Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 2 of 27
Found at i:203727 original size:164 final size:165
Alignment explanation
Indices: 203534--203973 Score: 412
Period size: 164 Copynumber: 2.7 Consensus size: 165
203524 AAACCTAGTT
* * *
203534 TTTCGG-AAACAGGAGAATTTCAAAAAAAATGAAAAATCT-ATGGAAAT-AAATGAATTTTTCAA
1 TTTCGGAAAACAGAAAAATTTCAAAAAAAATGAAAAAT-TAAT-GAAATAAAAGGAATTTTTCAA
* * ** *
203596 AACTAATTTAC-TATGAATTAGATGATGGTATTTTATGAATTTTAAAAATT-ATAAACCAAGAAA
64 AACTAATTT-CTTATGAATTAAATAATAATATTTAATGAATTTT-AAAATTGATAAACCAAGAAA
* * *
203659 AATCCCT-CGAAAACATTTACAGAGTAGAAAACTCCATA
127 AATCCCTCCAAAAAAATTTACAGAGAAGAAAACTCCATA
* **
203697 TTT-GGAAAACAGAAAAATTTCAAGAAAAAATGAAAACTTAATGAAATAAAAGGAATTTTTTGAA
1 TTTCGGAAAACAGAAAAATTTCAA-AAAAAATGAAAAATTAATGAAATAAAAGGAATTTTTCAAA
* * *
203761 ACTAATTTCTTGTGAGTTAAATAATAATATTTAATGAATTTTAAAATTGATAAACCAATAAAAAT
65 ACTAATTTCTTATGAATTAAATAATAATATTTAATGAATTTTAAAATTGATAAACCAAGAAAAAT
* *
203826 CCGTCCAAAAAAATTTACGGAGAAGAAAACTCCATA
130 CCCTCCAAAAAAATTTACAGAGAAGAAAACTCCATA
*** * * * ** *
203862 TTTCGG-AAACAATGGAAGTTTTAATGAAAAAAAATGAAAAACTCATGAAA-ATGAGTAAATTTT
1 TTTCGGAAAAC-A--GAAAAATT--TCAAAAAAAATGAAAAATTAATGAAATAAAAG-GAATTTT
* * *** *
203925 TGAAAACTGATTTAACATGAATTAAATAATAATATTTAATAAATTTTAA
60 TCAAAACTAATTTCTTATGAATTAAATAATAATATTTAATGAATTTTAA
203974 TATTTGAAAT
Statistics
Matches: 225, Mismatches: 38, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
162 2 0.01
163 31 0.14
164 79 0.35
165 34 0.15
166 3 0.01
168 8 0.04
169 65 0.29
170 3 0.01
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (165 bp):
TTTCGGAAAACAGAAAAATTTCAAAAAAAATGAAAAATTAATGAAATAAAAGGAATTTTTCAAAA
CTAATTTCTTATGAATTAAATAATAATATTTAATGAATTTTAAAATTGATAAACCAAGAAAAATC
CCTCCAAAAAAATTTACAGAGAAGAAAACTCCATA
Found at i:204833 original size:14 final size:15
Alignment explanation
Indices: 204805--204834 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
204795 TACCATCACT
204805 ACCCTTAGAAAATCG
1 ACCCTTAGAAAATCG
204820 ACCCTTAG-AAATCG
1 ACCCTTAGAAAATCG
204834 A
1 A
204835 GAGCAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
ACCCTTAGAAAATCG
Found at i:206207 original size:14 final size:15
Alignment explanation
Indices: 206188--206219 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
206178 CTTTCACTTT
206188 TTTATTTTT-AATTA
1 TTTATTTTTAAATTA
206202 TTTATTTTTAAATTA
1 TTTATTTTTAAATTA
206217 TTT
1 TTT
206220 TATATTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTTAAATTA
Found at i:206287 original size:25 final size:27
Alignment explanation
Indices: 206231--206290 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
206221 ATATTCATTT
* *
206231 ATTTTAATATAAATATAATTTTTAATT
1 ATTTTAATACAAATATAATTTTTAATA
206258 A-TTTAATACAAAT-TAA-TTTTAATA
1 ATTTTAATACAAATATAATTTTTAATA
206282 ATTTTAATA
1 ATTTTAATA
206291 AGTTATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 8 0.27
25 10 0.33
26 11 0.37
27 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTTAATACAAATATAATTTTTAATA
Found at i:206351 original size:24 final size:23
Alignment explanation
Indices: 206279--206352 Score: 76
Period size: 25 Copynumber: 3.1 Consensus size: 23
206269 ATTAATTTTA
* * *
206279 ATAATTTTAATAAGTTATTTAAC
1 ATAATTTTAATAATTTAATTAAT
* *
206302 ATAATTTTTATTATTTAATATAAAT
1 ATAATTTTAATAATTTAAT-T-AAT
206327 ATAATTTTAATAATTTCAATTAAT
1 ATAATTTTAATAATTT-AATTAAT
206351 AT
1 AT
206353 TTATAACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
23 15 0.37
24 6 0.15
25 17 0.41
26 3 0.07
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (23 bp):
ATAATTTTAATAATTTAATTAAT
Found at i:206355 original size:56 final size:56
Alignment explanation
Indices: 206245--206355 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 56
206235 TAATATAAAT
*
206245 ATAATTTTTAATTATTTAATACAAATTAATTTTAATAATTTTAATAAGTTATTTAAC
1 ATAATTTTTAATTATTTAATACAAATTAATTTTAATAATTTCAATAAG-TATTTAAC
*
206302 ATAATTTTT-ATTATTTAATATAAATATAATTTTAATAATTTCAATTAA-TATTTA
1 ATAATTTTTAATTATTTAATACAAAT-TAATTTTAATAATTTCAA-TAAGTATTTA
206356 TAACATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
56 21 0.42
57 26 0.52
58 3 0.06
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (56 bp):
ATAATTTTTAATTATTTAATACAAATTAATTTTAATAATTTCAATAAGTATTTAAC
Found at i:206420 original size:37 final size:37
Alignment explanation
Indices: 206307--206421 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 37
206297 TTAACATAAT
*
206307 TTTTATTATTTAATATAAATATAATTTTAATAATTTCA
1 TTTTATTATTTAATATAAATATAATTTTAATTATTT-A
* * *
206345 -ATTAATATTT-ATA-ACATATATAATTTT-ATT-TGTA
1 TTTTATTATTTAATATA-A-ATATAATTTTAATTATTTA
206379 TTTTATTATTTAATATAAATA-AATTTTAAATTATTTA
1 TTTTATTATTTAATATAAATATAATTTT-AATTATTTA
206416 TTTTAT
1 TTTTAT
206422 ATGTATACAC
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
34 7 0.11
35 14 0.23
36 13 0.21
37 28 0.45
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.57
Consensus pattern (37 bp):
TTTTATTATTTAATATAAATATAATTTTAATTATTTA
Found at i:209830 original size:11 final size:11
Alignment explanation
Indices: 209804--209852 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
209794 ATGCATGAAT
209804 TAAAAATAATAA
1 TAAAAATAA-AA
*
209816 TAAAGATAAAA
1 TAAAAATAAAA
*
209827 TAAAAATAAAT
1 TAAAAATAAAA
209838 TAAAAA-AAAA
1 TAAAAATAAAA
*
209848 GAAAA
1 TAAAA
209853 TCCAAGTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
10 7 0.22
11 17 0.53
12 8 0.25
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:209843 original size:17 final size:17
Alignment explanation
Indices: 209801--209847 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
209791 TTCATGCATG
*
209801 AATTAAAAATAATAATA
1 AATTAAAAATAAAAATA
*
209818 AA-GATAAAATAAAAATA
1 AATTA-AAAATAAAAATA
209835 AATTAAAAA-AAAA
1 AATTAAAAATAAAA
209848 GAAAATCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 5 0.20
17 19 0.76
18 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AATTAAAAATAAAAATA
Found at i:210032 original size:15 final size:17
Alignment explanation
Indices: 209996--210036 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
209986 AAAAAATGAA
209996 AATTTAAAAATAAATTTG
1 AATTTAAAAATAAA-TTG
210014 AATTTAAAAAT-AA-TG
1 AATTTAAAAATAAATTG
210029 AATTTAAA
1 AATTTAAA
210037 GATATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.43
17 2 0.09
18 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AATTTAAAAATAAATTG
Found at i:210586 original size:22 final size:22
Alignment explanation
Indices: 210556--210658 Score: 65
Period size: 22 Copynumber: 4.7 Consensus size: 22
210546 ATGAACAAAA
* *
210556 ATTTCATATTTATTTATTAATAT
1 ATTTAATATTTATTTATAAAT-T
* **
210579 ATTT-ATATATATAAATAAATT
1 ATTTAATATTTATTTATAAATT
210600 AATTT-ATGATTTATTTA-AAATTT
1 -ATTTAAT-ATTTATTTATAAA-TT
210623 ATTTAATATTT-TTTA-AAATT
1 ATTTAATATTTATTTATAAATT
*
210643 AATTTAA-ATTAATTTA
1 -ATTTAATATTTATTTA
210659 AATTTTATGA
Statistics
Matches: 66, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
20 5 0.08
21 18 0.27
22 29 0.44
23 14 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (22 bp):
ATTTAATATTTATTTATAAATT
Found at i:210622 original size:11 final size:11
Alignment explanation
Indices: 210608--210666 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
210598 TTAATTTATG
210608 ATTTATTTAAA
1 ATTTATTTAAA
*
210619 ATTTATTTAAT
1 ATTTATTTAAA
210630 ATTT-TTTAAA
1 ATTTATTTAAA
*
210640 ATTAATTT-AA
1 ATTTATTTAAA
*
210650 ATTAATTTAAA
1 ATTTATTTAAA
*
210661 TTTTAT
1 ATTTAT
210667 GATTATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 18 0.44
11 23 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTATTTAAA
Found at i:210637 original size:21 final size:21
Alignment explanation
Indices: 210595--210649 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
210585 ATATATAAAT
210595 AAATTAATTT-ATGATTTATTTA
1 AAATTAATTTAAT-ATTT-TTTA
*
210617 AAATTTATTTAATATTTTTTA
1 AAATTAATTTAATATTTTTTA
210638 AAATTAATTTAA
1 AAATTAATTTAA
210650 ATTAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 15 0.50
22 13 0.43
23 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTAATTTAATATTTTTTA
Found at i:210651 original size:10 final size:10
Alignment explanation
Indices: 210594--210662 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
210584 TATATATAAA
210594 TAAATTAATT
1 TAAATTAATT
* *
210604 TATGATTTATT
1 TA-AATTAATT
*
210615 TAAAATTTATT
1 T-AAATTAATT
*
210626 TAATATT-TTT
1 TAA-ATTAATT
210636 TAAAATTAATT
1 T-AAATTAATT
210647 TAAATTAATT
1 TAAATTAATT
210657 TAAATT
1 TAAATT
210663 TTATGATTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
10 25 0.51
11 23 0.47
12 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
TAAATTAATT
Found at i:210658 original size:21 final size:20
Alignment explanation
Indices: 210595--210660 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
210585 ATATATAAAT
*
210595 AAATTAATTTATGATTTATTTA
1 AAATTAATTTA--AATTATTTA
* *
210617 AAATTTATTTAATATTTTTTA
1 AAATTAATTTAA-ATTATTTA
210638 AAATTAATTTAAATTAATTTA
1 AAATTAATTTAAATT-ATTTA
210659 AA
1 AA
210661 TTTTATGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.11
21 23 0.62
22 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATTAATTTAAATTATTTA
Found at i:214944 original size:4 final size:4
Alignment explanation
Indices: 214935--214959 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
214925 TCAATGCTTT
214935 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
214960 AAGGTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:215348 original size:27 final size:27
Alignment explanation
Indices: 215309--215366 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
215299 TGCCACTCTC
215309 TGAGGCAACAATGAATGTTGAAGGCAG
1 TGAGGCAACAATGAATGTTGAAGGCAG
* * *
215336 TGAGGTAATAATGAATGTTGATGGCAG
1 TGAGGCAACAATGAATGTTGAAGGCAG
215363 TGAG
1 TGAG
215367 CATAACTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.24
Consensus pattern (27 bp):
TGAGGCAACAATGAATGTTGAAGGCAG
Found at i:224079 original size:20 final size:20
Alignment explanation
Indices: 224054--224130 Score: 145
Period size: 20 Copynumber: 3.9 Consensus size: 20
224044 GTAAAAAGAT
*
224054 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTGA
224074 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
224094 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
224114 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
224131 CTGGGTAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:224922 original size:43 final size:44
Alignment explanation
Indices: 224813--224927 Score: 144
Period size: 43 Copynumber: 2.6 Consensus size: 44
224803 TCTTTATCTC
*
224813 AAATTAAATTAAAATAAGAGATAAATGAAAAAAAAATTATCTCTAATT
1 AAATTAAATT-AATTAAGAGATAAATG---AAAAAATTATCTCTAATT
* * *
224861 -AATCAAATTAATTAAGAGATAAATG-AATAATTATCTTTAATT
1 AAATTAAATTAATTAAGAGATAAATGAAAAAATTATCTCTAATT
224903 AAATTAAATTAATTAAGAGATAAAT
1 AAATTAAATTAATTAAGAGATAAAT
224928 AAGAAAGATA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
42 15 0.25
43 23 0.38
46 15 0.25
47 8 0.13
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (44 bp):
AAATTAAATTAATTAAGAGATAAATGAAAAAATTATCTCTAATT
Found at i:229382 original size:13 final size:13
Alignment explanation
Indices: 229364--229388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229354 CTAAGATCAG
229364 TGTATCGATACAA
1 TGTATCGATACAA
229377 TGTATCGATACA
1 TGTATCGATACA
229389 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:229451 original size:13 final size:13
Alignment explanation
Indices: 229433--229484 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
229423 AGCTTCGTAG
229433 CGATACATTGTAT
1 CGATACATTGTAT
229446 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
229465 CGATACATTGTAT
1 CGATACATTGTAT
229478 CGATACA
1 CGATACA
229485 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:229465 original size:19 final size:19
Alignment explanation
Indices: 229441--229505 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
229431 AGCGATACAT
