Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold316
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: 597962
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 2 of 5
Found at i:164992 original size:16 final size:17
Alignment explanation
Indices: 164965--165005 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
164955 ATTTTGAAAT
164965 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
*
164980 TAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
164997 AAATTTTAT
1 AAATTTTAT
165006 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.32
16 6 0.27
17 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:169390 original size:104 final size:104
Alignment explanation
Indices: 169205--169413 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 104
169195 CTTGTTGAGC
*
169205 TCTGGAAACAGCTGTTGCAACCCATGAAAGTTAGAAGATATCAATGCCCACCGAAATTTAAGGTT
1 TCTGGAAACAGCTATTGCAACCCATGAAAGTTAGAAGATATCAATGCCCACCGAAATTTAAGGTT
169270 CAAGTAAATTAATTATCAGCTTTGTTACTTTGATTCGAG
66 CAAGTAAATTAATTATCAGCTTTGTTACTTTGATTCGAG
169309 TCTGGAAACAGCTATTGCAACCCATGAAAGTTAGAAGATATCAATGCCCACCGAAATTTAAGGTT
1 TCTGGAAACAGCTATTGCAACCCATGAAAGTTAGAAGATATCAATGCCCACCGAAATTTAAGGTT
*
169374 CAAGTAAATTAGTTATCAGCTTTGTTACTTTGATTCGAG
66 CAAGTAAATTAATTATCAGCTTTGTTACTTTGATTCGAG
169413 T
1 T
169414 ATTAGTGTCA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (104 bp):
TCTGGAAACAGCTATTGCAACCCATGAAAGTTAGAAGATATCAATGCCCACCGAAATTTAAGGTT
CAAGTAAATTAATTATCAGCTTTGTTACTTTGATTCGAG
Found at i:170306 original size:30 final size:30
Alignment explanation
Indices: 170266--170351 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
170256 TGTGTATAAA
170266 TAAATTTTTAATTTATATTTAAATAAATATT
1 TAAATTTTTAATTTATATTTAAATAAAT-TT
* * * * *
170297 T-TATTTTTAA-TTGTACTAAAATAAGTTT
1 TAAATTTTTAATTTATATTTAAATAAATTT
* *
170325 TAAAATTTTAATTTATATCTAAATAAA
1 TAAATTTTTAATTTATATTTAAATAAA
170352 CACTTAACAT
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
28 3 0.07
29 19 0.46
30 18 0.44
31 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
TAAATTTTTAATTTATATTTAAATAAATTT
Found at i:174469 original size:22 final size:21
Alignment explanation
Indices: 174437--174492 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
174427 TTTTCTAAAA
*
174437 AAAATTAATTTTTCATTGATTC
1 AAAATTTATTTTTCATTGA-TC
*
174459 AAAATTTATTTTTTATTGATC
1 AAAATTTATTTTTCATTGATC
174480 -AAA-TTATTTTTCA
1 AAAATTTATTTTTCA
174493 CCAAATAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.29
20 3 0.10
21 2 0.06
22 17 0.55
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.54
Consensus pattern (21 bp):
AAAATTTATTTTTCATTGATC
Found at i:174630 original size:22 final size:22
Alignment explanation
Indices: 174602--174644 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
174592 TAATTTATCC
*
174602 ATATTATTGA-TTATTTATCTAA
1 ATATTATT-ACTTATTAATCTAA
174624 ATATTATTACTTATTAATCTA
1 ATATTATTACTTATTAATCTA
174645 TTAATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTATTACTTATTAATCTAA
Found at i:174701 original size:2 final size:2
Alignment explanation
Indices: 174694--174725 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
174684 CATATGAGTT
174694 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
174726 AAGAGATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175031 original size:16 final size:15
Alignment explanation
Indices: 175012--175078 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
175002 ATTATATTGG
175012 GTTTAAAATTTTTTAA
1 GTTT-AAATTTTTTAA
*
175028 GTTTAAGTATTTTTAA
1 GTTTAAAT-TTTTTAA
*
175044 -ATTAAATTATTTTAA
1 GTTTAAATT-TTTTAA
* *
175059 ATTTAAGTTTTTTAA
1 GTTTAAATTTTTTAA
175074 GTTTA
1 GTTTA
175079 GTTTAGATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
14 1 0.02
15 24 0.57
16 17 0.40
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
GTTTAAATTTTTTAA
Found at i:175048 original size:15 final size:15
Alignment explanation
Indices: 175020--175082 Score: 67
Period size: 15 Copynumber: 4.2 Consensus size: 15
175010 GGGTTTAAAA
*
175020 TTTTTTAAGTTTAAG
1 TTTTTTAAATTTAAG
*
175035 TATTTTTAAA-TTAAA
1 T-TTTTTAAATTTAAG
175050 TTATTTTAAATTTAAG
1 TT-TTTTAAATTTAAG
*
175066 TTTTTTAAGTTT-AG
1 TTTTTTAAATTTAAG
175080 TTT
1 TTT
175083 AGATTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.15
15 22 0.54
16 13 0.32
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
TTTTTTAAATTTAAG
Found at i:177251 original size:39 final size:40
Alignment explanation
Indices: 177208--177288 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
177198 AATTAATACG
*
177208 ATTTCATATATAAAATTTTGATTTTA-TTTTCTTAAAAAA
1 ATTTCATATACAAAATTTTGATTTTATTTTTCTTAAAAAA
*
177247 ATTTCATATACAAAATTTTGATTTTATTTTTTTTAAAAAA
1 ATTTCATATACAAAATTTTGATTTTATTTTTCTTAAAAAA
177287 AT
1 AT
177289 CACTTACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 25 0.64
40 14 0.36
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (40 bp):
ATTTCATATACAAAATTTTGATTTTATTTTTCTTAAAAAA
Found at i:177337 original size:16 final size:17
Alignment explanation
Indices: 177316--177353 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
177306 AACTAATTCT
177316 TAATTATTTTT-TTTCA
1 TAATTATTTTTATTTCA
*
177332 TAATTATTTTTATTTTA
1 TAATTATTTTTATTTCA
177349 TAATT
1 TAATT
177354 TCATTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TAATTATTTTTATTTCA
Found at i:180199 original size:28 final size:29
Alignment explanation
Indices: 180152--180218 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
180142 AATTGTGATT
180152 ATTTTAT-TA-TTATATAATATATAG-TAA
1 ATTTTATATATTTATATAATAT-TAGATAA
*
180179 ATTTTATATATTTTTAT-ATATTAGATAA
1 ATTTTATATATTTATATAATATTAGATAA
*
180207 TTTTTATCATAT
1 ATTTTAT-ATAT
180219 AGAAATACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 10 0.29
28 15 0.44
29 9 0.26
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (29 bp):
ATTTTATATATTTATATAATATTAGATAA
Found at i:189091 original size:74 final size:72
Alignment explanation
Indices: 188964--189108 Score: 184
Period size: 74 Copynumber: 2.0 Consensus size: 72
188954 ATACCCGATA
* * * *
188964 GTGAAAAATCGATATTTTTGAAGTAAAAACAGGGTTGGAATATCCCCTTAAAAATGATGGGGTTG
1 GTGAAAAATCGATACTTTTGAAGTAAAAACAGGGTTGGAATATCCCATAAAAAATGATGGGATTG
189029 AAGTATG
66 AAGTATG
* * *
189036 GTGAAAAATTCGATGCTTTTGAGAGTAAAAACATGGTT-GAAGTATCTCATAAAAAATGATGGGA
1 GTGAAAAA-TCGATACTTTTGA-AGTAAAAACAGGGTTGGAA-TATCCCATAAAAAATGATGGGA
*
189100 TTGGAGTAT
63 TTGAAGTAT
189109 CCCCAATGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
72 8 0.13
73 14 0.23
74 40 0.65
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (72 bp):
GTGAAAAATCGATACTTTTGAAGTAAAAACAGGGTTGGAATATCCCATAAAAAATGATGGGATTG
AAGTATG
Found at i:193024 original size:16 final size:16
Alignment explanation
Indices: 192999--193030 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
192989 GATAAAAAAG
*
192999 ATTTTTTTATTATTTT
1 ATTTTGTTATTATTTT
193015 ATTTTGTTATTATTTT
1 ATTTTGTTATTATTTT
193031 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (16 bp):
ATTTTGTTATTATTTT
Found at i:195325 original size:42 final size:42
Alignment explanation
Indices: 195233--196023 Score: 643
Period size: 42 Copynumber: 18.9 Consensus size: 42
195223 ATATTCTCTT
* * * *
195233 GGGTCAAAGCCAACTA-GAAGACTTAGGGACAGAAAGT-TCCA
1 GGGTCAAAGCCGAC-AGGCAGACTGAGGGAAAGAAAGTCTCCA
* * * ** **
195274 AGGTCAAAGCCGACAGGTATACTGAGGG-TTGAAAAGTCTCTG
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAG-AAAGTCTCCA
195316 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* * *
195358 GGGTCAAAGCTGACAGGGAGACTGAGGGAAGGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
** * * * * **
195400 AAGACGAAGCTGACAGGCAGACTAAGGGAAA-AAAGTCTTTA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* * * * * *
195441 GGGACGAAGCTGACAAGCAGACTGAAGGAAGGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
** * * *
195483 ATGACGAAA-CCGACAGGCAGACT-ACGAGAAAGAAAGTCTCTA
1 GGGTC-AAAGCCGACAGGCAGACTGA-GGGAAAGAAAGTCTCCA
* * * *
195525 GGGACGAAGCCGACAGGCAGACT-AAGGATAAGAAAAGTCTTCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGA-AAG-AAAGTCTCCA
*
195568 AGGTCAAAGCCGACAGGCAGACTGA-GGAAAGGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAA-GAAAGTCTCCA
* * ***
195610 GGGTCAAGGCAGACAGGCAGACTGA-GGCTTGAAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAG-AAAGTCTCCA
* * *
195652 GGGACGAAGCCGACAGGCAGACTGAGGG-AAGAAAAGTCTCTA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAG-AAAGTCTCCA
* * * * *
195694 GGGACGAAGCCGATAGGCAGACTAAGGGAAAGAAAGTCTTCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* * * *
195736 GGGACGAATCCGACAGGCAGACTGAGGAAAAGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* * * * * * *
195778 GAGACGAAGTCGGCAGGCAGACTAAGGGAAAAAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* * * *
195820 AGGACGAAGCCGACAGGCAGACTGAGGGAGAGAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* * * * * * *
195862 GGGACGAAGCTGACAGGTAGATTGAAGGAAAAAAAAGTCTCCA
1 GGGTCAAAGCCGACAGGCAGACTG-AGGGAAAGAAAGTCTCCA
* * * *
195905 GGGACGAAGTCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCC-A
* * * * *
195948 GGAT-GAAGCCGACAGGCAGACTGAAGGAAGGAAAATCTCCA
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
* *
195989 GGGTCAAAGCCAACAGGCAGACTAAGGGAAA-AAAG
1 GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAG
196024 AAAAAATGAA
Statistics
Matches: 612, Mismatches: 120, Indels: 36
0.80 0.16 0.05
Matches are distributed among these distances:
40 2 0.00
41 72 0.12
42 460 0.75
43 77 0.13
