Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold57
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: 4071704
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82236 characters in sequence are not A, C, G, or T
File 18 of 27
Found at i:2384002 original size:19 final size:20
Alignment explanation
Indices: 2383976--2384024 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
2383966 AATTTTGATA
2383976 TGTTAATTTATTT-ATATATT
1 TGTTAATTTATTTAATA-ATT
2383996 T-TTAATTT-TTTAATAATT
1 TGTTAATTTATTTAATAATT
2384014 TGTTAATTTAT
1 TGTTAATTTAT
2384025 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (20 bp):
TGTTAATTTATTTAATAATT
Found at i:2384022 original size:52 final size:50
Alignment explanation
Indices: 2383951--2384088 Score: 113
Period size: 50 Copynumber: 2.7 Consensus size: 50
2383941 ATTTTATAAA
2383951 TAATATATTTGATTAAATTTTGATATGTTAATTTATTTATATATTTTTAATT-TTT
1 TAATA-ATTTG-TT-AATTTT-ATAT-TTAATTTATTTATATA-TTTTAATTATTT
* * *
2384006 TAATAATTTGTTAA-TTTATATTTATTTTTTGTTTTATATTTTAATTATTT
1 TAATAATTTGTTAATTTTATATTTAATTTAT-TTATATATTTTAATTATTT
* * *
2384056 T--TTATTTGTAAATTTTAATATATTTATTTATTT
1 TAATAATTTGTTAATTTT-ATAT-TTAATTTATTT
2384089 GTGTTGTATT
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
48 9 0.13
49 18 0.26
50 20 0.29
51 9 0.13
52 2 0.03
53 2 0.03
54 5 0.07
55 5 0.07
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (50 bp):
TAATAATTTGTTAATTTTATATTTAATTTATTTATATATTTTAATTATTT
Found at i:2384046 original size:24 final size:24
Alignment explanation
Indices: 2384019--2384109 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 24
2384009 TAATTTGTTA
2384019 ATTTATATTTATTTTTTGTTTTAT
1 ATTTATATTTATTTTTTGTTTTAT
* *
2384043 ATTT-TAATTATTTTTTATTTGTAAAT
1 ATTTATATTTATTTTTTGTTT-T--AT
* * *
2384069 TTTAATATATTTATTTATTTGTGTTGT
1 ATT--TATATTTATTT-TTTGTTTTAT
2384096 ATTTAT-TTTATTTT
1 ATTTATATTTATTTT
2384110 AATGTCATGT
Statistics
Matches: 52, Mismatches: 8, Indels: 15
0.69 0.11 0.20
Matches are distributed among these distances:
23 15 0.29
24 12 0.23
25 3 0.06
26 4 0.08
27 3 0.06
28 1 0.02
29 9 0.17
30 5 0.10
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (24 bp):
ATTTATATTTATTTTTTGTTTTAT
Found at i:2384055 original size:23 final size:24
Alignment explanation
Indices: 2384011--2384090 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 24
2384001 TTTTTTAATA
* *
2384011 ATTTGTTAATTTATATTTATTTTTT
1 ATTTGTAAATTT-TAATTATTTTTT
* *
2384036 GTTT-TATATTTTAATTATTTTTT
1 ATTTGTAAATTTTAATTATTTTTT
2384059 ATTTGTAAATTTTAATATATTTATTT
1 ATTTGTAAATTTTAAT-TATTT-TTT
2384085 ATTTGT
1 ATTTGT
2384091 GTTGTATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
23 14 0.30
24 15 0.33
25 8 0.17
26 9 0.20
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (24 bp):
ATTTGTAAATTTTAATTATTTTTT
Found at i:2384460 original size:37 final size:38
Alignment explanation
Indices: 2384412--2384491 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
2384402 TAAAACTAAT
2384412 ATCAAGTAAAAATTAACACAAAAGGTCATATAATCAAA
1 ATCAAGTAAAAATTAACACAAAAGGTCATATAATCAAA
* * * *
2384450 ATCAA-TAAAAATTAACCCACAATGTCCTATAATCAAA
1 ATCAAGTAAAAATTAACACAAAAGGTCATATAATCAAA
2384487 ATCAA
1 ATCAA
2384492 ACTTCTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 33 0.87
38 5 0.13
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.23
Consensus pattern (38 bp):
ATCAAGTAAAAATTAACACAAAAGGTCATATAATCAAA
Found at i:2386171 original size:24 final size:27
Alignment explanation
Indices: 2386144--2386202 Score: 88
Period size: 24 Copynumber: 2.3 Consensus size: 27
2386134 TTTATATATT
2386144 TTTATTAAATTAAATAATA-T-TTT-A
1 TTTATTAAATTAAATAATATTATTTAA
*
2386168 TTTATTTAATTAAATAATATTATTTAA
1 TTTATTAAATTAAATAATATTATTTAA
2386195 TTTATTAA
1 TTTATTAA
2386203 TAAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 18 0.60
25 1 0.03
26 3 0.10
27 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTATTAAATTAAATAATATTATTTAA
Found at i:2387372 original size:18 final size:18
Alignment explanation
Indices: 2387349--2387384 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2387339 ATCTCCTACT
*
2387349 TCTTCGACTACTTCATCG
1 TCTTCGACTACGTCATCG
*
2387367 TCTTCGCCTACGTCATCG
1 TCTTCGACTACGTCATCG
2387385 GTGGCTTCTC
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:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (18 bp):
TCTTCGACTACGTCATCG
Found at i:2389615 original size:12 final size:12
Alignment explanation
Indices: 2389600--2389624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2389590 TATTTTTTAA
2389600 TTTTTATAATTT
1 TTTTTATAATTT
2389612 TTTTTATAATTT
1 TTTTTATAATTT
2389624 T
1 T
2389625 AAATATGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATAATTT
Found at i:2389616 original size:21 final size:23
Alignment explanation
Indices: 2389581--2389624 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
2389571 GATATATTAA
*
2389581 TATAATATTTATTTTTTAATTTT
1 TATAATATTTATTTTATAATTTT
2389604 TATAAT-TTT-TTTTATAATTTT
1 TATAATATTTATTTTATAATTTT
2389625 AAATATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 3 0.15
23 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TATAATATTTATTTTATAATTTT
Found at i:2390060 original size:22 final size:21
Alignment explanation
Indices: 2390003--2390081 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 21
2389993 TATTAGATTA
2390003 AATTAAA-TTAT-TATTTTA-
1 AATTAAATTTATATATTTTAT
* *
2390021 AA-AAAATTTAAAATATTTT-T
1 AATTAAATTT-ATATATTTTAT
2390041 ATATTAATATTTATATATTTTAT
1 A-ATTAA-ATTTATATATTTTAT
2390064 AATTAAATTTA-AT-TTTTA
1 AATTAAATTTATATATTTTA
2390082 AAAAAATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
17 3 0.06
18 4 0.08
19 6 0.12
20 9 0.18
21 6 0.12
22 15 0.31
23 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTAAATTTATATATTTTAT
Found at i:2390325 original size:3 final size:3
Alignment explanation
Indices: 2390317--2390347 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2390307 ATAAATTGGA
2390317 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2390348 GTTGTCGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2390795 original size:2 final size:2
Alignment explanation
Indices: 2390788--2390812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2390778 ATGCAATAGA
2390788 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2390813 AATAATGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2390952 original size:5 final size:5
Alignment explanation
Indices: 2390944--2391074 Score: 58
Period size: 5 Copynumber: 26.0 Consensus size: 5
2390934 ATGATAATGT
* * * * *
2390944 TATAA TATAA -A-AA TATGA TATAA AATAA TTTAA -ATTTA TATAA AATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA-TAA TATAA TATAA
* * * * *
2390992 TTATTAA TATAT TAAAA T-TAA TATAA TTATAA AATAT TTTATA TATAA
1 -TA-TAA TATAA TATAA TATAA TATAA -TATAA TATAA TATA-A TATAA
*
2391040 TTATAA TTTAA TA-AA -ATAA TATAAA TATAA TATAA
1 -TATAA TATAA TATAA TATAA TAT-AA TATAA TATAA
2391075 AATTTTTAAG
Statistics
Matches: 91, Mismatches: 22, Indels: 26
0.65 0.16 0.19
Matches are distributed among these distances:
3 3 0.03
4 9 0.10
5 54 0.59
