Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 30 of 33
Found at i:5471358 original size:2 final size:2
Alignment explanation
Indices: 5471351--5471380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5471341 ATATTTTCTC
5471351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5471381 CGAGTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5471937 original size:2 final size:2
Alignment explanation
Indices: 5471930--5471964 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5471920 GGGCAAAAAC
5471930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5471965 AGAATTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5473071 original size:27 final size:27
Alignment explanation
Indices: 5473033--5473086 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5473023 ATGCTTGCTT
5473033 CTATTGATGAAAAGGCAAAGTAGCTGA
1 CTATTGATGAAAAGGCAAAGTAGCTGA
5473060 CTATTGATGAAAAGGCAAAGTAGCTGA
1 CTATTGATGAAAAGGCAAAGTAGCTGA
5473087 AATTCCACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (27 bp):
CTATTGATGAAAAGGCAAAGTAGCTGA
Found at i:5473274 original size:23 final size:23
Alignment explanation
Indices: 5473243--5473306 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
5473233 TATAAAAAAA
*
5473243 TAATATTTAATAAATTTAAT-TTT
1 TAATTTTTAA-AAATTTAATATTT
*
5473266 TAATTTTTAAAATTTTAATATTT
1 TAATTTTTAAAAATTTAATATTT
* * *
5473289 TTATATTAAAAAATTTAA
1 TAATTTTTAAAAATTTAA
5473307 AAATTAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 8 0.24
23 26 0.76
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAATTTTTAAAAATTTAATATTT
Found at i:5478251 original size:17 final size:17
Alignment explanation
Indices: 5478229--5478274 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5478219 ATATATTTTT
*
5478229 ATAATTAAATTTAAATA
1 ATAATTAAAATTAAATA
5478246 ATAATTAAAATTAAAT-
1 ATAATTAAAATTAAATA
*
5478262 -TAATTTAAATTAA
1 ATAATTAAAATTAA
5478275 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATTAAATA
Found at i:5478282 original size:27 final size:28
Alignment explanation
Indices: 5478231--5478284 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5478221 ATATTTTTAT
*
5478231 AATTAAATTTAAATAATAATTAAAATTA
1 AATTAAATTTAAATAATAATAAAAATTA
5478259 AATT-AATTTAAATTAATAA-AAAAATT
1 AATTAAATTTAAA-TAATAATAAAAATT
5478285 TATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AATTAAATTTAAATAATAATAAAAATTA
Found at i:5480550 original size:23 final size:24
Alignment explanation
Indices: 5480524--5480576 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
5480514 ATTTAATTTT
5480524 ATATTATTTTA-TTAATTAA-ATTA
1 ATATTATTTTATTTAA-TAACATTA
5480547 ATATTATTTTATTTAATAACATTA
1 ATATTATTTTATTTAATAACATTA
*
5480571 ACATTA
1 ATATTA
5480577 AATTTATCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTATTTTATTTAATAACATTA
Found at i:5483262 original size:12 final size:11
Alignment explanation
Indices: 5483245--5483440 Score: 96
Period size: 12 Copynumber: 17.9 Consensus size: 11
5483235 AAAAAATTAT
5483245 AAATTATTATCA
1 AAATTA-TATCA
5483257 AAATTATA-CA
1 AAATTATATCA
*
5483267 AAATGT-TATTA
1 AAAT-TATATCA
*
5483278 AAATTATATTTA
1 AAATTATA-TCA
5483290 AAATTAT-T-A
1 AAATTATATCA
*
5483299 AAATAAATTATCA
1 AAAT-TA-TATCA
5483312 AAATTATATCAATTA
1 AAATTATATC----A
5483327 AAATTAT-T-A
1 AAATTATATCA
*
5483336 AAATTATATAAA
1 AAATTATAT-CA
5483348 AAATTAT-T-A
1 AAATTATATCA
*
5483357 AAATTATATAAA
1 AAATTATAT-CA
5483369 AAATTA-AT-A
1 AAATTATATCA
**
5483378 AAATTATAAAA
1 AAATTATATCA
5483389 TAAATTAT-T-A
1 -AAATTATATCA
*
5483399 AAATTATATTAA
1 AAATTATA-TCA
5483411 AAATTAT-T-A
1 AAATTATATCA
5483420 AAATTATATCA
1 AAATTATATCA
*
5483431 AAATCATATC
1 AAATTATATC
5483441 CAAAGTTACT
Statistics
Matches: 152, Mismatches: 6, Indels: 53
0.72 0.03 0.25
Matches are distributed among these distances:
9 43 0.28
10 17 0.11
11 30 0.20
12 48 0.32
13 5 0.03
14 1 0.01
15 8 0.05
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (11 bp):
AAATTATATCA
Found at i:5483296 original size:21 final size:21
Alignment explanation
Indices: 5483250--5483433 Score: 170
Period size: 21 Copynumber: 9.0 Consensus size: 21
5483240 ATTATAAATT
* *
5483250 ATTATCAAAATTATA-CAAAA
1 ATTATTAAAATTATATTAAAA
* *
5483270 TGTTATTAAAATTATATTTAAA
1 -ATTATTAAAATTATATTAAAA
*
5483292 ATTATTAAAA-TAAATTATCAAA
1 ATTATTAAAATTATATTA--AAA
*
5483314 ATTA-T---ATCA-ATT-AAA
1 ATTATTAAAATTATATTAAAA
*
5483329 ATTATTAAAATTATATAAAAA
1 ATTATTAAAATTATATTAAAA
*
5483350 ATTATTAAAATTATATAAAAA
1 ATTATTAAAATTATATTAAAA
* *
5483371 ATTAATAAAATTATA-AAATAA
1 ATTATTAAAATTATATTAA-AA
5483392 ATTATTAAAATTATATTAAAA
1 ATTATTAAAATTATATTAAAA
*
5483413 ATTATTAAAATTATATCAAAA
1 ATTATTAAAATTATATTAAAA
5483434 TCATATCCAA
Statistics
Matches: 137, Mismatches: 14, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
15 7 0.05
16 1 0.01
18 4 0.03
19 4 0.03
20 10 0.07
21 99 0.72
22 12 0.09
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.39
Consensus pattern (21 bp):
ATTATTAAAATTATATTAAAA
Found at i:5483318 original size:34 final size:35
Alignment explanation
Indices: 5483272--5483402 Score: 111
Period size: 34 Copynumber: 3.9 Consensus size: 35
5483262 ATACAAAATG
*
5483272 TTATTAAAATTATAT-TTAAAATTATTAAAATAAA
1 TTATCAAAATTATATATTAAAATTATTAAAATAAA
*
5483306 TTATCAAAATTATATCAATTAAAATTATTAAAAT-TA
1 TTATCAAAATTATAT--ATTAAAATTATTAAAATAAA
*
5483342 -TAT-AAAA-AAT-TATTAAAATTA-TATAAA-AAA
1 TTATCAAAATTATATATTAAAATTATTA-AAATAAA
* *
5483372 TTAAT-AAAATTATAAAAT-AAATTATTAAAAT
1 TT-ATCAAAATTATATATTAAAATTATTAAAAT
5483403 TATATTAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
29 2 0.03
30 14 0.18
31 1 0.01
32 7 0.09
33 13 0.16
34 22 0.28
35 3 0.04
36 1 0.01
37 16 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (35 bp):
TTATCAAAATTATATATTAAAATTATTAAAATAAA
Found at i:5483333 original size:37 final size:34
Alignment explanation
Indices: 5483272--5483339 Score: 100
Period size: 37 Copynumber: 1.9 Consensus size: 34
5483262 ATACAAAATG
*
5483272 TTATTAAAATTATATTTAAAATTATTAAAATAAA
1 TTATCAAAATTATATTTAAAATTATTAAAATAAA
5483306 TTATCAAAATTATATCAATTAAAATTATTAAAAT
1 TTATCAAAATTATAT---TTAAAATTATTAAAAT
5483340 TATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 14 0.47
37 16 0.53
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (34 bp):
TTATCAAAATTATATTTAAAATTATTAAAATAAA
Found at i:5483336 original size:58 final size:55
Alignment explanation
Indices: 5483234--5483360 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 55
5483224 TAGATTTTTT
* **
5483234 TAAAAAATTA-T-AAAT-TATTATCAAAATTATACAAAATGTTATTAAAATTATA
1 TAAAAAATTATTAAAATAAATTATCAAAATTATACAAAAAATTATTAAAATTATA
**
5483286 TTTAAAATTATTAAAATAAATTATCAAAATTATATCAATTAAAATTATTAAAATTATA
1 TAAAAAATTATTAAAATAAATTATCAAAATTATA-CAA--AAAATTATTAAAATTATA
5483344 TAAAAAATTATTAAAAT
1 TAAAAAATTATTAAAAT
5483361 TATATAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
52 8 0.13
53 1 0.02
54 4 0.06
55 15 0.24
56 3 0.05
58 31 0.50
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (55 bp):
TAAAAAATTATTAAAATAAATTATCAAAATTATACAAAAAATTATTAAAATTATA
Found at i:5483632 original size:6 final size:6
Alignment explanation
Indices: 5483623--5483668 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
5483613 AATTCAAGTG
* *
5483623 TGGCTG TGGCTA TGGCTA TGGCTA TGGCTA TGGTTA TGGCTA TGGC
1 TGGCTA TGGCTA TGGCTA TGGCTA TGGCTA TGGCTA TGGCTA TGGC
5483669 ATGCTCAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.13, C:0.15, G:0.37, T:0.35
Consensus pattern (6 bp):
TGGCTA
Found at i:5490353 original size:24 final size:24
Alignment explanation
Indices: 5490326--5490376 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5490316 AAAGGTTAGT
*
5490326 TTCAACAAAGCCGTCAATGTTGGC
1 TTCAACAAAGCCGTCAAAGTTGGC
* *
5490350 TTCAACAAAGCTGTCAAAGTTTGC
1 TTCAACAAAGCCGTCAAAGTTGGC
5490374 TTC
1 TTC
5490377 GTTAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (24 bp):
TTCAACAAAGCCGTCAAAGTTGGC
Found at i:5495984 original size:59 final size:59
Alignment explanation
Indices: 5495907--5496025 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 59
5495897 AATTTAAATC
* * * *
5495907 TCTTATATTAAAGACTAATGCA-CTACTATTTAATTTAAATTACTTAATTTAATAAATTT
1 TCTTAAATTAAAGACTAATACATC-ACTATTTAATTTAAATTACTTAAATTAAAAAATTT
* *
5495966 TCTTAAATTAAAGACTAATACATCATTATTTAATTTAAATTCCTTAAATTAAAAAATTT
1 TCTTAAATTAAAGACTAATACATCACTATTTAATTTAAATTACTTAAATTAAAAAATTT
5496025 T
1 T
5496026 AAATTAAACC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 52 0.98
60 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.45
Consensus pattern (59 bp):
TCTTAAATTAAAGACTAATACATCACTATTTAATTTAAATTACTTAAATTAAAAAATTT
Found at i:5501845 original size:20 final size:20
