGCATCTTCTAAGGTACCG
** * * *
23934566 GGTTCGTTGTTGCGAG-CTCAACCTTTCCCATCACATCTTTTAAT-GTACCGGATTCGCCGTTGT
1 GGTTCGCCGTTGCG-GCCTCAACCTTTCCCGTCACATC--TTAATGGTATCGGATTCGCCGTTGC
* * * ** * *
23934629 GGCTTCAATCCTTCCCTTCAAATCTTC-ATGGTATCG
63 GACCTCAATCCTTCCCATCGCATCTTCTAAGGTACCG
** * * ** * ** * * * *
23934665 GGTTCATCGTTGTGGCCTCATCCTTT-TAGATCACGTCTTCTTTGGTACCGAGTTTTGCCGTTAC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCG-TCACATCTT-AATGGTATCG-GATTCGCCGTTGC
* * * * *
23934729 GGCCTCAA-CCTTTCCTAACGCATCTTCTTTTAGGTATCG
63 GACCTCAATCC-TTCCCATCGCATCTTC--TAAGGTACCG
* ** * * * * **
23934768 GATTTACTGTTGTGGCCTCAATCCTTT-CCATCACATCTTCTAA-GGTATCGGATTCGTCGTCAC
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCGTCACATC-T-TAATGGTATCGGATTCGCCGTTGC
* * * * * *
23934831 GGCCTCACTCCTTCCCTTCATC-TCTTC-ATGGTATCG
63 GACCTCAATCCTTCCCATC-GCATCTTCTAAGGTACCG
* * * * * ** ** * * * *
23934867 GGTTCGCCATTGTGGCCTCAACCTTTCCC-TTAGTATTTTCGTCATACCGGGTTCGCCATTGCGG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCA-CATCTTAATGGTATCGGATTCGCCGTTGCGA
*
23934931 CCTCAA-CCTTTCCCATCGCATCTTCTTAGGTACCG
65 CCTCAATCC-TTCCCATCGCATCTTCTAAGGTACCG
* * ** * *
23934966 GATTCACCGTCACAGCCTCAATCTTTCCC
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCC
23934995 TTCGTATCTC
Statistics
Matches: 468, Mismatches: 128, Indels: 64
0.71 0.19 0.10
Matches are distributed among these distances:
97 6 0.01
98 45 0.10
99 199 0.43
100 136 0.29
101 11 0.02
102 26 0.06
103 38 0.08
104 6 0.01
105 1 0.00
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (99 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCGTCACATCTTAATGGTATCGGATTCGCCGTTGCGAC
CTCAATCCTTCCCATCGCATCTTCTAAGGTACCG
Found at i:23934513 original size:149 final size:149
Alignment explanation
Indices: 23934236--23935162 Score: 579
Period size: 149 Copynumber: 6.2 Consensus size: 149
23934226 CATTGTGGCT
* * * * * * * *
23934236 TCAATCTTTCCCGTCAC-TTTTCTGAGGTGCTAGGTTAGCCGTTGCGGCCTCAACCTTTCCCTTT
1 TCAACCTTTCCCGTCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC
** ** * * * *
23934300 ATATCTTAAT-GGTATCGGATTCGCCGTTGCGACCTCAATCCTTCCCATCGTATCTTCTAAGGTA
66 GCATCTTCTTAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCATCATATCTTC-ATGGTA
*
23934364 CCGGGTTCGCCGTTCCGGCC
130 CCGGGTTCACCGTTCCGGCC
* *
23934384 TCAACCTTTCCCGTCACATCTTCTTAGGTATCAGGTTCGCCGTTGTGGCCTCAACCTTTCCCATC
1 TCAACCTTTCCCGTCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC
* * * * *
23934449 GCATCTTCTTAGGTACCGGGTTCGCCGTTGTGGCCTCAA-CCTTTCTCTTCGTATCTTCATGGTA
66 GCATCTTCTTAGGTACCGGATTCGCCGTTGCGGCCTCAATCC-TTCCCATCATATCTTCATGGTA
* ** * * *
23934513 CTGGGTTCACAATTGCAGTC
130 CCGGGTTCACCGTTCCGGCC
* * * * * **
23934533 TCATCCTTTCTCATCACATCTTTTTAGGTACCGGGTTCGTTGTTGCGAG-CTCAACCTTTCCCAT
1 TCAACCTTTCCCGTCACATCTTCTTAGGTACCAGGTTCGCCGTTGCG-GCCTCAACCTTTCCCAT
* * * * * *
23934597 CACATCTT-TTAATGTACCGGATTCGCCGTTGTGGCTTCAATCCTTCCCTTCAAATCTTCATGGT
65 CGCATCTTCTT-AGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCATCATATCTTCATGGT
* * **
23934661 ATCGGGTTCATCGTTGTGGCC
129 ACCGGGTTCACCGTTCCGGCC
* ** * * * * * *
23934682 TCATCCTTT-TAGATCACGTCTTCTTTGGTACCGAGTTTTGCCGTTACGGCCTCAACCTTTCCTA
1 TCAACCTTTCCCG-TCACATCTTCTTAGGTACC-AGGTTCGCCGTTGCGGCCTCAACCTTTCCCA
* * ** * * * * *
23934746 ACGCATCTTCTTTTAGGTATCGGATTTACTGTTGTGGCCTCAATCCTTTCCATCACATCTTCTAA
64 TCGCATCTTC--TTAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCATCATATCTTC-AT
* * **
23934811 GGTATCGGATTCGTCG-TCACGGCC
126 GGTACCGGGTTCACCGTTC-CGGCC
* * * * * * * *
23934835 TC-ACTCCTTCCCTTCATC-TCTTCAT-GGTATCGGGTTCGCCATTGTGGCCTCAACCTTTCCCT
1 TCAAC-CTTTCCCGTCA-CATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCA
* * * * * * ** *
23934897 TAGTATTTTCGTCA--TACCGGGTTCGCCATTGCGGCCTCAA-CCTTTCCCATCGCATCTTCTTA
64 TCGCATCTTC-TTAGGTACCGGATTCGCCGTTGCGGCCTCAATCC-TTCCCATCATATCTTCAT-
* *
23934959 GGTACCGGATTCACCG-TCACAGCC
126 GGTACCGGGTTCACCGTTC-CGGCC
* * ** * * * * * * *
23934983 TCAATCTTTCCCTTCGTATCTCCGT-GGTACCAGGTTTGCCATTACGGCCTCAACCTTTTCTATC
1 TCAACCTTTCCCGTCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC
* * * * ** * * * *
23935047 GCATATTTTTAGGTACCAGATTCGCTGTCACAGCGTCAATCCTTCCCTTCATCTCTTCATGGTAC
66 GCATCTTCTTAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCATCATATCTTCATGGTAC
* ** *
23935112 CGGGTTCGCTATTGCGGCC
131 CGGGTTCACCGTTCCGGCC
*
23935131 TCAACCTTTCCCATCACATCTTCTTAGGTACC
1 TCAACCTTTCCCGTCACATCTTCTTAGGTACC
23935163 GGATTCACTG
Statistics
Matches: 593, Mismatches: 160, Indels: 51
0.74 0.20 0.06
Matches are distributed among these distances:
147 4 0.01
148 158 0.27
149 246 0.41
150 74 0.12
151 29 0.05
152 46 0.08
153 35 0.06
154 1 0.00
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (149 bp):
TCAACCTTTCCCGTCACATCTTCTTAGGTACCAGGTTCGCCGTTGCGGCCTCAACCTTTCCCATC
GCATCTTCTTAGGTACCGGATTCGCCGTTGCGGCCTCAATCCTTCCCATCATATCTTCATGGTAC
CGGGTTCACCGTTCCGGCC
Found at i:23935024 original size:99 final size:99
Alignment explanation
Indices: 23934881--23935191 Score: 399
Period size: 99 Copynumber: 3.1 Consensus size: 99
23934871 CGCCATTGTG
* * **
23934881 GCCTCAA-CCTTTCCCTTAGTATTTTCGTCATACCGGGTTCGCCATTGCGGCCTCAACCTTTCCC
1 GCCTCAATCC-TTCCCTTCGTATCTTCGTGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCC
*
23934945 ATCGCATCTTCTTAGGTACCGGATTCACCGTCACA
65 ATCGCATCTTCTTAGGTACCGGATTCACTGTCACA
* * * * * * *
23934980 GCCTCAATCTTTCCCTTCGTATCTCCGTGGTACCAGGTTTGCCATTACGGCCTCAACCTTTTCTA
1 GCCTCAATCCTTCCCTTCGTATCTTCGTGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCA
* * * *
23935045 TCGCATATTTTTAGGTACCAGATTCGCTGTCACA
66 TCGCATCTTCTTAGGTACCGGATTCACTGTCACA
* * * * *
23935079 GCGTCAATCCTTCCCTTCATCTCTTCATGGTACCGGGTTCGCTATTGCGGCCTCAACCTTTCCCA
1 GCCTCAATCCTTCCCTTCGTATCTTCGTGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCA
* *
23935144 TCACATCTTCTTAGGTACCGGATTCACTGTCACG
66 TCGCATCTTCTTAGGTACCGGATTCACTGTCACA
23935178 GCCTCAATCCTTCC
1 GCCTCAATCCTTCC
23935192 TTGTCAAACC
Statistics
Matches: 176, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
99 175 0.99
100 1 0.01
ACGTcount: A:0.17, C:0.34, G:0.16, T:0.33
Consensus pattern (99 bp):
GCCTCAATCCTTCCCTTCGTATCTTCGTGGTACCGGGTTCGCCATTGCGGCCTCAACCTTTCCCA
TCGCATCTTCTTAGGTACCGGATTCACTGTCACA
Found at i:23935184 original size:50 final size:50
Alignment explanation
Indices: 23934268--23935164 Score: 525
Period size: 50 Copynumber: 18.0 Consensus size: 50
23934258 TGAGGTGCTA
* * * * ** *
23934268 GGTTAGCCGTTGCGGCCTCAACCTTTCCCTTTATATCTTAAT-GGTATCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * ** *
23934317 GATTCGCCGTTGCGACCTCAATCC-TTCCCATCGTATCTTCTAAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTTAGGTACCG
* * * *
23934367 GGTTCGCCGTTCCGGCCTCAACCTTTCCCGTCACATCTTCTTAGGTATCA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* *
23934417 GGTTCGCCGTTGTGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * * ** * *
