Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008786.1 Hibiscus syriacus cultivar Beakdansim tig00111920_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 306639
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:224146 original size:18 final size:18
Alignment explanation
Indices: 224010--224268 Score: 65
Period size: 18 Copynumber: 14.7 Consensus size: 18
224000 ATATACTATT
*
224010 TATATAAACTATAGTTTA
1 TATATGAACTATAGTTTA
* * *
224028 TAT-T-TA-TATACTATA
1 TATATGAACTATAGTTTA
224043 TATATGAACTATAGTTTA
1 TATATGAACTATAGTTTA
*
224061 CATATGAAC--T-G--TA
1 TATATGAACTATAGTTTA
*
224074 TATATAAACTATATAGTTTA
1 TATATGAAC--TATAGTTTA
* *
224094 CATATTAACTATA---TA
1 TATATGAACTATAGTTTA
* *
224109 TATACTAAAGTTGATA-TTTA
1 TATA-TGAA-CT-ATAGTTTA
224129 TATATGAACTATAGTTTA
1 TATATGAACTATAGTTTA
* *
224147 CATATAAACTATA---TA
1 TATATGAACTATAGTTTA
224162 -ATA--AACTATATAGTTTA
1 TATATGAAC--TATAGTTTA
224179 TATA--AACTATAGTTGATATTTA
1 TATATGAACTATA---G---TTTA
*
224201 TATATGAACCATAGTTTA
1 TATATGAACTATAGTTTA
* * *
224219 CATATGAACTACA-TATA
1 TATATGAACTATAGTTTA
*
224236 TATATAAACTATATAGTTTA
1 TATATGAAC--TATAGTTTA
* *
224256 CATATGACCTATA
1 TATATGAACTATA
224269 TATATATACT
Statistics
Matches: 178, Mismatches: 30, Indels: 66
0.65 0.11 0.24
Matches are distributed among these distances:
12 3 0.02
13 9 0.05
14 7 0.04
15 18 0.10
16 10 0.06
17 19 0.11
18 66 0.37
19 7 0.04
20 24 0.13
21 1 0.01
22 8 0.04
24 6 0.03
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (18 bp):
TATATGAACTATAGTTTA
Found at i:224161 original size:20 final size:19
Alignment explanation
Indices: 224075--224161 Score: 67
Period size: 18 Copynumber: 4.7 Consensus size: 19
224065 TGAACTGTAT
224075 ATATAAACTATATAGTTTAC
1 ATATAAACTATATA-TTTAC
* *
224095 ATATTAACTATATATATAC
1 ATATAAACTATATATTTAC
* *
224114 ---TAAAGT-TGATATTTAT
1 ATATAAACTAT-ATATTTAC
* *
224130 ATATGAACTATA-GTTTAC
1 ATATAAACTATATATTTAC
224148 ATATAAACTATATA
1 ATATAAACTATATA
224162 ATAAACTATA
Statistics
Matches: 49, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
15 1 0.02
16 10 0.20
18 15 0.31
19 9 0.18
20 14 0.29
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (19 bp):
ATATAAACTATATATTTAC
Found at i:224196 original size:72 final size:76
Alignment explanation
Indices: 224105--224255 Score: 238
Period size: 72 Copynumber: 2.0 Consensus size: 76
224095 ATATTAACTA
* *
224105 TATATATACTAAAGTTGATATTTATATATGAACTATAGTTTACATAT-AA-AC-TATATA-ATAA
1 TATATAAACTAAAGTTGATATTTATATATGAACCATAGTTTACATATGAACACATATATATATAA
224166 ACTATATAGTT
66 ACTATATAGTT
*
224177 TATATAAACTATAGTTGATATTTATATATGAACCATAGTTTACATATGAACTACATATATATATA
1 TATATAAACTAAAGTTGATATTTATATATGAACCATAGTTTACATATGAAC-ACATATATATATA
224242 AACTATATAGTT
65 AACTATATAGTT
224254 TA
1 TA
224256 CATATGACCT
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
72 44 0.62
73 2 0.03
75 2 0.03
76 6 0.08
77 17 0.24
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (76 bp):
TATATAAACTAAAGTTGATATTTATATATGAACCATAGTTTACATATGAACACATATATATATAA
ACTATATAGTT
Found at i:224275 original size:72 final size:67
Alignment explanation
Indices: 224122--224276 Score: 166
Period size: 72 Copynumber: 2.1 Consensus size: 67
224112 ACTAAAGTTG
* * *
224122 ATATTTATATATGAACTATAGTTTACATATAAACTATATAATAAACTATATAGTTTATATAAACT
1 ATATATATATATGAACCATAGTTTACATATAAACTATATAATAAACTATATAGTTTACATAAACT
224187 AT
66 AT
224189 AGTTGATATTTATATATGAACCATAGTTTACATATGAACTACATATATATATAAACTATATAGTT
1 A--T-ATA--TATATATGAACCATAGTTTACATAT-AA--AC-TATATA-ATAAACTATATAGTT
*
224254 TACATATGACCTAT
56 TACATA--AACTAT
224268 ATATATATA
1 ATATATATA
224277 CTAGTTGATA
Statistics
Matches: 72, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
67 1 0.01
69 1 0.01
70 2 0.03
72 24 0.33
73 2 0.03
74 4 0.06
75 2 0.03
76 9 0.12
77 21 0.29
79 6 0.08
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (67 bp):
ATATATATATATGAACCATAGTTTACATATAAACTATATAATAAACTATATAGTTTACATAAACT
AT
Found at i:224281 original size:29 final size:28
Alignment explanation
Indices: 224236--224327 Score: 88
Period size: 24 Copynumber: 3.4 Consensus size: 28
224226 ACTACATATA
*
224236 TATATAAACTATATAGTTTACATATGACC
1 TATATATA-TATATAGTTTACATATGACC
* *
224265 TATATATATATACTAG-TT-GATAT---T
1 TATATATATATA-TAGTTTACATATGACC
*
224289 TGTATAT-TATATAGTTTACATATGACC
1 TATATATATATATAGTTTACATATGACC
224316 TATATATATATA
1 TATATATATATA
224328 CTATAGTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
22 3 0.06
23 6 0.12
24 10 0.20
27 10 0.20
28 10 0.20
29 10 0.20
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.45
Consensus pattern (28 bp):
TATATATATATATAGTTTACATATGACC
Found at i:224288 original size:162 final size:155
Alignment explanation
Indices: 224041--224340 Score: 415
Period size: 162 Copynumber: 1.9 Consensus size: 155
224031 TTATATACTA
* * *
224041 TATATATGAACTATAGTTTACATATGAACTGTATATATAAACTATATAGTTTACATATTAACTAT
