Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 20 of 182
Found at i:8277760 original size:36 final size:34
Alignment explanation
Indices: 8277674--8277760 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 34
8277664 AGGGACTAAA
*
8277674 AAATATAAATTTTCATTTAATTAAAAACTTAAATT
1 AAAT-TAAAATTTCATTTAATTAAAAACTTAAATT
8277709 AAATTAATAATTTTCATTTAATTAAAAA-TTATATATT
1 AAATTAA-AA-TTTCATTTAATTAAAAACTTA-A-ATT
*
8277746 ACATGTAAAATTTCA
1 AAAT-TAAAATTTCA
8277761 ACTTGAGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
34 3 0.07
35 8 0.18
36 23 0.51
37 8 0.18
38 3 0.07
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (34 bp):
AAATTAAAATTTCATTTAATTAAAAACTTAAATT
Found at i:8282103 original size:23 final size:21
Alignment explanation
Indices: 8282062--8282103 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
8282052 AAATCTATAG
8282062 TAATTTATAAAAATGTTAAGA
1 TAATTTATAAAAATGTTAAGA
*
8282083 TAATTATATATAAAATTTTAA
1 TAATT-TATA-AAAATGTTAA
8282104 TAAATAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TAATTTATAAAAATGTTAAGA
Found at i:8283000 original size:114 final size:108
Alignment explanation
Indices: 8282799--8283080 Score: 381
Period size: 117 Copynumber: 2.5 Consensus size: 108
8282789 AGAAGAAGAA
*
8282799 GATGATGACAAATATTCACCAATGGGATCAATTTT--AGAAGAAGAAGAAGAAGATTCACTATCA
1 GATGATGACAAATATTCACCAATGGGATCATTTTTGAAGAAGAAGAAGAAGAAGATTCACTATCA
8282862 CAATCACCAACTTCAACAGAAGAAGAAGAAGAAGAATATGATGATGATGAT
66 CAATCACCAACTTCAAC-----AAGAAGAAGAAG-A-AT-ATGATGATGAT
8282913 GATGATGACAAATATTCACCAATGGGATCATTTTTAGAAGAAGAAGAAGAAGAAGATTCACTATC
1 GATGATGACAAATATTCACCAATGGGATCATTTTT-GAAGAAGAAGAAGAAGAAGATTCACTATC
8282978 ACAATCACCAACTTCAAC-AGAAGAAGAAGAATATGATGATGAT
65 ACAATCACCAACTTCAACAAGAAGAAGAAGAATATGATGATGAT
* * * *
8283021 GATGACGACAAAGATTCATCAATGGGATCATCGTTTTCGGAAGAAGAAGAAGATGAAGAT
1 GATGATGACAAATATTCACCAATGGGATCAT--TTTT--GAAGAAGAAGAAGAAGAAGAT
8283081 GAAGATGAAG
Statistics
Matches: 156, Mismatches: 6, Indels: 15
0.88 0.03 0.08
Matches are distributed among these distances:
108 39 0.25
109 2 0.01
110 5 0.03
111 31 0.20
114 34 0.22
117 45 0.29
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.22
Consensus pattern (108 bp):
GATGATGACAAATATTCACCAATGGGATCATTTTTGAAGAAGAAGAAGAAGAAGATTCACTATCA
CAATCACCAACTTCAACAAGAAGAAGAAGAATATGATGATGAT
Found at i:8283242 original size:6 final size:6
Alignment explanation
Indices: 8283072--8283242 Score: 216
Period size: 6 Copynumber: 28.5 Consensus size: 6
8283062 AGAAGAAGAA
* * * * * *
8283072 GATGAA GATGAA GATGAA GATGAT GATGAT GATGAA GATGAA GATGAA
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
* * * * * *
8283120 GATGAA GATGAA GAAGAT GATGAT GATGAT GAAGAT GAAGAT GAAGAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
* *
8283168 GAAGAA GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
8283216 GATGAT GATGAT GATGAT GATGAT GAT
1 GATGAT GATGAT GATGAT GATGAT GAT
8283243 AACAACGACA
Statistics
Matches: 156, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 156 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (6 bp):
GATGAT
Found at i:8297767 original size:11 final size:11
Alignment explanation
Indices: 8297751--8297777 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
8297741 TGTAACTTCA
8297751 AATTAAATTTT
1 AATTAAATTTT
8297762 AATTAAATTTT
1 AATTAAATTTT
8297773 AATTA
1 AATTA
8297778 TTATTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTAAATTTT
Found at i:8299542 original size:24 final size:24
Alignment explanation
Indices: 8299515--8299566 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
8299505 TAGTTTATCC
8299515 TTTTAGACAATTTATGTAAAACTA
1 TTTTAGACAATTTATGTAAAACTA
*
8299539 TTTTAGACAATTTGTGTAAAACTA
1 TTTTAGACAATTTATGTAAAACTA
8299563 TTTT
1 TTTT
8299567 CAAATAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTTAGACAATTTATGTAAAACTA
Found at i:8301130 original size:22 final size:19
Alignment explanation
Indices: 8301102--8301143 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
8301092 ATGTTCATTT
8301102 TAAATATAGTATTATAAAGTAA
1 TAAATATA-TATT-TAAA-TAA
8301124 TAAATATATATTTAAATAA
1 TAAATATATATTTAAATAA
8301143 T
1 T
8301144 GTTTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 4 0.20
22 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAATATATATTTAAATAA
Found at i:8301341 original size:14 final size:14
Alignment explanation
Indices: 8301306--8301347 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
8301296 CTATATTTTA
8301306 AATATTTAAATA-T
1 AATATTTAAATATT
8301319 AAT-TATTAAATATT
1 AATAT-TTAAATATT
*
8301333 TATATTTAAATATT
1 AATATTTAAATATT
8301347 A
1 A
8301348 GCATAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 1 0.04
13 10 0.42
14 12 0.50
15 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:8301346 original size:21 final size:21
Alignment explanation
Indices: 8301303--8301347 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8301293 AAACTATATT
*
8301303 TTAAATATTTAAATATAATTA
1 TTAAATATTTAAATATAAATA
* *
8301324 TTAAATATTTATATTTAAATA
1 TTAAATATTTAAATATAAATA
8301345 TTA
1 TTA
8301348 GCATAGTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAATATTTAAATATAAATA
Found at i:8308466 original size:29 final size:31
Alignment explanation
Indices: 8308423--8308525 Score: 121
Period size: 30 Copynumber: 3.5 Consensus size: 31
8308413 TCACAGGGGC
8308423 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
*
8308454 AAAATGG-AA-TTTT-G-GAAAGTTCGGGGGT--
1 AAAATGGTAATTTTTGGTGAAA--TC-GAGGTCA
8308482 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCA
8308513 AAAATGG-AATTTT
1 AAAATGGTAATTTT
8308526 GGAAAGTTCG
Statistics
Matches: 61, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
27 4 0.07
28 8 0.13
29 12 0.20
30 18 0.30
31 15 0.25
32 4 0.07
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTCA
Found at i:8308486 original size:59 final size:59
Alignment explanation
Indices: 8308418--8308564 Score: 269
Period size: 59 Copynumber: 2.5 Consensus size: 59
8308408 TGGACTCACA
*
8308418 GGGGCAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCG
8308477 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCG
*
8308536 GGGGTGAAATGGTAA-TTTTGGTGAAATCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCG
8308565 GGACTAATTG
Statistics
Matches: 86, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
58 14 0.16
59 72 0.84
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.30
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCG
Found at i:8308565 original size:29 final size:30
Alignment explanation
Indices: 8308423--8308566 Score: 119
Period size: 29 Copynumber: 4.9 Consensus size: 30
8308413 TCACAGGGGC
*
8308423 AAAATGGTAATTTTTGGTGAAATC-GAGGTCA
1 AAAATGGTAA-TTTTGGTGAAATCGGGGGT-A
8308454 AAAATGG-AATTTT-G-GAAAGTTCGGGGGT-
1 AAAATGGTAATTTTGGTGAAA--TCGGGGGTA
*
8308482 AAAATGGTAATTTTTGGTGAAATC-GAGGTCA
1 AAAATGGTAA-TTTTGGTGAAATCGGGGGT-A
8308513 AAAATGG-AATTTT-G-GAAAGTTCGGGGGT-
1 AAAATGGTAATTTTGGTGAAA--TCGGGGGTA
*
8308541 GAAATGGTAATTTTGGTGAAATCGGG
1 AAAATGGTAATTTTGGTGAAATCGGG
8308567 ACTAATTGCA
Statistics
Matches: 94, Mismatches: 4, Indels: 32
0.72 0.03 0.25
Matches are distributed among these distances:
27 8 0.09
28 15 0.16
29 29 0.31
30 19 0.20
31 19 0.20
32 4 0.04
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATCGGGGGTA
Found at i:8309518 original size:16 final size:14
Alignment explanation
Indices: 8309477--8309520 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
8309467 TTTCGTTTTA
8309477 TTATTTTATTAATT
1 TTATTTTATTAATT
8309491 TTATTTAATATTAATAT
1 TTATTT--TATTAAT-T
8309508 TTATTGTTATTAA
1 TTATT-TTATTAA
8309521 AATGTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.23
16 13 0.50
17 6 0.23
18 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTTATTAATT
Found at i:8310300 original size:11 final size:11
Alignment explanation
Indices: 8310286--8310327 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
8310276 AAATTATTTC
8310286 AAATTTAAACT
1 AAATTTAAACT
*
8310297 AAATTTAAATTT
1 AAATTTAAA-CT
*
8310309 AAATTTAAAGT
1 AAATTTAAACT
8310320 AAATTTAA
1 AAATTTAA
8310328 TTTTAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAATTTAAACT
Found at i:8310306 original size:17 final size:18
Alignment explanation
Indices: 8310302--8310346 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
8310292 AAACTAAATT
*
8310302 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
8310319 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
8310337 TAAATTTAAA
1 TAAATTTAAA
8310347 AATCATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:8310307 original size:6 final size:6
Alignment explanation
Indices: 8310260--8310346 Score: 58
Period size: 6 Copynumber: 15.0 Consensus size: 6
8310250 TTTTGGGTTT
* * * *
8310260 TTTAAT TTTAAT TTTAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* * *
8310306 TTTAAA TTTAAA -GTAAA TTTAAT TTTAGAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
8310347 AATCATTTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
4 3 0.05
5 10 0.16
6 45 0.71
7 5 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:8310312 original size:23 final size:23
Alignment explanation
Indices: 8310281--8310332 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
8310271 TTTTAAAATT
8310281 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATTTAAACTAAATTTAA
*
8310305 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATTTAAACTAAATTTAA
*
8310328 TTTTA
1 ATTTA
8310333 GAAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAAATTTAAACTAAATTTAA
Found at i:8310340 original size:23 final size:23
Alignment explanation
Indices: 8310281--8310340 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
8310271 TTTTAAAATT
*
8310281 ATTTCAAATTTAAACTAAATTTAA
1 ATTT-AAATATAAACTAAATTTAA
* *
8310305 ATTTAAATTTAAAGTAAATTTAA
1 ATTTAAATATAAACTAAATTTAA
*
8310328 TTTTAGAA-ATAAA
1 ATTTA-AATATAAA
8310341 TTTAAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (23 bp):
ATTTAAATATAAACTAAATTTAA
Found at i:8321030 original size:17 final size:17
Alignment explanation
Indices: 8320995--8321030 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8320985 AAAAATAATA
* *
8320995 ATTAATTATGGAAACAG
1 ATTAATTATGAAAAAAG
8321012 ATTAATTATGAAAAAAG
1 ATTAATTATGAAAAAAG
8321029 AT
1 AT
8321031 ATTTGTTACG
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:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (17 bp):
ATTAATTATGAAAAAAG
Found at i:8329381 original size:30 final size:29
Alignment explanation
Indices: 8329358--8329429 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
8329348 AAATTACATT
8329358 TTAATT-TTCTAAAAATTATAAAATTCTGA
1 TTAATTATT-TAAAAATTATAAAATTCTGA
*
8329387 TTAATTATTTAAAAATTATAAAA--AT-A
1 TTAATTATTTAAAAATTATAAAATTCTGA
8329413 TTAATTA-TTAAAAATTA
1 TTAATTATTTAAAAATTA
8329430 AAATTTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
25 10 0.24
26 8 0.20
27 1 0.02
29 20 0.49
30 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAATTATTTAAAAATTATAAAATTCTGA
Found at i:8329426 original size:26 final size:28
Alignment explanation
Indices: 8329368--8329426 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 28
8329358 TTAATTTTCT
* *
8329368 AAAAATTATAAAATTCTGATTAATTATTT
1 AAAAATTATAAAA-TATGATTAATTATTA
8329397 AAAAATTATAAAA-AT-ATTAATTATTA
1 AAAAATTATAAAATATGATTAATTATTA
8329423 AAAA
1 AAAA
8329427 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.50
27 1 0.04
29 13 0.46
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
AAAAATTATAAAATATGATTAATTATTA
Found at i:8339466 original size:11 final size:11
Alignment explanation
Indices: 8339450--8339474 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8339440 ATTCTTAAAT
8339450 ATTAAAAATTA
1 ATTAAAAATTA
8339461 ATTAAAAATTA
1 ATTAAAAATTA
8339472 ATT
1 ATT
8339475 TTTCGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAAAATTA
Found at i:8343156 original size:24 final size:21
Alignment explanation
Indices: 8343121--8343173 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
8343111 TCCAGAAATT
*
8343121 GAGAGAAAGAGATAGAACAAAA
1 GAGAGAAAGAGAAAGAA-AAAA
*
8343143 GAGAGAAATTGAGAAAGAAGAAA
1 GAGAGAAA--GAGAAAGAAAAAA
8343166 GAGAGAAA
1 GAGAGAAA
8343174 ATATTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 8 0.30
23 11 0.41
24 8 0.30
ACGTcount: A:0.62, C:0.02, G:0.30, T:0.06
Consensus pattern (21 bp):
GAGAGAAAGAGAAAGAAAAAA
Found at i:8350439 original size:16 final size:16
Alignment explanation
Indices: 8350420--8350450 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8350410 TTTTTGAGAT
*
8350420 AATAATTTTTGTTTAA
1 AATAATTGTTGTTTAA
8350436 AATAATTGTTGTTTA
1 AATAATTGTTGTTTA
8350451 GGACAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
AATAATTGTTGTTTAA
Found at i:8351327 original size:21 final size:21
Alignment explanation
Indices: 8351303--8351349 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
8351293 TAGCATAATA
8351303 CAAATATAAAGTTTAGAAATC
1 CAAATATAAAGTTTAGAAATC
* *
8351324 CAAATATAAAGTTTATAAATT
1 CAAATATAAAGTTTAGAAATC
8351345 CAAAT
1 CAAAT
8351350 TACATAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32
Consensus pattern (21 bp):
CAAATATAAAGTTTAGAAATC
Found at i:8364848 original size:16 final size:16
Alignment explanation
Indices: 8364808--8364852 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
8364798 TTTTAGGGAT
*
8364808 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
8364825 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
8364839 TTAAAAATTTATTT
1 TTAAAAATTTATTT
8364853 TCGTCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:8365212 original size:7 final size:7
Alignment explanation
Indices: 8365200--8365232 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
8365190 GACTAAATGC
8365200 AAAGGGA
1 AAAGGGA
8365207 AAAGGGA
1 AAAGGGA
8365214 AAAGGGA
1 AAAGGGA
8365221 AAAGGGA
1 AAAGGGA
8365228 AAAGG
1 AAAGG
8365233 CGACTAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
AAAGGGA
Found at i:8366508 original size:16 final size:16
Alignment explanation
Indices: 8366487--8366517 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8366477 AGGGTTGTTT
8366487 CAATTAGCAATGCTAC
1 CAATTAGCAATGCTAC
8366503 CAATTAGCAATGCTA
1 CAATTAGCAATGCTA
8366518 GCCATGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (16 bp):
CAATTAGCAATGCTAC
Found at i:8379545 original size:65 final size:66
Alignment explanation
Indices: 8379432--8379564 Score: 205
Period size: 65 Copynumber: 2.0 Consensus size: 66
8379422 AAATATTTGA
*
8379432 AAGGGGGAATTAAAGGAATAAAAAAAAAAGTTGTACAAGTACTTATTATATAGCTATATATGATT
1 AAGGGGGAATTAAAGGAATAAAAAAAAAAGTTGTACAAGTACTGATTATATAGCTATATATGATT
8379497 T
66 T
* * * * *
8379498 AAGGGGGAATTATAGGAAT-AAAAAATAAGTTGTATAAGTACTGATTATATTGTTATATATGATT
1 AAGGGGGAATTAAAGGAATAAAAAAAAAAGTTGTACAAGTACTGATTATATAGCTATATATGATT
8379562 T
66 T
8379563 AA
1 AA
8379565 ATTTTAAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
65 43 0.70
66 18 0.30
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.33
Consensus pattern (66 bp):
AAGGGGGAATTAAAGGAATAAAAAAAAAAGTTGTACAAGTACTGATTATATAGCTATATATGATT
T
Found at i:8379935 original size:102 final size:102
Alignment explanation
Indices: 8379794--8379993 Score: 271
Period size: 102 Copynumber: 2.0 Consensus size: 102
8379784 GTTCGATTTG
* * * * *
8379794 TTGTTTTCTTTGTATTTTAAATTTTGCTTCCCTTTTATTTCAATGTCTT-AGAGATTTTTCTTTC
1 TTGTTTTCTTTATATTTTAAATTTTGATTCCCTTTTATTTCAATGTCTTAAAAAATTTCTCTTTC
8379858 ATCTTTTGACTT-AAGTAGATTTGAAGCAAAAGAGAT
66 ATCTTTTGACTTAAAGTAGATTTGAAGCAAAAGAGAT
* * *
8379894 TTGTTCTTCTTTATATTTTTTAATTTTGATTCCGC-TTTATTTTAGTGTCTTAAAAAATTTCTCT
1 TTGTT-TTCTTTATA-TTTTAAATTTTGATTCC-CTTTTATTTCAATGTCTTAAAAAATTTCTCT
8379958 TTCATCTTTTGACTTAAAAGTAGATTTGAAGCAAAA
63 TTCATCTTTTGACTT-AAAGTAGATTTGAAGCAAAA
8379994 ATATCACTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
100 5 0.06
101 8 0.09
102 29 0.34
103 25 0.29
105 19 0.22
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (102 bp):
TTGTTTTCTTTATATTTTAAATTTTGATTCCCTTTTATTTCAATGTCTTAAAAAATTTCTCTTTC
ATCTTTTGACTTAAAGTAGATTTGAAGCAAAAGAGAT
Found at i:8386498 original size:6 final size:6
Alignment explanation
Indices: 8386487--8386516 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
8386477 CTTAAAGCCT
8386487 GGGTCA GGGTCA GGGTCA GGGTCA GGGTCA
1 GGGTCA GGGTCA GGGTCA GGGTCA GGGTCA
