Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 131 of 190
Found at i:38853159 original size:18 final size:18
Alignment explanation
Indices: 38853115--38853161 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
38853105 CCTACGCCTC
* *
38853115 CACCACCACCAGCTCCTA
1 CACCACCACCAGCCCCAA
* *
38853133 CTCCTCCACCAGCCCCAA
1 CACCACCACCAGCCCCAA
38853151 CACCACCACCA
1 CACCACCACCA
38853162 ATACCTGCAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.60, G:0.04, T:0.09
Consensus pattern (18 bp):
CACCACCACCAGCCCCAA
Found at i:38853232 original size:18 final size:18
Alignment explanation
Indices: 38853209--38853370 Score: 73
Period size: 18 Copynumber: 8.7 Consensus size: 18
38853199 CGCCAACACT
38853209 ACCTCCACCACCTCCACC
1 ACCTCCACCACCTCCACC
38853227 ACCTCCACCACCAACTCCTA-C
1 ACCTCCACCA-C--CTCC-ACC
* * *
38853248 TCCTCCACCGCCTCCAGC
1 ACCTCCACCACCTCCACC
*
38853266 ACCTCCACCAGCTCCTA-C
1 ACCTCCACCACCTCC-ACC
* *
38853284 TCCTCCACCAACCCCGACACC
1 ACCTCCACC-ACCTC--CACC
* *
38853305 ACCACTACCACCTACTC-CC
1 ACCTCCACCACCT-C-CACC
* *
38853324 A-CTCCAGCACCTCCTCC
1 ACCTCCACCACCTCCACC
* **
38853341 TA-CACCACCACCAACACC
1 -ACCTCCACCACCTCCACC
38853359 ACCTCCACCACC
1 ACCTCCACCACC
38853371 CCTAGCACCA
Statistics
Matches: 108, Mismatches: 22, Indels: 28
0.68 0.14 0.18
Matches are distributed among these distances:
16 1 0.01
17 5 0.05
18 65 0.60
19 8 0.07
20 6 0.06
21 22 0.20
22 1 0.01
ACGTcount: A:0.24, C:0.60, G:0.03, T:0.13
Consensus pattern (18 bp):
ACCTCCACCACCTCCACC
Found at i:38853370 original size:12 final size:12
Alignment explanation
Indices: 38853325--38853410 Score: 50
Period size: 12 Copynumber: 7.2 Consensus size: 12
38853315 CCTACTCCCA
* *
38853325 CTCCAGCACCTC
1 CTCCACCACCAC
38853337 CTCCTA-CACCAC
1 CTCC-ACCACCAC
* *
38853349 CACCAACACCAC
1 CTCCACCACCAC
38853361 CTCCACCACC-C
1 CTCCACCACCAC
*
38853372 CTAGCACCACCAC
1 CT-CCACCACCAC
* * *
38853385 TTGCACCTCCAC
1 CTCCACCACCAC
* *
38853397 TTCCACCCCCAC
1 CTCCACCACCAC
38853409 CT
1 CT
38853411 GCTCCTACTC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
11 4 0.07
12 53 0.88
13 3 0.05
ACGTcount: A:0.23, C:0.59, G:0.03, T:0.14
Consensus pattern (12 bp):
CTCCACCACCAC
Found at i:38856485 original size:37 final size:37
Alignment explanation
Indices: 38856423--38856545 Score: 187
Period size: 36 Copynumber: 3.3 Consensus size: 37
38856413 AAATTAAAAC
38856423 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAAGTATTTT-AAAATATTTTAAAATTA
*
38856461 AAAAACTT-AAAAAGTATTTTAAAATATTTT-AAATTT
1 AAAAA-TTAAAAAAGTATTTTAAAATATTTTAAAATTA
*
38856497 AAAAATTAAAAAAGTATTTTAAAGTATTTTAAAATTA
1 AAAAATTAAAAAAGTATTTTAAAATATTTTAAAATTA
*
38856534 AAAAAATAAAAA
1 AAAAATTAAAAA
38856546 TAAAAATATT
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
35 2 0.03
36 31 0.40
37 26 0.33
38 17 0.22
39 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (37 bp):
AAAAATTAAAAAAGTATTTTAAAATATTTTAAAATTA
Found at i:38857188 original size:31 final size:31
Alignment explanation
Indices: 38857153--38857217 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
38857143 AACAGTCCAG
*
38857153 TGACTTAAATAAAAACTTTCCAATAGTTCAA
1 TGACTTAAATAAAAACTTTCCAATAGCTCAA
* **
38857184 TGACTTAAATGAAAACTTTTGAATAGCTCAA
1 TGACTTAAATAAAAACTTTCCAATAGCTCAA
38857215 TGA
1 TGA
38857218 TCATTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCCAATAGCTCAA
Found at i:38867172 original size:13 final size:12
Alignment explanation
Indices: 38867154--38867188 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
38867144 ATAACACGAG
38867154 TAAAAACAAAAAA
1 TAAAAA-AAAAAA
*
38867167 TAAAAAAAAAGA
1 TAAAAAAAAAAA
38867179 TAAAAAAAAA
1 TAAAAAAAAA
38867189 TCAATTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.09
Consensus pattern (12 bp):
TAAAAAAAAAAA
Found at i:38868059 original size:11 final size:11
Alignment explanation
Indices: 38868045--38868069 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38868035 TTAAAAAGGG
38868045 AAAAAAAGAAA
1 AAAAAAAGAAA
38868056 AAAAAAAGAAA
1 AAAAAAAGAAA
38868067 AAA
1 AAA
38868070 TTCGAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:38868902 original size:44 final size:45
Alignment explanation
Indices: 38868854--38869000 Score: 133
Period size: 44 Copynumber: 3.4 Consensus size: 45
38868844 GACCTACCGT
* * ** * *
38868854 AACTTCAGAGG-TATAGGATTCATATTTTTAATCCGCTCCACTGC
1 AACTTCAGAGGAGATAGGATTAATAGCTTCAATCCACTCCACTGC
*
38868898 AACTTCA-AGGAGATAGGATTAATAGCTTCAATCTACTCCACTGC
1 AACTTCAGAGGAGATAGGATTAATAGCTTCAATCCACTCCACTGC
* *** * *
38868942 AACTTCAG-GGAGATAAGATTGGCATCTTCAA-CCTGCTCCACTGC
1 AACTTCAGAGGAGATAGGATTAATAGCTTCAATCC-ACTCCACTGC
38868986 AACTTCAG-GGAGATA
1 AACTTCAGAGGAGATA
38869001 AGACTTGTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 4 0.05
44 82 0.95
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (45 bp):
AACTTCAGAGGAGATAGGATTAATAGCTTCAATCCACTCCACTGC
Found at i:38869001 original size:44 final size:44
Alignment explanation
Indices: 38868888--38869003 Score: 160
Period size: 44 Copynumber: 2.6 Consensus size: 44
38868878 TTTTTAATCC
* * * *
38868888 GCTCCACTGCAACTTCAAGGAGATAGGATTAATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAACAGCTTCAACCT
* ** *
38868932 ACTCCACTGCAACTTCAGGGAGATAAGATTGGCATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAACAGCTTCAACCT
38868976 GCTCCACTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
38869004 CTTGTTTTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAACAGCTTCAACCT
Found at i:38869162 original size:132 final size:132
Alignment explanation
Indices: 38869010--38869358 Score: 565
Period size: 132 Copynumber: 2.6 Consensus size: 132
38869000 AAGACTTGTT
* *
38869010 TTTGATCTGCTCTACTACTGCTTAGGGAGACATGATCTATAATCTTCAACCTACTCCACTGCTGC
1 TTTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAACCTACTCCACTGCTGC
* * *
38869075 TCAAGGAGAT-AGGACTGGTGGCTTAAATCTTCTTCCCTACTACCTTGGAAAGATAAGATTCGCC
66 TCAGGGAGATAAGG-CTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACC
38869139 GTA
130 GTA
* *
38869142 TTTGATCTGCTCCACTACTGCTTAAGGAGACATGATCTACAATCTTCAACCTACTCCACTACTGC
1 TTTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAACCTACTCCACTGCTGC
* *
38869207 TCAGGGAGATAATGTTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCG
66 TCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCG
*
38869272 TC
131 TA
* * *
38869274 TTTGATCTGCTTCACTACTGCTTAGGGAGACAGGATTTACAATCTTCAACCTACTCCACTGCTGC
1 TTTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAACCTACTCCACTGCTGC
38869339 TCAGGGAGATAAGGCTGGTG
66 TCAGGGAGATAAGGCTGGTG
38869359 TTTCAGATCT
Statistics
Matches: 199, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 197 0.99
133 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (132 bp):
TTTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAACCTACTCCACTGCTGC
TCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCG
TA
Found at i:38874814 original size:14 final size:14
Alignment explanation
Indices: 38874795--38874844 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
38874785 GATTAATAAT
38874795 AAAGAAAAAACAGA
1 AAAGAAAAAACAGA
38874809 AAAGAAAAAA-ACGCA
1 AAAGAAAAAACA-G-A
38874824 AAGAGAAAAAGAC-GA
1 AA-AGAAAAA-ACAGA
38874839 AAAGAA
1 AAAGAA
38874845 CACCTTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 15 0.48
15 6 0.19
16 8 0.26
17 1 0.03
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAACAGA
Found at i:38874830 original size:16 final size:15
Alignment explanation
Indices: 38874799--38874844 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
38874789 AATAATAAAG
38874799 AAAAAACAGAAA-AGA
1 AAAAAAC-GAAAGAGA
38874814 AAAAAACGCAAAGAGA
1 AAAAAACG-AAAGAGA
*
38874830 AAAAGACGAAA-AGA
1 AAAAAACGAAAGAGA
38874844 A
1 A
38874845 CACCTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.18
15 13 0.46
16 10 0.36
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAACGAAAGAGA
Found at i:38881274 original size:27 final size:26
Alignment explanation
Indices: 38881203--38881275 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 26
38881193 AAGTAATTAC
38881203 ATAATAAAATAT-ATAATAAAACAAAAT
1 ATAATAAAATATAATAAT--AACAAAAT
* * *
38881230 ATATTTAAAAT-TTA-AATAAGAAAAT
1 ATA-ATAAAATATAATAATAACAAAAT
38881255 ATAATAATAATATAATAATAA
1 ATAATAA-AATATAATAATAA
38881276 ATGATAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
24 3 0.08
25 13 0.35
26 2 0.05
27 12 0.32
28 7 0.19
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAATAAAATATAATAATAACAAAAT
Found at i:38881282 original size:24 final size:24
Alignment explanation
Indices: 38881251--38881300 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
38881241 TTAAATAAGA
38881251 AAATATAATAATAAT-ATAATAAT
1 AAATATAATAATAATCATAATAAT
*
38881274 AAATGATAATAATAATCATCATAAT
1 AAAT-ATAATAATAATCATAATAAT
38881299 AA
1 AA
38881301 CATCAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATATAATAATAATCATAATAAT
Found at i:38886095 original size:2 final size:2
Alignment explanation
Indices: 38886088--38886114 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38886078 TTGAGATCTC
38886088 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 T
38886115 TTATGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38889527 original size:50 final size:50
Alignment explanation
Indices: 38889452--38889615 Score: 249
Period size: 50 Copynumber: 3.3 Consensus size: 50
38889442 ATACATGTAT
38889452 GCTCATACGAGCT-ATGAATCGGTATGCTCTCATGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTGA-GAATCGGTATGCTCTCATGAGCTGTGAATCGGTAA
*
38889502 GCTCATATGAGCTGAGAATCGGTATGCTCTCATGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTATGCTCTCATGAGCTGTGAATCGGTAA
* * ** *
38889552 GCTCATACGAGCTGAGAATCGGTAAGCTCTCACGAGCTGCAAATCGGGAA
1 GCTCATACGAGCTGAGAATCGGTATGCTCTCATGAGCTGTGAATCGGTAA
*
38889602 GCTCATACAAGCTG
1 GCTCATACGAGCTG
38889616 TGGTGTGTCT
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