1 TATATATGAACCATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTAT
224106 ATATATACTAAAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAATAAACTA-
66 ATATATACTAAAGTTGATATTTATATAT-AA-TATAGTTTACATATAAACTATAT-ATAAA-TAC
224170 TATAGTTTATATAAACTATAGTTGATATT
127 TATAGTTTATATAAACTATAGTTGATATT
*
224199 TATATATGAACCATAGTTTACATATGAACTACATATATATATAAACTATATAGTTTACATATGAC
1 TATATATGAACCATAGTTTACATATG-A--AC-TATATATATAAACTATATAGTTTACATATGAA
* * * * * *
224264 CTATATATATA-TACTAGTTGATATTTGTATATTATATAGTTTACATATGACCTATATATATATA
62 CTATATATATACTA-AAGTTGATATTTATATATAATATAGTTTACATATAAACTATATATAAATA
224328 CTATAGTTTATAT
126 CTATAGTTTATAT
224341 TTATATACTA
Statistics
Matches: 126, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
158 27 0.21
159 17 0.13
160 21 0.17
161 5 0.04
162 56 0.44
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (155 bp):
TATATATGAACCATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGAACTAT
ATATATACTAAAGTTGATATTTATATATAATATAGTTTACATATAAACTATATATAAATACTATA
GTTTATATAAACTATAGTTGATATT
Found at i:224306 original size:51 final size:52
Alignment explanation
Indices: 224076--224354 Score: 187
Period size: 51 Copynumber: 5.2 Consensus size: 52
224066 GAACTGTATA
* * *
224076 TATAAACTATATAGTTTACATATTAACTATATATATACTA-A-AGTTGATATT
1 TATATACTATATAGTTTACATATGACCTATATATATA-TACATAGTTGATATT
* * * * * *
224127 TATATA-TGAACTATAGTTTACATATAAACTATATAATAAACTATATAGTTTATATA
1 TATATACT--A-TATAGTTTACATATGACCTATAT-ATATA-TACATAGTTGATATT
* * * * * ** *
224183 AACTATAGT-TGATA-TTTATATATGAACCATAGTTTACATATGA-ACTACAT-ATATA
1 TA-TATACTAT-ATAGTTTACATATG-ACC-TA-TATATATAT-ACA-TAGTTGATATT
*
224238 TATAAACTATATAGTTTACATATGACCTATATATATATAC-TAGTTGATATT
1 TATATACTATATAGTTTACATATGACCTATATATATATACATAGTTGATATT
* * *
224289 TGTATATTATATAGTTTACATATGACCTATATATATATACTATAGTTTATATT
1 TATATACTATATAGTTTACATATGACCTATATATATATAC-ATAGTTGATATT
224342 TATATACTATATA
1 TATATACTATATA
224355 TATATATATA
Statistics
Matches: 179, Mismatches: 29, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
50 4 0.02
51 47 0.26
52 8 0.04
53 45 0.25
54 26 0.15
55 24 0.13
56 18 0.10
57 6 0.03
58 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (52 bp):
TATATACTATATAGTTTACATATGACCTATATATATATACATAGTTGATATT
Found at i:224383 original size:37 final size:37
Alignment explanation
Indices: 224316--224389 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
224306 ACATATGACC
* * * *
224316 TATATATATATACTATAGTTTATATTTATATACTATA
1 TATATATATATACTAAACTCTATATCTATATACTATA
*
224353 TATATATATATA-TAAACTCTATATACTATATAGTATA
1 TATATATATATACTAAACTCTATAT-CTATATACTATA
224390 ATTTACATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 9 0.29
37 22 0.71
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATATATATACTAAACTCTATATCTATATACTATA
Found at i:224444 original size:53 final size:50
Alignment explanation
Indices: 224322--224457 Score: 138
Period size: 53 Copynumber: 2.7 Consensus size: 50
224312 GACCTATATA
* * *
224322 TATATACTATAGTTTAT-ATTTATATACTATATATATATATATATAAACTC
1 TATATACTATAGTTGATAATTTATATACTATATATATAAACATATAAAC-C
*
224372 TATATACTATA-TAGTATAATTTACATATGAACTATATATA-AAACCATATAAA-C
1 TATATACTATAGTTG-ATAATTT--ATAT--ACTATATATATAAA-CATATAAACC
224425 TATATACTATAGTTGATAA-TTATATACTATATA
1 TATATACTATAGTTGATAATTTATATACTATATA
224458 AAATAATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
48 8 0.11
49 1 0.01
50 17 0.23
51 4 0.05
52 2 0.03
53 20 0.27
54 4 0.05
55 17 0.23
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (50 bp):
TATATACTATAGTTGATAATTTATATACTATATATATAAACATATAAACC
Found at i:224457 original size:7 final size:6
Alignment explanation
Indices: 224445--224620 Score: 52
Period size: 7 Copynumber: 29.0 Consensus size: 6
224435 AGTTGATAAT
* *
224445 TATATA CTATATA -AAATA -ATTTA TACTATA T-TATA TATA-A CTATATA
1 TATATA -TATATA TATATA TATATA TA-TATA TATATA TATATA -TATATA
* *
224492 -ATATA TATAAA CTATATA T-TATA TAGT-TCA T-TAGTA TATATA AACTATA
1 TATATA TATATA -TATATA TATATA TA-TAT-A TATA-TA TATATA TA-TATA
* * * * *
224541 TA-ATA TATATA AACTATA TGGTATA TATAAA CTATACA T-TATA TATATT
1 TATATA TATATA TA-TATA T-ATATA TATATA -TATATA TATATA TATATA
*
224590 TGAT-TA GTATATA TAAACTA TATAT- TATATA
1 T-ATATA -TATATA TATA-TA TATATA TATATA
224621 GTTCATTAGT
Statistics
Matches: 126, Mismatches: 19, Indels: 49
0.65 0.10 0.25
Matches are distributed among these distances:
5 38 0.30
6 37 0.29
7 51 0.40
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:224506 original size:18 final size:18
Alignment explanation
Indices: 224445--224620 Score: 127
Period size: 18 Copynumber: 10.1 Consensus size: 18
224435 AGTTGATAAT
* *
224445 TATATACTATATAAAATAA
1 TATAAACTATATAATAT-A
* *
224464 TTTATACTATAT--TATA
1 TATAAACTATATAATATA
224480 TAT-AACTATATAATATA
1 TATAAACTATATAATATA
224497 TATAAACTATAT-AT-TA