44 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.11
Consensus pattern (42 bp):
GGGTCAAAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCA
Found at i:195397 original size:84 final size:84
Alignment explanation
Indices: 195251--196023 Score: 747
Period size: 84 Copynumber: 9.2 Consensus size: 84
195241 GCCAACTAGA
* * * * * * * ** *
195251 AGACTTAGGGACAGAAAGT-TCCAAGGTCAAAGCCGACAGGTATACTGAGGGTTGAAAAGTCTCT
1 AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCC
* *
195315 GGGGTCAAAGCCGACAGGC
66 AGGGACAAAGCCGACAGGC
* * * * *
195334 AGACTGAGGGAAAGAAAGTCTCCAGGGTCAAAGCTGACAGGGAGACTGAGGGAAGGAAAGTCTCC
1 AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCC
** * *
195399 AAAGACGAAGCTGACAGGC
66 AGGGACAAAGCCGACAGGC
* ** * * * *
195418 AGACTAAGGGAAA-AAAGTCTTTAGGGACGAAGCTGACAAGCAGACTGAAGGAAGGAAAGTCTCC
1 AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCC
**
195482 AATGACGAAA-CCGACAGGC
66 AGGGAC-AAAGCCGACAGGC
* * * *
195501 AGACT-ACGAGAAAGAAAGTCTCTAGGGACGAAGCCGACAGGCAGACTAAGGATAAGAAAAGTCT
1 AGACTGA-GGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGG-GAAGAAAAGTCT
* * *
195565 TCAAGGTCAAAGCCGACAGGC
64 CCAGGGACAAAGCCGACAGGC
* * ***
195586 AGACTGA-GGAAAGGAAAGTCTCCAGGGTC-AAGGCAGACAGGCAGACTGAGGCTTGAAAAGTCT
1 AGACTGAGGGAAA-GAAAGTCTCCAGGGACGAA-GCCGACAGGCAGACTGAGGGAAGAAAAGTCT
*
195649 CCAGGGACGAAGCCGACAGGC
64 CCAGGGACAAAGCCGACAGGC
* * *
195670 AGACTGAGGG-AAGAAAAGTCTCTAGGGACGAAGCCGATAGGCAGACTAAGGGAA-AGAAAGTCT
1 AGACTGAGGGAAAG-AAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAAGA-AAAGTCT
* * *
195733 TCAGGGACGAATCCGACAGGC
64 CCAGGGACAAAGCCGACAGGC
* * * * * *
195754 AGACTGAGGAAAAGAAAGTCTCCAGAGACGAAGTCGGCAGGCAGACTAAGGGAAAAAAAGTCTCC
1 AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCC
* *
195819 AAGGACGAAGCCGACAGGC
66 AGGGACAAAGCCGACAGGC
* * * * * *
195838 AGACTGAGGGAGAGAAAGTCTCCAGGGACGAAGCTGACAGGTAGATTGAAGGAAAAAAAAGTCTC
1 AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTG-AGGGAAGAAAAGTCTC
* *
195903 CAGGGACGAAGTCGACAGGC
65 CAGGGACAAAGCCGACAGGC
* * * *
195923 AGACTAAGGGAAAGAAAGTCTCCAAGGATGAAGCCGACAGGCAGACTGAAGGAAGGAAAA-TCTC
1 AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAA-GAAAAGTCTC
* *
195987 CAGGGTCAAAGCCAACAGGC
65 CAGGGACAAAGCCGACAGGC
*
196007 AGACTAAGGGAAA-AAAG
1 AGACTGAGGGAAAGAAAG
196024 AAAAAATGAA
Statistics
Matches: 578, Mismatches: 95, Indels: 34
0.82 0.13 0.05
Matches are distributed among these distances:
82 1 0.00
83 90 0.16
84 340 0.59
85 146 0.25
86 1 0.00
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.11
Consensus pattern (84 bp):
AGACTGAGGGAAAGAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCC
AGGGACAAAGCCGACAGGC
Found at i:196012 original size:211 final size:209
Alignment explanation
Indices: 195322--196022 Score: 852
Period size: 211 Copynumber: 3.3 Consensus size: 209
195312 TCTGGGGTCA
* * * * *
195322 AAGCCGACAGGCAGACTGAGGGAAAGAAAGTCTCCAGGGTCAAAGCTGACAGGGAGACTGAGGGA
1 AAGCCGACAGGCAGACTGAAGGAAAGAAAATCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGA
** * * * * **
195387 AGGAAAGTCTCCAAAGACGAAGCTGACAGGCAGACTAAGGGAAAAAAGTCTTTAGGGACGAAGCT
66 AAAAAAGTCTCCAAGGACGAAGCAGACAGGCAGACTGAGGGAGAAAAGTCTCCAGGGACGAAGCT
* * ** * * *
195452 GACAAGCAGACTGAAGGAAGGAAAGTCTCCAATGACGAAACCGACAGGCAGACTACGAGAAAGAA
131 GACAGGCAGACTGAAGGAAGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGGAAAGAA
*
195517 AGTCTCTAGGGACG
196 AGTCTCCAGGGACG
* * *
195531 AAGCCGACAGGCAGACT-AAGGATAAGAAAAGTCTTCAAGGTCAAAGCCGACAGGCAGACTGA-G
1 AAGCCGACAGGCAGACTGAAGGA-AAGAAAA-TCTCCAGGGTCAAAGCCGACAGGCAGACTAAGG
* * * **
195594 GAAAGGAAAGTCTCCAGGGTC-AAGGCAGACAGGCAGACTGAGGCTTGAAAAGTCTCCAGGGACG
64 GAAA-AAAAGTCTCCAAGGACGAA-GCAGACAGGCAGACTGAGG-GAGAAAAGTCTCCAGGGACG
* * * *
195658 AAGCCGACAGGCAGACTGAGGGAAGAAAAGTCTCTAGGGACGAAGCCGATAGGCAGACTAAGGGA
126 AAGCTGACAGGCAGACTGAAGGAAGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGGA
*
195723 AAGAAAGTCTTCAGGGACG
191 AAGAAAGTCTCCAGGGACG
* * * * * * *
195742 AATCCGACAGGCAGACTG-AGGAAAAGAAAGTCTCCAGAGACGAAGTCGGCAGGCAGACTAAGGG
1 AAGCCGACAGGCAGACTGAAGG-AAAGAAAATCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGG
*
195806 AAAAAAAGTCTCCAAGGACGAAGCCGACAGGCAGACTGAGGGAGAGAAAGTCTCCAGGGACGAAG
65 AAAAAAAGTCTCCAAGGACGAAGCAGACAGGCAGACTGAGGGAGA-AAAGTCTCCAGGGACGAAG
* * * *
195871 CTGACAGGTAGATTGAAGGAAAAAAAAGTCTCCAGGGACGAAGTCGACAGGCAGACTAAGGGAAA
129 CTGACAGGCAGACTGAAGG-AAGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGGAAA
* *
195936 GAAAGTCTCCAAGGATG
193 GAAAGTCTCCAGGGACG
* *
195953 AAGCCGACAGGCAGACTGAAGGAAGGAAAATCTCCAGGGTCAAAGCCAACAGGCAGACTAAGGGA
1 AAGCCGACAGGCAGACTGAAGGAAAGAAAATCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGA
196018 AAAAA
66 AAAAA
196023 GAAAAAATGA
Statistics
Matches: 414, Mismatches: 66, Indels: 22
0.82 0.13 0.04
Matches are distributed among these distances:
208 4 0.01
209 31 0.07
210 145 0.35
211 230 0.56
212 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.32, T:0.11
Consensus pattern (209 bp):
AAGCCGACAGGCAGACTGAAGGAAAGAAAATCTCCAGGGTCAAAGCCGACAGGCAGACTAAGGGA
AAAAAAGTCTCCAAGGACGAAGCAGACAGGCAGACTGAGGGAGAAAAGTCTCCAGGGACGAAGCT
GACAGGCAGACTGAAGGAAGAAAAGTCTCCAGGGACGAAGCCGACAGGCAGACTAAGGGAAAGAA
AGTCTCCAGGGACG
Found at i:208690 original size:16 final size:15
Alignment explanation
Indices: 208664--208704 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
208654 ATAAAAAAGA
208664 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
208679 ATTTTGTTATTATTTTTT
1 ATTTT-TTATTA--TTTT
208697 ATTTTTTA
1 ATTTTTTA
208705 ATTCTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 3 0.13
18 9 0.39
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:210755 original size:20 final size:20
Alignment explanation
Indices: 210727--210770 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
210717 ACATGGTTCA
* *
210727 GTATTGATATATTTACTTAT
1 GTATGGATACATTTACTTAT
210747 GTATGGATACATTTACTTAT
1 GTATGGATACATTTACTTAT
210767 GTAT
1 GTAT
210771 CAATACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
GTATGGATACATTTACTTAT
Found at i:210776 original size:20 final size:20
Alignment explanation
Indices: 210737--210777 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
210727 GTATTGATAT
**
210737 ATTTACTTATGTATGGATAC
1 ATTTACTTATGTATCAATAC
210757 ATTTACTTATGTATCAATAC
1 ATTTACTTATGTATCAATAC
210777 A
1 A
210778 AATTGTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
ATTTACTTATGTATCAATAC
Found at i:215463 original size:20 final size:20
Alignment explanation
Indices: 215425--215463 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
215415 ACGGACTCGA
**
215425 AATTTGTTTTCTATGAACAC
1 AATTTGTTTTCTACAAACAC
*
215445 AATTTGTTTTCTGCAAACA
1 AATTTGTTTTCTACAAACA
215464 ATTATGATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
AATTTGTTTTCTACAAACAC
Found at i:218003 original size:17 final size:16
Alignment explanation
Indices: 217971--218023 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
217961 ATAAGAAATG
*
217971 AAGAAAAACAAGAAAGA
1 AAGAAAAA-AAAAAAGA
*
217988 AAGAAAAAAGAAAAAGG
1 AAGAAAAAA-AAAAAGA
218005 AAGAAAAAAAAAAA-A
1 AAGAAAAAAAAAAAGA
218020 AAGA
1 AAGA
218024 GACCTAGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 4 0.12
16 6 0.19
17 22 0.69
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAAGA
Found at i:218008 original size:21 final size:19
Alignment explanation
Indices: 217974--218022 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
217964 AGAAATGAAG
* *
217974 AAAAACAAGAAAGAAAGAAA
1 AAAAAAAAGGAAGAAA-AAA
217994 AAAGAAAAAGGAAGAAAAAA
1 AAA-AAAAAGGAAGAAAAAA
218014 AAAAAAAAG
1 AAAAAAAAG
218023 AGACCTAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 6 0.23
20 9 0.35
21 11 0.42
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGGAAGAAAAAA
Found at i:218008 original size:25 final size:24
Alignment explanation
Indices: 217971--218023 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
217961 ATAAGAAATG
* *
217971 AAGAAAAACAAGAAAGAAAGAAAA
1 AAGAAAAACAAGAAAAAAAAAAAA
*
217995 AAGAAAAAGGAAGAAAAAAAAAAAA
1 AAGAAAAA-CAAGAAAAAAAAAAAA
218020 AAGA
1 AAGA
218024 GACCTAGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (24 bp):
AAGAAAAACAAGAAAAAAAAAAAA
Found at i:222502 original size:13 final size:13
Alignment explanation
Indices: 222486--222544 Score: 68
Period size: 13 Copynumber: 4.6 Consensus size: 13
222476 ATTTTATTTT
222486 TTTATTATTAATA
1 TTTATTATTAATA
*
222499 TTTATAATTAATA
1 TTTATTATTAATA
222512 TTTATT-TTAATTA
1 TTTATTATTAA-TA
* *
222525 ATTA-TAATAATA
1 TTTATTATTAATA
222537 TTTATTAT
1 TTTATTAT
222545 ATTCATAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.27
13 27 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:225306 original size:18 final size:19
Alignment explanation
Indices: 225280--225317 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
225270 AAATTTAATT
225280 ATTTGTATT-CAAATTAAA
1 ATTTGTATTACAAATTAAA
* *
225298 ATTTTTATTACTAATTAAA
1 ATTTGTATTACAAATTAAA
225317 A
1 A
225318 ATAAAATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTGTATTACAAATTAAA
Found at i:225459 original size:17 final size:17
Alignment explanation
Indices: 225433--225466 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
225423 TTTTTCTAAT
*
225433 CAAATTTAAATAATTTA
1 CAAATATAAATAATTTA
*
225450 CAAATATAAATACTTTA
1 CAAATATAAATAATTTA
225467 TTTTTGTCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
CAAATATAAATAATTTA
Found at i:225699 original size:13 final size:12
Alignment explanation
