Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold433
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: 558157
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Warning! 7244 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:121647 original size:28 final size:29
Alignment explanation
Indices: 121616--121670 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
121606 TTTAATTATT
*
121616 AATTTATAAATAAA-AAA-TTTTTATATCA
1 AATTT-TAAAAAAATAAATTTTTTATATCA
121644 AATTTTAAAAAAATAAATTTTTTATAT
1 AATTTTAAAAAAATAAATTTTTTATAT
121671 TAGGATCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 8 0.33
29 9 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTTTAAAAAAATAAATTTTTTATATCA
Found at i:124977 original size:43 final size:43
Alignment explanation
Indices: 124916--125005 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
124906 AAAGCTGTAT
**
124916 TAATGTGGTAGTAAAAGTAAAAAATTTTTATCAAGATTGTGTC
1 TAATGTGACAGTAAAAGTAAAAAATTTTTATCAAGATTGTGTC
* * *
124959 TAATGTGACAGTAAAAGTAAGAATTTTTTATCAAGGTTGTGTC
1 TAATGTGACAGTAAAAGTAAAAAATTTTTATCAAGATTGTGTC
125002 TAAT
1 TAAT
125006 AATAAATATG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (43 bp):
TAATGTGACAGTAAAAGTAAAAAATTTTTATCAAGATTGTGTC
Found at i:125083 original size:11 final size:11
Alignment explanation
Indices: 125066--125098 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
125056 TAACAAATTA
125066 AATAATTATTT
1 AATAATTATTT
*
125077 GATAATTATTT
1 AATAATTATTT
125088 AATAA-TATTT
1 AATAATTATTT
125098 A
1 A
125099 CATGAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
AATAATTATTT
Found at i:126501 original size:2 final size:2
Alignment explanation
Indices: 126496--126526 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
126486 TTGTGGTTTG
*
126496 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 A
126527 AATGCTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:126572 original size:15 final size:17
Alignment explanation
Indices: 126552--126583 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
126542 ATACTCTTAT
126552 TTTTTAA-A-ATATTTA
1 TTTTTAATATATATTTA
126567 TTTTTAATATATATTTA
1 TTTTTAATATATATTTA
126584 AATATGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAATATATATTTA
Found at i:132576 original size:18 final size:17
Alignment explanation
Indices: 132555--132600 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
132545 TATTTAAAAA
132555 TATATTAAAAATTATTTT
1 TATATTAAAAATTA-TTT
* *
132573 TATATTAATATTTATTT
1 TATATTAAAAATTATTT
132590 TATAATTAAAA
1 TAT-ATTAAAA
132601 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTAAAAATTATTT
Found at i:133717 original size:11 final size:11
Alignment explanation
Indices: 133701--133725 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
133691 ATAAAAATAA
133701 TTTTTATAATT
1 TTTTTATAATT
133712 TTTTTATAATT
1 TTTTTATAATT
133723 TTT
1 TTT
133726 AATAATAAAA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:134278 original size:20 final size:20
Alignment explanation
Indices: 134228--134280 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
134218 AATATGATAT
*
134228 AAATATATAATATAAAATAAAA
1 AAATATA-AAAAT-AAATAAAA
*
134250 AAATTTAAAAATAAAT-AAA
1 AAATATAAAAATAAATAAAA
134269 AAATAATAAAAA
1 AAAT-ATAAAAA
134281 AGATATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 7 0.26
20 10 0.37
21 4 0.15
22 6 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATATAAAAATAAATAAAA
Found at i:134605 original size:27 final size:29
Alignment explanation
Indices: 134567--134638 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 29
134557 TTTAAAATAA
*
134567 AAAT-TAATAATATATTAAAA-ATTA-TAT
1 AAATATAA-AATATATTAAAATATGATTAT
134594 AAATATAAAATATA-TAAAATATGATTAT
1 AAATATAAAATATATTAAAATATGATTAT
134622 AATATAATAAAATATAT
1 AA-AT-ATAAAATATAT
134639 AAATAGTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
26 5 0.13
27 13 0.34
28 8 0.21
29 2 0.05
30 10 0.26
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (29 bp):
AAATATAAAATATATTAAAATATGATTAT
Found at i:134608 original size:9 final size:9
Alignment explanation
Indices: 134550--134641 Score: 61
Period size: 9 Copynumber: 10.4 Consensus size: 9
134540 AAGAATTTTT
*
134550 TAAAATATT
1 TAAAATATA
134559 TAAAATA-A
1 TAAAATATA
*
134567 -AAATTA-A
1 TAAAATATA
*
134574 TAATATAT-
1 TAAAATATA
134582 TAAAA-ATTA
1 TAAAATA-TA
*
134591 TATAA-ATA
1 TAAAATATA
134599 TAAAATATA
1 TAAAATATA
134608 TAAAATATGA
1 TAAAATAT-A
*
134618 TTATAATATAA
1 -TAAAATAT-A
134629 TAAAATATA
1 TAAAATATA
134638 TAAA
1 TAAA
134642 TAGTATTGCT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
7 7 0.11
8 15 0.23
9 28 0.42
10 8 0.12
11 8 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (9 bp):
TAAAATATA
Found at i:134612 original size:49 final size:45
Alignment explanation
Indices: 134550--134643 Score: 116
Period size: 49 Copynumber: 2.0 Consensus size: 45
134540 AAGAATTTTT
* *
134550 TAAAATATTTAAAATAAAAATTAATAATATATTAAAAATTATATAAATA
1 TAAAATATATAAAAT-AAAATT-ATAATATAAT-AAAA-TATATAAATA
**
134599 TAAAATATATAAAATATGATTATAATATAATAAAATATATAAATA
1 TAAAATATATAAAATAAAATTATAATATAATAAAATATATAAATA
134644 GTATTGCTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 10 0.24
46 4 0.10
47 9 0.22
48 4 0.10
49 14 0.34
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (45 bp):
TAAAATATATAAAATAAAATTATAATATAATAAAATATATAAATA
Found at i:155846 original size:6 final size:6
Alignment explanation
Indices: 155835--155875 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
155825 CATGGTTAAA
155835 AAATTT AAATTT AAATTT -AA-TT AAATTT AATAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT -A-AATTT AAATT
155876 ATTATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.06
5 4 0.13
6 18 0.58
7 2 0.06
8 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:155927 original size:18 final size:19
Alignment explanation
Indices: 155896--155938 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
155886 ATAAAATAAA
155896 ATATAATAAATTAT-TTTT
1 ATATAATAAATTATATTTT
**
155914 ATATAATATTTTATATTTT
1 ATATAATAAATTATATTTT
155933 -TATAAT
1 ATATAAT
155939 TATATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATAATAAATTATATTTT
Found at i:155995 original size:5 final size:5
Alignment explanation
Indices: 155977--156006 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
155967 TAATACATAA
155977 TAATT TATATT TAATT TAATT TAATT TAAT
1 TAATT TA-ATT TAATT TAATT TAATT TAAT
156007 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:156335 original size:5 final size:5
Alignment explanation
Indices: 156302--156458 Score: 64
Period size: 5 Copynumber: 31.8 Consensus size: 5
156292 AATATTTAAA
* * * *
156302 ATATT AT-TT ATTTT ATTTT A-ATT TTATT ATATT A-ATA AT-TT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
* * * * *
156348 ATATAA ATTTT AATATA ATAAT ATATT -T-TT CT-TT ATATT AATATT
1 ATAT-T ATATT -ATATT ATATT ATATT ATATT ATATT ATATT -ATATT
* *
156393 ATATTT ATACTT AT-TT TTATT ATATT ATATT TTAATT ATATT -T-TT
1 ATA-TT ATA-TT ATATT ATATT ATATT ATATT AT-ATT ATATT ATATT
*
156438 TTATT ATATTT ATAATT ATAT
1 ATATT ATA-TT AT-ATT ATAT
156459 AATTCGTATT
Statistics
Matches: 116, Mismatches: 20, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
3 4 0.03
4 22 0.19
5 57 0.49
6 32 0.28
7 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (5 bp):
ATATT
Found at i:156357 original size:32 final size:33
Alignment explanation
Indices: 156301--156375 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
156291 TAATATTTAA
* * * * *
156301 AATATTATTTATTTTATTTTAATTTTATTATATT
1 AATA-TATTTATATTATATAAATTTTAATATAAT