229441 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
229460 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
229473 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
229492 TGTATAGATACAAA
1 TGTATCGATACAAA
229506 TCGTTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:229474 original size:32 final size:32
Alignment explanation
Indices: 229433--229503 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
229423 AGCTTCGTAG
229433 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
229465 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
229497 AGATACA
1 CGATACA
229504 AATCGTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:230282 original size:52 final size:51
Alignment explanation
Indices: 230148--231173 Score: 1023
Period size: 49 Copynumber: 20.8 Consensus size: 51
230138 GATAAATGGA
* * * * **
230148 CCAATACGCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAG---AAGG-TG
* * * ** * * * *
230203 TCAATGTGCTGATTCACGGTTAGCAACATTAGACTTGAAGATGAGAAGAATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAG-GTG
* * * **
230255 CCAATATGCTGATTCAAGGCCAACAACAGTGGGTTTTAAAGATGACGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACA-TTGGACTTAAAGATGA-GAAGGTG
*
230308 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * * *
230357 CCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGGCG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
* *
230409 CCAATATGCTGATTCAAGGCCAGCGATATTAGAC-T-----T-A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* *
230452 CCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAG--GGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGAGAAGGTG
* * *
230502 CCAATATGCTGATTCAAGGCTAGCGATATTGGAC-T-----CG-GAA-GTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* *
230545 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* *
230594 CCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TG-G-AGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * *
230637 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--GATGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
*
230686 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--GAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* *
230735 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTATAGATGACGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
* *
230787 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAATGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
* *
230839 CCAATATGCTGATTCAAGGCCAGCGATATTGGATTTAAAGATGACGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-GAAGGTG
** *
230891 CCAATATGCTGATTCAAGGCCAGTAATATTGGACTTAAAGATGAAGGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-A-GAAGGTG
* *
230944 CCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT--GAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * *
230993 CCAATGTGCTGATTCAAGGCCAGTGACATTGGGCTTAAAAGATGAG--GGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGAGAAGGTG
* *
231043 CCAATATGCTGATTTAAGGCCAGCGATATTGGAC-T-----TG-G-AGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* * * *
231086 CCAATGTGCTAATTCAAGGCCAGCTACATTGGACATAAAGAT-A-AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
* *
231135 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA
231174 AGGGTTGCCA
Statistics
Matches: 822, Mismatches: 99, Indels: 106
0.80 0.10 0.10
Matches are distributed among these distances:
42 2 0.00
43 142 0.17
44 4 0.00
45 1 0.00
46 1 0.00
48 4 0.00
49 251 0.31
50 74 0.09
51 2 0.00
52 219 0.27
53 85 0.10
54 4 0.00
55 33 0.04
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (51 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGAAGGTG
Found at i:230373 original size:49 final size:49
Alignment explanation
Indices: 230253--231173 Score: 1035
Period size: 49 Copynumber: 18.8 Consensus size: 49
230243 ATGAGAAGAA
* * * * **
230253 TGCCAATATGCTGATTCAAGGCCAACAACAGTGGGTTTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATA-TTGGACTTAAAGAT---GAAGG
230306 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
230355 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
* *
230407 CGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
230450 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTTAAAAGATGAGGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGATGAAGG
* *
230500 TGCCAATATGCTGATTCAAGGCTAGCGATATTGGAC-T--CG--GAA-G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
230543 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
230592 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT---G--G-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
230635 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
230684 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
230733 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTATAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-A-A-GATGAAGG
* * *
230785 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAATG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
*
230837 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGATTTAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
**
230889 TGCCAATATGCTGATTCAAGGCCAGTAATATTGGACTTAAAGATGAAGGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT----GAAGG
*
230942 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
230991 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGGCTTAAAAGATGAGGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGATGAAGG
*
231041 TGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTT---G--G-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * *
231084 TGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACATAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
231133 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
231174 AGGGTTGCCA
Statistics
Matches: 750, Mismatches: 82, Indels: 76
0.83 0.09 0.08
Matches are distributed among these distances:
43 143 0.19
44 4 0.01
46 6 0.01
48 5 0.01
49 249 0.33
50 80 0.11
51 2 0.00
52 187 0.25
53 74 0.10
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:231277 original size:35 final size:35
Alignment explanation
Indices: 231231--231512 Score: 267
Period size: 35 Copynumber: 8.2 Consensus size: 35
231221 TTGTTGACTT
* * *
231231 AAAAGGAAAAGGATGCCACAAAGTTGTGGACTTTG
1 AAAAGAAAAAGGATGCCACGAAGTTGTGGGCTTTG
* * * *
231266 AAAAGAAAAAGGGTGCCACGGAGTTGTGGACTTTA
1 AAAAGAAAAAGGATGCCACGAAGTTGTGGGCTTTG
* * * *
231301 AAAAGAAAAAAGAGTGCCACGGAGTGGTGGGCTTTA
1 AAAAGAAAAAGGA-TGCCACGAAGTTGTGGGCTTTG
* *
231337 AAAAGAAAAAGGGTGCCATAGAA-TTGTGGGCTTTG
1 AAAAGAAAAAGGATGCCA-CGAAGTTGTGGGCTTTG
* * * *
231372 AAAAG-AAAAGAAGTGCCACGGAGTGGTGGGCTTTA
1 AAAAGAAAAAGGA-TGCCACGAAGTTGTGGGCTTTG
* *
231407 AAAAGAAAAAGGGTGCCACGGAA-TTGTAGGCTTTG
1 AAAAGAAAAAGGATGCCAC-GAAGTTGTGGGCTTTG
231442 AAAAGAAAAAGG-TGCCACGAAGTTGTGGGCTTTG
1 AAAAGAAAAAGGATGCCACGAAGTTGTGGGCTTTG
* *
231476 --AAG-AAAA-GATGCCACTG-AGTCGTGGACTTTG
1 AAAAGAAAAAGGATGCCAC-GAAGTTGTGGGCTTTG
231507 AAAAGA
1 AAAAGA
231513 GATTGCCACT
Statistics
Matches: 205, Mismatches: 30, Indels: 25
0.79 0.12 0.10
Matches are distributed among these distances:
30 1 0.00
31 22 0.11
32 4 0.02
33 6 0.03
34 24 0.12
35 108 0.53
36 40 0.20
ACGTcount: A:0.38, C:0.11, G:0.31, T:0.20
Consensus pattern (35 bp):
AAAAGAAAAAGGATGCCACGAAGTTGTGGGCTTTG
Found at i:231354 original size:106 final size:105
Alignment explanation
Indices: 231231--231512 Score: 342
Period size: 106 Copynumber: 2.7 Consensus size: 105
231221 TTGTTGACTT
* * * *
231231 AAAAGGAAAAGGATGCCACAAAGTTGTGGACTTTGAAAAGAAAAAGGGTGCCACGGAGTTGTGGA
1 AAAAGAAAAAGGGTGCCACAAAGTTGTGGGCTTTGAAAAG-AAAAGGGTGCCACGGAGTCGTGGA
* *
231296 CTTTAAAAAGAAAAAAGAGTGCCACGGAGTGGTGGGCTTTA
65 CTTTAAAAAGAAAAAAGAGTGCCACGGAATGGTAGGCTTTA
* * *
231337 AAAAGAAAAAGGGTGCCATAGAA-TTGTGGGCTTTGAAAAGAAAAGAAGTGCCACGGAGTGGTGG
1 AAAAGAAAAAGGGTGCCACA-AAGTTGTGGGCTTTGAAAAGAAAAG-GGTGCCACGGAGTCGTGG
* * * *
231401 GCTTTAAAAAG-AAAAAGGGTGCCACGGAATTGTAGGCTTTG
64 ACTTTAAAAAGAAAAAAGAGTGCCACGGAATGGTAGGCTTTA
* * *
231442 AAAAGAAAAA-GGTGCCACGAAGTTGTGGGCTTTG--AAGAAAA-GATGCCACTGAGTCGTGGAC
1 AAAAGAAAAAGGGTGCCACAAAGTTGTGGGCTTTGAAAAGAAAAGGGTGCCACGGAGTCGTGGAC
*
231503 TTTGAAAAGA
66 TTTAAAAAGA
231513 GATTGCCACT
Statistics
Matches: 152, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
100 23 0.15
102 7 0.05
103 2 0.01
104 19 0.12
105 40 0.26
106 59 0.39
107 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.31, T:0.20
Consensus pattern (105 bp):
AAAAGAAAAAGGGTGCCACAAAGTTGTGGGCTTTGAAAAGAAAAGGGTGCCACGGAGTCGTGGAC
TTTAAAAAGAAAAAAGAGTGCCACGGAATGGTAGGCTTTA
Found at i:231415 original size:70 final size:69
Alignment explanation
Indices: 231256--231474 Score: 312
Period size: 70 Copynumber: 3.1 Consensus size: 69
231246 CCACAAAGTT
* * * * *
231256 GTGGACTTTGAAAAGAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAAGAGTGCCAC
1 GTGGGCTTTAAAAAGAAAAAGGGTGCCACGGAATTGTGGGCTTTGAAAAG-AAAAA-AGTGCCAC
231321 GGAGTG
64 GGAGTG
**
231327 GTGGGCTTTAAAAAGAAAAAGGGTGCCATAGAATTGTGGGCTTTGAAAAGAAAAGAAGTGCCACG
1 GTGGGCTTTAAAAAGAAAAAGGGTGCCACGGAATTGTGGGCTTTGAAAAGAAAA-AAGTGCCACG
231392 GAGTG
65 GAGTG
* * *
231397 GTGGGCTTTAAAAAGAAAAAGGGTGCCACGGAATTGTAGGCTTTGAAAAGAAAAAGGTGCCACGA
1 GTGGGCTTTAAAAAGAAAAAGGGTGCCACGGAATTGTGGGCTTTGAAAAGAAAAAAGTGCCACGG
*
231462 AGTT
66 AGTG
231466 GTGGGCTTT
1 GTGGGCTTT
231475 GAAGAAAAGA
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
69 21 0.16
70 69 0.51
71 44 0.33
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (69 bp):
GTGGGCTTTAAAAAGAAAAAGGGTGCCACGGAATTGTGGGCTTTGAAAAGAAAAAAGTGCCACGG
AGTG
Found at i:231537 original size:62 final size:60
Alignment explanation
Indices: 231454--231602 Score: 187
Period size: 62 Copynumber: 2.5 Consensus size: 60
231444 AAGAAAAAGG
* *
231454 TGCCAC-GAAGTTGTGGGCTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTT-GAAAAGAGA
1 TGCCACTG-AGTTGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGGAAAA-A-A
* *
231515 TTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCCACTGAGTCGTGGACTTTGGGACAAAA
1 -TGCCACTGAGTTGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTT-GGAAAAAA
*
231577 TGCCACTGAGTCGTGGACTTT-AAGAA
1 TGCCACTGAGTTGTGGACTTTGAAGAA
231603 GGTATTTGAA
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
60 4 0.05
61 20 0.26
62 48 0.62
63 2 0.03
64 4 0.05
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (60 bp):
TGCCACTGAGTTGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGGAAAAAA
Found at i:231553 original size:31 final size:31
Alignment explanation
Indices: 231466--231597 Score: 171
Period size: 31 Copynumber: 4.3 Consensus size: 31
231456 CCACGAAGTT
* * *
231466 GTGGGCTTTGAAGAAAAGATGCCACTGAGTC
1 GTGGACTTTGGAGAAAAAATGCCACTGAGTC
* *
231497 GTGGACTTT-GA-AAAGAGATTGCCACTGAGTT
1 GTGGACTTTGGAGAAA-A-AATGCCACTGAGTC
231528 GTGGACTTTGGAGAAAAAATGCCACTGAGTC
1 GTGGACTTTGGAGAAAAAATGCCACTGAGTC
*
231559 GTGGACTTTGG-GACAAAATGCCACTGAGTC
1 GTGGACTTTGGAGAAAAAATGCCACTGAGTC
231589 GTGGACTTT
1 GTGGACTTT
231598 AAGAAGGTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.03
30 29 0.33
31 51 0.57
32 3 0.03
33 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (31 bp):
GTGGACTTTGGAGAAAAAATGCCACTGAGTC
Found at i:232914 original size:14 final size:12
Alignment explanation
Indices: 232871--232908 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
232861 CCTTTGCACC
*
232871 TTTTTTCTGTGT
1 TTTTTTTTGTGT
232883 TTTTTTTTGT-T
1 TTTTTTTTGTGT
232894 TTGTTTTTTGTGT
1 TT-TTTTTTGTGT
232907 TT
1 TT
232909 ACTTTTGACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 3 0.13
12 17 0.74
13 3 0.13
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.82
Consensus pattern (12 bp):
TTTTTTTTGTGT
Found at i:235230 original size:18 final size:18
Alignment explanation
Indices: 235207--235244 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
235197 AGGGATGTCG
235207 TCATGATTTCCATGAGTT
1 TCATGATTTCCATGAGTT
235225 TCATGATTTCCATGAGTT
1 TCATGATTTCCATGAGTT
235243 TC
