Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 30 of 208
Found at i:11894052 original size:21 final size:22
Alignment explanation
Indices: 11894016--11894065 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11894006 TGAAAATTAC
*
11894016 TACATAATTGTTAAAACTTATA
1 TACAAAATTGTTAAAACTTATA
*
11894038 TACAAAATT-TTAAAATTTATA
1 TACAAAATTGTTAAAACTTATA
*
11894059 TAAAAAA
1 TACAAAA
11894066 CATAAATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAAATTGTTAAAACTTATA
Found at i:11897885 original size:22 final size:23
Alignment explanation
Indices: 11897860--11897919 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
11897850 TGGACTGAAT
11897860 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
11897882 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
11897904 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
11897920 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:11897887 original size:4 final size:4
Alignment explanation
Indices: 11897869--11897902 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
11897859 TATAAAAATT
11897869 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
11897903 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:11904359 original size:22 final size:23
Alignment explanation
Indices: 11904334--11904393 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
11904324 TGGACTGAAT
11904334 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
11904356 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
11904378 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
11904394 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:11904361 original size:4 final size:4
Alignment explanation
Indices: 11904343--11904376 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
11904333 TATAAAAATT
11904343 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
11904377 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:11912697 original size:11 final size:11
Alignment explanation
Indices: 11912681--11912711 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11912671 ATACCCATAC
11912681 CCCATACCTTG
1 CCCATACCTTG
*
11912692 CCCATACCTTT
1 CCCATACCTTG
11912703 CCCATACCT
1 CCCATACCT
11912712 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:11913286 original size:18 final size:18
Alignment explanation
Indices: 11913263--11913364 Score: 168
Period size: 18 Copynumber: 5.7 Consensus size: 18
11913253 CGTTTACAAT
11913263 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
11913281 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
*
11913299 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
11913317 ACTATTCACGTATACGGA
1 ACTATTCACGTATACGGC
*
11913335 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
11913353 ACTGTTCACGTA
1 ACTATTCACGTA
11913365 CACAGTAGTT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 80 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:11915016 original size:14 final size:14
Alignment explanation
Indices: 11914997--11915024 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11914987 AGACAGGTCG
11914997 AAAGGTCAAACGAC
1 AAAGGTCAAACGAC
11915011 AAAGGTCAAACGAC
1 AAAGGTCAAACGAC
11915025 TTCGATCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.07
Consensus pattern (14 bp):
AAAGGTCAAACGAC
Found at i:11917450 original size:11 final size:11
Alignment explanation
Indices: 11917434--11917464 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
11917424 ATACCCATAC
11917434 CCCATACCTTG
1 CCCATACCTTG
*
11917445 CCCATACCTTT
1 CCCATACCTTG
11917456 CCCATACCT
1 CCCATACCT
11917465 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:11927868 original size:6 final size:6
Alignment explanation
Indices: 11927848--11927896 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
11927838 CTGTCGCTTC
* * *
11927848 CACTGT CACTG- --CTGT CACTGT CACTAT CACTAT CACTGC CACTGT
1 CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT
11927893 CACT
1 CACT
11927897 AGCACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
6 33 0.92
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (6 bp):
CACTGT
Found at i:11927885 original size:18 final size:18
Alignment explanation
Indices: 11927862--11927902 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11927852 GTCACTGCTG
*
11927862 TCACTGTCACTATCACTA
1 TCACTGCCACTATCACTA
*
11927880 TCACTGCCACTGTCACTA
1 TCACTGCCACTATCACTA
*
11927898 GCACT
1 TCACT
11927903 ATTTGCTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTATCACTA
Found at i:11933018 original size:359 final size:359
Alignment explanation
Indices: 11932359--11933081 Score: 1419
Period size: 359 Copynumber: 2.0 Consensus size: 359
11932349 AATCAAAATA
11932359 AAATTTAATCCATCCTGCACTAAATTCTTGTGCTGATGATATAAGGATTTATTTACCATCAAACT
1 AAATTTAATCCATCCTGCACTAAATTCTTGTGCTGATGATATAAGGATTTATTTACCATCAAACT
11932424 GACCATGCAAATGATACAACCTTTTGCTGATACGCAAGAACTACCAACATTGGTAGACAGTGATA
66 GACCATGCAAATGATACAACCTTTTGCTGATACGCAAGAACTACCAACATTGGTAGACAGTGATA
*
11932489 GCTATCATTTTAAACAAGTTGACTAGATTTGCTTGCTTTTCTTCAAATGCATACTTTTTTCAGAG
131 GCTATCATTTTAAACAAGTTGACTAGATTTGCTTGCTTTTCTGCAAATGCATACTTTTTTCAGAG
11932554 GTTTAGGTATGTGAACAATCCTGCATTAAACTTTCATTTTTACATGTTTTACAACTGCTCCTACC
196 GTTTAGGTATGTGAACAATCCTGCATTAAACTTTCATTTTTACATGTTTTACAACTGCTCCTACC
11932619 TAAAGTGACCCTCTATCATATCTTGTACACATGGACTTAAAAGCCATATCATATTCAAAGTAGGA
261 TAAAGTGACCCTCTATCATATCTTGTACACATGGACTTAAAAGCCATATCATATTCAAAGTAGGA
11932684 ATCACCAAATTCAGAACCTAAATCATCAGATACT
326 ATCACCAAATTCAGAACCTAAATCATCAGATACT
11932718 AAATTTAATCCATCCTGCACTAAATTCTTGTGCTGATGATATAAGGATTTATTTACCATCAAACT
1 AAATTTAATCCATCCTGCACTAAATTCTTGTGCTGATGATATAAGGATTTATTTACCATCAAACT
*
11932783 GACCATGCAAATGATACAACCTTTTGTTGATACGCAAGAACTACCAACATTGGTAGACAGTGATA
66 GACCATGCAAATGATACAACCTTTTGCTGATACGCAAGAACTACCAACATTGGTAGACAGTGATA
*
11932848 GCTATCATTTTAAACAAGTTGACTAGATTTGCTTTCTTTTCTGCAAATGCATACTTTTTTCAGAG
131 GCTATCATTTTAAACAAGTTGACTAGATTTGCTTGCTTTTCTGCAAATGCATACTTTTTTCAGAG
11932913 GTTTAGGTATGTGAACAATCCTGCATTAAACTTTCATTTTTACATGTTTTACAACTGCTCCTACC
196 GTTTAGGTATGTGAACAATCCTGCATTAAACTTTCATTTTTACATGTTTTACAACTGCTCCTACC
11932978 TAAAGTGACCCTCTATCATATCTTGTACACATGGACTTAAAAGCCATATCATATTCAAAGTAGGA
261 TAAAGTGACCCTCTATCATATCTTGTACACATGGACTTAAAAGCCATATCATATTCAAAGTAGGA
11933043 ATCACCAAATTCAGAACCTAAATCATCAGATACT
326 ATCACCAAATTCAGAACCTAAATCATCAGATACT
11933077 AAATT
1 AAATT
11933082 AACCAACAAG
Statistics
Matches: 361, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