8386517 AGGTGAGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
GGGTCA
Found at i:8386532 original size:18 final size:18
Alignment explanation
Indices: 8386487--8386525 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
8386477 CTTAAAGCCT
*
8386487 GGGTCAGGGTCAGGGTCA
1 GGGTCAGGGTCAAGGTCA
*
8386505 GGGTCAGGGTCAAGGTGA
1 GGGTCAGGGTCAAGGTCA
8386523 GGG
1 GGG
8386526 CGAGGGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.54, T:0.15
Consensus pattern (18 bp):
GGGTCAGGGTCAAGGTCA
Found at i:8390009 original size:10 final size:10
Alignment explanation
Indices: 8389996--8390027 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
8389986 AATGGACAAT
8389996 AATGGGAAAC
1 AATGGGAAAC
8390006 AATGGGAAAC
1 AATGGGAAAC
*
8390016 AATGGTAAAC
1 AATGGGAAAC
8390026 AA
1 AA
8390028 CTCTGCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.25, T:0.12
Consensus pattern (10 bp):
AATGGGAAAC
Found at i:8392401 original size:29 final size:30
Alignment explanation
Indices: 8392338--8392403 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
8392328 TTAAAGGGCC
* * *
8392338 CTAAATTTTTTTTACTAACTTTTAAGCAAT
1 CTAAAATTTTTTTACCAACTTTTAAACAAT
* *
8392368 TTAAAATTTTTTT-CCAACTTTTAAATAAT
1 CTAAAATTTTTTTACCAACTTTTAAACAAT
8392397 CTAAAAT
1 CTAAAAT
8392404 CCCATTTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (30 bp):
CTAAAATTTTTTTACCAACTTTTAAACAAT
Found at i:8396797 original size:6 final size:6
Alignment explanation
Indices: 8396786--8396815 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
8396776 ATCTCTCTCA
*
8396786 AGAAGC AGAAGC CGAAGC AGAAGC AGAAGC
1 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC
8396816 CGTGGTCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:8398738 original size:6 final size:6
Alignment explanation
Indices: 8398727--8398773 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
8398717 AGTCCAAGTG
* * *
8398727 GGAGCA GGAGCA GGAGTA GGAGCA GGAGCA GGAGCA AGAGCA AGAGC
1 GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGC
8398774 GTATCCAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.36, C:0.15, G:0.47, T:0.02
Consensus pattern (6 bp):
GGAGCA
Found at i:8421453 original size:18 final size:20
Alignment explanation
Indices: 8421412--8421455 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
8421402 TTTCTTCTCC
*
8421412 AAAATAATATTTTTAAATTA
1 AAAATAATATTTTAAAATTA
*
8421432 AAAATAA-A-TTTAAAATTT
1 AAAATAATATTTTAAAATTA
8421450 AAAATA
1 AAAATA
8421456 TAAATAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 1 0.05
20 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAATATTTTAAAATTA
Found at i:8421646 original size:18 final size:18
Alignment explanation
Indices: 8421623--8421662 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
8421613 GACTCCACCA
8421623 AAATTAAAAAATATATTT
1 AAATTAAAAAATATATTT
**
8421641 AAATTAAAGTATATATTT
1 AAATTAAAAAATATATTT
8421659 AAAT
1 AAAT
8421663 ATTATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
AAATTAAAAAATATATTT
Found at i:8421954 original size:94 final size:89
Alignment explanation
Indices: 8421850--8422019 Score: 207
Period size: 94 Copynumber: 1.9 Consensus size: 89
8421840 TAAAAAAAAT
*** * * *
8421850 AAAAATATTTAGGGAAAATGATGGCGCCATGTAATATGGCATCA-CAAAAAAAATTTAAATTTAT
1 AAAAATATTTAAAAAAAATGATGACGCCATGTAATATGACACCATC-AAAAAAATTTAAA--T-T
8421914 TTTAAAAATATAAATAATAATTCGTTTAA
62 TTTAAAAA-ATAAATAATAATTCGTTTAA
* *
8421943 AAAAATGATTTAAAAAAAATGATGACGCTATTTAATATGACACCATCAAAAAAATTTAAATTTTT
1 AAAAAT-ATTTAAAAAAAATGATGACGCCATGTAATATGACACCATCAAAAAAATTTAAATTTTT
8422008 AAAAAATAAATA
65 AAAAAATAAATA
8422020 TTAAATAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
90 7 0.10
91 9 0.13
92 1 0.01
93 6 0.09
94 43 0.64
95 1 0.01
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (89 bp):
AAAAATATTTAAAAAAAATGATGACGCCATGTAATATGACACCATCAAAAAAATTTAAATTTTTA
AAAAATAAATAATAATTCGTTTAA
Found at i:8426541 original size:7 final size:7
Alignment explanation
Indices: 8426529--8426582 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
8426519 TGTTTAGTGG
8426529 ATGGGCA
1 ATGGGCA
8426536 ATGGGCA
1 ATGGGCA
8426543 ATGGGCA
1 ATGGGCA
8426550 ATGGGCA
1 ATGGGCA
8426557 ATGGGCA
1 ATGGGCA
8426564 ATGGGCA
1 ATGGGCA
8426571 ATGGGCA
1 ATGGGCA
8426578 ATGGG
1 ATGGG
8426583 AGAGATGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.28, C:0.13, G:0.44, T:0.15
Consensus pattern (7 bp):
ATGGGCA
Found at i:8429756 original size:65 final size:66
Alignment explanation
Indices: 8429629--8429759 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 66
8429619 TTGCAAAATT
* * *
8429629 GTGAGAAACTAGATAGGCAAAATAAGTACAAGCAATAATGAAAATTAGGTTTCCCGAAATATAGA
1 GTGAAAAACTAGATAGGCAAAATAAGTAAAAGCAATAATGAAAATAAGGTTTCCCGAAATATAGA
8429694 C
66 C
* * * *
8429695 GTGAAAAACTAGATAGGCAAAAT-AGTAAAAGCAATGAT-ACAAGTAAGGTTTCCTGAGATATAG
1 GTGAAAAACTAGATAGGCAAAATAAGTAAAAGCAATAATGA-AAATAAGGTTTCCCGAAATATAG
8429758 AC
65 AC
8429760 ATAAAGAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
64 1 0.02
65 34 0.60
66 22 0.39
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (66 bp):
GTGAAAAACTAGATAGGCAAAATAAGTAAAAGCAATAATGAAAATAAGGTTTCCCGAAATATAGA
C
Found at i:8459388 original size:166 final size:166
Alignment explanation
Indices: 8459114--8459453 Score: 671
Period size: 166 Copynumber: 2.0 Consensus size: 166
8459104 ATGTTTAAGG
8459114 ATGAATATGATTTGATGCATAGAAAAAGCCATAAAGTATAGTGTTTGAAGGGAAACTGTACGCAC
1 ATGAATATGATTTGATGCATAGAAAAAGCCATAAAGTATAGTGTTTGAAGGGAAACTGTACGCAC
8459179 TACTAGCCTTTAACAAGATTGAAAGAAGAATTTGCTACGAACTCAGTACTTTTGGGAACAATCCC
66 TACTAGCCTTTAACAAGATTGAAAGAAGAATTTGCTACGAACTCAGTACTTTTGGGAACAATCCC
8459244 TACTTGAGTTAAGCCACCAAAACTTTTCAGTTTAAA
131 TACTTGAGTTAAGCCACCAAAACTTTTCAGTTTAAA
*
8459280 ATGAATATGATTTGATGCATAGAAAAAGCCATAACGTATAGTGTTTGAAGGGAAACTGTACGCAC
1 ATGAATATGATTTGATGCATAGAAAAAGCCATAAAGTATAGTGTTTGAAGGGAAACTGTACGCAC
8459345 TACTAGCCTTTAACAAGATTGAAAGAAGAATTTGCTACGAACTCAGTACTTTTGGGAACAATCCC
66 TACTAGCCTTTAACAAGATTGAAAGAAGAATTTGCTACGAACTCAGTACTTTTGGGAACAATCCC
8459410 TACTTGAGTTAAGCCACCAAAACTTTTCAGTTTAAA
131 TACTTGAGTTAAGCCACCAAAACTTTTCAGTTTAAA
8459446 ATGAATAT
1 ATGAATAT
8459454 TGGTGAACCA
Statistics
Matches: 173, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 173 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (166 bp):
ATGAATATGATTTGATGCATAGAAAAAGCCATAAAGTATAGTGTTTGAAGGGAAACTGTACGCAC
TACTAGCCTTTAACAAGATTGAAAGAAGAATTTGCTACGAACTCAGTACTTTTGGGAACAATCCC
TACTTGAGTTAAGCCACCAAAACTTTTCAGTTTAAA
Found at i:8465016 original size:5 final size:6
Alignment explanation
Indices: 8465001--8465025 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
8464991 AGCGCAAAGA
8465001 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
8465026 TTGAAAGCTT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:8466853 original size:17 final size:18
Alignment explanation
Indices: 8466831--8466864 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8466821 CAATTTTTCT
*
8466831 AATTAAATTAA-TAAAAA
1 AATTAAAATAACTAAAAA
8466848 AATTAAAATAACTAAAA
1 AATTAAAATAACTAAAA
8466865 TAAAAGTGAC
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:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AATTAAAATAACTAAAAA
Found at i:8467322 original size:28 final size:28
Alignment explanation
Indices: 8467290--8467343 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
8467280 TTTAAAAAAT
*
8467290 AATTAAATATCAAAATGAATTATTTACA
1 AATTAAATATCAAAATGAATAATTTACA
* * *
8467318 AATTAATTATCGAAATGGATAATTTA
1 AATTAAATATCAAAATGAATAATTTA
8467344 TTATAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (28 bp):
AATTAAATATCAAAATGAATAATTTACA
Found at i:8473437 original size:24 final size:23
Alignment explanation
Indices: 8473393--8473437 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
8473383 AGACAGAAGT
*
8473393 GTGCCACAAGGCAGAGCAAAAGC
1 GTGCCACAAGGCAGAGAAAAAGC
*
8473416 GTGCCACAAAGGCAGATAAAAA
1 GTGCCAC-AAGGCAGAGAAAAA
8473438 CTAGAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07
Consensus pattern (23 bp):
GTGCCACAAGGCAGAGAAAAAGC
Found at i:8478304 original size:6 final size:6
Alignment explanation
Indices: 8478295--8478339 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