1 TC
235245 CTGCATTTCG
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:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (18 bp):
TCATGATTTCCATGAGTT
Found at i:235244 original size:10 final size:9
Alignment explanation
Indices: 235208--235245 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
235198 GGGATGTCGT
235208 CATGATTTC
1 CATGATTTC
235217 CATGAGTTT-
1 CATGA-TTTC
235226 CATGATTTC
1 CATGATTTC
235235 CATGAGTTTC
1 CATGA-TTTC
235245 C
1 C
235246 TGCATTTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 3 0.12
9 15 0.58
10 8 0.31
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (9 bp):
CATGATTTC
Found at i:241737 original size:31 final size:31
Alignment explanation
Indices: 241699--241793 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
241689 CCTAATAAAA
* *
241699 ATGATGCTCTTAAACAAGAGCTTAAA-TAGTT
1 ATGATGCTCATAAGCAAGAGCTTAAACTA-TT
* *
241730 ATGATGCTCCTAAGCAAAAGCTTAAACTATT
1 ATGATGCTCATAAGCAAGAGCTTAAACTATT
*
241761 AT-ATTGCTCATAAGCATGAGCTTAAACTATT
1 ATGA-TGCTCATAAGCAAGAGCTTAAACTATT
241792 AT
1 AT
241794 ATTGTTTCTA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.02
31 53 0.95
32 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (31 bp):
ATGATGCTCATAAGCAAGAGCTTAAACTATT
Found at i:241794 original size:31 final size:30
Alignment explanation
Indices: 241716--241817 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 30
241706 TCTTAAACAA
*
241716 GAGCTTAAA-TAGTTATGA-TGCTCCTAAGCAA
1 GAGCTTAAACTA-TTAT-ATTGCT-CTAAGCAT
*
241747 AAGCTTAAACTATTATATTGCTCATAAGCAT
1 GAGCTTAAACTATTATATTGCTC-TAAGCAT
*
241778 GAGCTTAAACTATTATATTGTTTCTAAGCAT
1 GAGCTTAAACTATTATATTG-CTCTAAGCAT
241809 GAGCTTAAA
1 GAGCTTAAA
241818 TTGTTACATT
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
30 2 0.03
31 57 0.90
32 4 0.06
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (30 bp):
GAGCTTAAACTATTATATTGCTCTAAGCAT
Found at i:241994 original size:42 final size:42
Alignment explanation
Indices: 241937--242043 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 42
241927 TAAAGAAACA
* * * **
241937 ATGCTCCTAAGCATGAGCTTAAATTTTTTTTTTCAAA-AAATG
1 ATGCTTCTAAACATGAGCTTAAA-TTGTTCCTTCAAACAAATG
* * *
241979 ATGTTTTTAAACATGAGCTTAGATTGTTCCTTCAAACAAATG
1 ATGCTTCTAAACATGAGCTTAAATTGTTCCTTCAAACAAATG
* *
242021 ATGCTTCTAACCATGAGTTTAAA
1 ATGCTTCTAAACATGAGCTTAAA
242044 CTACATATGC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (42 bp):
ATGCTTCTAAACATGAGCTTAAATTGTTCCTTCAAACAAATG
Found at i:244072 original size:34 final size:35
Alignment explanation
Indices: 244003--244075 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
243993 GGTGTTCGTA
*
244003 GAAAGAATAAGCAAAAAAGAATACAAATGAGCTTT
1 GAAAGAATAAGCAAAAAAGAATACAAAAGAGCTTT
* * **
244038 GAAAGAATAA-CAATAAATAATACAAAAGCTCTTT
1 GAAAGAATAAGCAAAAAAGAATACAAAAGAGCTTT
244072 GAAA
1 GAAA
244076 TGTAGAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.58, C:0.10, G:0.14, T:0.19
Consensus pattern (35 bp):
GAAAGAATAAGCAAAAAAGAATACAAAAGAGCTTT
Found at i:244432 original size:19 final size:20
Alignment explanation
Indices: 244410--244450 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
244400 TTCAAGGTGT
*
244410 TCGACACTATG-AATATGTA
1 TCGACACTAAGCAATATGTA
*
244429 TCGATACTAAGCAATATGTA
1 TCGACACTAAGCAATATGTA
244449 TC
1 TC
244451 AATACATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
TCGACACTAAGCAATATGTA
Found at i:244969 original size:13 final size:13
Alignment explanation
Indices: 244951--244975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
244941 ATATTCAATA
244951 AAGTCTCGAAATT
1 AAGTCTCGAAATT
244964 AAGTCTCGAAAT
1 AAGTCTCGAAAT
244976 ATTCTTTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
AAGTCTCGAAATT
Found at i:249387 original size:27 final size:28
Alignment explanation
Indices: 249355--249410 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
249345 ATTTACCAAG
* *
249355 GTTTTTTTTTCCATTATTTAATACAAAA
1 GTTTTCTTTTCCAGTATTTAATACAAAA
*
249383 GTTTTCTTTTCCAGTCTTTAATACAAAA
1 GTTTTCTTTTCCAGTATTTAATACAAAA
249411 CATTTACATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.50
Consensus pattern (28 bp):
GTTTTCTTTTCCAGTATTTAATACAAAA
Found at i:251384 original size:24 final size:24
Alignment explanation
Indices: 251353--251409 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
251343 CCACCATAGC
251353 CTTCTTCTTTGGCTTGTTTAAATT
1 CTTCTTCTTTGGCTTGTTTAAATT
251377 CTTCTTCTTTGGCTTGTTTAAATT
1 CTTCTTCTTTGGCTTGTTTAAATT
251401 CTTCTTCTT
1 CTTCTTCTT
251410 CAACGTTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.60
Consensus pattern (24 bp):
CTTCTTCTTTGGCTTGTTTAAATT
Found at i:253458 original size:22 final size:22
Alignment explanation
Indices: 253432--253485 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
253422 TTATTTTTAC
**
253432 CTGAAAACATATGATTTATAACT
1 CTGAAAACAT-TGATACATAACT
253455 -TGAAAAACATTGATACATAACT
1 CTG-AAAACATTGATACATAACT
253477 CT-AAAACAT
1 CTGAAAACAT
253486 CTTTGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.26
22 12 0.44
23 8 0.30
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (22 bp):
CTGAAAACATTGATACATAACT
Found at i:256943 original size:79 final size:76
Alignment explanation
Indices: 256855--257477 Score: 419
Period size: 79 Copynumber: 8.0 Consensus size: 76
256845 CAGAGTACCT
* * * *
256855 CCTCAAAAATAACAGGGTTGGAGTATCCCTAATGGTGGAAAATCGATGTTTTGGAAAAAAAAATC
1 CCTCGAAAATAAC-GGGTTGGAGTATCCC-GATTGTGAAAAATCGATGTTTTGG-AAAAAAAATC
256920 GGGGTTGGAGTATC
63 GGGGTTGGAGTATC
* * * **
256934 CCTCGAAAATAACGAAGTTGGAGTATCTCCGATTGTGAAAAATCGATGTTTTAGAAATAAAGCCG
1 CCTCGAAAATAACG-GGTTGGAGTATC-CCGATTGTGAAAAATCGATGTTTTGGAAAAAAAATCG
256999 GGGTTGGAGTATC
64 GGGTTGGAGTATC
* * * * *
257012 CCTTCGAAAATAACGAGGTTGGAGTATCCTCGATGGTGGAAAATCGGTGTTTTGGAAATAAAATT
1 CC-TCGAAAATAACG-GGTTGGAGTATCC-CGATTGTGAAAAATCGATGTTTTGGAAAAAAAATC
*
257077 GGGGTTGAAGTAT-
63 GGGGTTGGAGTATC
* ** * * **
257090 CC-C-----TAACGGGTTTGGAGTATCCCGATTGTGGAAAATCGATAACTTTAGAAATAAGGTCG
1 CCTCGAAAATAACGGG-TTGGAGTATCCCGATTGTGAAAAATCGAT-GTTTTGGAAAAAAAATCG
257149 GGGTTGGAGTATC
64 GGGTTGGAGTATC
* * * * * * *
257162 CTCTTGGAAATAATGAGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGTAATAAAA-C
1 C-CTCGAAAATAACG-GGTTGGAGTAT-CCCGATTGTGAAAAATCGATGTTTTGGAAAAAAAATC
*
257226 TGAGGTTGGAGTATCC
63 -GGGGTTGGAGTAT-C
** * ** **
257242 CCTC-AATTTTAACGGGGTTGGAGTATCCCCGATTAT-AGAAAATTAACATTTT--AAAAATAAA
1 CCTCGAA-AATAAC-GGGTTGGAGTAT-CCCGATTGTGA-AAAATCGATGTTTTGGAAAAA-AAA
*
257303 GTCAGGGTTGGAGTATC
61 -TCGGGGTTGGAGTATC
* * ** *
257320 TCCTC-AGAAATAACAGGGTTGGAGTATTCCCGATTGTGAAAAATCAATGTTTTAG-AACTAAAG
1 -CCTCGA-AAATAAC-GGGTTGGAGTA-TCCCGATTGTGAAAAATCGATGTTTTGGAAAAAAAAT
257383 CTGGGGTTGGAGTATC
62 C-GGGGTTGGAGTATC
* * * * * * * *
257399 CAATTGGAAATAACAGGGTTAGAGTATCTCCGATGGTGAAAAATCGGTAGTTTTGGAAATAAAAC
1 C-CTCGAAAATAAC-GGGTTGGAGTATC-CCGATTGTGAAAAATCGAT-GTTTTGGAAAAAAAAT
257464 CGGGGTTGGAGTAT
62 CGGGGTTGGAGTAT
257478 TCTTGATGGT
Statistics
Matches: 433, Mismatches: 75, Indels: 71
0.75 0.13 0.12
Matches are distributed among these distances:
70 18 0.04
71 39 0.09
72 1 0.00
73 1 0.00
76 1 0.00
77 3 0.01
78 38 0.09
79 277 0.64
80 49 0.11
81 6 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (76 bp):
CCTCGAAAATAACGGGTTGGAGTATCCCGATTGTGAAAAATCGATGTTTTGGAAAAAAAATCGGG
GTTGGAGTATC
Found at i:257034 original size:158 final size:157
Alignment explanation
Indices: 256860--257477 Score: 511
Period size: 158 Copynumber: 4.0 Consensus size: 157
256850 TACCTCCTCA
* *
256860 AAAATAACAGGGTTGGAGTATCCCTAATGGTGGAAAATCGATGTTTTGGAAAAAAAAATCGGGGT
1 AAAATAACAGGGTTGGAGTATCCCTGATGGTGAAAAATCGATGTTTTGGAAAAAAAAAT-GGGGT
* *
256925 TGGAGTATCCCTCGAAAATAACGAAGTTGGAGTATCTCCGATTGTGAAAAATCGAT-GTTTTAGA
65 TGGAGTATCCCTC-AAAATAACGAGGTTGGAGTATCTCCGATTGTGAAAAATCGATAATTTTAGA
256989 AATAAAGCCGGGGTTGGAGTATCCCTTCG
129 AATAAAGCCGGGGTTGGAGTATCCCTTCG
* * * *
257018 AAAATAAC-GAGGTTGGAGTAT-CCTCGATGGTGGAAAATCGGTGTTTTGGAAATAAAATTGGGG
1 AAAATAACAG-GGTTGGAGTATCCCT-GATGGTGAAAAATCGATGTTTTGGAAAAAAAAATGGGG
* * *
257081 TTGAAGTAT-CC-C----TAACG-GGTTTGGAGTATC-CCGATTGTGGAAAATCGATAACTTTAG
64 TTGGAGTATCCCTCAAAATAACGAGG-TTGGAGTATCTCCGATTGTGAAAAATCGATAATTTTAG
* *
257138 AAATAAGGTCGGGGTTGGAGTATCCTCTT-G
128 AAATAAAGCCGGGGTTGGAGTATCC-CTTCG
* * * ** * * * * *
257168 GAAATAA-TGAGGTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGGTAATAAAACTGAGGT
1 AAAATAACAG-GGTTGGAGTATCCCTGATGGTGAAAAATCGATGTTTTGGAAAAAAAAATGGGGT
** * * * *
257232 TGGAGTATCCCCTCAATTTTAACGGGGTTGGAGTATCCCCGATTAT-AGAAAAT-TA-ACATTTT
65 TGGAGTAT-CCCTCAA-AATAACGAGGTTGGAGTATCTCCGATTGTGA-AAAATCGATA-ATTTT
* * *
257294 AAAAATAAAGTCAGGGTTGGAGTATCTCC-TC-
126 AGAAATAAAGCCGGGGTTGGAGTATC-CCTTCG
* * * ** **
257325 AGAAATAACAGGGTTGGAGTATTCCC-GATTGTGAAAAATCAATGTTTTAGAACTAAAGCTGGGG
1 A-AAATAACAGGGTTGGAGTA-TCCCTGATGGTGAAAAATCGATGTTTTGGAAAAAAAAATGGGG
* ** * * * *
257389 TTGGAGTATCCAATTGGAAATAAC-AGGGTTAGAGTATCTCCGATGGTGAAAAATCGGTAGTTTT
64 TTGGAGTATCC--CTCAAAATAACGA-GGTTGGAGTATCTCCGATTGTGAAAAATCGATAATTTT
* *
257453 GGAAATAAAACCGGGGTTGGAGTAT
126 AGAAATAAAGCCGGGGTTGGAGTAT
257478 TCTTGATGGT
Statistics
Matches: 375, Mismatches: 55, Indels: 59
0.77 0.11 0.12
Matches are distributed among these distances:
149 19 0.05
150 103 0.27
151 5 0.01
152 2 0.01
153 1 0.00
155 1 0.00
156 2 0.01
157 20 0.05
158 174 0.46
159 47 0.13
160 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.28
Consensus pattern (157 bp):
AAAATAACAGGGTTGGAGTATCCCTGATGGTGAAAAATCGATGTTTTGGAAAAAAAAATGGGGTT
GGAGTATCCCTCAAAATAACGAGGTTGGAGTATCTCCGATTGTGAAAAATCGATAATTTTAGAAA
TAAAGCCGGGGTTGGAGTATCCCTTCG
Found at i:257141 original size:71 final size:71
Alignment explanation
Indices: 257022--257162 Score: 169
Period size: 71 Copynumber: 2.0 Consensus size: 71
257012 CCTTCGAAAA
* ** * *
257022 TAACGAGGTTGGAGTATCCTCGATGGTGGAAAATCGGTGTTTTGGAAATAAAATTGGGGTTGAAG
1 TAACGAGGTTGGAGTATCCTCGATGGTGGAAAATCGATACTTTAGAAATAAAATCGGGGTTGAAG
257087 TATCCC
66 TATCCC
* ** *
257093 TAACG-GGTTTGGAGTATCC-CGATTGTGGAAAATCGATAACTTTAGAAATAAGGTCGGGGTTGG
1 TAACGAGG-TTGGAGTATCCTCGATGGTGGAAAATCGAT-ACTTTAGAAATAAAATCGGGGTTGA
257156 AGTATCC
64 AGTATCC
257163 TCTTGGAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
70 18 0.31
71 41 0.69
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.29
Consensus pattern (71 bp):
TAACGAGGTTGGAGTATCCTCGATGGTGGAAAATCGATACTTTAGAAATAAAATCGGGGTTGAAG
TATCCC
Found at i:257477 original size:52 final size:51
Alignment explanation
Indices: 257414--257513 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 51
257404 GGAAATAACA
*
257414 GGGTTAGAGTA-TCTCCGATGGTGAAAAATCGGTAGTTTTGGAAATAAAACCG
1 GGGTTAGAGTATTCT-CGATGGTGAAAAATCGGT-GTTTTAGAAATAAAACCG
* * * *
257466 GGGTTGGAGTATTCTTGATGGTGGAAAATTGGTGTTTTAGAAATAAAA
1 GGGTTAGAGTATTCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAA
257514 ACATGAATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 14 0.33
52 25 0.60
53 3 0.07
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (51 bp):
GGGTTAGAGTATTCTCGATGGTGAAAAATCGGTGTTTTAGAAATAAAACCG
Found at i:259156 original size:23 final size:22
Alignment explanation
Indices: 259111--259164 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
259101 GTTTTTTTGT
* * *
259111 AGTAGTTTTTGGAGCTACGGGA
1 AGTAGTGTTTGAAGCTAAGGGA
*
259133 ATGTAGTGTTTGAAGCTAATGGA
1 A-GTAGTGTTTGAAGCTAAGGGA
259156 A-TAGTGTTT
1 AGTAGTGTTT
259165 TTTAAGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.30
22 1 0.04
23 18 0.67
ACGTcount: A:0.26, C:0.06, G:0.31, T:0.37
Consensus pattern (22 bp):
AGTAGTGTTTGAAGCTAAGGGA
Found at i:259765 original size:50 final size:50
Alignment explanation
Indices: 259636--259769 Score: 182
Period size: 49 Copynumber: 2.7 Consensus size: 50
259626 AAAAATGCCT
*
259636 GAATGTATCGATAC-ATTAAGAAATGTATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGAAG-AATGTATCGATACATCTGGGTAAAACCCA
* * * * * *
259686 G-ATGCATTGATACAATGAAAAATGTATCGATTCTTCTTGGTAAAACCCA
1 GAATGTATCGATACAATGAAGAATGTATCGATACATCTGGGTAAAACCCA