50 104 0.99
51 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
GCTCATACGAGCTGAGAATCGGTATGCTCTCATGAGCTGTGAATCGGTAA
Found at i:38889589 original size:75 final size:75
Alignment explanation
Indices: 38889460--38889598 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 75
38889450 ATGCTCATAC
* * * *
38889460 GAGCTATGAATCGGTATGCTCTCATGAGCTGTGAATCGGTAAGCTCATATGAGCTG-AGAATCGG
1 GAGCTATGAATCGGTAAGCTCTCACGAGCTGAGAATCGGTAAGCTCATACGAGCTGCA-AATCGG
38889524 TATGCTCTCAT
65 TATGCTCTCAT
*
38889535 GAGCTGTGAATCGGTAAGCTCAT-ACGAGCTGAGAATCGGTAAGCTC-TCACGAGCTGCAAATCG
1 GAGCTATGAATCGGTAAGCTC-TCACGAGCTGAGAATCGGTAAGCTCAT-ACGAGCTGCAAATCG
38889598 G
64 G
38889599 GAAGCTCATA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
74 1 0.02
75 53 0.95
76 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (75 bp):
GAGCTATGAATCGGTAAGCTCTCACGAGCTGAGAATCGGTAAGCTCATACGAGCTGCAAATCGGT
ATGCTCTCAT
Found at i:38889614 original size:25 final size:25
Alignment explanation
Indices: 38889452--38889615 Score: 167
Period size: 25 Copynumber: 6.6 Consensus size: 25
38889442 ATACATGTAT
*
38889452 GCTCATACGAGCT-ATGAATCGGTAT
1 GCTCATACGAGCTGA-GAATCGGTAA
* *
38889477 GCTC-TCATGAGCTGTGAATCGGTAA
1 GCTCAT-ACGAGCTGAGAATCGGTAA
* *
38889502 GCTCATATGAGCTGAGAATCGGTAT
1 GCTCATACGAGCTGAGAATCGGTAA
* *
38889527 GCTC-TCATGAGCTGTGAATCGGTAA
1 GCTCAT-ACGAGCTGAGAATCGGTAA
38889552 GCTCATACGAGCTGAGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
*
38889577 GCTC-TCACGAGCTGCA-AATCGGGAA
1 GCTCAT-ACGAGCTG-AGAATCGGTAA
*
38889602 GCTCATACAAGCTG
1 GCTCATACGAGCTG
38889616 TGGTGTGTCT
Statistics
Matches: 120, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.03
25 113 0.94
26 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGGTAA
Found at i:38890729 original size:13 final size:13
Alignment explanation
Indices: 38890711--38890746 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
38890701 GTAAACAGTA
38890711 AAATTTCTTA-ACG
1 AAATTT-TTATACG
38890724 AAATTTTTATACG
1 AAATTTTTATACG
38890737 AAATTTTTAT
1 AAATTTTTAT
38890747 CATACTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (13 bp):
AAATTTTTATACG
Found at i:38892425 original size:21 final size:20
Alignment explanation
Indices: 38892401--38892444 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
38892391 AATTTAGCCA
*
38892401 TTTTTATTTTTATTTTAATAT
1 TTTTTATTTTTAATTTAAT-T
38892422 TTTTTATTTTTAATTTAATT
1 TTTTTATTTTTAATTTAATT
38892442 TTT
1 TTT
38892445 ACATTCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTTTTAATTTAATT
Found at i:38895406 original size:21 final size:21
Alignment explanation
Indices: 38895380--38895420 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
38895370 TCAAAATGGC
38895380 ATAATTTT-ACCTTTTAACTTA
1 ATAATTTTGA-CTTTTAACTTA
38895401 ATAATTTTGACTTTTAACTT
1 ATAATTTTGACTTTTAACTT
38895421 TAGAAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (21 bp):
ATAATTTTGACTTTTAACTTA
Found at i:38909224 original size:21 final size:21
Alignment explanation
Indices: 38909169--38909268 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
38909159 GTGCCAAACA
*
38909169 GAAACCCATAAGGGTTGAACG
1 GAAACCCATAAGAGTTGAACG
* * *
38909190 GAAGCTCATAAGAGCTGAACG
1 GAAACCCATAAGAGTTGAACG
* *
38909211 GAAACCCATTAGAGTTGAACA
1 GAAACCCATAAGAGTTGAACG
* *
38909232 GAAACCCCTTAAG-GTTAAACG
1 GAAA-CCCATAAGAGTTGAACG
* *
38909253 GAAACTCATATGAGTT
1 GAAACCCATAAGAGTT
38909269 AACAGAAGCT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
20 5 0.08
21 50 0.82
22 6 0.10
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
GAAACCCATAAGAGTTGAACG
Found at i:38909379 original size:24 final size:24
Alignment explanation
Indices: 38909347--38909394 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
38909337 TACTTGCGTA
*
38909347 ATTTGCCGTCAATTCATCATTTGC
1 ATTTACCGTCAATTCATCATTTGC
38909371 ATTTACCGTCAATTCATCATTTGC
1 ATTTACCGTCAATTCATCATTTGC
38909395 CACAGAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (24 bp):
ATTTACCGTCAATTCATCATTTGC
Found at i:38913246 original size:50 final size:50
Alignment explanation
Indices: 38913139--38913385 Score: 232
Period size: 50 Copynumber: 4.8 Consensus size: 50
38913129 ATTTGGGTAA
*
38913139 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---AG---ATG
* *
38913195 AGAGGTCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCAAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* ** * * * *
38913245 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGCCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * * *
38913295 AGA-ACTCCCATGCAAGACCATATCTAGGATATGGCATTGGCAGTACAAGA--
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCAAGATG
* *
38913345 A-ACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
38913386 TGTTATTATC
Statistics
Matches: 160, Mismatches: 27, Indels: 15
0.79 0.13 0.07
Matches are distributed among these distances:
49 33 0.21
50 80 0.50
52 3 0.02
53 2 0.01
56 42 0.26
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:38915116 original size:21 final size:21
Alignment explanation
Indices: 38915068--38915116 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
38915058 CCAAGCATAG
*
38915068 TCGTGTGGTTATCCCACACGC
1 TCGTGTGGTTATCCCACACAC
* *
38915089 CCATGTGGTTA-CTCCACACAC
1 TCGTGTGGTTATC-CCACACAC
38915110 TCGTGTG
1 TCGTGTG
38915117 CTCACTCGTG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.16, C:0.33, G:0.22, T:0.29
Consensus pattern (21 bp):
TCGTGTGGTTATCCCACACAC
Found at i:38919227 original size:27 final size:27
Alignment explanation
Indices: 38919178--38919229 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
38919168 ACTCTATATG
* *
38919178 AATTATTTATATATTAATTCCCCTATT
1 AATTATTTATATATAAATCCCCCTATT
38919205 AATTATTTATA-AGTAAATCCCCCTA
1 AATTATTTATATA-TAAATCCCCCTA
38919230 GATACAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTATTTATATATAAATCCCCCTATT
Found at i:38924540 original size:21 final size:21
Alignment explanation
Indices: 38924488--38924544 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
38924478 TACTGATACG
*
38924488 CCCGAGTCACCCGATTCCACA
1 CCCGAGTCACCTGATTCCACA
*
38924509 CCCGAATCACCTGATTCCACA
1 CCCGAGTCACCTGATTCCACA
*
38924530 CCCGAGGCACCTGAT
1 CCCGAGTCACCTGAT
38924545 GATGACTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.44, G:0.16, T:0.16
Consensus pattern (21 bp):
CCCGAGTCACCTGATTCCACA
Found at i:38933079 original size:31 final size:31
Alignment explanation
Indices: 38933033--38933099 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
38933023 GCCATTGATG
*
38933033 AAAATATAAAAAAAATTTAAAATTATTTTTAA
1 AAAATATAAAAAAAATTTAAAATTA-TTTAAA
*
38933065 AAAATAT-AAAAAAATTTGAAATTATTTAAA
1 AAAATATAAAAAAAATTTAAAATTATTTAAA
38933095 AAAAT
1 AAAAT
38933100 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 10 0.30
31 16 0.48
32 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAAATTTAAAATTATTTAAA
Found at i:38933081 original size:21 final size:21
Alignment explanation
Indices: 38933042--38933081 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38933032 GAAAATATAA
* **
38933042 AAAAAATTTAAAATTATTTTT
1 AAAAAATATAAAAAAATTTTT
38933063 AAAAAATATAAAAAAATTT
1 AAAAAATATAAAAAAATTT
38933082 GAAATTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATATAAAAAAATTTTT
Found at i:38933158 original size:22 final size:21
Alignment explanation
Indices: 38933133--38933183 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
38933123 TAATATGGAT
*
38933133 TTGAGAGATTTTTGGAATGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
38933155 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGA-GATTTTGGAAGGAAA
38933177 TTGAGAG
1 TTGAGAG
38933184 TTTAAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:38933200 original size:52 final size:52
Alignment explanation
Indices: 38933136--38933234 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
38933126 TATGGATTTG
* *
38933136 AGAGATTTTTGGAATGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
*
38933188 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAATGAAATTGAGA
1 AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGA
38933235 TATGATTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.30
Consensus pattern (52 bp):
AGAGAATTTTGGAAGGAAATTGAGAGGATTTTGGAAGGAAATTGAGAGTTTA
Found at i:38933218 original size:22 final size:22
Alignment explanation
Indices: 38933188--38933234 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
38933178 TGAGAGTTTA
38933188 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
* *
38933210 AGAGGATTTTGGAATGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
38933232 AGA
1 AGA
38933235 TATGATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:38933502 original size:29 final size:29
Alignment explanation
Indices: 38933436--38933502 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
38933426 CGATTTCCCG
* *
38933436 AAAAATGGACCATTCCGGTAAATAATCAA
1 AAAAACGGCCCATTCCGGTAAATAATCAA
* * ** *
38933465 AAAATCGGCCCATTTCGGTAAATTTTGAA
1 AAAAACGGCCCATTCCGGTAAATAATCAA
38933494 AAAAACGGC
1 AAAAACGGC
38933503 TTTTTTAGGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAAACGGCCCATTCCGGTAAATAATCAA
Found at i:38933599 original size:16 final size:16
Alignment explanation
Indices: 38933580--38933617 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38933570 CTTATTACAT
*
38933580 TATAAT-GTTATATGGA
1 TATAATGGTTATGT-GA
38933596 TATAATGGTTATGTGA
1 TATAATGGTTATGTGA
38933612 TATAAT
1 TATAAT
38933618 TATATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TATAATGGTTATGTGA
Found at i:38934797 original size:26 final size:23
Alignment explanation
Indices: 38934730--38934797 Score: 55
Period size: 26 Copynumber: 2.7 Consensus size: 23
38934720 TTAATGAATT
*
38934730 TTTATTTTTATACTTTATTATTA
1 TTTATTTTTATAGTTTATTATTA
* *
38934753 TATATTTTTTGAATTGTTTATATATTTA
1 TTTA-TTTTT--ATAGTTTAT-TA-TTA
38934781 TTTATATTTTATAGTTT
1 TTTAT-TTTTATAGTTT