Indices: 225683--225729 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
225673 AATTTTAAAT
225683 TTTATTATTAATA
1 TTTATTA-TAATA
225696 TTTATTATAATTA
1 TTTATTATAA-TA
* *
225709 ATTATGATAATA
1 TTTATTATAATA
225721 TTTATTATA
1 TTTATTATA
225730 TTTATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
TTTATTATAATA
Found at i:225724 original size:25 final size:24
Alignment explanation
Indices: 225691--225737 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
225681 ATTTTATTAT
225691 TAATATTTATTATAATTAATTATGA
1 TAATATTTATTAT-ATTAATTATGA
*
225716 TAATATTTATTATATTTATTAT
1 TAATATTTATTATATTAATTAT
225738 AAATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TAATATTTATTATATTAATTATGA
Found at i:226321 original size:20 final size:19
Alignment explanation
Indices: 226296--226335 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
226286 TCGAGAAAGA
226296 AATAAATATGTACTAAATAT
1 AATAAATATGTA-TAAATAT
*
226316 AATAAATATTTATAAATAT
1 AATAAATATGTATAAATAT
226335 A
1 A
226336 TGTATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATAAATATGTATAAATAT
Found at i:227983 original size:20 final size:19
Alignment explanation
Indices: 227933--227984 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
227923 TAAATCAATT
* *
227933 TTTCACTTTTCTTAAAAAG
1 TTTCACTTTTCTAAAAAAC
227952 TATTCA-TCTTTCTAAAAAAC
1 T-TTCACT-TTTCTAAAAAAC
227972 TTTCAGCTTTTCT
1 TTTCA-CTTTTCT
227985 TATAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 6 0.22
20 20 0.74
21 1 0.04
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (19 bp):
TTTCACTTTTCTAAAAAAC
Found at i:229195 original size:17 final size:17
Alignment explanation
Indices: 229166--229232 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 17
229156 AGACTAAAAT
229166 ATTTTATTAATTATGATA
1 ATTTTA-TAATTATGATA
* *
229184 ATCTTATAATTAAT-AAA
1 ATTTTATAATT-ATGATA
229201 ATATTATATTAATTATGATA
1 AT-TT-TA-TAATTATGATA
229221 ATTTTATAATTA
1 ATTTTATAATTA
229233 AGATTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
17 15 0.38
18 10 0.25
19 6 0.15
20 9 0.22
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTTATAATTATGATA
Found at i:229227 original size:20 final size:21
Alignment explanation
Indices: 229163--229233 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
229153 CCAAGACTAA
*
229163 AATATT-TTATTAATTATGAT
1 AATATTATAATTAATTATGAT
*
229183 AATCTTATAATTAA-TA--A-
1 AATATTATAATTAATTATGAT
229200 AATATTAT-ATTAATTATGAT
1 AATATTATAATTAATTATGAT
*
229220 AATTTTATAATTAA
1 AATATTATAATTAA
229234 GATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
16 5 0.12
17 9 0.22
18 1 0.02
19 1 0.02
20 14 0.34
21 11 0.27
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (21 bp):
AATATTATAATTAATTATGAT
Found at i:229228 original size:37 final size:37
Alignment explanation
Indices: 229160--229233 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
229150 GTTCCAAGAC
*
229160 TAAAATATTTTATTAATTATGATAATCTTATAATTAA
1 TAAAATATTATATTAATTATGATAATCTTATAATTAA
*
229197 TAAAATATTATATTAATTATGATAATTTTATAATTAA
1 TAAAATATTATATTAATTATGATAATCTTATAATTAA
229234 GATTTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
TAAAATATTATATTAATTATGATAATCTTATAATTAA
Found at i:229360 original size:27 final size:27
Alignment explanation
Indices: 229318--229378 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
229308 AAAATATATT
*
229318 ATTT-AAA-ATAAAATATTATTTTTAT-
1 ATTTAAAATATAAAATATT-TTCTTATA
*
229343 TTTTAAAATATAAAATATTTTCTTATA
1 ATTTAAAATATAAAATATTTTCTTATA
229370 ATTTAAAAT
1 ATTTAAAAT
229379 GAAGTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 9 0.30
27 18 0.60
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTTAAAATATAAAATATTTTCTTATA
Found at i:230800 original size:10 final size:10
Alignment explanation
Indices: 230785--230834 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
230775 TCAATAAAAT
230785 TTTAATTAAA
1 TTTAATTAAA
*
230795 TTTAATTTAA
1 TTTAATTAAA
230805 -TTAA--AAA
1 TTTAATTAAA
*
230812 TTTATTTAAA
1 TTTAATTAAA
*
230822 TTTAATTTAA
1 TTTAATTAAA
230832 TTT
1 TTT
230835 TAAAATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
7 2 0.06
8 3 0.09
9 4 0.12
10 23 0.72
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTAATTAAA
Found at i:230810 original size:27 final size:27
Alignment explanation
Indices: 230779--230853 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
230769 TATATATCAA
*
230779 TAAAATTTTAATTAAATTTAATTTAAT
1 TAAAAATTTAATTAAATTTAATTTAAT
*
230806 TAAAAATTTATTTAAATTTAATTTAATT
1 TAAAAATTTAATTAAATTTAATTTAA-T
*
230834 TTAAAA-TTAA-TAAA-TTAATT
1 TAAAAATTTAATTAAATTTAATT
230854 CTCAAACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.14
26 4 0.09
27 27 0.63
28 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAAAATTTAATTAAATTTAATTTAAT
Found at i:230836 original size:17 final size:16
Alignment explanation
Indices: 230785--230844 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 16
230775 TCAATAAAAT
230785 TTTAA-TTAAATTTAA
1 TTTAATTTAAATTTAA
230800 TTTAA-TTAAA---AA
1 TTTAATTTAAATTTAA
230812 TTT-ATTTAAATTTAA
1 TTTAATTTAAATTTAA
*
230827 TTTAATTTTAAAATTAA
1 TTTAA-TTTAAATTTAA
230844 T
1 T
230845 AAATTAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 1 0.03
12 10 0.26
15 15 0.39
16 1 0.03
17 11 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATTTAAATTTAA
Found at i:231339 original size:3 final size:3
Alignment explanation
Indices: 231331--231366 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
231321 TATGTTATTT
* *
231331 ATA ATA ATA ATA ATA ATA ATA CTA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
231367 TTATTGTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:233008 original size:6 final size:7
Alignment explanation
Indices: 232974--233005 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
232964 TAATTATTTT
*
232974 AAAATTA
1 AAAAATA
232981 AAAAATA
1 AAAAATA
232988 AAAAATA
1 AAAAATA
232995 AAAAATA
1 AAAAATA
233002 AAAA
1 AAAA
233006 TAATTGCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:236095 original size:2 final size:2
Alignment explanation
Indices: 236011--236083 Score: 62
Period size: 2 Copynumber: 36.5 Consensus size: 2
236001 ATATATCCTA
* * *
236011 AT AT AT AT AT AT AT AT AT AG CT TT AT -T AT ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
236053 AT AT AT AT -T AGT AT AA AGT -T AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT A
236084 CACTAATATA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
1 3 0.05
2 51 0.88
3 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:238157 original size:2 final size:2
Alignment explanation
Indices: 238150--238201 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
238140 ATTGTATAAC
* * * * * *
238150 AT AT AT AT AT AT AT AT AC AT AT AT AA AA AA AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238192 AT AT AT AT AT
1 AT AT AT AT AT
238202 TACGTCTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (2 bp):
AT
Found at i:238784 original size:2 final size:2
Alignment explanation
Indices: 238740--238772 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
238730 CTTAGAAAGT
*
238740 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
238773 TAAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:238799 original size:13 final size:13
Alignment explanation
Indices: 238781--238810 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
238771 ATTAAAAAAT
238781 ATATCGAATACGA
1 ATATCGAATACGA
*
238794 ATATCGAATATGA
1 ATATCGAATACGA
238807 ATAT
1 ATAT
238811 TTCAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (13 bp):
ATATCGAATACGA
Found at i:238885 original size:3 final size:3
Alignment explanation
Indices: 238877--238929 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
238867 GAATGACAAT
* *
238877 TAA TAA TAA TAA TAA TAA CAA CAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
238925 TAA TA
1 TAA TA
238930 GAAATTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:240596 original size:12 final size:13
Alignment explanation
Indices: 240579--240641 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 13
240569 AAATACAAAT
*
240579 ATAAATATGTATA
1 ATAAATATATATA
240592 A-AAATATATATA
1 ATAAATATATATA
240604 ATAAATTATTATTATA
1 ATAAA-TA-TA-TATA
* *
240620 TTAAA-ATTTAT-
1 ATAAATATATATA
240631 ATAAATATATA
1 ATAAATATATA
240642 GCCCGATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
11 4 0.10
12 18 0.45
13 5 0.12
14 3 0.08
15 2 0.05
16 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATAAATATATATA
Found at i:242222 original size:2 final size:2
Alignment explanation
Indices: 242215--242249 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
242205 ATCAAATTTA
242215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
242250 AAATTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:242716 original size:17 final size:17
Alignment explanation
Indices: 242670--242720 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
242660 TACTTTTTTC
*
242670 AAAATTTTAAAATAAATT
1 AAAA-TTTATAATAAATT
242688 AAAATTT-T-ATAAATT
1 AAAATTTATAATAAATT
**
242703 TTAATTTATAATAAATT
1 AAAATTTATAATAAATT
242720 A
1 A
242721 GTAAATTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 12 0.44
16 1 0.04
17 10 0.37
18 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTTATAATAAATT
Found at i:244638 original size:35 final size:33
Alignment explanation
Indices: 244581--244645 Score: 78
Period size: 35 Copynumber: 1.9 Consensus size: 33
244571 CAATGTCACA
*
244581 ATTATTATATTTAATAATTTATATATTTATATCTT