259735 GAATGTATCGATACAATGAAGAATGTATCGATACA
1 GAATGTATCGATACAATGAAGAATGTATCGATACA
259770 AATTTTGAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 37 0.53
50 33 0.47
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (50 bp):
GAATGTATCGATACAATGAAGAATGTATCGATACATCTGGGTAAAACCCA
Found at i:260405 original size:34 final size:34
Alignment explanation
Indices: 260364--260649 Score: 187
Period size: 40 Copynumber: 7.8 Consensus size: 34
260354 GGAAAGGGCA
*
260364 TCCTGCTCTTTGAGGACAAAGGAAAAAGAGCACG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGAGAACG
* *
260398 TCCTGCTCTTTAAGGACAAAGGAAAACAGAATGAAATGGG
1 TCCTGCTCTTTGAGGACAAAGGAAAA-AG-A-G-AA--CG
* * * *
260438 TCATGCTCCTTGAGGACAAA-GAAGAAAGGAGTACA
1 TCCTGCTCTTTGAGGACAAAGGAA-AAA-GAGAACG
* * * *
260473 TCTTGCTCTTTGAGGATAAAGGAAAAAAGGAATAAAATGCA
1 TCCTGCTCTTTGAGGACAAAGG-AAAAA-G---AGAA--CG
* *
260514 TTCTGCTCTTTGAGGACAAAGGAAAAAGAGTACG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAGAGAACG
* *
260548 TCCTGCTCTTCGAGGACAAAGGAAAAGAGAATGAAATGGG
1 TCCTGCTCTTTGAGGACAAAGGAAAA-AG-A-G-AA--CG
* * * *
260588 TCCTGCTCCTTGAGGACGAAGGAAAAAGGAGTACA
1 TCCTGCTCTTTGAGGACAAAGGAAAAA-GAGAACG
*
260623 TCCTGCACTTTGAGGACAAAGGAAAAA
1 TCCTGCTCTTTGAGGACAAAGGAAAAA
260650 AGGAAATAAA
Statistics
Matches: 197, Mismatches: 33, Indels: 43
0.72 0.12 0.16
Matches are distributed among these distances:
34 50 0.25
35 45 0.23
36 10 0.05
37 6 0.03
38 4 0.02
39 10 0.05
40 51 0.26
41 21 0.11
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (34 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAGAGAACG
Found at i:260456 original size:40 final size:39
Alignment explanation
Indices: 260364--260777 Score: 163
Period size: 42 Copynumber: 10.7 Consensus size: 39
260354 GGAAAGGGCA
* * *
260364 TCCTGCTCTTTGAGGACAAAGGAAAAAG-A-G-CA--CG
1 TCCTGCTCCTTGAGGACAAAGGAAAAAGAATGAAATGGG
* *
260398 TCCTGCTCTTTAAGGACAAAGGAAAACAGAATGAAATGGG
1 TCCTGCTCCTTGAGGACAAAGGAAAA-AGAATGAAATGGG
* * *
260438 TCATGCTCCTTGAGGACAAA-GAAGAAAGGA-GTACA----
1 TCCTGCTCCTTGAGGACAAAGGAA-AAAGAATG-AAATGGG
* * * * **
260473 TCTTGCTCTTTGAGGATAAAGGAAAAAAGGAATAAAATGCA
1 TCCTGCTCCTTGAGGACAAAGG-AAAAA-GAATGAAATGGG
* * **
260514 TTCTGCTCTTTGAGGACAAAGGAAAAAG-A-G---TACG
1 TCCTGCTCCTTGAGGACAAAGGAAAAAGAATGAAATGGG
260548 TCCTGCT-CTTCGAGGACAAAGGAAAAGAGAATGAAATGGG
1 TCCTGCTCCTT-GAGGACAAAGGAAAA-AGAATGAAATGGG
* * *
260588 TCCTGCTCCTTGAGGACGAAGGAAAAAGGA-GTACA----
1 TCCTGCTCCTTGAGGACAAAGGAAAAAGAATG-AAATGGG
* * * **
260623 TCCTGCACTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCA
1 TCCTGCTCCTTGAGGACAAAGG-AAAAA-G-AATGAAATGGG
* * * *
260665 TCATGCTCTTTGAGGACAAAGGAAAAGAAAGAAATTAAATGTG
1 TCCTGCTCCTTGAGGACAAAGG--AA-AAAG-AATGAAATGGG
* * **
260708 TCCTACTCTTTGAGGACAAAGGAGAAAAGGAAAT-AAAGTTCG
1 TCCTGCTCCTTGAGGACAAAGGA-AAAA-G-AATGAAA-TGGG
* * *
260750 TCCTACTCTTTGAGGACAAAGGGAAAAG
1 TCCTGCTCCTTGAGGACAAAGGAAAAAG
260778 GAAATAAAGT
Statistics
Matches: 299, Mismatches: 43, Indels: 70
0.73 0.10 0.17
Matches are distributed among these distances:
33 2 0.01
34 48 0.16
35 40 0.13
36 11 0.04
37 9 0.03
38 7 0.02
39 14 0.05
40 49 0.16
41 33 0.11
42 50 0.17
43 33 0.11
44 3 0.01
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (39 bp):
TCCTGCTCCTTGAGGACAAAGGAAAAAGAATGAAATGGG
Found at i:260487 original size:35 final size:35
Alignment explanation
Indices: 260441--260690 Score: 173
Period size: 35 Copynumber: 6.7 Consensus size: 35
260431 AAATGGGTCA
* *
260441 TGCTCCTTGAGGACAAA-GAAGAAAGGAGTACATCT
1 TGCTCTTTGAGGACAAAGGAA-AAAGGAGTACATCC
* * *
260476 TGCTCTTTGAGGATAAAGGAAAAAAGGAATAAAATGCATTC
1 TGCTCTTTGAGGACAAAGG-AAAAAGGAGT---A--CATCC
*
260517 TGCTCTTTGAGGACAAAGGAAAAA-GAGTACGTCC
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGTACATCC
* * *
260551 TGCTCTTCGAGGACAAAGG-AAAAGAGAATGAAATGGGTCC
1 TGCTCTTTGAGGACAAAGGAAAAAG-GAGT-ACA----TCC
* *
260591 TGCTCCTTGAGGACGAAGGAAAAAGGAGTACATCC
1 TGCTCTTTGAGGACAAAGGAAAAAGGAGTACATCC
* * *
260626 TGCACTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCA
1 TGCTCTTTGAGGACAAAGG-AAAAAGG-AGT---A--CATCC
260668 TGCTCTTTGAGGACAAAGGAAAA
1 TGCTCTTTGAGGACAAAGGAAAA
260691 GAAAGAAATT
Statistics
Matches: 169, Mismatches: 24, Indels: 38
0.73 0.10 0.16
Matches are distributed among these distances:
33 4 0.02
34 21 0.12
35 37 0.22
36 17 0.10
37 4 0.02
39 6 0.04
40 28 0.17
41 30 0.18
42 22 0.13
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.20
Consensus pattern (35 bp):
TGCTCTTTGAGGACAAAGGAAAAAGGAGTACATCC
Found at i:260498 original size:75 final size:74
Alignment explanation
Indices: 260367--260692 Score: 370
Period size: 75 Copynumber: 4.3 Consensus size: 74
260357 AAGGGCATCC
* * * * *
260367 TGCTCTTTGAGGACAAAGGAAAAAGAGCACGTCCTGCTCTTTAAGGACAAAGGAAAACA-GAATG
1 TGCTCTTTGAGGACAAA-GAAAAAGAGTACATCCTGCTCTTTGAGGACAAAGGAAAAAAGGAATA
260431 AAATGGGTCA
65 AAATGGGTCA
* * *
260441 TGCTCCTTGAGGACAAAGAAGAAAGGAGTACATCTTGCTCTTTGAGGATAAAGGAAAAAAGGAAT
1 TGCTCTTTGAGGACAAAGAA-AAA-GAGTACATCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAT
**
260506 AAAATGCATTC-
64 AAAATG-GGTCA
* * * *
260517 TGCTCTTTGAGGACAAAGGAAAAAGAGTACGTCCTGCTCTTCGAGGACAAAGGAAAAGA-GAATG
1 TGCTCTTTGAGGACAAA-GAAAAAGAGTACATCCTGCTCTTTGAGGACAAAGGAAAAAAGGAATA
*
260581 AAATGGGTCC
65 AAATGGGTCA
* * *
260591 TGCTCCTTGAGGACGAAGGAAAAAGGAGTACATCCTGCACTTTGAGGACAAAGGAAAAAAGGAAA
1 TGCTCTTTGAGGAC-AAAGAAAAA-GAGTACATCCTGCTCTTTGAGGACAAAGGAAAAAAGG-AA
**
260656 TAAAATGCATCA
63 TAAAATGGGTCA
*
260668 TGCTCTTTGAGGACAAAGGAAAAGA
1 TGCTCTTTGAGGACAAAGAAAAAGA
260693 AAGAAATTAA
Statistics
Matches: 210, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
73 5 0.02
74 47 0.22
75 94 0.45
76 36 0.17
77 28 0.13
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (74 bp):
TGCTCTTTGAGGACAAAGAAAAAGAGTACATCCTGCTCTTTGAGGACAAAGGAAAAAAGGAATAA
AATGGGTCA
Found at i:260536 original size:33 final size:34
Alignment explanation
Indices: 260516--260649 Score: 126
Period size: 34 Copynumber: 3.7 Consensus size: 34
260506 AAAATGCATT
* *
260516 CTGCTCTTTGAGGACAAAGGAAAAAGAGTACGTC
1 CTGCTCTTCGAGGACAAAGGAAAAAGAGTACATC
* *
260550 CTGCTCTTCGAGGACAAAGGAAAAGAGAATGAAATGGGTC
1 CTGCTCTTCGAGGACAAAGGAAAA-AGAGT-ACA----TC
*
260590 CTGCTCCTT-GAGGACGAAGGAAAAAGGAGTACATC
1 CTGCT-CTTCGAGGACAAAGGAAAAA-GAGTACATC
* *
260625 CTGCACTTTGAGGACAAAGGAAAAA
1 CTGCTCTTCGAGGACAAAGGAAAAA
260650 AGGAAATAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
34 26 0.32
35 25 0.30
36 1 0.01
39 3 0.04
40 24 0.29
41 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (34 bp):
CTGCTCTTCGAGGACAAAGGAAAAAGAGTACATC
Found at i:260637 original size:150 final size:151
Alignment explanation
Indices: 260361--260690 Score: 531
Period size: 150 Copynumber: 2.2 Consensus size: 151
260351 AAAGGAAAGG
* *
260361 GCATCCTGCTCTTTGAGGACAAAGGAAAAAGAGCACGTCCTGCTCTTTAAGGACAAAGGAAAACA
1 GCATTCTGCTCTTTGAGGACAAAGGAAAAAGAGCACGTCCTGCTCTTCAAGGACAAAGGAAAACA
* * *
260426 GAATGAAATGGGTCATGCTCCTTGAGGACAAAGAAGAAAGGAGTACATCTTGCTCTTTGAGGATA
66 GAATGAAATGGGTCATGCTCCTTGAGGACAAAGAAGAAAGGAGTACATCCTGCACTTTGAGGACA
260491 AAGGAAAAAAGG-AATAAAAT
131 AAGGAAAAAAGGAAATAAAAT
* * *
260511 GCATTCTGCTCTTTGAGGACAAAGGAAAAAGAGTACGTCCTGCTCTTCGAGGACAAAGGAAAAGA
1 GCATTCTGCTCTTTGAGGACAAAGGAAAAAGAGCACGTCCTGCTCTTCAAGGACAAAGGAAAACA
* *
260576 GAATGAAATGGGTCCTGCTCCTTGAGGACGAAGGAA-AAAGGAGTACATCCTGCACTTTGAGGAC
66 GAATGAAATGGGTCATGCTCCTTGAGGAC-AAAGAAGAAAGGAGTACATCCTGCACTTTGAGGAC
260640 AAAGGAAAAAAGGAAATAAAAT
130 AAAGGAAAAAAGGAAATAAAAT
260662 GCA-TCATGCTCTTTGAGGACAAAGGAAAA
1 GCATTC-TGCTCTTTGAGGACAAAGGAAAA
260691 GAAAGAAATT
Statistics
Matches: 167, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
150 128 0.77
151 39 0.23
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.19
Consensus pattern (151 bp):
GCATTCTGCTCTTTGAGGACAAAGGAAAAAGAGCACGTCCTGCTCTTCAAGGACAAAGGAAAACA
GAATGAAATGGGTCATGCTCCTTGAGGACAAAGAAGAAAGGAGTACATCCTGCACTTTGAGGACA
AAGGAAAAAAGGAAATAAAAT
Found at i:260794 original size:41 final size:42
Alignment explanation
Indices: 260630--260807 Score: 218
Period size: 42 Copynumber: 4.2 Consensus size: 42
260620 ACATCCTGCA
* * ** * *
260630 CTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCATGCT
1 CTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTACT
* *
260672 CTTTGAGGACAAAGGAAAAGAAAGAAATTAAA-TGTGTCCTACT
1 CTTTGAGGACAAAGGAGAA-AAGGAAA-TAAAGTGTGTCCTACT
260715 CTTTGAGGACAAAGGAGAAAAGGAAATAAAGT-TCGTCCTACT
1 CTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGT-GTCCTACT
*
260757 CTTTGAGGACAAAGG-GAAAAGGAAATAAAGTGTGTCCTGCT
1 CTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTACT
*
260798 CTTTGGGGAC
1 CTTTGAGGAC
260808 TAAAAGGTGC
Statistics
Matches: 122, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
41 37 0.30
42 50 0.41
43 31 0.25
44 4 0.03
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (42 bp):
CTTTGAGGACAAAGGAGAAAAGGAAATAAAGTGTGTCCTACT
Found at i:260814 original size:85 final size:83
Alignment explanation
Indices: 260623--260807 Score: 239
Period size: 85 Copynumber: 2.2 Consensus size: 83
260613 AAGGAGTACA
* *
260623 TCCTGCACTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCATGCTCTTTGAGGACAAAGGA
1 TCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCATACTCTTTGAGGACAAAGGA
260688 AAAGAAAGAAATTAAATGTG
66 AAAG--AGAAATTAAATGTG
* * * * * *
260708 TCCTACTCTTTGAGGACAAAGGAGAAAAGGAAATAAAGTTCGTCCTACTCTTTGAGGACAAAGGG
1 TCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCATACTCTTTGAGGACAAA-GG
260773 AAAAG-GAAA-TAAAGTGTG
65 AAAAGAGAAATTAAA-TGTG
*
260791 TCCTGCTCTTTGGGGAC
1 TCCTGCTCTTTGAGGAC
260808 TAAAAGGTGC
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
82 4 0.05
83 23 0.26
85 54 0.61
86 7 0.08
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (83 bp):
TCCTGCTCTTTGAGGACAAAGGAAAAAAGGAAATAAAATGCATCATACTCTTTGAGGACAAAGGA
AAAGAGAAATTAAATGTG
Found at i:262164 original size:46 final size:45
Alignment explanation
Indices: 262097--262231 Score: 173
Period size: 46 Copynumber: 3.0 Consensus size: 45
262087 ACCAGTCGAG
*
262097 TTTATCTCTAATTAAATTAAATTAATTAAGATATAAAAGAAGAAAT
1 TTTATCTCTAATTAAATTAAATTAATTAAGATATAAAA-AAGAAAA
*
262143 TTTATCTCTAATTAAATTAAATTAATTATAAGATA-AATAAAGAAAA
1 TTTATCTCTAATTAAATTAAATTAA-T-TAAGATATAAAAAAGAAAA
* * * * *
262189 CTCATCTTTAATTAAATTAAATTAATTAAGAAATAAATAAGAA
1 TTTATCTCTAATTAAATTAAATTAATTAAGATATAAAAAAGAA
262232 TAATAAATTC
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
44 6 0.08
45 8 0.10
46 53 0.68
47 4 0.05
48 7 0.09
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (45 bp):
TTTATCTCTAATTAAATTAAATTAATTAAGATATAAAAAAGAAAA
Found at i:263970 original size:2 final size:2
Alignment explanation
Indices: 263959--263989 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
263949 TATTTTTAAG
263959 AT AT -T 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
263990 TTGGCACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:265288 original size:16 final size:17
Alignment explanation
Indices: 265262--265296 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
265252 AGAAAAAAGG
265262 AAAAAGAAAAGAAGAAA
1 AAAAAGAAAAGAAGAAA
*
265279 AAAAAG-AAAGAATAAA
1 AAAAAGAAAAGAAGAAA
265295 AA
1 AA
265297 GTGGCATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAGAAGAAA
Found at i:265578 original size:43 final size:43
Alignment explanation
Indices: 265517--265605 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
265507 TAATTACATC
265517 TTTTATTATTATGAAATATTCGTTTAAATGCCTTTTAATGATG
1 TTTTATTATTATGAAATATTCGTTTAAATGCCTTTTAATGATG
265560 TTTTATTATTATGAAATATTCGTTTAAATGCCTTTTAATGATG
1 TTTTATTATTATGAAATATTCGTTTAAATGCCTTTTAATGATG
265603 TTT
1 TTT
265606 GGAAATTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (43 bp):
TTTTATTATTATGAAATATTCGTTTAAATGCCTTTTAATGATG
Found at i:268049 original size:81 final size:81
Alignment explanation
Indices: 267960--268124 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
267950 TTCGTTTGTT
*
267960 TGTGTTTTTTTGTGTGTTGAAAATATATAAATTTATAGAAATATTTACATGTTGATAGTTCGTTT
1 TGTGTTTTTTTGTGTGTTGAAAATATATAAATTTATAAAAATATTTACATGTTGATAGTTCGTTT