359 361 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (359 bp):
AAATTTAATCCATCCTGCACTAAATTCTTGTGCTGATGATATAAGGATTTATTTACCATCAAACT
GACCATGCAAATGATACAACCTTTTGCTGATACGCAAGAACTACCAACATTGGTAGACAGTGATA
GCTATCATTTTAAACAAGTTGACTAGATTTGCTTGCTTTTCTGCAAATGCATACTTTTTTCAGAG
GTTTAGGTATGTGAACAATCCTGCATTAAACTTTCATTTTTACATGTTTTACAACTGCTCCTACC
TAAAGTGACCCTCTATCATATCTTGTACACATGGACTTAAAAGCCATATCATATTCAAAGTAGGA
ATCACCAAATTCAGAACCTAAATCATCAGATACT
Found at i:11935114 original size:20 final size:20
Alignment explanation
Indices: 11935074--11935122 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11935064 AATTAAGTTT
*
11935074 ATTTAAA-TAAAAATATTAA
1 ATTTAAATTAAAAATATGAA
11935093 ATTTAAATTAAAAA-ATAGAA
1 ATTTAAATTAAAAATAT-GAA
11935113 ATTTATAATT
1 ATTTA-AATT
11935123 TTAAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 13 0.50
21 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATTTAAATTAAAAATATGAA
Found at i:11935328 original size:15 final size:14
Alignment explanation
Indices: 11935292--11935338 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
11935282 TACAATATAT
11935292 AATATATAATTTAA
1 AATATATAATTTAA
11935306 AA-ACTATAATTCTAA
1 AATA-TATAATT-TAA
*
11935321 AATATATAATTTTA
1 AATATATAATTTAA
11935335 AATA
1 AATA
11935339 GTTAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 15 0.52
15 12 0.41
16 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATATAATTTAA
Found at i:11935491 original size:20 final size:20
Alignment explanation
Indices: 11935466--11935530 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
11935456 AAATAATTTT
11935466 TATTTTTA-AACTTTTTTAAC
1 TATTTTTACAA-TTTTTTAAC
11935486 TATTTTTACAATTTTTT-A-
1 TATTTTTACAATTTTTTAAC
* *
11935504 TAGTTTTTACATTTTTTTTAC
1 TA-TTTTTACAATTTTTTAAC
11935525 -ATTTTT
1 TATTTTT
11935531 GTAACAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 2 0.05
19 20 0.50
20 16 0.40
21 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTTTTACAATTTTTTAAC
Found at i:11936482 original size:13 final size:13
Alignment explanation
Indices: 11936441--11936502 Score: 61
Period size: 13 Copynumber: 4.7 Consensus size: 13
11936431 TTAAACTAAA
* *
11936441 TTTTTCAAAAATAT
1 TTTTT-AAAAACAC
*
11936455 TTTTTAAAAATAC
1 TTTTTAAAAACAC
* *
11936468 TTTTTCACAACAC
1 TTTTTAAAAACAC
11936481 TTTTTAAAAACAC
1 TTTTTAAAAACAC
*
11936494 TTTTCAAAA
1 TTTTTAAAA
11936503 GTATTACTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
13 36 0.88
14 5 0.12
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTTAAAAACAC
Found at i:11936832 original size:40 final size:40
Alignment explanation
Indices: 11936774--11936854 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
11936764 TATAAATCAT
*
11936774 TAACACTATTATTAATATAACATCATTTCACATTAACATA
1 TAACACAATTATTAATATAACATCATTTCACATTAACATA
* * *
11936814 TAACACAATTATTGATATAACGTCATTTTACATTAACATA
1 TAACACAATTATTAATATAACATCATTTCACATTAACATA
11936854 T
1 T
11936855 TGCGTACATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.38
Consensus pattern (40 bp):
TAACACAATTATTAATATAACATCATTTCACATTAACATA
Found at i:11944094 original size:40 final size:39
Alignment explanation
Indices: 11944050--11944127 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
11944040 CCTCAAGAAA
11944050 GCACTTT-GTCCACGTGGACAAAAAACGCTTCCTTGAGGGC
1 GCACTTTGGTCCACGT-GA-AAAAAACGCTTCCTTGAGGGC
* * *
11944090 GCACTTTGGGTTCACGTGAACAAAGCGCTTCCTTGAGG
1 GCACTTT-GGTCCACGTGAAAAAAACGCTTCCTTGAGG
11944128 AATTACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 24 0.73
41 2 0.06
42 7 0.21
ACGTcount: A:0.23, C:0.26, G:0.27, T:0.24
Consensus pattern (39 bp):
GCACTTTGGTCCACGTGAAAAAAACGCTTCCTTGAGGGC
Found at i:11945018 original size:83 final size:83
Alignment explanation
Indices: 11944924--11945085 Score: 254
Period size: 83 Copynumber: 2.0 Consensus size: 83
11944914 ACTAAACCCC
* * *
11944924 AATCTATTTTTTAAAAAATTTTTAATTAATTTACTCGAA-TAATCCTAAACCCTAATTTATTTGA
1 AATCTAATTTTTAAAAAATTTATAATTAATTTACTC-AAGTAACCCTAAACCCTAATTTATTTGA
11944988 TTTTTTCCTTAAAAATCCT
65 TTTTTTCCTTAAAAATCCT
** *
11945007 AATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCTTAATTTATTTGAT
1 AATCTAATTTTTAAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTGAT
11945072 TTTTTCCTTAAAAA
66 TTTTTCCTTAAAAA
11945086 CCATAAACAC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 2 0.03
83 70 0.97
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (83 bp):
AATCTAATTTTTAAAAAATTTATAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTGAT
TTTTTCCTTAAAAATCCT
Found at i:11945126 original size:96 final size:96
Alignment explanation
Indices: 11945004--11945179 Score: 266
Period size: 96 Copynumber: 1.8 Consensus size: 96
11944994 CCTTAAAAAT
* **
11945004 CCTAATCTAATTTTTTTAAAATTTATAATTAATTTACTCAAGTAACCCTAAA-CCTTAATTTATT
1 CCTAATCTAATTTTTTTAAAATTTATAATTAATTTAATCAAAAAACCCTAAACCCTT-ATTTATT
*
11945068 TGATTTTTTCCTTAAAAACCATAAACACTAAAC
65 T-AATTTTTCCTTAAAAACCATAAACACTAAAC
* *
11945101 CCTAATCTAA-TTTTTTAAAATTTATAATTAATTTAATTAAAAAACCTTAAACCCTTATTTATTT
1 CCTAATCTAATTTTTTTAAAATTTATAATTAATTTAATCAAAAAACCCTAAACCCTTATTTATTT
11945165 AATTTTTCCTTAAAA
66 AATTTTTCCTTAAAA
11945180 CTCTAAAATC
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
95 14 0.19
96 44 0.61
97 14 0.19
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (96 bp):
CCTAATCTAATTTTTTTAAAATTTATAATTAATTTAATCAAAAAACCCTAAACCCTTATTTATTT
AATTTTTCCTTAAAAACCATAAACACTAAAC
Found at i:11949709 original size:35 final size:35
Alignment explanation
Indices: 11949670--11949736 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
11949660 GTTCAAATAA
11949670 AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
1 AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
* *
11949705 AAATATGGCTTGTGATTGATTCAAATAGAGAA
1 AAATATGGCATGTGACTGATTCAAATAGAGAA
11949737 CGTCATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (35 bp):
AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
Found at i:11952000 original size:25 final size:25
Alignment explanation
Indices: 11951945--11952009 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
11951935 GGTGGGACAG
* **
11951945 AGAAGAAAGAAAAGGAATTAAAAAA
1 AGAAGAAAAAAAAGGAAGGAAAAAA
* *
11951970 AAAAGAAATAAAAGG-AGGAAAAGAA
1 AGAAGAAAAAAAAGGAAGGAAAA-AA
11951995 AGAAGAGAAAAAAAG
1 AGAAGA-AAAAAAAG
11952010 AAAAGAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 5 0.16
25 20 0.62
26 7 0.22
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (25 bp):
AGAAGAAAAAAAAGGAAGGAAAAAA
Found at i:11957338 original size:15 final size:15