8478285 GAACAGAAGT
* * *
8478295 TAGGGT TAGGGT TTGGGC TAGGGC TAGGGC TAGGGC TAGGGC TAG
1 TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC TAG
8478340 TTGAAAGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.16, C:0.11, G:0.49, T:0.24
Consensus pattern (6 bp):
TAGGGC
Found at i:8478630 original size:5 final size:5
Alignment explanation
Indices: 8478620--8478648 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
8478610 TATATGTTTA
8478620 GGTTG GGTTG GGTTG GGTTG GGTTG GGTT
1 GGTTG GGTTG GGTTG GGTTG GGTTG GGTT
8478649 TTGAACGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.59, T:0.41
Consensus pattern (5 bp):
GGTTG
Found at i:8480044 original size:17 final size:17
Alignment explanation
Indices: 8480022--8480056 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8480012 TGCCCCAAAC
8480022 CTTTTTCTTTCTTTTTT
1 CTTTTTCTTTCTTTTTT
8480039 CTTTTTCTTTCTTTTTT
1 CTTTTTCTTTCTTTTTT
8480056 C
1 C
8480057 CTTGCCTTAC
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTTTCTTTCTTTTTT
Found at i:8480582 original size:21 final size:21
Alignment explanation
Indices: 8480558--8480614 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
8480548 ACATTCATTT
8480558 AAACCAAACCCATTTAAAACC
1 AAACCAAACCCATTTAAAACC
8480579 AAACCAAACCCATTTAAAACC
1 AAACCAAACCCATTTAAAACC
*
8480600 TAACCAAACCCATTT
1 AAACCAAACCCATTT
8480615 GAATCAAACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCAAACCCATTTAAAACC
Found at i:8480593 original size:36 final size:37
Alignment explanation
Indices: 8480524--8480596 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
8480514 TCCATCAAGC
* **
8480524 CCAAATCCCATTTAAACCAAACCCACATTCATTTAAA
1 CCAAATCCCATTTAAACCAAACCCAAACCCATTTAAA
8480561 CCAAA-CCCATTTAAAACCAAA-CCAAACCCATTTAAA
1 CCAAATCCCATTT-AAACCAAACCCAAACCCATTTAAA
8480597 ACCTAACCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 19 0.59
37 13 0.41
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.21
Consensus pattern (37 bp):
CCAAATCCCATTTAAACCAAACCCAAACCCATTTAAA
Found at i:8480599 original size:16 final size:15
Alignment explanation
Indices: 8480553--8480583 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
8480543 AACCCACATT
8480553 CATTTAAACCAAACC
1 CATTTAAACCAAACC
8480568 CATTTAAAACCAAACC
1 CATTT-AAACCAAACC
8480584 AAACCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.19
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:8481789 original size:3 final size:3
Alignment explanation
Indices: 8481777--8481821 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
8481767 TATTCTATTC
8481777 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
8481822 TTGGGATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:8487277 original size:17 final size:17
Alignment explanation
Indices: 8487255--8487289 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
8487245 TGCCCCAAAC
8487255 CTTTTTCTTTCTTTTTT
1 CTTTTTCTTTCTTTTTT
*
8487272 CTTTTTCTTTTTTTTTT
1 CTTTTTCTTTCTTTTTT
8487289 C
1 C
8487290 CTTGCCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
CTTTTTCTTTCTTTTTT
Found at i:8487816 original size:21 final size:21
Alignment explanation
Indices: 8487792--8487859 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
8487782 CATTCATTTG
8487792 AACCAAACCCATTTAAAACCA
1 AACCAAACCCATTTAAAACCA
*
8487813 AACCAAACCCATTTAAAACCT
1 AACCAAACCCATTTAAAACCA
*
8487834 AACCAAACCCATTT-GAACCA
1 AACCAAACCCATTTAAAACCA
8487854 AACCAA
1 AACCAA
8487860 TTGAACCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 10 0.23
21 34 0.77
ACGTcount: A:0.50, C:0.34, G:0.01, T:0.15
Consensus pattern (21 bp):
AACCAAACCCATTTAAAACCA
Found at i:8487826 original size:36 final size:37
Alignment explanation
Indices: 8487757--8487826 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
8487747 TCCATCAAGC
* **
8487757 CCAAATCCCATTTAAACCAAACCCACATTCATTTGAA
1 CCAAATCCCATTTAAACCAAACCCAAACCCATTTGAA
8487794 CCAAA-CCCATTTAAAACCAAA-CCAAACCCATTT
1 CCAAATCCCATTT-AAACCAAACCCAAACCCATTT
8487827 AAAACCTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 16 0.55
37 13 0.45
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.21
Consensus pattern (37 bp):
CCAAATCCCATTTAAACCAAACCCAAACCCATTTGAA
Found at i:8487865 original size:14 final size:15
Alignment explanation
Indices: 8487834--8487868 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
8487824 TTTAAAACCT
*
8487834 AACCAAACCCATTTG
1 AACCAAACCCAATTG
8487849 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
8487863 AACCAA
1 AACCAA
8487869 GTCCAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:8489023 original size:3 final size:3
Alignment explanation
Indices: 8489011--8489055 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
8489001 TATTCTATTC
8489011 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
8489056 TTGGGATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:8491368 original size:18 final size:18
Alignment explanation
Indices: 8491318--8491368 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
8491308 TGACATGTGG
8491318 TAAAAAATAATACAAAATA
1 TAAAAAATAATA-AAAATA
* **
8491337 -AAAAAACAATTAAAGTTA
1 TAAAAAATAA-TAAAAATA
8491355 TAAAAAATAATAAA
1 TAAAAAATAATAAA
8491369 TTTTAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
TAAAAAATAATAAAAATA
Found at i:8491722 original size:19 final size:18
Alignment explanation
Indices: 8491700--8491802 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 18
8491690 TATTTTTTTA
8491700 ATTTTTATAAAAGTTTAAT
1 ATTTTTATAAAA-TTTAAT
*
8491719 ATTTTTTTATAATTATTT-AT
1 A--TTTTTATAA-AATTTAAT
** *
8491739 GATTTTTATAAAAAAT-CT
1 -ATTTTTATAAAATTTAAT
*
8491757 ATTTTTA-ATAAATTTTAT
1 ATTTTTATA-AAATTTAAT
8491775 ATTTTTATTAAAATTTAAT
1 ATTTTTA-TAAAATTTAAT
8491794 AATTTTTAT
1 -ATTTTTAT
8491803 TTATTATAGT
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
16 1 0.02
17 11 0.17
18 11 0.17
19 19 0.29
20 10 0.15
21 13 0.20
22 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTTTATAAAATTTAAT
Found at i:8491777 original size:18 final size:19
Alignment explanation
Indices: 8491700--8491801 Score: 61
Period size: 20 Copynumber: 5.4 Consensus size: 19
8491690 TATTTTTTTA
8491700 ATTTTT-ATAAAAGTTTAAT
1 ATTTTTAATAAAA-TTTAAT
* *
8491719 ATTTTTTTATAATTATTT-AT
1 A-TTTTTAATAA-AATTTAAT
** *
8491739 GATTTTT-ATAAAAAAT-CT
1 -ATTTTTAATAAAATTTAAT
*
8491757 ATTTTTAAT-AAATTTTAT
1 ATTTTTAATAAAATTTAAT
*
8491775 ATTTTTATTAAAATTTAAT
1 ATTTTTAATAAAATTTAAT
8491794 AATTTTTA
1 -ATTTTTA
8491802 TTTATTATAG
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
17 10 0.15
18 14 0.22
19 13 0.20
20 19 0.29
21 8 0.12
22 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTTTAATAAAATTTAAT
Found at i:8491799 original size:38 final size:37
Alignment explanation
Indices: 8491695--8491801 Score: 105
Period size: 36 Copynumber: 2.9 Consensus size: 37
8491685 TATTTTATTT
* * *
8491695 TTTTA-ATTTTTATAAAAGTTTAATATTTTTTTATAAT
1 TTTTATATTTTTATAAAA-TTTAATAATTTTTAATAAA
*
8491732 TATTTATGATTTTTATAAAA---AATCTATTTTTAATAAA
1 T-TTTAT-ATTTTTATAAAATTTAAT-AATTTTTAATAAA
8491769 TTTTATATTTTTATTAAAATTTAATAATTTTTA
1 TTTTATATTTTTA-TAAAATTTAATAATTTTTA
8491802 TTTATTATAG
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
35 7 0.12
36 13 0.23
37 11 0.19
38 11 0.19
39 3 0.05
40 12 0.21
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (37 bp):
TTTTATATTTTTATAAAATTTAATAATTTTTAATAAA
Found at i:8503101 original size:13 final size:13
Alignment explanation
Indices: 8503083--8503107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8503073 AGATAAGTTT
8503083 ATTTTTAAAAATA
1 ATTTTTAAAAATA
8503096 ATTTTTAAAAAT
1 ATTTTTAAAAAT
8503108 TTAGATAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTTAAAAATA
Found at i:8505076 original size:38 final size:38
Alignment explanation
Indices: 8505030--8505138 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 38
8505020 TTAAAAAATA
*
8505030 AAAATAATTTAAAAATAAATTGGGATAATTTTGTTTCC
1 AAAATAATTTAAAAATAAATTGAGATAATTTTGTTTCC
* ** **
8505068 AAAGTAATTTTAAAAAT---TTTTGATAATTTT-TCTTTT
1 AAAATAA-TTTAAAAATAAATTGAGATAATTTTGT-TTCC
*
8505104 AAAATAATATAAAAATAAATTGAGATAA-TTTGTTT
1 AAAATAATTTAAAAATAAATTGAGATAATTTTGTTT