156335 AATA-ATTTATATTATATAAATTTTAATATAAT
1 AATATATTTATATTATATAAATTTTAATATAAT
156367 AATATATTT
1 AATATATTT
156376 TTCTTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 27 0.77
33 4 0.11
34 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
AATATATTTATATTATATAAATTTTAATATAAT
Found at i:156430 original size:11 final size:11
Alignment explanation
Indices: 156416--156458 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 11
156406 TTTTTATTAT
156416 ATTATATTTTA
1 ATTATATTTTA
*
156427 ATTATATTTTTTT
1 ATTATA--TTTTA
156440 ATTATATTTATA
1 ATTATATTT-TA
156452 ATTATAT
1 ATTATAT
156459 AATTCGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 9 0.33
12 8 0.30
13 10 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTATATTTTA
Found at i:156443 original size:13 final size:13
Alignment explanation
Indices: 156406--156448 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 13
156396 TTTATACTTA
156406 TTTTTATTATATT
1 TTTTTATTATATT
156419 ATATTTTAATTATATT
1 -T-TTTT-ATTATATT
156435 TTTTTATTATATT
1 TTTTTATTATATT
156448 T
1 T
156449 ATAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 5 0.19
15 5 0.19
16 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTATTATATT
Found at i:157786 original size:12 final size:11
Alignment explanation
Indices: 157767--157808 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
157757 TAATATTTTA
157767 TATT-TAAATT
1 TATTATAAATT
157777 TAATTATAAATT
1 T-ATTATAAATT
157789 TA-TATAAATAT
1 TATTATAAAT-T
157800 TATTATAAA
1 TATTATAAA
157809 AATAATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 7 0.25
12 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATTATAAATT
Found at i:157926 original size:28 final size:28
Alignment explanation
Indices: 157895--157949 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
157885 TATATTTAAA
* *
157895 TTTAATTAT-AAATTTATAAAAATAATAT
1 TTTAATAATAAAATTAATAAAAA-AATAT
157923 TTTAATAATAAAATTAATAAAAAAATA
1 TTTAATAATAAAATTAATAAAAAAATA
157950 GATTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TTTAATAATAAAATTAATAAAAAAATAT
Found at i:158312 original size:19 final size:19
Alignment explanation
Indices: 158290--158327 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
158280 TATTTTTAAT
158290 TAAAT-TTAATTATAAAATA
1 TAAATATTAA-TATAAAATA
158309 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
158328 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATATTAATATAAAATA
Found at i:159444 original size:16 final size:17
Alignment explanation
Indices: 159413--159445 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
159403 ATAACGTATC
*
159413 AAAATTTATATAAATAT
1 AAAATATATATAAATAT
159430 AAAATATAT-TAAATAT
1 AAAATATATATAAATAT
159446 GATTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATATATAAATAT
Found at i:160000 original size:21 final size:21
Alignment explanation
Indices: 159941--160004 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
159931 TTTAAATTAT
* *
159941 TATTCAAATATTAAGAT-AAA
1 TATTTAAATATTAATATAAAA
*
159961 TATTTTTAAT-TTAATTATAAAA
1 TA-TTTAAATATTAA-TATAAAA
159983 TATTTAAATATTAATATAAAA
1 TATTTAAATATTAATATAAAA
160004 T
1 T
160005 TAATTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 6 0.17
21 21 0.58
22 9 0.25
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TATTTAAATATTAATATAAAA
Found at i:160326 original size:331 final size:335
Alignment explanation
Indices: 159904--160646 Score: 935
Period size: 345 Copynumber: 2.2 Consensus size: 335
159894 ATTGAGCTTG
* * * * *
159904 AGTATTAATTTTTATGATTTAAAGTATTTTAAATTATTATTCAAATATTAAGATAAATATTTTTA
1 AGTATTGATTTTTATGATTTAAA-TATCTTAAATCACTATT-AAATATTAAAAT-AATATTTTTA
* * *
159969 ATTTAATTATAAAATATTTAAATATTAATATAAAATTAATTTTTTAATATTTTTAAAAATTTAAA
63 ATTTAATTATAAAATATATAAATATTAACATAAAATTAATTTTTTAATATTTTTAAAAAATTAAA
** ** * * * *
160034 CAATAAATTTGAATTTGTAAGGTTGAGTTGAACTAAATTAGGGTTTGAGCTTGAATTTTAAAA-T
128 CAATAAATTTGAATTCATAAGGTCAAGTTGAACTAAATTAAGATTTGAACTTAAATTTTAAAATT
* * *
160098 T-CTG-G-CT-CT-ATTTAATAGCAAGTTTAGTTAGATATTTTAACGTAAAAATATTATTTAAGA
193 TACTGAGCCTACTAATTTAATAACAAGTCTAGTTAGATATTTTAACATAAAAATATTATTTAAGA
* * * *
160158 ATAAAAAAATTATATATACCTTATTATGTTATAATTAAATTTATTTAAAAGTTAAATAG-CTTTC
258 ATAAAAAAATTATATATACATTATTATGTTATAATTAAAATTATTCAAAAGTTAAATAGTCTGT-
160222 TCGGA-TCGAGTTTA
322 TC-GACTCGAGTTTA
* * *
160236 AGTATTGATTTTTATGATTTGAGATATCTCAAATCACTATTAAATATTAAAATAATTTTTTTAAT
1 AGTATTGATTTTTATGATTT-AAATATCTTAAATCACTATTAAATATTAAAATAATATTTTTAAT
160301 TTAATTATAAAAATATATAAATATTAACATAAAATTAATTTTTTAATATTTTTAAAAAATTAAAC
65 TTAATTAT-AAAATATATAAATATTAACATAAAATTAATTTTTTAATATTTTTAAAAAATTAAAC
* * *
160366 AGTAAATTTTAATTCATCAGGTCAAGTTGAACTAAATTAAGATTTGAACTTAAATTTTAAAATTT
129 AATAAATTTGAATTCATAAGGTCAAGTTGAACTAAATTAAGATTTGAACTTAAATTTTAAAA---
*
160431 TTTTAATTGAAGCCTAGCTCAATTTAATAACAAGTCTAGTTAGATATTTTAACATAAAAATATTA
191 -TTT-ACTG-AGCCTA-CT-AATTTAATAACAAGTCTAGTTAGATATTTTAACATAAAAATATTA
* * * * *
160496 TTTAATAGTAAAAAATTTATATATATATTATTATGTTATAATTAAAATTATTCAAAATTTAAATA
251 TTTAAGAATAAAAAAATTATATATACATTATTATGTTATAATTAAAATTATTCAAAAGTTAAATA
*
160561 GTCTGTTCGACTTGAGTTTA
316 GTCTGTTCGACTCGAGTTTA
* *
160581 AATATTGATTTTTATGATTTAAAATATCTTGAATCACTATTTAAATATTAAAATAATATTTTTAA
1 AGTATTGATTTTTATGATTT-AAATATCTTAAATCACTA-TTAAATATTAAAATAATATTTTTAA
160646 T
64 T
160647 ATTTTAAAAA
Statistics
Matches: 350, Mismatches: 42, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
330 19 0.05
331 115 0.33
332 32 0.09
333 2 0.01
336 2 0.01
338 2 0.01
340 1 0.00
341 2 0.01
343 2 0.01
344 2 0.01
345 143 0.41
346 28 0.08
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (335 bp):
AGTATTGATTTTTATGATTTAAATATCTTAAATCACTATTAAATATTAAAATAATATTTTTAATT
TAATTATAAAATATATAAATATTAACATAAAATTAATTTTTTAATATTTTTAAAAAATTAAACAA
TAAATTTGAATTCATAAGGTCAAGTTGAACTAAATTAAGATTTGAACTTAAATTTTAAAATTTAC
TGAGCCTACTAATTTAATAACAAGTCTAGTTAGATATTTTAACATAAAAATATTATTTAAGAATA
AAAAAATTATATATACATTATTATGTTATAATTAAAATTATTCAAAAGTTAAATAGTCTGTTCGA
CTCGAGTTTA
Found at i:171913 original size:15 final size:15
Alignment explanation
Indices: 171893--171922 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
171883 TCCAGTTGGA
171893 GCTTTTCTTAGTTTG
1 GCTTTTCTTAGTTTG
171908 GCTTTTCTTAGTTTG
1 GCTTTTCTTAGTTTG
171923 TTAATGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.20, T:0.60
Consensus pattern (15 bp):
GCTTTTCTTAGTTTG
Found at i:172962 original size:3 final size:3
Alignment explanation
Indices: 172946--172987 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
172936 GATCACATTC
*
172946 TTA TTA TTGA -TA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
172988 GTATGATGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:174098 original size:25 final size:26
Alignment explanation
Indices: 174064--174137 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 26
174054 TAAATATGTT
174064 AATAATTTATATTATA-TATATTTTAA
1 AATAATTTAT-TTATATTATATTTTAA
174090 AATAA-TTATTTATATTATATTTT-A
1 AATAATTTATTTATATTATATTTTAA
* * *
174114 ATTACTTTATTTATATAATATTTT
1 AATAATTTATTTATATTATATTTT
174138 TATAATAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 9 0.21
25 29 0.67
26 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
AATAATTTATTTATATTATATTTTAA
Found at i:174115 original size:20 final size:20
Alignment explanation
Indices: 174092--174129 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
174082 TATTTTAAAA
174092 TAATTA-TTTATATTATATTT
1 TAATTACTTTAT-TTATATTT
174112 TAATTACTTTATTTATAT
1 TAATTACTTTATTTATAT
174130 AATATTTTTA
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:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATTACTTTATTTATATTT
Found at i:174561 original size:15 final size:17
Alignment explanation
Indices: 174522--174556 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
174512 ATTGGATGAG
*
174522 TATTGAATATAAATATA
1 TATTTAATATAAATATA
174539 TATTTAATATAAATATA
1 TATTTAATATAAATATA
174556 T
1 T
174557 TTAATTTTTT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATTTAATATAAATATA
Found at i:174639 original size:13 final size:13
Alignment explanation
Indices: 174617--174649 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
174607 TTTAAGTATG
*
174617 TATTAGATATAAA
1 TATTAAATATAAA
174630 TATTAAATATAAA
1 TATTAAATATAAA
174643 TATTAAA
1 TATTAAA
174650 AAAAAAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:180075 original size:22 final size:21
Alignment explanation
Indices: 180035--180079 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
180025 ATATTTATTA
*
180035 TAATTATAAATATAATAAATAT
1 TAATTATAAATAAAATAAA-AT
180057 TAATTATAAA-AAAATTAAAAT
1 TAATTATAAATAAAA-TAAAAT
180078 TA
1 TA
180080 TAAAATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATTATAAATAAAATAAAAT
Found at i:180334 original size:3 final size:3
Alignment explanation
Indices: 180326--180354 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
180316 CTAATTATCT
180326 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
180355 TCACAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:180696 original size:21 final size:21
Alignment explanation
Indices: 180670--180710 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
180660 TTTTAATAAA
*
180670 ATATTTT-TTATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
180691 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
180711 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:180863 original size:14 final size:15
Alignment explanation
Indices: 180844--180880 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
180834 TCAATGATAA
180844 AAAAAATTAA-AATT
1 AAAAAATTAATAATT
180858 AAAAAA-TAATAATT
1 AAAAAATTAATAATT
*
180872 ATAAAATTA
1 AAAAAATTA
180881 TATTATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 15 0.75
15 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAAATTAATAATT
Found at i:181581 original size:21 final size:22
Alignment explanation
Indices: 181557--181601 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
181547 TATTAAATTT
181557 TTTAAAA-AATA-ATTTTATATA
1 TTTAAAATAATATATTTT-TATA
*
181578 TTTAAAATATTATATTTTTATA
1 TTTAAAATAATATATTTTTATA
181600 TT
1 TT
181602 GATATTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 9 0.43
23 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAAAATAATATATTTTTATA
Found at i:182209 original size:26 final size:26
Alignment explanation
Indices: 182160--182209 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
182150 ATTTAAAATA
*
182160 ATATTAAAATTTAAAAATATATTTTT
1 ATATTAAAATTTAAAAATAAATTTTT
* *
182186 ATATTAATATTTAAAATTAAATTT
1 ATATTAAAATTTAAAAATAAATTT
182210 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTAAAATTTAAAAATAAATTTTT
Found at i:182236 original size:44 final size:43
Alignment explanation
Indices: 182140--182233 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 43
182130 ATTAGAAAAC
* *
182140 TTATATCACTATTTAAAATAATATTAAAATTTAAAAATATATTT
1 TTATATTAATATTTAAAATAATATTAAAA-TTAAAAATATATTT
*
182184 TTATATTAATATTTAAAATTAA-ATTTAAA-TAAAAATA-ATTT
1 TTATATTAATATTTAAAA-TAATATTAAAATTAAAAATATATTT
182225 TT-TATTAAT
1 TTATATTAAT
182234 TAAAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
40 7 0.15
41 6 0.13
42 8 0.17
44 22 0.48
45 3 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (43 bp):
TTATATTAATATTTAAAATAATATTAAAATTAAAAATATATTT
Found at i:183035 original size:25 final size:25
Alignment explanation
Indices: 183007--183059 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
182997 ATTATAATTT
183007 AAAA-AATTTAGTACAATATGATAAA
1 AAAAGAATTTAGTACAAT-TGATAAA
* *
183032 AAAAGTATTTCGTACAATTGATAAA
1 AAAAGAATTTAGTACAATTGATAAA
183057 AAA
1 AAA
183060 TGATATAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (25 bp):
AAAAGAATTTAGTACAATTGATAAA
Found at i:185035 original size:11 final size:13
Alignment explanation
Indices: 185026--185144 Score: 73
Period size: 13 Copynumber: 9.8 Consensus size: 13
185016 TTGATAATTT
185026 TAATATAATTATA
1 TAATATAATTATA
*
185039 TAATATAAATATA
1 TAATATAATTATA
*
185052 AAATATAA--A-A
1 TAATATAATTATA
185062 TAAGTATAA-TATA
1 TAA-TATAATTATA
185075 -AA-ATAA-TATA
1 TAATATAATTATA
185085 -AATATAA-TAT-
1 TAATATAATTATA
*
185095 TAATATTAA-AATA
1 TAATA-TAATTATA
* *
185108 TATTAAAATTATA
1 TAATATAATTATA
185121 TAATATAAATTAT-
1 TAATAT-AATTATA
*
185134 TAATTTAATTA
1 TAATATAATTA
185145 AAATTTTATA
Statistics
Matches: 87, Mismatches: 10, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
10 13 0.15
11 17 0.20
12 15 0.17
13 36 0.41
14 6 0.07
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (13 bp):
TAATATAATTATA
Found at i:185044 original size:5 final size:5
Alignment explanation
Indices: 185026--185128 Score: 72
Period size: 5 Copynumber: 20.6 Consensus size: 5
185016 TTGATAATTT
* *
185026 TAATA TAAT- T-ATA TAATA TAA-A T-ATA AAATA TAAAA TAAGTA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA-TA TAATA
* * * *
185073 TAAAA TAATA TAAATA TAATA TTAATA TTAAAA T-ATA TTAAAA TTATA
1 TAATA TAATA T-AATA TAATA -TAATA -TAATA TAATA -TAATA TAATA
185121 TAATA TAA
1 TAATA TAA
185129 ATTATTAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
3 3 0.04
4 7 0.09
5 46 0.60
6 21 0.27
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:185074 original size:16 final size:15
Alignment explanation
Indices: 185036--185129 Score: 80
Period size: 13 Copynumber: 6.8 Consensus size: 15
185026 TAATATAATT
185036 ATATAATAT-AAAT-
1 ATATAATATAAAATA
*
185049 ATAAAATATAAAATA
1 ATATAATATAAAATA
185064 AGTATAATATAAAATA
1 A-TATAATATAAAATA
*
185080 ATATAA-ATATAAT-
1 ATATAATATAAAATA
*
185093 AT-TAATAT-TAA-A
1 ATATAATATAAAATA
*
185105 ATAT-AT-TAAAATT
1 ATATAATATAAAATA
185118 ATATAATATAAA
1 ATATAATATAAA
185130 TTATTAATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
11 1 0.02
12 12 0.18
13 17 0.26
14 12 0.18
15 10 0.15
16 14 0.21
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (15 bp):
ATATAATATAAAATA
Found at i:185122 original size:32 final size:32
Alignment explanation
Indices: 185086--185187 Score: 90
Period size: 32 Copynumber: 3.3 Consensus size: 32
185076 AATAATATAA
185086 ATATAATATTAATATTAAAATATATTAAAATT
1 ATATAATATTAATATTAAAATATATTAAAATT
* **
185118 ATATAATATAAATTATTAATTTA-ATTAAAATT
1 ATATAATATTAA-TATTAAAATATATTAAAATT
* *
185150 TTAT-ATA-TAAT-TATAAAATATA--AAAAAT
1 ATATAATATTAATAT-TAAAATATATTAAAATT
185178 ATATTAATAT
1 ATA-TAATAT
185188 GATTAAGATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
28 8 0.15
29 7 0.13
30 6 0.11
31 3 0.05
32 23 0.42
33 8 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATTAATATTAAAATATATTAAAATT
Found at i:185142 original size:44 final size:43
Alignment explanation
Indices: 185032--185173 Score: 120
Period size: 44 Copynumber: 3.4 Consensus size: 43
185022 ATTTTAATAT
*
185032 AATTATATAATATAAATATAA-AAT-A-TAAAA-TA-AGTATAA
1 AATTATATAATATAAATATAATATTAATTAAAATTATA-TATAA
* * *
185071 TATAAAATAATATAAATATAATATTAATATTAAAA-TATAT-TAA
1 AATTATATAATATAAATATAATATT-A-ATTAAAATTATATATAA
* *
185114 AATTATATAATATAAATTATTAAT-TTAATTAAAATTTTATATAT
1 AATTATATAATATAAA-TA-TAATATTAATTAAAATTATATATAA
*
185158 AATTATAAAATATAAA
1 AATTATATAATATAAA
185174 AAATATATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
39 18 0.22
40 2 0.02
42 7 0.08
43 22 0.27
44 29 0.35
45 5 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (43 bp):