268025 TATATTTATTTTAATA
66 TATATTTATTTTAATA
*
268041 TGTGTTTTTTTGTGTGTTGAAAATATATAAATTTATAAAAATGTTTACATGTTGATAGTTCGTTT
1 TGTGTTTTTTTGTGTGTTGAAAATATATAAATTTATAAAAATATTTACATGTTGATAGTTCGTTT
268106 TATATTTATTTTAATA
66 TATATTTATTTTAATA
268122 TGT
1 TGT
268125 TCGTATATTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.53
Consensus pattern (81 bp):
TGTGTTTTTTTGTGTGTTGAAAATATATAAATTTATAAAAATATTTACATGTTGATAGTTCGTTT
TATATTTATTTTAATA
Found at i:270382 original size:4 final size:4
Alignment explanation
Indices: 270368--270400 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
270358 GCATTTCTTG
*
270368 TTCT GTCT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
270401 CTGATGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:275385 original size:19 final size:18
Alignment explanation
Indices: 275338--275423 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
275328 ATTTCAACTA
*
275338 TTTGTATCGATACAAACAG
1 TTTGTATCGATAC-ATCAG
*
275357 TAAATGTATCGATACATCAG
1 T--TTGTATCGATACATCAG
275377 TGTTGTATCGATACA--A-
1 T-TTGTATCGATACATCAG
*
275393 --TGTATCAATACATCAG
1 TTTGTATCGATACATCAG
275409 TATTGTATCGATACA
1 T-TTGTATCGATACA
275424 ATGTATCGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
13 11 0.21
15 1 0.02
17 1 0.02
19 24 0.45
20 5 0.09
21 11 0.21
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (18 bp):
TTTGTATCGATACATCAG
Found at i:275404 original size:32 final size:32
Alignment explanation
Indices: 275359--275430 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
275349 ACAAACAGTA
* *
275359 AATGTATCGATACATCAGTGTTGTATCGATAC
1 AATGTATCAATACATCAGTATTGTATCGATAC
275391 AATGTATCAATACATCAGTATTGTATCGATAC
1 AATGTATCAATACATCAGTATTGTATCGATAC
275423 AATGTATC
1 AATGTATC
275431 GCTACAAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
AATGTATCAATACATCAGTATTGTATCGATAC
Found at i:284681 original size:32 final size:32
Alignment explanation
Indices: 284640--284707 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
284630 GGCAGTAGCT
284640 TACATTGTATCGATACAAAACTTATATATCGA
1 TACATTGTATCGATACAAAACTTATATATCGA
* *
284672 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATATATCGA
284704 TACA
1 TACA
284708 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATATATCGA
Found at i:284701 original size:19 final size:19
Alignment explanation
Indices: 284645--284708 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
284635 TAGCTTACAT
*
284645 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
284664 TATATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
284677 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
284696 TGTATCGATACAA
1 TGTATCGATACAA
284709 ATCGTTGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.58
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:285691 original size:15 final size:15
Alignment explanation
Indices: 285652--285698 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
285642 AACACACAAA
*
285652 TTTTTTCTTTGTCTC
1 TTTTTTCTTTCTCTC
285667 TTTTTT-TTTCTCT-
1 TTTTTTCTTTCTCTC
*
285680 TTATTTTCTTTCTTTC
1 TT-TTTTCTTTCTCTC
285696 TTT
1 TTT
285699 CTCCCATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 10 0.37
15 13 0.48
16 2 0.07
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTTCTCTC
Found at i:288137 original size:22 final size:22
Alignment explanation
Indices: 288101--288142 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
288091 AAAGAAAATA
* * *
288101 ATTTTTTTTATAAAATGTGAGT
1 ATTTTTTTAAAAAAAAGTGAGT
288123 ATTTTTTTAAAAAAAAGTGA
1 ATTTTTTTAAAAAAAAGTGA
288143 ATAGTTGGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (22 bp):
ATTTTTTTAAAAAAAAGTGAGT
Found at i:288782 original size:18 final size:18
Alignment explanation
Indices: 288759--288793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
288749 ATTTTGTGAA
* *
288759 TTTTTTGTTTTTTTTAAT
1 TTTTTTATTTTCTTTAAT
288777 TTTTTTATTTTCTTTAA
1 TTTTTTATTTTCTTTAA
288794 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTTTATTTTCTTTAAT
Found at i:288787 original size:17 final size:18
Alignment explanation
Indices: 288757--288793 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
288747 AGATTTTGTG
288757 AATTTTTTGTTTTT-TTT
1 AATTTTTTGTTTTTCTTT
288774 AATTTTTT-TATTTTCTTT
1 AATTTTTTGT-TTTTCTTT
288792 AA
1 AA
288794 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 12 0.67
18 5 0.28
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (18 bp):
AATTTTTTGTTTTTCTTT
Found at i:289269 original size:19 final size:19
Alignment explanation
Indices: 289241--289300 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
289231 CTAAAAGATG
289241 ATAT-AAAATATAATATTA
1 ATATAAAAATATAATATTA
289259 ATATAAAAATATAA-ATATA
1 ATATAAAAATATAATAT-TA
*
289278 ATATTAATATATATATATATTA
1 ATA-TAA-AAATATA-ATATTA
289300 A
1 A
289301 AATTTTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 6 0.17
19 14 0.40
20 3 0.09
21 6 0.17
22 4 0.11
23 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAAAATATAATATTA
Found at i:289289 original size:8 final size:8
Alignment explanation
Indices: 289278--289331 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
289268 TATAAATATA
289278 ATATTAAT
1 ATATTAAT
289286 ATA-TATAT
1 ATATTA-AT
*
289294 ATATTAAA
1 ATATTAAT
*
289302 ATTTTAAT
1 ATATTAAT
*
289310 ATATAAAT
1 ATATTAAT
289318 -TATTAAT
1 ATATTAAT
289325 ATATTAA
1 ATATTAA
289332 AATTTATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 8 0.22
8 27 0.73
9 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATTAAT
Found at i:295385 original size:13 final size:13
Alignment explanation
Indices: 295367--295392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295357 CAAGGTAGCT
295367 TTGTATCGATACA
1 TTGTATCGATACA
295380 TTGTATCGATACA
1 TTGTATCGATACA
295393 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:298930 original size:22 final size:23
Alignment explanation
Indices: 298892--298935 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
298882 TTTTATATTA
*
298892 TTATTATAAAAATTAA-TAAAAT
1 TTATTATAAAAAATAATTAAAAT
298914 TTATT-TAAATAAATAATTAAAA
1 TTATTATAAA-AAATAATTAAAA
298936 AATAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTATTATAAAAAATAATTAAAAT
Found at i:299150 original size:19 final size:20
Alignment explanation
Indices: 299126--299163 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
299116 TCACAACGAC
299126 AAAGAA-AAAATAATTTATA
1 AAAGAATAAAATAATTTATA
299145 AAAGAATAAAATAATTTAT
1 AAAGAATAAAATAATTTAT
299164 TATTAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAGAATAAAATAATTTATA
Found at i:300897 original size:25 final size:25
Alignment explanation
Indices: 300869--300921 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
300859 GTTGCTGGAA
300869 AAGGTGGGAGAACCTTAAGAAAGAT
1 AAGGTGGGAGAACCTTAAGAAAGAT
300894 AAGGTGGGAGAACCTTAAGAAAGAT
1 AAGGTGGGAGAACCTTAAGAAAGAT
300919 AAG
1 AAG
300922 TTGTCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.32, T:0.15
Consensus pattern (25 bp):
AAGGTGGGAGAACCTTAAGAAAGAT
Found at i:305368 original size:19 final size:19
Alignment explanation
Indices: 305344--305380 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
305334 GATATGTTTA
305344 GATTCAGTATCTGTTTCTG
1 GATTCAGTATCTGTTTCTG
*
305363 GATTCAGTATTTGTTTCT
1 GATTCAGTATCTGTTTCT
305381 CATTATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (19 bp):
GATTCAGTATCTGTTTCTG
Found at i:308345 original size:6 final size:6
Alignment explanation
Indices: 308325--308374 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
308315 TTCTGAAGTG
* *
308325 AAAATCT AAAACT AAAGCT AAAACT AAAACA AAAACT AAAACT AAAACT
1 AAAA-CT AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT
308374 A
1 A
308375 GTTTTGGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 35 0.90
7 4 0.10
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAACT
Found at i:314735 original size:5 final size:5
Alignment explanation
Indices: 314703--314747 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
314693 AAGTTAATCA
*
314703 ATTAT TTTAT AATTAT A-TA- ATT-T ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT -ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
314748 AAAATATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
3 1 0.03
4 6 0.18
5 23 0.68
6 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:314786 original size:17 final size:18
Alignment explanation
Indices: 314766--314809 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
314756 TAAATAATTT
314766 AAAATTAAAAAT-TT-AA
1 AAAATTAAAAATATTGAA
*
314782 CAAAATAAAAAATATTGAA
1 -AAAATTAAAAATATTGAA
314801 AAAATTAAA
1 AAAATTAAA
314810 GAAAATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 11 0.48
18 10 0.43
19 2 0.09
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAATTAAAAATATTGAA
Found at i:315210 original size:23 final size:23
Alignment explanation
Indices: 315184--315230 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
315174 AATTTATTTT
315184 ATTAAATTTTAAAAT-AAAATAAA
1 ATTAAA-TTTAAAATAAAAATAAA
315207 ATTAAATTTAAAATAAAAATAAA
1 ATTAAATTTAAAATAAAAATAAA
315230 A
1 A
315231 AAATAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATTAAATTTAAAATAAAAATAAA
Found at i:317242 original size:13 final size:13
Alignment explanation
Indices: 317224--317259 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
317214 ATTTATGATG
*
317224 TATCGATACACTA
1 TATCGATACAATA
*
317237 TATCGATACAATG
1 TATCGATACAATA
317250 TATCGATACA
1 TATCGATACA
317260 TGAATAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:317325 original size:21 final size:22
Alignment explanation
Indices: 317269--317348 Score: 117
Period size: 21 Copynumber: 3.6 Consensus size: 22
317259 ATGAATAGTG
* *
317269 ATGAACAGTGATTTTTAACGATAC
1 ATGAACAGTGA--TGTATCGATAC
317293 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
317315 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
317336 ATGAACAGTGATG
1 ATGAACAGTGATG
317349 AATAGTGATG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 21 0.40
22 21 0.40
24 11 0.21
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:317355 original size:10 final size:10
Alignment explanation
Indices: 317336--317366 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
317326 GTATCGATAC
317336 ATGAACAGTG
1 ATGAACAGTG
*
317346 ATGAATAGTG
1 ATGAACAGTG
317356 ATGAACAGTG
1 ATGAACAGTG
317366 A
1 A
317367 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:317454 original size:53 final size:53
Alignment explanation
Indices: 317390--317526 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
317380 CTACTTCCAA
317390 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
317443 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
*
317496 TGTATCGATACATATTTGTGTATATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
317527 TATACAATTT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 67 0.85
54 12 0.15
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:317541 original size:20 final size:19
Alignment explanation
Indices: 317496--317567 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
317486 GCCAATGTCC
**
317496 TGTATCGATAC-ATATTTG
1 TGTATCGATACTATAAATG
*
317514 TGTATATCGATACTATACAATT
1 TG--TATCGATACTATA-AATG
*
317536 TGTATCGATACATTTAAATG
1 TGTATCGATAC-TATAAATG
317556 TGTATCGATACT
1 TGTATCGATACT
317568 TTTCAGGGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 32 0.73
21 6 0.14
22 3 0.07
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACTATAAATG
Found at i:317632 original size:21 final size:21
Alignment explanation
Indices: 317606--317646 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
317596 GTCAACCTTG
317606 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
317627 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
317647 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:319718 original size:50 final size:50
Alignment explanation
Indices: 319642--319807 Score: 147