8505139 GATACTAGGA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
35 9 0.16
36 19 0.34
37 5 0.09
38 14 0.25
39 9 0.16
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (38 bp):
AAAATAATTTAAAAATAAATTGAGATAATTTTGTTTCC
Found at i:8505928 original size:53 final size:51
Alignment explanation
Indices: 8505862--8505966 Score: 124
Period size: 52 Copynumber: 2.0 Consensus size: 51
8505852 TAATCGAATT
* * *
8505862 AAATTATTATTTTA-AATTTTTTAATAAAACAAGATAAA-CTATAAATTTAAAA
1 AAATTATAATTTTACAATTATTT--TAAAACAAGATAAATCAAT-AATTTAAAA
*
8505914 AAATATATAATTTTACAATTATTTTAAAATAAGATAAATCAATAATTTAAAA
1 AAAT-TATAATTTTACAATTATTTTAAAACAAGATAAATCAATAATTTAAAA
8505966 A
1 A
8505967 TAAGATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
52 27 0.59
53 12 0.26
54 7 0.15
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (51 bp):
AAATTATAATTTTACAATTATTTTAAAACAAGATAAATCAATAATTTAAAA
Found at i:8505961 original size:24 final size:24
Alignment explanation
Indices: 8505929--8505976 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
8505919 TATAATTTTA
* *
8505929 CAATTATTTTAAAATAAGATAAAT
1 CAATAATTTAAAAATAAGATAAAT
8505953 CAATAATTTAAAAATAAGATAAAT
1 CAATAATTTAAAAATAAGATAAAT
8505977 TGTATTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
CAATAATTTAAAAATAAGATAAAT
Found at i:8507477 original size:32 final size:35
Alignment explanation
Indices: 8507428--8507500 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 35
8507418 TAAGTGTTGA
8507428 AAAATTAAATGATACAT-ATT-GATT-TTAAATTAT
1 AAAA-TAAATGATACATAATTAGATTGTTAAATTAT
**
8507461 AAAATAAATTGA-ACATAATTAGATTGTTTGATTAT
1 AAAATAAA-TGATACATAATTAGATTGTTAAATTAT
8507496 AAAAT
1 AAAAT
8507501 TTAAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
32 8 0.24
33 10 0.29
34 4 0.12
35 12 0.35
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (35 bp):
AAAATAAATGATACATAATTAGATTGTTAAATTAT
Found at i:8507666 original size:16 final size:15
Alignment explanation
Indices: 8507625--8507679 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
8507615 TAAATATAAA
*
8507625 ATATTATAAATCTAG
1 ATATTATAAATCTAC
* * *
8507640 AAATAATAAATACTAT
1 ATATTATAAAT-CTAC
8507656 ATATTATAAATCTAAC
1 ATATTATAAATCT-AC
8507672 ATATTATA
1 ATATTATA
8507680 CTAAATATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (15 bp):
ATATTATAAATCTAC
Found at i:8517148 original size:31 final size:28
Alignment explanation
Indices: 8517111--8517189 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 28
8517101 TTTTTTTAAA
*
8517111 ATTTTAAAAATTCAAAAAAAGATATAAAATT
1 ATTTTAAAAATT--AAAAAACAT-TAAAATT
*
8517142 ATTTTAAAAATTAAAAATCATTAAAATT
1 ATTTTAAAAATTAAAAAACATTAAAATT
*
8517170 GTTTTAAAAACTATAAAAAA
1 ATTTTAAAAA-T-TAAAAAA
8517190 TATTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 16 0.38
29 8 0.19
30 6 0.14
31 12 0.29
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (28 bp):
ATTTTAAAAATTAAAAAACATTAAAATT
Found at i:8517157 original size:28 final size:27
Alignment explanation
Indices: 8517111--8517192 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 27
8517101 TTTTTTTAAA
8517111 ATTTTAAAAATTCAAAAAAAGATATAAAATT
1 ATTTTAAAAATT---AAAAA-ATATAAAATT
8517142 ATTTTAAAAATT-AAAAATCATTAAAATT
1 ATTTTAAAAATTAAAAAAT-A-TAAAATT
*
8517170 GTTTTAAAAACTATAAAAAATAT
1 ATTTTAAAAA-T-TAAAAAATAT
8517193 TTTTAATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
26 2 0.04
27 5 0.11
28 16 0.36
29 2 0.04
30 2 0.04
31 18 0.40
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
ATTTTAAAAATTAAAAAATATAAAATT
Found at i:8518994 original size:15 final size:15
Alignment explanation
Indices: 8518974--8519036 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
8518964 AGAATATTTG
8518974 AAATATTTTAATATA
1 AAATATTTTAATATA
*
8518989 AAATATTTT-ATTTCCA
1 AAATATTTTAATAT--A
* *
8519005 AATATAATTTAAAATA
1 AA-ATATTTTAATATA
8519021 AAATATTTTAATATA
1 AAATATTTTAATATA
8519036 A
1 A
8519037 TTTAATATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
14 3 0.08
15 21 0.55
16 6 0.16
17 6 0.16
18 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:8519071 original size:10 final size:10
Alignment explanation
Indices: 8519051--8519097 Score: 69
Period size: 10 Copynumber: 4.6 Consensus size: 10
8519041 ATATAAAAAT
8519051 AATTATATTA
1 AATTATATTA
8519061 AATGT-TATTA
1 AAT-TATATTA
8519071 AATTATATTA
1 AATTATATTA
8519081 AATTATGATTA
1 AATTAT-ATTA
8519092 AATTAT
1 AATTAT
8519098 TTATTATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.03
10 22 0.65
11 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (10 bp):
AATTATATTA
Found at i:8519293 original size:44 final size:46
Alignment explanation
Indices: 8519237--8519330 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
8519227 TATATTATCT
* *
8519237 ATTATATTCAACCAAAC-A-TAACATTACT-ATTACAGTTCTATTCC
1 ATTACATTCAACCAAACAATTAA-ATTACTGATTACAATTCTATTCC
* *
8519281 ATTACATTCAACCAAACAATTAAATTATTGATTACAATTTTATTCC
1 ATTACATTCAACCAAACAATTAAATTACTGATTACAATTCTATTCC
8519327 ATTA
1 ATTA
8519331 TGACTCTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 16 0.37
45 6 0.14
46 21 0.49
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (46 bp):
ATTACATTCAACCAAACAATTAAATTACTGATTACAATTCTATTCC
Found at i:8534705 original size:19 final size:19
Alignment explanation
Indices: 8534666--8534717 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
8534656 TATATGATAC
*
8534666 ATAACAAAATATCTCCTAA
1 ATAACAATATATCTCCTAA
8534685 ATAACAATATATCTCAC-AA
1 ATAACAATATATCTC-CTAA
*
8534704 ATAATAATAT-TCTC
1 ATAACAATATATCTC
8534718 TTACAACTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 4 0.13
19 25 0.83
20 1 0.03
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAACAATATATCTCCTAA
Found at i:8534907 original size:19 final size:19
Alignment explanation
Indices: 8534883--8534943 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
8534873 AAAAAAATTT
* *
8534883 ATAATTTTTACGATTTTAA
1 ATAATTTTTATGATTTTTA
*
8534902 ATAATTATTATGATTTTTA
1 ATAATTTTTATGATTTTTA
*
8534921 ATATTTTTTTATGATTTTTA
1 ATA-ATTTTTATGATTTTTA
8534941 ATA
1 ATA
8534944 TATATCTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (19 bp):
ATAATTTTTATGATTTTTA
Found at i:8534942 original size:20 final size:20
Alignment explanation
Indices: 8534886--8534946 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
8534876 AAAATTTATA
* *
8534886 ATTTTTACGATTTTAAATA-
1 ATTTTTATGATTTTTAATAT
*
8534905 ATTATTATGATTTTTAATAT
1 ATTTTTATGATTTTTAATAT
*
8534925 TTTTTTATGATTTTTAATAT
1 ATTTTTATGATTTTTAATAT
8534945 AT
1 AT
8534947 ATCTATTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTTATGATTTTTAATAT
Found at i:8536913 original size:29 final size:27
Alignment explanation
Indices: 8536881--8536944 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
8536871 AGTTATAAAA
* *
8536881 AATAAATTTTAGAAAAAATATTAAATTTT
1 AATAAAATTTA-AAAAAAT-TTAAAATTT
8536910 AATAAAAATTTAAAAAAATTTAAAATTT
1 AAT-AAAATTTAAAAAAATTTAAAATTT
*
8536938 ATTAAAA
1 AATAAAA
8536945 ATTCAAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 10 0.32
29 10 0.32
30 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
AATAAAATTTAAAAAAATTTAAAATTT
Found at i:8536922 original size:18 final size:19
Alignment explanation
Indices: 8536883--8536923 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8536873 TTATAAAAAA
8536883 TAAATTTTAGAAAAAATAT
1 TAAATTTTAGAAAAAATAT
8536902 TAAATTTTA-ATAAAAAT-T
1 TAAATTTTAGA-AAAAATAT
8536920 TAAA
1 TAAA
8536924 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAATTTTAGAAAAAATAT
Found at i:8536924 original size:28 final size:28
Alignment explanation
Indices: 8536888--8536947 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
8536878 AAAAATAAAT
*
8536888 TTTAGAAAAAATATTAAATTTTAATAAAAA
1 TTTA-AAAAAAT-TTAAAATTTAATAAAAA
*
8536918 TTTAAAAAAATTTAAAATTTATTAAAAA
1 TTTAAAAAAATTTAAAATTTAATAAAAA
8536946 TT
1 TT
8536948 CAAACTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 17 0.61
29 7 0.25
30 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTAAAAAAATTTAAAATTTAATAAAAA
Found at i:8537287 original size:10 final size:10
Alignment explanation
Indices: 8537274--8537365 Score: 55