1 ATTAATATATTTAATAATTTATA-A-TTATATCTT
*
244616 ATTAATATATTT-TTAATATTATAATTATAT
1 ATTAATATATTTAATAAT-TTATAATTATAT
244646 TTAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.22
34 5 0.19
35 16 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (33 bp):
ATTAATATATTTAATAATTTATAATTATATCTT
Found at i:244644 original size:20 final size:20
Alignment explanation
Indices: 244594--244658 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
244584 ATTATATTTA
* *
244594 ATAATTTATATATTTATATCTT
1 ATAA-TTATATTTTTA-ATATT
244616 ATTAA-TATATTTTTAATATT
1 A-TAATTATATTTTTAATATT
**
244636 ATAATTATATTTAAAATATT
1 ATAATTATATTTTTAATATT
244656 ATA
1 ATA
244659 TATATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 3 0.08
20 21 0.57
21 9 0.24
22 1 0.03
23 3 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATTATATTTTTAATATT
Found at i:244664 original size:20 final size:19
Alignment explanation
Indices: 244618--244663 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
244608 TATATCTTAT
**
244618 TAATATATTTTTAATATTA
1 TAATATATTTAAAATATTA
244637 TAATTATATTTAAAATATTA
1 TAA-TATATTTAAAATATTA
244657 T-ATATAT
1 TAATATAT
244664 AATATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 4 0.17
20 15 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATATTTAAAATATTA
Found at i:244667 original size:34 final size:33
Alignment explanation
Indices: 244629--244717 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 33
244619 AATATATTTT
*
244629 TAATATTATAATTATATTTAAAATATTATATATA
1 TAATATTAT-ATTATATTTAAAATATCATATATA
*
244663 TAATATTATATT-T-TTTAATTATATCATATATA
1 TAATATTATATTATATTTAA-AATATCATATATA
244695 T-ATA-TATATATATTATTTAAAAT
1 TAATATTATAT-TA-TATTTAAAAT
244718 TATCTTATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
30 5 0.11
31 9 0.19
32 13 0.28
33 6 0.13
34 14 0.30
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (33 bp):
TAATATTATATTATATTTAAAATATCATATATA
Found at i:244719 original size:36 final size:32
Alignment explanation
Indices: 244580--244720 Score: 94
Period size: 34 Copynumber: 4.2 Consensus size: 32
244570 TCAATGTCAC
*
244580 AATTATTATATTTAATAAT-TTATA-TATTTATA
1 AATTATTATATAT-ATAATATTATATTATTTA-A
** *
244612 TCTTATTAATATATTTTTAATATTATAATTATATTTAA
1 AATTATT-ATATA--TATAATATTAT-A-T-TATTTAA
*
244650 AA-TATTATATATATAATATTATATT-TTT-T
1 AATTATTATATATATAATATTATATTATTTAA
244679 AATTATATCATATATATATATATATATATTATTTAA
1 AATTAT-T-ATATATATA-ATAT-TATATTATTTAA
244715 AATTAT
1 AATTAT
244721 CTTATCTAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
29 2 0.02
30 6 0.07
31 2 0.02
32 15 0.18
33 9 0.11
34 20 0.24
35 8 0.09
36 12 0.14
37 4 0.05
38 1 0.01
39 6 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (32 bp):
AATTATTATATATATAATATTATATTATTTAA
Found at i:246249 original size:32 final size:32
Alignment explanation
Indices: 246213--246277 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
246203 TATCATTCAC
246213 AGGACAAACTTGGCTGGTATTTATATATATAT
1 AGGACAAACTTGGCTGGTATTTATATATATAT
246245 AGGACAAACTTGGCTGGTATTTATATATATAT
1 AGGACAAACTTGGCTGGTATTTATATATATAT
246277 A
1 A
246278 TATATACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (32 bp):
AGGACAAACTTGGCTGGTATTTATATATATAT
Found at i:247315 original size:7 final size:7
Alignment explanation
Indices: 247272--247296 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
247262 AAAAAAATTT
247272 AAAAAAC
1 AAAAAAC
247279 AAAAAAC
1 AAAAAAC
247286 AAAAAAC
1 AAAAAAC
247293 AAAA
1 AAAA
247297 GTTTTAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:247715 original size:15 final size:16
Alignment explanation
Indices: 247695--247724 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
247685 CAAAATAACA
247695 TTATAATCTT-TTATT
1 TTATAATCTTATTATT
247710 TTATAATCTTATTAT
1 TTATAATCTTATTAT
247725 ATAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATAATCTTATTATT
Found at i:256622 original size:66 final size:66
Alignment explanation
Indices: 256513--256642 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
256503 GCATTAATTT
* * * *
256513 GAAGTAATAAGAACAGGAACCAGAAATTGGACAATGAACAGAAAACCCATGATGGAGCATCCATC
1 GAAGTAATAAGAACAGGAACCAAAAATTGGACAATGAAAAGAAAACCCATCATGCAGCATCCATC
256578 C
66 C
* * * *
256579 GAAGTAATGAGAACATGAATCAAAAATTGGTA-AATGAAAAGAAATCCCATCATGCAGCATCCAT
1 GAAGTAATAAGAACAGGAACCAAAAATTGG-ACAATGAAAAGAAAACCCATCATGCAGCATCCAT
256643 TAGAGGAAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 54 0.98
67 1 0.02
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.17
Consensus pattern (66 bp):
GAAGTAATAAGAACAGGAACCAAAAATTGGACAATGAAAAGAAAACCCATCATGCAGCATCCATC
C
Found at i:260859 original size:47 final size:50
Alignment explanation
Indices: 260806--260905 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 50
260796 AAATAATTTA
* *
260806 AATATTTATATTATTTTTTAA-AAA-AT-ATTAAAAATTATTTTTA-TATT
1 AATATTTATA-TATTTTATAATAAATATAAATAAAAATTATTTTTATTATT
*
260853 AATATTTATATATTTTATAATTAAATTTAAATAAAAATTATTTTTATTATT
1 AATATTTATATATTTTATAA-TAAATATAAATAAAAATTATTTTTATTATT
260904 AA
1 AA
260906 ATAATAATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
46 9 0.20
47 10 0.22
48 3 0.07
49 1 0.02
50 16 0.36
51 6 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (50 bp):
AATATTTATATATTTTATAATAAATATAAATAAAAATTATTTTTATTATT
Found at i:262018 original size:3 final size:3
Alignment explanation
Indices: 262010--262070 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
262000 AACGTATGTT
*
262010 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
262058 GT- TTA ATA ATA AT
1 ATA ATA ATA ATA AT
262071 TCAATAGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
2 1 0.02
3 51 0.98
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:262397 original size:8 final size:8
Alignment explanation
Indices: 262384--262443 Score: 56
Period size: 8 Copynumber: 7.9 Consensus size: 8
262374 TAGACATTAA
262384 TTATATAT
1 TTATATAT
262392 TTATATAT
1 TTATATAT
262400 TT-TATTAT
1 TTATA-TAT
*
262408 TT-TATAA
1 TTATATAT
262415 TTATAT-T
1 TTATATAT
* *
262422 TTAAAAAT
1 TTATATAT
262430 TT-TATAT
1 TTATATAT
262437 TTATATA
1 TTATATA
262444 AATATTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
7 15 0.36
8 27 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATATAT
Found at i:265286 original size:174 final size:171
Alignment explanation
Indices: 264926--265493 Score: 428
Period size: 172 Copynumber: 3.3 Consensus size: 171
264916 AATTATTATT
* * * * * *
264926 GATATTTTAATAATAAAATATATTTTCTAATTTAAAAATTAAGAAATATTAATTCTAAAAAAAAC
1 GATATTTTAATAATAAAATACATTTACCAATTAAAAAATTAAGAAATAATAAGTCTAAAAAAAAC
* ***
264991 GTAAATTGAAACTTTCATATTAAAATATAGTAGTTTCTCAAGCCAAAATTTTATTTTACATAATT
66 GTAAATTGAAACTTTCATATTAAAATATAATAGTTTCTCAAGCCAAAAAAATATTTTACATAATT
265056 TTAAAGTTTAAAAATATTTAAATATTTAAAGTATAATTTTA
131 TTAAAGTTTAAAAATATTTAAATATTTAAAGTATAATTTTA
*
265097 GATATTTTAATAATAAAATACATTTACCATATTAAAAAATTACGAAATAATAAGT-TAAGAAAAA
1 GATATTTTAATAATAAAATACATTTACCA-ATTAAAAAATTAAGAAATAATAAGTCTAA-AAAAA
** ** * * *
265161 ACGTAAATTGATGCTTTTGTGTTAAAATATAAT-GTTTCAT-AA-CTGTAAAAAAATAGTTTTAT
64 ACGTAAATTGAAACTTTCATATTAAAATATAATAGTTTC-TCAAGC--CAAAAAAATA-TTTTAC
** *
265223 ATAATTTTAGATTTTTGAAAAAT-TTTAAATATTTATAAG-ATCATTTTA
125 ATAATTTTA-AAGTTT-AAAAATATTTAAATATTTA-AAGTATAATTTTA
*** *
265271 GATATTTTAATAATAAAATACA--T-CGGGTTAAAAATTTACA-AAATAATAAGTCTCAAAGAAA
1 GATATTTTAATAATAAAATACATTTACCAATTAAAAAATTA-AGAAATAATAAGTCT-AAA-AAA
** * * * * * * * ** **
265332 AATATATATTGACACTTTTATATTAAAATACAATAACTTT-TTAA-ACATCAAAATTTATTTTTT
63 AACGTAAATTGAAACTTTCATATTAAAATATAAT-AGTTTCTCAAGCCA--AAAAAATATTTTAC
* * * * **
265395 ATAATTTTAGA-TTTTAATATTTTTGAAATATTT-ATTTGATAATTTTA
125 ATAATTTTAAAGTTTAAAAATATTT-AAATATTTAAAGT-ATAATTTTA
* * * * *
265442 AATATCTTAATAATAAAATATATTTACCAAGTAAAATAATT-ATAAATAATAA
1 GATATTTTAATAATAAAATACATTTACCAATTAAAA-AATTAAGAAATAATAA
265494 ACTGAAAAAA
Statistics
Matches: 315, Mismatches: 55, Indels: 51
0.75 0.13 0.12
Matches are distributed among these distances:
169 5 0.02
170 28 0.09
171 75 0.24
172 107 0.34
173 24 0.08
174 64 0.20
175 12 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (171 bp):
GATATTTTAATAATAAAATACATTTACCAATTAAAAAATTAAGAAATAATAAGTCTAAAAAAAAC
GTAAATTGAAACTTTCATATTAAAATATAATAGTTTCTCAAGCCAAAAAAATATTTTACATAATT
TTAAAGTTTAAAAATATTTAAATATTTAAAGTATAATTTTA
Found at i:265641 original size:29 final size:29
Alignment explanation
Indices: 265584--265647 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
265574 ACCACACAAG
265584 CAAAATAATAATATTTTAATAAATAATTT
1 CAAAATAATAATATTTTAATAAATAATTT
* * * *
265613 TAAAATAATATTATTTTAATAATTTATTT
1 CAAAATAATAATATTTTAATAAATAATTT
265642 CAAAAT
1 CAAAAT
265648 TAAAACTGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
CAAAATAATAATATTTTAATAAATAATTT
Found at i:267106 original size:17 final size:19
Alignment explanation
Indices: 267072--267109 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
267062 TAATTTTTTT
*
267072 AAGAATATTATATTTTAAA
1 AAGAATATTATATATTAAA
267091 AAGAATATTA-A-ATTAAA
1 AAGAATATTATATATTAAA
267108 AA
1 AA
267110 TAAGTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAGAATATTATATATTAAA
Found at i:267222 original size:14 final size:15
Alignment explanation
Indices: 267193--267226 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
267183 AGTTTTTTAC
*
267193 TTAATAGTTAATTTT
1 TTAATAGATAATTTT
*
267208 TTAATAGATATTTTT
1 TTAATAGATAATTTT
267223 TTAA
1 TTAA
267227 AGTAAAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (15 bp):
TTAATAGATAATTTT