38934798 TTTAAAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
23 3 0.09
24 5 0.15
26 13 0.38
27 3 0.09
28 10 0.29
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTATTTTTATAGTTTATTATTA
Found at i:38939237 original size:13 final size:14
Alignment explanation
Indices: 38939203--38939246 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
38939193 AGGGTTTGTT
38939203 TGTTTTACT-GAAAA
1 TGTTTT-CTGGAAAA
38939217 TAGTTTTC-GGAAAA
1 T-GTTTTCTGGAAAA
38939231 TGTTTTCTGGAAAA
1 TGTTTTCTGGAAAA
38939245 TG
1 TG
38939247 ACCTACTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 6 0.22
14 16 0.59
15 5 0.19
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (14 bp):
TGTTTTCTGGAAAA
Found at i:38939306 original size:31 final size:32
Alignment explanation
Indices: 38939268--38939341 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
38939258 TGGAAAAGTT
* * *
38939268 AATATTTTTTGGTGTTTGGATGAGTC-TATAA
1 AATATTTTCTGGTATTTGGATGAATCGTATAA
*
38939299 AATATTTTCTGTTATTTGGATGAATCTGTATAA
1 AATATTTTCTGGTATTTGGATGAATC-GTATAA
38939332 AATATTTTCT
1 AATATTTTCT
38939342 ATTGTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 22 0.59
33 15 0.41
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.50
Consensus pattern (32 bp):
AATATTTTCTGGTATTTGGATGAATCGTATAA
Found at i:38939761 original size:15 final size:15
Alignment explanation
Indices: 38939741--38939808 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
38939731 ACACTACAAA
38939741 ATATTTATTATTGAT
1 ATATTTATTATTGAT
*
38939756 ATATTTATAATTGTAAT
1 ATATTTATTATTG--AT
* *
38939773 AAGTATTTATTATTAAA
1 -A-TATTTATTATTGAT
*
38939790 ATA-TTAATATTGA-
1 ATATTTATTATTGAT
38939803 ATATTT
1 ATATTT
38939809 TTAATAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
13 3 0.07
14 10 0.24
15 14 0.33
16 1 0.02
17 3 0.07
18 1 0.02
19 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTGAT
Found at i:38939864 original size:13 final size:14
Alignment explanation
Indices: 38939826--38939876 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
38939816 TATGTGAAGA
38939826 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
38939841 ATCATTTTTAAAATT
1 AT-ATTATTAAAATT
*
38939856 -TATTATTAAAATA
1 ATATTATTAAAATT
38939869 ATA-TATTA
1 ATATTATTA
38939877 TAGTAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 15 0.48
14 3 0.10
15 10 0.32
16 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:38945664 original size:19 final size:18
Alignment explanation
Indices: 38945613--38945668 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
38945603 TGAAAATAAA
38945613 TATAATTG-TAATAATTT
1 TATAATTGTTAATAATTT
*
38945630 T-TAATCAT-TTATTAATTT
1 TATAAT--TGTTAATAATTT
38945648 TATAATTGTTAAATAATTT
1 TATAATTGTT-AATAATTT
38945667 TA
1 TA
38945669 AAAATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
16 4 0.13
17 2 0.06
18 12 0.39
19 13 0.42
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
TATAATTGTTAATAATTT
Found at i:38945806 original size:21 final size:21
Alignment explanation
Indices: 38945782--38945834 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
38945772 CGCTGTTTCT
* *
38945782 AATCTCACTGCTACAGTACCC
1 AATCTCACCGCTACAGTAACC
*
38945803 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
38945824 AATCTCACCGC
1 AATCTCACCGC
38945835 CACCGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:38946716 original size:6 final size:6
Alignment explanation
Indices: 38946705--38946733 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38946695 GTTTATCAAC
38946705 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
38946734 GAAATTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:38947468 original size:22 final size:22
Alignment explanation
Indices: 38947420--38947469 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
38947410 TTATTTTCAA
*
38947420 TTTTCACAAAAAGTATCGATAC
1 TTTTTACAAAAAGTATCGATAC
*
38947442 -CTTTACAAAAAGTATCGATAC
1 TTTTTACAAAAAGTATCGATAC
38947463 TTTTTAC
1 TTTTTAC
38947470 CATGTATCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (22 bp):
TTTTTACAAAAAGTATCGATAC
Found at i:38950202 original size:5 final size:5
Alignment explanation
Indices: 38950186--38950246 Score: 113
Period size: 5 Copynumber: 12.2 Consensus size: 5
38950176 TGAACATGTG
*
38950186 CATAT CACAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
38950236 CATAT CATAT C
1 CATAT CATAT C
38950247 TTTGTACTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (5 bp):
CATAT
Found at i:38950537 original size:24 final size:24
Alignment explanation
Indices: 38950492--38950577 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
38950482 TCCGGGCTAT
*
38950492 ATAACAGGAAGCTCATAAGAGCC-
1 ATAACGGGAAGCTCATAAGAGCCA
**
38950515 ATAATCGGGAAGCTCATGCGAGCCA
1 ATAA-CGGGAAGCTCATAAGAGCCA
*
38950540 ATAACGGGTAA-CTC-TGAAAAGCCA
1 ATAACGGG-AAGCTCAT-AAGAGCCA
* *
38950564 TTAACGGGAGGCTC
1 ATAACGGGAAGCTC
38950578 CGGATAGTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 6 0.12
24 38 0.76
25 6 0.12
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (24 bp):
ATAACGGGAAGCTCATAAGAGCCA
Found at i:38952252 original size:134 final size:134
Alignment explanation
Indices: 38952031--38952298 Score: 536
Period size: 134 Copynumber: 2.0 Consensus size: 134
38952021 TGAAGACCAA
38952031 ATTGGTGACAAAGGAAAACAAGTGGTCATTGAGTGAAAATAAAGGAAAACATATTATCCAAGATT
1 ATTGGTGACAAAGGAAAACAAGTGGTCATTGAGTGAAAATAAAGGAAAACATATTATCCAAGATT
38952096 TGGTTGTAAGTATTTCAAGTGTTTTTGCTTTGTTTTATTTAAATTTAAATAAAAATAGTGTTAAA
66 TGGTTGTAAGTATTTCAAGTGTTTTTGCTTTGTTTTATTTAAATTTAAATAAAAATAGTGTTAAA
38952161 TAGT
131 TAGT
38952165 ATTGGTGACAAAGGAAAACAAGTGGTCATTGAGTGAAAATAAAGGAAAACATATTATCCAAGATT
1 ATTGGTGACAAAGGAAAACAAGTGGTCATTGAGTGAAAATAAAGGAAAACATATTATCCAAGATT
38952230 TGGTTGTAAGTATTTCAAGTGTTTTTGCTTTGTTTTATTTAAATTTAAATAAAAATAGTGTTAAA
66 TGGTTGTAAGTATTTCAAGTGTTTTTGCTTTGTTTTATTTAAATTTAAATAAAAATAGTGTTAAA
38952295 TAGT
131 TAGT
38952299 TAGTTTAATT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (134 bp):
ATTGGTGACAAAGGAAAACAAGTGGTCATTGAGTGAAAATAAAGGAAAACATATTATCCAAGATT
TGGTTGTAAGTATTTCAAGTGTTTTTGCTTTGTTTTATTTAAATTTAAATAAAAATAGTGTTAAA
TAGT
Found at i:38959244 original size:22 final size:21
Alignment explanation
Indices: 38959218--38959266 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 21
38959208 TTCATTGATT
38959218 AAATTAGAGAAAAATAAAT-TTA
1 AAATT-GA-AAAAATAAATATTA
*
38959240 AAATTTAAAAAATAAATATTA
1 AAATTGAAAAAATAAATATTA
38959261 ACAATT
1 A-AATT
38959267 TTAACATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.42
21 5 0.21
22 9 0.38
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAATTGAAAAAATAAATATTA
Found at i:38959252 original size:20 final size:22
Alignment explanation
Indices: 38959227--38959267 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
38959217 TAAATTAGAG
38959227 AAAAATAAAT-TTAA-AATTTA
1 AAAAATAAATATTAACAATTTA
38959247 AAAAATAAATATTAACAATTT
1 AAAAATAAATATTAACAATTT
38959268 TAACATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAATAAATATTAACAATTTA
Found at i:38960637 original size:30 final size:32
Alignment explanation
Indices: 38960603--38960666 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 32
38960593 AGTTCCTATA
*
38960603 TTTATAATTTTTAA-AGAATTAAATTA-AATT
1 TTTATAATTTTTAAGAGAATTAAAATATAATT
*
38960633 TTTATTATTTTTAAGAGAATTAAAATATAATT
1 TTTATAATTTTTAAGAGAATTAAAATATAATT
38960665 TT
1 TT
38960667 ATATTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.43
31 11 0.37
32 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (32 bp):
TTTATAATTTTTAAGAGAATTAAAATATAATT
Found at i:38960672 original size:30 final size:29
Alignment explanation
Indices: 38960603--38960677 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 29
38960593 AGTTCCTATA
*
38960603 TTTATAATTTTTAAAGAATTAAATTAAATT
1 TTTAT-ATTTTTAAAGAATTAAAATAAATT
38960633 TTTATTATTTTTAAGAGAATTAAAATATAA-T
1 TTTA-TATTTTTAA-AGAATTAAAATA-AATT
38960664 TTTATATTTATTAA
1 TTTATATTT-TTAA
38960678 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 17 0.43
31 21 0.52
32 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTATATTTTTAAAGAATTAAAATAAATT
Found at i:38967802 original size:23 final size:23
Alignment explanation
Indices: 38967769--38967818 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
38967759 ATGTTTATTG
*
38967769 TTAATATATTTGAAG-ATATTTT
1 TTAATATATTTGAAGAATATTAT
38967791 TTAATAATATTTGAAGAATATTAT
1 TTAAT-ATATTTGAAGAATATTAT
38967815 TTAA
1 TTAA
38967819 ACTTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.20
23 10 0.40
24 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (23 bp):
TTAATATATTTGAAGAATATTAT
Found at i:38968744 original size:13 final size:13
Alignment explanation
Indices: 38968728--38968752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38968718 GAAATTTTTA
38968728 GCTTTTCAAAAGT
1 GCTTTTCAAAAGT
38968741 GCTTTTCAAAAG
1 GCTTTTCAAAAG
38968753 CACTTCTGAA
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):
GCTTTTCAAAAGT
Found at i:38968957 original size:32 final size:34
Alignment explanation
Indices: 38968895--38968957 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
38968885 GCTTATTTAC
*
38968895 AATATTGTGTTAAAATCATTAATTAAAAATAAAA
1 AATATTGTGTTAAAATCACTAATTAAAAATAAAA
* *
38968929 AATATT-TTTTAAAAT-ACTAATTACAAATA
1 AATATTGTGTTAAAATCACTAATTAAAAATA
38968958 TTTAATGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 12 0.46
33 8 0.31
34 6 0.23
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (34 bp):
AATATTGTGTTAAAATCACTAATTAAAAATAAAA
Found at i:38969063 original size:31 final size:29
Alignment explanation
Indices: 38969020--38969081 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
38969010 TTTTATAAAT
*
38969020 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
38969050 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
38969080 AA
1 AA