Period size: 10 Copynumber: 9.2 Consensus size: 10
8537264 CTTTATAAAA
8537274 TTTTATATTT
1 TTTTATATTT
*
8537284 TTTTATAAATT
1 TTTTAT-ATTT
*
8537295 TTTTACGA--T
1 TTTTA-TATTT
**
8537304 TTTTATAAAT
1 TTTTATATTT
* *
8537314 TTTTACAATT
1 TTTTATATTT
*
8537324 TTTTATATTA
1 TTTTATATTT
*
8537334 TTTTACGATTT
1 TTTTA-TATTT
*
8537345 TTATATATTT
1 TTTTATATTT
8537355 TTTTA-ATTT
1 TTTTATATTT
8537364 TT
1 TT
8537366 AAAAATATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
8 1 0.02
9 12 0.19
10 35 0.55
11 16 0.25
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATATTT
Found at i:8537290 original size:20 final size:20
Alignment explanation
Indices: 8537265--8537379 Score: 69
Period size: 19 Copynumber: 5.8 Consensus size: 20
8537255 TTCTTACGAC
*
8537265 TTTATAAAATTTTATATTTT
1 TTTATAAAATTTTATAATTT
*
8537285 TTTAT-AAATTTTTTACGA-TT
1 TTTATAAAATTTTATA--ATTT
* *
8537305 TTTATAAATTTTTACAATTT
1 TTTATAAAATTTTATAATTT
** **
8537325 TTTATATTATTTTACGA-TT
1 TTTATAAAATTTTATAATTT
* * *
8537344 TTTATATATTTTTTTAA-TT
1 TTTATAAAATTTTATAATTT
8537363 TTTA-AAAATATTTATAA
1 TTTATAAAAT-TTTATAA
8537380 CCTTTATTGA
Statistics
Matches: 73, Mismatches: 17, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
18 3 0.04
19 36 0.49
20 27 0.37
21 7 0.10
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATAAAATTTTATAATTT
Found at i:8537363 original size:19 final size:20
Alignment explanation
Indices: 8537283--8537366 Score: 79
Period size: 19 Copynumber: 4.3 Consensus size: 20
8537273 ATTTTATATT
*
8537283 TTTTTATA-AATTTTTTACGA
1 TTTTTATATATTTTTTTAC-A
*
8537303 TTTTTATA-A-ATTTTTACAA
1 TTTTTATATATTTTTTTAC-A
*
8537322 TTTTT-TATATTATTTTACGA
1 TTTTTATATATTTTTTTAC-A
8537342 TTTTTATATATTTTTTTA-A
1 TTTTTATATATTTTTTTACA
8537361 TTTTTA
1 TTTTTA
8537367 AAAATATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
18 2 0.04
19 21 0.38
20 21 0.38
21 11 0.20
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATATATTTTTTTACA
Found at i:8537375 original size:39 final size:39
Alignment explanation
Indices: 8537265--8537375 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
8537255 TTCTTACGAC
* * * * *
8537265 TTTATAAAATTTTATATTTTTTTATAAATTTTTTACGATT
1 TTTATAAATTTTTACA-ATTTTTAAAAATATTTTACGATT
* * *
8537305 TTTATAAATTTTTACAATTTTTTATATTATTTTACGATT
1 TTTATAAATTTTTACAATTTTTAAAAATATTTTACGATT
* **
8537344 TTTATATATTTTTTTAATTTTTAAAAATATTT
1 TTTATAAATTTTTACAATTTTTAAAAATATTT
8537376 ATAACCTTTA
Statistics
Matches: 57, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
39 43 0.75
40 14 0.25
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (39 bp):
TTTATAAATTTTTACAATTTTTAAAAATATTTTACGATT
Found at i:8538025 original size:18 final size:17
Alignment explanation
Indices: 8537994--8538041 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
8537984 TTAGTTTAGA
* * *
8537994 TTAATTTTAGATTTATT
1 TTAAATTTAAATTTACT
8538011 TCTAAATTTAAATTTACT
1 T-TAAATTTAAATTTACT
8538029 TTAAATTTGAAAT
1 TTAAATTT-AAAT
8538042 AATTTTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTTAAATTTACT
Found at i:8538852 original size:12 final size:12
Alignment explanation
Indices: 8538837--8538883 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
8538827 ACGACATTAA
*
8538837 TAATAATATTAT
1 TAATAATAATAT
8538849 TAATAATAATGA-
1 TAATAATAAT-AT
8538861 TAATAATTAATAT
1 TAATAA-TAATAT
8538874 TAAATAATAA
1 T-AATAATAA
8538884 AAAAGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 16 0.53
13 9 0.30
14 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:8540031 original size:29 final size:30
Alignment explanation
Indices: 8539991--8540263 Score: 170
Period size: 29 Copynumber: 9.5 Consensus size: 30
8539981 AACTATCCAA
*
8539991 AAAATTA-TATTTTTACCCTCGAACTTTCC
1 AAAATTACCATTTTTACCCTCGAACTTTCC
*
8540020 AAAATT-CCATTTTTGA-CCTCAAACTTTCC
1 AAAATTACCATTTTT-ACCCTCGAACTTTCC
**
8540049 AAGAATTACCA-TTTTACCC-CTGAACTTTTA
1 AA-AATTACCATTTTTACCCTC-GAACTTTCC
* * *
8540079 AAAATT-CCATTTTGA-CCT-TAATTTTTCC
1 AAAATTACCATTTTTACCCTCGAA-CTTTCC
*
8540107 AAAATTACCA-TTTTACCC-CTAAAC-TTCC
1 AAAATTACCATTTTTACCCTC-GAACTTTCC
* **
8540135 AAAAATT-CCATTTTGACCCT-GATTTTTCC
1 -AAAATTACCATTTTTACCCTCGAACTTTCC
**
8540164 AAAATTACCA-CATTACCC-CTGAAC-TTCC
1 AAAATTACCATTTTTACCCTC-GAACTTTCC
* * *
8540192 AAAAATCCCATTTTTACCCT-AAACTTTTCC
1 AAAATTACCATTTTTACCCTCGAAC-TTTCC
* * *
8540222 AAAATTACCA-TTTTGCCCTCG-AGTGTCC
1 AAAATTACCATTTTTACCCTCGAACTTTCC
8540250 AAAATTACCATTTT
1 AAAATTACCATTTT
8540264 GCCCCCAAGT
Statistics
Matches: 185, Mismatches: 33, Indels: 52
0.69 0.12 0.19
Matches are distributed among these distances:
27 2 0.01
28 66 0.36
29 81 0.44
30 33 0.18
31 3 0.02
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTTACCCTCGAACTTTCC
Found at i:8540132 original size:57 final size:57
Alignment explanation
Indices: 8540001--8540235 Score: 285
Period size: 57 Copynumber: 4.1 Consensus size: 57
8539991 AAAATTATAT
* **
8540001 TTTTA-CCCTCGAACTTTCC-AAAATTCCATTTTTGACCTCAAACTTTCCAAGAATTACCA
1 TTTTACCCCT-GAAC-TTCCAAAAATTCCA-TTTTGACCTTAATTTTTCCAA-AATTACCA
**
8540060 TTTTACCCCTGAACTTTTAAAAATTCCATTTTGACCTTAATTTTTCCAAAATTACCA
1 TTTTACCCCTGAACTTCCAAAAATTCCATTTTGACCTTAATTTTTCCAAAATTACCA
* * *
8540117 TTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCTGATTTTTCCAAAATTACCA
1 TTTTACCCCTGAACTTCCAAAAATTCCATTTTGACCTTAATTTTTCCAAAATTACCA
** * * * *
8540174 CATTACCCCTGAACTTCCAAAAATCCCATTTTTACCCTAAACTTTTCCAAAATTACCA
1 TTTTACCCCTGAACTTCCAAAAATTCCATTTTGA-CCTTAATTTTTCCAAAATTACCA
8540232 TTTT
1 TTTT
8540236 GCCCTCGAGT
Statistics
Matches: 152, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
57 89 0.59
58 41 0.27
59 18 0.12
60 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.37
Consensus pattern (57 bp):
TTTTACCCCTGAACTTCCAAAAATTCCATTTTGACCTTAATTTTTCCAAAATTACCA
Found at i:8540255 original size:28 final size:28
Alignment explanation
Indices: 8540219--8540281 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
8540209 CCTAAACTTT
* * *
8540219 TCCAAAATTACCATTTTGCCCTCGAGTG
1 TCCAAAATTACCATTTTGCCCCCAAGTA
8540247 TCCAAAATTACCATTTTGCCCCCAAGTA
1 TCCAAAATTACCATTTTGCCCCCAAGTA
8540275 TCCAAAA
1 TCCAAAA
8540282 ATCTCATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.29
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCCCAAGTA
Found at i:8540279 original size:86 final size:86
Alignment explanation
Indices: 8540103--8540291 Score: 201
Period size: 86 Copynumber: 2.2 Consensus size: 86
8540093 ACCTTAATTT
* * * *
8540103 TTCCAAAATTACCA-TTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCTGATTTTTCCAAA
1 TTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCTGATGTGTCCAAA
*
8540167 ATTACCACATTACCCCTGAAC
66 ATTACCACATTACCCCTCAAC
8540188 TTCCAAAAATCCCATTTTTA-CCCTAAACTTTTCC-AAAATTACCATTTTG-CCCTCGA-GTGTC
1 TTCCAAAAATCCCATTTTTACCCCTAAAC--TTCCAAAAATT-CCATTTTGACCCT-GATGTGTC
** * *
8540249 CAAAATTACCATTTTGCCCC-CAAG
62 CAAAATTACCACATTACCCCTCAAC
*
8540273 TATCCAAAAATCTCATTTT
1 T-TCCAAAAATCCCATTTT
8540292 CAATTCCGAT
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
85 23 0.26
86 51 0.58
87 14 0.16
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.34
Consensus pattern (86 bp):
TTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAATTCCATTTTGACCCTGATGTGTCCAAA
ATTACCACATTACCCCTCAAC
Found at i:8540289 original size:28 final size:28
Alignment explanation
Indices: 8540219--8540291 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
8540209 CCTAAACTTT
* * * *
8540219 TCCAAAATTACCATTTTGCCCTCGAGTG
1 TCCAAAAATACCATTTTGCCCCCAAGTA
*
8540247 TCCAAAATTACCATTTTGCCCCCAAGTA
1 TCCAAAAATACCATTTTGCCCCCAAGTA
8540275 TCCAAAAAT-CTCATTTT
1 TCCAAAAATAC-CATTTT
8540292 CAATTCCGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (28 bp):
TCCAAAAATACCATTTTGCCCCCAAGTA
Found at i:8542124 original size:23 final size:23
Alignment explanation
Indices: 8542096--8542152 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
8542086 ACATTATTTG
*
8542096 TAAACATGTTCATTTTATGTTCA
1 TAAACATGTTCATTTAATGTTCA
* *
8542119 TAAACATGTTAATTTAATGTTCG
1 TAAACATGTTCATTTAATGTTCA
*
8542142 TGAACATGTTC
1 TAAACATGTTC
8542153 GTGAATATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (23 bp):
TAAACATGTTCATTTAATGTTCA