23934467 GGTTCGCCGTTGTGGCCTCAACCTTTCTCTTCGTATCTTCAT-GGTACTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* ** * * * * *
23934516 GGTTCACAATTGCAGTCTCATCCTTTCTCATCACATCTTTTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
** *
23934566 GGTTCGTTGTTGCGAG-CTCAACCTTTCCCATCACATCTT-TTAATGTACCG
1 GGTTCGCCGTTGCG-GCCTCAACCTTTCCCATCACATCTTCTT-AGGTACCG
* * * * * * *
23934616 GATTCGCCGTTGTGGCTTCAATCC-TTCCCTTCAAATCTTCAT-GGTATCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTTAGGTACCG
** * * *** * *
23934665 GGTTCATCGTTGTGGCCTCATCCTTTTAGATCACGTCTTCTTTGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * * * * * *
23934715 AGTTTTGCCGTTACGGCCTCAACCTTTCCTAACGCATCTTCTTTTAGGTATCG
1 -GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTC--TTAGGTACCG
* ** * * * *
23934768 GATTTACTGTTGTGGCCTCAATCCTTT-CCATCACATCTTCTAAGGTATCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCACATCTTCTTAGGTACCG
* * ** * * * *
23934818 GATTCGTCGTCACGGCCTC-ACTCCTTCCCTTCATC-TCTTCAT-GGTATCG
1 GGTTCGCCGTTGCGGCCTCAAC-CTTTCCCATCA-CATCTTCTTAGGTACCG
* * * * * *
23934867 GGTTCGCCATTGTGGCCTCAACCTTTCCC-TTAGTATTTTCGTCA--TACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCA-CATCTTC-TTAGGTACCG
* *
23934916 GGTTCGCCATTGCGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * ** * * * ** * * *
23934966 GATTCACCGTCACAGCCTCAATCTTTCCCTTCGTATCTCCGT-GGTACCA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * * * * * * * *
23935015 GGTTTGCCATTACGGCCTCAACCTTTTCTATCGCATATTTTTAGGTACCA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
* * ** * * * *
23935065 GATTCGCTGTCACAGCGTCAATCC-TTCCCTTCATC-TCTTCAT-GGTACCG
1 GGTTCGCCGTTGCGGCCTCAA-CCTTTCCCATCA-CATCTTCTTAGGTACCG
**
23935114 GGTTCGCTATTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
23935164 G
1 G
23935165 ATTCACTGTC
Statistics
Matches: 638, Mismatches: 179, Indels: 61
0.73 0.20 0.07
Matches are distributed among these distances:
48 10 0.02
49 242 0.38
50 312 0.49
51 35 0.05
52 26 0.04
53 13 0.02
ACGTcount: A:0.16, C:0.31, G:0.18, T:0.35
Consensus pattern (50 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTTAGGTACCG
Found at i:23938621 original size:22 final size:22
Alignment explanation
Indices: 23938595--23938637 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
23938585 CTTCTAAACA
23938595 CATATCTTGCTCGAAACTAGGT
1 CATATCTTGCTCGAAACTAGGT
23938617 CATATCTTGCTCGAAACTAGG
1 CATATCTTGCTCGAAACTAGG
23938638 CTCTAAGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (22 bp):
CATATCTTGCTCGAAACTAGGT
Found at i:23942495 original size:16 final size:15
Alignment explanation
Indices: 23942476--23942513 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
23942466 CATGAACAAT
23942476 TATACGAATGAATAAA
1 TATACGAAT-AATAAA
23942492 TATACGAA-AATAAA
1 TATACGAATAATAAA
23942506 -ATACGAAT
1 TATACGAAT
23942514 CATGAATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 6 0.29
16 8 0.38
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (15 bp):
TATACGAATAATAAA
Found at i:23942676 original size:29 final size:29
Alignment explanation
Indices: 23942634--23942859 Score: 156
Period size: 29 Copynumber: 7.8 Consensus size: 29
23942624 GGAGAGTTCA
*
23942634 GGGTTAAAATATAATTTTGGAAAGTTTAG
1 GGGTAAAAATATAATTTTGGAAAGTTTAG
23942663 GGGTAAAAATATAATTTTGAGAAAGTTTA-
1 GGGTAAAAATATAATTTTG-GAAAGTTTAG
* * *
23942692 GGGTAAAAATGTAATTTTTGAGAAG-TTCG
1 GGGTAAAAATATAATTTTGGA-AAGTTTAG
* * * * **
23942721 AGGCAAAAATGTGAGTTTTGG-AAGTTCGG
1 GGGTAAAAATAT-AATTTTGGAAAGTTTAG
* * *
23942750 GGGCAAAAATATGATTTTTGG-AAG-TTCG
1 GGGTAAAAATAT-AATTTTGGAAAGTTTAG
** * *
23942778 GGGGCAAAATGTAATTTTTGAGAAGTTTAG
1 GGGTAAAAATATAATTTTGGA-AAGTTTAG
* * *
23942808 GGGTAAAAATGTGATTTTTGAAAGTTTAG
1 GGGTAAAAATATAATTTTGGAAAGTTTAG
* * **
23942837 AGATAAAAATATGGTTTTGGAAA
1 GGGTAAAAATATAATTTTGGAAA
23942860 TTCGAGGCAA
Statistics
Matches: 160, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
27 6 0.04
28 18 0.11
29 100 0.62
30 36 0.22
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATATAATTTTGGAAAGTTTAG
Found at i:23942707 original size:58 final size:58
Alignment explanation
Indices: 23942628--23943009 Score: 196
Period size: 58 Copynumber: 6.6 Consensus size: 58
23942618 AGTTTCGGAG
* * * *
23942628 AGTTCAGGGTTAAAATATAATTTTGGAAAGTTTAGGGGTAAAAATAT-AATTTTGAGAA
1 AGTTTAGGGTAAAAATGTAATTTTGGAAAGTTTAGGGGTAAAAATGTGAATTTTG-GAA
* * * * *
23942686 AGTTTAGGGTAAAAATGTAATTTTTGAGAAG-TTCGAGGCAAAAATGTGAGTTTTGG-A
1 AGTTTAGGGTAAAAATGTAATTTTGGA-AAGTTTAGGGGTAAAAATGTGAATTTTGGAA
** * * * * ** *
23942743 AGTTCGGGGGCAAAAATATGATTTTTGG-AAG-TTCGGGGGCAAAATGT-AATTTTTGAGA
1 AGTT-TAGGGTAAAAATGT-AATTTTGGAAAGTTTAGGGGTAAAAATGTGAATTTTGGA-A
* * * * * *
23942801 AGTTTAGGGGTAAAAATGTGATTTTTGAAAGTTTAGAGATAAAAATATG-GTTTTGGAA
1 AGTTTA-GGGTAAAAATGTAATTTTGGAAAGTTTAGGGGTAAAAATGTGAATTTTGGAA
* * * * * *
23942859 A--TTCGAGGCAAAAATGTAATTTTTTGAAAATTTTA-GGGTTAAAATGTGATTTTTGAGAA
1 AGTTTAG-GGTAAAAATGTAA--TTTTGGAAAGTTTAGGGGTAAAAATGTGAATTTTG-GAA
** * * *
23942918 AGTTCGGGGTTAAAAA-GGAATTTTTGG-AAG-TTAGAGGGTTAAAATGTGATTTTTGGAA
1 AGTTTAGGG-TAAAAATGTAA-TTTTGGAAAGTTTAG-GGGTAAAAATGTGAATTTTGGAA
* * *
23942976 AGTTTGGGGGTTAAAAGGTAATTTTTGGAAAGTT
1 AGTTT-AGGGTAAAAATGTAA-TTTTGGAAAGTT
23943010 CGAGGGCCTC
Statistics
Matches: 245, Mismatches: 55, Indels: 45
0.71 0.16 0.13
Matches are distributed among these distances:
55 1 0.00
56 19 0.08
57 38 0.16
58 96 0.39
59 75 0.31
60 8 0.03
61 8 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (58 bp):
AGTTTAGGGTAAAAATGTAATTTTGGAAAGTTTAGGGGTAAAAATGTGAATTTTGGAA
Found at i:23942855 original size:86 final size:85
Alignment explanation
Indices: 23942647--23943009 Score: 277
Period size: 87 Copynumber: 4.2 Consensus size: 85
23942637 TTAAAATATA
* * * **
23942647 ATTTTGGAAAGTTTAGGGGTAAAAATATAATTTTGAGAAAGTTTAGGGTAAAAATGTAATTTTTG
1 ATTTTTGAAAGTTTAGGGGTAAAAATATGATTTTG-G-AAG-TTCGGGGCAAAATGTAATTTTTG
* * *
23942712 AGAAG-TTCGAGGCAAAAATGTG
63 AGAAGTTTAGGGGTAAAAATGTG
* * ** *
23942734 AGTTTTGGAAGTTCGGGGGCAAAAATATGATTTTTGGAAGTTCGGGGGCAAAATGTAATTTTTGA
1 ATTTTTGAAAGTTTAGGGGTAAAAATATGA-TTTTGGAAGTTC-GGGGCAAAATGTAATTTTTGA
23942799 GAAGTTTAGGGGTAAAAATGTG
64 GAAGTTTAGGGGTAAAAATGTG
* * * * *
23942821 ATTTTTGAAAGTTTAGAGATAAAAATATGGTTTTGGAAATTCGAGGCAAAAATGTAATTTTTTGA
1 ATTTTTGAAAGTTTAGGGGTAAAAATATGATTTTGGAAGTTCGGGGC-AAAATGTAA-TTTTTGA
* * *
23942886 AAATTTTA-GGGTTAAAATGTG
64 GAAGTTTAGGGGTAAAAATGTG
* * * * * *
23942907 ATTTTTGAGAAAG-TTCGGGGTTAAAA-AGGAATTTTTGGAAGTTAGAGGGTTAAAATGTGATTT
1 ATTTTT--GAAAGTTTAGGGGTAAAAATATG-A-TTTTGGAAGTTCG-GGG-CAAAATGTAATTT
* * * *
23942970 TTG-GAAAGTTTGGGGGTTAAAAGGTA
60 TTGAG-AAGTTTAGGGGTAAAAATGTG
23942996 ATTTTTGGAAAGTT
1 ATTTTT-GAAAGTT
23943010 CGAGGGCCTC
Statistics
Matches: 219, Mismatches: 43, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
85 6 0.03
86 66 0.30
87 82 0.37
88 37 0.17