1 TATAAACTATATAATATA
** *
224513 TAT-AGTTCAT-TAGTATA
1 TATAAACT-ATATAATATA
224530 TATAAACTATATAATATA
1 TATAAACTATATAATATA
**
224548 TATAAACTATATGGTATA
1 TATAAACTATATAATATA
* *
224566 TATAAACTATACATTATA
1 TATAAACTATATAATATA
** *
224584 TAT-ATTTGAT-TAGTATA
1 TATAAACT-ATATAATATA
*
224601 TATAAACTATATATTATA
1 TATAAACTATATAATATA
224619 TA
1 TA
224621 GTTCATTAGT
Statistics
Matches: 124, Mismatches: 22, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
15 10 0.08
16 11 0.09
17 30 0.24
18 62 0.50
19 11 0.09
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TATAAACTATATAATATA
Found at i:224568 original size:58 final size:58
Alignment explanation
Indices: 224497--224786 Score: 205
Period size: 58 Copynumber: 5.1 Consensus size: 58
224487 ATATAATATA
* * *
224497 TATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAATATATATAAAC
1 TATATACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATATATAAAC
** * * *
224555 TATATGGTATATA-TAAACTA-TACATTA-TATATAT---TTGAT-TAG--TATAT--A-
1 TATATACTATATATTATA-TAGTTCATTACTATATATAAACT-ATATAGTATATATAAAC
* * ***
224603 TA-A-ACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGACTATGG
1 TATATACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATAT--A-TAAAC
* * *
224662 TATATACAAACTATATATTATATAGTTCATTACTATATATAACCTATATAGTATATGGTATA-
1 TATAT----ACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATAT-ATAAAC
* * * *
224724 TACAAACTATATATTATATAGTTCATTACTATATATAAATTATATAGCATATATAAAC
1 TATATACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATATATAAAC
224782 TATAT
1 TATAT
224787 GTTGAAAAGT
Statistics
Matches: 183, Mismatches: 25, Indels: 48
0.71 0.10 0.19
Matches are distributed among these distances:
46 8 0.04
47 10 0.05
48 9 0.05
49 1 0.01
50 2 0.01
51 9 0.05
53 6 0.03
54 2 0.01
55 1 0.01
56 8 0.04
57 12 0.07
58 59 0.32
59 2 0.01
60 1 0.01
62 3 0.02
63 3 0.02
64 1 0.01
65 46 0.25
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (58 bp):
TATATACTATATATTATATAGTTCATTACTATATATAAACTATATAGTATATATAAAC
Found at i:224608 original size:71 final size:68
Alignment explanation
Indices: 224471--224620 Score: 219
Period size: 71 Copynumber: 2.2 Consensus size: 68
224461 TAATTTATAC
*
224471 TATATTATATATAACTATATAATATATATAAACTATATATTATATAGTTCATTAGTATATATAAA
1 TATATTATATATAACTATATAATATATATAAACTATACATTATATAGTTCATTAGTATATATAAA
224536 CTA
66 CTA
* ** * *
224539 TATAATATATATAAACTATATGGTATATATAAACTATACATTATATATATTTGATTAGTATATAT
1 TATATTATATAT-AACTATATAATATATATAAACTATACA-T-TATATAGTTCATTAGTATATAT
224604 AAACTA
63 AAACTA
224610 TATATTATATA
1 TATATTATATA
224621 GTTCATTAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
68 11 0.15
69 24 0.33
70 1 0.01
71 36 0.50
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (68 bp):
TATATTATATATAACTATATAATATATATAAACTATACATTATATAGTTCATTAGTATATATAAA
CTA
Found at i:224629 original size:33 final size:33
Alignment explanation
Indices: 224493--224769 Score: 252
Period size: 33 Copynumber: 8.5 Consensus size: 33
224483 AACTATATAA
224493 TATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
** *
224526 TATATATAAACTATATAATATATATA-AACTATATGG
1 TATATATAAACTATAT-AT-TATATAGTTC-AT-TAG
* * *
224562 TATATATAAACTATACATTATATATATTTGATTAG
1 TATATATAAACTATATA-T-TATATAGTTCATTAG
224597 TATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATATTATATAGTTCATTAG
* * ** *
224630 TATATATAACCTATATAGTATAT-GGAC-TATGG
1 TATATATAAACTATATATTATATAGTTCAT-TAG
* *
224662 TATATACAAACTATATATTATATAGTTCATTAC
1 TATATATAAACTATATATTATATAGTTCATTAG
* *
224695 TATATATAACCTATATAGTATAT-G-------G
1 TATATATAAACTATATATTATATAGTTCATTAG
* *
224720 TATATACAAACTATATATTATATAGTTCATTAC
1 TATATATAAACTATATATTATATAGTTCATTAG
*
224753 TATATATAAATTATATA
1 TATATATAAACTATATA
224770 GCATATATAA
Statistics
Matches: 194, Mismatches: 33, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
25 20 0.10
26 1 0.01
31 1 0.01
32 25 0.13
33 88 0.45
34 5 0.03
35 27 0.14
36 27 0.14
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (33 bp):
TATATATAAACTATATATTATATAGTTCATTAG
Found at i:224637 original size:2 final size:2
Alignment explanation
Indices: 224316--224620 Score: 70
Period size: 2 Copynumber: 148.0 Consensus size: 2
224306 ACATATGACC
* *
224316 TA TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA TA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA
* * * *
224359 TA TA TA TA AA CTC TA TA TA CTA TA TA GTA TA -A TT TA CA TA TGA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA T-A
* * *
224402 -A CTA TA TA TA -A AA CCA TA TA AA CTA TA TA CTA TA GT- TGA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA -TA T-A TA
* *
224443 -A T- TA TA TA CTA TA TA -A AA TA -A TT TA TA CTA TA T- TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
224482 TA -A CTA TA TA -A TA TA TA TA AA CTA TA TA T- TA TA TA GT- TCA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA T-A