Alignment explanation
Indices: 11957318--11957347 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11957308 ACATTCAATT
11957318 TTATTTTTTATCATG
1 TTATTTTTTATCATG
11957333 TTATTTTTTATCATG
1 TTATTTTTTATCATG
11957348 AACAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (15 bp):
TTATTTTTTATCATG
Found at i:11963679 original size:17 final size:17
Alignment explanation
Indices: 11963655--11963688 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11963645 GTATTTAATA
11963655 AATTACAC-AAATTTAT
1 AATTACACTAAATTTAT
11963671 AATTAACACTAAATTTAT
1 AATT-ACACTAAATTTAT
11963689 TCCATAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTACACTAAATTTAT
Found at i:11966700 original size:28 final size:29
Alignment explanation
Indices: 11966669--11966729 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
11966659 GAAATTAATT
*
11966669 CTATCTAATTTTAA-AATCAATTTTTACA
1 CTATCTAATTTTAACAAACAATTTTTACA
**
11966697 CTAT-TTTTTTTAACAAACAATTTTTACA
1 CTATCTAATTTTAACAAACAATTTTTACA
11966725 CTATC
1 CTATC
11966730 ATAAATGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (29 bp):
CTATCTAATTTTAACAAACAATTTTTACA
Found at i:11971397 original size:16 final size:16
Alignment explanation
Indices: 11971360--11971390 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11971350 GTTGGGTTAG
11971360 GGTTTTATGGATTTTA
1 GGTTTTATGGATTTTA
*
11971376 GGTTTTATGGGTTTT
1 GGTTTTATGGATTTT
11971391 GAGTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (16 bp):
GGTTTTATGGATTTTA
Found at i:11971411 original size:9 final size:9
Alignment explanation
Indices: 11971398--11971448 Score: 59
Period size: 9 Copynumber: 5.4 Consensus size: 9
11971388 TTTGAGTTTT
11971398 TTTTTATATA
1 TTTTT-TATA
*
11971408 TTTTTTATG
1 TTTTTTATA
11971417 TTTTGTATATA
1 TTTT-T-TATA
11971428 TTTTTTAT-
1 TTTTTTATA
11971436 TTTTTTATA
1 TTTTTTATA
11971445 TTTT
1 TTTT
11971449 CTTGAGATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
8 8 0.22
9 14 0.39
10 7 0.19
11 7 0.19
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTTTATA
Found at i:11971420 original size:20 final size:19
Alignment explanation
Indices: 11971396--11971445 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 19
11971386 GTTTTGAGTT
11971396 TTTTTTTATATATTTTTTA
1 TTTTTTTATATATTTTTTA
*
11971415 TGTTTTGTATATATTTTTTA
1 T-TTTTTTATATATTTTTTA
11971435 TTTTTTTATAT
1 TTTTTTTATAT
11971446 TTTCTTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTTTTATATATTTTTTA
Found at i:11971503 original size:15 final size:15
Alignment explanation
Indices: 11971483--11971515 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11971473 TTTAATTTGA
11971483 TATTTACAACC-ATCG
1 TATTTAC-ACCAATCG
11971498 TATTTACACCAATCG
1 TATTTACACCAATCG
11971513 TAT
1 TAT
11971516 ATTTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
TATTTACACCAATCG
Found at i:11973998 original size:37 final size:38
Alignment explanation
Indices: 11973940--11974053 Score: 101
Period size: 40 Copynumber: 3.0 Consensus size: 38
11973930 TGTCAATTTA
*
11973940 TTACTTCAGATTTATTCGATGA-AGCACTGGGTGCCAAC
1 TTACTTCAGATTTAATCGATGAGA-CACTGGGTGCCAAC
* * *
11973978 TTACTTCTG-TTTAATCGATGAGACACTGGGTGTCAATT
1 TTACTTCAGATTTAATCGATGAGACACTGGGTGCCAA-C
* *
11974016 TACTACTTC-GAATT-ATCCGATGAGGCACTGGGTGCCAA
1 T--TACTTCAGATTTAAT-CGATGAGACACTGGGTGCCAA
11974054 ATTGGTGTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
37 23 0.37
38 10 0.16
39 3 0.05
40 27 0.43
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (38 bp):
TTACTTCAGATTTAATCGATGAGACACTGGGTGCCAAC
Found at i:11974037 original size:40 final size:39
Alignment explanation
Indices: 11973914--11974049 Score: 136
Period size: 37 Copynumber: 3.5 Consensus size: 39
11973904 ATAATTCGAG
* *
11973914 TCGATGAGACACTAGGTGTCAATTTATTACTTCAGATTTA
1 TCGATGAGACACTGGGTGTCAATTTACTACTTC-GATTTA
* * *
11973954 TTCGATGA-AGCACTGGGTGCCAACTTACTTC-T-G-TTTAA
1 -TCGATGAGA-CACTGGGTGTCAATTTACTACTTCGATTT-A
*
11973992 TCGATGAGACACTGGGTGTCAATTTACTACTTCGAATTA
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGATTTA
*
11974031 TCCGATGAGGCACTGGGTG
1 T-CGATGAGACACTGGGTG
11974050 CCAAATTGGT
Statistics
Matches: 78, Mismatches: 10, Indels: 15
0.76 0.10 0.15
Matches are distributed among these distances:
37 28 0.36
38 4 0.05
39 3 0.04
40 20 0.26
41 23 0.29
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTACTACTTCGATTTA
Found at i:11976677 original size:52 final size:48
Alignment explanation
Indices: 11976658--11976860 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
11976648 TGACAAGTGG
* *
11976658 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
11976704 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
11976756 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
11976802 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
11976848 AAAGTGATAAGTG
1 AAAGTGATAAGTG
11976861 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:11976712 original size:98 final size:98
Alignment explanation
Indices: 11976592--11976860 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
11976582 TTTGAGTACT
*
11976592 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
11976657 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
11976690 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
11976755 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
11976788 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
11976853 GATAAGTG
65 GAAAAGTG
11976861 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:11976868 original size:37 final size:37
Alignment explanation
Indices: 11976824--11976969 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
11976814 GATAGCTTTA
*
11976824 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
11976861 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
11976898 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
11976935 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
11976970 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:11982953 original size:17 final size:18
Alignment explanation
Indices: 11982917--11982956 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
11982907 TTTAACTATT
*
11982917 ATTTTAAATCTTTATGTA
1 ATTTTAAATCTTTATATA
*
11982935 ATTTTACAT-TTTATATA
1 ATTTTAAATCTTTATATA
11982952 ATTTT
1 ATTTT
11982957 TTAGTGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (18 bp):
ATTTTAAATCTTTATATA
Found at i:11983482 original size:26 final size:25
Alignment explanation