6 22 0.24
7 3 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:2391007 original size:20 final size:20
Alignment explanation
Indices: 2390954--2391009 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2390944 TATAATATAA
2390954 AAATATGATATAAAATAATTT
1 AAATAT-ATATAAAATAATTT
*
2390975 AAATTTATATAAAATAATTAT
1 AAATATATATAAAATAATT-T
*
2390996 TAATATAT-TAAAAT
1 AAATATATATAAAAT
2391010 TAATATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATATATATAAAATAATTT
Found at i:2391023 original size:37 final size:39
Alignment explanation
Indices: 2390982--2391066 Score: 97
Period size: 38 Copynumber: 2.2 Consensus size: 39
2390972 TTTAAATTTA
*
2390982 TATAAAATAATTATTA-ATAT-ATTA-AAATTAATATAAT
1 TATAAAATAATT-TTATATATAATTATAAATTAATAAAAT
*
2391019 TATAAAAT-ATTTTATATATAATTATAATTTAATAAAAT
1 TATAAAATAATTTTATATATAATTATAAATTAATAAAAT
*
2391057 AATATAAATA
1 TATA-AAATA
2391067 TAATATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
35 3 0.08
36 7 0.17
37 12 0.30
38 14 0.35
39 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (39 bp):
TATAAAATAATTTTATATATAATTATAAATTAATAAAAT
Found at i:2391024 original size:17 final size:20
Alignment explanation
Indices: 2390980--2391026 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2390970 AATTTAAATT
2390980 TATATAAAA-TAATTATTAA
1 TATATAAAATTAATTATTAA
2390999 TATATTAAAATTAA-TA-TAA
1 TATA-TAAAATTAATTATTAA
2391018 T-TATAAAAT
1 TATATAAAAT
2391027 ATTTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.23
18 2 0.08
19 8 0.31
20 7 0.27
21 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATAAAATTAATTATTAA
Found at i:2391033 original size:51 final size:50
Alignment explanation
Indices: 2390978--2391082 Score: 122
Period size: 51 Copynumber: 2.1 Consensus size: 50
2390968 ATAATTTAAA
* * * *
2390978 TTTATATAAAATAATTA-TTAATATATTAAAATTAATATAATTATAAAATAT
1 TTTATATAAAATAATAATTTAATAAAATAAAATAAATATAA-TATAAAAT-T
* * *
2391029 TTTATATATAATTATAATTTAATAAAATAATATAAATATAATATAAAATT
1 TTTATATAAAATAATAATTTAATAAAATAAAATAAATATAATATAAAATT
2391079 TTTA
1 TTTA
2391083 AGTATTGTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
50 5 0.11
51 22 0.48
52 19 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (50 bp):
TTTATATAAAATAATAATTTAATAAAATAAAATAAATATAATATAAAATT
Found at i:2391056 original size:30 final size:27
Alignment explanation
Indices: 2390981--2391074 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 27
2390971 ATTTAAATTT
* * *
2390981 ATATAAAATAATTATTAATATATTA-AA
1 ATATAATATAATTA-TAAAATAATATAA
* * *
2391008 AT-TAATATAATTATAAAATATTTTAT
1 ATATAATATAATTATAAAATAATATAA
2391034 ATATAATTATAATTTAATAAAATAATATAA
1 ATATAA-TATAA-TT-ATAAAATAATATAA
2391064 ATATAATATAA
1 ATATAATATAA
2391075 AATTTTTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
25 8 0.15
26 13 0.24
27 5 0.09
28 5 0.09
29 7 0.13
30 17 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATAATATAATTATAAAATAATATAA
Found at i:2391350 original size:11 final size:11
Alignment explanation
Indices: 2391334--2391374 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
2391324 CGTTGACTAA
2391334 TATATTTAAAT
1 TATATTTAAAT
2391345 TATA-TTAAAT
1 TATATTTAAAT
*
2391355 TAAATTTAAAT
1 TATATTTAAAT
2391366 TATTATTTA
1 TA-TATTTA
2391375 TATAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 9 0.35
11 12 0.46
12 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATTTAAAT
Found at i:2391436 original size:22 final size:22
Alignment explanation
Indices: 2391395--2391438 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2391385 AAATAAATTT
2391395 TTATATAAATTTAATAATAAAA
1 TTATATAAATTTAATAATAAAA
*
2391417 TTATATCAATATTAAT-ATAAAA
1 TTATATAAAT-TTAATAATAAAA
2391439 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTATATAAATTTAATAATAAAA
Found at i:2392524 original size:10 final size:11
Alignment explanation
Indices: 2392507--2392558 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
2392497 TTTATAAAAA
2392507 AATATAAAATT
1 AATATAAAATT
2392518 AAT-TAAAATAT
1 AATATAAAAT-T
*
2392529 GATATAAAATT
1 AATATAAAATT
*
2392540 -ATATAAAAAT
1 AATATAAAATT
2392550 AAT-TAAAAT
1 AATATAAAAT
2392559 GACATAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 20 0.57
11 9 0.26
12 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AATATAAAATT
Found at i:2392534 original size:22 final size:23
Alignment explanation
Indices: 2392508--2392550 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2392498 TTATAAAAAA
*
2392508 ATATAAAATTA-ATTAAAATATG
1 ATATAAAATTATATAAAAATATG
2392530 ATATAAAATTATATAAAAATA
1 ATATAAAATTATATAAAAATA
2392551 ATTAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
ATATAAAATTATATAAAAATATG
Found at i:2392736 original size:23 final size:23
Alignment explanation
Indices: 2392710--2392763 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
2392700 TCAATTTTTT
*
2392710 TAAATATATTATT-TAAAATAAAA
1 TAAA-ATAATATTCTAAAATAAAA
*
2392733 TAAAATAATATTCTCAAAT-AAA
1 TAAAATAATATTCTAAAATAAAA
2392755 TAATAATAA
1 TAA-AATAA
2392764 AAGAAAACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAAATAATATTCTAAAATAAAA
Found at i:2393187 original size:29 final size:29
Alignment explanation
Indices: 2393153--2393209 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2393143 TCTATATTTT
2393153 TAAAATT-TATTAAAATAATATATTAAATA
1 TAAAATTCTATTAAAATAATA-ATTAAATA
*
2393182 TAAAATTCTTTTAAAATAATAATTAAAT
1 TAAAATTCTATTAAAATAATAATTAAAT
2393210 TATTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAATTCTATTAAAATAATAATTAAATA
Found at i:2395867 original size:13 final size:13
Alignment explanation
Indices: 2395849--2395873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2395839 TTGAAAAGTA
2395849 TTAATATATATTT
1 TTAATATATATTT
2395862 TTAATATATATT
1 TTAATATATATT
2395874 AATATATAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATATATATTT
Found at i:2396532 original size:17 final size:18
Alignment explanation
Indices: 2396504--2396537 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2396494 CAAATTTTTA
*
2396504 AAATACTTATATGAATTT
1 AAATACTTATATAAATTT
2396522 AAATA-TTATATAAATT
1 AAATACTTATATAAATT
2396538 GTAGATATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATACTTATATAAATTT
Found at i:2397082 original size:21 final size:21
Alignment explanation
Indices: 2397058--2397112 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 21
2397048 AACTATTTAA
*
2397058 TAATAAAAAATTATTTAAAT-T
1 TAATAAAAAA-TATATAAATAT
* *
2397079 TAATTATAAATATATAAATAT
1 TAATAAAAAATATATAAATAT
*
2397100 TAAT-ATAAATATA
1 TAATAAAAAATATA
2397113 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAAAAAATATATAAATAT
Found at i:2397106 original size:20 final size:20
Alignment explanation
Indices: 2397073--2397112 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2397063 AAAAATTATT
2397073 TAAATTTAATTATAAATATA
1 TAAATTTAATTATAAATATA
2397093 TAAATATTAA-TATAAATATA
1 TAAAT-TTAATTATAAATATA
2397113 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAATTTAATTATAAATATA
Found at i:2397629 original size:41 final size:42
Alignment explanation
Indices: 2397544--2397638 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