Alignment explanation
Indices: 5501822--5501864 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
5501812 TTATTATTTA
5501822 AAATTTATAAAT-AAAAAAAT
1 AAATTTA-AAATCAAAAAAAT
5501842 AAATTTAAAATCAAAAAAAT
1 AAATTTAAAATCAAAAAAAT
5501862 AAA
1 AAA
5501865 AATTAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATTTAAAATCAAAAAAAT
Found at i:5501872 original size:20 final size:19
Alignment explanation
Indices: 5501829--5501875 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
5501819 TTAAAATTTA
*
5501829 TAAAT-AAAAAAATAAATT
1 TAAATCAAAAAAATAAAAT
5501847 TAAAATCAAAAAAATAAAAAT
1 T-AAATCAAAAAAAT-AAAAT
5501868 TAAATCAA
1 TAAATCAA
5501876 TTCTCAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 4 0.16
20 15 0.60
21 5 0.20
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAATCAAAAAAATAAAAT
Found at i:5502304 original size:15 final size:15
Alignment explanation
Indices: 5502280--5502327 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
5502270 TATGTTTATA
*
5502280 TATAAATATAAATTT
1 TATAATTATAAATTT
5502295 TATAATTATAAATATT
1 TATAATTATAAAT-TT
*
5502311 TA-ATATTAAAAATTT
1 TATA-ATTATAAATTT
5502326 TA
1 TA
5502328 ATTATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTATAAATTT
Found at i:5502309 original size:29 final size:29
Alignment explanation
Indices: 5502277--5502351 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
5502267 ATTTATGTTT
*
5502277 ATATATAAATATAAATTTTATAATTA-TAA
1 ATATATAAATATAAAATTT-TAATTATTAA
*
5502306 ATAT-TTAATATTAAAAATTTTAATTATTAA
1 ATATATAAATA-T-AAAATTTTAATTATTAA
* *
5502336 ATAAATAAGTATAAAA
1 ATATATAAATATAAAA
5502352 ATATTATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
28 5 0.14
29 15 0.41
30 13 0.35
31 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
ATATATAAATATAAAATTTTAATTATTAA
Found at i:5502335 original size:16 final size:16
Alignment explanation
Indices: 5502289--5502336 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
5502279 ATATAAATAT
* *
5502289 AAATTTT-ATAATTAT
1 AAATTTTAATTATTAA
5502304 AAATATTTAA-TATTAA
1 AAAT-TTTAATTATTAA
5502320 AAATTTTAATTATTAA
1 AAATTTTAATTATTAA
5502336 A
1 A
5502337 TAAATAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 9 0.32
16 18 0.64
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTAATTATTAA
Found at i:5504388 original size:25 final size:24
Alignment explanation
Indices: 5504335--5504388 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5504325 TTTGATACAA
*
5504335 TTTTAATTTTTTTTAATTTTACTT
1 TTTTAATTTTTATTAATTTTACTT
*
5504359 ATTTAATTTTTAATTAATTTTTA-TT
1 TTTTAATTTTT-ATTAA-TTTTACTT
5504384 TTTTA
1 TTTTA
5504389 TCTTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 10 0.40
25 10 0.40
26 5 0.20
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTAATTTTTATTAATTTTACTT
Found at i:5505061 original size:11 final size:11
Alignment explanation
Indices: 5505047--5505084 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
5505037 AATTATCTTT
5505047 AATTATTATTA
1 AATTATTATTA
*
5505058 AATTA-AATTA
1 AATTATTATTA
5505068 AATTATTATTA
1 AATTATTATTA
5505079 AATTAT
1 AATTAT
5505085 ATTTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTATTATTA
Found at i:5505061 original size:21 final size:21
Alignment explanation
Indices: 5505036--5505093 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
5505026 GTTAATCTCA
*
5505036 AAATTATCTTTAATTATTATT
1 AAATTATATTTAATTATTATT
* *
5505057 AAATTAAATTAAATTATTATT
1 AAATTATATTTAATTATTATT
5505078 AAATTATATTTTAATT
1 AAATTATA-TTTAATT
5505094 TAAATACATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTATATTTAATTATTATT
Found at i:5505087 original size:10 final size:10
Alignment explanation
Indices: 5505036--5505087 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
5505026 GTTAATCTCA
*
5505036 AAATTATCTT
1 AAATTATATT
*
5505046 TAATTATTATT
1 AAATTA-TATT
*
5505057 AAATTAAATT
1 AAATTATATT
5505067 AAATTATTATT
1 AAATTA-TATT
5505078 AAATTATATT
1 AAATTATATT
5505088 TTAATTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATTATATT
Found at i:5511931 original size:13 final size:13
Alignment explanation
Indices: 5511913--5511937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5511903 AACAGCTCAT
5511913 TCTTTGCACAATC
1 TCTTTGCACAATC
5511926 TCTTTGCACAAT
1 TCTTTGCACAAT
5511938 TCAATTGTAA
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:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (13 bp):
TCTTTGCACAATC
Found at i:5512810 original size:43 final size:44
Alignment explanation
Indices: 5512720--5512811 Score: 100
Period size: 43 Copynumber: 2.1 Consensus size: 44
5512710 AAAAATTTTT
* * **
5512720 AAAAATTACTAAAATTAAAATAATTTTATTCAAATAATTAATTA
1 AAAAATTACTAAAATTAAAATAATTTAATTCAAATAACTAAGCA
*
5512764 AAAAATT-GTAAAA-TAAAATTAATATTAATT-AAATAACTAAGCA
1 AAAAATTACTAAAATTAAAA-TAAT-TTAATTCAAATAACTAAGCA
5512807 AAAAA
1 AAAAA
5512812 AATAAATAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
42 5 0.12
43 24 0.59
44 12 0.29
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (44 bp):
AAAAATTACTAAAATTAAAATAATTTAATTCAAATAACTAAGCA
Found at i:5516261 original size:20 final size:20
Alignment explanation
Indices: 5516238--5516277 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5516228 TTTAGTATAT
* * *
5516238 TTTTATTATTTTATAATAAA
1 TTTTACTATTATAAAATAAA
5516258 TTTTACTATTATAAAATAAA
1 TTTTACTATTATAAAATAAA
5516278 CAGATAAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTTACTATTATAAAATAAA
Found at i:5517265 original size:16 final size:15
Alignment explanation
Indices: 5517239--5517275 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
5517229 TATTTAATTT
5517239 TTTTAAAAAAATTATA
1 TTTT-AAAAAATTATA
5517255 TATTTAAAAAATTATA
1 T-TTTAAAAAATTATA
5517271 TTTTA
1 TTTTA
5517276 CATGCATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 13 0.65
17 3 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAAAAAATTATA
Found at i:5525670 original size:20 final size:20
Alignment explanation
Indices: 5525647--5525688 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5525637 ATGTTTATAT
*
5525647 ATATTAT-TTATTATATTAAA
1 ATATTATATAATTATA-TAAA
5525667 ATATTATATAATTATATAAA
1 ATATTATATAATTATATAAA
5525687 AT
1 AT
5525689 TTGATATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATATAATTATATAAA
Found at i:5526831 original size:56 final size:56
Alignment explanation
Indices: 5526765--5526875 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
5526755 ATTTGAAGGA
5526765 TTCAGGTGGGAATCTGCTGCCACTTCCACAAGGCATGAGTCCACTAATCTAGCAAG
1 TTCAGGTGGGAATCTGCTGCCACTTCCACAAGGCATGAGTCCACTAATCTAGCAAG
*
5526821 TTCAGGTGGGAATCTGCTGCCACTTCCACAAGGTATGAGTCCACTAATCTAGCAA
1 TTCAGGTGGGAATCTGCTGCCACTTCCACAAGGCATGAGTCCACTAATCTAGCAA
5526876 CTTTTCTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (56 bp):
TTCAGGTGGGAATCTGCTGCCACTTCCACAAGGCATGAGTCCACTAATCTAGCAAG
Found at i:5532846 original size:2 final size:2
Alignment explanation
Indices: 5532839--5532872 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
5532829 AAAATAAAAA
*
5532839 TC TC TC TC GC TC TC TC TC TC TC TC TC TGC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC T
5532873 AGAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.00, C:0.47, G:0.06, T:0.47
Consensus pattern (2 bp):
TC
Found at i:5532943 original size:2 final size:2
Alignment explanation
Indices: 5532932--5532964 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5532922 ATAAATAGGG
5532932 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5532965 GTCTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5538785 original size:13 final size:14
Alignment explanation
Indices: 5538767--5538796 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
5538757 TAAATAAAAT
5538767 ATAAAATAAT-TAA
1 ATAAAATAATATAA
5538780 ATAAAATAATATAA
1 ATAAAATAATATAA
5538794 ATA
1 ATA
5538797 TGATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAAATAATATAA
Found at i:5538788 original size:29 final size:28
Alignment explanation
Indices: 5538759--5538824 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
5538749 ACACGATATA
5538759 AATA-AAATATAAAATAATTAAATAAAAT
1 AATATAAATATAAAATAA-TAAATAAAAT
* * *
5538787 AATATAAATATGATATAATAAATATAAAA
1 AATATAAATATAAAATAATAAATA-AAAT
5538816 ACATATAAA
1 A-ATATAAA
5538825 ATTTATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.31
29 15 0.47
30 7 0.22
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
AATATAAATATAAAATAATAAATAAAAT
Found at i:5538907 original size:19 final size:19
Alignment explanation
Indices: 5538885--5538923 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5538875 GTATTATTAT
* *