89 28 0.13
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (85 bp):
ATTTTTGAAAGTTTAGGGGTAAAAATATGATTTTGGAAGTTCGGGGCAAAATGTAATTTTTGAGA
AGTTTAGGGGTAAAAATGTG
Found at i:23942884 original size:29 final size:28
Alignment explanation
Indices: 23942696--23943014 Score: 115
Period size: 29 Copynumber: 11.0 Consensus size: 28
23942686 AGTTTAGGGT
*
23942696 AAAAATGTAATTTTTGAGAAGTTCGAGGC
1 AAAAATGTAATTTTTG-GAAATTCGAGGC
* * * *
23942725 AAAAATGTGAGTTTTGGAAGTTCGGGGGC
1 AAAAATGTAATTTTTGGAAATTC-GAGGC
* * * *
23942754 AAAAATATGATTTTTGGAAGTTCGGGGGC
1 AAAAATGTAATTTTTGGAAATTC-GAGGC
* * * *
23942783 -AAAATGTAATTTTTGAGAAGTTTAGGGGT
1 AAAAATGTAATTTTTG-GAA-ATTCGAGGC
* * **
23942812 AAAAATGTGATTTTT-GAAAGTTTAGAGAT
1 AAAAATGTAATTTTTGGAAA--TTCGAGGC
* **
23942841 AAAAATAT-GGTTTTGGAAATTCGAGGC
1 AAAAATGTAATTTTTGGAAATTCGAGGC
* ** *
23942868 AAAAATGTAATTTTTTGAAAATTTTAGGGT
1 AAAAATGTAA-TTTTTGGAAATTCGA-GGC
* * * *
23942898 TAAAATGTGATTTTTGAGAAAGTTCGGGGTT
1 AAAAATGTAATTTTTG-GAAA-TTCGAGG-C
* * * *
23942929 AAAAA-GGAATTTTTGGAAGTTAGAGGGT
1 AAAAATGTAATTTTTGGAAATTCGA-GGC
* * * * *
23942957 TAAAATGTGATTTTTGGAAAGTTTGGGGGT
1 AAAAATGTAATTTTTGGAAA--TTCGAGGC
* *
23942987 TAAAAGGTAATTTTTGGAAAGTTCGAGG
1 AAAAATGTAATTTTTGGAAA-TTCGAGG
23943015 GCCTCTTGAG
Statistics
Matches: 223, Mismatches: 50, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
27 12 0.05
28 35 0.16
29 107 0.48
30 59 0.26
31 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAATTCGAGGC
Found at i:23942905 original size:30 final size:30
Alignment explanation
Indices: 23942869--23943015 Score: 111
Period size: 30 Copynumber: 4.9 Consensus size: 30
23942859 ATTCGAGGCA
*
23942869 AAAATGTAATTTTTTGAAAATTTTAGGGTT
1 AAAATGTAATTTTTTGAAAATTTGAGGGTT
* *
23942899 AAAATGTGA-TTTTTGAGAAAGTTCG-GGGTT
1 AAAATGTAATTTTTTGA-AAA-TTTGAGGGTT
* * * * *
23942929 AAAAAGGAA-TTTTTGGAAGTTAGAGGGTT
1 AAAATGTAATTTTTTGAAAATTTGAGGGTT
* * * *
23942958 AAAATGTGATTTTTGGAAAGTTTGGGGGTT
1 AAAATGTAATTTTTTGAAAATTTGAGGGTT
* * * *
23942988 AAAAGGTAATTTTTGGAAAGTTCGAGGG
1 AAAATGTAATTTTTTGAAAATTTGAGGG
23943016 CCTCTTGAGC
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
28 3 0.03
29 20 0.22
30 68 0.73
31 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.29, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTTGAAAATTTGAGGGTT
Found at i:23946943 original size:17 final size:17
Alignment explanation
Indices: 23946913--23946950 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
23946903 AATAATAATG
23946913 AATTAAAAATTTATAAA
1 AATTAAAAATTTATAAA
23946930 AATTAGAAAA-TTATAAA
1 AATTA-AAAATTTATAAA
23946947 AATT
1 AATT
23946951 TTCTTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATTAAAAATTTATAAA
Found at i:23948037 original size:4 final size:4
Alignment explanation
Indices: 23948028--23948054 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
23948018 TTTCAAAAAT
23948028 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
23948055 TTCATAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:23950322 original size:30 final size:30
Alignment explanation
Indices: 23950245--23950356 Score: 93
Period size: 30 Copynumber: 3.8 Consensus size: 30
23950235 AAAAATAGAA
* * * * *
23950245 TTTCGAGAAATTCGAGATGAAAAT-GTAAT
1 TTTCGAAAAATTTGGGATCAAAATCGAAAT
*
23950274 TTTCGAGAAATTTGGGGATCAAAATCGAAAT
1 TTTCGAAAAATTT-GGGATCAAAATCGAAAT
* * *
23950305 TTTTGAAAAATTTGGGATTAAAATCGAACT
1 TTTCGAAAAATTTGGGATCAAAATCGAAAT
* * *
23950335 TTTGGAAAATTTTAGG-TCAAAA
1 TTTCGAAAAATTTGGGATCAAAA
23950357 ATGTGACTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.25
30 37 0.54
31 15 0.22
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (30 bp):
TTTCGAAAAATTTGGGATCAAAATCGAAAT
Found at i:23950414 original size:29 final size:28
Alignment explanation
Indices: 23950382--23950591 Score: 176
Period size: 29 Copynumber: 7.2 Consensus size: 28
23950372 ATTTGAACGC
*
23950382 AAAATGGTAATTTTTGGATGCTCGGGAGT
1 AAAATGGTAATTTTTGGATGTTCGGG-GT
23950411 AAAATGGTAATTTTTGGATGTTCGGGGGT
1 AAAATGGTAATTTTTGGATGTTC-GGGGT
* *
23950440 AAAATGGTAA--TTTGGAAAAGTTTGGGGT
1 AAAATGGTAATTTTTGG--ATGTTCGGGGT
* * * *
23950468 CAAAATGATAAATTTTGGATGTTCAAGGGC
1 -AAAATGGTAATTTTTGGATGTTC-GGGGT
*
23950498 AAAATGGTAATTTTTGGATGGTT-GAGGGC
1 AAAATGGTAATTTTTGGAT-GTTCG-GGGT
* *
23950527 AAAATGGTACTTTTTGGAATGTTCGAGAGT
1 AAAATGGTAATTTTTGG-ATGTTCG-GGGT
*
23950557 CAAAAT-GTAATTTTTGTAATGTTCGGGGTT
1 -AAAATGGTAATTTTTG-GATGTTCGGGG-T
23950587 AAAAT
1 AAAAT
23950592 ATGATTTTTG
Statistics
Matches: 150, Mismatches: 17, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
27 5 0.03
28 5 0.03
29 98 0.65
30 32 0.21
31 10 0.07
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGATGTTCGGGGT
Found at i:23950569 original size:87 final size:87
Alignment explanation
Indices: 23950411--23950572 Score: 204
Period size: 87 Copynumber: 1.9 Consensus size: 87
23950401 GCTCGGGAGT
* * * *
23950411 AAAATGGTAATTTTTGGATGTTCGGGGGTAAAATGGTAATTTGGAAAAGTTTGGGGTCAAAATGA
1 AAAATGGTAATTTTTGGATGTTCGAGGGCAAAATGGTAATTTGGAAAAGTTCGGAGTCAAAATGA
23950476 TAAATTTTGGATGTTCAAGGGC
66 TAAATTTTGGATGTTCAAGGGC
* *
23950498 AAAATGGTAATTTTTGGATGGTT-GAGGGCAAAATGGTACTTTTTGG-AATGTTCGAGAGTCAAA
1 AAAATGGTAATTTTTGGAT-GTTCGAGGGCAAAATGGTA--ATTTGGAAAAGTTCG-GAGTCAAA
*
23950561 ATG-TAATTTTTG
62 ATGATAAATTTTG
23950573 TAATGTTCGG
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
87 32 0.50
88 17 0.27
89 15 0.23
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.35
Consensus pattern (87 bp):
AAAATGGTAATTTTTGGATGTTCGAGGGCAAAATGGTAATTTGGAAAAGTTCGGAGTCAAAATGA
TAAATTTTGGATGTTCAAGGGC
Found at i:23950629 original size:29 final size:30
Alignment explanation
Indices: 23950581--23950727 Score: 154
Period size: 30 Copynumber: 4.9 Consensus size: 30
23950571 TGTAATGTTC
* * *
23950581 GGGGTTAAAATATGATTTTTGAGAAGTTTA
1 GGGGTTAAAATATAATTTTAGAAAAGTTTA
* *
23950611 GGGGTTAAAATGTAATTTTAGAGAAGTTTA
1 GGGGTTAAAATATAATTTTAGAAAAGTTTA
*
23950641 AGGGTTAAAATATAATTTTAGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAGAAAAGTTTA
* **
23950671 GGGGTCAAAATGCAATTTT-GAAAAAGTTT-
1 GGGGTTAAAATATAATTTTAG-AAAAGTTTA
* * * *
23950700 GGGGTCAAAATATGATTTTTGGAAAGTT
1 GGGGTTAAAATATAATTTTAGAAAAGTT
23950728 CAAAGACCTT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.23
30 78 0.77
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGGTTAAAATATAATTTTAGAAAAGTTTA
Found at i:23950698 original size:60 final size:59
Alignment explanation
Indices: 23950555--23950727 Score: 186
Period size: 60 Copynumber: 2.9 Consensus size: 59
23950545 ATGTTCGAGA
* * * * ** *
23950555 GTCAAAATGTAATTTTTGTAATGTTCGGGGTTAAAATATGATTTTTGAGAAGTTTAGGG
1 GTCAAAATGCAATTTTAGAAAAGTTTAGGGTTAAAATATGATTTTTGAAAAGTTTAGGG
* * * * *
23950614 GTTAAAATGTAATTTTAGAGAAGTTTAAGGGTTAAAATATAATTTTAGAAAAGTTTAGGG
1 GTCAAAATGCAATTTTAGAAAAGTTT-AGGGTTAAAATATGATTTTTGAAAAGTTTAGGG
* * *