* * *
224522 T- TA GTA TA TA TA AA CTA TA TA -A TA TA TA TA AA CTA TA TGG TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA T-A TA
* * *
224564 TA TA TA AA CTA TA CA T- TA TA TA TA TT TGA T- TA GTA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA
*
224605 AA CTA TA TA T- TA TA TA
1 TA -TA TA TA TA TA TA TA
224621 GTTCATTAGT
Statistics
Matches: 223, Mismatches: 35, Indels: 90
0.64 0.10 0.26
Matches are distributed among these distances:
1 18 0.08
2 170 0.76
3 35 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:224681 original size:65 final size:61
Alignment explanation
Indices: 224596--224778 Score: 264
Period size: 58 Copynumber: 3.0 Consensus size: 61
224586 TATTTGATTA
* *
224596 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGGACTATG
1 GTATATACAAACTATATATTATATAGTTCATTACTATATATAACCTATATAG-ATAT--A-TATG
224661 GTATATACAAACTATATATTATATAGTTCATTACTATATATAACCTATATAG---TATATG
1 GTATATACAAACTATATATTATATAGTTCATTACTATATATAACCTATATAGATATATATG
**
224719 GTATATACAAACTATATATTATATAGTTCATTACTATATATAAATTATATAGCATATATA
1 GTATATACAAACTATATATTATATAGTTCATTACTATATATAACCTATATAG-ATATATA
224779 AACTATATGT
Statistics
Matches: 110, Mismatches: 4, Indels: 11
0.88 0.03 0.09
Matches are distributed among these distances:
58 54 0.49
59 1 0.01
61 1 0.01
62 4 0.04
65 50 0.45
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (61 bp):
GTATATACAAACTATATATTATATAGTTCATTACTATATATAACCTATATAGATATATATG
Found at i:224733 original size:25 final size:25
Alignment explanation
Indices: 224695--224742 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
224685 AGTTCATTAC
* *
224695 TATATATAACCTATATAGTATATGG
1 TATATACAAACTATATAGTATATGG
*
224720 TATATACAAACTATATATTATAT
1 TATATACAAACTATATAGTATAT
224743 AGTTCATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
TATATACAAACTATATAGTATATGG
Found at i:224776 original size:51 final size:52
Alignment explanation
Indices: 224663--224821 Score: 128
Period size: 51 Copynumber: 3.0 Consensus size: 52
224653 GGACTATGGT
* * * * *
224663 ATATACAAACTATATATT-ATATAGTTCATTACTATATATAACCTATATAGTATATGGT
1 ATATACAAACTATATATTGA-AAAGTTCATTA--ATATATTA--TA-AT-CTATATAGC
* *
224721 ATATACAAACTATATATT-ATATAGTTCATTACTATA-TATAAAT-TATATAGC
1 ATATACAAACTATATATTGA-AAAGTTCATTAATATATTAT-AATCTATATAGC
* *
224772 ATATATAAACTATATGTTGAAAAGTTCATTAATATATTATAATCTATATA
1 ATATACAAACTATATATTGAAAAGTTCATTAATATATTATAATCTATATA
224822 TTAATTTATT
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
51 39 0.44
52 10 0.11
53 3 0.03
54 1 0.01
55 1 0.01
56 4 0.04
58 31 0.35
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.42
Consensus pattern (52 bp):
ATATACAAACTATATATTGAAAAGTTCATTAATATATTATAATCTATATAGC
Found at i:224824 original size:22 final size:24
Alignment explanation
Indices: 224799--224852 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
224789 TGAAAAGTTC
*
224799 ATTAATA-TATTATAATC-TATAT
1 ATTAATATTATTATAAACATATAT
224821 ATTAATTTATTATTATAAACATATAT
1 ATTAA--TATTATTATAAACATATAT
224847 ATTAAT
1 ATTAAT
224853 TGGGAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.19
24 3 0.11
25 9 0.33
26 10 0.37
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTAATATTATTATAAACATATAT
Found at i:224962 original size:61 final size:61
Alignment explanation
Indices: 224881--225017 Score: 190
Period size: 61 Copynumber: 2.2 Consensus size: 61
224871 TATAAGGATC
224881 AAATTGAATAAATTTTAAATATGAAGCTTAAATTAATAAACTAT-AAT-ATTAAATTTGGACT
1 AAATTGAATAAATTTTAAATATGAAGCTTAAATTAATAAA-T-TGAATCATTAAATTTGGACT
* * *
224942 AAATTGAA-AATTTTTGAAATATGAAGCTTAAATTAATATATTGCATCATTAAATTTGGACT
1 AAATTGAATAAATTTT-AAATATGAAGCTTAAATTAATAAATTGAATCATTAAATTTGGACT
*
225003 AAATTGAACAAATTT
1 AAATTGAATAAATTT
225018 AAAACTACGA
Statistics
Matches: 68, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
59 1 0.01
60 9 0.13
61 53 0.78
62 5 0.07
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (61 bp):
AAATTGAATAAATTTTAAATATGAAGCTTAAATTAATAAATTGAATCATTAAATTTGGACT
Found at i:225464 original size:113 final size:112
Alignment explanation
Indices: 225210--225533 Score: 492
Period size: 113 Copynumber: 2.9 Consensus size: 112
225200 GAAAATCAAT
* * *
225210 CGTGTTTTTCATTTGTTCATCCAGTTCATCCCCAAAAGCCTCTTTTGATCTTCAAAAACACCTAA
1 CGTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTC-TTTGATCTTCAAAAACACCTAA
*
225275 AC-CAAATCATTTTCGTGTTTTTTTCGATCAAACACCCAAATTTCTTC
65 ACACAAACCATTTTCGTGTTTTTTTCGATCAAACACCCAAATTTCTTC
* * * *
225322 TGTGTTCTTCATTTGTTCTTCCAGTTCTTCCCTAAAACCCTTCTTTGATCTTCACAAACACCTAA
1 CGTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCC-TCTTTGATCTTCAAAAACACCTAA
*
225387 ACACAAA-CATTTTCGTTTTTTTTTCGATCAAACACCCAAATATTCTTC
65 ACACAAACCATTTTCGTGTTTTTTTCGATCAAACACCCAAAT-TTCTTC
225435 CGTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCCTCTTTGATCTTCAAAAACACCTAA