5538885 AAATATAATTATAACATAA
1 AAATACAATAATAACATAA
*
5538904 AAATACAATAATAATATAA
1 AAATACAATAATAACATAA
5538923 A
1 A
5538924 TAAATAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATACAATAATAACATAA
Found at i:5539912 original size:12 final size:10
Alignment explanation
Indices: 5539884--5539917 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5539874 AAAATTAAAA
*
5539884 TTAAAATTTT
1 TTAATATTTT
5539894 TTAATATTTT
1 TTAATATTTT
*
5539904 TTAATATATT
1 TTAATATTTT
5539914 TTAA
1 TTAA
5539918 CATTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTAATATTTT
Found at i:5546322 original size:13 final size:13
Alignment explanation
Indices: 5546304--5546328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5546294 GGTGTCGCCA
5546304 AAAAAGAAAACTT
1 AAAAAGAAAACTT
5546317 AAAAAGAAAACT
1 AAAAAGAAAACT
5546329 CTATTCATTA
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:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAAGAAAACTT
Found at i:5549135 original size:2 final size:2
Alignment explanation
Indices: 5549130--5549158 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5549120 AAAAAAAGGA
5549130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5549159 GCAAATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5549233 original size:7 final size:7
Alignment explanation
Indices: 5549221--5549248 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
5549211 CCATTTAACT
5549221 TCACAGC
1 TCACAGC
5549228 TCACAGC
1 TCACAGC
5549235 TCACAGC
1 TCACAGC
5549242 TCACAGC
1 TCACAGC
5549249 ACAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.43, G:0.14, T:0.14
Consensus pattern (7 bp):
TCACAGC
Found at i:5567864 original size:14 final size:15
Alignment explanation
Indices: 5567841--5567894 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
5567831 ATTCATATTA
5567841 AATTATATTTTAATT
1 AATTATATTTTAATT
*
5567856 AATTA-ATTTTATTT
1 AATTATATTTTAATT
* *
5567870 AA-AATATTTTTATAT
1 AATTATATTTTAAT-T
5567885 AATTATATTT
1 AATTATATTT
5567895 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.03
14 16 0.52
15 8 0.26
16 6 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATTATATTTTAATT
Found at i:5567864 original size:44 final size:45
Alignment explanation
Indices: 5567792--5567894 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 45
5567782 ACATAAATAA
* *
5567792 ATAAATT-TATTTTTATATTTATATAATTTTATATAAATTATTCAT
1 ATAAATTATA-TTTTATATTAATATAATTTTATATAAAATATTCAT
* **
5567837 ATTAAATTATATTTTA-ATTAAT-TAATTTTATTTAAAATATTTTT
1 A-TAAATTATATTTTATATTAATATAATTTTATATAAAATATTCAT
5567881 ATATAATTATATTT
1 ATA-AATTATATTT
5567895 ATTTTTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 2 0.04
44 29 0.58
45 6 0.12
46 11 0.22
47 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (45 bp):
ATAAATTATATTTTATATTAATATAATTTTATATAAAATATTCAT
Found at i:5567868 original size:29 final size:30
Alignment explanation
Indices: 5567845--5567898 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
5567835 ATATTAAATT
5567845 ATATTTTAAT-TAATTA-ATTTTATTTAAA
1 ATATTTTAATATAATTATATTTTATTTAAA
*
5567873 ATATTTTTATATAATTATA-TTTATTT
1 ATATTTTAATATAATTATATTTTATTT
5567899 TTAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
28 9 0.39
29 13 0.57
30 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
ATATTTTAATATAATTATATTTTATTTAAA
Found at i:5567872 original size:30 final size:32
Alignment explanation
Indices: 5567798--5567907 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 32
5567788 ATAAATAAAT
* *
5567798 TTATTTTTATATTTATATA-ATTTT-ATATAA
1 TTATATTTATATTTAAATATATTTTAATATAA
* *
5567828 AT-TATTCATA-TTAAATTATATTTTAAT-TAA
1 TTATATTTATATTTAAA-TATATTTTAATATAA
*
5567858 TTA-ATTT-TATTTAAA-ATATTTTTATATAA
1 TTATATTTATATTTAAATATATTTTAATATAA
*
5567887 TTATATTTATTTTTAAATATA
1 TTATATTTATATTTAAATATA
5567908 ATATATAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
28 13 0.21
29 16 0.25
30 22 0.35
31 9 0.14
32 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
TTATATTTATATTTAAATATATTTTAATATAA
Found at i:5568358 original size:19 final size:18
Alignment explanation
Indices: 5568339--5568404 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
5568329 ATTAATTTTA
5568339 AAATATAAATATAATATT
1 AAATATAAATATAATATT
*
5568357 AATTATTAAATATTAAAATATT
1 AAATA-TAAATA-T--AATATT
*
5568379 AAATATAAATAAATATATT
1 AAATATAAATATA-ATATT
5568398 AAATATA
1 AAATATA
5568405 TTATATTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 5 0.12
19 18 0.45
20 1 0.03
21 6 0.15
22 10 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATAAATATAATATT
Found at i:5568363 original size:7 final size:7
Alignment explanation
Indices: 5568339--5568403 Score: 61
Period size: 7 Copynumber: 9.9 Consensus size: 7
5568329 ATTAATTTTA
5568339 AAATA-T
1 AAATATT
5568345 AAATA-T
1 AAATATT
5568351 -AATATT
1 AAATATT
*
5568357 AATTATT
1 AAATATT
5568364 AAATATT
1 AAATATT
5568371 AAAATATT
1 -AAATATT
5568379 AAATA-T
1 AAATATT
5568385 AAATA--
1 AAATATT
5568390 AATATATT
1 AA-ATATT
5568398 AAATAT
1 AAATAT
5568404 ATTATATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
5 6 0.12
6 16 0.31
7 20 0.39
8 9 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:5568382 original size:34 final size:33
Alignment explanation
Indices: 5568326--5568403 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 33
5568316 TTATATTTTT
* *
5568326 TATATT-AATTTTAAAATATAAATATAATATTAA
1 TATATTAAATATTAAAATATAAATATAA-ATAAA
5568359 T-TATTAAATATTAAAATATTAAATATAAATAAA
1 TATATTAAATATTAAAATA-TAAATATAAATAAA
5568392 TATATTAAATAT
1 TATATTAAATAT
5568404 ATTATATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 4 0.10
33 17 0.43
34 19 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
TATATTAAATATTAAAATATAAATATAAATAAA
Found at i:5568387 original size:14 final size:14
Alignment explanation
Indices: 5568327--5568418 Score: 59
Period size: 14 Copynumber: 6.9 Consensus size: 14
5568317 TATATTTTTT
* *
5568327 ATATTAATTTTAAA
1 ATATTAAATATAAA
5568341 ATA-TAAATAT--A
1 ATATTAAATATAAA
* *
5568352 ATATTAATTATTAA
1 ATATTAAATATAAA
*
5568366 ATATTAAAATATTAA
1 ATATT-AAATATAAA
*
5568381 ATA-TAAATA-AAT
1 ATATTAAATATAAA
**
5568393 ATATTAAATATATT
1 ATATTAAATATAAA
*
5568407 ATATTAATTATA
1 ATATTAAATATA
5568419 TTTAAATATT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
11 4 0.06
12 10 0.16
13 16 0.25
14 23 0.36
15 11 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTAAATATAAA
Found at i:5568402 original size:9 final size:9
Alignment explanation
Indices: 5568366--5568407 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
5568356 TAATTATTAA
5568366 ATATTAAA-
1 ATATTAAAT
5568374 ATATTAAAT
1 ATATTAAAT
*
5568383 ATAAATAAAT
1 AT-ATTAAAT
5568393 ATATTAAAT
1 ATATTAAAT
5568402 ATATTA
1 ATATTA
5568408 TATTAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
8 8 0.27
9 14 0.47
10 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATATTAAAT
Found at i:5568419 original size:14 final size:14
Alignment explanation
Indices: 5568392--5568449 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
5568382 TATAAATAAA
*
5568392 TATATTAAATATAT
1 TATATTAATTATAT
5568406 TATATTAATTATATT
1 TATATTAATTATA-T
5568421 TAAATATT--TTATAT
1 T--ATATTAATTATAT
*
5568435 TATATTTATTATAT
1 TATATTAATTATAT
5568449 T
1 T
5568450 TAAATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 5 0.13
14 21 0.55
15 7 0.18
17 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATTAATTATAT
Found at i:5568423 original size:24 final size:25
Alignment explanation
Indices: 5568391--5568467 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 25
5568381 ATATAAATAA
5568391 ATATATTAAATATATTATATTA-ATT
1 ATAT-TTAAATATATTATATTATATT
*
5568416 ATATTTAAATATTTTATATTATATTTATT
1 ATATTTAAATATATTATA-T-TA--TATT
5568445 ATATTTAAATAT-TT-TATTATATT
1 ATATTTAAATATATTATATTATATT
5568468 TTTAATGGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
23 4 0.09
24 13 0.28
25 7 0.15
26 3 0.07
27 2 0.04
28 2 0.04
29 15 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTTAAATATATTATATTATATT
Found at i:5568425 original size:33 final size:33
Alignment explanation
Indices: 5568360--5568456 Score: 103
Period size: 29 Copynumber: 3.0 Consensus size: 33
5568350 TAATATTAAT
** * **
5568360 TATTAAATATTAAAATATTAAATATAAATAAATA
1 TATTAAATA-TATTATATTAATTATATTTAAATA
5568394 TATTAAATATATTATATTAATTATATTTAAATA
1 TATTAAATATATTATATTAATTATATTTAAATA
*
5568427 T-TT---TATATTATATTTATTATATTTAAATA
1 TATTAAATATATTATATTAATTATATTTAAATA
5568456 T
1 T
5568457 TTTATTATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 26 0.46
32 2 0.04
33 20 0.35
34 9 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TATTAAATATATTATATTAATTATATTTAAATA