23950674 GTCAAAATGCAATTTT-GAAAAAGTTTGGGGTCAAAATATGATTTTTGGAAAGTT
1 GTCAAAATGCAATTTTAG-AAAAGTTTAGGGTTAAAATATGATTTTTGAAAAGTT
23950728 CAAAGACCTT
Statistics
Matches: 94, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
59 44 0.47
60 50 0.53
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (59 bp):
GTCAAAATGCAATTTTAGAAAAGTTTAGGGTTAAAATATGATTTTTGAAAAGTTTAGGG
Found at i:23951657 original size:13 final size:13
Alignment explanation
Indices: 23951639--23951663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23951629 TTTGTTTTTA
23951639 TTATTTATTATAT
1 TTATTTATTATAT
23951652 TTATTTATTATA
1 TTATTTATTATA
23951664 CTTAATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTATTATAT
Found at i:23952893 original size:39 final size:39
Alignment explanation
Indices: 23952850--23953305 Score: 291
Period size: 39 Copynumber: 11.7 Consensus size: 39
23952840 GATGGTTGCA
* *
23952850 ATCTGCCCTAAGCTCGGGATAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
** *
23952889 ATCTGCCTTAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * **
23952928 ATTTGCCCCAGGCTCGGGGTAAAAGA-T--CAAATGGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-TG
23952965 TAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * **
23953006 ATCTGCCTC-AGACTCGGGGTAAAAGA-T--CAAATGGCTG
1 ATCTGCCCCAAG-CTCGGGGTAAGAGATTGGCTGATGG-TG
* * * *
23953043 TAACTTGCCCCAAACTTGGGGTAAGAGATTGGCTAATGGTG
1 -ATC-TGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * ** * * ** * *
23953084 ATCTGCCTCAGGCTTAGGGTAAAAGATCGAATGGCT-GTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTG
* *
23953123 ATTTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* ** * * * * ** *
23953162 ATTTTTCCCAGGCTCGAGGTAAGAGATCGGATGGCGGTA
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * *
23953201 ATCTACCCCAGGCTCGAGGTAAAAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * * *
23953240 ATCT-ACCCTAGACTCAGGGTAAAAGATTGGATGATTGTG
1 ATCTGCCCCAAG-CTCGGGGTAAGAGATTGGCTGATGGTG
* * *
23953279 ATCTGCCTCATGATCGGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT
23953306 CGAAATCTTC
Statistics
Matches: 319, Mismatches: 80, Indels: 36
0.73 0.18 0.08
Matches are distributed among these distances:
36 10 0.03
37 4 0.01
38 12 0.04
39 269 0.84
40 9 0.03
41 4 0.01
42 11 0.03
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:23952971 original size:78 final size:78
Alignment explanation
Indices: 23952900--23953266 Score: 466
Period size: 78 Copynumber: 4.7 Consensus size: 78
23952890 TCTGCCTTAG
*
23952900 GCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG
23952965 TAATCTGCCCCAA
66 TAATCTGCCCCAA
* *
23952978 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCTCAGACTCGGGGTAAAAGATCAAATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG
23953043 TAA-CTTGCCCCAA
66 TAATC-TGCCCCAA
* * * * ** *
23953056 ACTTGGGGTAAGAGATTGGCTAATGGTGATCTGCCTCAGGCTTAGGGTAAAAGATCGAATGGCTG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG
*
23953121 TAATTTGCCCCAA
66 TAATCTGCCCCAA
* * ** * * ** *
23953134 GCTCGGGGTAAGAGATTGGCTGATAGTGATTTTTCCCAGGCTCGAGGTAAGAGATCGGATGGCGG
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG
* *
23953199 TAATCTACCCCAG
66 TAATCTGCCCCAA
* * * * * *
23953212 GCTCGAGGTAAAAGATTGGCTGATGGTGATCTACCCTAGACTCAGGGTAAAAGAT
1 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGAT
23953267 TGGATGATTG
Statistics
Matches: 248, Mismatches: 39, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
77 1 0.00
78 247 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (78 bp):
GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGGCTG
TAATCTGCCCCAA
Found at i:23965097 original size:30 final size:30
Alignment explanation
Indices: 23965061--23965125 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
23965051 ATTTTCGATG
* * *
23965061 AATTTGGGGATCAAAATTGAAGTTTTTG-A
1 AATTTGGGGATCAAAATCGAACTTTTAGAA
* *
23965090 AATTTTGGGATTAAAATCGAACTTTTAGAA
1 AATTTGGGGATCAAAATCGAACTTTTAGAA
23965120 AATTTG
1 AATTTG
23965126 AGGTCGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGGATCAAAATCGAACTTTTAGAA
Found at i:23965192 original size:29 final size:28
Alignment explanation
Indices: 23965160--23965318 Score: 135
Period size: 29 Copynumber: 5.5 Consensus size: 28
23965150 AATTAAGGGC
*
23965160 AAAATGGTAATTTTTGGATTCTCGGGGGT
1 AAAATGGTAATTTTTGGA-TGTCGGGGGT
23965189 AAAATGGTAATTTTTGGATGATCGGGGG-
1 AAAATGGTAATTTTTGGATG-TCGGGGGT
* ** **
23965217 -AAATGGTAA-TTTTGGAAAAGTTCAAGGCC
1 AAAATGGTAATTTTTGG--ATG-TCGGGGGT
23965246 AAAATGGTAATTTTTGGATGGTCGGGGGT
1 AAAATGGTAATTTTTGGAT-GTCGGGGGT
* ***
23965275 AAAATTGTAATTTTTGGATGTTTAAGGGT
1 AAAATGGTAATTTTTGGATG-TCGGGGGT
*
23965304 AAAATGGTACTTTTT
1 AAAATGGTAATTTTT
23965319 AGAAAGTTCG
Statistics
Matches: 105, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
26 6 0.06
27 9 0.09
28 8 0.08
29 66 0.63
30 10 0.10
31 6 0.06
ACGTcount: A:0.30, C:0.05, G:0.29, T:0.36
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGATGTCGGGGGT
Found at i:23965387 original size:46 final size:46
Alignment explanation
Indices: 23965335--23965422 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
23965325 TTCGAGGGTC
*
23965335 AAAATGTAATTGT-AAAAAGTATGGGGGTTAAAATATAATTTTAGAG
1 AAAATGTAATTGTGAAAAAGT-TGGGGGTCAAAATATAATTTTAGAG
* * * *
23965381 AAAATGTAATTTTGGAAAAGTTTGGGGTCAAAATATGATTTT
1 AAAATGTAATTGTGAAAAAGTTGGGGGTCAAAATATAATTTT
23965423 GGAAAGTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
46 30 0.83
47 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.22, T:0.35
Consensus pattern (46 bp):
AAAATGTAATTGTGAAAAAGTTGGGGGTCAAAATATAATTTTAGAG
Found at i:23967016 original size:14 final size:15
Alignment explanation
Indices: 23966997--23967026 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
23966987 TTAGGTTTTG
23966997 TAATTGGGCTT-GGT
1 TAATTGGGCTTAGGT
23967011 TAATTGGGCTTAGGT
1 TAATTGGGCTTAGGT
23967026 T
1 T
23967027 TAGGTGGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.17, C:0.07, G:0.33, T:0.43
Consensus pattern (15 bp):
TAATTGGGCTTAGGT
Found at i:23978341 original size:19 final size:20
Alignment explanation
Indices: 23978302--23978347 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
23978292 TTTATAACAA
* **
23978302 TATTTAATTTTTTTTTGAAT
1 TATTTAAATTTTTTTAAAAT
23978322 T-TTTAAATTTTTTTAAAAT
1 TATTTAAATTTTTTTAAAAT
23978341 TATTTAA
1 TATTTAA
23978348 GAAAAACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTAAATTTTTTTAAAAT
Found at i:23981846 original size:23 final size:22
Alignment explanation
Indices: 23981818--23981964 Score: 125
Period size: 23 Copynumber: 6.5 Consensus size: 22
23981808 ACATTAGCGC
*
23981818 GCTTACTGTTCAACACTGTGTGT
1 GCTTACTGTTC-GCACTGTGTGT
* *
23981841 GTTTACTATTCAGCACTGTGTGT
1 GCTTACTGTTC-GCACTGTGTGT
* * * *
23981864 GCTTACTGATTCACAATATATGT
1 GCTTACTG-TTCGCACTGTGTGT
23981887 GCTTACTGATT-GCACTGTGTGT