Found at i:8560978 original size:19 final size:18
Alignment explanation
Indices: 8560941--8560979 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8560931 TTGAAATATT
* *
8560941 TTAAAATTTTAAAATTAA
1 TTAAAAATTTAAAAATAA
8560959 TTAAAAATTTAAACAATAA
1 TTAAAAATTTAAA-AATAA
8560978 TT
1 TT
8560980 TGAGAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAAATTTAAAAATAA
Found at i:8562962 original size:18 final size:18
Alignment explanation
Indices: 8562941--8562978 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8562931 TGAATTTTCG
8562941 AATTCAAAT-AACTCGAAT
1 AATTCAAATAAACT-GAAT
*
8562959 AATTCGAATAAACTGAAT
1 AATTCAAATAAACTGAAT
8562977 AA
1 AA
8562979 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
AATTCAAATAAACTGAAT
Found at i:8563161 original size:34 final size:34
Alignment explanation
Indices: 8563118--8563190 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
8563108 AAACTAAATT
*
8563118 CAAATATTTTTAATCTTTTACCTTTTATCTTACC
1 CAAATATTTTTAATCTTTTACCTTTTACCTTACC
* *
8563152 CAAATATTTTTAATTTTTTATCTTTTACCTTACC
1 CAAATATTTTTAATCTTTTACCTTTTACCTTACC
8563186 CAAAT
1 CAAAT
8563191 GTTGTTTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (34 bp):
CAAATATTTTTAATCTTTTACCTTTTACCTTACC
Found at i:8573748 original size:3 final size:3
Alignment explanation
Indices: 8573742--8573767 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8573732 TTCTTCTTCT
8573742 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
8573768 CCTTCTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:8579126 original size:38 final size:38
Alignment explanation
Indices: 8579075--8579147 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
8579065 AAAGAAGAAA
*
8579075 TTCCCTTTTGGATTGTAGTAGCAATGTCCAGGCATTTC
1 TTCCCTCTTGGATTGTAGTAGCAATGTCCAGGCATTTC
8579113 TTCCCTCTTGGATTGTAGTAGCAATGTCCAGGCAT
1 TTCCCTCTTGGATTGTAGTAGCAATGTCCAGGCAT
8579148 ACTCCCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (38 bp):
TTCCCTCTTGGATTGTAGTAGCAATGTCCAGGCATTTC
Found at i:8579934 original size:13 final size:13
Alignment explanation
Indices: 8579916--8579941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8579906 CAAGACTATC
8579916 AATTTCTATAAAT
1 AATTTCTATAAAT
8579929 AATTTCTATAAAT
1 AATTTCTATAAAT
8579942 GATATTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTCTATAAAT
Found at i:8586758 original size:15 final size:15
Alignment explanation
Indices: 8586740--8586784 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 15
8586730 TATGATATAA
8586740 TTTAAAATAAAAAAT
1 TTTAAAATAAAAAAT
*
8586755 TTTAAAAAATAAAATAT
1 TTT--AAAATAAAAAAT
8586772 TTTAAAATAAAAA
1 TTTAAAATAAAAA
8586785 CAAAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.46
17 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTTAAAATAAAAAAT
Found at i:8587575 original size:31 final size:29
Alignment explanation
Indices: 8587506--8587576 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
8587496 AAGTTAAATT
* *
8587506 TTCATGTATAAAATTACACAAAATTAAAA
1 TTCATGTATAGAATTACACAAAACTAAAA
* * *
8587535 TACATGTATAGAATTACACATTAGACTAAAG
1 TTCATGTATAGAATTACACA--AAACTAAAA
8587566 TTCATGTATAG
1 TTCATGTATAG
8587577 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.32
Consensus pattern (29 bp):
TTCATGTATAGAATTACACAAAACTAAAA
Found at i:8590282 original size:39 final size:39
Alignment explanation
Indices: 8590239--8590316 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
8590229 TAAATTGAGT
8590239 TAATGACAAGTTGCATATATAACAGTATGCTAATGCACA
1 TAATGACAAGTTGCATATATAACAGTATGCTAATGCACA
8590278 TAATGACAAGTTGCATATATAACAGTATGCTAATGCACA
1 TAATGACAAGTTGCATATATAACAGTATGCTAATGCACA
8590317 ACATGTGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (39 bp):
TAATGACAAGTTGCATATATAACAGTATGCTAATGCACA
Found at i:8596669 original size:24 final size:24
Alignment explanation
Indices: 8596638--8596692 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
8596628 TCTACACTAC
*
8596638 ATATATTGCAAGAATTTTGAAATT
1 ATATATTGCAAGAATTTTGAAATG
*
8596662 ATATATTGCATGAATTTTGAAATG
1 ATATATTGCAAGAATTTTGAAATG
8596686 A-ATATTG
1 ATATATTG
8596693 ATGGGGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (24 bp):
ATATATTGCAAGAATTTTGAAATG
Found at i:8599766 original size:24 final size:24
Alignment explanation
Indices: 8599705--8599767 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
8599695 TAGACTAATA
* *
8599705 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
8599729 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
8599753 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
8599768 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:8602287 original size:24 final size:24
Alignment explanation
Indices: 8602202--8602288 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
8602192 TAGACTAATA
* *
8602202 AGAATTTGACTCAAACAAATAAAC
1 AGAATTTAACTGAAACAAATAAAC
* * *
8602226 AGAATTTAATTAAAACAAATAAAT
1 AGAATTTAACTGAAACAAATAAAC
* * *
8602250 AGAGTTTAATTGAAACAATTAAAC
1 AGAATTTAACTGAAACAAATAAAC
8602274 AGAATTTAACTGAAA
1 AGAATTTAACTGAAA
8602289 GATTATTTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.26
Consensus pattern (24 bp):
AGAATTTAACTGAAACAAATAAAC
Found at i:8604241 original size:24 final size:24
Alignment explanation
Indices: 8604213--8604278 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
8604203 TAGACTAATA
*
8604213 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
8604237 AGAGTTTAATTTAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
8604261 AGAGTTGAACT-AAA-AAAT
1 AGAGTTTAACTCAAACAAAT
8604279 TATTTCTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 4 0.11
23 3 0.08
24 30 0.81
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:8608376 original size:21 final size:21
Alignment explanation
Indices: 8608335--8608376 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
8608325 TTGATTAGGA
* *
8608335 AATTATAAAAATATTTTTTAT
1 AATTATAAAAAAATTTATTAT
8608356 AATTA-AAAAAAATTATATTAT
1 AATTATAAAAAAATT-TATTAT
8608377 TTGAAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTATAAAAAAATTTATTAT
Found at i:8621419 original size:505 final size:503
Alignment explanation
Indices: 8620471--8621479 Score: 1964
Period size: 505 Copynumber: 2.0 Consensus size: 503
8620461 AGTTTTTAAT
8620471 TAATCGAGCTCTGAATTTCTTCTTCTCTGTAATTTTCTTAATTTCTTGAGATCTCTCATCATCCT
1 TAATCGAGCTCTGAATTTCTTCTTCTCTGTAATTTTCTTAATTTCTTGAGATCTCTCATCATCCT
8620536 GTTTGAAAAACCTTCTTCTCAAGCTCTCTGCTTTTTTTCTTCTCCATAATTTTCTAAATTTCTTG
66 GTTTGAAAAACCTTCTTCTCAAGCTCTCTGCTTTTTTTCTTCTCCATAATTTTCTAAATTTCTTG
*
8620601 AGATCTGGACATTACAACAAATTCAAGGTATATTTGGTGATTTTGTTTCATGAACTACAATTTAA
131 AGATCTAGACATTACAACAAATTCAAGGTATATTTGGTGATTTTGTTTCATGAACTACAATTTAA
*
8620666 AGATCCAATTTTTTTTAACTTTTCTTTCAAAATCTAGGTCTAAATTTTCCTTCTTTCTTTCAAAA
196 AAATCCAATTTTTTTTAACTTTTCTTTCAAAATCTAGGTCTAAATTTTCCTTCTTTCTTTCAAAA
8620731 TCTGGGTACTTTACCAATTTATTAAAACTTGAAATATATTGGGGAGATTTAAGGTTAGCATTTTT
261 TCTGGGTACTTTACCAATTTATTAAAACTTGAAATATATTGGGGAGATTTAAGGTTAGCATTTTT
8620796 GTGTATATATTTTCACTATTTTTTCTACTAGTAATTTTGGCTGTAAATTTACTTGCTACTGACAG
326 GTGTATATATTTTCACTATTTTTTCTACTAGTAATTTTGGCTGTAAATTTACTTGCTACTGACAG
8620861 TTTTGCTAAAACAAATATACTAGCAAAGGTAGATTTACATGGACCTCATTTCTTAGTTATCAAAA
391 TTTTGCTAAAACAAATATACTAGCAAAGGTAGATTTACATGGACCTCATTTCTTAGTTATCAAAA
8620926 GAAAACCTGAATTTTTTGTTTCAAATTCGAGTTAGACAGGGTTTGTGA
456 GAAAACCTGAATTTTTTGTTTCAAATTCGAGTTAGACAGGGTTTGTGA
8620974 TAATCGAGCTCTGAATTTCTTCTTCTCTGTAATTTTCTTAATTTCTTGAGATCTCTCATCATCCT
1 TAATCGAGCTCTGAATTTCTTCTTCTCTGTAATTTTCTTAATTTCTTGAGATCTCTCATCATCCT
*
8621039 GTTTGAGAAACCTTCTTCTCAAGCTCTCTGCTTTTTTTTCTTCTCCATAATTTTCTAAATTTCTT
66 GTTTGAAAAACCTTCTTCTCAAGCTCTCTGC-TTTTTTTCTTCTCCATAATTTTCTAAATTTCTT
*
8621104 GGGATCTAGACATTACAACAAATTCAAGGTATATTTGGTGATTTTGTTTCATGAACTACAATTTA
130 GAGATCTAGACATTACAACAAATTCAAGGTATATTTGGTGATTTTGTTTCATGAACTACAATTTA
8621169 AAAATCCAATTTTTTTTTAACTTTTCTTTCAAAATCTAGGTCTAAATTTTCCTTCTTTCTTTCAA
195 AAAATCCAA-TTTTTTTTAACTTTTCTTTCAAAATCTAGGTCTAAATTTTCCTTCTTTCTTTCAA
8621234 AATCTGGGTACTTTACCAATTTATTAAAACTTGAAATATATTGGGGAGATTTAAGGTTAGCATTT
259 AATCTGGGTACTTTACCAATTTATTAAAACTTGAAATATATTGGGGAGATTTAAGGTTAGCATTT
8621299 TTGTGTATATATTTTCACTATTTTTTCTACTAGTAATTTTGGCTGTAAATTTACTTGCTACTGAC