Found at i:5568462 original size:18 final size:17
Alignment explanation
Indices: 5568407--5568468 Score: 71
Period size: 18 Copynumber: 3.9 Consensus size: 17
5568397 TAAATATATT
*
5568407 ATATTAATTATATTTAA
1 ATATTTATTATATTTAA
5568424 ATA-TT-TTATA-TT--
1 ATATTTATTATATTTAA
5568436 ATATTTATTATATTTAA
1 ATATTTATTATATTTAA
5568453 ATATTTTATTATATTT
1 ATA-TTTATTATATTT
5568469 TTAATGGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 7 0.18
15 7 0.18
16 1 0.03
17 6 0.16
18 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTTATTATATTTAA
Found at i:5568471 original size:29 final size:29
Alignment explanation
Indices: 5568401--5568468 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
5568391 ATATATTAAA
*
5568401 TATATTATATTAATTATATTTAAATATTT
1 TATATTATATTTATTATATTTAAATATTT
5568430 TATATTATATTTATTATATTTAAATA-TT
1 TATATTATATTTATTATATTTAAATATTT
5568458 T-TATTATATTT
1 TATATTATATTT
5568469 TTAATGGTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 10 0.26
28 3 0.08
29 25 0.66
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TATATTATATTTATTATATTTAAATATTT
Found at i:5569450 original size:3 final size:3
Alignment explanation
Indices: 5569442--5569471 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5569432 AATGCAGATG
5569442 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5569472 AACAACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5569853 original size:8 final size:8
Alignment explanation
Indices: 5569840--5569867 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5569830 TATTGATTCG
5569840 ATTATAAA
1 ATTATAAA
5569848 ATTATAAA
1 ATTATAAA
5569856 ATTATAAA
1 ATTATAAA
5569864 ATTA
1 ATTA
5569868 ATTAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTATAAA
Found at i:5570704 original size:19 final size:19
Alignment explanation
Indices: 5570677--5570790 Score: 58
Period size: 19 Copynumber: 5.8 Consensus size: 19
5570667 ATTAATACAT
*
5570677 TTATTTTATATTTATTTTA
1 TTATATTATATTTATTTTA
*
5570696 TTATATTATAATTT-TTAAAATA
1 TTATATTAT-ATTTATT---TTA
**
5570718 TTTATATTATATTTAAATTA
1 -TTATATTATATTTATTTTA
5570738 TT-T-TTATATATTATATTTA
1 TTATATTATAT-TTAT-TTTA
*
5570757 -TATAATTATATTTAATATTA
1 TTAT-ATTATATTT-ATTTTA
*
5570777 TTAAATT-TATTTAT
1 TTATATTATATTTAT
5570791 AAATATTTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 27
0.67 0.08 0.25
Matches are distributed among these distances:
17 6 0.08
18 7 0.10
19 21 0.29
20 14 0.19
21 10 0.14
22 6 0.08
23 9 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTATATTTATTTTA
Found at i:5570709 original size:16 final size:14
Alignment explanation
Indices: 5570682--5570801 Score: 56
Period size: 14 Copynumber: 8.8 Consensus size: 14
5570672 TACATTTATT
5570682 TTATATTTATTTTA
1 TTATATTTATTTTA
*
5570696 TTATATTATAATTT-
1 TTATATT-TATTTTA
**
5570710 TTA-AAATATTTATA
1 TTATATTTATTT-TA
*
5570724 TTATATTTA---AA
1 TTATATTTATTTTA
* *
5570735 TTATTTTTA-TATA
1 TTATATTTATTTTA
* *
5570748 TTATATTTATATAA
1 TTATATTTATTTTA
*
5570762 TTATATTTAATATTA
1 TTATATTT-ATTTTA
*
5570777 TTAAATTTA-TTTA
1 TTATATTTATTTTA
*
5570790 TAAATATTTATT
1 T-TATATTTATT
5570802 AAAATTTTTA
Statistics
Matches: 78, Mismatches: 18, Indels: 19
0.68 0.16 0.17
Matches are distributed among these distances:
11 9 0.12
12 4 0.05
13 15 0.19
14 29 0.37
15 21 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATTTATTTTA
Found at i:5570758 original size:11 final size:11
Alignment explanation
Indices: 5570675--5570777 Score: 71
Period size: 11 Copynumber: 10.0 Consensus size: 11
5570665 TAATTAATAC
*
5570675 ATTTATTTTAT
1 ATTTATATTAT
5570686 ATTTAT-TT-T
1 ATTTATATTAT
5570695 A-TTATATTAT
1 ATTTATATTAT
* **
5570705 AATTTTTAAAAT
1 -ATTTATATTAT
5570717 ATTTATATTAT
1 ATTTATATTAT
*
5570728 ATTTAAATTAT
1 ATTTATATTAT
5570739 -TTT-TA-TAT
1 ATTTATATTAT
5570747 A-TTATATT-T
1 ATTTATATTAT
*
5570756 ATATA-ATTAT
1 ATTTATATTAT
5570766 ATTTAATATTAT
1 ATTT-ATATTAT
5570778 TAAATTTATT
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
8 9 0.13
9 12 0.17
10 13 0.18
11 26 0.37
12 11 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:5570778 original size:24 final size:22
Alignment explanation
Indices: 5570708--5570789 Score: 59
Period size: 20 Copynumber: 3.7 Consensus size: 22
5570698 ATATTATAAT
5570708 TTTTAAA--ATATTT-ATATTA
1 TTTTAAATTATATTTAATATTA
*
5570727 TATTTAAATTATTTTTATATATTATA
1 T-TTTAAATTATATTTA-ATA-T-TA
5570753 TTTATATAATTATATTTAATATTA
1 TTT-TA-AATTATATTTAATATTA
5570777 --TTAAATT-TATTTA
1 TTTTAAATTATATTTA
5570790 TAAATATTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
19 7 0.13
20 10 0.19
21 2 0.04
22 6 0.12
24 5 0.10
25 4 0.08
26 8 0.15
27 10 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAATTATATTTAATATTA
Found at i:5570811 original size:22 final size:22
Alignment explanation
Indices: 5570770--5570821 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
5570760 AATTATATTT
*
5570770 AATATTATTAAATTTATTTATA
1 AATATTATTAAAATTATTTATA
*
5570792 AATATTTATTAAAATT-TTTATTT
1 AATA-TTATTAAAATTATTTA-TA
5570815 AATATTA
1 AATATTA
5570822 ATTTTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTATTAAAATTATTTATA
Found at i:5570818 original size:23 final size:24
Alignment explanation
Indices: 5570716--5570820 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
5570706 ATTTTTAAAA
*
5570716 TATTT-ATATTATATTTAAATTA-T
1 TATTTAATATT-TATTAAAATTATT
* * *
5570739 T-TTTATATATTATATTTATATAATT
1 TATTTA-ATATT-TATTAAAATTATT
*
5570764 ATATTTAATA-TTATTAAATTTATT
1 -TATTTAATATTTATTAAAATTATT
*
5570788 TA-TAAATATTTATTAAAATT-TT
1 TATTTAATATTTATTAAAATTATT
5570810 TATTTAATATT
1 TATTTAATATT
5570821 AATTTTTACA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
22 12 0.18
23 20 0.30
24 24 0.36
25 2 0.03
26 4 0.06
27 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTAATATTTATTAAAATTATT
Found at i:5571405 original size:8 final size:7
Alignment explanation
Indices: 5571380--5571410 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
5571370 CATTTTATAA
5571380 TAAAATT
1 TAAAATT
5571387 TAAAATT
1 TAAAATT
5571394 TAAAATTT
1 TAAAA-TT
5571402 TAAAATT
1 TAAAATT
5571409 TA
1 TA
5571411 CATTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAAATT
Found at i:5571405 original size:15 final size:14
Alignment explanation
Indices: 5571380--5571410 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
5571370 CATTTTATAA
5571380 TAAAATTTAAAATT
1 TAAAATTTAAAATT
5571394 TAAAATTTTAAAATT
1 TAAAA-TTTAAAATT
5571409 TA
1 TA
5571411 CATTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTTAAAATT
Found at i:5580107 original size:2 final size:2
Alignment explanation
Indices: 5580100--5580129 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5580090 TAAAATTCAA
*
5580100 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5580130 TTTCAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5581450 original size:65 final size:65
Alignment explanation
Indices: 5581346--5581482 Score: 265
Period size: 65 Copynumber: 2.1 Consensus size: 65
5581336 ATATAATGGT
5581346 AAAAATAAATAATAAAAAAAGTTGTCAAACTATAACTCCATAAACTTGTGAGGAAATGAGTTGAG
1 AAAAATAAATAATAAAAAAAGTTGTCAAACTATAACTCCATAAACTTGTGAGGAAATGAGTTGAG
*
5581411 AAAAATAAATAATAAAAAAAGTTGTCAAACTATAACTCCATAAACTTGTGAGGAAATGAGTTGGG
1 AAAAATAAATAATAAAAAAAGTTGTCAAACTATAACTCCATAAACTTGTGAGGAAATGAGTTGAG
5581476 AAAAATA
1 AAAAATA
5581483 CGTAGACTTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 71 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (65 bp):
AAAAATAAATAATAAAAAAAGTTGTCAAACTATAACTCCATAAACTTGTGAGGAAATGAGTTGAG
Found at i:5582808 original size:2 final size:2
Alignment explanation
Indices: 5582803--5582828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5582793 TATTTTTTTT
5582803 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
5582829 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5584302 original size:32 final size:33
Alignment explanation
Indices: 5584240--5584307 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
5584230 TTGATTAAAC
* *
5584240 TATTTTTATTTATAAAATTAATTATTAAAATAT
1 TATTATTATTTATAAAATTAATTATCAAAATAT
5584273 TATTATTATTT-TAAAA-TAATTTATCAAAATAT
1 TATTATTATTTATAAAATTAA-TTATCAAAATAT
5584305 TAT
1 TAT
5584308 CATTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 3 0.09
32 19 0.59
33 10 0.31
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
TATTATTATTTATAAAATTAATTATCAAAATAT
Found at i:5584517 original size:21 final size:20
Alignment explanation
Indices: 5584477--5584518 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
5584467 AGTAAGTGAG
*
5584477 TTTTTTTTTAAAGATTTATT
1 TTTTTTTTTAAAGATATATT