2397534 ATTAAATTAA
* * * * *
2397544 ATTTAAA-TTAATTTTATTTATAATATTAATATTATCTATTT
1 ATTTAAATTTAATTTAATTTAAAATATAAATATAATCTATGT
2397585 ATTTAAATTTAATTTAATTTAAAATATAAATATAAAT-T-TGT
1 ATTTAAATTTAATTTAATTTAAAATATAAATAT-AATCTATGT
2397626 ATTTAAATTTAAT
1 ATTTAAATTTAAT
2397639 ATTTTATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 22 0.47
42 23 0.49
43 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (42 bp):
ATTTAAATTTAATTTAATTTAAAATATAAATATAATCTATGT
Found at i:2398097 original size:16 final size:17
Alignment explanation
Indices: 2398078--2398110 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2398068 TATATTATAA
2398078 TTATATTTTAA-ATATT
1 TTATATTTTAATATATT
2398094 TTATATTTTAATATATT
1 TTATATTTTAATATATT
2398111 AATAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATATTTTAATATATT
Found at i:2398188 original size:19 final size:20
Alignment explanation
Indices: 2398157--2398194 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
2398147 TATATTATTT
2398157 TTATATTATATA-TATAAAA
1 TTATATTATATATTATAAAA
2398176 TTATATT-TAATATTATAAA
1 TTATATTAT-ATATTATAAA
2398195 TCTATCCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 10 0.59
20 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATTATATATTATAAAA
Found at i:2398375 original size:17 final size:17
Alignment explanation
Indices: 2398353--2398408 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
2398343 TTAAAATAAT
2398353 TAAAATATAATATAAAA
1 TAAAATATAATATAAAA
* *
2398370 TAAAATATGATAAAAAA
1 TAAAATATAATATAAAA
2398387 TAATATATATAATATATAAA
1 TAA-A-ATATAATATA-AAA
2398407 TA
1 TA
2398409 TTTCAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 18 0.56
18 1 0.03
19 8 0.25
20 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAAATATAATATAAAA
Found at i:2398423 original size:18 final size:18
Alignment explanation
Indices: 2398395--2398459 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 18
2398385 AATAATATAT
2398395 ATAATATATAAATATTTCA
1 ATAATATATAAA-ATTTCA
*
2398414 ATAA-ATATAAAATTTTA
1 ATAATATATAAAATTTCA
*
2398431 AT-ATAT-TAAACTTT-A
1 ATAATATATAAAATTTCA
2398446 TATAA-ATATAAAAT
1 -ATAATATATAAAAT
2398460 AATTTAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.03
16 12 0.31
17 15 0.38
18 7 0.18
19 4 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATATATAAAATTTCA
Found at i:2398433 original size:33 final size:33
Alignment explanation
Indices: 2398396--2398459 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
2398386 ATAATATATA
2398396 TAATATA-TAAATATTTCA-ATAAATATAAAATTT
1 TAATATATTAAA-ATTT-ATATAAATATAAAATTT
*
2398429 TAATATATTAAACTTTATATAAATATAAAAT
1 TAATATATTAAAATTTATATAAATATAAAAT
2398460 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.04
33 23 0.82
34 4 0.14
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (33 bp):
TAATATATTAAAATTTATATAAATATAAAATTT
Found at i:2398492 original size:83 final size:83
Alignment explanation
Indices: 2398331--2398488 Score: 209
Period size: 84 Copynumber: 1.9 Consensus size: 83
2398321 ACAACCTAAT
2398331 ATAAATATAATTTTAAAATAATTAAAATATAATATAAAATAAAATATGATAAAAAATAATATATA
1 ATAAATATAATTTTAAAATAATTAAAATATAATATAAAATAAAATATGATAAAAAATAATATATA
2398396 TAATATATAAATATTTCA
66 TAATATATAAATATTTCA
* * * *
2398414 ATAAATATAAAATTTTAATAT-ATTAAACT-TTATATAAATATAAAATAAT-TTAAAAAATAATA
1 ATAAATAT--AATTTTAAAATAATTAAAATATAATATAAA-ATAAAAT-ATGATAAAAAATAATA
2398476 -ATAT-ATATATAAA
62 TATATAATATATAAA
2398489 ATATAAATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
82 9 0.13
83 20 0.30
84 26 0.39
85 12 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (83 bp):
ATAAATATAATTTTAAAATAATTAAAATATAATATAAAATAAAATATGATAAAAAATAATATATA
TAATATATAAATATTTCA
Found at i:2400114 original size:23 final size:23
Alignment explanation
Indices: 2400070--2400114 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2400060 ATTTTAAAAT
*
2400070 GTAAAAATTATATTTATTTTTAA
1 GTAAAAATTATATTTATATTTAA
*
2400093 GTAAAATTTATA-TTATAATTTA
1 GTAAAAATTATATTTAT-ATTTA
2400115 TTTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
GTAAAAATTATATTTATATTTAA
Found at i:2400119 original size:17 final size:17
Alignment explanation
Indices: 2400099--2400134 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2400089 TTAAGTAAAA
*
2400099 TTTATATTATAATTTAT
1 TTTATATTATAATATAT
*
2400116 TTTATTTTATAATATAT
1 TTTATATTATAATATAT
2400133 TT
1 TT
2400135 ATCTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATAATATAT
Found at i:2400352 original size:16 final size:17
Alignment explanation
Indices: 2400320--2400356 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2400310 CTATAATATA
2400320 TTATAAATTAAATTTAT
1 TTATAAATTAAATTTAT
*
2400337 TTATAAGTTAAA-TTAT
1 TTATAAATTAAATTTAT
2400353 TTAT
1 TTAT
2400357 TGAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTATAAATTAAATTTAT
Found at i:2400453 original size:27 final size:27
Alignment explanation
Indices: 2400423--2400474 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2400413 GTAATGTAAA
2400423 TTAATATTTAATAATA-AAAAATATATT
1 TTAA-ATTTAATAATATAAAAATATATT
* *
2400450 TTAAATTTAATTATATAAATATATA
1 TTAAATTTAATAATATAAAAATATA
2400475 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
TTAAATTTAATAATATAAAAATATATT
Found at i:2400527 original size:43 final size:44
Alignment explanation
Indices: 2400432--2400528 Score: 101
Period size: 48 Copynumber: 2.2 Consensus size: 44
2400422 ATTAATATTT
2400432 AATAATAAAAAATATATTTTAAATTTAATTATATAAATATATAA
1 AATAATAAAAAATATATTTTAAATTTAATTATATAAATATATAA
* * * *
2400476 ATATTAATATAAATATTATATTTTTAATTT-GTTAT-T-AATTTATAA
1 A-A-TAATA-AAA-AATATATTTTAAATTTAATTATATAAATATATAA
2400521 AATAATAA
1 AATAATAA
2400529 TTTAAATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
42 1 0.02
43 5 0.11
44 2 0.04
45 10 0.22
46 6 0.13
47 7 0.16
48 14 0.31
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (44 bp):
AATAATAAAAAATATATTTTAAATTTAATTATATAAATATATAA
Found at i:2403801 original size:30 final size:30
Alignment explanation
Indices: 2403767--2403946 Score: 315
Period size: 30 Copynumber: 6.0 Consensus size: 30
2403757 GAATCTTGCC
2403767 TGTTGAGACTGATGATTTGAGTAGAGAGAA
1 TGTTGAGACTGATGATTTGAGTAGAGAGAA
*
2403797 TGTTGAGACTGATGATTTGAGCAGAGAGAA
1 TGTTGAGACTGATGATTTGAGTAGAGAGAA
* *
2403827 CGTTGAGACTGGTGATTTGAGTAGAGAGAA
1 TGTTGAGACTGATGATTTGAGTAGAGAGAA
2403857 TGTTGAGACTGATGATTTGAGTAGAGAGAA
1 TGTTGAGACTGATGATTTGAGTAGAGAGAA
*
2403887 TGTTGAGACTGATGATTTGAGTAGAGATAA
1 TGTTGAGACTGATGATTTGAGTAGAGAGAA
*
2403917 TGTTGAGACTGGTGATTTGAGTAGAGAGAA
1 TGTTGAGACTGATGATTTGAGTAGAGAGAA
2403947 ACAGGAATCT
Statistics
Matches: 141, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 141 1.00
ACGTcount: A:0.32, C:0.04, G:0.34, T:0.29
Consensus pattern (30 bp):
TGTTGAGACTGATGATTTGAGTAGAGAGAA
Found at i:2407006 original size:13 final size:12
Alignment explanation
Indices: 2406988--2407017 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2406978 AAATCTTGGT
2406988 TTTTTTTTTTAAA
1 TTTTTTTTTT-AA
2407001 TTTTTTTTTTAA
1 TTTTTTTTTTAA
2407013 TTTTT
1 TTTTT