1 CGTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAA-CCCTCTTTGATCTTCAAAAACACCTAA
* *
225500 ACACAAACCA-TATCGTGTTTATTTCGATCAAACA
65 ACACAAACCATTTTCGTGTTTTTTTCGATCAAACA
225534 ATCACAAATT
Statistics
Matches: 192, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
112 90 0.47
113 97 0.51
114 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.07, T:0.38
Consensus pattern (112 bp):
CGTGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCTTTGATCTTCAAAAACACCTAAA
CACAAACCATTTTCGTGTTTTTTTCGATCAAACACCCAAATTTCTTC
Found at i:225708 original size:12 final size:11
Alignment explanation
Indices: 225684--225727 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
225674 TTCATCTTCC
*
225684 CTAACCCTTAA
1 CTAACCCTAAA
225695 CTAGACCCTAAA
1 CTA-ACCCTAAA
225707 CTAATCCC-AAA
1 CTAA-CCCTAAA
225718 CTAACCCTAA
1 CTAACCCTAA
225728 CCCTGACCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
10 3 0.10
11 13 0.45
12 13 0.45
ACGTcount: A:0.41, C:0.36, G:0.02, T:0.20
Consensus pattern (11 bp):
CTAACCCTAAA
Found at i:225783 original size:17 final size:18
Alignment explanation
Indices: 225744--225785 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
225734 CCCTAACCCT
225744 CCCAAACACGAACCCAAA
1 CCCAAACACGAACCCAAA
* *
225762 TCCAAACA-GAACCCAAG
1 CCCAAACACGAACCCAAA
225779 CCCAAAC
1 CCCAAAC
225786 TAATCTTAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.48, C:0.43, G:0.07, T:0.02
Consensus pattern (18 bp):
CCCAAACACGAACCCAAA
Found at i:226094 original size:31 final size:31
Alignment explanation
Indices: 226065--226610 Score: 785
Period size: 31 Copynumber: 17.7 Consensus size: 31
226055 ATATATATAT
* *
226065 TGGTTTATTGATGTTGATGTAAATGATATAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* *
226096 TGGTTTATTGATGTTGATGTAAATGATATAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
226127 TGGTTTATTGTTATTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
226158 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
226189 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* *
226220 TGGTTTATTGCTGTTGATGTAAATTATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
226251 TGGTTTATTGTTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* * *
226282 TGGTTTATTGCTGTTGATGTTAATTATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* * *
226313 TGGTTTATTGTTG-TGATGTTAATTATGTAT
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
226343 TGGTTTATTGTTGATGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* * *
226374 TGGTTTA---TTATTGATGTAAATTATGTAT
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* *
226402 TGGTTTATTGTTATTGATGTACATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* * * *
226433 TGGTTTTTTGTTGTTGATGTTAATTATGGAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* **
226464 TGGTTTATTGTTGTTGATGTTAATTTTGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
226495 TGGTTTATTGTTGTTGATGTAGATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
* * *
226526 TAGTTTATTGCTATTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
*
226557 TGGTTTATTGCTGTTGATGTAAATGATGTAC
1 TGGTTTATTGTTGTTGATGTAAATGATGTAC
226588 TGGTTTATTGTTGTTGATGTAAA
1 TGGTTTATTGTTGTTGATGTAAA
226611 CTAACCATGT
Statistics
Matches: 468, Mismatches: 43, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
28 24 0.05
30 29 0.06
31 415 0.89
ACGTcount: A:0.23, C:0.04, G:0.24, T:0.49
Consensus pattern (31 bp):
TGGTTTATTGTTGTTGATGTAAATGATGTAC
Found at i:228630 original size:20 final size:19
Alignment explanation
Indices: 228592--228639 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
228582 TGCTTGATTC
*
228592 TGCTTGCTTTGTTTTATAT
1 TGCTTGCTTTGTTTGATAT
*
228611 TGTTTGCTTATGTTTGATAT
1 TGCTTGCTT-TGTTTGATAT
228631 TGCTTGCTT
1 TGCTTGCTT
228640 CTACTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (19 bp):
TGCTTGCTTTGTTTGATAT
Found at i:234562 original size:17 final size:17
Alignment explanation
Indices: 234540--234580 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
234530 ACTTTATTAA
*
234540 TTTTTTAGTTTTTAATT
1 TTTTTTAGTTTTTAAAT
234557 TTTTTTA-TTTTTAAAT
1 TTTTTTAGTTTTTAAAT
*
234573 ATTTTTAG
1 TTTTTTAG
234581 ATGGCGCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTTTAGTTTTTAAAT
Found at i:235672 original size:20 final size:20
Alignment explanation
Indices: 235642--235694 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
235632 TAAAGAAATA
*
235642 TAAATTAATTTTATTAGATTG
1 TAAA-TAATTTTATTACATTG
*
235663 TAAATAATTTT-TTACTTTG
1 TAAATAATTTTATTACATTG
*
235682 TAAACAATTTTAT
1 TAAATAATTTTAT
235695 CTTTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.57
20 8 0.29
21 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.53
Consensus pattern (20 bp):
TAAATAATTTTATTACATTG
Found at i:235698 original size:18 final size:18
Alignment explanation
Indices: 235660--235711 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