5584497 TTTTTATTTTATAA-ATATATT
1 TTTTT-TTTTA-AAGATATATT
5584518 T
1 T
5584519 AATTGTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 12 0.63
22 2 0.11
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTTTTTAAAGATATATT
Found at i:5584678 original size:11 final size:11
Alignment explanation
Indices: 5584657--5584710 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
5584647 GATATGAAAA
5584657 TTTAT-TATTT
1 TTTATATATTT
5584667 TTTATATATTT
1 TTTATATATTT
5584678 TTTATCATA-TT
1 TTTAT-ATATTT
*
5584689 TATAT-TATTT
1 TTTATATATTT
5584699 TTATATCATATT
1 TT-TAT-ATATT
5584711 CGTACTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 2 0.06
10 8 0.22
11 19 0.53
12 3 0.08
13 4 0.11
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATATTT
Found at i:5584692 original size:20 final size:22
Alignment explanation
Indices: 5584667--5584710 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5584657 TTTATTATTT
5584667 TTTATA-TATTTTT-TATCATA
1 TTTATATTATTTTTATATCATA
5584687 TTTATATTATTTTTATATCATA
1 TTTATATTATTTTTATATCATA
5584709 TT
1 TT
5584711 CGTACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
22 9 0.41
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTATATTATTTTTATATCATA
Found at i:5584721 original size:22 final size:21
Alignment explanation
Indices: 5584673--5584724 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
5584663 ATTTTTTATA
*
5584673 TATTTTTTATCATATTTATAT
1 TATTTTTTATCATATTCATAT
*
5584694 TATTTTTATATCATATTCGTACT
1 TATTTTT-TATCATATTCATA-T
5584717 T-TTTTTTA
1 TATTTTTTA
5584725 GTGTCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (21 bp):
TATTTTTTATCATATTCATAT
Found at i:5584851 original size:20 final size:20
Alignment explanation
Indices: 5584826--5584871 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
5584816 TTAATATTAA
*
5584826 TTTTTATATTAAATTTATAT
1 TTTTTATATCAAATTTATAT
*
5584846 TTTTTATATCATATTTATAT
1 TTTTTATATCAAATTTATAT
5584866 TATTTT
1 T-TTTT
5584872 TTACCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATATCAAATTTATAT
Found at i:5592209 original size:3 final size:3
Alignment explanation
Indices: 5592203--5592244 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
5592193 TAAAAAAATG
* *
5592203 TAA TAA TAA TAA TAA T-A GAA TAA TAA CAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5592245 TAAAGATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5597913 original size:26 final size:26
Alignment explanation
Indices: 5597884--5597938 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
5597874 GTCAATTATA
5597884 ATTCCATAAGACATAACATTACAAAC
1 ATTCCATAAGACATAACATTACAAAC
*
5597910 ATTCCATAAGACATAACGTTACAAAC
1 ATTCCATAAGACATAACATTACAAAC
5597936 ATT
1 ATT
5597939 ACAAATCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.22, G:0.05, T:0.25
Consensus pattern (26 bp):
ATTCCATAAGACATAACATTACAAAC
Found at i:5600125 original size:32 final size:32
Alignment explanation
Indices: 5600088--5600175 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 32
5600078 AAATAATTAA
*
5600088 AATATAAATATAATAAATATTTAATTATATAT
1 AATATAAATATATTAAATATTTAATTATATAT
*
5600120 AATATAAA-ATATTAAAT-TTT-A-TATACAT
1 AATATAAATATATTAAATATTTAATTATATAT
*
5600148 AA-AT-AATATCTTAAATA--TAATTATATAT
1 AATATAAATATATTAAATATTTAATTATATAT
5600176 TACATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 3 0.06
27 11 0.23
28 14 0.29
29 1 0.02
30 3 0.06
31 8 0.17
32 8 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATAAATATATTAAATATTTAATTATATAT
Found at i:5600129 original size:24 final size:24
Alignment explanation
Indices: 5600089--5600174 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
5600079 AATAATTAAA
5600089 ATATA-AATATAATAAATATTTAATT
1 ATATATAATAT-A-AAATATTTAATT
*
5600114 ATATATAATATAAAATATTAAATT
1 ATATATAATATAAAATATTTAATT
* *
5600138 TTATATACATA-AATAATATCTTAAAT
1 ATATATA-ATATAA-AATAT-TTAATT
*
5600164 ATA-ATTATATA
1 ATATATAATATA
5600175 TTACATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
24 22 0.44
25 17 0.34
26 11 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATAATATAAAATATTTAATT
Found at i:5600732 original size:19 final size:17
Alignment explanation
Indices: 5600707--5600754 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
5600697 TATTTTAAAA
5600707 AATTTAAATAAAAATATT
1 AATTTAAATAAAAAT-TT
5600725 ATATTTAAA-AATAAATTT
1 A-ATTTAAATAA-AAATTT
5600743 AA-TTAAATAAAA
1 AATTTAAATAAAA
5600755 TATAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.26
17 3 0.11
18 6 0.22
19 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAATAAAAATTT
Found at i:5601342 original size:22 final size:22
Alignment explanation
Indices: 5601317--5601359 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5601307 TATAAAAAAT
* *
5601317 TTAAAATTAATTTAATTTTATA
1 TTAAAATAAATGTAATTTTATA
*
5601339 TTAATATAAATGTAATTTTAT
1 TTAAAATAAATGTAATTTTAT
5601360 TTATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAAAATAAATGTAATTTTATA
Found at i:5601365 original size:20 final size:22
Alignment explanation
Indices: 5601329--5601372 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
5601319 AAAATTAATT
5601329 TAATTTTATATTAATATAAATG
1 TAATTTTATATTAATATAAATG
*
5601351 TAATTTTAT-TT-ATATATATG
1 TAATTTTATATTAATATAAATG
5601371 TA
1 TA
5601373 TTAGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TAATTTTATATTAATATAAATG
Found at i:5602160 original size:2 final size:2
Alignment explanation
Indices: 5602148--5602190 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
5602138 CAACGAATCA
5602148 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5602191 TGTTGAGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5602639 original size:33 final size:33
Alignment explanation
Indices: 5602602--5602699 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
5602592 ATCTCCTGTG
* *
5602602 ATTTATTTATTTTTAGCTGATAATAATTTATCA
1 ATTTATTTATTTTTATCTAATAATAATTTATCA
*
5602635 ATTTATTTATCTTTATCTAATAATAATTTATCA
1 ATTTATTTATTTTTATCTAATAATAATTTATCA
* *
5602668 ATTTATTTATTTTAATTTAATAATAATTTATC
1 ATTTATTTATTTTTATCTAATAATAATTTATC
5602700 TGATAAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (33 bp):
ATTTATTTATTTTTATCTAATAATAATTTATCA
Found at i:5603584 original size:24 final size:25
Alignment explanation
Indices: 5603533--5603602 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 25
5603523 ATAATATGAT
*
5603533 TATTCATTTAAAATTTAATTAAAATAA
1 TATT-ATTT-AAATTTTATTAAAATAA
* *
5603560 T-TTATTTAAATTTTATTTAATTAA
1 TATTATTTAAATTTTATTAAAATAA
*
5603584 TATT-TTTATTATTTTATTA
1 TATTATTTA-AATTTTATTA
5603603 TTTATTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
24 19 0.53
25 14 0.39
26 2 0.06
27 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTATTTAAATTTTATTAAAATAA
Found at i:5603595 original size:20 final size:21
Alignment explanation
Indices: 5603572--5603612 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5603562 TATTTAAATT
5603572 TTATTTAATTA-ATATTTTTA
1 TTATTTAATTATATATTTTTA
* *
5603592 TTATTTTATTATTTATTTTTA
1 TTATTTAATTATATATTTTTA
5603613 AATAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTTAATTATATATTTTTA
Found at i:5605981 original size:15 final size:15
Alignment explanation
Indices: 5605952--5605980 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5605942 TTTTTGAAGC
5605952 TTTTCCCAGGAAAAA
1 TTTTCCCAGGAAAAA
5605967 TTTT-CCAGGAAAAA
1 TTTTCCCAGGAAAAA
5605981 AAAGGAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (15 bp):
TTTTCCCAGGAAAAA
Found at i:5608641 original size:151 final size:151
Alignment explanation
Indices: 5608367--5608672 Score: 612
Period size: 151 Copynumber: 2.0 Consensus size: 151
5608357 TTACTGTAGC
5608367 ATACCGTAAATAGGGATTGGGTTCAAGACAACTACAAATCTTGAATACACCTTTGATCATATGAT
1 ATACCGTAAATAGGGATTGGGTTCAAGACAACTACAAATCTTGAATACACCTTTGATCATATGAT
5608432 AAGAAACATTGAATACTGCCAAGTGGGATCTTAGAACCAACATTTTCAAACAAGACATCTAGAAG
66 AAGAAACATTGAATACTGCCAAGTGGGATCTTAGAACCAACATTTTCAAACAAGACATCTAGAAG
5608497 ATCTTTGATACCTTAAAACTG
131 ATCTTTGATACCTTAAAACTG
5608518 ATACCGTAAATAGGGATTGGGTTCAAGACAACTACAAATCTTGAATACACCTTTGATCATATGAT
1 ATACCGTAAATAGGGATTGGGTTCAAGACAACTACAAATCTTGAATACACCTTTGATCATATGAT
5608583 AAGAAACATTGAATACTGCCAAGTGGGATCTTAGAACCAACATTTTCAAACAAGACATCTAGAAG
66 AAGAAACATTGAATACTGCCAAGTGGGATCTTAGAACCAACATTTTCAAACAAGACATCTAGAAG
5608648 ATCTTTGATACCTTAAAACTG
131 ATCTTTGATACCTTAAAACTG
5608669 ATAC
1 ATAC
5608673 GTCAGAATTT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 155 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (151 bp):
ATACCGTAAATAGGGATTGGGTTCAAGACAACTACAAATCTTGAATACACCTTTGATCATATGAT
AAGAAACATTGAATACTGCCAAGTGGGATCTTAGAACCAACATTTTCAAACAAGACATCTAGAAG