AATTATATAATATAAATATAATATTAATTAAAATTATATATAA
Found at i:185148 original size:18 final size:18
Alignment explanation
Indices: 185117--185162 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
185107 ATATTAAAAT
185117 TATATAA-TATAAATTATTA
1 TATATAATTA-AAATT-TTA
*
185136 -ATTTAATTAAAATTTTA
1 TATATAATTAAAATTTTA
185153 TATATAATTA
1 TATATAATTA
185163 TAAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 18 0.78
19 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATAATTAAAATTTTA
Found at i:185353 original size:23 final size:23
Alignment explanation
Indices: 185308--185353 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
185298 AATATTTATA
185308 TTTTATAATTAAATATAAATAATTT
1 TTTTATAATTAAATAT--ATAATTT
185333 TTTTAATAATTAAATAT-TAAT
1 TTTT-ATAATTAAATATATAAT
185354 CAAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
25 4 0.20
26 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTATAATTAAATATATAATTT
Found at i:185363 original size:10 final size:10
Alignment explanation
Indices: 185339--185436 Score: 76
Period size: 10 Copynumber: 9.8 Consensus size: 10
185329 ATTTTTTTAA
185339 TAATTAAATAT
1 TAATTAAA-AT
*
185350 TAATCAAAAT
1 TAATTAAAAT
* *
185360 TAATTTAATT
1 TAATTAAAAT
*
185370 TAATTTAAAT
1 TAATTAAAAT
185380 TAA-TAAAAT
1 TAATTAAAAT
185389 TATATTTAAAAT
1 TA-A-TTAAAAT
*
185401 TAATTAATAT
1 TAATTAAAAT
*
185411 AAATT-AAAT
1 TAATTAAAAT
*
185420 TTATT-AAAT
1 TAATTAAAAT
*
185429 TAAATAAA
1 TAATTAAA
185437 TAATTTAATC
Statistics
Matches: 70, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
9 20 0.29
10 34 0.49
11 8 0.11
12 8 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATTAAAAT
Found at i:185379 original size:20 final size:19
Alignment explanation
Indices: 185356--185431 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
185346 ATATTAATCA
185356 AAATTAATTTAATTTAATTT
1 AAATTAA-TTAATTTAATTT
* *
185376 AAATTAATAAAATTATATTT
1 AAATTAATTAATTTA-ATTT
* *
185396 AAAATTAATTAATATAAATT
1 -AAATTAATTAATTTAATTT
* *
185416 AAATTTATTAAATTAA
1 AAATTAATTAATTTAA
185432 ATAAATAATT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
19 19 0.42
20 14 0.31
21 12 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAATTAATTTAATTT
Found at i:188476 original size:18 final size:18
Alignment explanation
Indices: 188453--188490 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
188443 ATCTCTCTAT
188453 ATATCTATACTATATTAG
1 ATATCTATACTATATTAG
188471 ATATCTATACTATATTAG
1 ATATCTATACTATATTAG
188489 AT
1 AT
188491 TAATTGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATCTATACTATATTAG
Found at i:189629 original size:3 final size:3
Alignment explanation
Indices: 189623--189666 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
189613 TAGAAACAAC
189623 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
189667 GCAATATTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:190469 original size:2 final size:2
Alignment explanation
Indices: 190462--190506 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
190452 TTAGGTGGGT
*
190462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA 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
190504 TA T
1 TA T
190507 TAATGATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:190804 original size:22 final size:21
Alignment explanation
Indices: 190779--190821 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
190769 AAAAATGTAT
190779 TAAAAATATTAAT-ATTTTTAAA
1 TAAAAATA--AATAATTTTTAAA
*
190801 TAAAAGTAAATAATTTTTAAA
1 TAAAAATAAATAATTTTTAAA
190822 CTTAAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
TAAAAATAAATAATTTTTAAA
Found at i:193247 original size:16 final size:16
Alignment explanation
Indices: 193223--193254 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
193213 TAAAAATTTC
*
193223 CATGTCCATATTGTGT
1 CATGCCCATATTGTGT
193239 CATGCCCATATTGTGT
1 CATGCCCATATTGTGT
193255 GTCCAGAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (16 bp):
CATGCCCATATTGTGT
Found at i:197594 original size:15 final size:15
Alignment explanation
Indices: 197576--197811 Score: 78
Period size: 15 Copynumber: 16.2 Consensus size: 15
197566 AAAATAATTA
197576 AATTAAATTTAAAAT
1 AATTAAATTTAAAAT
**
197591 AATTAAATCGGATAAAT
1 AATTAAAT-TTA-AAAT
*
197608 --TTAAATATTAAATTT
1 AATTAAAT-TTAAA-AT
**
197623 AATT-AATTTATATTT
1 AATTAAATTTA-AAAT
197638 AATT-AATTT-AAAT
1 AATTAAATTTAAAAT
197651 -ATTAAATTT-AAAT
1 AATTAAATTTAAAAT
*
197664 CACTTAAATTTAAAAT
1 -AATTAAATTTAAAAT
*
197680 AA-T---TTAAAAAT
1 AATTAAATTTAAAAT
197691 AATTAACA--T-AAAT
1 AATTAA-ATTTAAAAT
197704 -ATTAAATTTAATTAAT
1 AATTAAATTTAA--AAT
* * *
197720 -TTTTAACTTAAAAT
1 AATTAAATTTAAAAT
*
197734 AATTTAAAATTAAAAT
1 AA-TTAAATTTAAAAT
*
197750 AATTAAAATTAAAA-
1 AATTAAATTTAAAAT
197764 AA-T-AATTTAAAAT
1 AATTAAATTTAAAAT
**
197777 TTTTAAAATATTAAAAT
1 AATT-AAAT-TTAAAAT
* * *
197794 AATTTAATATAAATT
1 AATTAAATTTAAAAT
197809 AAT
1 AAT
197812 CAACTCAAAA
Statistics
Matches: 167, Mismatches: 27, Indels: 54
0.67 0.11 0.22
Matches are distributed among these distances:
11 10 0.06
12 17 0.10
13 17 0.10
14 10 0.06
15 59 0.35
16 39 0.23
17 15 0.09
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTAAATTTAAAAT
Found at i:197638 original size:52 final size:52
Alignment explanation
Indices: 197570--197714 Score: 136
Period size: 53 Copynumber: 2.8 Consensus size: 52
197560 AATTTAAAAA
*
197570 TAATTAAATTAAATTTAAAATAA-TTAAATCGGA-TAAATTTAAAT-A-TTAAATT
1 TAATTAATTTAAATTT-AAATAATTTAAAT---ATTAAATTTAAATCACTTAAATT
* *
197622 TAATTAATTTATATTTAATTAATTTAAATATTAAATTTAAATCACTTAAATT
1 TAATTAATTTAAATTTAAATAATTTAAATATTAAATTTAAATCACTTAAATT
* ** * **
197674 TAAAATAATTTAAAAATAATTAACATAAATATTAAATTTAA
1 T-AATTAATTTAAATTTAAATAATTTAAATATTAAATTTAA
197715 TTAATTTTTA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
49 1 0.01
50 11 0.14
51 6 0.08
52 28 0.35
53 33 0.42
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (52 bp):
TAATTAATTTAAATTTAAATAATTTAAATATTAAATTTAAATCACTTAAATT
Found at i:197675 original size:37 final size:35
Alignment explanation
Indices: 197577--197721 Score: 114
Period size: 37 Copynumber: 3.9 Consensus size: 35
197567 AAATAATTAA
*** *
197577 ATTAAATTTAAAATAATTAAATCGGATAAATTTAAAT
1 ATTAAATTT-AAAT-ATTAAATTTAATTAATTTAAAT
* *
197614 ATTAAATTTAATTAATTTATATTTAATTAATTTAAAT
1 ATTAAATTTAAAT-A-TTAAATTTAATTAATTTAAAT
*
197651 ATTAAATTTAAATCACTTAAATTTAAAATAATTTAAAAAT
1 ATTAAATTTAAAT-A-TTAAATTT-AATTAATTT--AAAT
197691 AATTAACA--TAAATATTAAATTTAATTAATTT
1 -ATTAA-ATTTAAATATTAAATTTAATTAATTT
197722 TTAACTTAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
36 5 0.06
37 53 0.59
38 16 0.18
39 1 0.01
40 9 0.10
41 5 0.06
42 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (35 bp):
ATTAAATTTAAATATTAAATTTAATTAATTTAAAT
Found at i:197691 original size:11 final size:10
Alignment explanation
Indices: 197670--197810 Score: 56
Period size: 10 Copynumber: 14.7 Consensus size: 10
197660 AAATCACTTA
197670 AATTTAAAAT
1 AATTTAAAAT
197680 AATTTAAAAAT
1 AATTT-AAAAT
*
197691 AA-TTAACAT
1 AATTTAAAAT
*
197700 AAATATTAAATTT
1 -AAT-TTAAA-AT
**
197713 AA-TTAATTTTT
1 AATTTAA--AAT
*
197724 AACTTAAAAT
1 AATTTAAAAT
197734 AATTT--AA-
1 AATTTAAAAT
197741 AA-TTAAAAT
1 AATTTAAAAT
197750 AA-TTAAAATT
1 AATTTAAAA-T
197760 AA---AAAAT
1 AATTTAAAAT
197767 AATTTAAAAT
1 AATTTAAAAT
*
197777 -TTTTAAAAT
1 AATTTAAAAT
197786 -A-TTAAAAT
1 AATTTAAAAT
*
197794 AATTTAATAT
1 AATTTAAAAT
*
197804 AAATTAA
1 AATTTAA
197811 TCAACTCAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
6 2 0.02
7 5 0.05
8 15 0.15
9 21 0.20
10 38 0.37
11 11 0.11
12 10 0.10