Period size: 50 Copynumber: 3.5 Consensus size: 50
319632 AAAGTCACAT
* * *
319642 TTTTACCTAGATGTATTGATATATTTTTCAATGTATCGATATATTCTATC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTATC
319692 TTTTACCCAGATGTATCGATACATTTTTCAATGTATC-A-ATA--C-A--
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTATC
* ** * * * *
319735 -TGTA-TGA-ATGTATCGATACATTCTTT-AATGTATAGATACATTTTGTC
1 TTTTACCCAGATGTATCGATACATT-TTTCAATGTATCGATATATTCTATC
319782 TTTTTACCCAGATGTATCGATACATT
1 -TTTTACCCAGATGTATCGATACATT
319808 GAAAAATGTA
Statistics
Matches: 91, Mismatches: 13, Indels: 23
0.72 0.10 0.18
Matches are distributed among these distances:
40 22 0.24
41 5 0.05
42 5 0.05
45 1 0.01
46 1 0.01
48 3 0.03
49 4 0.04
50 35 0.38
51 15 0.16
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (50 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATATATTCTATC
Found at i:319727 original size:20 final size:19
Alignment explanation
Indices: 319702--319778 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
319692 TTTTACCCAG
319702 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTT-A
* * *
319722 ATGTATCAATACATGTATGA
1 ATGTATCGATACAT-TTTTA
319742 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATT-TTTA
*
319762 ATGTATAGATACATTTT
1 ATGTATCGATACATTTT
319779 GTCTTTTTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.06
20 43 0.90
21 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTTA
Found at i:319816 original size:91 final size:90
Alignment explanation
Indices: 319652--319826 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 90
319642 TTTTACCTAG
* * * *
319652 ATGTATTGATATATTTTTCAATGTATCGATATATTCTATCTTTTACCCAGATGTATCGATACATT
1 ATGTATCGATACATTTTTCAATGTATAGATACATTCTATCTTTTACCCAGATGTATCGATACATT
****
319717 TTTCAATGTATCAATACATGTATGA
66 GAAAAATGTATCAATACATGTATGA
* *
319742 ATGTATCGATACATTCTTT-AATGTATAGATACATTTTGTCTTTTTACCCAGATGTATCGATACA
1 ATGTATCGATACATT-TTTCAATGTATAGATACATTCTATC-TTTTACCCAGATGTATCGATACA
*
319806 TTGAAAAATGTATCGATACAT
64 TTGAAAAATGTATCAATACAT
319827 CTAGTTAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
90 30 0.42
91 42 0.58
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (90 bp):
ATGTATCGATACATTTTTCAATGTATAGATACATTCTATCTTTTACCCAGATGTATCGATACATT
GAAAAATGTATCAATACATGTATGA
Found at i:328672 original size:19 final size:18
Alignment explanation
Indices: 328647--328711 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
328637 ATTTCAACGA
328647 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
328665 TGTTGTATCGATAC---A-
1 T-TTGTATCGATACATAAG
328680 -TTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
328697 ATTTGTATCGATACA
1 -TTTGTATCGATACA
328712 ATGTATCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 12 0.30
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:328684 original size:32 final size:32
Alignment explanation
Indices: 328648--328719 Score: 119
Period size: 32 Copynumber: 2.2 Consensus size: 32
328638 TTTCAACGAT
328648 TTGTATCGATACATAAG-TGTTGTATCGATACA
1 TTGTATCGATACATAAGAT-TTGTATCGATACA
328680 TTGTATCGATACATAAGATTTGTATCGATACA
1 TTGTATCGATACATAAGATTTGTATCGATACA
*
328712 ATGTATCG
1 TTGTATCG
328720 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACATAAGATTTGTATCGATACA
Found at i:328685 original size:13 final size:13
Alignment explanation
Indices: 328667--328693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
328657 TACATAAGTG
328667 TTGTATCGATACA
1 TTGTATCGATACA
328680 TTGTATCGATACA
1 TTGTATCGATACA
328693 T
1 T
328694 AAGATTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:328842 original size:52 final size:52
Alignment explanation
Indices: 328797--328925 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
328787 CACTGATCTT
328797 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
328849 TGTATCGATACATACAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
328901 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
328926 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:337413 original size:28 final size:28
Alignment explanation
Indices: 337369--338012 Score: 664
Period size: 28 Copynumber: 22.5 Consensus size: 28
337359 ATACGAACTT
*
337369 TTTCAAAGCCCACAAGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
337397 TTTCAAAGCCCAAAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
337425 TTTCAAAGCCCACATGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
337453 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* ** * *
337481 TTCTTAAAGCCCACAAGTTGGTAGCAACC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
*
337510 TTTTTCAAAGCCCATAAGTCAGTGGCATCC
1 --TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
337540 TTCTCAAAGCCCATAAGTCAGTGGCATCT
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
*
337569 TTTCAAAGCCCACATGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** *
337597 TTTTCAAAGCCCATGAGTTAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
337626 TTCTCAAA-CCCACAAGTCGGTGGCAACCAC
1 TT-TCAAAGCCCACAAGTCAGTGGC-ATC-C
* * *
337656 TTTTAAAGCCCACAAGTTAGTGGTC-GCC
1 TTTCAAAGCCCACAAGTCAGTGG-CATCC
* *
337684 TTTCAAAGCTCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * * *
337712 TTTTGAAGCCCAAAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
337740 TTTTAAAGCCCACATGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
337768 TTTTCAAAGCCCACAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
337797 TTTCAAAGCCCACATGTGAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * *
337825 TTCTTTAAGCCCACACAAGTCGGTGGCAACC
1 TT-TCAAAG-CC-CACAAGTCAGTGGCATCC
* *
337856 TCTCTCAAAGCCCACAAGTCAGTGGTACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
* * *
337886 TTTCAAAGCCCATAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
337914 TTTCGAAGCCTACAAGTCAGTGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
337942 TTTCGAAGCCCACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
337969 TTTTCGAAGCTCACAAATCAGTGGCATCA
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
*
337998 TTTTAAAGCCCACAA
1 TTTCAAAGCCCACAA
338013 ATTGGTGGCA
Statistics
Matches: 519, Mismatches: 79, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.01
28 321 0.62
29 115 0.22
30 54 0.10
31 20 0.04
32 6 0.01
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:338045 original size:202 final size:199
Alignment explanation
Indices: 337368--338057 Score: 714
Period size: 202 Copynumber: 3.4 Consensus size: 199
337358 AATACGAACT
* * * **
337368 TTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCAAAAGTCAGTGGCATCCTT-TC-AA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAA-TTGGTGGCATCCTTCTCTAA
* * * * * * * *
337431 AGCCCACATGTCAGTGGC-ATC-CTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTTAAAGCCCA
65 AGCACACAAGTCGGTGGCAACCACTCTCAAAGCCCACAAGTCAGTGGTACCCTT-TCAAAGCCCA
* * * * * * * *
337494 CAAGTTGGTAGCAACCTTTTTCAAAGCCCATAAGTCAGTGGCATCCTTCTCAAAGCCCATAAGTC
129 CAAGTTAGTGGC-ACC-CTTTCGAAGCCCAAAAGTCAGTGGCAACCTT-TCAAAGCCCACAAGTT
*
337559 AGTGGCATC
191 AGTGGCACC
* * * *
337568 TTTTCAAAGCCCACATGTCAGTGGCATCCTTTTCAAAGCCCATGAGTTAGTGGCATCCTTCTC-A
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAGCCCA-CAATTGGTGGCATCCTTCTCTA
* * * * *
337632 AA-CCCACAAGTCGGTGGCAACCACTTTTAAAGCCCACAAGTTAGTGGT-CGCCTTTCAAAGCTC
64 AAGCACACAAGTCGGTGGCAACCACTCTCAAAGCCCACAAGTCAGTGGTAC-CCTTTCAAAGCCC
* * * * * *
337695 ACAAGTCAGTGGCACCCTTTTGAAGCCCAAAAGTTAGTGGCACCCTTTTAAAGCCCACATGTTAG
128 ACAAGTTAGTGGCACCCTTTCGAAGCCCAAAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAG
337760 TGGCATCC
193 TGGCA-CC
* *
337768 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCAC-ATGTGAGTGGCATCCTTCT-TT
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAT-TG-GTGGCATCCTTCTCTA
*
337831 AAGCCCACACAAGTCGGTGGCAACCTCTCTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCC
64 AAG--CACACAAGTCGGTGGCAACCACTCTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCC
* * * *
337896 CATAAGTTAGTGGCACCCTTTCGAAGCCTACAAGTCAGTGGCAACCTTTCGAAGCCCACAAGTTA
127 CACAAGTTAGTGGCACCCTTTCGAAGCCCAAAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTA
337961 GTGGCACC
192 GTGGCACC
* * * * *
337969 TTTTCGAAGCTCACAAATCAGTGGCATCATTTTAAAGCCCACAAATTGGTGGCAACCTTCTCTAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCAC-AATTGGTGGCATCCTTCTCTAA
* *
338034 AGCTTACACAAGTTGGTGGTAACC
65 AGC--ACACAAGTCGGTGGCAACC
338058 CTTCTAAACC
Statistics
Matches: 411, Mismatches: 60, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
197 1 0.00
198 1 0.00
199 42 0.10
200 88 0.21
201 89 0.22
202 161 0.39
203 29 0.07
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (199 bp):
TTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAATTGGTGGCATCCTTCTCTAAA
GCACACAAGTCGGTGGCAACCACTCTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCCCACA
AGTTAGTGGCACCCTTTCGAAGCCCAAAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTTAGTGG
CACC
Found at i:343765 original size:13 final size:13
Alignment explanation
Indices: 343747--343772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
343737 CTATTTATGA
343747 TGTATCGATACAC
1 TGTATCGATACAC
343760 TGTATCGATACAC
1 TGTATCGATACAC
343773 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:343867 original size:10 final size:10
Alignment explanation
Indices: 343840--343910 Score: 65
Period size: 10 Copynumber: 7.0 Consensus size: 10
343830 TAGTGATACG
343840 TGAACAGTG-
1 TGAACAGTGA
343849 TGAACAGTGA
1 TGAACAGTGA
*
343859 TGAATAGTGA
1 TGAACAGTGA
* *
343869 TGTATC-GATACA
1 TG-AACAG-T-GA
343881 TGAACAGTGA
1 TGAACAGTGA
*
343891 TGAATAGTGA
1 TGAACAGTGA
343901 TGAACAGTGA
1 TGAACAGTGA
343911 AAATGAGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 9 0.18
10 31 0.63
11 5 0.10
12 4 0.08
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.25
Consensus pattern (10 bp):
TGAACAGTGA
Found at i:343962 original size:19 final size:19
Alignment explanation
Indices: 343934--343988 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
343924 CTACTTCCAA
*
343934 TGTATTGATACATATTTTG
1 TGTATCGATACATATTTTG
343953 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
*
343972 TGTATCGATACAAATTT
1 TGTATCGATACATATTT
343989 GGATACTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:344017 original size:53 final size:53
Alignment explanation
Indices: 343953--344089 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
343943 ACATATTTTG
*
343953 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGATACTGTCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGATACTGCCAATGACC
* * *
344006 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGATACTGCCAATGACC
344059 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
344090 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGATACTGCCAATGACC
Found at i:344122 original size:20 final size:20
Alignment explanation
Indices: 344059--344129 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
344049 GCCAATGTCC
**
344059 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
344079 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
344099 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
344119 TGTATCGATAC
1 TGTATCGATAC
344130 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:344195 original size:21 final size:21
Alignment explanation
Indices: 344169--344209 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
344159 GTCAACCTTG
344169 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
344190 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
344210 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:353516 original size:26 final size:26
Alignment explanation
Indices: 353444--353516 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
353434 CCTTTTGCCA
* *
353444 TTTGTCAAGAAATTATCGTTAAGAACT
1 TTTGTCAAGAAATT-TCGTCAAAAACT
* *
353471 TTTGTCGAG-AATGTTTGTCAAAAAC-
1 TTTGTCAAGAAAT-TTCGTCAAAAACT
353496 TTTGTCAAGAAATTTCCGTCA
1 TTTGTCAAGAAATTT-CGTCA
353517 GTACGACCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
25 10 0.27
26 18 0.49