Indices: 11983452--11983512 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
11983442 TATTATTTTT
11983452 ATATAAAAATAAATTTTAAAAATA-TA
1 ATATAAAAATAAA--TTAAAAATATTA
* *
11983478 ATATATTAAATACATTAAAAATATTA
1 ATATA-AAAATAAATTAAAAATATTA
*
11983504 AAATAAAAA
1 ATATAAAAA
11983513 ATTCAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 12 0.41
26 11 0.38
27 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAAAAATAAATTAAAAATATTA
Found at i:11990230 original size:10 final size:10
Alignment explanation
Indices: 11990215--11990242 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
11990205 TACTATTTTT
11990215 TTATTTTACA
1 TTATTTTACA
11990225 TTATTTTACA
1 TTATTTTACA
11990235 TTATTTTA
1 TTATTTTA
11990243 GTACATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTTTACA
Found at i:11990702 original size:9 final size:9
Alignment explanation
Indices: 11990682--11990739 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
11990672 CAATTTAGGG
*
11990682 TAATTAGGT
1 TAATTCGGT
*
11990691 TAATTCGAT
1 TAATTCGGT
11990700 TAATTCGGT
1 TAATTCGGT
11990709 TAATTCGGT
1 TAATTCGGT
*
11990718 TAA-TCGGG
1 TAATTCGGT
*
11990726 TAATTCGGG
1 TAATTCGGT
11990735 TAATT
1 TAATT
11990740 TTTAACCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.16
9 37 0.84
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (9 bp):
TAATTCGGT
Found at i:11990729 original size:17 final size:17
Alignment explanation
Indices: 11990691--11990738 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
11990681 GTAATTAGGT
* *
11990691 TAATTCGATTAATTCGGT
1 TAATTCGGTTAA-TCGGG
11990709 TAATTCGGTTAATCGGG
1 TAATTCGGTTAATCGGG
*
11990726 TAATTCGGGTAAT
1 TAATTCGGTTAAT
11990739 TTTTAACCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (17 bp):
TAATTCGGTTAATCGGG
Found at i:11990738 original size:26 final size:27
Alignment explanation
Indices: 11990679--11990739 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
11990669 GGGCAATTTA
*
11990679 GGGTAATTAGGTTAATTCGATTAATTC
1 GGGTAATTAGGTTAATTCGAGTAATTC
* * *
11990706 GGTTAATTCGGTTAA-TCGGGTAATTC
1 GGGTAATTAGGTTAATTCGAGTAATTC
11990732 GGGTAATT
1 GGGTAATT
11990740 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 16 0.55
27 13 0.45
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (27 bp):
GGGTAATTAGGTTAATTCGAGTAATTC
Found at i:11991076 original size:8 final size:8
Alignment explanation
Indices: 11991063--11991098 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
11991053 TTAAAAAATA
11991063 TATTATTT
1 TATTATTT
11991071 TATTATTT
1 TATTATTT
11991079 TATTATTT
1 TATTATTT
11991087 TACATTATTT
1 T--ATTATTT
11991097 TA
1 TA
11991099 GTACATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.69
10 8 0.31
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTATTT
Found at i:11991417 original size:152 final size:149
Alignment explanation
Indices: 11991144--11991636 Score: 684
Period size: 155 Copynumber: 3.2 Consensus size: 149
11991134 TTTTTTATTG
* * * *
11991144 AAAGTAAGAAAATCCGAGAAAAAATACGAACAAAAGGCTGAAATAAGAGTTTTTTTAAAATTTAT
1 AAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGCCGAAATAAG-GTTTTTTT-AAATTTAT
11991209 TTAAAAAACACACTAAATTAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAATAAAA
64 TTAAAAAACACACTAAATTAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAA-AAAA
*
11991274 -TACAAAAATAATATATTTTTTA
128 TTA-AAAAATAGTATATTTTTTA
*
11991296 TTGAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGATTTTTT-AATTTA
1 ---AAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAATTTA
* *
11991360 TTTAAAAAACACACTAAATTAATACATTTCAAATATAATGTACTAAAATAATTTAAAATAAAAAA
63 TTTAAAAAACACACTAAATTAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAAAAAA
11991425 TTTAAAAAATAGTATATTTTTTA
128 -TTAAAAAATAGTATATTTTTTA
* ** * *
11991448 AAAGTAATAAAATTCGGGAAAAAAAATATTAACATAGGGTCGAAATAAGGGTTTTTTTTAAATTT
1 AAAGTAATAAAATCCGGG--AAAAAATACGAACAAAGGGCCGAAATAA-GG-TTTTTTTAAATTT
* *
11991513 ATTTAAAAAAACACAGTAAATTAATACATTTCAAATATGATATACTAAAATAATGTAAAATTAAA
62 ATTT-AAAAAACACACTAAATTAATACATTTCAAATATGATGTACTAAAATAATGTAAAA-TAAA
11991578 AAATTAAAAAATAGTATATTTTTTA
125 AAATTAAAAAATAGTATATTTTTTA
* *
11991603 AAAGTAATAAAATCTGGAAAAAAAATACGAACAA
1 AAAGTAATAAAATCCGG-GAAAAAATACGAACAA
11991637 TTGGTGCCGC
Statistics
Matches: 304, Mismatches: 24, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
149 17 0.06
151 28 0.09
152 85 0.28
153 8 0.03
154 28 0.09
155 131 0.43
156 7 0.02
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (149 bp):
AAAGTAATAAAATCCGGGAAAAAATACGAACAAAGGGCCGAAATAAGGTTTTTTTAAATTTATTT
AAAAAACACACTAAATTAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAAAAAATTA
AAAAATAGTATATTTTTTA
Found at i:11991428 original size:14 final size:15
Alignment explanation
Indices: 11991403--11991431 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11991393 TATAATGTAC
11991403 TAAAATAATTTAAAA
1 TAAAATAATTTAAAA
11991418 TAAAA-AATTTAAAA
1 TAAAATAATTTAAAA
11991432 AATAGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATAATTTAAAA
Found at i:11994890 original size:22 final size:24
Alignment explanation
Indices: 11994857--11994903 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
11994847 TATAAAAATA
11994857 TTATTAATTTT-ACAATATATTTT
1 TTATTAATTTTAACAATATATTTT
*
11994880 TTATT-ATTTTAATAATATATTTT
1 TTATTAATTTTAACAATATATTTT
11994903 T
1 T
11994904 ACATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATTAATTTTAACAATATATTTT
Found at i:11994910 original size:23 final size:24
Alignment explanation
Indices: 11994870--11994918 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
11994860 TTAATTTTAC
*
11994870 AATATATTTTTTATTATTTTA-AT
1 AATATATTTTTTAATATTTTATAT
11994893 AATATA-TTTTTACATATTTTATAT
1 AATATATTTTTTA-ATATTTTATAT
11994917 AA
1 AA
11994919 AAAATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATATTTTTTAATATTTTATAT
Found at i:11997741 original size:13 final size:13
Alignment explanation
Indices: 11997725--11997803 Score: 71
Period size: 13 Copynumber: 6.5 Consensus size: 13
11997715 AATTTTGAAT
11997725 TATTTAATGATAA
1 TATTTAATGATAA
*
11997738 TATTTAA--A-AT
1 TATTTAATGATAA
*
11997748 TATTTAACGATAA
1 TATTTAATGATAA
*
11997761 TATTTAA--A-AT
1 TATTTAATGATAA
*
11997771 TATTTAGTGATAA
1 TATTTAATGATAA
*
11997784 TATTTAGTGATAA
1 TATTTAATGATAA
11997797 TATTTAA
1 TATTTAA
11997804 AAAACAATCT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 15 0.28
11 2 0.04
12 2 0.04
13 35 0.65
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (13 bp):
TATTTAATGATAA
Found at i:11997742 original size:23 final size:23