13 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:197703 original size:53 final size:51
Alignment explanation
Indices: 197603--197742 Score: 147
Period size: 53 Copynumber: 2.7 Consensus size: 51
197593 TTAAATCGGA
* * ** **
197603 TAAATTTAAATATTAAATTT-AATTAATTTATATTTAATTAATTTAAATAT
1 TAAATTTAAATATTAAATTTAAAATAATTTAAAAATAATTAACATAAATAT
197653 TAAATTTAAATCACTTAAATTTAAAATAATTTAAAAATAATTAACATAAATAT
1 TAAATTTAAAT-A-TTAAATTTAAAATAATTTAAAAATAATTAACATAAATAT
* * *
197706 TAAATTTAATTAATTTTTAACTTAAAATAATTTAAAA
1 TAAATTT-A--AATATTAAATTTAAAATAATTTAAAA
197743 TTAAAATAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
50 11 0.15
51 1 0.01
52 8 0.11
53 31 0.41
54 21 0.28
56 3 0.04
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (51 bp):
TAAATTTAAATATTAAATTTAAAATAATTTAAAAATAATTAACATAAATAT
Found at i:197755 original size:9 final size:9
Alignment explanation
Indices: 197727--197797 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
197717 AATTTTTAAC
197727 TTAAAATAA
1 TTAAAATAA
*
197736 TT-TAA-AA
1 TTAAAATAA
197743 TTAAAATAA
1 TTAAAATAA
197752 TTAAAATTAA
1 TTAAAA-TAA
197762 --AAAATAA
1 TTAAAATAA
**
197769 TTTAAAATTT
1 -TTAAAATAA
197779 TTAAAAT-A
1 TTAAAATAA
197787 TTAAAATAA
1 TTAAAATAA
197796 TT
1 TT
197798 TAATATAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
7 7 0.14
8 15 0.30
9 20 0.40
10 8 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTAAAATAA
Found at i:197776 original size:27 final size:27
Alignment explanation
Indices: 197743--197810 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
197733 TAATTTAAAA
197743 TTAAAATAATTAAAAT-TAAAAAATAAT
1 TTAAAATAATTAAAATAT-AAAAATAAT
** *
197770 TTAAAATTTTTAAAATATTAAAATAAT
1 TTAAAATAATTAAAATATAAAAATAAT
*
197797 TTAATATAAATTAA
1 TTAAAAT-AATTAA
197811 TCAACTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 28 0.85
28 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TTAAAATAATTAAAATATAAAAATAAT
Found at i:197792 original size:17 final size:18
Alignment explanation
Indices: 197727--197793 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
197717 AATTTTTAAC
197727 TTAAAATAATTTAAAA---
1 TTAAAATAA-TTAAAATTT
197743 TTAAAATAATTAAAA-TT
1 TTAAAATAATTAAAATTT
**
197760 AAAAAATAATTTAAAATTT
1 TTAAAATAA-TTAAAATTT
197779 TTAAAAT-ATTAAAAT
1 TTAAAATAATTAAAAT
197794 AATTTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.14
16 9 0.21
17 14 0.33
18 7 0.16
19 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAATTAAAATTT
Found at i:199325 original size:17 final size:17
Alignment explanation
Indices: 199303--199336 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
199293 ATCATTTTAA
199303 AATTAAATAAAA-ATATT
1 AATT-AATAAAATATATT
199320 AATTAATAAAATATATT
1 AATTAATAAAATATATT
199337 TTTGTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAATAAAATATATT
Found at i:204209 original size:18 final size:18
Alignment explanation
Indices: 204176--204220 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
204166 CAAAGATTTA
* *
204176 ATAATATTAAACATAAAT
1 ATAATATAAAAAATAAAT
*
204194 ATAATATAAAAAATAATT
1 ATAATATAAAAAATAAAT
*
204212 AAAATATAA
1 ATAATATAA
204221 CACAATGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATATAAAAAATAAAT
Found at i:204298 original size:17 final size:17
Alignment explanation
Indices: 204258--204300 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
204248 ATTTATATAT
* * *
204258 TATAAAAATTATTAACA
1 TATAAAATTTATAAAAA
204275 TATTAAAATTTATAAAAA
1 TA-TAAAATTTATAAAAA
204293 TATAAAAT
1 TATAAAAT
204301 ATGTTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAAAATTTATAAAAA
Found at i:205348 original size:22 final size:21
Alignment explanation
Indices: 205300--205349 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
205290 GTTTACAATT
*
205300 ATAAAGTGGATAATTTTTTTGG
1 ATAAA-TGGATAATTTTTTAGG
* *
205322 CTAAATGGATAGTTTTTTAGG
1 ATAAATGGATAATTTTTTAGG
205343 AATAAAT
1 -ATAAAT
205350 AAATTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (21 bp):
ATAAATGGATAATTTTTTAGG
Found at i:207331 original size:2 final size:2
Alignment explanation
Indices: 207324--207352 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
207314 ACATATCAAA
207324 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
207353 ATAACTTAAG
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:208921 original size:9 final size:9
Alignment explanation
Indices: 208905--208949 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
208895 TTTCGTAAGC
208905 TAAAAAAAA
1 TAAAAAAAA
208914 TTAAAAAATAA
1 -TAAAAAA-AA
*
208925 TAAAAATAA
1 TAAAAAAAA
208934 TAGAAAAAAA
1 TA-AAAAAAA
208944 TAAAAA
1 TAAAAA
208950 TTATAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 8 0.26
10 21 0.68
11 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:208955 original size:9 final size:9
Alignment explanation
Indices: 208917--208955 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
208907 AAAAAAATTA
208917 AAAAATAAT
1 AAAAATAAT
208926 AAAAATAAT
1 AAAAATAAT
*
208935 AGAAAAAAAT
1 A-AAAATAAT
*
208945 AAAAATTAT
1 AAAAATAAT
208954 AA
1 AA
208956 TAAAGGGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:218337 original size:17 final size:16
Alignment explanation
Indices: 218312--218346 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
218302 CCATTTTTCC
218312 TTTTCCTTTTTGTTTTT
1 TTTTCCTTTTT-TTTTT
*
218329 TTTTTCTTTTTTTTTT
1 TTTTCCTTTTTTTTTT
218345 TT
1 TT
218347 AAATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTCCTTTTTTTTTT
Found at i:219888 original size:13 final size:14
Alignment explanation
Indices: 219870--219898 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
219860 TATCAAATAT
219870 ATATTCATA-TTAA
1 ATATTCATATTTAA
219883 ATATTCATATTTAA
1 ATATTCATATTTAA
219897 AT
1 AT
219899 TCGAACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATTCATATTTAA
Found at i:220637 original size:23 final size:23
Alignment explanation
Indices: 220607--220652 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
220597 TCCCAATCAC
*
220607 CAACTGGTCTTCTTCAGATGTTT
1 CAACTGGTCTCCTTCAGATGTTT
220630 CAACTGGTCTCCTTCAGATGTTT
1 CAACTGGTCTCCTTCAGATGTTT
220653 GAGGGCATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (23 bp):
CAACTGGTCTCCTTCAGATGTTT
Found at i:225183 original size:37 final size:40
Alignment explanation
Indices: 225142--225218 Score: 99
Period size: 38 Copynumber: 2.0 Consensus size: 40
225132 TTTAATTACT
*
225142 ATTTT-TAAAAAATATACT-TAAT-ATATT-TTTTTATTAA
1 ATTTTGTAAAAAA-ATAATGTAATAATATTGTTTTTATTAA
*
225179 ATTTTGTAAAAAAATAATGTATTAATATTGTTTTTATTAA
1 ATTTTGTAAAAAAATAATGTAATAATATTGTTTTTATTAA
225219 TATCATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 9 0.26
38 10 0.29
39 5 0.15
40 10 0.29
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (40 bp):
ATTTTGTAAAAAAATAATGTAATAATATTGTTTTTATTAA
Found at i:225708 original size:25 final size:26
Alignment explanation
Indices: 225680--225730 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
225670 AAAGTGAGAA
225680 AAATTATATTTT-TTATTTTTATAAT
1 AAATTATATTTTATTATTTTTATAAT
* *
225705 AAATTTTATTTTATTATTTTTTTAAT
1 AAATTATATTTTATTATTTTTATAAT
225731 TTATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
AAATTATATTTTATTATTTTTATAAT
Found at i:227733 original size:34 final size:34
Alignment explanation
Indices: 227688--227752 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
227678 AAACTTTAAA
*
227688 AAAAATAAACATATCTGTGTCAGACACATACCTG
1 AAAAATAAACATATCTATGTCAGACACATACCTG
* *
227722 AAAAATGAACATATCTATGTCGGACACATAC
1 AAAAATAAACATATCTATGTCAGACACATAC
227753 TTGTATCTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (34 bp):