2407018 CACATGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:2412754 original size:6 final size:6
Alignment explanation
Indices: 2412745--2412769 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2412735 AGCACAAGCT
2412745 ATTGCC ATTGCC ATTGCC ATTGCC A
1 ATTGCC ATTGCC ATTGCC ATTGCC A
2412770 ATGTGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (6 bp):
ATTGCC
Found at i:2413743 original size:3 final size:3
Alignment explanation
Indices: 2413735--2413765 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2413725 TCCATCTTTT
2413735 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2413766 CAAATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2413879 original size:21 final size:20
Alignment explanation
Indices: 2413855--2413894 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2413845 ATAAAAATAA
*
2413855 AAATTATAAAAATTCAAATTT
1 AAATTAAAAAAATT-AAATTT
2413876 AAATTAAAAAAATTAAATT
1 AAATTAAAAAAATTAAATT
2413895 CCAACCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATTAAAAAAATTAAATTT
Found at i:2414439 original size:2 final size:2
Alignment explanation
Indices: 2414432--2414481 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2414422 TCAAGTATAA
2414432 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2414474 AG AG AG AG
1 AG AG AG AG
2414482 GAGGTTAGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2415682 original size:55 final size:55
Alignment explanation
Indices: 2415619--2415729 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
2415609 AAACATTTTT
2415619 GAACATTATTTATCCTGCCAAATTTTTGGCATCTGAAGAATGGGTATTCATGTTG
1 GAACATTATTTATCCTGCCAAATTTTTGGCATCTGAAGAATGGGTATTCATGTTG
2415674 GAACATTATTTATCCTGCCAAATTTTTGGCATCTGAAGAATGGGTATTCATGTTG
1 GAACATTATTTATCCTGCCAAATTTTTGGCATCTGAAGAATGGGTATTCATGTTG
2415729 G
1 G
2415730 TTGTCAACTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (55 bp):
GAACATTATTTATCCTGCCAAATTTTTGGCATCTGAAGAATGGGTATTCATGTTG
Found at i:2418969 original size:2 final size:2
Alignment explanation
Indices: 2418962--2418988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2418952 ATTCATTGAT
2418962 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2418989 TTCTTTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2423417 original size:14 final size:16
Alignment explanation
Indices: 2423390--2423422 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2423380 TTTATGTTTA
2423390 TTTATAATTTAAAT-T
1 TTTATAATTTAAATAT
2423405 TTTATAA-TTAAATAT
1 TTTATAATTTAAATAT
2423420 TTT
1 TTT
2423423 TTATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATAATTTAAATAT
Found at i:2423935 original size:15 final size:15
Alignment explanation
Indices: 2423915--2423964 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
2423905 TATTACACTT
2423915 TTAAAAGTATAAAAA
1 TTAAAAGTATAAAAA
* *
2423930 TTAAAA-TATTAAAT
1 TTAAAAGTATAAAAA
* *
2423944 TTAATAGTACAAAAA
1 TTAAAAGTATAAAAA
2423959 TTAAAA
1 TTAAAA
2423965 TATTTTATTC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (15 bp):
TTAAAAGTATAAAAA
Found at i:2424189 original size:23 final size:23
Alignment explanation
Indices: 2424162--2424207 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2424152 ATGATTATAT
* *
2424162 AATATAATTTAAAAAATTATTAA
1 AATATAATATAAAAAAATATTAA
2424185 AATATAATATAAAAAAATATTAA
1 AATATAATATAAAAAAATATTAA
2424208 TATCATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AATATAATATAAAAAAATATTAA
Found at i:2424215 original size:26 final size:25
Alignment explanation
Indices: 2424158--2424223 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 25
2424148 TAACATGATT
* *
2424158 ATATAATATAATTTAAAAAATTATTA
1 ATAT-ATATAATATAAAAAAATATTA
2424184 A-A-ATATAATATAAAAAAATATTA
1 ATATATATAATATAAAAAAATATTA
2424207 ATATCATATAAATATAA
1 ATAT-ATAT-AATATAA
2424224 CGTATCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 20 0.59
24 1 0.03
25 1 0.03
26 5 0.15
27 7 0.21
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATATATAATATAAAAAAATATTA
Found at i:2425828 original size:17 final size:17
Alignment explanation
Indices: 2425797--2425840 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2425787 ACATAATTAT
**
2425797 AATATAAAAAATATAAA
1 AATATAAAATTTATAAA
* *
2425814 AATATTAAATTTATATA
1 AATATAAAATTTATAAA
2425831 AATATAAAAT
1 AATATAAAAT
2425841 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATAAAATTTATAAA
Found at i:2425868 original size:30 final size:31
Alignment explanation
Indices: 2425791--2425878 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 31
2425781 GATAAAACAT
2425791 AATTATAATATAA-AAAATA-TAAAAATATTA
1 AATTATAATATAATAAAATATTAAAAATA-TA
* **
2425821 AATT-TATATAAATATAAAATATTTTAAATA-A
1 AATTATA-ATATA-ATAAAATATTAAAAATATA
*
2425852 AATTATAATATAATAAAATATAAAAAA
1 AATTATAATATAATAAAATATTAAAAA
2425879 CAATAATAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
29 2 0.04
30 20 0.43
31 10 0.22
32 8 0.17
33 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AATTATAATATAATAAAATATTAAAAATATA
Found at i:2429007 original size:2 final size:2
Alignment explanation
Indices: 2429000--2429035 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2428990 TTCATCAAAT
2429000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2429036 ATTGCAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2430793 original size:25 final size:25
Alignment explanation
Indices: 2430733--2430801 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
2430723 ATTAAATTAT
2430733 ATTAAT-TTATTTATAGTTTTTAATAA
1 ATTAATATTATTT-TA-TTTTTAATAA
2430759 ATTTAA-ATTATTTTATTTTTAATAA
1 A-TTAATATTATTTTATTTTTAATAA
*
2430784 GA-TAATATTATTTAATTT
1 -ATTAATATTATTTTATTT
2430802 ATTTATAGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 3 0.08
25 21 0.55
26 4 0.11
27 10 0.26
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (25 bp):
ATTAATATTATTTTATTTTTAATAA
Found at i:2431408 original size:14 final size:14
Alignment explanation
Indices: 2431389--2431434 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
2431379 ATAAATCTAT
2431389 TAAAATTTATATAA
1 TAAAATTTATATAA
2431403 TAAAATTTATTAATATAA
1 TAAAA--T-TT-ATATAA
2431421 TAAAATTTATATAA
1 TAAAATTTATATAA
2431435 ATATATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.39
15 2 0.07
16 2 0.07
17 2 0.07
18 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATTTATATAA
Found at i:2432179 original size:17 final size:17
Alignment explanation
Indices: 2432159--2432199 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
2432149 TTTAATATAA
2432159 TTATATATTT-ATAATTT
1 TTATAT-TTTAATAATTT
*
2432176 TTATATTTTAATTATTT
1 TTATATTTTAATAATTT
2432193 TTATATT
1 TTATATT
2432200 ATATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTTAATAATTT
Found at i:2432182 original size:15 final size:15
Alignment explanation
Indices: 2432162--2432215 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
2432152 AATATAATTA
2432162 TATATTTATAATTTT
1 TATATTTATAATTTT
2432177 TATATTT-TAATTATT
1 TATATTTATAATT-TT
*
2432192 TTTATATTAT-A-TTT
1 TATAT-TTATAATTTT
2432206 TAT-TTTATAA
1 TATATTTATAA
2432216 ACATTTCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 9 0.27