235650 TTTTATTAGA
*
235660 TTGTAAATAATTTTTTACT
1 TTGTAAA-AATTTTATACT
235679 TTGTAAACAATTTTAT-CT
1 TTGTAAA-AATTTTATACT
*
235697 TTAATAAAAATTTTA
1 TT-GTAAAAATTTTA
235712 AATTTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (18 bp):
TTGTAAAAATTTTATACT
Found at i:236417 original size:19 final size:19
Alignment explanation
Indices: 236393--236465 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
236383 TGACCTCATT
* *
236393 GGTCGCCATGTGCTACATA
1 GGTCGCCAAGTGCTCCATA
236412 GGTCGCCAAGTGCTCCATA
1 GGTCGCCAAGTGCTCCATA
* *
236431 GGTCGTCAAATGCTCCATA
1 GGTCGCCAAGTGCTCCATA
236450 GGTCGCCAAGTGCTCC
1 GGTCGCCAAGTGCTCC
236466 TTGCGACAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (19 bp):
GGTCGCCAAGTGCTCCATA
Found at i:236595 original size:30 final size:30
Alignment explanation
Indices: 236554--236618 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
236544 AGTGCTCCAT
* *
236554 AGGTCGTCGTGTGCTCCTGGAGACCTATGG
1 AGGTCGCCGTGTACTCCTGGAGACCTATGG
236584 AGGTCGCCGTGTACTCCTGGAGACCTATGG
1 AGGTCGCCGTGTACTCCTGGAGACCTATGG
*
236614 TGGTC
1 AGGTC
236619 ACTGTAGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.25, G:0.35, T:0.26
Consensus pattern (30 bp):
AGGTCGCCGTGTACTCCTGGAGACCTATGG
Found at i:236756 original size:4 final size:4
Alignment explanation
Indices: 236747--236773 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
236737 TATTTTAGAC
236747 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
236774 AATTGGTGAT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:238325 original size:63 final size:66
Alignment explanation
Indices: 238162--238426 Score: 325
Period size: 63 Copynumber: 4.0 Consensus size: 66
238152 TAGGGATTTT
*
238162 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTAACT--ATTA
1 TTTAGGGTAAACTACCTATTTGGTCAC-T-TATATTATCTAATTTATGTTTTGGTCACTCGATTA
238225 TTA
64 TTA
238228 TTTAGGGTAAACTACCT-TTTCGGTCACTTATA-TATCTAATTTATGTTTTGGTCACTCGATTAT
1 TTTAGGGTAAACTACCTATTT-GGTCACTTATATTATCTAATTTATGTTTTGGTCACTCGATTAT
238291 TA
65 TA
* ** *
238293 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATATAAT-TCAT-AT-A-T--ATT
1 TTTAGGGTAAACTACCTATTTGGTCAC-T-TATATTATCTAAT-TTATGTTTTGGTCACTCGATT
*
238352 TTTA
63 ATTA
*
238356 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATTTTTTGGTCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCAC-T-TATATTATCTAATTTATGTTTTGGTCACTCGATTA
238421 TTA
64 TTA
238424 TTT
1 TTT
238427 TTTTCAAAAT
Statistics
Matches: 174, Mismatches: 11, Indels: 26
0.82 0.05 0.12
Matches are distributed among these distances:
62 3 0.02
63 74 0.43
64 5 0.03
65 36 0.21
66 29 0.17
67 5 0.03
68 19 0.11
69 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (66 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATTATCTAATTTATGTTTTGGTCACTCGATTATT
A
Found at i:238357 original size:131 final size:131
Alignment explanation
Indices: 238162--238426 Score: 380
Period size: 131 Copynumber: 2.0 Consensus size: 131
238152 TAGGGATTTT
* ** *
238162 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTAACTATTATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTAATGTCATGATAA--ATT-TT
238227 ATTTAGGGTAAACTACCT-TTTCGGTCAC-T-TATA-TATCTAATTTATGTTTTGGTCACTCGAT
63 ATTTAGGGTAAACTACCTATTT-GGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGAT
238288 TATTA
127 TATTA
*
238293 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATATAAT-TCAT-ATATATTTTTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAAT-TAATGTCATGATA-AATTTTA
*
238356 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATTTTTTGGTCACTCGATTA
64 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTA
238421 TTA
129 TTA
238424 TTT
1 TTT
238427 TTTTCAAAAT
Statistics
Matches: 122, Mismatches: 6, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
128 26 0.21
129 6 0.05
130 6 0.05
131 81 0.66
132 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.48
Consensus pattern (131 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTAATGTCATGATAAATTTTATT
TAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCGATTATT
A
Found at i:239804 original size:3 final size:3
Alignment explanation
Indices: 239796--239865 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
239786 CTAAAAAACT
239796 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
239844 ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
239866 CTAAACATGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:241752 original size:15 final size:16
Alignment explanation
Indices: 241727--241756 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
241717 ACGACCGCGC
241727 AGGGACCCCAAAAAAT
1 AGGGACCCCAAAAAAT
241743 AGGG-CCCCAAAAAA
1 AGGGACCCCAAAAAA
241757 GTATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.27, G:0.20, T:0.03
Consensus pattern (16 bp):
AGGGACCCCAAAAAAT
Found at i:249534 original size:25 final size:24