Found at i:268488 original size:2 final size:2
Alignment explanation
Indices: 268481--268511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
268471 ATGTAAACAA
268481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
268512 GTTTGATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:269841 original size:15 final size:15
Alignment explanation
Indices: 269821--269877 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
269811 GATTTATATA
269821 AATAAAATATTAAAT
1 AATAAAATATTAAAT
269836 AAT-AAA-ATTAAATT
1 AATAAAATATTAAA-T
269850 AA-ATAAATA-TAAAT
1 AATA-AAATATTAAAT
269864 GATATAAAATATTA
1 -A-ATAAAATATTA
269878 TTCAAATGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
13 6 0.18
14 7 0.21
15 11 0.32
16 7 0.21
17 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAAAATATTAAAT
Found at i:269972 original size:11 final size:11
Alignment explanation
Indices: 269928--269974 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
269918 TTTCAGCTAT
*
269928 TAATTGATTAA
1 TAATTTATTAA
269939 TAATTTATTCAA
1 TAATTTATT-AA
* *
269951 -CATTAATTAA
1 TAATTTATTAA
269961 TAATTTATTAA
1 TAATTTATTAA
269972 TAA
1 TAA
269975 CATGTGGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 2 0.07
11 25 0.86
12 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (11 bp):
TAATTTATTAA
Found at i:271004 original size:20 final size:21
Alignment explanation
Indices: 270979--271017 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
270969 ATTGGGAACG
270979 AATATTATTTAT-AATTTAAT
1 AATATTATTTATAAATTTAAT
270999 AATATTATTTATAAATTTA
1 AATATTATTTATAAATTTA
271018 TTAGAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTATTTATAAATTTAAT
Found at i:271866 original size:26 final size:26
Alignment explanation
Indices: 271830--271884 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
271820 TGTTTGACAA
* *
271830 AATCAAAATTTGAATATCTGGTTGTG
1 AATCAAAATTTGAATATCTGATTATG
*
271856 AATCGAAATTTGAATATCTGATTATG
1 AATCAAAATTTGAATATCTGATTATG
271882 AAT
1 AAT
271885 TTTTACATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (26 bp):
AATCAAAATTTGAATATCTGATTATG
Found at i:272299 original size:14 final size:13
Alignment explanation
Indices: 272282--272316 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
272272 AAATATTAAA
272282 TTAAAAAACATATT
1 TTAAAAAAC-TATT
*
272296 TTAAAAAACTTTT
1 TTAAAAAACTATT
272309 TTAAAAAA
1 TTAAAAAA
272317 TATAATGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAAAAACTATT
Found at i:277235 original size:21 final size:20
Alignment explanation
Indices: 277211--277284 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
277201 AATTGCATTT
*
277211 TTTCATCCAAAAAATTTATTC
1 TTTCATCCAAAAAATGTA-TC
*
277232 TTTCATCCAAAAAATGCACTC
1 TTTCATCCAAAAAATGTA-TC
**
277253 TTTCATCCAACCAATGTATC
1 TTTCATCCAAAAAATGTATC
277273 ATTTCATCCAAA
1 -TTTCATCCAAA
277285 TATACCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 2 0.04
21 43 0.96
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (20 bp):
TTTCATCCAAAAAATGTATC
Found at i:280583 original size:21 final size:21
Alignment explanation
Indices: 280565--280624 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
280555 TTATAAAAGT
*
280565 TATATTTTTTCATTCAAAAAA
1 TATATTCTTTCATTCAAAAAA
* **
280586 TGTATTCTTTCATTCAATCAA
1 TATATTCTTTCATTCAAAAAA
280607 TATA-TCATTTCATTCAAA
1 TATATTC-TTTCATTCAAA
280625 TACATCTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATTCTTTCATTCAAAAAA
Found at i:283605 original size:11 final size:11
Alignment explanation
Indices: 283567--283605 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
283557 TAATTTTAAA
*
283567 TTATAAAAAAT
1 TTATATAAAAT
283578 TTATA-AAAAT
1 TTATATAAAAT
283588 ATTATATAAAAT
1 -TTATATAAAAT
283600 TTATAT
1 TTATAT
283606 TCTTAAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTATATAAAAT
Found at i:283706 original size:73 final size:74
Alignment explanation
Indices: 283621--283759 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 74
283611 AGAAATAAAT
* * * * *
283621 TTTTACATAATTTTATGTTATGATTATATAATTATAATATTATAAT-AAAAAATTAT-AGATAAA
1 TTTTACATAATTTTATATTATAATTAAATAATAATAATAGTATAATAAAAAAATTATAAG-TAAA
283684 ATATTTTTTA
65 ATATTTTTTA
*
283694 TTTTATATAATTTTATATTATAATTAAATAATAATAATAGTATAATAAAAAAATTATAAGTAAAA
1 TTTTACATAATTTTATATTATAATTAAATAATAATAATAGTATAATAAAAAAATTATAAGTAAAA
283759 T
66 T
283760 GCTCTTGGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 40 0.69
74 16 0.28
75 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.46
Consensus pattern (74 bp):
TTTTACATAATTTTATATTATAATTAAATAATAATAATAGTATAATAAAAAAATTATAAGTAAAA
TATTTTTTA
Found at i:288629 original size:20 final size:20
Alignment explanation
Indices: 288587--288660 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
288577 CACATAGTCC
* **
288587 TGTATCAATACATTTCAGGTA
1 TGTATCGATACA-TTCACTTA
288608 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACTTA
*
288628 TGTATTGATACATT-ACCTTA
1 TGTATCGATACATTCA-CTTA
*
288648 TTGTATTGATACA
1 -TGTATCGATACA
288661 AATTGTTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 23 0.49
21 23 0.49
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTCACTTA
Found at i:288654 original size:21 final size:20
Alignment explanation
Indices: 288606--288660 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
288596 ACATTTCAGG
*
288606 TATGTATCGATACATTCACT
1 TATGTATTGATACATTCACT
288626 TATGTATTGATACATT-ACCT
1 TATGTATTGATACATTCA-CT
288646 TATTGTATTGATACA
1 TA-TGTATTGATACA
288661 AATTGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 19 0.59
21 12 0.38
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
TATGTATTGATACATTCACT
Found at i:290649 original size:28 final size:28
Alignment explanation
Indices: 290614--291086 Score: 444
Period size: 28 Copynumber: 17.0 Consensus size: 28
290604 GGCCTTAAAA
* *
290614 AAAGG-TGCCACTGACCTGTGGACTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
290641 GAAGGGTGCCACCGACTTGTGGGC-TTA
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
290668 AAAAGAGTGCCACTTG-CTTGTGGGCTTTG
1 AAAGGA-TGCCAC-TGACTTGTGGGCTTTG
* * * * **
290697 GAAGGGTGCCACCGACTTATGGGCTTAAA
1 AAAGGATGCCACTGACTTGTGGGCTT-TG
* *
290726 AAAGG-TGTCACTGACTTGTGGACTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
*
290753 AAAGGATGCCACTGACCTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
** * **
290781 AAAAAATGCCACTAACTTGTGGATTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
290809 AAAAGATACTACTGACCTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
290837 -AAGAGATGCCACTGACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
*
290865 -AAGAGATGCCACTAACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
* *
290893 AAAGGATGCTACTGA-TCTGTAGGCTTTG
1 AAAGGATGCCACTGACT-TGTGGGCTTTG
* *
290921 AAAAGATACCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* * * *
290949 AAAGGATGCCACTAACCTATGAGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
290977 -AAGAGATGCCACTGACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
* * *
291005 AAAGGATGCCATTGACCTATGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTG
* *
291033 -AAGAGATG-TACTAACTTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTG
*
291060 AAAGGATGCTACTGACTTGTGGGCTTT
1 AAAGGATGCCACTGACTTGTGGGCTTT
291087 CAAGAGATAA
Statistics
Matches: 359, Mismatches: 71, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
27 42 0.12
28 300 0.84
29 17 0.05
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
AAAGGATGCCACTGACTTGTGGGCTTTG
Found at i:290690 original size:56 final size:56
Alignment explanation
Indices: 290581--290890 Score: 261
Period size: 56 Copynumber: 5.4 Consensus size: 56
290571 GTGTTTTGAA
* *
290581 AAGGGTTGCCACTGACTTGTGTGGGCCTTAAAAAAAGGTGCCACTGACCTGTGGACTTTGG
1 AAGGG-TGCCACCGAC-T-TGTGGG-CTT-AAAAAAGGTGCCACTGACTTGTGGACTTTGG
*
290642 AAGGGTGCCACCGACTTGTGGGCTT-AAAAAGAGTGCCACTTG-CTTGTGGGCTTTGG
1 AAGGGTGCCACCGACTTGTGGGCTTAAAAAAG-GTGCCAC-TGACTTGTGGACTTTGG
* * *
290698 AAGGGTGCCACCGACTTATGGGCTTAAAAAAGGTGTCACTGACTTGTGGACTTTGA
1 AAGGGTGCCACCGACTTGTGGGCTTAAAAAAGGTGCCACTGACTTGTGGACTTTGG
* * * * * *
290754 AAGGATGCCACTGACCTGTGGGCTTTGAAAAAA--TGCCACTAACTTGTGGATTTTGA
1 AAGGGTGCCACCGACTTGTGGGC-TT-AAAAAAGGTGCCACTGACTTGTGGACTTTGG
* * * * * * ** * * *
290810 AAAGATACTACTGACCTGTGGGCTTTGAAGAGATGCCACTGACTTGTGGGCTTT-G
1 AAGGGTGCCACCGACTTGTGGGCTTAAAAAAGGTGCCACTGACTTGTGGACTTTGG
* **
290865 AAGAGATGCCACTAACTTGTGGGCTT
1 AAG-GGTGCCACCGACTTGTGGGCTT
290891 TGAAAGGATG
Statistics
Matches: 211, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
54 3 0.01
55 12 0.06
56 156 0.74
57 13 0.06
58 12 0.06
59 1 0.00
60 9 0.04
61 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (56 bp):
AAGGGTGCCACCGACTTGTGGGCTTAAAAAAGGTGCCACTGACTTGTGGACTTTGG
Found at i:308345 original size:40 final size:40
Alignment explanation
Indices: 308282--308441 Score: 158
Period size: 40 Copynumber: 3.8 Consensus size: 40
308272 TTTTAACTAG
* *
308282 ATGTATCGATACATTGAAGAATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAAATATATCGATACATTCATAC
* * * *
308322 ATGTATCGATACATTTAAAAATGTATCGATACATCTGGGTAAAAGAC
1 ATGTATCGATACATTGAAAAATATATCGATACA--T---T--CATAC
*
308369 AGAATGTATCGATACATTGAAGAATATATCGATACATTCATAC
1 ---ATGTATCGATACATTGAAAAATATATCGATACATTCATAC
*
308412 ATGTATCGATACATTTAAAAATATATCGAT
1 ATGTATCGATACATTGAAAAATATATCGAT
308442 GCATCTGGGT
Statistics
Matches: 99, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
40 59 0.60
42 1 0.01
43 3 0.03
45 2 0.02
47 3 0.03
48 1 0.01
50 30 0.30