15 14 0.42
16 3 0.09
17 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATTTATAATTTT
Found at i:2432318 original size:16 final size:17
Alignment explanation
Indices: 2432297--2432329 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2432287 ATTAATTAAA
2432297 TTAAATTAATT-ATTTT
1 TTAAATTAATTAATTTT
2432313 TTAAATTAATTAATTTT
1 TTAAATTAATTAATTTT
2432330 AAAAATTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAAATTAATTAATTTT
Found at i:2432973 original size:8 final size:8
Alignment explanation
Indices: 2432911--2433033 Score: 53
Period size: 8 Copynumber: 15.8 Consensus size: 8
2432901 TTTAAAAATA
*
2432911 ATATAAAT
1 ATATTAAT
*
2432919 ATTTTAAT
1 ATATTAAT
*
2432927 ATTTTAAT
1 ATATTAAT
* *
2432935 ATTTTAAA
1 ATATTAAT
2432943 AT-TTATAT
1 ATATTA-AT
2432951 AATATTAAT
1 -ATATTAAT
2432960 -TATTAAT
1 ATATTAAT
2432967 ATATTAA-
1 ATATTAAT
2432974 A-ATT--T
1 ATATTAAT
*
2432979 ATATAAAT
1 ATATTAAT
*
2432987 ATA-AAAT
1 ATATTAAT
*
2432994 ATTTTAAAT
1 ATATT-AAT
*
2433003 ATAATAAT
1 ATATTAAT
*
2433011 ATAATAAT
1 ATATTAAT
*
2433019 AATATAAAT
1 -ATATTAAT
*
2433028 AAATTA
1 ATATTA
2433034 TAATTTAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
5 1 0.01
6 5 0.05
7 17 0.19
8 49 0.54
9 16 0.18
10 3 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
ATATTAAT
Found at i:2433340 original size:26 final size:26
Alignment explanation
Indices: 2433311--2433363 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
2433301 AATATAAATA
2433311 TTTTAAATTT-T-TTTAAAAATTTTTAT
1 TTTTAAATTTATATTT--AAATTTTTAT
*
2433337 TTTTATATTTATATTTAAATTTTTAT
1 TTTTAAATTTATATTTAAATTTTTAT
2433363 T
1 T
2433364 AAATATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 20 0.83
27 1 0.04
28 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTAAATTTATATTTAAATTTTTAT
Found at i:2433369 original size:25 final size:26
Alignment explanation
Indices: 2433327--2433380 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
2433317 ATTTTTTTAA
** **
2433327 AAATTTTTATTTTTATATTTATATTT
1 AAATTTTTATTTAAATATAAATATTT
2433353 AAATTTTTA-TTAAATATAAATATTT
1 AAATTTTTATTTAAATATAAATATTT
2433378 AAA
1 AAA
2433381 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AAATTTTTATTTAAATATAAATATTT
Found at i:2433399 original size:18 final size:17
Alignment explanation
Indices: 2433364--2433408 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
2433354 AATTTTTATT
*
2433364 AAATATAAATATTTAAAA
1 AAATA-AAAAATTTAAAA
2433382 AAATAAAAAATTTAAAA
1 AAATAAAAAATTTAAAA
2433399 AACATAAAAA
1 AA-ATAAAAA
2433409 GCGTCAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAAATTTAAAA
Found at i:2438656 original size:3 final size:3
Alignment explanation
Indices: 2438650--2438681 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2438640 AAAAAAAATA
2438650 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2438682 ATCTTAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2443189 original size:2 final size:2
Alignment explanation
Indices: 2443182--2443258 Score: 118
Period size: 2 Copynumber: 38.5 Consensus size: 2
2443172 TTTAATTGCT
2443182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2443224 TG TA CA TA TA TG GA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2443259 GAAAATAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2443447 original size:18 final size:18
Alignment explanation
Indices: 2443424--2443467 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2443414 AATTAATTAA
2443424 TTTATAA-GATTTTATATT
1 TTTATAATGA-TTTATATT
2443442 TTTATATATGATTTATATT
1 TTTATA-ATGATTTATATT
*
2443461 TTAATAA
1 TTTATAA
2443468 ATCGATCACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 14 0.61
20 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTATAATGATTTATATT
Found at i:2445116 original size:3 final size:3
Alignment explanation
Indices: 2445108--2445146 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2445098 AGGATACTTC
2445108 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2445147 TAATCGTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2446231 original size:23 final size:23
Alignment explanation
Indices: 2446205--2446250 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2446195 TAAATATCAA
2446205 TTAAAAATAATTTA-ATTATTATT
1 TTAAAAA-AATTTATATTATTATT
* *
2446228 TTAATAAAATTTATATTTTTATT
1 TTAAAAAAATTTATATTATTATT
2446251 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTAAAAAAATTTATATTATTATT
Found at i:2446244 original size:17 final size:17
Alignment explanation
Indices: 2446224--2446257 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2446214 ATTTAATTAT
2446224 TATTTTAATAAAATTTA
1 TATTTTAATAAAATTTA
* *
2446241 TATTTTTATTAAATTTA
1 TATTTTAATAAAATTTA
2446258 AAAATTAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTAATAAAATTTA
Found at i:2446298 original size:25 final size:24
Alignment explanation
Indices: 2446205--2446297 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 24
2446195 TAAATATCAA
2446205 TTAAAAA-TAATTTAATTATTATTT
1 TTAAAAATTAATTT-ATTATTATTT
* **
2446229 TAATAAAATTTATATTT-TTATTAAAT
1 T--TAAAAATTA-ATTTATTATTATTT
**
2446255 TTAAAAATTAACATATTAATTATTT
1 TTAAAAATTAATTTATT-ATTATTT
2446280 TTAAAAATTAATTTATTA
1 TTAAAAATTAATTTATTA
2446298 AGTATTATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
23 2 0.04
24 12 0.23
25 20 0.38
26 13 0.25
27 2 0.04
28 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAAAAATTAATTTATTATTATTT
Found at i:2446303 original size:25 final size:25
Alignment explanation
Indices: 2446254--2446303 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2446244 TTTTATTAAA
*
2446254 TTTAAAAATTAACATATTAATTATT
1 TTTAAAAATTAACATATTAAGTATT
**
2446279 TTTAAAAATTAATTTATTAAGTATT
1 TTTAAAAATTAACATATTAAGTATT
2446304 ATTTGATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTAAAAATTAACATATTAAGTATT
Found at i:2448116 original size:18 final size:19
Alignment explanation
Indices: 2448079--2448127 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2448069 TAATAAATAC
*
2448079 TATATTTAATATATTATTTT
1 TATATTTAA-ATAATATTTT
2448099 TATATTTAAA-AATATTTT
1 TATATTTAAATAATATTTT
*
2448117 TATAATTAAAT
1 TATATTTAAAT
2448128 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 16 0.62
19 1 0.04
20 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTTAAATAATATTTT
Found at i:2448936 original size:8 final size:10
Alignment explanation
Indices: 2448907--2448931 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2448897 TTTTTTTTTT
2448907 TTAAATAATA
1 TTAAATAATA
2448917 TTAAATAATA
1 TTAAATAATA
2448927 TTAAA
1 TTAAA
2448932 ATATTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTAAATAATA
Found at i:2450570 original size:29 final size:30
Alignment explanation
Indices: 2450526--2450591 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
2450516 GAAAGTGCTT
*
2450526 TTAATTTTTAAATAAATTATCAAAATAATA
1 TTAATTTTGAAATAAATTATCAAAATAATA
* *
2450556 TTAA-TTTGAAATAAATTATCATAATATTA
1 TTAATTTTGAAATAAATTATCAAAATAATA
2450585 TT-ATTTT
1 TTAATTTT
2450592 ATCTTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 27 0.84