Alignment explanation
Indices: 249464--249526 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
249454 ATGACTAAGA
249464 TAATAATAAAATAATAATG--AAAG
1 TAATAATAAAATAAT-ATGCAAAAG
*
249487 TAATAATTTAAATATATAT-CAAAAG
1 TAATAA-TAAAATA-ATATGCAAAAG
249512 TAATAATAAAATAAT
1 TAATAATAAAATAAT
249527 GTTGCAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 8 0.24
24 14 0.41
25 12 0.35
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (24 bp):
TAATAATAAAATAATATGCAAAAG
Found at i:249609 original size:15 final size:16
Alignment explanation
Indices: 249576--249610 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
249566 TATAAAATTA
*
249576 AAATGCAAAATATATT
1 AAATGAAAAATATATT
249592 AAATGAAAAATATA-T
1 AAATGAAAAATATATT
249607 AAAT
1 AAAT
249611 TAATGACCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATGAAAAATATATT
Found at i:250778 original size:11 final size:12
Alignment explanation
Indices: 250738--250776 Score: 64
Period size: 11 Copynumber: 3.4 Consensus size: 12
250728 TTTATTATTT
250738 AATAATAATAT-
1 AATAATAATATA
250749 AATAATAATATA
1 AATAATAATATA
250761 AATAA-AATATA
1 AATAATAATATA
250772 AATAA
1 AATAA
250777 AAACAAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 22 0.81
12 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATAATATA
Found at i:251149 original size:24 final size:24
Alignment explanation
Indices: 251103--251149 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
251093 AAAATTGTTG
* **
251103 ATTTTTTTCACCGATAAGTATTAC
1 ATTTTTTTCACCAATAAAAATTAC
251127 ATTTTTTTCACCAATAAAAATTA
1 ATTTTTTTCACCAATAAAAATTA
251150 AATTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTTTTTCACCAATAAAAATTAC
Found at i:253119 original size:17 final size:17
Alignment explanation
Indices: 253097--253130 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
253087 AAAGATAAAA
*
253097 GTTGAAGAGGTTTAATT
1 GTTGAAAAGGTTTAATT
253114 GTTGAAAAGGTTTAATT
1 GTTGAAAAGGTTTAATT
253131 TGATTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (17 bp):
GTTGAAAAGGTTTAATT
Found at i:256508 original size:65 final size:64
Alignment explanation
Indices: 256366--256521 Score: 244
Period size: 65 Copynumber: 2.4 Consensus size: 64
256356 TGCACTAAGG
* *
256366 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAACCGGAGTGCATCGATGCATGGCTT
*
256430 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-AATCGGAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AAATAACCGGAGTGCATCGATGCATGGCT
256493 AT
64 -T
256495 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
256522 AATTCAATTT
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
64 34 0.40
65 49 0.57
66 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAACCGGAGTGCATCGATGCATGGCTT
Found at i:258086 original size:2 final size:2
Alignment explanation
Indices: 258079--258112 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
258069 GCTAAAGTCC
258079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
258113 TAAATCCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:271569 original size:45 final size:44
Alignment explanation
Indices: 271490--271583 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 44
271480 TTGTGGATCG
*
271490 ATGCACATTCAAGGCGTGCATCGGTGCATCTTCAT-GATGTATCA
1 ATGCACATTCAAGGCGTGCATCGATGCATCTTCATAG-TGTATCA
*
271534 ATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCATAGTGTATCG
1 ATGCACATTC-AAGGCG-TGCATCGATGCATC-TTCATAGTGTATCA
271579 ATGCA
1 ATGCA
271584 TTATGCACAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
44 12 0.27
45 31 0.70
46 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
ATGCACATTCAAGGCGTGCATCGATGCATCTTCATAGTGTATCA
Found at i:277413 original size:32 final size:35
Alignment explanation
Indices: 277372--277438 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
277362 TATGTGCAGG
277372 GGGAACAGA-TCC-CCT-GGGGGTATCGATTCCCC
1 GGGAACAGATTCCTCCTGGGGGGTATCGATTCCCC
*
277404 GGGAACAGATTCCTCTTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCTCCTGGGGGGTATCGATTCCCC
277439 CTAAATGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 9 0.29
33 3 0.10
34 2 0.06
35 17 0.55
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.22
Consensus pattern (35 bp):
GGGAACAGATTCCTCCTGGGGGGTATCGATTCCCC
Found at i:278040 original size:31 final size:31
Alignment explanation
Indices: 278002--278157 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
277992 AGGGTTGAGG
*
278002 GTTTACCTATGTTCTTCGGTACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
278033 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
278064 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
278095 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
278126 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
278157 G
1 G
278158 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:281948 original size:35 final size:36