Alignment explanation
Indices: 11997722--11997789 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
11997712 TTAAATTTTG
11997722 AATTATTTAATGATAATATTTAA
1 AATTATTTAATGATAATATTTAA
*
11997745 AATTATTTAACGATAATATTTAA
1 AATTATTTAATGATAATATTTAA
*
11997768 AATTATTTAGTGATAATATTTA
1 AATTATTTAATGATAATATTTA
11997790 GTGATAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (23 bp):
AATTATTTAATGATAATATTTAA
Found at i:12012813 original size:31 final size:29
Alignment explanation
Indices: 12012743--12012813 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
12012733 AAATCAAAAT
** *
12012743 TTCATGTATAAAATTACACAAAATTAAAT
1 TTCATGTATAAAATTACACAAAAGCAAAG
*
12012772 TTCATATATAAAATTACA-AGTTAAAGCAAAG
1 TTCATGTATAAAATTACACA---AAAGCAAAG
12012803 TTCATGTATAA
1 TTCATGTATAA
12012814 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.03
29 17 0.50
31 16 0.47
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (29 bp):
TTCATGTATAAAATTACACAAAAGCAAAG
Found at i:12017681 original size:35 final size:38
Alignment explanation
Indices: 12017634--12017711 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
12017624 TTTTTAATAA
12017634 ATTAAATAAAAATAATAC-T-C-TGGTAAAAGAAAGTAC
1 ATTAAATAAAAATAAT-CTTACATGGTAAAAGAAAGTAC
12017670 ATTAAA-AAAAATAATCTTTACAATGGTAAAAGAAAGTAC
1 ATTAAATAAAAATAATC-TTAC-ATGGTAAAAGAAAGTAC
12017709 ATT
1 ATT
12017712 TATAAGAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
34 1 0.03
35 9 0.24
36 7 0.19
37 1 0.03
39 19 0.51
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (38 bp):
ATTAAATAAAAATAATCTTACATGGTAAAAGAAAGTAC
Found at i:12018611 original size:5 final size:5
Alignment explanation
Indices: 12018601--12018625 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12018591 AGAAAGAAAG
12018601 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
12018626 GCGTATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:12027583 original size:29 final size:30
Alignment explanation
Indices: 12027549--12027643 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
12027539 TGTATATGAT
*
12027549 ACATG-AACTTTAATTTGGTGT-AATTATAC
1 ACATGAAACTTTAATTTGGT-TCAAATATAC
* *
12027578 ACATGAAACTTTGATTGTGGTTCAAATATAT
1 ACATGAAACTTTAATT-TGGTTCAAATATAC
* *
12027609 AAATGAAACTTTAATTTTGATTC-AATCATAC
1 ACATGAAACTTTAA-TTTGGTTCAAAT-ATAC
12027640 ACAT
1 ACAT
12027644 TTAATGAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
29 5 0.09
30 13 0.25
31 33 0.62
32 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (30 bp):
ACATGAAACTTTAATTTGGTTCAAATATAC
Found at i:12040833 original size:31 final size:29
Alignment explanation
Indices: 12040763--12040836 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
12040753 GGCTCAGGTT
* *
12040763 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
12040792 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
12040823 ACATTTTAGTCACT
1 ACATTTTAGTCACT
12040837 AAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:12042266 original size:24 final size:24
Alignment explanation
Indices: 12042224--12042272 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
12042214 ACAGTAATCC
* *
12042224 TTTATTTTATCTTATCTTATTTTA
1 TTTACTTTATCTTATCTTAATTTA
12042248 TTTACTTTATCTT-TGCTTAATTTA
1 TTTACTTTATCTTAT-CTTAATTTA
12042272 T
1 T
12042273 AGGATTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTACTTTATCTTATCTTAATTTA
Found at i:12042461 original size:8 final size:8
Alignment explanation
Indices: 12042442--12042471 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12042432 GCATGGCATC
12042442 CAATCACTT
1 CAATC-CTT
12042451 CAATCCTT
1 CAATCCTT
12042459 CAATCCTT
1 CAATCCTT
12042467 CAATC
1 CAATC
12042472 ATATTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (8 bp):
CAATCCTT
Found at i:12047164 original size:58 final size:58
Alignment explanation
Indices: 12047094--12047207 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
12047084 TTTCAAGGTT
*
12047094 AGCCAGTTTCCGTCCATC-AACAGGGTTTCATTGTATTCAATTTAGTAGTGTGATTGTC
1 AGCCAGTTTCCGTCCATCGAA-AGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
*
12047152 AGCCAGTTTCCGTCCATCGAAAGGGTTTCTTTGTATTCAATTTAATAGTGTGATTG
1 AGCCAGTTTCCGTCCATCGAAAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
12047208 AATATCAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
58 51 0.96
59 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.39
Consensus pattern (58 bp):
AGCCAGTTTCCGTCCATCGAAAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
Found at i:12062516 original size:30 final size:32
Alignment explanation
Indices: 12062456--12062519 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
12062446 CACTTATTTT
12062456 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
12062489 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
12062520 ATACATATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:12062781 original size:41 final size:41
Alignment explanation
Indices: 12062736--12062848 Score: 217
Period size: 41 Copynumber: 2.8 Consensus size: 41
12062726 ACCGGCTCTT
*
12062736 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
12062777 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
12062818 AGCCTGCTAGACTTATAGTCTGAAATGTGTC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTC
12062849 TGTAACACCC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:12063510 original size:37 final size:37
Alignment explanation
Indices: 12063449--12063595 Score: 235
Period size: 37 Copynumber: 4.0 Consensus size: 37
12063439 TACGTATGAT
* *
12063449 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
12063484 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
12063521 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
* *
12063558 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
12063595 C
1 C
12063596 GAAGCTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:12063637 original size:52 final size:52
Alignment explanation
Indices: 12063558--12063774 Score: 293
Period size: 52 Copynumber: 4.2 Consensus size: 52
12063548 TAAGTGTAGC
* *
12063558 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
12063611 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
12063663 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * ** *
12063709 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
12063761 CACTTTGTCACTTG
1 CACTTT-TCACTTG
12063775 ATCAGAAGTA
Statistics
Matches: 145, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.30
49 1 0.01
52 86 0.59