38969082 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:38969272 original size:13 final size:13
Alignment explanation
Indices: 38969251--38969280 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38969241 TTTAAGCCAA
*
38969251 ACTTTTCAAAATC
1 ACTTCTCAAAATC
38969264 ACTTCTCAAAATC
1 ACTTCTCAAAATC
38969277 ACTT
1 ACTT
38969281 TTCCACTTGT
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:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (13 bp):
ACTTCTCAAAATC
Found at i:38969724 original size:136 final size:137
Alignment explanation
Indices: 38969568--38969878 Score: 518
Period size: 136 Copynumber: 2.3 Consensus size: 137
38969558 CTCATATTTA
*
38969568 TATTTTTTAGTTCATGTTGCTTCAACCTTTTTTTTAATTAATATTTTTAACATATTAACTCATTT
1 TATTTTTTATTTCATGTTGCTTCAACCTTTTTTTTAATTAATATTTTTAACATATTAACTCATTT
* * *
38969633 GATTAAATGGTTAAATAATTGTGATTACATCCTTGAGTCTCAAGTTCTAGTATTTTTATAAGCAT
66 GATTAAATGGTTAAATAATTGCGATTACATCCTTAAGTCTCAAGTTCCAGTATTTTTATAAGCAT
*
38969698 ATTAATG
131 ATTAACG
38969705 TA-TTTTTATTTCATGTTGCTTCAACCTTTTTTTTAATTAATATTTTTAACATATTAACTCATTT
1 TATTTTTTATTTCATGTTGCTTCAACCTTTTTTTTAATTAATATTTTTAACATATTAACTCATTT
* * *
38969769 GATTAAATGGTTAGATAATTGCGATTACATCTTTAAGTCTCAAGTTCCATTATTTTTATAAGCAT
66 GATTAAATGGTTAAATAATTGCGATTACATCCTTAAGTCTCAAGTTCCAGTATTTTTATAAGCAT
38969834 ATTAACG
131 ATTAACG
* *
38969841 TATTTTTTATTTCATGTTGTTTCAA-GTTTTTTTTAATT
1 TATTTTTTATTTCATGTTGCTTCAACCTTTTTTTTAATT
38969879 TTTAATTAAT
Statistics
Matches: 163, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
136 140 0.86
137 23 0.14
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (137 bp):
TATTTTTTATTTCATGTTGCTTCAACCTTTTTTTTAATTAATATTTTTAACATATTAACTCATTT
GATTAAATGGTTAAATAATTGCGATTACATCCTTAAGTCTCAAGTTCCAGTATTTTTATAAGCAT
ATTAACG
Found at i:38969894 original size:13 final size:13
Alignment explanation
Indices: 38969876--38969902 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38969866 GTTTTTTTTA
38969876 ATTTTTAATTAAT
1 ATTTTTAATTAAT
38969889 ATTTTTAATTAAT
1 ATTTTTAATTAAT
38969902 A
1 A
38969903 AATATATTAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTTAATTAAT
Found at i:38971174 original size:51 final size:51
Alignment explanation
Indices: 38971098--38971316 Score: 375
Period size: 51 Copynumber: 4.3 Consensus size: 51
38971088 CGGATCACAT
* *
38971098 TTATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGTTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
38971149 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCAACCAT
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
38971200 TTATCACTTGTTACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
38971251 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
38971302 TTATCACTTGTCACT
1 TTATCACTTGTCACT
38971317 GATTAGAAGT
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 158 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:38973715 original size:46 final size:46
Alignment explanation
Indices: 38973662--38973894 Score: 378
Period size: 46 Copynumber: 5.0 Consensus size: 46
38973652 ACAATGCTAT
*
38973662 AACTCAGTATGGTTTTCTTCA-CGAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCG-AAATACCATACCTACTTTTCAC
*
38973708 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* *
38973754 AACTCGGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTAC-TTTTCAC
38973801 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
* *
38973847 AACTCGGTATGGTTTTCTTTACCGAATTACCATACCTACTTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTAC-TTTTCAC
38973894 A
1 A
38973895 CTTTGCCATG
Statistics
Matches: 177, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
46 123 0.69
47 54 0.31
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
Found at i:38973831 original size:93 final size:92
Alignment explanation
Indices: 38973662--38973894 Score: 396
Period size: 93 Copynumber: 2.5 Consensus size: 92
38973652 ACAATGCTAT
* *
38973662 AACTCAGTATGGTTTTCTTCACGAAAATACCATACCTAC-TTTTCACAACTCAGTATGGTTTTCT
1 AACTCGGTATGGTTTTCTTTACG-AAATACCATACCTACTTTTTCACAACTCAGTATGGTTTTCT
38973726 TCACCGAAATACCATACCTACTTTTCAC
65 TCACCGAAATACCATACCTACTTTTCAC
38973754 AACTCGGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTTCACAACTCAGTATGGTTTTCT
1 AACTCGGTATGGTTTTCTTTAC-GAAATACCATACCTACTTTTTCACAACTCAGTATGGTTTTCT
*
38973819 TTACCGAAATACCATACCTACTTTTCAC
65 TCACCGAAATACCATACCTACTTTTCAC
*
38973847 AACTCGGTATGGTTTTCTTTACCGAATTACCATACCTACTTTTTCACA
1 AACTCGGTATGGTTTTCTTTA-CGAAATACCATACCTACTTTTTCACA
38973895 CTTTGCCATG
Statistics
Matches: 134, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
92 35 0.26
93 98 0.73
94 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.37
Consensus pattern (92 bp):
AACTCGGTATGGTTTTCTTTACGAAATACCATACCTACTTTTTCACAACTCAGTATGGTTTTCTT
CACCGAAATACCATACCTACTTTTCAC
Found at i:38981883 original size:10 final size:10
Alignment explanation
Indices: 38981868--38981914 Score: 58
Period size: 11 Copynumber: 4.4 Consensus size: 10
38981858 ACCTAAATCC
38981868 TTTCTCTCAA
1 TTTCTCTCAA
38981878 TTTCTCTCCAA
1 TTTCTCT-CAA
38981889 TATTCTCTCAA
1 T-TTCTCTCAA
*
38981900 ATTCTTCTCAA
1 TTTC-TCTCAA
38981911 TTTC
1 TTTC
38981915 CTCTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 10 0.31
11 16 0.50
12 6 0.19
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:38983655 original size:30 final size:30
Alignment explanation
Indices: 38983619--38983723 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
38983609 GACGACGCAG
38983619 GCGCCCACACAATCACTCGGCCCATCAACA
1 GCGCCCACACAATCACTCGGCCCATCAACA
* *
38983649 GCGCCCACACAATCACTCGACCCATCAGCA
1 GCGCCCACACAATCACTCGGCCCATCAACA
* *
38983679 GCGCCCATACAAT-AC-CAGGCCCAGCAACA
1 GCGCCCACACAATCACTC-GGCCCATCAACA
* * *
38983708 GCACCGACACAGTCAC
1 GCGCCCACACAATCAC
38983724 CCAGCCCAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.02
29 20 0.32
30 42 0.67
ACGTcount: A:0.31, C:0.45, G:0.15, T:0.09
Consensus pattern (30 bp):
GCGCCCACACAATCACTCGGCCCATCAACA
Found at i:38983808 original size:18 final size:18
Alignment explanation
Indices: 38983785--38983827 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38983775 TGCCAGGTGC
* *
38983785 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
38983803 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
38983821 GTTTCCT
1 GTATCCT
38983828 TTTTTTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:38987634 original size:126 final size:126
Alignment explanation
Indices: 38987409--38987696 Score: 477
Period size: 126 Copynumber: 2.3 Consensus size: 126
38987399 GCCAAACAGG
* * * *
38987409 AGCTACTGTAACAAAAGCGTGTCCATGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
1 AGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
* * *
38987474 TGCTTAAAGCGTTTTTGACATTATTTTCTCAGAAACGTCTTCTCGAAATTATTTTTTCAGA
66 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCGAAATTATTTTTTCAGA
* * *
38987535 AGCTATTGTAGCAAAAGAGCGTCCACGTGGGAGTTTCTTTCAGTACTTTTGTTGACAATGCATCC
1 AGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
*
38987600 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCGAAATTATTTTTTCAGG
66 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCGAAATTATTTTTTCAGA
38987661 AGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
1 AGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
38987697 TTTTAAATTA
Statistics
Matches: 149, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 149 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (126 bp):
AGCTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCC
TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCGAAATTATTTTTTCAGA
Found at i:38987781 original size:7 final size:7
Alignment explanation
Indices: 38987769--38987812 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
38987759 TTTTCTTTAA
38987769 AAACTCT
1 AAACTCT
38987776 AAACTCT
1 AAACTCT
38987783 AAACTCT
1 AAACTCT
38987790 AAACTCT
1 AAACTCT
*
38987797 AAACCCT
1 AAACTCT
*
38987804 AAACCCT
1 AAACTCT
38987811 AA
1 AA
38987813 TCTAATTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACTCT
Found at i:38988023 original size:97 final size:90
Alignment explanation
Indices: 38987804--38988056 Score: 233
Period size: 95 Copynumber: 2.7 Consensus size: 90
38987794 TCTAAACCCT
* * *
38987804 AAACCCTAATCTAATTTT--TTTAATTTATAATTAAATTACTCAAGTAACCCTAAACCTTAATTT
1 AAACCCTAATCTAATTTTAATTT--TTT-TAATTAATTTACTTAAGTAACCCTAAACCATAATTT
* *
38987867 ATTTGATTTTTTTAAAAACCCTTAACACT
63 AATTGATTTTTTTAAAAA-CCTTAACACG
* * *
38987896 AAACCCTAATATGATTTTTTTTAAAATTTTTTTAATTAATTTACTTAAGTAACCCTAAACCCTAA
1 AAACCCTAATCT-A---ATTTT--AATTTTTTTAATTAATTTACTTAAGTAACCCTAAACCATAA
*
38987961 TTTAATTGATTTTTTCTTTAAAAA-TTATAAGCACG
60 TTTAATTGA--TTTT-TTTAAAAACCT-TAA-CACG
* * *
38987996 AAACCCTAATCTAATTTTGAATTTTTTTAATTAATTTAATTAAGAAACCTTAAACCATAAT
1 AAACCCTAATCTAATTTT-AATTTTTTTAATTAATTTACTTAAGTAACCCTAAACCATAAT
38988057 CCCTTATTTA
Statistics
Matches: 133, Mismatches: 15, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
92 11 0.08
93 1 0.01
95 38 0.29
96 8 0.06
97 38 0.29
98 4 0.03
99 8 0.06
100 25 0.19
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.43
Consensus pattern (90 bp):
AAACCCTAATCTAATTTTAATTTTTTTAATTAATTTACTTAAGTAACCCTAAACCATAATTTAAT
TGATTTTTTTAAAAACCTTAACACG
Found at i:38988767 original size:39 final size:41
Alignment explanation
Indices: 38988688--38988777 Score: 139
Period size: 39 Copynumber: 2.2 Consensus size: 41
38988678 TAAAAAGTAT
*
38988688 TTATATTAAAAAACACTATTATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
*
38988729 TTATATTAAAAAACAC-A-AATAAATATAATAAATGTTTTA
1 TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
*
38988768 TTGTATTAAA
1 TTATATTAAA
38988778 TATAAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 29 0.63
40 1 0.02
41 16 0.35
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (41 bp):
TTATATTAAAAAACACTATAATAAATATAATAAATATTTTA
Found at i:38999590 original size:45 final size:44
Alignment explanation