AAAAATAAACATATCTATGTCAGACACATACCTG
Found at i:230046 original size:2 final size:2
Alignment explanation
Indices: 230039--230071 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
230029 TAAGAGCAAC
230039 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
230072 CTAAGAGATT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:234132 original size:13 final size:13
Alignment explanation
Indices: 234109--234158 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
234099 ATGTGTATAT
234109 TTTTATTATATTTA
1 TTTT-TTATATTTA
234123 TTTTTTATA-TTA
1 TTTTTTATATTTA
* *
234135 TGTTTTA-ATTATT
1 TTTTTTATATT-TA
234148 TTTTTTATATT
1 TTTTTTATATT
234159 CAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.03
12 10 0.33
13 12 0.40
14 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTTATATTTA
Found at i:237528 original size:18 final size:16
Alignment explanation
Indices: 237507--237541 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
237497 TTAACTTATC
237507 AAATATTATATAAATATA
1 AAATATT-T-TAAATATA
237525 AAATATTTTAAATATA
1 AAATATTTTAAATATA
237541 A
1 A
237542 TTATAATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATTTTAAATATA
Found at i:237577 original size:29 final size:31
Alignment explanation
Indices: 237508--237578 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
237498 TAACTTATCA
*
237508 AATATTATATAAATATAAAATATTTTAAATAT
1 AATATTA-ATAAATATAAAATATTATAAATAT
*
237540 AAT-TATAATACA-ATAAAATA-TATAAATAT
1 AATAT-TAATAAATATAAAATATTATAAATAT
237569 AATATTAATA
1 AATATTAATA
237579 TATAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 16 0.46
30 9 0.26
31 5 0.14
32 5 0.14
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
AATATTAATAAATATAAAATATTATAAATAT
Found at i:239080 original size:18 final size:18
Alignment explanation
Indices: 239038--239080 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
239028 TATATAATAT
239038 AAATTA-CTAATATATAA
1 AAATTATCTAATATATAA
239055 AAATTTATCTAA-ATATAA
1 AAA-TTATCTAATATATAA
239073 AATATTAT
1 AA-ATTAT
239081 AAAAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTATCTAATATATAA
Found at i:239093 original size:12 final size:11
Alignment explanation
Indices: 239068--239100 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
239058 TTTATCTAAA
239068 TATAAAAT-AT
1 TATAAAATAAT
239078 TATAAAAATAAT
1 TAT-AAAATAAT
239090 TATAAAATAAT
1 TATAAAATAAT
239101 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 13 0.62
12 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:239113 original size:27 final size:28
Alignment explanation
Indices: 239046--239114 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 28
239036 ATAAATTACT
*
239046 AATATATAAA-AATTTATCTAAATATAA
1 AATATATAAATAATTTATCAAAATATAA
239073 AATATTATAAA-AATAATTAT-AAAATAATAA
1 AATA-TATAAATAAT--TTATCAAAAT-ATAA
239103 AATATATAAATA
1 AATATATAAATA
239115 CGATATAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 4 0.11
28 9 0.25
29 10 0.28
30 13 0.36
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
AATATATAAATAATTTATCAAAATATAA
Found at i:243160 original size:38 final size:34
Alignment explanation
Indices: 243118--243206 Score: 92
Period size: 38 Copynumber: 2.5 Consensus size: 34
243108 TGATGTGATT
243118 TATATAAATAATATTATATCATATGTAAAAGATAAATA
1 TATATAAATAATATTATATCAT-T-TAAAA-A-AAATA
** *
243156 TATATGATGTAAT-TTATATCATTTATAAAAAATA
1 TATAT-AAATAATATTATATCATTTAAAAAAAATA
243190 -ATATAAATAATATTATA
1 TATATAAATAATATTATA
243207 GTGTAAACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
32 5 0.11
33 9 0.20
34 5 0.11
35 1 0.02
36 4 0.09
37 1 0.02
38 14 0.32
39 5 0.11
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (34 bp):
TATATAAATAATATTATATCATTTAAAAAAAATA
Found at i:243311 original size:21 final size:21
Alignment explanation
Indices: 243269--243311 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
243259 AAAAATTATT
*
243269 AAATTAAAAATATATATTTAA
1 AAATTAAAAATATATATATAA
243290 AAATTAAAAA-ATATAATATAA
1 AAATTAAAAATATAT-ATATAA
243311 A
1 A
243312 TAAATCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTAAAAATATATATATAA
Found at i:243416 original size:46 final size:45
Alignment explanation
Indices: 243328--243477 Score: 160
Period size: 46 Copynumber: 3.2 Consensus size: 45
243318 TGAACGAACT
* *
243328 ATAAATTTAAAATATAAATAAATATAAATAATTTTAAAATTTATATTTTAA
1 ATAAA-TT-AAATTTAAATAAATAT--ATAATATT--AATTTATATTTTAA
243379 ATCAAATTAAATTTAAATAAATATATAATATTAATTTATATTTTAA
1 AT-AAATTAAATTTAAATAAATATATAATATTAATTTATATTTTAA
* *
243425 ATTAAATTAAATTTAAATAAATAAAT-ATA-TAATATTATTATTATAA
1 A-TAAATTAAATTTAAATAAATATATAATATTAAT-TTA-TATTTTAA
243471 ATAAATT
1 ATAAATT
243478 TGATCTAATT
Statistics
Matches: 91, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
44 4 0.04
45 12 0.13
46 45 0.49
47 1 0.01
48 7 0.08
50 15 0.16
51 4 0.04
52 3 0.03
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (45 bp):
ATAAATTAAATTTAAATAAATATATAATATTAATTTATATTTTAA
Found at i:243428 original size:17 final size:16
Alignment explanation
Indices: 243374--243450 Score: 58
Period size: 16 Copynumber: 5.1 Consensus size: 16
243364 AAATTTATAT
*
243374 TTTAAATCAAATTAAA
1 TTTAAATTAAATTAAA
243390 TTTAAA-TAAA-T--A
1 TTTAAATTAAATTAAA
* * *
243402 TATAATATTAATTTATAT
1 TTTAA-ATTAAATTA-AA
243420 TTTAAATTAAATTAAA
1 TTTAAATTAAATTAAA
243436 TTTAAA-TAAA-TAAA
1 TTTAAATTAAATTAAA
243450 T
1 T
243451 ATATAATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
12 5 0.10
13 1 0.02
14 9 0.19
15 8 0.17
16 13 0.27
17 8 0.17
18 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:243448 original size:50 final size:47
Alignment explanation
Indices: 243334--243461 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 47
243324 AACTATAAAT
* *
243334 TTAAAATATAAATAAATATAAATAATTTTAAAATTTATATTTTAAATCAAA
1 TTAAATTATAAATAAATAT--ATAATATT--AATTTATATTTTAAATCAAA
*
243385 TTAAATT-TAAATAAATATATAATATTAATTTATATTTTAAATTAAA
1 TTAAATTATAAATAAATATATAATATTAATTTATATTTTAAATCAAA
243431 TTAAATTTAAATAAATAAATATATAATATTA
1 TTAAA-TT--ATAAATAAATATATAATATTA
243462 TTATTATAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
46 24 0.34
47 2 0.03
48 7 0.10
50 31 0.44
51 6 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (47 bp):
TTAAATTATAAATAAATATATAATATTAATTTATATTTTAAATCAAA
Found at i:243489 original size:50 final size:50
Alignment explanation
Indices: 243341--243477 Score: 131
Period size: 50 Copynumber: 2.7 Consensus size: 50
243331 AATTTAAAAT
* ** *
243341 ATAAATAAATATAAATAATTTTAAAATTTATATTTTAAATCAAATTAAA-TT--
1 ATAAATAAATAT--ATAATATT--AATTTATATAATAAATTAAATTAAATTTAA
**
243392 -TAAATAAATATATAATATTAATTTATATTTTAAATTAAATTAAATTTAA
1 ATAAATAAATATATAATATTAATTTATATAATAAATTAAATTAAATTTAA
*
243441 ATAAATAAATATATAATATTATTATTATA-AATAAATT
1 ATAAATAAATATATAATATTAAT-TTATATAATAAATT
243478 TGATCTAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
46 24 0.32
47 2 0.03
48 7 0.09
50 38 0.50
51 5 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.45
Consensus pattern (50 bp):
ATAAATAAATATATAATATTAATTTATATAATAAATTAAATTAAATTTAA
Found at i:243740 original size:16 final size:16
Alignment explanation
Indices: 243719--243790 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
243709 TCAGTTTAAT
243719 ATATTAAATTTAATTA
1 ATATTAAATTTAATTA
*
243735 ATATTAAAATTAATTA
1 ATATTAAATTTAATTA
* *
243751 A-A-TCAATTCATATTA
1 ATATTAAATTTA-ATTA
*
243766 ATATTAAAATTAA--A
1 ATATTAAATTTAATTA
243780 ATAATTAAATT
1 AT-ATTAAATT
243791 AATATTAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
14 8 0.18
15 13 0.30
16 18 0.41
17 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTAAATTTAATTA
Found at i:243766 original size:31 final size:28
Alignment explanation
Indices: 243725--243808 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 28
243715 TAATATATTA
*
243725 AATTTAATTAATATTAAAATTAATTAAAT
1 AATTAAATTAATATTAAAATT-ATTAAAT
*
243754 CAATTCATATTAATATTAAAATTA--AAAT
1 -AATT-AAATTAATATTAAAATTATTAAAT
243782 AATTAAATTAATATTAAAATTGATTAA
1 AATTAAATTAATATTAAAATT-ATTAA
243809 TTTTTTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 16 0.34
27 5 0.11
28 4 0.09
29 2 0.04
30 5 0.11
31 15 0.32
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
AATTAAATTAATATTAAAATTATTAAAT
Found at i:243830 original size:11 final size:12
Alignment explanation
Indices: 243813--243853 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
243803 GATTAATTTT
243813 TTATTTTAAATA
1 TTATTTTAAATA
243825 -TATTTTAAATA
1 TTATTTTAAATA
243836 TTATTTT---TA
1 TTATTTTAAATA
243845 TTATTTTAA
1 TTATTTTAA
243854 TTTAATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.35
11 11 0.42
12 6 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTATTTTAAATA
Found at i:243951 original size:14 final size:15
Alignment explanation
Indices: 243932--243964 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
243922 CGATCAAAAT
*
243932 TTAAATTAAA-TTAA
1 TTAAATCAAATTTAA
243946 TTAAATCAAATTTAA
1 TTAAATCAAATTTAA
243961 TTAA
1 TTAA
243965 TTTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAATCAAATTTAA
Found at i:243992 original size:25 final size:26
Alignment explanation
Indices: 243945--243996 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
243935 AATTAAATTA
243945 ATTAAATCAAATTTAATTAATTTTTT
1 ATTAAATCAAATTTAATTAATTTTTT
* * * *
243971 ATTAAATTAATTTTAATCATTTTTTT
1 ATTAAATCAAATTTAATTAATTTTTT
243997 CTCCCCATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (26 bp):
ATTAAATCAAATTTAATTAATTTTTT
Found at i:244417 original size:42 final size:42
Alignment explanation
Indices: 244332--244418 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
244322 TCTTATTCGA
* *
244332 TTATAATAGAATTAATAATATTATTATTCGTTATTTATTTAT
1 TTATAATAGAATTAATAATATTATTATTCATTATTTATATAT
* *
244374 TTATAATATAATTAATAATATTTATGT-TTTATTATTT-TATAT
1 TTATAATAGAATTAATAATA-TTAT-TATTCATTATTTATATAT
244416 TTA
1 TTA
244419 AAACTAACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 26 0.67
43 12 0.31
44 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (42 bp):
TTATAATAGAATTAATAATATTATTATTCATTATTTATATAT
Found at i:246244 original size:16 final size:17
Alignment explanation
Indices: 246223--246257 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
246213 ATGAGTTATT
*
246223 TTTATTTTTATTTA-AA
1 TTTATTTATATTTATAA
246239 TTTATTTATATTTATAA
1 TTTATTTATATTTATAA
246256 TT
1 TT
246258 AAATAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTTATATTTATAA
Found at i:246250 original size:22 final size:22
Alignment explanation
Indices: 246218--246261 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
246208 GAAATATGAG
* * *
246218 TTATTTTTATTTTTATTTAAAT
1 TTATTTATATTTATAATTAAAT
246240 TTATTTATATTTATAATTAAAT
1 TTATTTATATTTATAATTAAAT
246262 AATCTCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTATATTTATAATTAAAT
Found at i:246459 original size:20 final size:19
Alignment explanation
Indices: 246419--246485 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
246409 AACTAGTAAA
*
246419 ATAAAAT-TACAATATTATT
1 ATAAAATATAAAAT-TTATT
* *
246438 ATAAAATGTATAATTATATT
1 ATAAAATATAAAATT-TATT
*
246458 ATAAAATATAAAATTTATA
1 ATAAAATATAAAATTTATT
246477 ATAAAATAT
1 ATAAAATAT
246486 TTTATTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.48
20 22 0.52
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (19 bp):
ATAAAATATAAAATTTATT
Found at i:246919 original size:2 final size:2
Alignment explanation
Indices: 246912--246946 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
246902 TCACTATCAC
246912 TA 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 TA T
246947 GACAATCATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:247206 original size:16 final size:15
Alignment explanation
Indices: 247149--247205 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 15
247139 AAAAAGATGG
*
247149 ATTAATTT-ATTATA
1 ATTAATTTAATTAAA
*
247163 ATTAA-TTAATCAAA
1 ATTAATTTAATTAAA
247177 TATTAATTTAATTTAAA
1 -ATTAATTTAA-TTAAA
247194 ATTAATTTAATT
1 ATTAATTTAATT
247206 TTTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 2 0.06
14 9 0.25
15 7 0.19
16 14 0.39
17 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTAATTTAATTAAA
Found at i:247540 original size:29 final size:29
Alignment explanation
Indices: 247507--247573 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
247497 ATTTTCAAAT
* *
247507 AAATTTAAATTTATTTAAATAT-AAATTAA
1 AAATTAAAATTAATTTAAAT-TCAAATTAA
247536 AAATTAAAATTAATTTAAATTCAAATTAA
1 AAATTAAAATTAATTTAAATTCAAATTAA
*
247565 AAATAAAAA
1 AAATTAAAA
247574 AATTTATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (29 bp):
AAATTAAAATTAATTTAAATTCAAATTAA
Found at i:247561 original size:16 final size:15
Alignment explanation
Indices: 247506--247564 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
247496 TATTTTCAAA
*
247506 TAAATTTAAATTTATT
1 TAAA-TTAAATTAATT
247522 TAAATATAAATTAA--
1 TAAAT-TAAATTAATT
247536 -AAATTAAAATTAATT
1 TAAATT-AAATTAATT
247551 TAAATTCAAATTAA
1 TAAATT-AAATTAA
247565 AAATAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
12 1 0.03
13 11 0.31
15 1 0.03
16 23 0.64
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATTAAATTAATT
Found at i:247631 original size:21 final size:22
Alignment explanation
Indices: 247605--247651 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
247595 TAGTACCAAG
247605 ATTTTTTTAATATTT-TATTTT-
1 ATTTTTTTAAT-TTTCTATTTTC
*
247626 ATTTTTTTCATTTTCTATTTTC
1 ATTTTTTTAATTTTCTATTTTC
247648 ATTT
1 ATTT
247652 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 3 0.13
21 16 0.70
22 4 0.17
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTTTTAATTTTCTATTTTC
Found at i:257353 original size:2 final size:2
Alignment explanation
Indices: 257346--257387 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
257336 TAGTATAAAA
257346 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
257388 TCCACATCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:258192 original size:25 final size:25
Alignment explanation
Indices: 258158--258209 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
258148 TGCTGCCTCT
258158 TTCTCTTTGTTAACGATGACTAAAC
1 TTCTCTTTGTTAACGATGACTAAAC
**
258183 TTCTCTTTGTTAGTGATGACTAAAC
1 TTCTCTTTGTTAACGATGACTAAAC
258208 TT
1 TT
258210 ACTGTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (25 bp):
TTCTCTTTGTTAACGATGACTAAAC
Found at i:259447 original size:19 final size:20
Alignment explanation
Indices: 259424--259483 Score: 72
Period size: 19 Copynumber: 3.1 Consensus size: 20
259414 TTATTTAGAT
*
259424 TTTAATATAAATATTAAATA
1 TTTAATATAAATAATAAATA
*
259444 -TTAATAT-AATAATATATA
1 TTTAATATAAATAATAAATA
*
259462 TTTAATATAAA-AATATATA
1 TTTAATATAAATAATAAATA
259481 TTT
1 TTT
259484 TTTAAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 9 0.25
19 25 0.69
20 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATATAAATAATAAATA
Found at i:259555 original size:20 final size:21
Alignment explanation
Indices: 259517--259555 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
259507 TAATTTTTAA
**
259517 AAAAATTATATTATTTATATT
1 AAAAATTATATTAAATATATT
259538 AAAAA-TATATTAAATATA
1 AAAAATTATATTAAATATA
259556 AATATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAATTATATTAAATATATT
Found at i:260824 original size:2 final size:2