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (40 bp):
ATGTATCGATACATTGAAAAATATATCGATACATTCATAC
Found at i:308399 original size:50 final size:50
Alignment explanation
Indices: 308322--308505 Score: 208
Period size: 50 Copynumber: 3.9 Consensus size: 50
308312 ACATTCATAC
* *
308322 ATGTATCGATACATTTAAAAATGTATCGATACATCTGGGTAAAAGACAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAGACAGA
* * *
308372 ATGTATCGATACATTGAAGAATATATCGATACA--T---T--CATAC---
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAGACAGA
* * *
308412 ATGTATCGATACATTTAAAAATATATCGATGCATCTGGGTAAAAGATAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAGACAGA
* *
308462 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAA
308506 ATGAGACTTT
Statistics
Matches: 109, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
40 30 0.28
42 1 0.01
43 3 0.03
45 2 0.02
47 2 0.02
48 1 0.01
50 70 0.64
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAGACAGA
Found at i:308399 original size:90 final size:90
Alignment explanation
Indices: 308282--308495 Score: 383
Period size: 90 Copynumber: 2.4 Consensus size: 90
308272 TTTTAACTAG
*
308282 ATGTATCGATACATTGAAGAATGTATCGATACATTCATACATGTATCGATACATTTAAAAATGTA
1 ATGTATCGATACATTGAAGAATGTATCGATACATTCATACATGTATCGATACATTTAAAAATATA
308347 TCGATACATCTGGGTAAAAGACAGA
66 TCGATACATCTGGGTAAAAGACAGA
*
308372 ATGTATCGATACATTGAAGAATATATCGATACATTCATACATGTATCGATACATTTAAAAATATA
1 ATGTATCGATACATTGAAGAATGTATCGATACATTCATACATGTATCGATACATTTAAAAATATA
* *
308437 TCGATGCATCTGGGTAAAAGATAGA
66 TCGATACATCTGGGTAAAAGACAGA
*
308462 ATGTATCGATACATTGAAAAATGTATCGATACAT
1 ATGTATCGATACATTGAAGAATGTATCGATACAT
308496 CTAGGTAAAA
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 118 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (90 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATTCATACATGTATCGATACATTTAAAAATATA
TCGATACATCTGGGTAAAAGACAGA
Found at i:308508 original size:24 final size:20
Alignment explanation
Indices: 308282--308495 Score: 131
Period size: 20 Copynumber: 9.7 Consensus size: 20
308272 TTTTAACTAG
*
308282 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
308302 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
308322 ATGTATCGATACATTTAAAA
1 ATGTATCGATACATTGAAAA
308342 ATGTATCGATACATCTGGGTAAAAGACAGA
1 ATGTATCGATACAT-T--G----A-A-A-A
*
308372 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * * *
308392 ATATATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
308412 ATGTATCGATACATTTAAAA
1 ATGTATCGATACATTGAAAA
* *
308432 ATATATCGATGCATCTGGGTAAAAGATAGA
1 ATGTATCGATACAT-T--G----A-A-A-A
308462 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
308482 ATGTATCGATACAT
1 ATGTATCGATACAT
308496 CTAGGTAAAA
Statistics
Matches: 151, Mismatches: 23, Indels: 40
0.71 0.11 0.19
Matches are distributed among these distances:
20 106 0.70
21 3 0.02
22 2 0.01
23 2 0.01
27 4 0.03
28 2 0.01
29 4 0.03
30 28 0.19
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:308874 original size:19 final size:20
Alignment explanation
Indices: 308834--308876 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
308824 CTCCTTTTTT
308834 TTAAAAAAAAAAGGCCCAAA
1 TTAAAAAAAAAAGGCCCAAA
*
308854 TTAAAAGAAATAA-GCCC-AA
1 TTAAAA-AAAAAAGGCCCAAA
308873 TTAA
1 TTAA
308877 TCTGGATCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 10 0.48
21 5 0.24
ACGTcount: A:0.60, C:0.14, G:0.09, T:0.16
Consensus pattern (20 bp):
TTAAAAAAAAAAGGCCCAAA
Found at i:309657 original size:13 final size:13
Alignment explanation
Indices: 309639--309663 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
309629 AAATATACTA
309639 CAAATAATAAATC
1 CAAATAATAAATC
309652 CAAATAATAAAT
1 CAAATAATAAAT
309664 ATAGATGCGA
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:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (13 bp):
CAAATAATAAATC
Found at i:314190 original size:19 final size:19
Alignment explanation
Indices: 314165--314219 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
314155 GTCATCAAAT
314165 TTAAAAATTTTAAAAAT-A
1 TTAAAAATTTTAAAAATAA
*
314183 TATAAAAA-TTTAAATATAA
1 T-TAAAAATTTTAAAAATAA
*
314202 TTAAAAAATATTAAAAAT
1 TT-AAAAATTTTAAAAAT
314220 TCCTTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 10 0.33
19 13 0.43
20 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAATTTTAAAAATAA
Found at i:314276 original size:18 final size:18
Alignment explanation
Indices: 314161--314284 Score: 54
Period size: 18 Copynumber: 6.6 Consensus size: 18
314151 CCATGTCATC
*
314161 AAATTTAAAAATTTTAAA
1 AAATTTAAAAATTATAAA
*
314179 AATATATAAAAATT-TAAA
1 AA-ATTTAAAAATTATAAA
*
314197 TATAA-TTAAAAAATATTAAA
1 -A-AATTTAAAAATTA-TAAA
* * * *
314217 AATTCCTTTTAAAATAAAAAA
1 AA---ATTTAAAAATTATAAA
** * * *
314238 AAAAGTAAAAAATCTACA
1 AAATTTAAAAATTATAAA
314256 AAATTTAAAAATTATAAA
1 AAATTTAAAAATTATAAA
*
314274 AAATTCAAAAA
1 AAATTTAAAAA
314285 CCTTAGAATT
Statistics
Matches: 74, Mismatches: 23, Indels: 18
0.64 0.20 0.16
Matches are distributed among these distances:
18 44 0.59
19 13 0.18
20 5 0.07
21 5 0.07
22 7 0.09
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.31
Consensus pattern (18 bp):
AAATTTAAAAATTATAAA
Found at i:314284 original size:26 final size:25
Alignment explanation
Indices: 314244--314342 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 25
314234 AAAAAAAAGT
*
314244 AAAAAATCTACAAAATTTAAAAATTAT
1 AAAAAAT-TA-AAAATTTAAAAATTAA
* *
314271 AAAAAATTCAAAAACCTT-AGAATTAA
1 AAAAAATT-AAAAA-TTTAAAAATTAA
* *
314297 AAAAAATTAATAAATATAAAAATTAC
1 AAAAAATTAA-AAATTTAAAAATTAA
*
314323 AAAAAATT-AAAATTAAAAAA
1 AAAAAATTAAAAATTTAAAAA
314343 GAAAAAGAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
24 9 0.15
25 4 0.07
26 36 0.61
27 10 0.17
ACGTcount: A:0.68, C:0.06, G:0.01, T:0.25
Consensus pattern (25 bp):
AAAAAATTAAAAATTTAAAAATTAA
Found at i:314337 original size:42 final size:43
Alignment explanation
Indices: 314255--314342 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 43
314245 AAAAATCTAC
* * *
314255 AAAATTTAAAAATTATAAAAAATTCAAAAACCTTAGAATTAAA
1 AAAAATTAAAAATTATAAAAAATTCAAAAACATTAAAATTAAA
314298 AAAAATTAATAAA-TAT-AAAAATTACAAAAA-ATTAAAATTAAA
1 AAAAATTAA-AAATTATAAAAAATT-CAAAAACATTAAAATTAAA
314340 AAA
1 AAA
314343 GAAAAAGAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
42 20 0.50
43 17 0.43
44 3 0.08
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (43 bp):
AAAAATTAAAAATTATAAAAAATTCAAAAACATTAAAATTAAA
Found at i:315010 original size:9 final size:9
Alignment explanation
Indices: 314998--315111 Score: 62
Period size: 9 Copynumber: 12.6 Consensus size: 9
314988 TTTTAGATGC
314998 TTTTTAA-T
1 TTTTTAATT
315006 TTTTT-A-T
1 TTTTTAATT
*
315013 TTTATAGATTT
1 TTTTTA-AT-T
315024 TTTTTATAATT
1 TTTTTA--ATT
*
315035 TTTTAAATT
1 TTTTTAATT
315044 GATTTTTAATT
1 --TTTTTAATT
315055 TTTTTAATT
1 TTTTTAATT
315064 TTTTTGAATT
1 TTTTT-AATT
315074 TTTATT--TT
1 TTT-TTAATT
* *
315082 ATTTTAAAT
1 TTTTTAATT
315091 TTTTTAA--
1 TTTTTAATT
*
315098 CTTTTAATT
1 TTTTTAATT
315107 TTTTT
1 TTTTT
315112 TTAAATTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 25
0.70 0.08 0.21
Matches are distributed among these distances:
7 14 0.17
8 9 0.11
9 29 0.35
10 7 0.08
11 22 0.27
12 2 0.02
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.72
Consensus pattern (9 bp):
TTTTTAATT
Found at i:315049 original size:21 final size:20
Alignment explanation
Indices: 315025--315097 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
315015 TATAGATTTT
315025 TTTTATAATTTTTTAAATTGA
1 TTTT-TAATTTTTTAAATTGA
*
315046 TTTTTAATTTTTTTAATT--
1 TTTTTAATTTTTTAAATTGA
* *
315064 TTTTTGAA-TTTTT-ATTTTA
1 TTTTT-AATTTTTTAAATTGA
*
315083 TTTTAAATTTTTTAA
1 TTTTTAATTTTTTAA
315098 CTTTTAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.07
18 12 0.27
19 11 0.25
20 14 0.32
21 4 0.09
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTTAATTTTTTAAATTGA
Found at i:315055 original size:20 final size:19
Alignment explanation
Indices: 315025--315097 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 19
315015 TATAGATTTT
315025 TTTTATAATTTTTTAAATTGA
1 TTTT-TAATTTTTTAAATT-A
*
315046 TTTTTAATTTTTTTAATT-
1 TTTTTAATTTTTTAAATTA
**
315064 TTTTTGAA-TTTTTATTTTA
1 TTTTT-AATTTTTTAAATTA
*
315083 TTTTAAATTTTTTAA
1 TTTTTAATTTTTTAA
315098 CTTTTAATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 14 0.33
19 12 0.28
20 13 0.30
21 4 0.09
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTTTAATTTTTTAAATTA
Found at i:315076 original size:27 final size:25
Alignment explanation
Indices: 314978--315128 Score: 99
Period size: 26 Copynumber: 5.5 Consensus size: 25
314968 TTTAATAATT
* *
314978 ATTTTTTAAATTTTAGATGCTTTTT-A
1 ATTTTTTAATTTTTA-AT-TTTTTTAA
315004 ATTTTTT-ATTTTATAGATTTTTTTTATA
1 ATTTTTTAATTTT-TA-A-TTTTTTTA-A
315032 ATTTTTTAAATTGATTTTTAATTTTTTTAA
1 ATTTTTT--A---ATTTTTAATTTTTTTAA
* *
315062 TTTTTTTGAATTTTTATTTTATTTTAA
1 ATTTTTT-AATTTTTAATTT-TTTTAA
*
315089 ATTTTTTAACTTTTAATTTTTTTTTAA
1 ATTTTTTAATTTTTAA--TTTTTTTAA
315116 ATTTTTTATATTT
1 ATTTTTTA-ATTT
315129 AAAAATTATT
Statistics
Matches: 102, Mismatches: 9, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
25 4 0.04
26 33 0.32
27 27 0.26
28 14 0.14
29 1 0.01
30 7 0.07
31 8 0.08
32 1 0.01
33 2 0.02
34 5 0.05
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (25 bp):
ATTTTTTAATTTTTAATTTTTTTAA
Found at i:315120 original size:9 final size:9
Alignment explanation
Indices: 315023--315128 Score: 56
Period size: 9 Copynumber: 11.3 Consensus size: 9
315013 TTTATAGATT