ATCTTTGATACCTTAAAACTG
Found at i:5609464 original size:20 final size:20
Alignment explanation
Indices: 5609439--5609476 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5609429 AATTTCAGCT
5609439 AACTTTTG-AGCAAGACTGGC
1 AACTTTTGTAGCAA-ACTGGC
5609459 AACTTTTGTAGCAAACTG
1 AACTTTTGTAGCAAACTG
5609477 TTCCAGTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
AACTTTTGTAGCAAACTGGC
Found at i:5613345 original size:2 final size:2
Alignment explanation
Indices: 5613332--5613372 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
5613322 CTAGATATGG
* *
5613332 TA TA TG TA TA TA TA T- TT 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
5613373 CACACACTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5615118 original size:2 final size:2
Alignment explanation
Indices: 5615111--5615140 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5615101 CCATGTCGGT
5615111 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5615141 GCGTAGCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5620341 original size:35 final size:35
Alignment explanation
Indices: 5620302--5620371 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
5620292 TTCAATTGTC
*
5620302 GTTTTGCTTACA-CACACCACACATGGAGCGATGTG
1 GTTTTGCTTACATCA-ACCACACATGGAGCAATGTG
* * *
5620337 GTTTTGTTTACATTAACCACACATTGAGCAATGTG
1 GTTTTGCTTACATCAACCACACATGGAGCAATGTG
5620372 CACCTGCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (35 bp):
GTTTTGCTTACATCAACCACACATGGAGCAATGTG
Found at i:5629043 original size:32 final size:32
Alignment explanation
Indices: 5629007--5629076 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
5628997 TAAAATTAAA
* *
5629007 ATTTTACCTACTTAAATTTTATTAAAAA-ATTT
1 ATTTTA-CTACTTAAATTATATTAAAAATATAT
* *
5629039 ATTTTATTATTTAAATTATATTAAAAATATAT
1 ATTTTACTACTTAAATTATATTAAAAATATAT
5629071 ATTTTA
1 ATTTTA
5629077 TATTAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 18 0.55
32 15 0.45
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (32 bp):
ATTTTACTACTTAAATTATATTAAAAATATAT
Found at i:5629061 original size:31 final size:32
Alignment explanation
Indices: 5629018--5629077 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
5629008 TTTTACCTAC
* *
5629018 TTAAATTTTATTAAAAA-ATTTATTTTATTAT
1 TTAAATTATATTAAAAATATATATTTTATTAT
5629049 TTAAATTATATTAAAAATATATATTTTAT
1 TTAAATTATATTAAAAATATATATTTTAT
5629078 ATTAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTAAATTATATTAAAAATATATATTTTATTAT
Found at i:5629504 original size:19 final size:19
Alignment explanation
Indices: 5629473--5629528 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
5629463 AACATGAATA
* *
5629473 ATAAAAATAAAATTTTAAT
1 ATAAAAATTAAATTATAAT
* *
5629492 TTATAAATTAAATTATAAT
1 ATAAAAATTAAATTATAAT
*
5629511 ATAAAAATTAAATAATAA
1 ATAAAAATTAAATTATAA
5629529 ATTAATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATTAAATTATAAT
Found at i:5630813 original size:228 final size:227
Alignment explanation
Indices: 5630180--5630814 Score: 615
Period size: 228 Copynumber: 2.8 Consensus size: 227
5630170 AATCACTCTC
* * * * * * * * * *
5630180 GAAGTCGAGAGTTCCGACACTATCGACAACGTGAAGGCAAAAATTCAAGACAAGGAAGGTATTCC
1 GAAGTCGAGAGCTCTGACACGATCGACAACGTTAAGGCGAAGATCCAAGACAAAGAAGGAATCCC
* * ** * * * * * * *
5630245 GCCAGACCAACAGCGTCTCATCTTCGCTGGGAAGCAGCTAGAAGACGGCAGAACCTTGGCCGATT
66 ACCAGACCAGCAAAGGCTTATCTTTGCTGGGAAGCAG-TTGAAGACGGAAGAACTTTGGCTGATT
* * * * * * * *
5630310 ATAACATCCAAAAGGAGTCAACTCTCCACCTCGTCCTCCGTCTACGTGGCGGTATGCAAATCTTC
130 ATAATATTCAGAAGGAGTCGACCCTTCACCTCGTCCTCCGTCTTCGTGGCGGGATGCAAATCTTC
5630375 GTCAAAACTCTGACTGGCAAAACCATAACCTTG
195 GTCAAAACTCTGACTGGCAAAACCATAACCTTG
*
5630408 GAAGTCGAGAGCTCTGACACGATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGAATCCC
1 GAAGTCGAGAGCTCTGACACGATCGACAACGTTAAGGCGAAGATCCAAGACAAAGAAGGAATCCC
* * * **
5630473 ACCGGACCAGCAAAGGCTTATCTTTGCTGGAAAGCAGCTTGAGGACGGTCGAACTTTGGCTGATT
66 ACCAGACCAGCAAAGGCTTATCTTTGCTGGGAAGCAG-TTGAAGACGGAAGAACTTTGGCTGATT
* ** * * ** * * *
5630538 ATAATATTCAGAAGGAATCGACCCTTCATTTGGTTCTGAGGCTTCGTGGCGGGATGCAGATCTTT
130 ATAATATTCAGAAGGAGTCGACCCTTCACCTCGTCCTCCGTCTTCGTGGCGGGATGCAAATCTTC
* * * * * * *
5630603 GTCAAGACTTTGACTGGGAAGACGATTACTTTG
195 GTCAAAACTCTGACTGGCAAAACCATAACCTTG
* * * * * * * * * * *
5630636 GAGGTGGAGAGTTCTGACACGGTCGATAATGTTAAGGCGAAGATTCAGGATAAAGAAGGGATTCC
1 GAAGTCGAGAGCTCTGACACGATCGACAACGTTAAGGCGAAGATCCAAGACAAAGAAGGAATCCC
* * * *
5630701 ACCAGATCAGCAAAGG-TTGATTTTTGCTGGGAAGCAGTTGGAAGATGGAAGGACTTTGGCTGAT
66 ACCAGACCAGCAAAGGCTT-ATCTTTGCTGGGAAGCAGTT-GAAGACGGAAGAACTTTGGCTGAT
*
5630765 TACAATATTCAGAAGGAGTCGACCCTTCACCTCGTCCTCCGTCTTCGTGG
129 TATAATATTCAGAAGGAGTCGACCCTTCACCTCGTCCTCCGTCTTCGTGG
5630815 TGGTCTCTAA
Statistics
Matches: 326, Mismatches: 79, Indels: 4
0.80 0.19 0.01
Matches are distributed among these distances:
227 4 0.01
228 322 0.99
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (227 bp):
GAAGTCGAGAGCTCTGACACGATCGACAACGTTAAGGCGAAGATCCAAGACAAAGAAGGAATCCC
ACCAGACCAGCAAAGGCTTATCTTTGCTGGGAAGCAGTTGAAGACGGAAGAACTTTGGCTGATTA
TAATATTCAGAAGGAGTCGACCCTTCACCTCGTCCTCCGTCTTCGTGGCGGGATGCAAATCTTCG
TCAAAACTCTGACTGGCAAAACCATAACCTTG
Found at i:5635814 original size:45 final size:45
Alignment explanation
Indices: 5635763--5635851 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
5635753 TTCACAGATA
* * *
5635763 AGCACAATGGGCTGAACTAACTGGAATCATCTTAATCTCAATGCC
1 AGCACAATGGACCGAACTAACTAGAATCATCTTAATCTCAATGCC
** * *
5635808 AGCACAATGGACCGGGCTAACTAGAATCGTCTTCATCTCAATGC
1 AGCACAATGGACCGAACTAACTAGAATCATCTTAATCTCAATGC
5635852 AGGAAAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (45 bp):
AGCACAATGGACCGAACTAACTAGAATCATCTTAATCTCAATGCC
Found at i:5642595 original size:2 final size:2
Alignment explanation
Indices: 5642588--5642616 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5642578 AGTATAATCG
5642588 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5642617 GATCTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5651322 original size:15 final size:17
Alignment explanation
Indices: 5651297--5651340 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
5651287 TGTAAATTCG
5651297 TATATTTATATTAT-TTT
1 TATA-TTATATTATGTTT
5651314 T-TATTATATTATGTTT
1 TATATTATATTATGTTT
5651330 TATATTATATT
1 TATATTATATT
5651341 TATAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.36
16 6 0.24
17 10 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TATATTATATTATGTTT
Found at i:5651714 original size:2 final size:2
Alignment explanation
Indices: 5651707--5651739 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5651697 TTAGGTCATG
*
5651707 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5651740 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5652267 original size:23 final size:22
Alignment explanation
Indices: 5652224--5652278 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5652214 TTAATTACAA
5652224 AATT-TATA-TTTTTATAATAT
1 AATTATATATTTTTTATAATAT
*
5652244 AATTATATATTTTTTATGATTAT
1 AATTATATATTTTTTAT-AATAT
*
5652267 AGTTATA-ATTTT
1 AATTATATATTTT
5652279 ATTTTATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 4 0.13
21 4 0.13
22 12 0.40
23 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (22 bp):
AATTATATATTTTTTATAATAT
Found at i:5659080 original size:2 final size:2
Alignment explanation
Indices: 5659073--5659105 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5659063 TAGGAGGTTT
5659073 TA 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 TA T
5659106 TAAAATTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5659817 original size:2 final size:2
Alignment explanation
Indices: 5659810--5659836 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5659800 ACTTGAATGA
5659810 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5659837 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5660579 original size:17 final size:17
Alignment explanation
Indices: 5660559--5660605 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5660549 TAATTAACAG
5660559 ATTTTAATTTATTTTTT
1 ATTTTAATTTATTTTTT
* *
5660576 ATTTTAAGTTAATTTTT
1 ATTTTAATTTATTTTTT
*
5660593 AATTT-ATTTATTT
1 ATTTTAATTTATTT
5660606 ATATCAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTTAATTTATTTTTT
Found at i:5660614 original size:18 final size:19
Alignment explanation
Indices: 5660593--5660634 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5660583 GTTAATTTTT
*
5660593 AATTTATT-TATTTATATC
1 AATTTATTATATTTATATA
*
5660611 AA-TTATTATATTTTTATA
1 AATTTATTATATTTATATA
5660629 AATTTA
1 AATTTA
5660635 ATAAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.25
18 12 0.60