1 GCTTACTG-TTCGCACTGTGTGT
*
23981909 GCTTACTGTTTTGCACTGTGTGT
1 GCTTACTG-TTCGCACTGTGTGT
* * * *
23981932 GCCTGCTGATTTGCACTATGTGT
1 GCTTACTG-TTCGCACTGTGTGT
23981955 GCTTACTGTT
1 GCTTACTGTT
23981965 TCCCCAGCAC
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
22 19 0.19
23 80 0.78
24 3 0.03
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (22 bp):
GCTTACTGTTCGCACTGTGTGT
Found at i:23981910 original size:45 final size:46
Alignment explanation
Indices: 23981853--23981962 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 46
23981843 TTACTATTCA
*
23981853 GCACTGTGTGTGCTTACTGATTCACAATATATGTGCTTACTGA-TT
1 GCACTGTGTGTGCTTACTGATTCACAATATATGTGCCTACTGATTT
* ** * * * *
23981898 GCACTGTGTGTGCTTACTGTTTTGCACTGTGTGTGCCTGCTGATTT
1 GCACTGTGTGTGCTTACTGATTCACAATATATGTGCCTACTGATTT
*
23981944 GCACTATGTGTGCTTACTG
1 GCACTGTGTGTGCTTACTG
23981963 TTTCCCCAGC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
45 35 0.64
46 20 0.36
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.41
Consensus pattern (46 bp):
GCACTGTGTGTGCTTACTGATTCACAATATATGTGCCTACTGATTT
Found at i:23981928 original size:68 final size:68
Alignment explanation
Indices: 23981831--23981962 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 68
23981821 TACTGTTCAA
* *
23981831 CACTGTGTGTGTTTACTATTCAGCACTGTGTGTGCTTACTGATTCACAATATATGTGCTTACTGA
1 CACTGTGTGTGCTTACTATTCAGCACTGTGTGTGCCTACTGATTCACAATATATGTGCTTACTGA
23981896 TTG
66 TTG
* ** * ** * *
23981899 CACTGTGTGTGCTTACTGTTTTGCACTGTGTGTGCCTGCTGATTTGCACTATGTGTGCTTACTG
1 CACTGTGTGTGCTTACTATTCAGCACTGTGTGTGCCTACTGATTCACAATATATGTGCTTACTG
23981963 TTTCCCCAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (68 bp):
CACTGTGTGTGCTTACTATTCAGCACTGTGTGTGCCTACTGATTCACAATATATGTGCTTACTGA
TTG
Found at i:23993743 original size:17 final size:18
Alignment explanation
Indices: 23993721--23993758 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
23993711 GGGCTTATAA
* *
23993721 AAATATGAACATG-AATT
1 AAATATAAACAAGCAATT
23993738 AAATATAAACAAGCAATT
1 AAATATAAACAAGCAATT
23993756 AAA
1 AAA
23993759 CACAATCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (18 bp):
AAATATAAACAAGCAATT
Found at i:23997575 original size:209 final size:209
Alignment explanation
Indices: 23996852--23997725 Score: 1133
Period size: 210 Copynumber: 4.2 Consensus size: 209
23996842 TTGGCGTCAT
* * *
23996852 TTGATTTGGTCTATTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
* * * * *
23996917 CTCTGTGTCTCATCAGGAAGAC-GATTCTGGTTCACTTCTTTGTATCTTA-CCAG--G--AA-GG
66 CTCTGTGTCTCATCAGGAAGACGGATT-TGGTTCACTTCTCTATATCTCATCAAGAAGTTAACCG
* * * * *
23996975 TTTTATTGCTTCG---TCCTACTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTTGCTCAC
130 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGA-TTTGCTCAC
*
23997037 TTTGAGTCTGGTTTCA
194 TTTGAGCCTGGTTTCA
* * *
23997053 TTGATTTGGTCTACTTCTCAGTATCTCATTAGGAAGATGACCGCATCAATTGTTTTGATCCACTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
** * *
23997118 CTCTGTGTCTCATCAAAAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGTTAACCGC
66 CTCTGTGTCTCATCAGGAAGACGGATTTGGTTCACTTCTCTATATCTCATCAAGAAGTTAACCGC
* * * * * *
23997183 TTTATTTCTTTGACCTGCTTCTTAGTATCTCATAAGGAAGCTGGGGTTCAAAAATTTGCTCACTT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTT
23997248 TGAGCCTGGTTTTCA
196 TGAGCCTGG-TTTCA
*
23997263 TTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
* *
23997328 CTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAAGAAGTTAACCGC
66 CTCTGTGTCTCATCAGGAAGACGGATTTGGTTCACTTCTCTATATCTCATCAAGAAGTTAACCGC
* *
23997393 TTTATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAG-TTTCGCTCACA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCTCACT
* *
23997457 TTGAGCTTTGTTTCA
195 TTGAGCCTGGTTTCA
* * ** *
23997472 TTGATTTGGTCTACTTCTCAGTATTTCATCAGGAAGATGATCGCATTACTTGTTTCAATCCGCTT
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
* * * * * *
23997537 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT-TAGTATCTCATCAGGAAGCTAACCA
66 CTCTGTGTCTCATCAGGAAGACGGATTTGGTTCACTTCTCTA-TATCTCATCAAGAAGTTAACCG
* * *
23997601 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTACTCACT
130 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC-
* *
23997666 TTTAAGCCTTGTTTCA
194 TTTGAGCCTGGTTTCA
* * *
23997682 TTGATTTGGTATACTTCTCTGTATCTCATCAGGGAGATGATCGC
1 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGC
23997726 CTCGTTGTTT
Statistics
Matches: 590, Mismatches: 68, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
201 101 0.17
202 6 0.01
204 1 0.00
206 2 0.00
207 11 0.02
208 2 0.00
209 195 0.33
210 272 0.46
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (209 bp):
TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTT
CTCTGTGTCTCATCAGGAAGACGGATTTGGTTCACTTCTCTATATCTCATCAAGAAGTTAACCGC
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTT
TGAGCCTGGTTTCA
Found at i:23997631 original size:419 final size:411
Alignment explanation
Indices: 23996855--23997725 Score: 1158
Period size: 419 Copynumber: 2.1 Consensus size: 411
23996845 GCGTCATTTG
* * *
23996855 ATTTGGTCTATTTCTTAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTC
* * * * * *
23996920 TGTGTCTCATCAGGAAGACGATTCTGGTTCACTTCTTTGTATCTTACCAGGAAGGTTTTATTGCT
66 TGTGTCTCATCAGGAAGACGATTCTGGTTCACTTCTCTATATCTCACAAGGAACGCTTTATTGCT
* * *
23996985 TCGTCCTACTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTTGCTCACTTTGAGTCTGGTT
131 TCGTCCTACTCAATATCTCATCAGAAAGCTGGGATTCGAAGATTTCGCTCACATTGAGTCTGGTT
* **
23997050 TCATTGATTTGGTCTACTTCTCAGTATCTCATTAGGAAGATGACCGCATCAATTGTTTTGATCCA
196 TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCAATTGTTTCAATCCA
* * * *
23997115 CTTCTCTGTGTCTCATCAAAAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGAAGTTAAC
261 CTTCTCTGTATCTCATCAAAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAAC
* * * * *
23997180 CGCTTTATTTCTTTGACCTGCTTCTTAGTATCTCATAAGGAAGCTGGGGTTCAAAAATTTGCTCA
326 CACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTGGGGTTCAAAAATTTACTCA
*
23997245 C-TTTGAGCCTGGTTTTCATTA
391 CTTTTAAGCCTGG-TTTCATTA
*
23997266 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTT
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTC
23997331 TGTGTCTCATCAGGAAGACGGA-TCTGGTTCACTTCTCTATATCTCATCAAGAAGTTAACCGCTT
66 TGTGTCTCATCAGGAAGAC-GATTCTGGTTCACTTCTCTATATCTCA-CAAG--G--AA-CGCTT
* * * *
23997395 TATTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAG-TTTCGCTCACATT
124 TATTGCTTCG---TCCTACTCAATATCTCATCAGAAAGCTGGGATTCGAAGATTTCGCTCACATT
* * * * *
23997459 GAG-CTTTGTTTCATTGATTTGGTCTACTTCTCAGTATTTCATCAGGAAGATGATCGCATTACTT
186 GAGTC-TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCAATT
* **
23997523 GTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT-TAGTATCTCAT
250 GTTTCAATCCACTTCTCTGTATCTCATCAAAAAGACGAATTTGGTCCACTTCTCT-GTATCTCAT
* * * *