Indices: 38999394--38999916 Score: 291
Period size: 44 Copynumber: 11.8 Consensus size: 44
38999384 GACTTGTATA
*
38999394 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATTTGCTTTC
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTTC
* * ** * *** *
38999439 TTCAATCTACTTTA-CGTCAATACATGAAGACAAGATCTGTTTTA
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTTC
* * * *** * **** * *
38999483 TTCAATCTGCTTTA-TGTCAATACATAAAGATAAGATTTGCTTTC
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTTC
* * *
38999527 TTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCTTTA
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTTC
* * * *
38999572 TTCGATCTACTCCACCACCAGTATGGGGAGACAATATCTGGTATC
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCT-GTTTC
* * *** *
38999617 TTCGATCTACTTCA-CGCCAATACATGAAGATAAGATCTGTTTTC
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTTC
* * *
38999661 TTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGATATC
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TTTC
* * * *** * * *
38999706 TTTGATCTACTTCA-CGCCAATACATGAAGACAATATCTATTTTTT
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATC--TGTTTC
* * * * * * *
38999751 TTCGATCTGCTTCGCCACTAGTATGGGAAGGCGAGATCTGTATA
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTTC
* ***
38999795 TTCGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGTATTCC
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGT-TT-C
* * * *
38999840 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTATA
1 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTTC
* * * * * *
38999884 TTCAATCCACTTCGCTACCAATATAGGAAGACA
1 TTCGATCTACTTCACCACCAGTATGGGAAGACA
38999917 GGACCTGCTG
Statistics
Matches: 357, Mismatches: 111, Indels: 21
0.73 0.23 0.04
Matches are distributed among these distances:
43 20 0.06
44 159 0.45
45 140 0.39
46 38 0.11
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTTC
Found at i:38999646 original size:89 final size:88
Alignment explanation
Indices: 38999394--38999896 Score: 432
Period size: 89 Copynumber: 5.6 Consensus size: 88
38999384 GACTTGTATA
* * * * * * *
38999394 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATTTGCTTTCTTCAATCTACTTTACGTCAA
1 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTG-TATATTCGATCTACTTCACGCCAA
*
38999459 TACATGAAGACAAGATCTGTTTTA
65 TACATGAAGACAAGATCTGTTTTC
* * ** *** * **** * * * * * *
38999483 TTCAATCTGCTTTA-TGTCAATACATAAAGATAAGATTTGCTTTCTTCGATCTACTTCGCCACCA
1 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTG-TATATTCGATCTACTTC-ACGCCA
* *** * * *
38999547 GTATGGGAAGACAATATCTGCTTTA
64 ATACATGAAGACAAGATCTGTTTTC
* * *
38999572 TTCGATCTACTCCACCACCAGTATGGGGAGACAATATCTGGTATCTTCGATCTACTTCACGCCAA
1 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCT-GTATATTCGATCTACTTCACGCCAA
*
38999637 TACATGAAGATAAGATCTGTTTTC
65 TACATGAAGACAAGATCTGTTTTC
* * *
38999661 TTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGATATCTTTGATCTACTTCACGCCAA
1 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTG-TATATTCGATCTACTTCACGCCAA
* * *
38999726 TACATGAAGACAATATCTATTTTTT
65 TACATGAAGACAAGATCT-GTTTTC
* * * * * * *
38999751 TTCGATCTGCTTCGCCACTAGTATGGGAAGGCGAGATCTGTATATTCGATCTACTTCACGCCAGT
1 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTATATTCGATCTACTTCACGCCAAT
*
38999816 ACATGAAGACAAGATCTGTATTCC
66 ACATGAAGACAAGATCTGT-TTTC
* * * * *
38999840 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTATATTCAATCCACTTC
1 TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTATATTCGATCTACTTC
38999897 GCTACCAATA
Statistics
Matches: 333, Mismatches: 75, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
88 34 0.10
89 233 0.70
90 65 0.20
91 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (88 bp):
TTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTATATTCGATCTACTTCACGCCAAT
ACATGAAGACAAGATCTGTTTTC
Found at i:38999737 original size:178 final size:180
Alignment explanation
Indices: 38999553--38999884 Score: 463
Period size: 179 Copynumber: 1.9 Consensus size: 180
38999543 ACCAGTATGG
* * *
38999553 GAAGACAATATCT-GCTTTATTCGATCTACTCCACCACCAGTATGGGGAGACAATATCTGGTATC
1 GAAGACAATATCTAGCTTTATTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCT-GTATA
* *
38999617 TTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGT-TTTCTTCGATCTACTCCACCACCA
65 TTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTATTCCTTCGATCTACTCCACCACCA
*
38999681 GTATGGGGAGACAAGATCTG-ATATCTTTGATCTACTTCACGCCAATACAT
130 GTATGGGAAGACAAGATCTGTATATCTTTGATCTACTTCACGCCAATACAT
** * * * * * * *
38999731 GAAGACAATATCTATTTTTTTTCGATCTGCTTCGCCACTAGTATGGGAAGGCGAGATCTGTATAT
1 GAAGACAATATCTAGCTTTATTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTATAT
* * * *
38999796 TCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTATTCCTTCGATCTGCTTCGCCACCAG
66 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTATTCCTTCGATCTACTCCACCACCAG
38999861 TATGGGAAGACAAGATCTGTATAT
131 TATGGGAAGACAAGATCTGTATAT
38999885 TCAATCCACT
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
178 55 0.42
179 73 0.55
180 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (180 bp):
GAAGACAATATCTAGCTTTATTCGATCTACTCCACCACCAGTATGGGAAGACAAGATCTGTATAT
TCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTATTCCTTCGATCTACTCCACCACCAG
TATGGGAAGACAAGATCTGTATATCTTTGATCTACTTCACGCCAATACAT
Found at i:38999914 original size:44 final size:43
Alignment explanation
Indices: 38999527--38999916 Score: 231
Period size: 45 Copynumber: 8.7 Consensus size: 43
38999517 ATTTGCTTTC
* * *
38999527 TTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCTTTA
1 TTCGATCTACTTCG-CACCAGTATAGGAAGACAAGATCTG-TATA
* * * * * *
38999572 TTCGATCTACTCCACCACCAGTATGGGGAGACAATATCTGGTATC
1 TTCGATCTACTTC-GCACCAGTATAGGAAGACAAGATCT-GTATA
* * * * * * * *
38999617 TTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGTTTTC
1 TTCGATCTACTTCGCACCAGTATAGGAAGACAAGATCTG-TATA
* * * * *
38999661 TTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGATATC
1 TTCGATCTACTTC-GCACCAGTATAGGAAGACAAGATCTG-TATA
* * * * * * * * * *
38999706 TTTGATCTACTTCACGCCAATACATGAAGACAATATCTATTTTTT
1 TTCGATCTACTTCGCACCAGTATAGGAAGACAAGATC--TGTATA
* * * * *
38999751 TTCGATCTGCTTCGCCACTAGTATGGGAAGGCGAGATCTGTATA
1 TTCGATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGTATA
* * * * *
38999795 TTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTATTCC
1 TTCGATCTACTTCGCACCAGTATAGGAAGACAAGATCTGTA-T-A
* *
38999840 TTCGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGTATA
1 TTCGATCTACTTCG-CACCAGTATAGGAAGACAAGATCTGTATA
* * *
38999884 TTCAATCCACTTCGCTACCAATATAGGAAGACA
1 TTCGATCTACTTCGC-ACCAGTATAGGAAGACA
38999917 GGACCTGCTG
Statistics
Matches: 257, Mismatches: 77, Indels: 23
0.72 0.22 0.06
Matches are distributed among these distances:
43 22 0.09
44 89 0.35
45 107 0.42
46 39 0.15
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
TTCGATCTACTTCGCACCAGTATAGGAAGACAAGATCTGTATA
Found at i:39001264 original size:45 final size:45
Alignment explanation
Indices: 39001196--39001284 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
39001186 AGCCTCTCCA
* * *
39001196 TTTTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGGTCT
1 TTTTTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTCT
39001241 TTTTTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTC
1 TTTTTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTC
39001285 CCACCTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (45 bp):
TTTTTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTCT
Found at i:39001294 original size:46 final size:45
Alignment explanation
Indices: 39001199--39001296 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
39001189 CTCTCCATTT
* * * ****
39001199 TTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCTTGGTCTTTT
1 TTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTCCACC
39001244 TTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTCCCACC
1 TTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGT-CCACC
39001290 TTTTTTA
1 TTTTTTA
39001297 AGCAGAGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 37 0.82
46 8 0.18
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.46
Consensus pattern (45 bp):
TTTTTTACTCAAAGCACCCTTTGTAGGCTTTCACCTTGGTCCACC
Found at i:39016826 original size:135 final size:137
Alignment explanation
Indices: 39016583--39016901 Score: 472
Period size: 135 Copynumber: 2.3 Consensus size: 137
39016573 CGGGACACGG
* ***
39016583 TATTTAACTCCGATT---ACACTCTCTAAATCAAATTCAAAATTAAGTTAATATTTTTTTTCAAA
1 TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATTAATA-TTTTTAAAAAA
* *
39016645 GTTACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCGGCACAAAAGAAACTAAAATCAAATTC
65 GATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAACT-AAATCAAATTC
39016710 AAATTTTGA
129 AAATTTTGA
39016719 TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATT-A-A-TTTTAAAAAAG
1 TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATTAATATTTTTAAAAAAG
*
39016781 ATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAGCTAAATCAAATTCAA
66 ATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAACTAAATCAAATTCAA
39016846 ATTTTGA
131 ATTTTGA
*
39016853 TATTTTAACTCCGATTGCAACACGT-TATAAATCAAATATCAAAATTAAA
1 TA-TTTAACTCCGATTGCAACAC-TCTCTAAATCAAAT-TCAAAATTAAA
39016902 ACTTTTTAAG
Statistics
Matches: 169, Mismatches: 8, Indels: 12
0.89 0.04 0.06
Matches are distributed among these distances:
134 22 0.13
135 88 0.52
136 27 0.16
137 1 0.01
138 1 0.01
139 30 0.18
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (137 bp):
TATTTAACTCCGATTGCAACACTCTCTAAATCAAATTCAAAATTAAATTAATATTTTTAAAAAAG
ATACTAACTTGGAACTGAAATTAAAAGTTCAAAATTCAGCACAAAAGAAACTAAATCAAATTCAA
ATTTTGA
Found at i:39026689 original size:4 final size:4
Alignment explanation
Indices: 39026680--39026723 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