19 3 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTATTATATTTATATA
Found at i:5661947 original size:3 final size:3
Alignment explanation
Indices: 5661941--5661992 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
5661931 GATGATGCTG
* *
5661941 TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5661989 TTA T
1 TTA T
5661993 ATATCTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5662388 original size:2 final size:2
Alignment explanation
Indices: 5662381--5662410 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5662371 GACATGTCAA
*
5662381 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5662411 TAGTATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5669514 original size:18 final size:18
Alignment explanation
Indices: 5669491--5669529 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5669481 AAAAATATTT
*
5669491 AACAGCGTTTTTAATACA
1 AACAGCGCTTTTAATACA
5669509 AACAGCGCTTTTAATACA
1 AACAGCGCTTTTAATACA
5669527 AAC
1 AAC
5669530 TCCATTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (18 bp):
AACAGCGCTTTTAATACA
Found at i:5669681 original size:80 final size:82
Alignment explanation
Indices: 5669517--5669712 Score: 211
Period size: 80 Copynumber: 2.4 Consensus size: 82
5669507 CAAACAGCGC
* ** ** * *
5669517 TTTTAATACAAACT-CCATTAATAGAAAAAATTTAGTGACGTTTTTTTTTAAAATGCTGCTAATA
1 TTTTAATACAAA-TGCCAATAATAGAAAAAATTTAACGACGTTTTTTAATAAAACGCTACTAATA
***
5669581 GAAAAAATTTAACGGTAT
65 GAAAAAATTTAACAACAT
* ** *
5669599 TTTT-TTA-AAATGCCGCTAATAAAAAAAATTTAACGACG-TTTTTAATACAAACGCTACTAATA
1 TTTTAATACAAATGCCAATAATAGAAAAAATTTAACGACGTTTTTTAATA-AAACGCTACTAATA
*
5669661 GAAAAAATTTAGCAACAT
65 GAAAAAATTTAACAACAT
5669679 TTTTAATACAAATGCCAATAATAGAAAAAATTTA
1 TTTTAATACAAATGCCAATAATAGAAAAAATTTA
5669713 GCGATATTTA
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
79 8 0.09
80 54 0.59
81 4 0.04
82 26 0.28
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (82 bp):
TTTTAATACAAATGCCAATAATAGAAAAAATTTAACGACGTTTTTTAATAAAACGCTACTAATAG
AAAAAATTTAACAACAT
Found at i:5669682 original size:41 final size:41
Alignment explanation
Indices: 5669517--5669753 Score: 187
Period size: 41 Copynumber: 5.8 Consensus size: 41
5669507 CAAACAGCGC
* * *
5669517 TTTTAATACAAACT-CCATTAATAGAAAAAATTTAGTGACGTT
1 TTTTAATACAAA-TGCCACTAATAGAAAAAATTTAGCGAC-AT
** ** * **
5669559 TTTTTTTA-AAATGCTGCTAATAGAAAAAATTTAACGGTAT
1 TTTTAATACAAATGCCACTAATAGAAAAAATTTAGCGACAT
* * * * *
5669599 TTTT-TTA-AAATGCCGCTAATAAAAAAAATTTAACGACGT
1 TTTTAATACAAATGCCACTAATAGAAAAAATTTAGCGACAT
* * *
5669638 TTTTAATACAAACGCTACTAATAGAAAAAATTTAGCAACAT
1 TTTTAATACAAATGCCACTAATAGAAAAAATTTAGCGACAT
* *
5669679 TTTTAATACAAATGCCAATAATAGAAAAAATTTAGCGATAT
1 TTTTAATACAAATGCCACTAATAGAAAAAATTTAGCGACAT
* * * * *
5669720 TTAGT-GTAAAAATGTCGCTAATAGAAAAAATTTA
1 TT-TTAATACAAATGCCACTAATAGAAAAAATTTA
5669754 ATTGCGTTCT
Statistics
Matches: 157, Mismatches: 34, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
39 34 0.22
40 8 0.05
41 108 0.69
42 7 0.04
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (41 bp):
TTTTAATACAAATGCCACTAATAGAAAAAATTTAGCGACAT
Found at i:5669939 original size:41 final size:40
Alignment explanation
Indices: 5669882--5670020 Score: 165
Period size: 40 Copynumber: 3.4 Consensus size: 40
5669872 CGAAATGTCA
* *
5669882 CTAATAGAAAAAATTTAACAGCGTTTTTAATGCAAATACCG
1 CTAATA-AAAAAATTTAACAACGTTTTTAATGCAAATATCG
* ** *
5669923 CTAATAAAAAAAATTTAACAACGTTTTTAATACAAACGTCA
1 CTAAT-AAAAAAATTTAACAACGTTTTTAATGCAAATATCG
*
5669964 CTAATAAAAAAATTTAACAACG--TTTAATGTAAAAATATCG
1 CTAATAAAAAAATTTAACAACGTTTTTAATG--CAAATATCG
5670004 CTAATAAAAAAATTTAA
1 CTAATAAAAAAATTTAA
5670021 TGACATTCAT
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
38 6 0.07
40 39 0.46
41 38 0.45
42 1 0.01
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (40 bp):
CTAATAAAAAAATTTAACAACGTTTTTAATGCAAATATCG
Found at i:5669973 original size:40 final size:40
Alignment explanation
Indices: 5669878--5669988 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 40
5669868 TTTTCGAAAT
* * *
5669878 GTCACTAATAGAAAAAATTTAACAGCGTTTTTAATGCAAAT
1 GTCACTAATA-AAAAAATTTAACAACGTTTTTAATACAAAC
** *
5669919 ACCGCTAATAAAAAAAATTTAACAACGTTTTTAATACAAAC
1 GTCACTAAT-AAAAAAATTTAACAACGTTTTTAATACAAAC
5669960 GTCACTAATAAAAAAATTTAACAACGTTT
1 GTCACTAATAAAAAAATTTAACAACGTTT
5669989 AATGTAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
40 20 0.33
41 39 0.65
42 1 0.02
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (40 bp):
GTCACTAATAAAAAAATTTAACAACGTTTTTAATACAAAC
Found at i:5670843 original size:10 final size:10
Alignment explanation
Indices: 5670827--5670867 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5670817 GAAGACAGAC
5670827 ATATAAATAT
1 ATATAAATAT
*
5670837 GTATAAATAT
1 ATATAAATAT
*
5670847 ATATATATAT
1 ATATAAATAT
5670857 ATATGAAATAT
1 ATAT-AAATAT
5670868 TTTTGGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 21 0.81
11 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (10 bp):
ATATAAATAT
Found at i:5671434 original size:45 final size:46
Alignment explanation
Indices: 5671368--5671456 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 46
5671358 AATTTAAACT
* *
5671368 TTAAAATTTAGAATTCCTGTT-AATGAATAAAATACTGATATATTGG
1 TTAAAATTTAAAACTCCTGTTAAAT-AATAAAATACTGATATATTGG
* *
5671414 TTAAAA-TTAAAACTCCTGTTAAATAATGAAATCCTGATATATT
1 TTAAAATTTAAAACTCCTGTTAAATAATAAAATACTGATATATT
5671457 AATAAAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 29 0.76
46 9 0.24
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (46 bp):
TTAAAATTTAAAACTCCTGTTAAATAATAAAATACTGATATATTGG
Found at i:5674886 original size:22 final size:22
Alignment explanation
Indices: 5674846--5674887 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5674836 TATTAAAAAT
*
5674846 TATTTTTATTTTAATATTTATA
1 TATTTTTATATTAATATTTATA
5674868 TATTTTTATAATTAA-ATTTA
1 TATTTTTAT-ATTAATATTTA
5674888 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:5678070 original size:2 final size:2
Alignment explanation
Indices: 5678063--5678102 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5678053 GACCTACTCA
*
5678063 AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5678103 GGAGATCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5689552 original size:16 final size:16
Alignment explanation
Indices: 5689521--5689564 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5689511 TTTAAAATAA
*
5689521 ATTTAATAATTAAATTT
1 ATTTAA-AATTTAATTT
*
5689538 TTTTAAAATTTAATTT
1 ATTTAAAATTTAATTT
*
5689554 ACTTAAAATTT
1 ATTTAAAATTT
5689565 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAAAATTTAATTT
Found at i:5695451 original size:17 final size:17
Alignment explanation
Indices: 5695429--5695464 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5695419 CATTTCATAT
* *
5695429 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
5695446 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
5695463 TT
1 TT
5695465 CATCTTCCTT
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:5696672 original size:45 final size:48
Alignment explanation
Indices: 5696571--5696676 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 48
5696561 AATGTGCCAT
* *
5696571 TTCAAGGTCAGCGACATCGGGCTAAGGGAAAAGTGGACCAATGTGCTGA
1 TTCAAGGCCAGCGACATCGGGCTAA-GGAAAAGTGGACCAATATGCTGA
* * * *
5696620 CTCAAGGCCAGCGACATTGGGCTTA-GAAAGGT-G-CCAATATGCTGA
1 TTCAAGGCCAGCGACATCGGGCTAAGGAAAAGTGGACCAATATGCTGA
5696665 TTCAAGGCCAGC
1 TTCAAGGCCAGC
5696677 AATATCGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 22 0.44
46 1 0.02
47 6 0.12
49 21 0.42
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (48 bp):
TTCAAGGCCAGCGACATCGGGCTAAGGAAAAGTGGACCAATATGCTGA
Found at i:5696758 original size:32 final size:32
Alignment explanation
Indices: 5696709--5697240 Score: 724
Period size: 32 Copynumber: 17.2 Consensus size: 32
5696699 AAAATGGTGA
* ** **
5696709 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5696741 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5696773 TTTGAAAAGGGTCGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696805 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696837 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696869 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696901 TTTGAAATGGG-TGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696932 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696964 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5696996 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5697028 TTTGGAATGGGTTGTCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * **
5697058 TTTGAAA--AGATGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5697086 TTTGAAATGGATTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5697116 TTTGAAA--GGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
5697144 TTTGAAA--GGATGCCACCAACTTGTGTGGAC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
5697174 TTTGAAA--AGATGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5697202 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5697234 TTTGAAA
1 TTTGAAA
5697241 AAGGTGCCAC
Statistics
Matches: 454, Mismatches: 37, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
28 72 0.16
29 2 0.00
30 69 0.15
31 33 0.07
32 278 0.61
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:5696999 original size:159 final size:158
Alignment explanation
Indices: 5696709--5697240 Score: 734
Period size: 159 Copynumber: 3.4 Consensus size: 158
5696699 AAAATGGTGA
* ** *
5696709 TTTGAAAAGGGTTGCCACTAACTTGCATGGGCTTTTAAATGGGTTGCCACCGACTTGTGTGGGCT
1 TTTGAAATGGGTTGCCACCGACTTG--TGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCT
* *
5696774 TTGAAAAGGGTCGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTT
64 TTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTT
5696839 TGAAATGGGTTGCCACCGACTTGTGTGGGC
129 TGAAATGGGTTGCCACCGACTTGTGTGGGC
5696869 TTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGG-TGCCACCGACTTGTGTGGGCT
1 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCT
5696933 TTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTT
64 TTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTT
5696998 TGAAATGGGTTGCCACCGACTTGTGTGGGC
129 TGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * * **
5697028 TTTGGAATGGGTTGTCACCGACTTGTGGGCTTTGAAA--AGATGCCACTAAC-T-TGTGGGCTTT
1 TTTGAAATGGGTTGCCACCGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
* * *
5697089 GAAATGGATTGCCACCGAC-T-TGTGGGCTTTGAAA--GGATGCCACTGAC-T-TGTGGGCTTTG
66 GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTG
* * *
5697148 AAA--GGATGCCACCAACTTGTGTGGAC
131 AAATGGGTTGCCACCGACTTGTGTGGGC
* * *
5697174 TTTGAAA--AGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
1 TTTGAAATGGGTTGCCACCGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
5697237 GAAA
66 GAAA
5697241 AAGGTGCCAC
Statistics
Matches: 339, Mismatches: 26, Indels: 26
0.87 0.07 0.07
Matches are distributed among these distances:
144 24 0.07
146 35 0.10
147 1 0.00
148 28 0.08
149 1 0.00
150 11 0.03
152 14 0.04
153 1 0.00
154 28 0.08
155 2 0.01
156 8 0.02
157 14 0.04
158 1 0.00
159 134 0.40
160 34 0.10
161 1 0.00
162 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (158 bp):
TTTGAAATGGGTTGCCACCGACTTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTT
GAAATGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTG
AAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:5697288 original size:30 final size:28
Alignment explanation
Indices: 5696753--5697784 Score: 464
Period size: 27 Copynumber: 35.6 Consensus size: 28
5696743 TTAAATGGGT
*
5696753 TGCCACCGACTTGTGTGGGCTTTGAAAAGGG
1 TGCCACCGAC-T-TGTGGGCTTTG-AAAGGA
*
5696784 TCGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 T-GCCACCGAC-T-TGTGGGCTTTGAAA--GGA
*
5696817 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGAC-T-TGTGGGCTTTGAAA--GGA
*
5696849 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGAC-T-TGTGGGCTTTGAAA--GGA
*
5696881 TGCCACCGACTTGTGTGGGCTTTGAAATGGG
1 TGCCACCGAC-T-TGTGGGCTTTGAAA-GGA
*
5696912 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGAC-T-TGTGGGCTTTGAAA--GGA
*
5696944 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGAC-T-TGTGGGCTTTGAAA--GGA
*
5696976 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACCGAC-T-TGTGGGCTTTGAAA--GGA
* *
5697008 TGCCACCGACTTGTGTGGGCTTTGGAATGGGT
1 TGCCACCGAC-T-TGTGGGCTTT-GAA-AGGA
* *
5697040 TGTCACCGACTTGTGGGCTTTGAAAAGA
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
**
5697068 TGCCACTAACTTGTGGGCTTTGAAATGGA
1 TGCCACCGACTTGTGGGCTTTGAAA-GGA
5697097 TTGCCACCGACTTGTGGGCTTTGAAAGGA
1 -TGCCACCGACTTGTGGGCTTTGAAAGGA
*
5697126 TGCCACTGACTTGTGGGCTTTGAAAGGA
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* *
5697154 TGCCACCAACTTGTGTGGACTTTGAAAAGA
1 TGCCACCGACTTGTG-GG-CTTTGAAAGGA
* *
5697184 TGCCACTGACTTGTGGGCTTTGAAATGGGT
1 TGCCACCGACTTGTGGGCTTTGAAA--GGA
5697214 TGCCACCGACTTGTGTGGGCTTTGAAAAAGG-
1 TGCCACCGAC-T-TGTGGGCTTTG--AAAGGA
** *
5697245 TGCCACTAACTTGTGGGCTTTAGAAGGGAA
1 TGCCACCGACTTGTGGGCTTT-GAAAGG-A
* * ** *
5697275 TGCCACCGCCTTGTGGACTTAAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* ** *
5697303 TGCCA-CGAAGTTGTGAAC-TTAAAAGGGA
1 TGCCACCG-ACTTGTGGGCTTTGAAA-GGA
* * * * *
5697331 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * * * *
5697358 TGCCACGGAGTTATGGAC-TTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * *
5697385 TGCCACGGAGTTGTGGAC-TTAAAAGGGA
1 TGCCACCGACTTGTGGGCTTTGAAA-GGA
* * * *
5697413 TGCCACGGAGTTGTGGAC-TTAAAAGGA
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * *
5697440 TGCCACGGAGC-TGTGGAC-TTAAAAGGGA
1 TGCCACCGA-CTTGTGGGCTTTGAAA-GGA
* * * * *
5697468 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * * ** *
5697495 TGCCACGGAGTTGCGGAC-TAAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * * *
5697522 TGCCACGGAGTTGTGGACTTTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * *
5697550 TGCCACAGAGTTGTGGAC-TTAAAAGGGA
1 TGCCACCGACTTGTGGGCTTTGAAA-GGA
* * * * *
5697578 TGCCACGGAGTTGTGGAC-TTAAAAAGA
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * *
5697605 TGCCACAGAGTTGTGGAC-TTAAAAGGA
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * * *
5697632 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * * *
5697659 TGCCACGGAGTTGTGGAC-TTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * * *
5697686 TGCCACGGATTTGTGGAC-TTAAAAGGG
1 TGCCACCGACTTGTGGGCTTTGAAAGGA
* * * *
5697713 TGCCACGGAGTTGTGGAC-TTAAAAGGGA
1 TGCCACCGACTTGTGGGCTTTGAAA-GGA
* * * *
5697741 TGCCACAGAGTTGTGGAC-TTAAAAGGGA
1 TGCCACCGACTTGTGGGCTTTGAAA-GGA
* *
5697769 TGCCACAGAGTTGTGG
1 TGCCACCGACTTGTGG
5697785 ACTTAAAAAG
Statistics
Matches: 906, Mismatches: 66, Indels: 61
0.88 0.06 0.06
Matches are distributed among these distances:
27 261 0.29
28 255 0.28
29 27 0.03
30 84 0.09
31 43 0.05
32 227 0.25
33 6 0.01
34 3 0.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (28 bp):
TGCCACCGACTTGTGGGCTTTGAAAGGA
Found at i:5697327 original size:27 final size:27
Alignment explanation
Indices: 5697285--5697952 Score: 1066
Period size: 27 Copynumber: 24.4 Consensus size: 27
5697275 TGCCACCGCC
*
5697285 TTGTGGACTTAAAAAGGGTGCCACGAAG
1 TTGTGGACTT-AAAAGGGTGCCACGGAG
*
5697313 TTGTGAACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
5697341 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
5697368 TTATGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697395 TTGTGGACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
*
5697423 TTGTGGACTTAAAAGGATGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
5697450 CTGTGGACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
5697478 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
* *
5697505 TTGCGGACTAAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
5697532 TTGTGGACTTTAAAAGGGTGCCACAGAG
1 TTGTGGAC-TTAAAAGGGTGCCACGGAG
5697560 TTGTGGACTTAAAAGGGATGCCACGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
* * *
5697588 TTGTGGACTTAAAAAGATGCCACAGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
* *
5697615 TTGTGGACTTAAAAGGATGCCACAGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697642 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
5697669 TTGTGGACTTAAAAGGGTGCCACGGAT
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697696 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
5697723 TTGTGGACTTAAAAGGGATGCCACAGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
*
5697751 TTGTGGACTTAAAAGGGATGCCACAGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
* *
5697779 TTGTGGACTTAAAAAGGTGCCATGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697806 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697833 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
*
5697860 TTGTGGACTTAAAAGGGATGCCATGGAG
1 TTGTGGACTTAAAAGGG-TGCCACGGAG
* *
5697888 TTATGGACTTAAAAGAGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697915 TTGTGGACTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTAAAAGGGTGCCACGGAG
5697942 TTGTGGACTTA
1 TTGTGGACTTA
5697953 TTTTAATTGA
Statistics
Matches: 598, Mismatches: 35, Indels: 15
0.92 0.05 0.02
Matches are distributed among these distances:
27 386 0.65
28 212 0.35
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (27 bp):
TTGTGGACTTAAAAGGGTGCCACGGAG
Done.