23997587 CAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCG
314 CAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTGGGGTTCA
* * *
23997652 AAGATTTACTCACTTTTAAGCCTTGTTTCATTG
379 AAAATTTACTCACTTTTAAGCCTGGTTTCATTA
* * *
23997685 ATTTGGTATACTTCTCTGTATCTCATCAGGGAGATGATCGC
1 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGC
23997726 CTCGTTGTTT
Statistics
Matches: 399, Mismatches: 48, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
411 101 0.25
412 5 0.01
414 1 0.00
416 2 0.01
417 13 0.03
418 2 0.01
419 233 0.58
420 42 0.11
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (411 bp):
ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACTTCTC
TGTGTCTCATCAGGAAGACGATTCTGGTTCACTTCTCTATATCTCACAAGGAACGCTTTATTGCT
TCGTCCTACTCAATATCTCATCAGAAAGCTGGGATTCGAAGATTTCGCTCACATTGAGTCTGGTT
TCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCAATTGTTTCAATCCA
CTTCTCTGTATCTCATCAAAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAAC
CACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATAAGGAAGCTGGGGTTCAAAAATTTACTCA
CTTTTAAGCCTGGTTTCATTA
Found at i:24005920 original size:23 final size:24
Alignment explanation
Indices: 24005875--24005920 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
24005865 AATATGCAAA
* *
24005875 TATGCAATGCGAATAAAATGCATG
1 TATGCAATGCGAAGAAAAGGCATG
*
24005899 TATGTAATGC-AAGAAAAGGCAT
1 TATGCAATGCGAAGAAAAGGCAT
24005921 TGATTTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (24 bp):
TATGCAATGCGAAGAAAAGGCATG
Found at i:24009954 original size:29 final size:30
Alignment explanation
Indices: 24009832--24010218 Score: 183
Period size: 29 Copynumber: 13.4 Consensus size: 30
24009822 TTTAGATGCC
* * *
24009832 CGAGGGTAAAACGGTAA-TTTTAGACACTT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* * * * * *
24009861 CGAGAGCAAAACGATAATTTTTAGACA-CT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* * *
24009890 CG-GGGTAAAATTGTAATTTTTA-TATGTT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* * *
24009918 -AAAGGTAAAATGGTAATTTTTAGATA-TT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* *
24009946 CGGGGGTAAAAAT-ATAAATTTTT-GAAAGTT
1 CGAGGGT-AAAATGGT-AATTTTTAGAAAGTT
24009976 C-AGGGTCAAAAT-GTAA-TTTTAGAAAGTT
1 CGAGGGT-AAAATGGTAATTTTTAGAAAGTT
* * *
24010004 CGAGGGTAAAATGGTGATTTTTGGAAAATT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* * *
24010034 TGA-GTTCAAAATTGG-AA-TTTTGGAAA-TT
1 CGAGGGT-AAAA-TGGTAATTTTTAGAAAGTT
* *
24010062 CGAGGGTAAAATGGT-ATTTTTGGAAAATT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* ** *
24010091 TGAGTTTAAAAAAGG-AATTTTT-GAAAGTT
1 CGAGGGT-AAAATGGTAATTTTTAGAAAGTT
* * * *
24010120 TG-GGGTTAAAT-ATAATTTTTGGAAA-TT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
**
24010147 TAAGGGTAAAATGGTAATTTTTAGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTAGAAAGTT
* *
24010177 TG-GGGTTAAAAATGG-AATTTTT-GGAAGTT
1 CGAGGG-T-AAAATGGTAATTTTTAGAAAGTT
*
24010206 CGGGGGTTAAAAT
1 CGAGGG-TAAAAT
24010219 ATGATTTTTG
Statistics
Matches: 278, Mismatches: 52, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
27 21 0.08
28 82 0.29
29 96 0.35
30 69 0.25
31 10 0.04
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
CGAGGGTAAAATGGTAATTTTTAGAAAGTT
Found at i:24010000 original size:28 final size:28
Alignment explanation
Indices: 24009921--24010286 Score: 120
Period size: 29 Copynumber: 12.6 Consensus size: 28
24009911 ATATGTTAAA
* *
24009921 GGTAAAATGGTAATTTTTAGATA-TTCGGG
1 GGTAAAAT-GTAA-TTTTAGAAAGTTCGAG
* *
24009950 GGTAAAAATATAAATTTTTGAAAGTTC-AG
1 GGT-AAAATGT-AATTTTAGAAAGTTCGAG
24009979 GGTCAAAATGTAATTTTAGAAAGTTCGAG
1 GGT-AAAATGTAATTTTAGAAAGTTCGAG
* * * *
24010008 GGTAAAATGGTGATTTTTGGAAAATTTGA-
1 GGTAAAAT-GT-AATTTTAGAAAGTTCGAG
* * *
24010037 GTTCAAAATTGGAATTTTGGAAA-TTCGAG
1 GGT-AAAA-TGTAATTTTAGAAAGTTCGAG
* * * *
24010066 GGTAAAATGGTATTTTTGGAAAATTTGAG
1 GGTAAAAT-GTAATTTTAGAAAGTTCGAG
** * * * *
24010095 TTTAAAAAAGGAATTTTTGAAAGTTTG-G
1 GGT-AAAATGTAATTTTAGAAAGTTCGAG
* * * **
24010123 GGTTAAATATAATTTTTGGAAA-TTTAAG
1 GGTAAAATGTAA-TTTTAGAAAGTTCGAG
*
24010151 GGTAAAATGGTAATTTTTAGAAAGTTTG-G
1 GGTAAAAT-GTAA-TTTTAGAAAGTTCGAG
* * * *
24010180 GGTTAAAAATGGAATTTTTGGAAGTTCGGG
1 GG-T-AAAATGTAATTTTAGAAAGTTCGAG
* * * * * *
24010210 GGTTAAAATATGATTTTTGAAAAATTTGAT
1 GG-TAAAATGTAATTTTAG-AAAGTTCGAG
24010240 GGTCAAAATGTAATTTTTA-AGAAGTTC-ATG
1 GGT-AAAATGTAA-TTTTAGA-AAGTTCGA-G
*
24010270 GGTCAAAATGTGATTTT
1 GGT-AAAATGTAATTTT
24010287 TAAATAGTTT
Statistics
Matches: 256, Mismatches: 57, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
27 9 0.04
28 56 0.22
29 107 0.42
30 74 0.29
31 10 0.04
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (28 bp):
GGTAAAATGTAATTTTAGAAAGTTCGAG
Found at i:24010026 original size:57 final size:58
Alignment explanation
Indices: 24009962--24010286 Score: 197
Period size: 57 Copynumber: 5.6 Consensus size: 58
24009952 TAAAAATATA
*
24009962 AATTTTT-GAAAGTTCAGGGTCAAAATGTAATTTTAGAAAGTTCGAGGGTAAAATGGT
1 AATTTTTGGAAAGTTCAGGGTCAAAATGTAATTTTAGAAAGTTTGAGGGTAAAATGGT
* * * * * * *
24010019 GATTTTTGGAAAATT-TGAGTTCAAAATTGGAATTTTGGAAA-TTCGAGGGTAAAATGGT
1 AATTTTTGGAAAGTTCAG-GGTCAAAA-TGTAATTTTAGAAAGTTTGAGGGTAAAATGGT
* * ** * * * * * *
24010077 -ATTTTTGGAAAATTTGAGTTTAAAAAAGGAATTTTTGAAAGTTTG-GGGTTAAAT-AT
1 AATTTTTGG-AAAGTTCAGGGTCAAAATGTAATTTTAGAAAGTTTGAGGGTAAAATGGT
* *
24010133 AATTTTTGGAAATTTAAGGGT-AAAATGGTAATTTTTAGAAAGTTTG-GGGTTAAAAATGG-
1 AATTTTTGGAAAGTTCAGGGTCAAAAT-GTAA-TTTTAGAAAGTTTGAGGG-T-AAAATGGT
* * * * * * *
24010192 AATTTTTGG-AAGTTCGGGGGTTAAAATATGATTTTTGAAAAATTTGATGGTCAAAAT-GT
1 AATTTTTGGAAAGTTC-AGGGTCAAAATGTAATTTTAG-AAAGTTTGAGGGT-AAAATGGT
* *
24010251 AATTTTT-AAGAAGTTCATGGGTCAAAATGTGATTTT
1 AATTTTTGGA-AAGTTCA-GGGTCAAAATGTAATTTT
24010287 TAAATAGTTT
Statistics
Matches: 212, Mismatches: 36, Indels: 37
0.74 0.13 0.13
Matches are distributed among these distances:
55 4 0.02
56 13 0.06
57 59 0.28
58 55 0.26
59 52 0.25
60 29 0.14
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (58 bp):
AATTTTTGGAAAGTTCAGGGTCAAAATGTAATTTTAGAAAGTTTGAGGGTAAAATGGT
Found at i:24010043 original size:58 final size:57
Alignment explanation
Indices: 24009981--24010202 Score: 213
Period size: 57 Copynumber: 3.8 Consensus size: 57
24009971 AAGTTCAGGG
* *
24009981 TCAAAATGTAATTTTAGAAAGTTCGAGGGTAAAATGGTGATTTTTGGAAAATTTGAGT
1 TCAAAATGGAATTTTAGAAAGTTCG-GGGTAAAATGGTAATTTTTGGAAAATTTGAGT
*
24010039 TCAAAATTGGAATTTTGGAAA-TTCGAGGGTAAAATGGT-ATTTTTGGAAAATTTGAGTT
1 TCAAAA-TGGAATTTTAGAAAGTTCG-GGGTAAAATGGTAATTTTTGGAAAATTTGAG-T
* * * * * * * *
24010097 TAAAAAAGGAATTTTTGAAAGTTTGGGGTTAAAT-ATAATTTTTGG-AAATTTAAGGG
1 TCAAAATGGAATTTTAGAAAGTTCGGGGTAAAATGGTAATTTTTGGAAAATTTGA-GT
*
24010153 T-AAAATGGTAATTTTTAGAAAGTTTGGGGTTAAAAATGG-AATTTTTGGAA
1 TCAAAATGG-AA-TTTTAGAAAGTTCGGGG-T-AAAATGGTAATTTTTGGAA
24010203 GTTCGGGGGT
Statistics
Matches: 139, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