30 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
TTAATTTTGAAATAAATTATCAAAATAATA
Found at i:2450714 original size:32 final size:32
Alignment explanation
Indices: 2450655--2450715 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2450645 ATGATTAGAG
*
2450655 AATCTAATGTGTAATTACTAAAAGCTTTAACA
1 AATCTAATGTGTAATAACTAAAAGCTTTAACA
*
2450687 AATCTAATGTGTAATAACTAAACGCTTTA
1 AATCTAATGTGTAATAACTAAAAGCTTTA
2450716 CTAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (32 bp):
AATCTAATGTGTAATAACTAAAAGCTTTAACA
Found at i:2451104 original size:17 final size:18
Alignment explanation
Indices: 2451082--2451121 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2451072 TCGCTTACTG
2451082 AATTAACAA-TTT-AAAAT
1 AATTAA-AATTTTAAAAAT
2451099 AATTAAAATTTTAAAAAT
1 AATTAAAATTTTAAAAAT
2451117 AATTA
1 AATTA
2451122 GATAATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 10 0.48
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAATTTTAAAAAT
Found at i:2451171 original size:41 final size:45
Alignment explanation
Indices: 2451102--2451188 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 45
2451092 TTAAAATAAT
2451102 TAAAATTTTAAAAATAATTAGATAATTACAA-CC-TAA-TTAAAA
1 TAAAATTTTAAAAATAATTAGATAATTACAATCCTTAATTTAAAA
* *
2451144 TAAAATTTT-AAAGTAATTAGATGATTACAATCCTTAATTTAAAA
1 TAAAATTTTAAAAATAATTAGATAATTACAATCCTTAATTTAAAA
2451188 T
1 T
2451189 TAGAGGGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 19 0.47
42 11 0.28
43 3 0.08
44 7 0.17
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.37
Consensus pattern (45 bp):
TAAAATTTTAAAAATAATTAGATAATTACAATCCTTAATTTAAAA
Found at i:2451268 original size:31 final size:31
Alignment explanation
Indices: 2451207--2451266 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2451197 TACTACTCTT
* *
2451207 AATAATTAGATGTTTATAATTTAAATTTTAA
1 AATAATTAGATGATTACAATTTAAATTTTAA
*
2451238 AATAATTAGATGATTACAACTTTTAATTT
1 AATAATTAGATGATTACAA-TTTAAATTT
2451267 AAGTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (31 bp):
AATAATTAGATGATTACAATTTAAATTTTAA
Found at i:2451278 original size:38 final size:38
Alignment explanation
Indices: 2451223--2451297 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
2451213 TAGATGTTTA
* *
2451223 TAATTTAAATTTTAAAATAATTAGATGATTACAACTTT
1 TAATTTAAATTTAAAAATAATTAAATGATTACAACTTT
* *
2451261 TAATTTAAGTTTAAAAATAATTAAATGATTATAACTT
1 TAATTTAAATTTAAAAATAATTAAATGATTACAACTT
2451298 AAATTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (38 bp):
TAATTTAAATTTAAAAATAATTAAATGATTACAACTTT
Found at i:2451312 original size:38 final size:38
Alignment explanation
Indices: 2451227--2451313 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
2451217 TGTTTATAAT
* *
2451227 TTAAATTTT-AAAATAATTAGATGATTACAACTTTTAA
1 TTAAATTTTAAAAATAATTAAATGATTACAACTTTAAA
* * *
2451264 TTTAAGTTTAAAAATAATTAAATGATTATAAC-TTAAA
1 TTAAATTTTAAAAATAATTAAATGATTACAACTTTAAA
2451301 TTAAAATTTTAAA
1 TT-AAATTTTAAA
2451314 TTAGATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
37 13 0.32
38 28 0.68
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (38 bp):
TTAAATTTTAAAAATAATTAAATGATTACAACTTTAAA
Found at i:2451462 original size:16 final size:19
Alignment explanation
Indices: 2451417--2451462 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
2451407 TATTATTATA
2451417 TTTA-TAATAATATTATCT
1 TTTATTAATAATATTATCT
*
2451435 TTTATTAATAATA-TATTTT
1 TTTATTAATAATATTA-TCT
2451454 TTTATTAAT
1 TTTATTAAT
2451463 TTTAAAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATTAATAATATTATCT
Found at i:2451738 original size:14 final size:14
Alignment explanation
Indices: 2451719--2451773 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 14
2451709 TGTGAGTTAA
*
2451719 AATAATAATATTTT
1 AATAATATTATTTT
2451733 AATAAT-TTATTTT
1 AATAATATTATTTT
2451746 AAATTAATATTATTTT
1 -AA-TAATATTATTTT
*
2451762 GATAAT-TTATTT
1 AATAATATTATTT
2451774 AGAAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
13 12 0.33
14 12 0.33
15 5 0.14
16 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
AATAATATTATTTT
Found at i:2451748 original size:29 final size:29
Alignment explanation
Indices: 2451715--2451783 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
2451705 TTTTTGTGAG
2451715 TTAAAATAATAATATTTTAATAATTTATT
1 TTAAAATAATAATATTTTAATAATTTATT
* * *
2451744 TTAAATTAATATTATTTTGATAATTTATT
1 TTAAAATAATAATATTTTAATAATTTATT
*
2451773 TAGAAAATAAT
1 T-TAAAATAAT
2451784 CATACTGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 27 0.79
30 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAAAATAATAATATTTTAATAATTTATT
Found at i:2453122 original size:23 final size:22
Alignment explanation
Indices: 2453092--2453134 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2453082 GATTTACTAA
*
2453092 TATTTTATGGGTATTAAATTAT
1 TATTTTATGAGTATTAAATTAT
*
2453114 TATTATTATGATTATTAAATT
1 TATT-TTATGAGTATTAAATT
2453135 GGTATTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (22 bp):
TATTTTATGAGTATTAAATTAT
Found at i:2453329 original size:2 final size:2
Alignment explanation
Indices: 2453322--2453352 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2453312 TTTCGAAGGT
2453322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2453353 TAGATCCGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2453451 original size:16 final size:16
Alignment explanation
Indices: 2453425--2453480 Score: 71
Period size: 16 Copynumber: 3.4 Consensus size: 16
2453415 AAATTTTTAA
2453425 ATTATTTTTGAGATTAG
1 ATTA-TTTTGAGATTAG
2453442 ATTATTTTGA-ATTTAG
1 ATTATTTTGAGA-TTAG
2453458 ATTATTTTGAG-TTCAG
1 ATTATTTTGAGATT-AG
2453474 ATTATTT
1 ATTATTT
2453481 AAGGTTCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.08
16 29 0.81
17 4 0.11
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (16 bp):
ATTATTTTGAGATTAG
Found at i:2453504 original size:16 final size:15
Alignment explanation
Indices: 2453431--2453520 Score: 67
Period size: 16 Copynumber: 5.7 Consensus size: 15
2453421 TTAAATTATT
2453431 TTTGAGATT-AGATTA
1 TTTG-GATTCAGATTA
* *
2453446 TTTTGAATTTAGATTA
1 -TTTGGATTCAGATTA
*
2453462 TTTTGAGTTCAGATTA
1 TTTGGA-TTCAGATTA
2453478 TTTAAGG-TTCAGATTA
1 TTT--GGATTCAGATTA
* *
2453494 TTTCGGATTCAGGTCA
1 TTT-GGATTCAGATTA
2453510 TTTGGATTCAG
1 TTTGGATTCAG
2453521 GTTAATTGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
15 17 0.28
16 43 0.70
18 1 0.02
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
TTTGGATTCAGATTA
Found at i:2453518 original size:15 final size:16
Alignment explanation
Indices: 2453493--2453522 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2453483 GGTTCAGATT
2453493 ATTTCGGATTCAGGTC
1 ATTTCGGATTCAGGTC
2453509 ATTT-GGATTCAGGT
1 ATTTCGGATTCAGGT
2453523 TAATTGGGTT
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:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (16 bp):
ATTTCGGATTCAGGTC
Found at i:2453875 original size:59 final size:59
Alignment explanation
Indices: 2453808--2453926 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2453798 ATGGTTGAAT
2453808 TTTAAAATTTCAATTTATCACGACTCAAATTTTTTTTAATTCTATTGTTAAGTTCTAGC
1 TTTAAAATTTCAATTTATCACGACTCAAATTTTTTTTAATTCTATTGTTAAGTTCTAGC