Alignment explanation
Indices: 281889--281959 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
281879 TATGTACAGG
281889 GGGAACAGATTCTCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCTCCCCTGGGGGGTATCGATTCCCC
281925 GGGAACAGATTC-CCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCTCCCCTGGGGGGTATCGATTCCCC
281960 CCTAAATGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCTCCCCTGGGGGGTATCGATTCCCC
Found at i:282667 original size:31 final size:31
Alignment explanation
Indices: 282525--282665 Score: 219
Period size: 31 Copynumber: 4.5 Consensus size: 31
282515 AGGGTCGAGG
282525 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
282556 GTTTACCTATGTTCTTCGGGATATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
282587 GTTTACCTATGTTCTTCGGGACATATGGGCT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
282618 GTTTACCTATGTTATTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
282649 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
282666 AGAATCTATG
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:284379 original size:65 final size:65
Alignment explanation
Indices: 284296--284465 Score: 306
Period size: 65 Copynumber: 2.6 Consensus size: 65
284286 TTTAAAATAG
* *
284296 CGATGCATGGCT-TGTGCATCGATGCATAAAATACATTCGTTGTTTTCATAAAAACCGGAGTGCA
1 CGATGCATGG-TATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCGGAGTGCA
284360 T
65 T
284361 CGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCGGAGTGCAT
1 CGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCGGAGTGCAT
284426 CGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGA
1 CGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGA
284466 AATTCAATTT
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
64 1 0.01
65 101 0.99
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (65 bp):
CGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCGGAGTGCAT
Found at i:296617 original size:22 final size:23
Alignment explanation
Indices: 296574--296618 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
296564 AATTTTAGTC
**
296574 TATTTTAGTAAATAATTTTTTAAT
1 TATTTTAG-AAATAATACTTTAAT
296598 TATTTTA-AAATAATACTTTAA
1 TATTTTAGAAATAATACTTTAA
296619 GTTTAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTTTAGAAATAATACTTTAAT
Found at i:297661 original size:2 final size:2
Alignment explanation
Indices: 297654--297679 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
297644 AAATTTAATA
297654 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
297680 TACAATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:299748 original size:16 final size:17
Alignment explanation
Indices: 299719--299750 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
299709 CTACTATTAT
299719 CGGAAATAAGACTTGTA
1 CGGAAATAAGACTTGTA
299736 CGGAAAT-AGACTTGT
1 CGGAAATAAGACTTGT
299751 CACAAGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (17 bp):
CGGAAATAAGACTTGTA
Found at i:304120 original size:3 final size:3
Alignment explanation
Indices: 304112--304153 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
304102 TAGAGTCAAT
304112 ATA ATA ATA A-A ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
304154 CAATTCACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:304126 original size:11 final size:11
Alignment explanation
Indices: 304112--304153 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
304102 TAGAGTCAAT
304112 ATAATAATAAA
1 ATAATAATAAA
304123 ATAATAATAAA
1 ATAATAATAAA
304134 ATAATAATAATA
1 ATAATAATAA-A
304146 ATAATAAT
1 ATAATAAT
304154 CAATTCACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:304131 original size:14 final size:15
Alignment explanation
Indices: 304112--304153 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
304102 TAGAGTCAAT
304112 ATAATAATAA-AATA
1 ATAATAATAATAATA
304126 ATAATAA-AATAATA
1 ATAATAATAATAATA
304140 ATAATAATAATAAT
1 ATAATAATAATAAT
304154 CAATTCACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.08
14 18 0.69
15 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAATAATAATA
Found at i:304827 original size:8 final size:8
Alignment explanation
Indices: 304815--304849 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
304805 CGACGTTACC
*
304815 CAATATTC
1 CAATATTA
304823 CAATATTA
1 CAATATTA
304831 CAATATTA
1 CAATATTA
304839 CAATATTA
1 CAATATTA
304847 CAA
1 CAA
304850 CACTGGCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (8 bp):
CAATATTA
Found at i:306019 original size:16 final size:16
Alignment explanation
Indices: 305994--306027 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
305984 ACCCCAATAT
*
305994 TACAATATTACAACAC
1 TACAACATTACAACAC
306010 TACAACATTACAACAC
1 TACAACATTACAACAC
306026 TA
1 TA
306028 GTTGCGGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (16 bp):
TACAACATTACAACAC
Done.