39026670 TGCAAAAGGA
39026680 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
39026724 CATGCATGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:39027193 original size:3 final size:3
Alignment explanation
Indices: 39027113--39027174 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
39027103 AAATGGAAAT
* * * * *
39027113 ATA ATG ATA ATA ACA ATA ATA TTA ATA ATA ATA CTA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
39027161 ACA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
39027175 TTATTAATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39037546 original size:6 final size:7
Alignment explanation
Indices: 39037531--39037556 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
39037521 ATAAAAGAAG
39037531 AAAATAA
1 AAAATAA
39037538 AAAATAA
1 AAAATAA
39037545 AAAATAA
1 AAAATAA
39037552 AAAAT
1 AAAAT
39037557 CAAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:39040692 original size:18 final size:18
Alignment explanation
Indices: 39040658--39040698 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
39040648 TAAAATTATT
*
39040658 TTATAAATTTCTAATTTA
1 TTATAAACTTCTAATTTA
39040676 CTTATAAACTT-TAATTTA
1 -TTATAAACTTCTAATTTA
39040694 TTATA
1 TTATA
39040699 CGATTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 9 0.43
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAAACTTCTAATTTA
Found at i:39045376 original size:22 final size:19
Alignment explanation
Indices: 39045343--39045388 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
39045333 TAGTTGTTTC
*
39045343 TAAATTATTTTTAGGGCTCCG
1 TAAATTAATTTTA-GGC-CCG
39045364 TAAACTTAATTTTAGGCCCG
1 TAAA-TTAATTTTAGGCCCG
39045384 TAAAT
1 TAAAT
39045389 GTATTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 7 0.30
22 8 0.35
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (19 bp):
TAAATTAATTTTAGGCCCG
Found at i:39045917 original size:23 final size:23
Alignment explanation
Indices: 39045891--39045937 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
39045881 TTCAATTGGA
39045891 TTCGAAGTAAGTAAATTAATGTT
1 TTCGAAGTAAGTAAATTAATGTT
39045914 TTCGAAGTAAGTAAATTAATGTT
1 TTCGAAGTAAGTAAATTAATGTT
39045937 T
1 T
39045938 ACTTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (23 bp):
TTCGAAGTAAGTAAATTAATGTT
Found at i:39061959 original size:3 final size:3
Alignment explanation
Indices: 39061951--39061980 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39061941 AAGATGATAT
39061951 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39061981 ACTTTAATAT
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:39068382 original size:15 final size:15
Alignment explanation
Indices: 39068357--39068391 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39068347 AACTCTATTT
*
39068357 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
39068371 TAATTAATATTAAGA
1 TAATTAATATTAAGA
39068386 TAATTA
1 TAATTA
39068392 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:39068633 original size:9 final size:9
Alignment explanation
Indices: 39068619--39068644 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
39068609 AATTTCCATT
39068619 TTTATTTTA
1 TTTATTTTA
39068628 TTTATTTTA
1 TTTATTTTA
39068637 TTTATTTT
1 TTTATTTT
39068645 CTTTTCCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:39070487 original size:105 final size:105
Alignment explanation
Indices: 39070305--39070509 Score: 347
Period size: 105 Copynumber: 2.0 Consensus size: 105
39070295 ATATGGTAGA
* *
39070305 CGCCGCTCGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGAAAGAGACTTGATCTCCGCGA
1 CGCCGCTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGAAAGAGACTTGATCTCCACGA
*
39070370 TGGCTGCAAATTCTTAGCAGTTCCGAGCCAATACTGAACT
66 TGGCTGCAAATTCTCAGCAGTTCCGAGCCAATACTGAACT
**
39070410 CGCCGCTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGCGAGAGACTTGATCTCCACGA
1 CGCCGCTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGAAAGAGACTTGATCTCCACGA
* *
39070475 TGGCTGTAAATTCTCAGCAGTTTCGAGCCAATACT
66 TGGCTGCAAATTCTCAGCAGTTCCGAGCCAATACT
39070510 AAACCCCCTA
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 93 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.21
Consensus pattern (105 bp):
CGCCGCTAGTAGAGGAGCATTGGTCAACATGACTCCCCAACAAGAAAGAGACTTGATCTCCACGA
TGGCTGCAAATTCTCAGCAGTTCCGAGCCAATACTGAACT
Found at i:39074966 original size:4 final size:4
Alignment explanation
Indices: 39074957--39075032 Score: 61
Period size: 4 Copynumber: 18.5 Consensus size: 4
39074947 CAACTCAATT
*
39074957 TTTA TTTA -TTA TTTA TTTA -TTA TTTTA TTTTA TTTT TTTA CTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA -TTTA TTTA
39075006 -TTA CTTTA TTTTA TTT- TATTA TTTA TT
1 TTTA -TTTA -TTTA TTTA T-TTA TTTA TT
39075033 AATTATTTGG
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
3 10 0.16
4 31 0.51
5 20 0.33
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:39074986 original size:5 final size:5
Alignment explanation
Indices: 39074976--39075025 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
39074966 TATTTATTTA
* *
39074976 TTATT TTATT TTA-T TT-TT TTACT TTATTT ATTACT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT -TTATT TTATT TTATT TTATT
39075026 ATTTATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 6 0.16
5 26 0.70
6 2 0.05
7 3 0.08
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:39075004 original size:30 final size:29
Alignment explanation
Indices: 39074956--39075040 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 29
39074946 GCAACTCAAT
39074956 TTTTA-TTTATTATTTATTTATTATTTTA
1 TTTTATTTTATTATTTATTTATTATTTTA
* *
39074984 TTTTATTTTTTTACTTTATTTATTACTTTA
1 TTTTATTTTATTA-TTTATTTATTATTTTA
*
39075014 TTTTATTTTATTATTTATTAATTATTT
1 TTTTATTTTATTATTTATTTATTATTT
39075041 GGATATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 5 0.10
29 18 0.36
30 27 0.54
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTATTTTATTATTTATTTATTATTTTA
Found at i:39075234 original size:22 final size:22
Alignment explanation
Indices: 39075187--39075246 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
39075177 GTCCAGAATG
* *
39075187 CCTGCAGCCAAACTA-CCATATT
1 CCTGCAGCC-AACCACCCATATC
*
39075209 CCTGCAGCCAACCACCCTTATC
1 CCTGCAGCCAACCACCCATATC
* *
39075231 CCTGCACCCAAGCACC
1 CCTGCAGCCAACCACC
39075247 ACCCCTCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.27, C:0.47, G:0.10, T:0.17
Consensus pattern (22 bp):
CCTGCAGCCAACCACCCATATC
Found at i:39076984 original size:9 final size:9
Alignment explanation
Indices: 39076970--39077000 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39076960 GTTAAACGAA
39076970 TCGAGTTAT
1 TCGAGTTAT
*
39076979 TCGAGTTAA
1 TCGAGTTAT
39076988 TCGAGTTAT
1 TCGAGTTAT
39076997 TCGA
1 TCGA
39077001 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:39084879 original size:25 final size:25
Alignment explanation
Indices: 39084707--39084896 Score: 77
Period size: 25 Copynumber: 7.6 Consensus size: 25
39084697 CATGTAATAT
* * * *
39084707 GAAGCTCATGTGAGCTATATAACGA
1 GAAGCTCATGAGAGCCAAATATCGA
* * *
39084732 GAAGCTC-TTATGAGCCAATTATCGG
1 GAAGCTCATGA-GAGCCAAATATCGA
* *
39084757 GAAGCTCAT-ACAAGCCATATATC-A
1 GAAGCTCATGA-GAGCCAAATATCGA
* * * *
39084781 GGAAACTCAAGAGAGCTATTAAT-T-GG
1 -GAAGCTCATGAGAGCCA--AATATCGA
* ** *
39084807 GAAGCTCATGAGAGCTAAATAAAGG
1 GAAGCTCATGAGAGCCAAATATCGA
* * *
39084832 GAATCTCGTGAGAGCCAAGTATCGA
1 GAAGCTCATGAGAGCCAAATATCGA
*
39084857 GAAGCTCATGAAAGCCAAATATC-A
1 GAAGCTCATGAGAGCCAAATATCGA
* *
39084881 GGACGCTCATAAGAGC
1 -GAAGCTCATGAGAGC
39084897 TGTGGTGTGT
Statistics
Matches: 120, Mismatches: 35, Indels: 20
0.69 0.20 0.11
Matches are distributed among these distances:
23 3 0.03
24 2 0.02
25 110 0.92
26 3 0.03
27 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (25 bp):
GAAGCTCATGAGAGCCAAATATCGA
Found at i:39093252 original size:32 final size:32
Alignment explanation
Indices: 39093165--39093256 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 32
39093155 TAGAAGTTCT
* * *
39093165 AGAGGGTTTAATTAAAATTTTTAAAAATTTGG
1 AGAGAGTTTAATTGAAATTTTAAAAAATTTGG
* *
39093197 AG-GA-TATAA-TGAGAATTTTAAAAAATTTTG
1 AGAGAGTTTAATTGA-AATTTTAAAAAATTTGG
*
39093227 AGAGAGTTTAATTGAAACTTTAAAAAATTT
1 AGAGAGTTTAATTGAAATTTTAAAAAATTT
39093257 AGGGGGACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 2 0.04
30 21 0.43
31 3 0.06
32 20 0.41
33 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (32 bp):
AGAGAGTTTAATTGAAATTTTAAAAAATTTGG
Found at i:39107951 original size:31 final size:30
Alignment explanation
Indices: 39107889--39107954 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
39107879 TTTAGTCATA
*
39107889 TAATAAATTATTAATATAATTTATTATTTT
1 TAATAAATTATTAATATAAATTATTATTTT
39107919 TAATAAATTATTTAATATTTAAATT-TTA-TTT
1 TAATAAATTA-TTAATA--TAAATTATTATTTT
39107950 TAATA
1 TAATA
39107955 GTAAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 14 0.44
32 3 0.09
33 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATAAATTATTAATATAAATTATTATTTT
Found at i:39115309 original size:14 final size:15
Alignment explanation
Indices: 39115292--39115335 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
39115282 TTAAAGATTA
39115292 ATGATTAA-TTAATT
1 ATGATTAAGTTAATT
39115306 ATGATTAAGTTAATT
1 ATGATTAAGTTAATT
39115321 A--ATTAAGTTTAATT
1 ATGATTAAG-TTAATT
39115335 A
1 A
39115336 AAACTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.21
14 15 0.54
15 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (15 bp):
ATGATTAAGTTAATT
Found at i:39115332 original size:19 final size:18
Alignment explanation
Indices: 39115295--39115336 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
39115285 AAGATTAATG
*
39115295 ATTAATTAATTATGATTA
1 ATTAATTAATTAAGATTA
*
39115313 AGTTAATTAATTAAGTTTA
1 A-TTAATTAATTAAGATTA
39115332 ATTAA
1 ATTAA
39115337 AACTAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
ATTAATTAATTAAGATTA