2453867 TTTAAAATTTCAATTTATCACGACTCAAATTTTTTTTAATTCTATTGTTAAGTTCTAGC
1 TTTAAAATTTCAATTTATCACGACTCAAATTTTTTTTAATTCTATTGTTAAGTTCTAGC
2453926 T
1 T
2453927 AAAGAAATAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (59 bp):
TTTAAAATTTCAATTTATCACGACTCAAATTTTTTTTAATTCTATTGTTAAGTTCTAGC
Found at i:2454418 original size:16 final size:16
Alignment explanation
Indices: 2454397--2454429 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2454387 TTAATTGTAC
2454397 GGATCATTTCGAGTTT
1 GGATCATTTCGAGTTT
2454413 GGATCATTTCGAGTTT
1 GGATCATTTCGAGTTT
2454429 G
1 G
2454430 AGTTATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.42
Consensus pattern (16 bp):
GGATCATTTCGAGTTT
Found at i:2454437 original size:16 final size:16
Alignment explanation
Indices: 2454402--2454450 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
2454392 TGTACGGATC
*
2454402 ATTTCGAGTTTG-GATC
1 ATTTCGAGTTTGAG-TT
2454418 ATTTCGAGTTTGAGTT
1 ATTTCGAGTTTGAGTT
*
2454434 ATTTCGGGTTTCGAGTT
1 ATTTCGAGTTT-GAGTT
2454451 GTTGATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.16, C:0.10, G:0.27, T:0.47
Consensus pattern (16 bp):
ATTTCGAGTTTGAGTT
Found at i:2454676 original size:16 final size:16
Alignment explanation
Indices: 2454631--2454678 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2454621 TCACGATTTT
*
2454631 ATAATATTATTTTAAA
1 ATAATATTAATTTAAA
*
2454647 ATTAATATTGATTTAAA
1 A-TAATATTAATTTAAA
*
2454664 ATAATAATAATTTAA
1 ATAATATTAATTTAA
2454679 TTTAATAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
ATAATATTAATTTAAA
Found at i:2456095 original size:17 final size:17
Alignment explanation
Indices: 2456073--2456107 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2456063 AAAAAGAGTG
2456073 TCGAGATCTTTGAAGTT
1 TCGAGATCTTTGAAGTT
2456090 TCGAGATCTTTGAAGTT
1 TCGAGATCTTTGAAGTT
2456107 T
1 T
2456108 GCCTTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (17 bp):
TCGAGATCTTTGAAGTT
Found at i:2456452 original size:13 final size:13
Alignment explanation
Indices: 2456436--2456484 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
2456426 TTTTAATTTT
*
2456436 ATATTTTTTAAAA
1 ATATTTATTAAAA
2456449 ATATTTATTAAAA
1 ATATTTATTAAAA
2456462 ATA-TTA--AAAA
1 ATATTTATTAAAA
2456472 A-ATTTATTAAAA
1 ATATTTATTAAAA
2456484 A
1 A
2456485 AATTAAGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
9 1 0.03
10 8 0.25
12 8 0.25
13 15 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTATTAAAA
Found at i:2456470 original size:22 final size:22
Alignment explanation
Indices: 2456443--2456490 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
2456433 TTTATATTTT
* *
2456443 TTAAAAATATTTATTAAAAATA
1 TTAAAAAAATTTATTAAAAAAA
2456465 TTAAAAAAATTTATTAAAAAAA
1 TTAAAAAAATTTATTAAAAAAA
2456487 TTAA
1 TTAA
2456491 GAATGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAAAAAAATTTATTAAAAAAA
Found at i:2456783 original size:5 final size:5
Alignment explanation
Indices: 2456775--2456819 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
2456765 AAAAAATAAA
*
2456775 AATAT AATA- AACAT AATAT AATA- AATAT AATAT AATAT AAATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT A
2456820 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 7 0.20
5 23 0.66
6 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (5 bp):
AATAT
Found at i:2456794 original size:14 final size:14
Alignment explanation
Indices: 2456775--2456811 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2456765 AAAAAATAAA
2456775 AATATAATAAACAT
1 AATATAATAAACAT
*
2456789 AATATAATAAATAT
1 AATATAATAAACAT
2456803 AATATAATA
1 AATATAATA
2456812 TAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
AATATAATAAACAT
Found at i:2456801 original size:9 final size:10
Alignment explanation
Indices: 2456775--2456819 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
2456765 AAAAAATAAA
2456775 AATATAATA-
1 AATATAATAT
*
2456784 AACATAATAT
1 AATATAATAT
2456794 AATA-AATAT
1 AATATAATAT
2456803 AATATAATAT
1 AATATAATAT
2456813 AAATATA
1 -AATATA
2456820 TTTAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 17 0.55
10 8 0.26
11 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AATATAATAT
Found at i:2456817 original size:25 final size:25
Alignment explanation
Indices: 2456770--2456845 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 25
2456760 AATTAAAAAA
*
2456770 ATAA-AAATATAATA-AACAT-AAT
1 ATAATAAATATAATATAATATAAAT
2456792 ATAATAAATATAATATAATATAAAT
1 ATAATAAATATAATATAATATAAAT
* *
2456817 ATATTTAAAATTTTAATATAAT-TAAAT
1 ATA-AT-AAA-TATAATATAATATAAAT
2456844 AT
1 AT
2456846 TTTTTATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
22 4 0.09
23 10 0.22
24 4 0.09
25 6 0.13
26 1 0.02
27 10 0.22
28 10 0.22
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATAAATATAATATAATATAAAT
Found at i:2456836 original size:17 final size:18
Alignment explanation
Indices: 2456814--2456848 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2456804 ATATAATATA
*
2456814 AATATATTTAAA-ATTTT
1 AATATAATTAAATATTTT
2456831 AATATAATTAAATATTTT
1 AATATAATTAAATATTTT
2456849 TTATTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATAATTAAATATTTT
Found at i:2457510 original size:17 final size:17
Alignment explanation
Indices: 2457484--2457518 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2457474 GTTACATGAC
*
2457484 TAAAATTAATAATATTT
1 TAAAAATAATAATATTT
*
2457501 TAAAAATAATTATATTT
1 TAAAAATAATAATATTT
2457518 T
1 T
2457519 GATAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAAATAATAATATTT
Found at i:2457810 original size:31 final size:31
Alignment explanation
Indices: 2457773--2457838 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2457763 ATATAATATA
*
2457773 TTTAATAATAAAAATTTATAATTAAATTTTT
1 TTTAATAATAAAAATTTATAATTAAATATTT
* * *
2457804 TTTAATAATAACAGTTTATATTTAAATATTT
1 TTTAATAATAAAAATTTATAATTAAATATTT
2457835 TTTA
1 TTTA
2457839 TTTTAATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (31 bp):
TTTAATAATAAAAATTTATAATTAAATATTT
Found at i:2457871 original size:23 final size:21
Alignment explanation
Indices: 2457818--2457873 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
2457808 ATAATAACAG
* *
2457818 TTTATATTTAAATATTTTTTAT
1 TTTA-ATTTAAATATTTTTAAA
2457840 TTTAA-TTAAATCATTTTATAAA
1 TTTAATTTAAAT-ATTTT-TAAA
2457862 TTTAATTTAAAT
1 TTTAATTTAAAT
2457874 TAACTATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 6 0.21
21 6 0.21
22 11 0.38
23 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTAATTTAAATATTTTTAAA
Found at i:2458212 original size:18 final size:17
Alignment explanation
Indices: 2458169--2458225 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
2458159 TTTATTTTTA
2458169 AAAATTTA-TAATATAAT
1 AAAATTTATTAATAT-AT
2458186 ATAAA-TTATTAATATAT
1 A-AAATTTATTAATATAT
2458203 CAAAATTTATATAA-ATAT
1 -AAAATTTAT-TAATATAT
2458221 AAAAT
1 AAAAT
2458226 ACAAACATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 14 0.40
18 18 0.51
19 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTTATTAATATAT
Found at i:2458802 original size:18 final size:19
Alignment explanation