27 9 0.24
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (26 bp):
TTTGTCAAGAAATTTCGTCAAAAACT
Found at i:353566 original size:28 final size:29
Alignment explanation
Indices: 353535--354212 Score: 410
Period size: 29 Copynumber: 23.6 Consensus size: 29
353525 TTTTTCTAAG
* * *
353535 CCCATAAGTCAGTGACATTCTT-TCAAAA
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
*
353563 CCCACAAGTAAGTGGCATCCTT-TC-AAA
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * *
353590 GCCATACA-TCAGTGGCATCCTTCTCAAAG
1 CCCACA-AGTCAGTGGCATCCTTCTCAAAA
* *
353619 CCCACAAATCAGTGGCATCCTTCTCAAAT
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * *
353648 CCCCCAAGTCAATGGCATCCTT-TTAAAT
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * * * *
353676 CGCATATGTTAGTGGCATCCTTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * *
353705 CCCACGAGTTAGTGGCATCTTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * * * *
353734 CCTACAAGTCGGTGGCAACCACTCTTAAAT
1 CCCACAAGTCAGTGGCATCC-TTCTCAAAA
* * *
353764 CCCACAGGTTAGTGGCATCCTTCTCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* *
353793 CTCACAAGTCAGTGGCATCCTT-TCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * * *
353821 CCCACATGTTAGTGGCATCATTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * *
353850 CCCACGAGTCAGTGGCATCCTTCTTAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * *
353879 CCCACAAGTCGGTGGCAACCTCTCTCAAAG
1 CCCACAAGTCAGTGGCATCCT-TCTCAAAA
* * * * * *
353909 CCAATAAGTTAGTGGTAGCCTT-TCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * *
353937 CCCACAAGTTAGTGGCACCCTT-TTAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * ** *
353965 CCCATAAGTTAGTGGCA-CCTTTTTGAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * *
353993 CCCACACGTTAGTGGCA-CCCTCTCAAAGA
1 CCCACAAGTCAGTGGCATCCTTCTCAAA-A
* * * * * *
354022 -TCACATGTCGGTGGCATCTTTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * *
354050 CTCACAAGTCAGTGGCAT-CTTTTTAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * * *
354078 CCCACATGTCCGTGGCATCCTTTTCAAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
* * *
354107 CCCATAAGTCAGTGGCATCCTTCTTTAAGA
1 CCCACAAGTCAGTGGCATCCTTC-TCAAAA
* * * *
354137 CCACACAAGTCGGTGCCAACCTCTCTCAAAG
1 CC-CACAAGTCAGTGGCATCCT-TCTCAAAA
* * *
354168 CCCACAAGTCAGTGGCACCCTT-TCGAAG
1 CCCACAAGTCAGTGGCATCCTTCTCAAAA
354196 CCCACAAGTCAGTGGCA
1 CCCACAAGTCAGTGGCA
354213 CTCTTTTGAA
Statistics
Matches: 517, Mismatches: 117, Indels: 32
0.78 0.18 0.05
Matches are distributed among these distances:
27 24 0.05
28 197 0.38
29 210 0.41
30 64 0.12
31 20 0.04
32 2 0.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (29 bp):
CCCACAAGTCAGTGGCATCCTTCTCAAAA
Found at i:353637 original size:29 final size:28
Alignment explanation
Indices: 353527--354316 Score: 593
Period size: 28 Copynumber: 27.6 Consensus size: 28
353517 GTACGACCTT
* * * *
353527 TTTCTAAGCCCATAAGTCAGTGACATTC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
353555 TTTCAAAACCCACAAGTAAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
353583 TTTCAAAG-CCATACA-TCAGTGGCATCC
1 TTTCAAAGCCCACA-AGTCAGTGGCATCC
*
353610 TTCTCAAAGCCCACAAATCAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* * *
353639 TTCTCAAATCCCCCAAGTCAATGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* * * * * *
353668 TTTTAAATCGCATATGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
353696 TTTTCAAAGCCCACGAGTTAGTGGCATCT
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
353725 TTCTCAAAGCCTACAAGTCGGTGGCAACCAC
1 TT-TCAAAGCCCACAAGTCAGTGGC-ATC-C
* * *
353756 TCTT-AAATCCCACAGGTTAGTGGCATCC
1 T-TTCAAAGCCCACAAGTCAGTGGCATCC
*
353784 TTCTCAAAGCTCACAAGTCAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* * *
353813 TTTCAAAGCCCACATGTTAGTGGCATCAT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
*
353842 TTTCAAAGCCCACGAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
353870 TTCTTAAAGCCCACAAGTCGGTGGCAACC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* * * * *
353899 TCTCTCAAAGCCAATAAGTTAGTGGTAGCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
* *
353929 TTTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
353957 TTTTAAAGCCCATAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * * *
353984 TTTTTGAAGCCCACACGTTAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* ** * * *
354013 TCTCAAAGATCACATGTCGGTGGCATCTT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* *
354042 TTTCAAAGCTCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
354070 TTTTAAAGCCCACATGTCCGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
354098 TTTTCAAAGCCCATAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
** * * *
354127 TTCTTTAAGACCACACAAGTCGGTGCCAACC
1 TT-TCAAAG-CC-CACAAGTCAGTGGCATCC
*
354158 TCTCTCAAAGCCCACAAGTCAGTGGCACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
*
354188 TTTCGAAGCCCACAAGTCAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
** * *
354216 TTTTGAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * *
354244 TTTTGAAGCCTACAAGGT-AGTGGCACCC
1 TTTCAAAGCCCACAA-GTCAGTGGCATCC
** * * *
354272 TTTTGAAGCTCACAAATTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
354300 TTTTAAAGCCCACAAGT
1 TTTCAAAGCCCACAAGT
354317 TGGTGGCAAC
Statistics
Matches: 619, Mismatches: 117, Indels: 52
0.79 0.15 0.07
Matches are distributed among these distances:
27 22 0.04
28 303 0.49
29 211 0.34
30 57 0.09
31 19 0.03
32 7 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:353707 original size:86 final size:85
Alignment explanation
Indices: 353526--354331 Score: 501
Period size: 86 Copynumber: 9.4 Consensus size: 85
353516 AGTACGACCT
* * * * * *
353526 TTTTCTAAGCCCATAAGTCAGTGACATTCTT-TCAAAACCCACAAGT-AAGTGGCATCCTTTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAA-TGGCATCCTTTTAA
*
353589 AG-CCATACATCAGTGGCATCC
65 AGCCCATA-GTCAGTGGCATCC
* * * *
353610 TTCTCAAAGCCCACAAATCAGTGGCATCCTTCTCAAATCCCCCAAGTCAATGGCATCCTTTTAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTTTAAA
* * *
353675 TCGCATATGTTAGTGGCATCC
66 GCCCATA-GTCAGTGGCATCC
* * * * ** * *
353696 TTTTCAAAGCCCACGAGTTAGTGGCATCTTTCTCAAAGCCTACAAGTCGGTGGCAACCACTCTTA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGC-ATC-CTTTTA
* * *
353761 AATCCCACAGGTTAGTGGCATCC
64 AAGCCCATA-GTCAGTGGCATCC
* * * * * *
353784 TTCTCAAAGCTCACAAGTCAGTGGCATCCTT-TCAAAGCCCACATGTTAGTGGCATCATTTTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTTT-AA
*
353848 AGCCCACGAGTCAGTGGCATCC
65 AGCCCA-TAGTCAGTGGCATCC
* * * * * * * * *
353870 TTCTT-AAAGCCCACAAGTCGGTGGCAACCTCTCTCAAAGCCAATAAGTTAGTGGTAGCCTTTCA
1 TT-TTCAAAGCCCACAAGTCAGTGGCATCCT-TCTCAAAGCCCACAAGTCAATGGCATCCTTTTA
* * *
353934 AAGCCCACAAGTTAGTGGCACCC
64 AAGCCCA-TAGTCAGTGGCATCC
* * * ** * * * * * *
353957 TTTT-AAAGCCCATAAGTTAGTGGCA-CCTTTTTGAAGCCCACACGTTAGTGGCACCCTCTCAAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTTTAAA
* * *
354020 GATCACAT-GTCGGTGGCATCT
66 G--CCCATAGTCAGTGGCATCC
* * * * **
354041 TTTTCAAAGCTCACAAGTCAGTGGCAT-CTTTTTAAAGCCCACATGTCCGTGGCATCCTTTTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTTT-AA
354105 AGCCCATAAGTCAGTGGCATCC
65 AGCCCAT-AGTCAGTGGCATCC
* * * * * *
354127 TTCTT-TAAGACCACACAAGTCGGTGCCAACCTCTCTCAAAGCCCACAAGTCAGTGGCACCCTTT
1 TT-TTCAAAG-CC-CACAAGTCAGTGGCATCCT-TCTCAAAGCCCACAAGTCAATGGCATCCTTT
** *
354191 CGAAGCCCACAAGTCAGTGGCA-CTC
62 TAAAGCCCA-TAGTCAGTGGCATC-C
* * * ** * * * *
354216 TTTT-GAAGCCCACAAGTTAGTGGCACCCTT-TTGAAGCCTACAAGGT-AGTGGCACCCTTTTGA
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAA-GTCAATGGCATCCTTTTAA
* *
354278 AGCTCACA-AATTAGTGGCATCC
65 AGC-C-CATAGTCAGTGGCATCC
** *
354300 TTTT-AAAGCCCACAAGTTGGTGGCAACCTTCT
1 TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCT
354332 TTAAAACCCA
Statistics
Matches: 577, Mismatches: 116, Indels: 57
0.77 0.15 0.08
Matches are distributed among these distances:
84 134 0.23
85 84 0.15
86 166 0.29
87 51 0.09
88 93 0.16
89 23 0.04
90 26 0.05
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (85 bp):
TTTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCACAAGTCAATGGCATCCTTTTAAA
GCCCATAGTCAGTGGCATCC
Found at i:353788 original size:145 final size:144
Alignment explanation
Indices: 353532--354327 Score: 661
Period size: 145 Copynumber: 5.6 Consensus size: 144
353522 ACCTTTTTCT
* * * * * * *
353532 AAGCCCATAAGTCAGTGACATTC-TTTCAAAACCCACAAGTAAGTGGCATCCTT-TCAAAGCCAT
1 AAGCCCATATGTTAGTGGCATCCTTTTCAAAGCCCACGAGTTAGTGGCATCCTTCTCAAAGCC-T
* * * * * * *
353595 AC-A-TCAGTGGCATCCTTCTCAAAGCCCACAAATCAGTGGCATCCTTCTCAAATCCCCCAAGTC
65 ACAAGTCGGTGGCAACCCTCTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTC
*
353658 AATGGCATCCTTTTA
130 AGTGGCATCCTTTTA
* * *
353673 AATCGCATATGTTAGTGGCATCCTTTTCAAAGCCCACGAGTTAGTGGCATCTTTCTCAAAGCCTA
1 AAGCCCATATGTTAGTGGCATCCTTTTCAAAGCCCACGAGTTAGTGGCATCCTTCTCAAAGCCTA
* * * *
353738 CAAGTCGGTGGCAACCACTCTTAAATCCCACAGGTTAGTGGCATCCTTCTCAAAGCTCACAAGTC
66 CAAGTCGGTGGCAACC-CTCTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTC
*
353803 AGTGGCATCCTTTCA
130 AGTGGCATCCTTTTA
* * * * *
353818 AAGCCCACATGTTAGTGGCATCATTTTCAAAGCCCACGAGTCAGTGGCATCCTTCTTAAAGCCCA
1 AAGCCCATATGTTAGTGGCATCCTTTTCAAAGCCCACGAGTTAGTGGCATCCTTCTCAAAGCCTA
* * * * *
353883 CAAGTCGGTGGCAACCTCTCTCAAAGCCAATAAGTTAGTGGTAGCCTT-TCAAAGCCCACAAGTT
66 CAAGTCGGTGGCAACC-CTCTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTC
*
353947 AGTGGCACCCTTTTA
130 AGTGGCATCCTTTTA
* ** * *
353962 AAGCCCATAAGTTAGTGGCA-CCTTTTTGAAGCCCAC-ACGTTAGTGGCA-CCCTCTCAAAG-AT
1 AAGCCCATATGTTAGTGGCATCCTTTTCAAAGCCCACGA-GTTAGTGGCATCCTTCTCAAAGCCT
* * ** * * * * * *
354023 CACATGTCGGTGGCATCTTTTTCAAAGCTCACAAGTCAGTGGCAT-CTTTTTAAAGCCCACATGT
65 -ACAAGTCGGTGGCAACCCTCTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGT
*
354087 CCGTGGCATCCTTTTCA
129 CAGTGGCATCCTTTT-A
* * * * ** * *
354104 AAGCCCATAAGTCAGTGGCATCCTTCTT-TAAGACCACACAAGTCGGTGCCAACCTCTCTCAAAG
1 AAGCCCATATGTTAGTGGCATCCTT-TTCAAAG-CC-CACGAGTTAGTGGCATCCT-TCTCAAAG
* * * * * **
354168 CCCACAAGTCAGTGGC-ACCCTTTCGAAGCCCACAAGTCAGTGGCA-CTCTT-TTGAAGCCCACA
62 CCTACAAGTCGGTGGCAACCCTCTCAAAGCCCACAAGTTAGTGGCATC-CTTCTCAAAGCCCACA
* * *
354230 AGTTAGTGGCACCCTTTTG
126 AGTCAGTGGCATCCTTTTA
* * * * * * * * * * *
354249 AAGCCTACAAGGTAGTGGCACCCTTTT-GAAGCTCACAAATTAGTGGCATCCTT-TTAAAGCCCA
1 AAGCCCATATGTTAGTGGCATCCTTTTCAAAGCCCACGAGTTAGTGGCATCCTTCTCAAAGCCTA
*
354312 CAAGTTGGTGGCAACC
66 CAAGTCGGTGGCAACC
354328 TTCTTTAAAA
Statistics
Matches: 530, Mismatches: 105, Indels: 40
0.79 0.16 0.06
Matches are distributed among these distances:
140 22 0.04
141 65 0.12
142 87 0.16
143 39 0.07
144 64 0.12
145 179 0.34
146 52 0.10
147 22 0.04
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (144 bp):
AAGCCCATATGTTAGTGGCATCCTTTTCAAAGCCCACGAGTTAGTGGCATCCTTCTCAAAGCCTA
CAAGTCGGTGGCAACCCTCTCAAAGCCCACAAGTTAGTGGCATCCTTCTCAAAGCCCACAAGTCA
GTGGCATCCTTTTA
Found at i:354171 original size:61 final size:58
Alignment explanation
Indices: 353532--354331 Score: 326
Period size: 57 Copynumber: 14.0 Consensus size: 58
353522 ACCTTTTTCT
* * * * * ** * *
353532 AAGCCCATAAGTCAGTGACATTC-TTTCAAAACCCACAAGTAAGTGGCATCCTT-TCA
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * * * *
353588 AAG-CCATACA-TCAGTGGCATCCTTCTCAAAGCCCACAAATCAGTGGCATCCTTCTCA
1 AAGCCCACA-AGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * * * * ** * * *
353645 AATCCCCCAAGTCAATGGCATCC-TTTTAAATCGCATATGTTAGTGGCATCCTTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * * * * *
353702 AAGCCCACGAGTTAGTGGCAT-CTTTCTCAAAGCCTACAAGTCGGTGGCAACCACTCTTA
1 AAGCCCACAAGTCAGTGGCATCCTTT-TTAAAGCCCACAAGTCCGTGCCAACC-TTCTCA
* * * * * * * * *
353761 AATCCCACAGGTTAGTGGCATCCTTCTCAAAGCTCACAAGTCAGTGGCATCCTT-TCA
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * * * * * *
353818 AAGCCCACATGTTAGTGGCATCATTTTCAAAGCCCACGAGTCAGTGGCATCCTTCTTA
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * * * ** ** *
353876 AAGCCCACAAGTCGGTGGCAACCTCTCTCAAAGCCAATAAGTTAGTGGTAGCCTT-TCA
1 AAGCCCACAAGTCAGTGGCATCCT-TTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * ** * * **