55 6 0.04
56 11 0.08
57 63 0.45
58 33 0.24
59 25 0.18
60 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (57 bp):
TCAAAATGGAATTTTAGAAAGTTCGGGGTAAAATGGTAATTTTTGGAAAATTTGAGT
Found at i:24010256 original size:30 final size:30
Alignment explanation
Indices: 24010222--24010295 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
24010212 TTAAAATATG
* *
24010222 ATTTTTGAAAAATTTGAT-GGTCAAAATGTA
1 ATTTTT-AAAAAGTTCATGGGTCAAAATGTA
* *
24010252 ATTTTTAAGAAGTTCATGGGTCAAAATGTG
1 ATTTTTAAAAAGTTCATGGGTCAAAATGTA
*
24010282 ATTTTTAAATAGTT
1 ATTTTTAAAAAGTT
24010296 TAGGGATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (30 bp):
ATTTTTAAAAAGTTCATGGGTCAAAATGTA
Found at i:24011435 original size:18 final size:18
Alignment explanation
Indices: 24011412--24011447 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24011402 ATCATTATTT
* *
24011412 TAATAAATTTATTATTAA
1 TAATAAATGTACTATTAA
24011430 TAATAAATGTACTATTAA
1 TAATAAATGTACTATTAA
24011448 AGGATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TAATAAATGTACTATTAA
Found at i:24013463 original size:60 final size:58
Alignment explanation
Indices: 24013292--24013799 Score: 361
Period size: 60 Copynumber: 8.6 Consensus size: 58
24013282 ACCCCAAATA
* * * *
24013292 TTTCCAAAATTACATTTTAACCCCTTCAACATTT-T-TAAAATTATATTTTCACCCCT-AAAC
1 TTTCCAAAATTACATTTTAA-CCC-T-AA-ATTTATCCAAAATCACATTTT-AACCCTAAAAC
** * * *
24013352 TTTTTAAAAATTATATTTTAACCCTCGAA-CT-TCCTAAAATCACATTTTAACCCTAAAAC
1 -TTTCCAAAATTACATTTTAACCCT-AAATTTATCC-AAAATCACATTTTAACCCTAAAAC
* * * *
24013411 TTTCCTAAAATCACATTTTAATCCCTAAATTTATCCAAAATCATAATTTAACCTTAAAAC
1 TTTCC-AAAATTACATTTTAA-CCCTAAATTTATCCAAAATCACATTTTAACCCTAAAAC
** * * *
24013471 TTCTCCAAAATTACATTTTAACTTTTAAATTTATCCAAAATCACATATTAGCCTTAAAA-
1 TT-TCCAAAATTACATTTTAAC-CCTAAATTTATCCAAAATCACATTTTAACCCTAAAAC
* * * * *
24013530 ATT-CAAAATTACATTTTGACCCTAAAATTTATCTAAAATTACATTTTGACCCCT-AAAC
1 TTTCCAAAATTACATTTTAACCCT-AAATTTATCCAAAATCACATTTT-AACCCTAAAAC
* ** * *
24013588 TTTTCCAAAATTACATTTTAACCCTTAAATTTCTTTAAAATTACATTTTGACCCT-AAAC
1 -TTTCCAAAATTACATTTTAACCC-TAAATTTATCCAAAATCACATTTTAACCCTAAAAC
** * * * * * * *
24013647 TTTTATAAAATTACATTTTGACCCTAAACTTCTCAAAAATCACCTTTTGACCCTTAAAC
1 -TTTCCAAAATTACATTTTAACCCTAAATTTATCCAAAATCACATTTTAACCCTAAAAC
* * * * * * *
24013706 TTCTCCAAAATTATATTTTAACCCTTAAACTTCTCTAAAATCACATTTTAACCTCCAATAT
1 TT-TCCAAAATTACATTTTAACCC-TAAATTTATCCAAAATCACATTTTAACC-CTAAAAC
*
24013767 TTTCCAAAATTACATTTTAACCTTAAA-TTATCC
1 TTTCCAAAATTACATTTTAACCCTAAATTTATCC
24013800 TAAACTTCAT
Statistics
Matches: 365, Mismatches: 63, Indels: 41
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.00
57 41 0.11
58 45 0.12
59 91 0.25
60 158 0.43
61 29 0.08
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (58 bp):
TTTCCAAAATTACATTTTAACCCTAAATTTATCCAAAATCACATTTTAACCCTAAAAC
Found at i:24013568 original size:117 final size:118
Alignment explanation
Indices: 24013358--24013753 Score: 392
Period size: 117 Copynumber: 3.4 Consensus size: 118
24013348 AAACTTTTTA
* ** * * *
24013358 AAAATTATATTTTAACCCTCGAACTTC-CTAAAATCACATTTTA-ACCCTAAA-ACTTTCCTAAA
1 AAAATTACATTTTAACCCTTAAATTTCTCTAAAATCACA-TTTAGACCCTAAACA-ATTAC-AAA
* * * * * *
24013420 ATCACATTTTAATCCCTAAATTTATCCAAAATCATAATTT-AACCTTAAAACTTCTCC
63 ATTACATTTTGA-CCCTAAATTTATCAAAAATCACATTTTGACCCTT-AAACTTCTCC
** * * *
24013477 AAAATTACATTTTAACTTTTAAATTTATCCAAAATCACATATTAG-CCTTAAA-AATT-CAAAAT
1 AAAATTACATTTTAACCCTTAAATTTCTCTAAAATCACAT-TTAGACCCTAAACAATTACAAAAT
* * * *
24013539 TACATTTTGACCCTAAAATTTATCTAAAATTACATTTTGACCCCTAAACTTTTCC
65 TACATTTTGACCCT-AAATTTATCAAAAATCACATTTTGACCCTTAAACTTCTCC
* * * ** *
24013594 AAAATTACATTTTAACCCTTAAATTTCTTTAAAATTACATTTTGACCCTAAACTTTTATAAAATT
1 AAAATTACATTTTAACCCTTAAATTTCTCTAAAATCACATTTAGACCCTAAACAATTACAAAATT
* * *
24013659 ACATTTTGACCCTAAACTTCTCAAAAATCACCTTTTGACCCTTAAACTTCTCC
66 ACATTTTGACCCTAAATTTATCAAAAATCACATTTTGACCCTTAAACTTCTCC
* *
24013712 AAAATTATATTTTAACCCTTAAACTTCTCTAAAATCACATTT
1 AAAATTACATTTTAACCCTTAAATTTCTCTAAAATCACATTT
24013754 TAACCTCCAA
Statistics
Matches: 228, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
116 7 0.03
117 81 0.36
118 78 0.34
119 42 0.18
120 20 0.09
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.38
Consensus pattern (118 bp):
AAAATTACATTTTAACCCTTAAATTTCTCTAAAATCACATTTAGACCCTAAACAATTACAAAATT
ACATTTTGACCCTAAATTTATCAAAAATCACATTTTGACCCTTAAACTTCTCC
Found at i:24013789 original size:30 final size:28
Alignment explanation
Indices: 24013277--24013812 Score: 315
Period size: 30 Copynumber: 18.1 Consensus size: 28
24013267 TAGAAATTTG
* *
24013277 TTTTGACCCCAAATATTTCCAAAATTACA
1 TTTTAACCCTAAAT-TTTCCAAAATTACA
* *
24013306 TTTTAACCCCTTCAACATTTT-TAAAATTATA
1 TTTTAA-CCC-T-AA-ATTTTCCAAAATTACA
* ** *
24013337 TTTTCACCCCTAAACTTTTTAAAAATTATA
1 TTTT-AACCCTAAA-TTTTCCAAAATTACA
* * *
24013367 TTTTAACCCTCGAA-CTTCCTAAAATCACA
1 TTTTAACCCT-AAATTTTCC-AAAATTACA
* *
24013396 TTTTAACCCTAAAACTTTCCTAAAATCACA
1 TTTTAACCCT-AAATTTTCC-AAAATTACA
* *
24013426 TTTTAATCCCTAAATTTATCCAAAATCATA
1 TTTTAA-CCCTAAATTT-TCCAAAATTACA
* * *
24013456 ATTTAACCTTAAAACTTCTCCAAAATTACA
1 TTTTAACCCT-AAA-TTTTCCAAAATTACA
** *
24013486 TTTTAACTTTTAAATTTATCCAAAATCACA
1 TTTTAAC-CCTAAATTT-TCCAAAATTACA
* * * **
24013516 TATTAGCCTTAAAAATT-CAAAATTACA
1 TTTTAACCCTAAATTTTCCAAAATTACA
* *
24013543 TTTTGACCCTAAAATTTATCTAAAATTACA
1 TTTTAACCCT-AAATTT-TCCAAAATTACA
*
24013573 TTTTGACCCCTAAACTTTTCCAAAATTACA
1 TTTT-AACCCTAAA-TTTTCCAAAATTACA
**
24013603 TTTTAACCCTTAAATTTCTTTAAAATTACA
1 TTTTAACCC-TAAATTT-TCCAAAATTACA
* **
24013633 TTTTGACCCTAAACTTTTATAAAATTACA
1 TTTTAACCCTAAA-TTTTCCAAAATTACA
* * * * *
24013662 TTTTGACCCTAAACTTCTCAAAAATCACC
1 TTTTAACCCTAAA-TTTTCCAAAATTACA
* * *
24013691 TTTTGACCCTTAAACTTCTCCAAAATTATA
1 TTTTAACCC-TAAA-TTTTCCAAAATTACA
* * *
24013721 TTTTAACCCTTAAACTTCTCTAAAATCACA
1 TTTTAACCC-TAAA-TTTTCCAAAATTACA
*
24013751 TTTTAACCTCCAATATTTTCCAAAATTACA
1 TTTTAACC-CTAA-ATTTTCCAAAATTACA
* * *
24013781 TTTTAACCTTAAATTATCCTAAACTT-CA
1 TTTTAACCCTAAATTTTCC-AAAATTACA
24013809 TTTT
1 TTTT
24013813 TGACCCCTTT
Statistics
Matches: 410, Mismatches: 69, Indels: 57
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.04
28 20 0.05
29 109 0.27
30 223 0.54
31 35 0.09
32 6 0.01
33 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTTAACCCTAAATTTTCCAAAATTACA
Found at i:24015738 original size:12 final size:12
Alignment explanation
Indices: 24015691--24015724 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
24015681 ATTTCCACGA
*
24015691 GATCTTCCTCAG
1 GATCTTCTTCAG
24015703 GATCTTCTTCAG
1 GATCTTCTTCAG
24015715 GATCTTCTTC
1 GATCTTCTTC
24015725 TTCTTCAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (12 bp):
GATCTTCTTCAG
Found at i:24019466 original size:46 final size:46
Alignment explanation
Indices: 24019414--24019508 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