Found at i:39121032 original size:26 final size:26
Alignment explanation
Indices: 39120991--39121050 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
39120981 CAGTAAGATA
* *
39120991 AAATGACCATAATGCCCCT-AGAGGGT
1 AAATGACTATAATGCCCATCA-AGGGT
*
39121017 AAATGACTATATTGCCCATCAAGGGT
1 AAATGACTATAATGCCCATCAAGGGT
39121043 AAATGACT
1 AAATGACT
39121051 GATTTGTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (26 bp):
AAATGACTATAATGCCCATCAAGGGT
Found at i:39132137 original size:23 final size:24
Alignment explanation
Indices: 39132101--39132165 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 24
39132091 AATAATACCA
*
39132101 AAATCATTCAATAAATAAAAA-ACT
1 AAATCATGCAATAAA-AAAAATACT
39132125 AAATCATGC-ATAAAAAAAATACT
1 AAATCATGCAATAAAAAAAATACT
39132148 -AATCTAT--AATAAAAAAAA
1 AAATC-ATGCAATAAAAAAAA
39132166 GCCACAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
22 19 0.51
23 10 0.27
24 8 0.22
ACGTcount: A:0.65, C:0.11, G:0.02, T:0.23
Consensus pattern (24 bp):
AAATCATGCAATAAAAAAAATACT
Found at i:39133650 original size:16 final size:17
Alignment explanation
Indices: 39133620--39133652 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39133610 ATTAAAAATA
39133620 TTTTAATTTATATTAAT
1 TTTTAATTTATATTAAT
39133637 TTTTAATTTA-ATTAAT
1 TTTTAATTTATATTAAT
39133653 CCAAAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAATTTATATTAAT
Found at i:39135344 original size:2 final size:2
Alignment explanation
Indices: 39135339--39135370 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39135329 ATATATCTGT
39135339 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
39135371 AAGTTTAGAA
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:39138436 original size:3 final size:3
Alignment explanation
Indices: 39138424--39138517 Score: 77
Period size: 3 Copynumber: 31.3 Consensus size: 3
39138414 GGTTTTCTTT
* * * *
39138424 TTA TTA -TA TTA TTA ATA TTGT TTA TTA GTA TTA TTA TTA CTA -TA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * *
39138468 TTA TTA TTA TTT TTT TTA TTTA TTA -TA TCA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA
39138514 TTA T
1 TTA T
39138518 ACCTACATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
2 6 0.08
3 61 0.82
4 7 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:39140942 original size:413 final size:413
Alignment explanation
Indices: 39140175--39141001 Score: 1636
Period size: 413 Copynumber: 2.0 Consensus size: 413
39140165 GCTATGTTCA
39140175 GAACCAATTGTATTCTCATCCATTGTTATACCCTTTTTGCAAGCGTGTTGCATTGGAATAATGAT
1 GAACCAATTGTATTCTCATCCATTGTTATACCCTTTTTGCAAGCGTGTTGCATTGGAATAATGAT
39140240 TAATGGACTAATAAAACTTTCAAAAGGGAAGTTTGGCATATTACTCTAGAAGTTTCTAAATAATA
66 TAATGGACTAATAAAACTTTCAAAAGGGAAGTTTGGCATATTACTCTAGAAGTTTCTAAATAATA
39140305 CAGGAACCTGAAACACGACTATTGTTTAGAACACACCACATTTAAAGGTTGGAAATCTGAAAAGG
131 CAGGAACCTGAAACACGACTATTGTTTAGAACACACCACATTTAAAGGTTGGAAATCTGAAAAGG
39140370 AAGAGTCTAAATTAGGACTTTCTCTTTAGATTTTGTTGTTAAAAACATTGATTGAACAAAATGAC
196 AAGAGTCTAAATTAGGACTTTCTCTTTAGATTTTGTTGTTAAAAACATTGATTGAACAAAATGAC
39140435 AAAGCTTAAATAAAAAACTAAGCAATGATCACCCTGACATTGCAGTGGAGTAGATTGAAGCACTA
261 AAAGCTTAAATAAAAAACTAAGCAATGATCACCCTGACATTGCAGTGGAGTAGATTGAAGCACTA
39140500 GTTCCTATACCTCTGAAGATGCAGTAGGAAGGAATGAGACTACTTGAAGAAGAATAGTACCAAGG
326 GTTCCTATACCTCTGAAGATGCAGTAGGAAGGAATGAGACTACTTGAAGAAGAATAGTACCAAGG
39140565 TCCAGCACGACCGGGCAAAATTG
391 TCCAGCACGACCGGGCAAAATTG
39140588 GAACCAATTGTATTCTCATCCATTGTTATACCCTTTTTGCAAGCGTGTTGCATTGGAATAATGAT
1 GAACCAATTGTATTCTCATCCATTGTTATACCCTTTTTGCAAGCGTGTTGCATTGGAATAATGAT
39140653 TAATGGACTAATAAAACTTTCAAAAGGGAAGTTTGGCATATTACTCTAGAAGTTTCTAAATAATA
66 TAATGGACTAATAAAACTTTCAAAAGGGAAGTTTGGCATATTACTCTAGAAGTTTCTAAATAATA
39140718 CAGGAACCTGAAACACGACTATTGTTTAGAACACACCACATTTAAAGGTTGGAAATCTGAAAAGG
131 CAGGAACCTGAAACACGACTATTGTTTAGAACACACCACATTTAAAGGTTGGAAATCTGAAAAGG
*
39140783 AAGAGTCTAAATTAGGACTTTCTCTTTAGATTTTGTTGTTAAAAATATTGATTGAACAAAATGAC
196 AAGAGTCTAAATTAGGACTTTCTCTTTAGATTTTGTTGTTAAAAACATTGATTGAACAAAATGAC
39140848 AAAGCTTAAATAAAAAACTAAGCAATGATCACCCTGACATTGCAGTGGAGTAGATTGAAGCACTA
261 AAAGCTTAAATAAAAAACTAAGCAATGATCACCCTGACATTGCAGTGGAGTAGATTGAAGCACTA
*
39140913 GTTCCTATACCTCTGAAGATGCAGTAGGAAGGAATGAGGCTACTTGAAGAAGAATAGTACCAAGG
326 GTTCCTATACCTCTGAAGATGCAGTAGGAAGGAATGAGACTACTTGAAGAAGAATAGTACCAAGG
39140978 TCCAGCACGACCGGGCAAAATTG
391 TCCAGCACGACCGGGCAAAATTG
39141001 G
1 G
39141002 CTATTTTTAA
Statistics
Matches: 412, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
413 412 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (413 bp):
GAACCAATTGTATTCTCATCCATTGTTATACCCTTTTTGCAAGCGTGTTGCATTGGAATAATGAT
TAATGGACTAATAAAACTTTCAAAAGGGAAGTTTGGCATATTACTCTAGAAGTTTCTAAATAATA
CAGGAACCTGAAACACGACTATTGTTTAGAACACACCACATTTAAAGGTTGGAAATCTGAAAAGG
AAGAGTCTAAATTAGGACTTTCTCTTTAGATTTTGTTGTTAAAAACATTGATTGAACAAAATGAC
AAAGCTTAAATAAAAAACTAAGCAATGATCACCCTGACATTGCAGTGGAGTAGATTGAAGCACTA
GTTCCTATACCTCTGAAGATGCAGTAGGAAGGAATGAGACTACTTGAAGAAGAATAGTACCAAGG
TCCAGCACGACCGGGCAAAATTG
Found at i:39142213 original size:3 final size:3
Alignment explanation
Indices: 39142201--39142293 Score: 63
Period size: 3 Copynumber: 31.3 Consensus size: 3
39142191 GGTGTTCTTT
* * *
39142201 TTA TTA -TA TTA TTA ATA CTGT- TTA TTA GTA TTA TTA TTA CTA -TA
1 TTA TTA TTA TTA TTA TTA -T-TA TTA TTA TTA TTA TTA TTA TTA TTA
*
39142245 TTA TTA TTA GTT- TT- TTA TTTA TTA -TA TCA TATA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA
39142290 TTA T
1 TTA T
39142294 ACCTACATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
2 11 0.15
3 54 0.74
4 7 0.10
5 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:39142446 original size:35 final size:36
Alignment explanation
Indices: 39142365--39142456 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
39142355 AATACATATG
* * *
39142365 CATATTATGTATATATTTTAT-TATTATTTTATTTT
1 CATAATATTTATATATTTTATATATCATTTTATTTT
* *
39142400 CATAGTTTTTATATATTTTATATA-CATTTATATTTT
1 CATAATATTTATATATTTTATATATCATTT-TATTTT
*
39142436 -ATAATATTTATAT-TTTCATAT
1 CATAATATTTATATATTTTATAT
39142457 TTTATAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.15
35 33 0.69
36 8 0.17
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (36 bp):
CATAATATTTATATATTTTATATATCATTTTATTTT
Found at i:39142450 original size:52 final size:50
Alignment explanation
Indices: 39142376--39142472 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 50
39142366 ATATTATGTA
*
39142376 TATATTTTATTATTATTTTATTTTCATAGTTTTTATATATTT-TATATACATT
1 TATATTTTATTAATATTTTATTTTCATA--TTTTATA-ATTTATATATACATT
39142428 TATATTTTA-TAATATTTATATTTTCATATTTTATAATTTATATAT
1 TATATTTTATTAATATTT-TATTTTCATATTTTATAATTTATATAT
39142473 GTTTATACAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
49 4 0.10
50 12 0.29
51 7 0.17
52 19 0.45
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (50 bp):
TATATTTTATTAATATTTTATTTTCATATTTTATAATTTATATATACATT
Found at i:39142458 original size:14 final size:16
Alignment explanation
Indices: 39142411--39142479 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
39142401 ATAGTTTTTA
*
39142411 TATATTTTATATACATT
1 TATATTTTATA-ATATT
39142428 TATATTTTATAATATT
1 TATATTTTATAATATT
39142444 TATATTTTCAT-AT-TT
1 TATATTTT-ATAATATT
* *
39142459 TATAATTTATATATGTT
1 TATATTTTATA-ATATT
39142476 TATA
1 TATA
39142480 CATTCTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.04
15 9 0.20
16 16 0.35
17 19 0.41
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (16 bp):
TATATTTTATAATATT
Found at i:39142466 original size:22 final size:23
Alignment explanation
Indices: 39142377--39142470 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 23
39142367 TATTATGTAT
39142377 ATATTTTATTATTATTT-TATTTTC
1 ATATTTTA-TA-TATTTATATTTTC
39142401 ATAGTTTTTATATATTTTATATACATTT-
1 ATA--TTTTATATA-TTTATAT---TTTC
39142429 ATATTTTATAATATTTATATTTTC
1 ATATTTTAT-ATATTTATATTTTC
39142453 ATATTTTATA-ATTTATAT
1 ATATTTTATATATTTATAT
39142471 ATGTTTATAC
Statistics
Matches: 61, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
22 8 0.13
23 4 0.07
24 14 0.23
25 5 0.08
26 21 0.34
27 3 0.05
28 3 0.05
29 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (23 bp):
ATATTTTATATATTTATATTTTC
Found at i:39142479 original size:8 final size:7
Alignment explanation
Indices: 39142411--39142470 Score: 57
Period size: 7 Copynumber: 7.7 Consensus size: 7
39142401 ATAGTTTTTA
39142411 TATATTT
1 TATATTT
39142418 TATATACATT
1 TATAT---TT
39142428 TATATTT
1 TATATTT
39142435 TATAATATT
1 TAT-AT-TT
39142444 TATATTT
1 TATATTT
39142451 TCATATTT
1 T-ATATTT
*
39142459 TATAATT
1 TATATTT
39142466 TATAT
1 TATAT
39142471 ATGTTTATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
7 22 0.49
8 11 0.24
9 5 0.11
10 7 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (7 bp):
TATATTT
Found at i:39144759 original size:8 final size:8
Alignment explanation
Indices: 39144742--39144805 Score: 55
Period size: 7 Copynumber: 8.5 Consensus size: 8
39144732 CATTTTGCAT
*
39144742 GTTTTGGG
1 GTTTTAGG
39144750 GTTTTAGG
1 GTTTTAGG
*
39144758 G-TTTATG
1 GTTTTAGG
39144765 GTTTTAGG
1 GTTTTAGG
*
39144773 GTTTTA-A
1 GTTTTAGG
*
39144780 CTTTTAGG
1 GTTTTAGG
*
39144788 G-TTTAAG
1 GTTTTAGG
39144795 G-TTTAGG
1 GTTTTAGG
39144802 GTTT
1 GTTT
39144806 ATGGTTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
7 23 0.52
8 21 0.48
ACGTcount: A:0.14, C:0.02, G:0.33, T:0.52
Consensus pattern (8 bp):
GTTTTAGG
Found at i:39144769 original size:15 final size:15
Alignment explanation
Indices: 39144749--39144811 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
39144739 CATGTTTTGG
39144749 GGTTTTAGGGTTTAT
1 GGTTTTAGGGTTTAT
39144764 GGTTTTAGGGTTT-T
1 GGTTTTAGGGTTTAT
** *
39144778 AACTTTTAGGGTTTAA
1 -GGTTTTAGGGTTTAT
39144794 GG-TTTAGGGTTTAT
1 GGTTTTAGGGTTTAT
39144808 GGTT
1 GGTT
39144812 AAAAATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 14 0.36
15 25 0.64
ACGTcount: A:0.16, C:0.02, G:0.32, T:0.51