324 TTGTGTATATATTTTCACTATTTTTTCTACTAGTAATTTTGGCTGTAAATTTACTTGCTACTGAC
8621364 AGTTTTGCTAAAACAAATATACTAGCAAAGGTAGATTTACATGGACCTCATTTCTTAGTTATCAA
389 AGTTTTGCTAAAACAAATATACTAGCAAAGGTAGATTTACATGGACCTCATTTCTTAGTTATCAA
8621429 AAGAAAACCTGAATTTTTTGTTTCAAATTCGAGTTAGACAGGGTTTGTGA
454 AAGAAAACCTGAATTTTTTGTTTCAAATTCGAGTTAGACAGGGTTTGTGA
8621479 T
1 T
8621480 TTGTATTTTT
Statistics
Matches: 500, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
503 95 0.19
504 104 0.21
505 301 0.60
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (503 bp):
TAATCGAGCTCTGAATTTCTTCTTCTCTGTAATTTTCTTAATTTCTTGAGATCTCTCATCATCCT
GTTTGAAAAACCTTCTTCTCAAGCTCTCTGCTTTTTTTCTTCTCCATAATTTTCTAAATTTCTTG
AGATCTAGACATTACAACAAATTCAAGGTATATTTGGTGATTTTGTTTCATGAACTACAATTTAA
AAATCCAATTTTTTTTAACTTTTCTTTCAAAATCTAGGTCTAAATTTTCCTTCTTTCTTTCAAAA
TCTGGGTACTTTACCAATTTATTAAAACTTGAAATATATTGGGGAGATTTAAGGTTAGCATTTTT
GTGTATATATTTTCACTATTTTTTCTACTAGTAATTTTGGCTGTAAATTTACTTGCTACTGACAG
TTTTGCTAAAACAAATATACTAGCAAAGGTAGATTTACATGGACCTCATTTCTTAGTTATCAAAA
GAAAACCTGAATTTTTTGTTTCAAATTCGAGTTAGACAGGGTTTGTGA
Found at i:8621694 original size:34 final size:33
Alignment explanation
Indices: 8621629--8621694 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
8621619 TTAAAATATA
* * *
8621629 TTTTTTTAGAATATTTACTGTTTACATTATAAT
1 TTTTTTTACAATATTTAATGTTTACAGTATAAT
* *
8621662 TTTTTATTACAATTTTTAATGTTTACGGTATAA
1 TTTTT-TTACAATATTTAATGTTTACAGTATAA
8621695 ATATTTCTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (33 bp):
TTTTTTTACAATATTTAATGTTTACAGTATAAT
Found at i:8622031 original size:24 final size:24
Alignment explanation
Indices: 8621998--8622055 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
8621988 TATCTTGATA
* *
8621998 TTTTGGTGTTGTTTTTGCTATTAT
1 TTTTGTTGTTATTTTTGCTATTAT
* * *
8622022 TTTTGTTGTTATTTTTTCTGTTGT
1 TTTTGTTGTTATTTTTGCTATTAT
8622046 TTTTGTTGTT
1 TTTTGTTGTT
8622056 TTGCCGTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.05, C:0.03, G:0.19, T:0.72
Consensus pattern (24 bp):
TTTTGTTGTTATTTTTGCTATTAT
Found at i:8622055 original size:12 final size:12
Alignment explanation
Indices: 8621998--8622055 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
8621988 TATCTTGATA
* *
8621998 TTTTGGTGTTGT
1 TTTTGTTGTTAT
* *
8622010 TTTTGCTATTAT
1 TTTTGTTGTTAT
8622022 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
8622034 TTTT-TCTGTTGT
1 TTTTGT-TGTTAT
8622046 TTTTGTTGTT
1 TTTTGTTGTT
8622056 TTGCCGTTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
11 1 0.03
12 36 0.95
13 1 0.03
ACGTcount: A:0.05, C:0.03, G:0.19, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:8622381 original size:49 final size:45
Alignment explanation
Indices: 8622301--8622456 Score: 122
Period size: 49 Copynumber: 3.2 Consensus size: 45
8622291 TTTTATAATT
8622301 CTTTTTAATAT-TATT-ATAATTTTTATTTTTTTTAACAATTCTTTTACAA
1 CTTTTTAATATAT-TTAATAATTTTTA--TTTTTTAA-AA-T-TTTTACAA
* *
8622350 CTTTTTAATATATTTAAATAATTTTTATTTTTAAATAAATTTTA-AA
1 CTTTTTAATATATTT-AATAATTTTTATTTTTTAA-AATTTTTACAA
* *
8622396 GTTTTCTAA-ATACCTTTACTAATTTTTATATTTTTAAAGAATTTTTACAA
1 CTTTT-TAATATA--TTTAATAATTTTTAT-TTTTT-AA-AATTTTTACAA
8622446 CTTTTTAATAT
1 CTTTTTAATAT
8622457 TTTTTAAAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
46 9 0.10
47 19 0.22
48 7 0.08
49 34 0.39
50 9 0.10
51 10 0.11
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (45 bp):
CTTTTTAATATATTTAATAATTTTTATTTTTTAAAATTTTTACAA
Found at i:8628268 original size:13 final size:13
Alignment explanation
Indices: 8628250--8628275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8628240 CAGAAGAAAG
8628250 TAAAAAATAAAAA
1 TAAAAAATAAAAA
8628263 TAAAAAATAAAAA
1 TAAAAAATAAAAA
8628276 CCTAAATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:8630671 original size:19 final size:20
Alignment explanation
Indices: 8630636--8630674 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
8630626 GATTGGCTTT
8630636 ATTATAAATATTTTATAATA
1 ATTATAAATATTTTATAATA
8630656 ATTA-AAAT-TTTGTATAATA
1 ATTATAAATATTT-TATAATA
8630675 TAATCTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 11 0.61
20 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTATAAATATTTTATAATA
Found at i:8633413 original size:30 final size:30
Alignment explanation
Indices: 8633379--8633449 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
8633369 TAGCAAAATG
8633379 GGACCTGGTGGACCGGGAGGA-GGGCCG-GGA
1 GGACCTGGTGGACCGGGAGGATGGG--GAGGA
8633409 GGACCTGGTGGACCGGGAGGATGGGGAGGA
1 GGACCTGGTGGACCGGGAGGATGGGGAGGA
8633439 GGACCTGGTGG
1 GGACCTGGTGG
8633450 TTGGGGTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 1 0.03
30 35 0.90
31 3 0.08
ACGTcount: A:0.17, C:0.17, G:0.56, T:0.10
Consensus pattern (30 bp):
GGACCTGGTGGACCGGGAGGATGGGGAGGA
Found at i:8633426 original size:18 final size:18
Alignment explanation
Indices: 8633379--8633429 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
8633369 TAGCAAAATG
8633379 GGACCTGGTGGACCGGGA
1 GGACCTGGTGGACCGGGA
8633397 GGA----G-GG-CCGGGA
1 GGACCTGGTGGACCGGGA
8633409 GGACCTGGTGGACCGGGA
1 GGACCTGGTGGACCGGGA
8633427 GGA
1 GGA
8633430 TGGGGAGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 1 0.04
16 1 0.04
17 2 0.07
18 12 0.44
ACGTcount: A:0.18, C:0.20, G:0.55, T:0.08
Consensus pattern (18 bp):
GGACCTGGTGGACCGGGA
Found at i:8633538 original size:24 final size:24
Alignment explanation
Indices: 8633502--8633548 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
8633492 AGGTCCTGGT
* *
8633502 TGGGGTCCTGGGCCTGGAGGTCCC
1 TGGGGGCCAGGGCCTGGAGGTCCC
8633526 TGGGGGCCAGGGCCTGGAGGTCC
1 TGGGGGCCAGGGCCTGGAGGTCC
8633549 TGGTTTTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.28, G:0.49, T:0.17
Consensus pattern (24 bp):
TGGGGGCCAGGGCCTGGAGGTCCC
Found at i:8633708 original size:13 final size:13
Alignment explanation
Indices: 8633690--8633754 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
8633680 AATTTAACAT
* *
8633690 TGCTTTTGAGAAG
1 TGCTTTTAAAAAG
8633703 TGCTTTTAAAAAG
1 TGCTTTTAAAAAG
* *
8633716 TGCTTTGAAAAAA
1 TGCTTTTAAAAAG
*
8633729 TGATTTTAAAAAG
1 TGCTTTTAAAAAG
*
8633742 TACTTTTGAAAAA
1 TGCTTTT-AAAAA
8633755 TTTGGTTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
13 37 0.88
14 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (13 bp):
TGCTTTTAAAAAG
Found at i:8633720 original size:26 final size:26
Alignment explanation
Indices: 8633690--8633755 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
8633680 AATTTAACAT
* * *
8633690 TGCTTTTGAGAAGTGCTTTTAAAAAG
1 TGCTTTTGAAAAATGATTTTAAAAAG
8633716 TGC-TTTGAAAAAATGATTTTAAAAAG
1 TGCTTTTG-AAAAATGATTTTAAAAAG
*
8633742 TACTTTTGAAAAAT
1 TGCTTTTGAAAAAT
8633756 TTGGTTTAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.12
26 26 0.76
27 4 0.12
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (26 bp):
TGCTTTTGAAAAATGATTTTAAAAAG
Found at i:8640899 original size:31 final size:29
Alignment explanation
Indices: 8640864--8640935 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
8640854 ATACCAAAAT
* * *
8640864 TATACATGAACTATGGTTTAATGTGTAATTG
1 TATACATGAAATATGATTT--TGTGCAATTG
*
8640895 TATACATGAAATTTGATTTTGTGCAATTG
1 TATACATGAAATATGATTTTGTGCAATTG
8640924 TATACATGAAAT
1 TATACATGAAAT
8640936 TTTGATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (29 bp):
TATACATGAAATATGATTTTGTGCAATTG
Found at i:8640924 original size:29 final size:30
Alignment explanation
Indices: 8640885--8640943 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
8640875 TATGGTTTAA
*
8640885 TGTGTAATTGTATACATGAAA-TTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
8640914 TGTGCAATTGTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
8640944 GATTTAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:8651737 original size:27 final size:27
Alignment explanation
Indices: 8651714--8651768 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
8651704 AGAAGTTGAT
*
8651714 AATTTTTTTTGA-CCTTTAAAAGTTAA
1 AATTTTTTTAGACCCTTTAAAAGTTAA
*
8651740 AATTTTTTTAGACCCTTTAAAAATTAA
1 AATTTTTTTAGACCCTTTAAAAGTTAA
8651767 AA
1 AA
8651769 AAACAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (27 bp):
AATTTTTTTAGACCCTTTAAAAGTTAA
Done.