315023 TTTTTTATAA
1 TTTTTTA-AA
315033 TTTTTTAAA
1 TTTTTTAAA
*
315042 TTGATTTTTAAT
1 -T--TTTTTAAA
*
315054 TTTTTTAAT
1 TTTTTTAAA
*
315063 TTTTTTGAA
1 TTTTTTAAA
**
315072 -TTTTTATT
1 TTTTTTAAA
315080 TTATTTTAAA
1 TT-TTTTAAA
315090 TTTTTT-AA
1 TTTTTTAAA
* *
315098 -CTTTTAATTT
1 TTTTTTAA--A
315108 TTTTTTAAA
1 TTTTTTAAA
*
315117 TTTTTTATA
1 TTTTTTAAA
315126 TTT
1 TTT
315129 AAAAATTATT
Statistics
Matches: 74, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
7 4 0.05
8 8 0.11
9 33 0.45
10 15 0.20
11 7 0.09
12 7 0.09
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:315129 original size:15 final size:14
Alignment explanation
Indices: 315078--315131 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
315068 TGAATTTTTA
315078 TTTTATTTTAAATT
1 TTTTATTTTAAATT
315092 TTTTAACTTTT-AA-T
1 TTTT-A-TTTTAAATT
315106 TTTT-TTTTAAATT
1 TTTTATTTTAAATT
315119 TTTTATATTTAAA
1 TTTTAT-TTTAAA
315132 AATTATTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
11 4 0.12
12 2 0.06
13 5 0.15
14 10 0.29
15 9 0.26
16 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTTAAATT
Found at i:315130 original size:26 final size:26
Alignment explanation
Indices: 315053--315128 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
315043 TGATTTTTAA
* *
315053 TTTTTTTAATTTTTTTGAATTTTTATT
1 TTTTTTTAAATTTTTT-AATTTTAATT
*
315080 TTATTTTAAATTTTTTAACTTTTAATT
1 TTTTTTTAAATTTTTTAA-TTTTAATT
315107 TTTTTTTAAATTTTTTATATTT
1 TTTTTTTAAATTTTTTA-ATTT
315129 AAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (26 bp):
TTTTTTTAAATTTTTTAATTTTAATT
Found at i:315671 original size:15 final size:15
Alignment explanation
Indices: 315628--315681 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
315618 GATCTACATG
*
315628 AATAAATGATAAAATA
1 AATAAAT-ATAAATTA
315644 CAAT-AAT-TAAATTA
1 -AATAAATATAAATTA
315658 AATAAATATAAATTA
1 AATAAATATAAATTA
*
315673 TATAAATAT
1 AATAAATAT
315682 TTATAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 3 0.09
14 9 0.27
15 15 0.45
16 3 0.09
17 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAAATATAAATTA
Found at i:315675 original size:9 final size:10
Alignment explanation
Indices: 315656--315773 Score: 69
Period size: 10 Copynumber: 11.8 Consensus size: 10
315646 ATAATTAAAT
*
315656 TAAATAAATA
1 TAAATATATA
315666 TAAAT-TATA
1 TAAATATATA
*
315675 TAAATATTTA
1 TAAATATATA
* *
315685 TAAATGTATG
1 TAAATATATA
*
315695 TAAA-ATTAATT
1 TAAATA-T-ATA
* *
315706 TAATTTTATA
1 TAAATATATA
*
315716 TAAATATAAA
1 TAAATATATA
* * *
315726 TGAATCTTTA
1 TAAATATATA
*
315736 TATATATATA
1 TAAATATATA
*
315746 TATATATATA
1 TAAATATATA
*
315756 TATATATATA
1 TAAATATATA
*
315766 TATATATA
1 TAAATATA
315774 GTGTGTGTGA
Statistics
Matches: 83, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
9 8 0.10
10 69 0.83
11 6 0.07
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (10 bp):
TAAATATATA
Found at i:315678 original size:19 final size:19
Alignment explanation
Indices: 315656--315721 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
315646 ATAATTAAAT
315656 TAAATAAATATAAATTATA
1 TAAATAAATATAAATTATA
** *
315675 TAAATATTTATAAATGTATG
1 TAAATAAATATAAAT-TATA
* * *
315695 TAAAATTAATTTAATTTTATA
1 T-AAATAAATATAA-ATTATA
315716 TAAATA
1 TAAATA
315722 TAAATGAATC
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
19 13 0.38
20 8 0.24
21 12 0.35
22 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TAAATAAATATAAATTATA
Found at i:315741 original size:2 final size:2
Alignment explanation
Indices: 315734--315773 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
315724 AATGAATCTT
315734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
315774 GTGTGTGTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:316567 original size:16 final size:17
Alignment explanation
Indices: 316542--316576 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
316532 AATAATTATA
*
316542 TTTTACATATA-AATTT
1 TTTTAAATATATAATTT
316558 TTTTAAATATATAATTT
1 TTTTAAATATATAATTT
316575 TT
1 TT
316577 AAAAATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAATATATAATTT
Found at i:319552 original size:22 final size:22
Alignment explanation
Indices: 319509--319552 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
319499 TTTTTTAGTT
* * *
319509 AATATTAATTATTTATTATTAA
1 AATATAAAATATTTATGATTAA
*
319531 AATATAAAATATTTATGCTTAA
1 AATATAAAATATTTATGATTAA
319553 TAATTTTCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AATATAAAATATTTATGATTAA
Found at i:327458 original size:14 final size:16
Alignment explanation
Indices: 327427--327473 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
327417 AAAAAAGGTT
327427 AAAA-GCAAAAGCACAA
1 AAAATGCAAAAGCA-AA
327443 AAAATG-AAAAG-AAA
1 AAAATGCAAAAGCAAA
*
327457 AAAGTGCAAAAGCAAA
1 AAAATGCAAAAGCAAA
327473 A
1 A
327474 TAAAAAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 13 0.48
17 1 0.04
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAATGCAAAAGCAAA
Found at i:328642 original size:27 final size:27
Alignment explanation
Indices: 328585--328984 Score: 493
Period size: 27 Copynumber: 14.7 Consensus size: 27
328575 TTTTAAAATT
**
328585 CACAACTTCGTGGCATTCTTTTAAAGTC
1 CACAACTTCGTGGCACCCTTTT-AAGTC
*
328613 CACAACTTCGTGGCACCCTTTAAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
*
328640 CACAAC-TCTGTGGCACCTTTTTAAGTC
1 CACAACTTC-GTGGCACCCTTTTAAGTC
*
328667 CACAACTCCGTGGCACCCTTTTAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
**
328694 CGTAACTTCGTGGCACCCTTTTAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
* ** *
328721 CATAACCCCGTGGCACCCTTTAAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
*
328748 CACAAC-TCTGTGGCACCTTTTTAAGTC
1 CACAACTTC-GTGGCACCCTTTTAAGTC
* *
328775 CACAACTCCGTGACACCCTTTTAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
328802 CACAACTTCGTGGCACCCTTTTAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
**
328829 CACAACCCCGTGGCACCCTTTTAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
* *
328856 CACAACTTTGTGGCACCATTTTAAGTC
1 CACAACTTCGTGGCACCCTTTTAAGTC
*
328883 CACAACTCCGTGGCA-CCTTTTGAAGTC
1 CACAACTTCGTGGCACCCTTTT-AAGTC
* * *
328910 CACAACTCCGTGGCACACTTTTGAAATC
1 CACAACTTCGTGGCACCCTTTT-AAGTC
* *
328938 CATAAC-TCTGTGGCATCCTTTTAAGTC
1 CACAACTTC-GTGGCACCCTTTTAAGTC
*
328965 CACAACTCCGTGGCACCCTT
1 CACAACTTCGTGGCACCCTT
328985 CAAAGCCCAC
Statistics
Matches: 322, Mismatches: 42, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
26 8 0.02
27 266 0.83
28 48 0.15
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (27 bp):
CACAACTTCGTGGCACCCTTTTAAGTC
Found at i:328743 original size:108 final size:109
Alignment explanation
Indices: 328585--328981 Score: 577
Period size: 108 Copynumber: 3.7 Consensus size: 109
328575 TTTTAAAATT
** **
328585 CACAACTTCGTGGCATTCTTTTAAAGTCCACAACTTCGTGGCACCCTTTAAAGTCCACAACTCTG
1 CACAACTTCGTGGCACCCTTTTAAAGTCCACAACCCCGTGGCACCCTTTAAAGTCCACAACTCTG
328650 TGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
66 TGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
** *
328694 CGTAACTTCGTGGCACCCTTTT-AAGTCCATAACCCCGTGGCACCCTTTAAAGTCCACAACTCTG
1 CACAACTTCGTGGCACCCTTTTAAAGTCCACAACCCCGTGGCACCCTTTAAAGTCCACAACTCTG
*
328758 TGGCACCTTTTTAAGTCCACAACTCCGTGACACCCTTTTAAGTC
66 TGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
* *
328802 CACAACTTCGTGGCACCCTTTT-AAGTCCACAACCCCGTGGCACCCTTTTAAGTCCACAACTTTG
1 CACAACTTCGTGGCACCCTTTTAAAGTCCACAACCCCGTGGCACCCTTTAAAGTCCACAACTCTG
*
328866 TGGCACCATTTTAAGTCCACAACTCCGTGGCA-CCTTTTGAAGTC
66 TGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
* * * * * * * *
328910 CACAACTCCGTGGCACACTTTTGAAA-TCCATAACTCTGTGGCATCCTTTTAAGTCCACAACTCC
1 CACAACTTCGTGGCACCCTTTT-AAAGTCCACAACCCCGTGGCACCCTTTAAAGTCCACAACTCT
328974 GTGGCACC
65 GTGGCACC
328982 CTTCAAAGCC
Statistics
Matches: 262, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
107 6 0.02
108 196 0.75
109 58 0.22
110 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28
Consensus pattern (109 bp):
CACAACTTCGTGGCACCCTTTTAAAGTCCACAACCCCGTGGCACCCTTTAAAGTCCACAACTCTG
TGGCACCTTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
Found at i:329049 original size:28 final size:28
Alignment explanation
Indices: 328983--329471 Score: 559
Period size: 28 Copynumber: 17.1 Consensus size: 28
328973 CGTGGCACCC
328983 TTCAAAGCCCACAAGTCAGTGGCATC-T
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329010 TTCCAAGCCCACAAGTCAGTGGCAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329038 TTCAAAGCCCACGAGTCAGTGGCAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329066 TTCAAAGCCCACGAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* ** *
329094 TTCAAAACCCACACAAGTTGGTGGCAACCTAT
1 TTC-AAAGCC-CACAAGTCAGTGGC-ATCT-T
** *
329126 TTCAAAGCCCACACAAGTTGGTGGCAACCTAT
1 TTCAAAG-CC-CACAAGTCAGTGGC-ATCT-T
329158 TTCAAAGCCTACACAAGTCAGTGGCATCTT
1 TTCAAAGCC--CACAAGTCAGTGGCATCTT
* *
329188 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
329216 TTCAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329244 TTCAATGTCCACAAGTC-GATGGCATCTT
1 TTCAAAGCCCACAAGTCAG-TGGCATCTT
*
329272 TTCAAAGCCCACAAGTCAATGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
329300 TTCCAAGCCCACAAGTCAGTGGCAACTC
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* * *
329328 TTCAAAGCCCACGAGTCAGTGGAAACTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329356 TTCAAAGCCCACGAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329384 TCCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329412 TTCAAAGCCCACAAGTCAGTGGTATCTC