Consensus pattern (15 bp):
GGTTTTAGGGTTTAT
Found at i:39144799 original size:14 final size:14
Alignment explanation
Indices: 39144752--39144811 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
39144742 GTTTTGGGGT
*
39144752 TTTAGGGTTTATGG
1 TTTAGGGTTTAAGG
**
39144766 TTTTAGGGTTTTAACT
1 -TTTAGGG-TTTAAGG
39144782 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
*
39144796 TTTAGGGTTTATGG
1 TTTAGGGTTTAAGG
39144810 TT
1 TT
39144812 AAAAATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 20 0.53
15 14 0.37
16 4 0.11
ACGTcount: A:0.17, C:0.02, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:39145764 original size:226 final size:221
Alignment explanation
Indices: 39145235--39145858 Score: 955
Period size: 226 Copynumber: 2.8 Consensus size: 221
39145225 GAACACCTCT
*
39145235 AGTTTAGGGTTTGTCAATTAAATTA--TATAAATTTTTCATAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTCGTGTTTAT
** * * *
39145298 TATTTTTT--TTAAAATCACTTAAATTAGGGTGTAGGGTTACTTGAGTAATTTAATTAAAAATTT
66 TATTTTTTAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAA-AT
*
39145361 TGAAAAATTAGATTAGGGTTAGGGTTA--G---GGTTTAGGGTGTTTTTAAGTTAAGAGTTTTTA
130 T-AAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGTTTAGGGTGTTTTTAAGTTAAGAGGTTTTA
39145421 AGGAAAAATCAAATAAATTAGGGTTTAG
194 AGGAAAAATCAAATAAATTAGGGTTTAG
39145449 AGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTCGTGTTTAT
*
39145514 TATCTTTTATGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAT
66 TATTTTTTA-GAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAT
39145579 TAAAAATTAGATTAGGGTTAGGGTTAGGGTTAAGGTTTAGGGTGTTTTTAAGTTAAG-GGTTTTA
130 TAAAAATTAGATTAGGGTTAGGGTTAGGGTT-AGGTTTAGGGTGTTTTTAAGTTAAGAGGTTTTA
39145643 AGGAAAAAT-AAATAAATTAGGGTTTAG
194 AGGAAAAATCAAATAAATTAGGGTTTAG
*
39145670 AGTTTAGGGTTTGTCAATTAAATTATTTATAAATATTCGTAGCCAAAATTGGATTAGTTTTCGTG
1 AGTTTAGGGTTTGTCAATTAAATTATTTATAAAT-TT--T--TCAAAATTGGATTAGTTTTCGTG
39145735 TTTATTATTTTTTAAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAA
61 TTTATTATTTTTT-AGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAA
* * *
39145800 AAAATTTAAAAATCAGATTAGAGTTAGGGTTAGGGTTAGGGTTTAGAGTGTTTTTAAGT
125 AAAA-TTAAAAATTAGATTAGGGTTAGGGTTAGGGTTA-GGTTTAGGGTGTTTTTAAGT
39145859 AAAGTTTATA
Statistics
Matches: 378, Mismatches: 13, Indels: 25
0.91 0.03 0.06
Matches are distributed among these distances:
214 25 0.07
216 44 0.12
217 25 0.07
218 2 0.01
219 49 0.13
221 52 0.14
222 17 0.04
223 24 0.06
224 1 0.00
226 89 0.24
227 50 0.13
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.42
Consensus pattern (221 bp):
AGTTTAGGGTTTGTCAATTAAATTATTTATAAATTTTTCAAAATTGGATTAGTTTTCGTGTTTAT
TATTTTTTAGAAAAAATCAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATT
AAAAATTAGATTAGGGTTAGGGTTAGGGTTAGGTTTAGGGTGTTTTTAAGTTAAGAGGTTTTAAG
GAAAAATCAAATAAATTAGGGTTTAG
Found at i:39149924 original size:49 final size:51
Alignment explanation
Indices: 39149855--39149952 Score: 139
Period size: 49 Copynumber: 2.0 Consensus size: 51
39149845 AATAATTAAA
*
39149855 AAATAGGGATTTAAGAGAAATTT-GAGAGGAAATT-A-AGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGCAAATTGAGAGCAAATTGAGATT
* *
39149904 AAATATGGATTTGAGAGAAATTTAGAAGCAAATTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGCAAATTGAGAGCAAATTGAGA
39149953 GGAAATTGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
49 28 0.65
50 3 0.07
51 12 0.28
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGCAAATTGAGAGCAAATTGAGATT
Found at i:39149926 original size:11 final size:11
Alignment explanation
Indices: 39149914--39149963 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
39149904 AAATATGGAT
39149914 TTGAGAG-AAA
1 TTGAGAGCAAA
*
39149924 TTTAGAAGCAAA
1 TTGAG-AGCAAA
39149936 TTGAGAGCAAA
1 TTGAGAGCAAA
*
39149947 TTGAGAGGAAA
1 TTGAGAGCAAA
39149958 TTGAGA
1 TTGAGA
39149964 TGTTGTTGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 4 0.11
11 24 0.69
12 7 0.20
ACGTcount: A:0.46, C:0.04, G:0.28, T:0.22
Consensus pattern (11 bp):
TTGAGAGCAAA
Found at i:39150658 original size:55 final size:54
Alignment explanation
Indices: 39150581--39150704 Score: 135
Period size: 55 Copynumber: 2.3 Consensus size: 54
39150571 CTGCTCTTAT
* * *** *
39150581 TAAAAATTAGAAAAATTATT-AAATAATAAATTTTAGAAAAATTATTAAATTTTAA
1 TAAAAATCATAAAAATTATTAAAATAATAAAAAATA-AAAAATTATAAAATTTT-A
* *
39150636 TAAAAA-CATAAAAATTAGTTAAAATCATAAAAAATAAAAAATTGTAAAATTTTA
1 TAAAAATCATAAAAATTA-TTAAAATAATAAAAAATAAAAAATTATAAAATTTTA
39150690 TAAAAATCATAAAAA
1 TAAAAATCATAAAAA
39150705 ATTAACTACC
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
54 16 0.28
55 31 0.53
56 11 0.19
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.32
Consensus pattern (54 bp):
TAAAAATCATAAAAATTATTAAAATAATAAAAAATAAAAAATTATAAAATTTTA
Found at i:39150676 original size:27 final size:28
Alignment explanation
Indices: 39150617--39150708 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 28
39150607 TAAATTTTAG
* * *
39150617 AAAAATTATTAAATTTTAATAAAAACAT-
1 AAAAATTAGTAAA-ATTCATAAAAACATA
39150645 AAAAATTAGTTAAAA-TCATAAAAA-ATA
1 AAAAATTAG-TAAAATTCATAAAAACATA
*
39150672 AAAAATT-GTAAAATTTTATAAAAATCATA
1 AAAAATTAGTAAAA-TTCATAAAAA-CATA
39150701 AAAAATTA
1 AAAAATTA
39150709 ACTACCCCTA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
25 5 0.09
26 3 0.06
27 23 0.43
28 8 0.15
29 14 0.26
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAAATTAGTAAAATTCATAAAAACATA
Found at i:39150702 original size:19 final size:19
Alignment explanation
Indices: 39150608--39150703 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 19
39150598 ATTAAATAAT
* * *
39150608 AAATTTTAGAAAAATTATT
1 AAATTTTATAAAAATCATA
39150627 AAATTTTAATAAAAA-CATA
1 AAATTTT-ATAAAAATCATA
* *
39150646 AAA-ATTAGTTAAAATCATA
1 AAATTTTA-TAAAAATCATA
** **
39150665 AAA-AATA-AAAAATTGTA
1 AAATTTTATAAAAATCATA
39150682 AAATTTTATAAAAATCATA
1 AAATTTTATAAAAATCATA
39150701 AAA
1 AAA
39150704 AATTAACTAC
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
17 11 0.19
18 9 0.15
19 33 0.56
20 6 0.10
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATTTTATAAAAATCATA
Found at i:39150899 original size:20 final size:20
Alignment explanation
Indices: 39150871--39151011 Score: 68
Period size: 19 Copynumber: 7.2 Consensus size: 20
39150861 GAAAATTATA
*
39150871 TTTCTTTACATTTTGTATAAT
1 TTTC-TTACATTTTTTATAAT
* * *
39150892 TTTCTTACGACTTTATAAAAT
1 TTTCTTAC-ATTTTTTATAAT
*
39150913 TTT-ATA-ATTTTTTAT-A-
1 TTTCTTACATTTTTTATAAT
*
39150929 TTTC-TATATTTTTTATAAT
1 TTTCTTACATTTTTTATAAT
*
39150948 TTT-TTACGA-TTTTTATAAA
1 TTTCTTAC-ATTTTTTATAAT
*
39150967 ATT-TTACAATTTTTTAT-AT
1 TTTCTTAC-ATTTTTTATAAT
* *
39150986 TTT-TAACGATTTTTATATATT
1 TTTCTTAC-ATTTTT-TATAAT
39151007 TTTCT
1 TTTCT
39151012 AGTTTTTAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 21
0.72 0.12 0.16
Matches are distributed among these distances:
16 5 0.05
17 10 0.11
18 7 0.08
19 33 0.35
20 17 0.18
21 20 0.22
22 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTCTTACATTTTTTATAAT
Found at i:39150925 original size:10 final size:10
Alignment explanation
Indices: 39150912--39150989 Score: 67
Period size: 10 Copynumber: 8.3 Consensus size: 10
39150902 CTTTATAAAA
39150912 TTTTATAATT
1 TTTTATAATT
39150922 TTTTAT-A-T
1 TTTTATAATT
*
39150930 TTCTAT-ATT
1 TTTTATAATT
39150939 TTTTATAATT
1 TTTTATAATT
**
39150949 TTTTACGA-T
1 TTTTATAATT
**
39150958 TTTTATAAAA
1 TTTTATAATT
*
39150968 TTTTACAATT
1 TTTTATAATT
39150978 TTTTAT-ATT
1 TTTTATAATT
39150987 TTT
1 TTT
39150990 AACGATTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
8 7 0.13
9 20 0.37
10 27 0.50
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (10 bp):
TTTTATAATT
Found at i:39150940 original size:56 final size:57
Alignment explanation
Indices: 39150866--39151009 Score: 179
Period size: 56 Copynumber: 2.5 Consensus size: 57
39150856 TTTATGAAAA
*
39150866 TTATATTTCTTTACATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTTATAATTTT
1 TTATATTTC-TTACATTTTGTATAATTTT-TTACGATCTTTATAAAATTTTACAATTTT
* * *
39150924 TTATATTTC-TATATTTTTTATAATTTTTTACGATTTTTATAAAATTTTACAATTTT
1 TTATATTTCTTACATTTTGTATAATTTTTTACGATCTTTATAAAATTTTACAATTTT
39150980 TTATATTT-TTAACGATTTT-TATATATTTTT
1 TTATATTTCTT-AC-ATTTTGTATA-ATTTTT
39151010 CTAGTTTTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
55 6 0.08
56 45 0.59
57 5 0.07
58 20 0.26
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (57 bp):
TTATATTTCTTACATTTTGTATAATTTTTTACGATCTTTATAAAATTTTACAATTTT
Found at i:39150960 original size:19 final size:19
Alignment explanation
Indices: 39150938--39151030 Score: 84
Period size: 19 Copynumber: 4.8 Consensus size: 19
39150928 ATTTCTATAT
39150938 TTTTTATAATTTTTTACGA
1 TTTTTATAATTTTTTACGA
** *
39150957 TTTTTATAAAATTTTACAA
1 TTTTTATAATTTTTTACGA
*
39150976 TTTTT-TATATTTTTAACGA
1 TTTTTATA-ATTTTTTACGA
39150995 TTTTTATATATTTTTCTA-G-
1 TTTTTATA-ATTTTT-TACGA
*
39151014 TTTTTAATAACTTTTTA
1 TTTTT-ATAATTTTTTA
39151031 ATATTTGAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
18 4 0.07
19 43 0.70
20 13 0.21
21 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTATAATTTTTTACGA
Found at i:39151007 original size:10 final size:10
Alignment explanation
Indices: 39150912--39151009 Score: 68
Period size: 9 Copynumber: 10.4 Consensus size: 10
39150902 CTTTATAAAA
39150912 TTTTATA-AT
1 TTTTATATAT
39150921 TTTT-TATAT
1 TTTTATATAT
*
39150930 TTCTATAT-T
1 TTTTATATAT
39150939 TTTTATA-AT
1 TTTTATATAT
*
39150948 TTTT-TACGAT
1 TTTTATA-TAT
* *
39150958 TTTTATAAAA
1 TTTTATATAT
*
39150968 TTTTACA-AT
1 TTTTATATAT
39150977 TTTT-TATAT
1 TTTTATATAT
*
39150986 TTTTA-ACGAT
1 TTTTATA-TAT
39150996 TTTTATATAT
1 TTTTATATAT
39151006 TTTT
1 TTTT
39151010 CTAGTTTTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 19
0.71 0.09 0.19
Matches are distributed among these distances:
8 5 0.07
9 33 0.47
10 29 0.41
11 3 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Done.