353934 AAGCCCACAAGTTAGTGGCA-CCCTTTTAAAGCCCATAAGTTAGTGGC-ACCTTTTTG
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * * ** * * * * * *
353990 AAGCCCACACGTTAGTGGCA-CCCTCTCAAAGATCACATGTCGGTGGCATCTTTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* * * * *
354047 AAGCTCACAAGTCAGTGGCAT-CTTTTTAAAGCCCACATGTCCGTGGCATCCTTTTCA
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
* *
354104 AAGCCCATAAGTCAGTGGCATCCTTCTTT-AAGACCACACAAGTCGGTGCCAACCTCTCTCA
1 AAGCCCACAAGTCAGTGGCATCCTT-TTTAAAG-CC-CACAAGTCCGTGCCAACCT-TCTCA
* ** * * **
354165 AAGCCCACAAGTCAGTGGCA-CCCTTTCGAAGCCCACAAGTCAGTGGC-ACTCTT-TTG
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAAC-CTTCTCA
* * * * * * * **
354221 AAGCCCACAAGTTAGTGGCA-CCCTTTTGAAGCCTACAAGGT-AGTGGCACCCTT-TTG
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAA-GTCCGTGCCAACCTTCTCA
* * * ** *
354277 AAGCTCACAAATTAGTGGCATCC-TTTTAAAGCCCACAAGTTGGTGGCAACCTTCT
1 AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCT
354332 TTAAAACCCA
Statistics
Matches: 595, Mismatches: 123, Indels: 51
0.77 0.16 0.07
Matches are distributed among these distances:
55 21 0.04
56 179 0.30
57 180 0.30
58 93 0.16
59 75 0.13
60 24 0.04
61 23 0.04
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (58 bp):
AAGCCCACAAGTCAGTGGCATCCTTTTTAAAGCCCACAAGTCCGTGCCAACCTTCTCA
Found at i:355388 original size:20 final size:20
Alignment explanation
Indices: 355365--355414 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
355355 CAGATGTACT
355365 GATACATTTTTAAATGTATC
1 GATACATTTTTAAATGTATC
* * * * *
355385 GATATATGTATGATTGTATC
1 GATACATTTTTAAATGTATC
355405 GATACATTTT
1 GATACATTTT
355415 ATCTTTTTAC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (20 bp):
GATACATTTTTAAATGTATC
Found at i:361347 original size:52 final size:52
Alignment explanation
Indices: 361277--361397 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
361267 GAAAATTTAT
*
361277 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
361329 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
361381 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
361398 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:361410 original size:52 final size:51
Alignment explanation
Indices: 361277--361417 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
361267 GAAAATTTAT
361277 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
361329 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
361381 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
361418 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:361424 original size:13 final size:13
Alignment explanation
Indices: 361406--361430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361396 CAAAGATCAG
361406 TGTATCGATACAA
1 TGTATCGATACAA
361419 TGTATCGATACA
1 TGTATCGATACA
361431 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:361514 original size:13 final size:13
Alignment explanation
Indices: 361496--361520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361486 CAAAAAAATA
361496 TGTATCGATACAT
1 TGTATCGATACAT
361509 TGTATCGATACA
1 TGTATCGATACA
361521 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:361516 original size:33 final size:33
Alignment explanation
Indices: 361474--361540 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
361464 AGTAGCTTAA
361474 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
361507 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
361540 A
1 A
361541 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:362571 original size:43 final size:45
Alignment explanation
Indices: 362510--362643 Score: 191
Period size: 43 Copynumber: 2.9 Consensus size: 45
362500 GATGGAAAAT
362510 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G-
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGA
* *
362553 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-ATG-A
*
362601 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
362644 AATGATGATG
Statistics
Matches: 80, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
43 37 0.46
44 2 0.03
45 1 0.01
46 1 0.01
47 1 0.01
48 3 0.04
49 35 0.44
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGA
Found at i:362609 original size:49 final size:49
Alignment explanation
Indices: 362467--362653 Score: 233
Period size: 49 Copynumber: 3.9 Consensus size: 49
362457 GATGTCAACG
* *
362467 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
362519 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
362562 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
362611 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATG
362654 AGAAGAGTGA
Statistics
Matches: 119, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
43 36 0.30
44 2 0.02
45 1 0.01
46 1 0.01
48 2 0.02
49 46 0.39
50 1 0.01
51 2 0.02
52 28 0.24
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:362640 original size:92 final size:94
Alignment explanation
Indices: 362466--362643 Score: 306
Period size: 92 Copynumber: 1.9 Consensus size: 94
362456 GGATGTCAAC
362466 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA-GTGCCAATATGCTGATTCAAG
*
362531 GCCAGCTATATTGGACTTAAAGGTGCCAAT
65 GCCAGCGATATTGGACTTAAAGGTGCCAAT
* *
362561 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA-TGCCAATATGCTGATTCAAGG
1 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTGCCAATATGCTGATTCAAGG
362624 CCAGCGATATTGGACTTAAA
66 CCAGCGATATTGGACTTAAA
362644 AATGATGATG
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
92 40 0.50
94 4 0.05
95 36 0.45
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (94 bp):
GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTGCCAATATGCTGATTCAAGG
CCAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:362765 original size:55 final size:52
Alignment explanation
Indices: 362705--363893 Score: 392
Period size: 49 Copynumber: 24.0 Consensus size: 52
362695 CGATATTGGG
* *
362705 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
362760 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
362812 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
362855 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
362904 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
362947 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* ** * * * * *
362996 CTTAAAAATGATGATGAGAAGAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTG
1 CTT--AAA-GATG--GAAAAG-GTG--CCA-A---C---ATGCTGATTCAAGGCCAGCTACATTG
**
363061 GG
51 AA
* *
363063 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
363118 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** *
363170 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
363213 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
363262 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
363305 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
363354 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
363397 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
363446 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
363489 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
363538 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
363581 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
** * *
363630 C-T-----T---AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * * * *
363673 CTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* ** * * * * *
363722 CTTAAAAATGATGATGAGAAGAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTG
1 CTT--AAA-GATG--GAAAAG-GTG--CCA-A---C---ATGCTGATTCAAGGCCAGCTACATTG
**
363787 GG
51 AA
* *
363789 CTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
* * *
363844 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTG
363894 GGCTTAGAGG
Statistics
Matches: 901, Mismatches: 131, Indels: 207
0.73 0.11 0.17
Matches are distributed among these distances:
43 292 0.32
44 8 0.01
46 2 0.00
48 6 0.01
49 294 0.33
51 8 0.01
52 97 0.11
53 15 0.02
54 3 0.00
55 72 0.08
57 6 0.01
58 6 0.01
60 2 0.00
61 4 0.00
62 2 0.00
63 4 0.00
64 20 0.02
65 6 0.01
67 54 0.06
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:362811 original size:266 final size:266
Alignment explanation
Indices: 362337--362909 Score: 1101
Period size: 266 Copynumber: 2.2 Consensus size: 266
362327 ATGATAAAGG
* *
362337 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAAGTGATAAA
362402 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACG
66 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACG
362467 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
131 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
362532 CCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
196 CCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
362597 TGAAGA
261 TGAAGA
* *
362603 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAGAGTGATAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAAGTGATAAA
*
362668 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACG
66 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACG
362733 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
131 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
362798 CCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
196 CCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
362863 TGAAGA
261 TGAAGA
362869 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
362910 GGTGCCAATG
Statistics
Matches: 302, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 302 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (266 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGAAGATGAGAAAAGTGATAAA
GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCAACG
TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGG
CCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
TGAAGA
Found at i:362837 original size:43 final size:43
Alignment explanation
Indices: 362776--363727 Score: 705
Period size: 49 Copynumber: 21.0 Consensus size: 43
362766 GATGGAAAAT
362776 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
362819 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
362865 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
362911 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
362957 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AAA-G
** * * * * * *
363006 ATGATGAGAAGA-G-TGA-TAAAGATGCCA-ATATGTT-GA-TT-CAT
1 --G-TGCCAATATGCTGATTCAAG--GCCAGCTATATTGGACTTAAAG
* * * * * * ** *
363047 G-GCC-A-ACGAT-ATT--GGGCTTA--AAGA-TGAGA-AAAAGG
1 GTGCCAATATGCTGATTCAAGGC-CAGCTATATTG-GACTTAAAG
* * ** * *
363082 ATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G
363129 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 -----GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
363177 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
363223 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
363269 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
363315 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
363361 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
363407 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
363453 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
363499 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
363545 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
363591 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
363637 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G
*
363683 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
363728 AATGATGATG
Statistics
Matches: 733, Mismatches: 99, Indels: 150
0.75 0.10 0.15
Matches are distributed among these distances:
32 1 0.00
33 3 0.00
34 3 0.00
35 2 0.00
36 5 0.01
37 4 0.01
38 2 0.00
39 4 0.01
40 1 0.00
41 3 0.00
42 4 0.01
43 280 0.38
44 24 0.03
45 10 0.01
46 20 0.03
47 15 0.02
48 28 0.04
49 285 0.39
50 4 0.01
51 2 0.00
52 33 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
Done.