1 TTCAAAGCCCACAAGTCAGTGGCATCTT
* *
329440 TTCAAAGCCCACAAAAGTTAGTGGCACCTT
1 TTCAAAGCCCAC--AAGTCAGTGGCATCTT
329470 TT
1 TT
329472 TTTTAAAAGC
Statistics
Matches: 405, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
27 25 0.06
28 282 0.70
29 5 0.01
30 35 0.09
31 10 0.02
32 48 0.12
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTT
Found at i:329130 original size:32 final size:32
Alignment explanation
Indices: 329093--329228 Score: 158
Period size: 32 Copynumber: 4.4 Consensus size: 32
329083 AGTGGCATCC
*
329093 TTTCAAAACCCACACAAGTTGGTGGCAACCTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
329125 TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
* ** *
329157 TTTCAAAGCCTACACAAGTCAGTGGC-ATCT-
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
** *
329187 TTTCAAAG-CC-CACAAGTCAGTGGC-ACC-C
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
329215 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
329229 AGTCAGTGGC
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
28 24 0.26
29 3 0.03
30 10 0.11
31 3 0.03
32 54 0.57
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAACCTA
Found at i:329685 original size:47 final size:47
Alignment explanation
Indices: 329576--329724 Score: 235
Period size: 48 Copynumber: 3.1 Consensus size: 47
329566 GGCACCTTTA
* * *
329576 TTAGCTCAATGTCGCTGGCATTGAATCAACACATTGTCTGCTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTC-CCTTTTCCC
329624 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCCTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCCTTTTCCC
* *
329671 TTAGCTCAATGTCGCTAGCCTTAAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCC-CTTTTCCC
329719 TTAGCT
1 TTAGCT
329725 TGATGTCATT
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
47 45 0.47
48 50 0.53
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (47 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCCTTTTCCC
Found at i:329754 original size:48 final size:47
Alignment explanation
Indices: 329576--329744 Score: 230
Period size: 48 Copynumber: 3.6 Consensus size: 47
329566 GGCACCTTTA
* * * *
329576 TTAGCTCAATGTCGCTGGCATTGAATCAACACATTGTCTGCTTTTCCC
1 TTAGCTCAATGTCGCTAGCCTTGAATCAGCACATTGTC-CCTTTTCCC
*
329624 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTGTCCCTTTTCCC
1 TTAGCTCAATGTCGCTAGCCTTGAATCAGCACATTGTCCCTTTTCCC
*
329671 TTAGCTCAATGTCGCTAGCCTTAAATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTAGCCTTGAATCAGCACATTGTCC-CTTTTCCC
** **
329719 TTAGCTTGATGTCATTAGCCTTGAAT
1 TTAGCTCAATGTCGCTAGCCTTGAAT
329745 TGGTACATTG
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
47 45 0.41
48 65 0.59
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.36
Consensus pattern (47 bp):
TTAGCTCAATGTCGCTAGCCTTGAATCAGCACATTGTCCCTTTTCCC
Found at i:330423 original size:24 final size:24
Alignment explanation
Indices: 330396--330449 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
330386 AATGTTGGAT
330396 AAAAAAAAGGGAGTCGAGTAAAGG
1 AAAAAAAAGGGAGTCGAGTAAAGG
** *
330420 AAAAAAGGGGGAGTCTAGTAAAGG
1 AAAAAAAAGGGAGTCGAGTAAAGG
330444 AAAAAA
1 AAAAAA
330450 TGGGGGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.31, T:0.09
Consensus pattern (24 bp):
AAAAAAAAGGGAGTCGAGTAAAGG
Found at i:330454 original size:24 final size:24
Alignment explanation
Indices: 330404--330455 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 24
330394 ATAAAAAAAA
330404 GGGAGTCGAGTAAAGGAAAAAAGG
1 GGGAGTCGAGTAAAGGAAAAAAGG
*
330428 GGGAGTCTAGTAAAGGAAAAAATGG
1 GGGAGTCGAGTAAAGGAAAAAA-GG
330453 GGG
1 GGG
330456 GAGAGGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.42, T:0.12
Consensus pattern (24 bp):
GGGAGTCGAGTAAAGGAAAAAAGG
Found at i:334970 original size:3 final size:3
Alignment explanation
Indices: 334962--334991 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
334952 AAAATCAGAT
334962 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
334992 AATTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:335047 original size:13 final size:13
Alignment explanation
Indices: 335026--335068 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
335016 ATTAATGAAG
*
335026 ATTAAATTTAAAA
1 ATTATATTTAAAA
335039 ATTATATTTCAAAA
1 ATTATATTT-AAAA
*
335053 AATATATTATAAAA
1 ATTATATT-TAAAA
335067 AT
1 AT
335069 AAAATAGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 8 0.32
14 16 0.64
15 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATATTTAAAA
Found at i:335425 original size:18 final size:18
Alignment explanation
Indices: 335404--335495 Score: 84
Period size: 18 Copynumber: 5.3 Consensus size: 18
335394 AAAATCTCAT
*
335404 ATTTTCTAGGAATCTTAG
1 ATTTTCTAGGAATCATAG
* * *
335422 ATTTTCTAGAAATCACAA
1 ATTTTCTAGGAATCATAG
* *
335440 ATTTTCTAAGAATCATAT
1 ATTTTCTAGGAATCATAG
* *
335458 ATTTT-T-GTAATAATAG
1 ATTTTCTAGGAATCATAG
335474 A-TTTCTA-GAATCATAG
1 ATTTTCTAGGAATCATAG
335490 ATTTTC
1 ATTTTC
335496 AATCATAATA
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
15 3 0.05
16 16 0.28
17 5 0.09
18 33 0.58
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (18 bp):
ATTTTCTAGGAATCATAG
Found at i:340314 original size:18 final size:18
Alignment explanation
Indices: 340269--340365 Score: 106
Period size: 18 Copynumber: 5.4 Consensus size: 18
340259 AAAAATCAGA
* *
340269 TTTTAAAAATCACATATT
1 TTTTAGAAATCACAGATT
* * **
340287 TTCTATAAATCTTAGATT
1 TTTTAGAAATCACAGATT
*
340305 TTTTAGAAATAACAGATT
1 TTTTAGAAATCACAGATT
340323 TTTTAGAAATCACAGATT
1 TTTTAGAAATCACAGATT
* *
340341 TTTTAAAAATCATAGA-T
1 TTTTAGAAATCACAGATT
340358 TTTTAGAA
1 TTTTAGAA
340366 TAATATATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
17 8 0.12
18 57 0.88
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (18 bp):
TTTTAGAAATCACAGATT
Found at i:340391 original size:16 final size:15
Alignment explanation
Indices: 340348--340408 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
340338 ATTTTTTAAA
340348 AATCATAGATTTTTAG
1 AATCATAGATTTTT-G
* *
340364 AATAATATATTTTTG
1 AATCATAGATTTTTG
**
340379 TAATCATAGATTTCTAA
1 -AATCATAGATTT-TTG
340396 AATCATAGATTTT
1 AATCATAGATTTT
340409 CAACCGTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 2 0.05
16 34 0.92
17 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (15 bp):
AATCATAGATTTTTG
Found at i:340408 original size:32 final size:32
Alignment explanation
Indices: 340348--340408 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
340338 ATTTTTTAAA
* * *
340348 AATCATAGATTTTTAGAATAATATATTTTTGT
1 AATCATAGATTTCTAAAATAATAGATTTTTGT
*
340380 AATCATAGATTTCTAAAATCATAGATTTT
1 AATCATAGATTTCTAAAATAATAGATTTT
340409 CAACCGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (32 bp):
AATCATAGATTTCTAAAATAATAGATTTTTGT
Found at i:341230 original size:28 final size:28
Alignment explanation
Indices: 341197--341257 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
341187 GTTTTTATTT
341197 TTTAAATAAATTATTAAAATAATATTAA
1 TTTAAATAAATTATTAAAATAATATTAA
* *
341225 TTTAAATAAATTATTAAAATATTATTAT
1 TTTAAATAAATTATTAAAATAATATTAA
341253 TTTAA
1 TTTAA
341258 TACATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAAATAAATTATTAAAATAATATTAA
Found at i:341457 original size:19 final size:19
Alignment explanation
Indices: 341433--341515 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
341423 TATTTTTAAA
341433 ATTAATAAAAAATTATATT
1 ATTAATAAAAAATTATATT
* *
341452 ATTAATAAAAGATAATATT
1 ATTAATAAAAAATTATATT
*
341471 ATT-ATAAATATAATAATAATTTT
1 ATTAATAAA-A-AAT--T-ATATT
* *
341494 ATTATTAAAAAATTATTTT
1 ATTAATAAAAAATTATATT
341513 ATT
1 ATT
341516 TACAATTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.10
19 29 0.56
20 3 0.06
22 3 0.06
23 8 0.15
24 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
ATTAATAAAAAATTATATT
Found at i:341498 original size:45 final size:43
Alignment explanation
Indices: 341422--341505 Score: 107
Period size: 45 Copynumber: 1.9 Consensus size: 43
341412 TATTATGTTT
*
341422 ATATTTTTAAAATTAATAAAAAATTATATTATTAATAAAAGATA
1 ATATTATTAAAATTAATAAAAAATTATATTATTAA-AAAAGATA
* *
341466 ATATTATTATAAATATAAT-AATAATTTTATTATTAAAAAA
1 ATATTATTA-AAAT-TAATAAAAAATTATATTATTAAAAAA
341506 TTATTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
44 12 0.34
45 19 0.54
46 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (43 bp):
ATATTATTAAAATTAATAAAAAATTATATTATTAAAAAAGATA
Found at i:341733 original size:30 final size:31
Alignment explanation
Indices: 341699--341763 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
341689 TTGTCTAATT
*
341699 ATTAAG-GATAATAAT-ATTTAATTATTTTAA
1 ATTAAGAG-TAATAATCATCTAATTATTTTAA
*
341729 ATTAAGAGTTATAATCATCTAATTATTTTAA
1 ATTAAGAGTAATAATCATCTAATTATTTTAA
341760 ATTA
1 ATTA
341764 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (31 bp):
ATTAAGAGTAATAATCATCTAATTATTTTAA
Found at i:341826 original size:51 final size:49
Alignment explanation
Indices: 341711--341831 Score: 131
Period size: 51 Copynumber: 2.4 Consensus size: 49
341701 TAAGGATAAT
*
341711 AATA-TTTAATTATTTTAAATTAAGAGTTATAATCATCTAATTATTTTA
1 AATATTTTAATTATTTTAAATTAAAAGTTATAATCATCTAATTATTTTA
* * * * *
341759 AATTATTTTAA-AATTTTAATTTAATTAAGTTGTATTTATCTAATTATTTTTA
1 AA-TATTTTAATTATTTTAAATTAA--AAGTTATAATCATCTAATTA-TTTTA
341811 AA-ATTTTAATTATTTTAAATT
1 AATATTTTAATTATTTTAAATT
341832 GCTAAACGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
48 2 0.03
49 13 0.22
50 12 0.20
51 25 0.42
52 7 0.12
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (49 bp):
AATATTTTAATTATTTTAAATTAAAAGTTATAATCATCTAATTATTTTA
Done.