24019404 TTTAGAAAAA
* *
24019414 TTTTAAAAATTTAACTTTCTTTATATATTTTT-TAAAGATTTAT-AAT
1 TTTTAAAAATATAA-TTTCTTTATAAATTTTTATAAAGATTT-TGAAT
* * *
24019460 TTTTAAAAATATAATTTTTTTTTAAATTTTTATAAATATTTTGAAT
1 TTTTAAAAATATAATTTCTTTATAAATTTTTATAAAGATTTTGAAT
24019506 TTT
1 TTT
24019509 ATTTTGTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 15 0.36
46 27 0.64
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (46 bp):
TTTTAAAAATATAATTTCTTTATAAATTTTTATAAAGATTTTGAAT
Found at i:24019524 original size:14 final size:12
Alignment explanation
Indices: 24019496--24019529 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
24019486 TTTTTATAAA
24019496 TATTTTGAATTT
1 TATTTTGAATTT
24019508 TATTTTGTAATTTT
1 TATTTTG-AA-TTT
24019522 TATTTTGA
1 TATTTTGA
24019530 GAAAGACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 3 0.15
14 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
TATTTTGAATTT
Found at i:24020819 original size:3 final size:3
Alignment explanation
Indices: 24020811--24020839 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
24020801 TCTACATGCA
24020811 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24020840 CTTGCACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24032318 original size:18 final size:18
Alignment explanation
Indices: 24032297--24032350 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
24032287 TATTGCTCAT
24032297 ACGAGCTAGTATGCTATA
1 ACGAGCTAGTATGCTATA
* *
24032315 ACGAACTAGTATGCTCAAA
1 ACGAGCTAGTATGCT-ATA
**
24032334 ACGAGCCCGTATGCTAT
1 ACGAGCTAGTATGCTAT
24032351 TCCTTTCATG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (18 bp):
ACGAGCTAGTATGCTATA
Found at i:24033776 original size:14 final size:15
Alignment explanation
Indices: 24033757--24033785 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24033747 GAGAGAGGCG
24033757 AGAGAGTTTT-TTTT
1 AGAGAGTTTTGTTTT
24033771 AGAGAGTTTTGTTTT
1 AGAGAGTTTTGTTTT
24033786 TTTTTTTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.00, G:0.24, T:0.55
Consensus pattern (15 bp):
AGAGAGTTTTGTTTT
Found at i:24034412 original size:30 final size:29
Alignment explanation
Indices: 24034312--24034439 Score: 132
Period size: 29 Copynumber: 4.3 Consensus size: 29
24034302 CTGTTTTATT
* *
24034312 TAAAAATTATATTTTAACCCTCGAACTTC
1 TAAAAATTACATTTTAACCCTCAAACTTC
* * *
24034341 -ACAAAATTATATTTTTACCCCCAAACTTC
1 TA-AAAATTACATTTTAACCCTCAAACTTC
* * * *
24034370 TCAAAATCACATTTTGACCCTTAAACTTTC
1 TAAAAATTACATTTTAACCCTCAAAC-TTC
24034400 TAAAAATTACATTTTAACCCTCAAACTTC
1 TAAAAATTACATTTTAACCCTCAAACTTC
*
24034429 TCTAAAATTAC
1 T-AAAAATTAC
24034440 CCTTAAAGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.01
29 47 0.58
30 33 0.41
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
TAAAAATTACATTTTAACCCTCAAACTTC
Found at i:24034522 original size:29 final size:28
Alignment explanation
Indices: 24034480--24034612 Score: 83
Period size: 29 Copynumber: 4.6 Consensus size: 28
24034470 CTTAAACTTT
*
24034480 TCCAAAATT-GCATTTTTATCCCAAAACA
1 TCCAAAATTACCATTTTTA-CCCAAAACA
* **
24034508 TCCAAAATTACCATTTTGA-CCATAAATTTT
1 TCCAAAATTACCATTTTTACCCA-AAA--CA
* * **
24034538 TCCAAAATTA-TATTTTTGCCCCCGAACA
1 TCCAAAATTACCATTTTT-ACCCAAAACA
* **
24034566 TCCAAAAATTACCATTTTGACCCCTAACA
1 TCC-AAAATTACCATTTTTACCCAAAACA
24034595 TCCAAAAATTACCATTTT
1 TCC-AAAATTACCATTTT
24034613 ATCCTCGAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 15
0.73 0.13 0.13
Matches are distributed among these distances:
27 3 0.04
28 15 0.18
29 45 0.55
30 17 0.21
31 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.34
Consensus pattern (28 bp):
TCCAAAATTACCATTTTTACCCAAAACA
Found at i:24034540 original size:58 final size:58
Alignment explanation
Indices: 24034451--24034587 Score: 168
Period size: 58 Copynumber: 2.4 Consensus size: 58
24034441 CTTAAAGTTT
* * * * *
24034451 TCCAAAATCA-CATTTTCACCTTAAACTTTTCCAAAATTGCATTTTTATCCCAAAACA
1 TCCAAAATTACCATTTTGACCATAAACTTTTCCAAAATTACATTTTTACCCCAAAACA
* * * **
24034508 TCCAAAATTACCATTTTGACCATAAATTTTTCCAAAATTATATTTTTGCCCCCGAACA
1 TCCAAAATTACCATTTTGACCATAAACTTTTCCAAAATTACATTTTTACCCCAAAACA
24034566 TCCAAAAATTACCATTTTGACC
1 TCC-AAAATTACCATTTTGACC
24034588 CCTAACATCC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 9 0.13
58 41 0.60
59 18 0.26
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
TCCAAAATTACCATTTTGACCATAAACTTTTCCAAAATTACATTTTTACCCCAAAACA
Found at i:24034671 original size:29 final size:29
Alignment explanation
Indices: 24034551--24034732 Score: 170
Period size: 29 Copynumber: 6.2 Consensus size: 29
24034541 AAAATTATAT
*
24034551 TTTTGCCCCCGAACATCCAAAAATTACCA
1 TTTTGACCCCGAACATCCAAAAATTACCA
*
24034580 TTTTGACCCCTAACATCCAAAAATTACCA
1 TTTTGACCCCGAACATCCAAAAATTACCA
* * **
24034609 TTTT-ATCCTCGAAAAGTAAAAAAAATTACCA
1 TTTTGA-CCCCGAACA-T-CCAAAAATTACCA
*
24034640 TTTTGACCCCGAACATCCAAAAATTATCA
1 TTTTGACCCCGAACATCCAAAAATTACCA
** *
24034669 TTTTG-CTCTTGAACGTCCAAAAATTACCA
1 TTTTGAC-CCCGAACATCCAAAAATTACCA
* * * **
24034698 TTTTGATCTCGAACTTTTACAAAATTACCA
1 TTTTGACCCCGAACATCCA-AAAATTACCA
24034728 TTTTG
1 TTTTG
24034733 CCCTAAAATT
Statistics
Matches: 125, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.02
29 83 0.66
30 17 0.14
31 22 0.18
32 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
TTTTGACCCCGAACATCCAAAAATTACCA
Found at i:24034816 original size:30 final size:29
Alignment explanation
Indices: 24034764--24034858 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
24034754 TTTTCGACCT
* *
24034764 CAAATTTTCCAAAAGTTTGATTTTAATCC
1 CAAATTTTCCAAAAATTCGATTTTAATCC
*
24034793 CAAATTTTCCAAAAAATTCGATTTTGATCCC
1 CAAATTTTCC-AAAAATTCGATTTTAAT-CC
* *
24034824 CAAA-TTCCTCAAAAATTAC-ATTTTCATCC
1 CAAATTTTC-CAAAAATT-CGATTTTAATCC
24034853 CAAATT
1 CAAATT
24034859 CTCCTAAGCT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
29 16 0.29
30 32 0.57
31 8 0.14
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (29 bp):
CAAATTTTCCAAAAATTCGATTTTAATCC
Found at i:24037562 original size:22 final size:23
Alignment explanation
Indices: 24037536--24037579 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
24037526 TTTCTTTTCT
*
24037536 TTTAG-TTGTTTTTCTATTATTG
1 TTTAGTTTGTTTTTCTAATATTG
*
24037558 TTTAGTTTTTTTTTCTAATATT
1 TTTAGTTTGTTTTTCTAATATT
24037580 TGATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTAGTTTGTTTTTCTAATATTG
Found at i:24039423 original size:24 final size:24
Alignment explanation
Indices: 24039388--24039444 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
24039378 AATCTTCCAG
24039388 TTAAACTCTGTTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTTCAA
* *
24039412 TTAAACTTTGTTTATTTGTTTCAG
1 TTAAACTCTGTTTATTTGTTTCAA
*
24039436 TCAAACTCT
1 TTAAACTCT
24039445 TATTCTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.53
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTTCAA
Done.