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:12063689 original size:98 final size:98
Alignment explanation
Indices: 12063557--12063780 Score: 394
Period size: 98 Copynumber: 2.3 Consensus size: 98
12063547 ATAAGTGTAG
* *
12063557 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
*
12063622 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
* *
12063655 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
*
12063720 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
12063753 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
12063781 AGTACTCAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 119 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
Found at i:12072953 original size:30 final size:32
Alignment explanation
Indices: 12072893--12072956 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
12072883 CACTTATTTT
12072893 CACCTATGCCGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
12072926 CACCTATGCCGAATGCAACATATATATATAT
1 CACCTATGCCGAATGCAACACATAAATATAT
12072957 ACATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.27
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Found at i:12073216 original size:41 final size:41
Alignment explanation
Indices: 12073171--12073326 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
12073161 ACCGGCTCTT
*
12073171 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
12073212 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
12073253 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
* *
12073294 AGCCTGCTAGACTTATAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
12073327 TAACGATAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:12076171 original size:22 final size:23
Alignment explanation
Indices: 12076142--12076216 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
12076132 ATTAAATTGA
12076142 TTAT-ATAATTTATTAAAAT-AT
1 TTATAATAATTTATTAAAATAAT
**
12076163 TTATAATAAAATATTAGAAGATACAT
1 TTATAATAATTTATTA-AA-ATA-AT
*
12076189 TT-TAATAATTTATTAAATTAAT
1 TTATAATAATTTATTAAAATAAT
12076211 TTATAA
1 TTATAA
12076217 ATTCACATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.09
22 13 0.30
23 7 0.16
24 4 0.09
25 11 0.26
26 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (23 bp):
TTATAATAATTTATTAAAATAAT
Found at i:12078767 original size:6 final size:6
Alignment explanation
Indices: 12078756--12078784 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12078746 TTTAGATATC
12078756 AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAAT
12078785 CCACTTCTTA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:12088800 original size:21 final size:20
Alignment explanation
Indices: 12088776--12088818 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12088766 AATCTAATTA
12088776 TTTATGATTTTAATCAATTTT
1 TTTAT-ATTTTAATCAATTTT
* * *
12088797 TTTATTTTTTTATTAATTTT
1 TTTATATTTTAATCAATTTT
12088817 TT
1 TT
12088819 AGAAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATATTTTAATCAATTTT
Found at i:12091480 original size:2 final size:2
Alignment explanation
Indices: 12091467--12091498 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12091457 CTCATCCACA
*
12091467 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12091499 CCACTCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:12091890 original size:14 final size:14
Alignment explanation
Indices: 12091873--12091905 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12091863 TGTCTTTGGA
*
12091873 TTTTCTTTTTT-CC
1 TTTTTTTTTTTCCC
12091886 TTTTTTTTTTTCCC
1 TTTTTTTTTTTCCC
12091900 TTTTTT
1 TTTTTT
12091906 GGTTTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTTCCC
Found at i:12098073 original size:19 final size:19
Alignment explanation
Indices: 12098051--12098095 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12098041 TTATATTTTG
*
12098051 AAATATAATT-TATATAAAA
1 AAATACAATTATA-ATAAAA
12098070 AAATACAATTATAATAAAA
1 AAATACAATTATAATAAAA
*
12098089 CAATACA
1 AAATACA
12098096 TTCATACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATACAATTATAATAAAA
Found at i:12099822 original size:13 final size:13
Alignment explanation
Indices: 12099801--12099833 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12099791 GAGAGTATTG
*
12099801 CATGCGCCCTCTA
1 CATGGGCCCTCTA
12099814 CATGGGCCCTCTA
1 CATGGGCCCTCTA
12099827 CATGGGC
1 CATGGGC
12099834 TTCTGCCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.21
Consensus pattern (13 bp):
CATGGGCCCTCTA
Found at i:12108628 original size:26 final size:26
Alignment explanation
Indices: 12108598--12108648 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
12108588 TTCAAAGAAT
*
12108598 TTTGATCTCTGTTGAAAAATAATTCA
1 TTTGATATCTGTTGAAAAATAATTCA
*
12108624 TTTGATATCTGTTGACAAATAATTC
1 TTTGATATCTGTTGAAAAATAATTC
12108649 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGAAAAATAATTCA
Found at i:12126192 original size:20 final size:19
Alignment explanation
Indices: 12126164--12126204 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12126154 ATCAAAGTAA
*
12126164 TTTTCAAAATTTGAAAATAT
1 TTTTCAAAA-TTCAAAATAT
*
12126184 TTTTTAAAATTCAAAATAT
1 TTTTCAAAATTCAAAATAT
12126203 TT
1 TT
12126205 ATAGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (19 bp):
TTTTCAAAATTCAAAATAT
Found at i:12126212 original size:19 final size:20
Alignment explanation
Indices: 12126177--12126219 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
12126167 TCAAAATTTG
*
12126177 AAAATATTTTTTAAAATTC-
1 AAAATATTTTATAAAATTCT
12126196 AAAATA-TTTATAGAAATTCT
1 AAAATATTTTATA-AAATTCT
12126216 AAAA
1 AAAA
12126220 AAATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (20 bp):
AAAATATTTTATAAAATTCT
Found at i:12126226 original size:20 final size:19
Alignment explanation
Indices: 12126190--12126238 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
12126180 ATATTTTTTA
* *
12126190 AAATTCAAAATATTTATAG
1 AAATTCAAAAAAATTATAG
12126209 AAATTCTAAAAAAATTAT--
1 AAATTC-AAAAAAATTATAG
12126227 AAATT-AAAAAAA
1 AAATTCAAAAAAA
12126239 ACTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 7 0.26
18 5 0.19
19 6 0.22
20 9 0.33
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATTCAAAAAAATTATAG
Found at i:12126592 original size:21 final size:21
Alignment explanation
Indices: 12126568--12126608 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12126558 ACCTTTTCTA
*
12126568 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
*
12126589 AAGTTAAAAGGCAAATCTAT
1 AAGTTAAAAGGCAAAACTAT