Alignment explanation
Indices: 260817--260860 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
260807 TAATGACAGC
260817 AT AT AT 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
260859 AT
1 AT
260861 GAATTTCGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261402 original size:3 final size:3
Alignment explanation
Indices: 261394--261452 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
261384 CCTAAACATG
261394 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
261442 TAA TAA TAA TA
1 TAA TAA TAA TA
261453 TATGTACCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:261487 original size:161 final size:161
Alignment explanation
Indices: 261299--261589 Score: 537
Period size: 161 Copynumber: 1.8 Consensus size: 161
261289 GATTGATTTG
* *
261299 CACATCCATCTATATAAAAGCTTGAAAATATCAATTTCAAATGTAAATTAATATGATATACAATG
1 CACATCCATCTATATAAAAACTTGAAAATATCAATTCCAAATGTAAATTAATATGATATACAATG
*
261364 CTCAACCTTACTAATTCAAGCCTAAACATGTAATAATAATAATAATAATAATAATAATAATAATA
66 CTCAACCTTACTAATTCAAGCCTAAACATGCAATAATAATAATAATAATAATAATAATAATAATA
261429 ATAATAATAATAATAATAATAATATATGTAC
131 ATAATAATAATAATAATAATAATATATGTAC
* *
261460 CACATCCATCTATATAAAAATTTGAAAATATCAATTCCAAATGTATATTAATATGATATACAATG
1 CACATCCATCTATATAAAAACTTGAAAATATCAATTCCAAATGTAAATTAATATGATATACAATG
261525 CTCAACCTTACTAATTCAAGCCTAAACATGCAATAATAATAATAATAATAATAATAATAATAATA
66 CTCAACCTTACTAATTCAAGCCTAAACATGCAATAATAATAATAATAATAATAATAATAATAATA
261590 TATGTATATG
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
161 125 1.00
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (161 bp):
CACATCCATCTATATAAAAACTTGAAAATATCAATTCCAAATGTAAATTAATATGATATACAATG
CTCAACCTTACTAATTCAAGCCTAAACATGCAATAATAATAATAATAATAATAATAATAATAATA
ATAATAATAATAATAATAATAATATATGTAC
Found at i:261564 original size:3 final size:3
Alignment explanation
Indices: 261556--261589 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
261546 CTAAACATGC
261556 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
261590 TATGTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:263460 original size:18 final size:19
Alignment explanation
Indices: 263422--263465 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
263412 TTAGGATGAT
*
263422 TATTATGTCGTAATAATAA
1 TATTATGTAGTAATAATAA
263441 TATTATGTAGTAAT-ATAA
1 TATTATGTAGTAATAATAA
263459 TATTATG
1 TATTATG
263466 ATGATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.45
Consensus pattern (19 bp):
TATTATGTAGTAATAATAA
Found at i:264245 original size:21 final size:21
Alignment explanation
Indices: 264203--264245 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
264193 TAGATTCGAA
* *
264203 TCTTATTTCTACATTTACTTC
1 TCTTATTTCTACATTGAATTC
* *
264224 TCTTATTTTTATATTGAATTC
1 TCTTATTTCTACATTGAATTC
264245 T
1 T
264246 TCATTATACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.02, T:0.60
Consensus pattern (21 bp):
TCTTATTTCTACATTGAATTC
Found at i:265122 original size:38 final size:37
Alignment explanation
Indices: 265080--265162 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 37
265070 TATATAAAAA
265080 TTATATTAAATTTAGAAAT-TCAAAATAAAAATTTACAG
1 TTATATTAAATTTAGAAATCT-AAAAT-AAAATTTACAG
*
265118 TTATATTAAATTTAGAAATCTAAAATAAAATTTATAG
1 TTATATTAAATTTAGAAATCTAAAATAAAATTTACAG
265155 TATATATT
1 T-TATATT
265163 TATTTTCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
37 11 0.26
38 30 0.71
39 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.41
Consensus pattern (37 bp):
TTATATTAAATTTAGAAATCTAAAATAAAATTTACAG
Found at i:268120 original size:2 final size:2
Alignment explanation
Indices: 268113--268153 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
268103 TAACAATTTA
268113 AT AT AT 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 AT AT AT A
268154 ACTAGGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:268480 original size:3 final size:3
Alignment explanation
Indices: 268472--268531 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
268462 TGACCAAAAT
268472 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
268520 ATA ATA ATA ATA
1 ATA ATA ATA ATA
268532 TTTTCCATCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:271407 original size:32 final size:32
Alignment explanation
Indices: 271371--271440 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
271361 TATTAAATAT
* *
271371 TTATATAAATTTTGATACATTAATA-ATTTATA
1 TTATATAAA-TTTAAAACATTAATATATTTATA
* *
271403 TTATATAAATTTAAAATATTTATATATTTATA
1 TTATATAAATTTAAAACATTAATATATTTATA
271435 TTATAT
1 TTATAT
271441 CCATATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 11 0.33
32 22 0.67
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
TTATATAAATTTAAAACATTAATATATTTATA
Found at i:271712 original size:14 final size:14
Alignment explanation
Indices: 271661--271713 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
271651 TTTTATCATA
271661 TTTATATATTTTAT
1 TTTATATATTTTAT
271675 TTTATCATAATTTTAT
1 TTTAT-AT-ATTTTAT
* *
271691 TTAAAATATTTTAT
1 TTTATATATTTTAT
271705 ATTTA-ATAT
1 -TTTATATAT
271714 AAATTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 16 0.48
15 7 0.21
16 10 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATATATTTTAT
Found at i:272238 original size:19 final size:18
Alignment explanation
Indices: 272214--272258 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
272204 CATGTAAATA
*
272214 TAAATATAATTAAATTTAT
1 TAAATATAATTAAAATT-T
272233 TAAATAT-ATTAAAATTT
1 TAAATATAATTAAAATTT
272250 TAAATATAA
1 TAAATATAA
272259 ATACGTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 8 0.33
18 9 0.38
19 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATATAATTAAAATTT
Found at i:272247 original size:10 final size:9
Alignment explanation
Indices: 272214--272257 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
272204 CATGTAAATA
272214 TAAATATAAT
1 TAAATAT-AT
*
272224 TAAATTTAT
1 TAAATATAT
272233 TAAATATAT
1 TAAATATAT
*
272242 TAAA-ATTT
1 TAAATATAT
272250 TAAATATA
1 TAAATATA
272258 AATACGTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 7 0.24
9 16 0.55
10 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TAAATATAT
Found at i:272254 original size:17 final size:18
Alignment explanation
Indices: 272214--272257 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
272204 CATGTAAATA
*
272214 TAAATATAATTAAATTTAT
1 TAAATAT-ATTAAAATTAT
272233 TAAATATATTAAAATT-T
1 TAAATATATTAAAATTAT
272250 TAAATATA
1 TAAATATA
272258 AATACGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 8 0.33
19 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATATTAAAATTAT
Found at i:273042 original size:16 final size:16
Alignment explanation
Indices: 273023--273057 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
273013 TTTTTTATTT
273023 TTTAAATTATATTTAA
1 TTTAAATTATATTTAA
* *
273039 TTTAATTTATATTTTA
1 TTTAAATTATATTTAA
273055 TTT
1 TTT
273058 TATTATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAAATTATATTTAA
Found at i:273413 original size:43 final size:44
Alignment explanation
Indices: 273348--273454 Score: 105
Period size: 43 Copynumber: 2.5 Consensus size: 44
273338 ATTAAAATAT
* *
273348 TTTTTAAT-TTTAT-AACTATTTATCCTATAT-TTTAATTTAAAA
1 TTTTTAATATTTATAAAATATTTATCATATATATTTAATTT-AAA
* * *
273390 TTTTTAATATTTATAAAAT-TTTATGATATATATTTTATTTAAT
1 TTTTTAATATTTATAAAATATTTATCATATATATTTAATTTAAA
* *
273433 TTTTTAAAAATTTATATAATAT
1 TTTTT-AATATTTATAAAATAT
273455 AAAATTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
42 8 0.15
43 22 0.42
44 22 0.42
45 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (44 bp):
TTTTTAATATTTATAAAATATTTATCATATATATTTAATTTAAA
Done.