Indices: 2458769--2458805 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2458759 AATATAAAAA
2458769 TATTTTAAATTTTTAATAT
1 TATTTTAAATTTTTAATAT
2458788 TATTTTAAA-TTTTAATAT
1 TATTTTAAATTTTTAATAT
2458806 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTAAATTTTTAATAT
Found at i:2458811 original size:19 final size:19
Alignment explanation
Indices: 2458770--2458812 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2458760 ATATAAAAAT
*
2458770 ATTTTAAATTTTTAATATT
1 ATTTTAAATTTTTAATATA
2458789 ATTTTAAA-TTTTAATATAA
1 ATTTTAAATTTTTAATAT-A
2458808 ATTTT
1 ATTTT
2458813 TAAGTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAAATTTTTAATATA
Found at i:2461194 original size:26 final size:25
Alignment explanation
Indices: 2461152--2461204 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
2461142 TTTTATATTA
2461152 ATAATAAATTAAATTAAATTAAATT
1 ATAATAAATTAAATTAAATTAAATT
*
2461177 ATAA-AAATTAAAATTTAATTTAAATT
1 ATAATAAATT-AAA-TTAAATTAAATT
2461203 AT
1 AT
2461205 TTCAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 7 0.28
26 13 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATAAATTAAATTAAATTAAATT
Found at i:2461936 original size:53 final size:53
Alignment explanation
Indices: 2461879--2461980 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
2461869 TTCAATCATA
* *
2461879 CCATTAACAACTTTCGAAGAAAGTAAGTTATGAAAGGTACTAATCCAATCGGG
1 CCATTAACAACTCTCGAAGAAAGTAAGTTATGAAAGGAACTAATCCAATCGGG
* *
2461932 CCATTAACAACTCTCGAAGAAAGTTAGTTATGAAAGGAACTTATCCAAT
1 CCATTAACAACTCTCGAAGAAAGTAAGTTATGAAAGGAACTAATCCAAT
2461981 GGCAGCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (53 bp):
CCATTAACAACTCTCGAAGAAAGTAAGTTATGAAAGGAACTAATCCAATCGGG
Found at i:2462274 original size:23 final size:23
Alignment explanation
Indices: 2462236--2462279 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2462226 TTGAATTAAA
2462236 TTTAAATAATAAAA-TTAAATAT
1 TTTAAATAATAAAATTTAAATAT
*
2462258 TTTAAATTAATATAATTTAAAT
1 TTTAAA-TAATAAAATTTAAAT
2462280 TATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 7 0.37
24 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAATAATAAAATTTAAATAT
Found at i:2462276 original size:15 final size:14
Alignment explanation
Indices: 2462231--2462281 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
2462221 CCATATTGAA
2462231 TTAAATTTAAATAA-
1 TTAAA-TTAAATAAT
* *
2462245 TAAAATTAAATATT
1 TTAAATTAAATAAT
2462259 TTAAATTAATATAAT
1 TTAAATTAA-ATAAT
2462274 TTAAATTA
1 TTAAATTA
2462282 TTATTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
15 12 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATTAAATAAT
Found at i:2463753 original size:10 final size:10
Alignment explanation
Indices: 2463738--2463764 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2463728 ATTTAATTAA
2463738 AAAATTATAT
1 AAAATTATAT
2463748 AAAATTATAT
1 AAAATTATAT
2463758 AAAATTA
1 AAAATTA
2463765 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTATAT
Found at i:2464563 original size:22 final size:22
Alignment explanation
Indices: 2464535--2464576 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2464525 GGAGAGAGGT
2464535 CGAGTGAGATAACGGAAGATGC
1 CGAGTGAGATAACGGAAGATGC
2464557 CGAGTGAGATAACGGAAGAT
1 CGAGTGAGATAACGGAAGAT
2464577 CTGCATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.36, T:0.14
Consensus pattern (22 bp):
CGAGTGAGATAACGGAAGATGC
Found at i:2470406 original size:15 final size:14
Alignment explanation
Indices: 2470384--2470414 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2470374 ATAAATCAAT
2470384 TAATAT-TTTTTAA
1 TAATATATTTTTAA
2470397 TAATATATTTTTAA
1 TAATATATTTTTAA
2470411 TAAT
1 TAAT
2470415 TTTTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATATATTTTTAA
Found at i:2470409 original size:14 final size:13
Alignment explanation
Indices: 2470384--2470418 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2470374 ATAAATCAAT
2470384 TAATATTTTTTAA
1 TAATATTTTTTAA
2470397 TAATATATTTTTAA
1 TAATAT-TTTTTAA
2470411 TAAT-TTTT
1 TAATATTTT
2470419 ATTATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.14
13 7 0.33
14 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATATTTTTTAA
Found at i:2473919 original size:108 final size:108
Alignment explanation
Indices: 2473730--2473946 Score: 407
Period size: 108 Copynumber: 2.0 Consensus size: 108
2473720 AAGTCATATC
* *
2473730 AAACTTTTTAAGTGTAATGTAGCTAGTTCTAGACTTATACTAATCTTTTCCCTTTAGTCTGAAAA
1 AAACTTTTTAAGTGTAATGTAGCTAGTTCTAGACTTATACTAATCTTCTCCCTTTAATCTGAAAA
*
2473795 TATGATATGCTTTTAGTATTGATTCAATTATCAAGAGTGTAAG
66 TATGATATGCTTTTAGTATTGATTCAATTATCAAGAGTCTAAG
2473838 AAACTTTTTAAGTGTAATGTAGCTAGTTCTAGACTTATACTAATCTTCTCCCTTTAATCTGAAAA
1 AAACTTTTTAAGTGTAATGTAGCTAGTTCTAGACTTATACTAATCTTCTCCCTTTAATCTGAAAA
2473903 TATGATATGCTTTTAGTATTGATTCAATTATCAAGAGTCTAAG
66 TATGATATGCTTTTAGTATTGATTCAATTATCAAGAGTCTAAG
2473946 A
1 A
2473947 CGGAAAATAT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (108 bp):
AAACTTTTTAAGTGTAATGTAGCTAGTTCTAGACTTATACTAATCTTCTCCCTTTAATCTGAAAA
TATGATATGCTTTTAGTATTGATTCAATTATCAAGAGTCTAAG
Found at i:2477782 original size:2 final size:2
Alignment explanation
Indices: 2477775--2477801 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2477765 ATGAGCTATG
2477775 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2477802 CGAGCTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2486676 original size:9 final size:9
Alignment explanation
Indices: 2486617--2486702 Score: 54
Period size: 9 Copynumber: 9.2 Consensus size: 9
2486607 TATCAATTTA
2486617 TAAATATA-
1 TAAATATAT
2486625 -AAATATAACT
1 TAAATAT-A-T
2486635 TAAAT-TAT
1 TAAATATAT
2486643 TAAATATAT
1 TAAATATAT
*
2486652 TAGAAT-TTT
1 TA-AATATAT
2486661 ATAAATATAT
1 -TAAATATAT
2486671 TAAATATAT
1 TAAATATAT
*
2486680 CATAAACATAAT
1 --TAAATAT-AT
*
2486692 TAAACATAT
1 TAAATATAT
2486701 TA
1 TA
2486703 TATTTTATTT
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
7 6 0.09
8 7 0.11
9 24 0.38
10 15 0.23
11 10 0.16
12 2 0.03
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (9 bp):
TAAATATAT
Found at i:2486694 original size:21 final size:20
Alignment explanation
Indices: 2486661--2486700 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2486651 TTAGAATTTT
* *
2486661 ATAAATATATTAAATATATC
1 ATAAACATATTAAACATATC
2486681 ATAAACATAATTAAACATAT
1 ATAAACAT-ATTAAACATAT
2486701 TATATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAACATATTAAACATATC
Found at i:2486702 original size:49 final size:44
Alignment explanation
Indices: 2486613--2486710 Score: 106
Period size: 49 Copynumber: 2.1 Consensus size: 44
2486603 TTCATATCAA
* * *
2486613 TTTATAAATATAAAATATAACTTAAATTATTAAATATATTAGAAT
1 TTTATAAATATAAAATATAACTAAAATAATTAAACATATTA-AAT
* *
2486658 TTTATAAATATATTAAATATATCATAAACATAATTAAACATATTATAT
1 TTTATAAATATA--AAATATAAC-TAAA-ATAATTAAACATATTAAAT
2486706 TTTAT
1 TTTAT
2486711 TTATTATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
45 12 0.27
47 8 0.18
48 10 0.23
49 14 0.32
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (44 bp):
TTTATAAATATAAAATATAACTAAAATAATTAAACATATTAAAT
Done.