12126609 GTTGTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:12128078 original size:20 final size:21
Alignment explanation
Indices: 12128055--12128093 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12128045 ACTAAAAAAA
12128055 TTAAATAATAAAAT-AAAAGT
1 TTAAATAATAAAATGAAAAGT
*
12128075 TTAAATATTAAAATGAAAA
1 TTAAATAATAAAATGAAAA
12128094 AAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
TTAAATAATAAAATGAAAAGT
Found at i:12134333 original size:3 final size:3
Alignment explanation
Indices: 12134325--12134367 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
12134315 TGGAATCCAA
12134325 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12134368 ATTGCAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12137657 original size:21 final size:20
Alignment explanation
Indices: 12137628--12137676 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 20
12137618 TCTCTAAAAT
12137628 TTTGATAAA-TATTTATATTTA
1 TTTG-TAAAGTATTT-TATTTA
12137649 TCTTGTAAATGTATTTTATTTA
1 T-TTGTAAA-GTATTTTATTTA
12137671 TTTGTA
1 TTTGTA
12137677 GAGGCAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.40
22 10 0.40
23 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTGTAAAGTATTTTATTTA
Found at i:12138414 original size:24 final size:24
Alignment explanation
Indices: 12138386--12138434 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12138376 AAATTATGTC
12138386 AATCTTCTTATTAGTCTTCAATAA
1 AATCTTCTTATTAGTCTTCAATAA
12138410 AATCTTCTTATTAGTCTTCAATAA
1 AATCTTCTTATTAGTCTTCAATAA
12138434 A
1 A
12138435 GGGATAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (24 bp):
AATCTTCTTATTAGTCTTCAATAA
Found at i:12139459 original size:54 final size:54
Alignment explanation
Indices: 12139396--12139505 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
12139386 GCGGTGTGTC
12139396 TAACTTATTTTTTGTCTCATGCTACAGTATTTAATTTCACCTCACCGTTGTTTT
1 TAACTTATTTTTTGTCTCATGCTACAGTATTTAATTTCACCTCACCGTTGTTTT
12139450 TAACTTATTTTTTGTCTCATGCTACAGTATTTAATTTCACCTCACCGTTGTTTT
1 TAACTTATTTTTTGTCTCATGCTACAGTATTTAATTTCACCTCACCGTTGTTTT
12139504 TA
1 TA
12139506 CACAAACAAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.21, C:0.20, G:0.09, T:0.50
Consensus pattern (54 bp):
TAACTTATTTTTTGTCTCATGCTACAGTATTTAATTTCACCTCACCGTTGTTTT
Found at i:12144167 original size:10 final size:12
Alignment explanation
Indices: 12144138--12144166 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
12144128 TCTTATATAG
12144138 ATATATAACTTT
1 ATATATAACTTT
12144150 ATATATAACTTT
1 ATATATAACTTT
12144162 ATATA
1 ATATA
12144167 AAATTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATAACTTT
Found at i:12147765 original size:21 final size:22
Alignment explanation
Indices: 12147741--12147813 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
12147731 TTTAACAAAG
12147741 TTATAATATTTTTTTATAA-TT
1 TTATAATATTTTTTTATAATTT
*
12147762 TTAT-ATA-ATTTTTATAATTTT
1 TTATAATATTTTTTTATAA-TTT
* *
12147783 TTATAATATTTTTCATATTATTT
1 TTATAATATTTTT-TTATAATTT
*
12147806 TTAAAATA
1 TTATAATA
12147814 CAAATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.21
20 3 0.07
21 10 0.24
22 3 0.07
23 13 0.31
24 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATAATATTTTTTTATAATTT
Found at i:12147774 original size:41 final size:43
Alignment explanation
Indices: 12147690--12147775 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 43
12147680 ACCTTCAAAA
*
12147690 TAACAAATATATATATATTTCTTTTATAATCTTCATAACTTTT
1 TAACAAATATATATATATTTCTTTTATAATCTTCATAAATTTT
*
12147733 TAACAAAGT-TATA-ATATTT-TTTTATAAT-TTTATATAATTTT
1 TAACAAA-TATATATATATTTCTTTTATAATCTTCATA-AATTTT
12147774 TA
1 TA
12147776 TAATTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 5 0.13
41 16 0.41
42 6 0.15
43 11 0.28
44 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.53
Consensus pattern (43 bp):
TAACAAATATATATATATTTCTTTTATAATCTTCATAAATTTT
Found at i:12147775 original size:19 final size:18
Alignment explanation
Indices: 12147751--12147892 Score: 82
Period size: 17 Copynumber: 7.7 Consensus size: 18
12147741 TTATAATATT
12147751 TTTTTATAATTTTATATAA
1 TTTTTATAATTTTATA-AA
12147770 TTTTTATAATTTTTTATAATA
1 TTTTTATAA--TTTTATAA-A
12147791 TTTTTCATATTATTTT-TAAA
1 TTTTT-ATA--ATTTTATAAA
* **
12147811 -ATACA-AATTTTATAAA
1 TTTTTATAATTTTATAAA
*
12147827 TTTTCTATAATTTTCA-CAA
1 TTTT-TATAATTTT-ATAAA
* *
12147846 TTTTTA-ATTTATTAT-AT
1 TTTTTATAATT-TTATAAA
*
12147863 TTTTTATAAATTTA-AAA
1 TTTTTATAATTTTATAAA
12147880 TTTTTATAATTTT
1 TTTTTATAATTTT
12147893 TTTTCTATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.05
16 4 0.04
17 29 0.31
18 8 0.08
19 22 0.23
20 3 0.03
21 16 0.17
22 7 0.07
24 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTATAAA
Found at i:12147777 original size:9 final size:9
Alignment explanation
Indices: 12147751--12147893 Score: 76
Period size: 10 Copynumber: 14.6 Consensus size: 9
12147741 TTATAATATT
12147751 TTTTTATAA
1 TTTTTATAA
12147760 TTTTATATAA
1 TTTT-TATAA
12147770 TTTTTATAA
1 TTTTTATAA
12147779 TTTTTTATAATA
1 -TTTTTAT-A-A
12147791 TTTTTCATATTA
1 TTTTT-ATA--A
12147803 TTTTTAAAATACAA
1 TTTTT---AT--AA
*
12147817 ATTTTATAAA
1 TTTTTAT-AA
12147827 TTTTCTATAA
1 TTTT-TATAA
* *
12147837 TTTTCACAA
1 TTTTTATAA
12147846 -TTTT-TAA
1 TTTTTATAA
*
12147853 TTTATTATAT
1 TTT-TTATAA
12147863 TTTTTATAA
1 TTTTTATAA
* *
12147872 -ATTTAAAA
1 TTTTTATAA
12147880 TTTTTATAA
1 TTTTTATAA
12147889 TTTTT
1 TTTTT
12147894 TTTCTATATT
Statistics
Matches: 105, Mismatches: 14, Indels: 30
0.70 0.09 0.20
Matches are distributed among these distances:
7 2 0.02
8 11 0.10
9 30 0.29
10 32 0.30
11 12 0.11
12 10 0.10
14 7 0.07
16 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12147855 original size:35 final size:34
Alignment explanation
Indices: 12147819--12147885 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
12147809 AAATACAAAT
* *
12147819 TTTA-TAAATTTTCTATAATTTTCACAATTTTTAA
1 TTTATTAAATTTTCTATAAATTT-AAAATTTTTAA
* *
12147853 TTTATTATATTTTTTATAAATTTAAAATTTTTA
1 TTTATTAAATTTTCTATAAATTTAAAATTTTTA
12147886 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTATTAAATTTTCTATAAATTTAAAATTTTTAA
Found at i:12147893 original size:26 final size:25
Alignment explanation
Indices: 12147819--12147893 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
12147809 AAATACAAAT
* *
12147819 TTTATAAATTTTCTATAATTTTCACAA
1 TTTA-AAATTTT-TATAATTTTTAAAA
** *
12147846 TTTTTAATTTATTATATTTTTTATAAA
1 TTTAAAATTT-TTATAATTTTTA-AAA
12147873 TTTAAAATTTTTATAATTTTT
1 TTTAAAATTTTTATAATTTTT
12147894 TTTCTATATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
26 24 0.63
27 14 0.37
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTAAAATTTTTATAATTTTTAAAA
Found at i:12147980 original size:31 final size:31
Alignment explanation
Indices: 12147945--12148004 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
12147935 TGTTAAAAAT
*
12147945 TCTTATAAAATAA-TTAAAAACTCAATTAAGA
1 TCTTAAAAAATAATTTAAAAAC-CAATTAAGA
12147976 TCTTAAAAAATAATTTAAAAACCAATTAA
1 TCTTAAAAAATAATTTAAAAACCAATTAA
12148005 ACAGTCACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.32
Consensus pattern (31 bp):
TCTTAAAAAATAATTTAAAAACCAATTAAGA
Found at i:12151818 original size:7 final size:7
Alignment explanation
Indices: 12151808--12151841 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
12151798 CATAATATAT
12151808 AACCTTG
1 AACCTTG
12151815 AACCCTTG
1 AA-CCTTG
12151823 AACCTTG
1 AACCTTG
*
12151830 AGCCTTG
1 AACCTTG
12151837 AACCT
1 AACCT
12151842 AAACATGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.26
Consensus pattern (7 bp):
AACCTTG
Found at i:12157097 original size:50 final size:50
Alignment explanation
Indices: 12157038--12157139 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 50
12157028 TTTGCCAGCT
12157038 CAACATTAGCATCTACAAAAACAATTTAAAAA-ATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAA-TTAAAAATATCCACATGTATCCAGTC
* *
12157088 CAACATTAGCATCTGCTAAAACAATTAAAAATATCCACATGTATCCAGTC
1 CAACATTAGCATCTACAAAAACAATTAAAAATATCCACATGTATCCAGTC
12157138 CA
1 CA
12157140 CCTTGTTGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 7 0.14
50 42 0.86
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.25
Consensus pattern (50 bp):
CAACATTAGCATCTACAAAAACAATTAAAAATATCCACATGTATCCAGTC
Found at i:12161602 original size:137 final size:139
Alignment explanation
Indices: 12161382--12161658 Score: 434
Period size: 137 Copynumber: 2.0 Consensus size: 139
12161372 AAAACAGCTA
* *
12161382 AAAATTGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAAC
1 AAAATTGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAAC
* * * *
12161447 ACTAGCTACAAAAGTAATTTACCAATATCATGTGGTAACAAGTCCACCTGAAAGTG-AGATATGA
66 ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTCCACATGAAAGTGCA-ATATGA
*
12161511 AAGATATGCC
130 AAGACATGCC
* *
12161521 AAAA-TGAAATCATTTATGGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAAC
1 AAAATTGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAAC
*
12161584 ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTTCACATGAAAGTGCAATATGAA
66 ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTCCACATGAAAGTGCAATATGAA
12161649 AGACATGCC
131 AGACATGCC
12161658 A
1 A
12161659 TTTTCTGAAA
Statistics
Matches: 127, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
137 85 0.67
138 38 0.30
139 4 0.03
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (139 bp):
AAAATTGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAAC
ACTAACTACAAAAGTAATTTAACAATATCATGTAGTAACAAGTCCACATGAAAGTGCAATATGAA
AGACATGCC
Found at i:12164542 original size:23 final size:24
Alignment explanation
Indices: 12164497--12164543 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
12164487 CACTTGATTT
* *
12164497 TATAATTTTTTAATTCATTAAATAA
1 TATAATTTTATAATT-ATAAAATAA
12164522 TATAATTTTATAATT-TAAAATA
1 TATAATTTTATAATTATAAAATA
12164544 TTTTTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
25 14 0.70
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATTTTATAATTATAAAATAA
Found at i:12174358 original size:3 final size:3
Alignment explanation
Indices: 12174350--12174378 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12174340 TCAAAACTTG
12174350 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12174379 TCTTTTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12179427 original size:16 final size:15
Alignment explanation
Indices: 12179406--12179435 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12179396 AGTAAAAGTT
12179406 AATTTAATTATTGATG
1 AATTTAATT-TTGATG
12179422 AATTTAATTTTGAT
1 AATTTAATTTTGAT
12179436 ACTCAAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (15 bp):
AATTTAATTTTGATG
Found at i:12183412 original size:18 final size:18
Alignment explanation
Indices: 12183385--12183429 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
12183375 ATTTAAAATT
*
12183385 TATTTAAAAATACAAAAA
1 TATTTAAAAATAAAAAAA
*
12183403 TATTTCAAAATAAAAAAA
1 TATTTAAAAATAAAAAAA
12183421 TATTATAAA
1 TATT-TAAA
12183430 GTTACAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
TATTTAAAAATAAAAAAA
Found at i:12183665 original size:25 final size:26
Alignment explanation
Indices: 12183615--12183666 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
12183605 GTAAACTTTG
* *
12183615 ATTTATAAAGTTTTAAAAATATTAAA
1 ATTTATAAAGTTTAAAAAATAGTAAA
*
12183641 ATTTCTAAA-TTTAAAAAATAGTAAA
1 ATTTATAAAGTTTAAAAAATAGTAAA
12183666 A
1 A
12183667 ATTAGTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
ATTTATAAAGTTTAAAAAATAGTAAA
Found at i:12183667 original size:26 final size:26
Alignment explanation
Indices: 12183615--12183669 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12183605 GTAAACTTTG
* *
12183615 ATTTATAAAGTTTTAAAAATATTAAA
1 ATTTATAAAGTTTAAAAAATATAAAA
*
12183641 ATTTCTAAA-TTTAAAAAATAGTAAAA
1 ATTTATAAAGTTTAAAAAATA-TAAAA
12183667 ATT
1 ATT
12183670 AGTTTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (26 bp):
ATTTATAAAGTTTAAAAAATATAAAA
Found at i:12196332 original size:31 final size:31
Alignment explanation
Indices: 12196294--12196356 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
12196284 CTTCTTCTGT
*
12196294 ATCTCTTCCTTGCTGATCCCACACATCAACA
1 ATCTCTTCCTTGCTAATCCCACACATCAACA
12196325 ATCTCTTCCTTGCTAATCCCACACATCAACA
1 ATCTCTTCCTTGCTAATCCCACACATCAACA
12196356 A
1 A
12196357 GGGTATCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.38, G:0.05, T:0.29
Consensus pattern (31 bp):
ATCTCTTCCTTGCTAATCCCACACATCAACA
Found at i:12201841 original size:4 final size:4
Alignment explanation
Indices: 12201834--12201875 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
12201824 AGATAGAAAC
* *
12201834 AGAA AGAA AGAA AGAA AGAAA AAAA AGAA A-AA GGAA AGAA AG
1 AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AG
12201876 GAAGGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 2 0.06
4 27 0.84
5 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:12202799 original size:41 final size:39
Alignment explanation
Indices: 12202753--12202888 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 39
12202743 CGACTTCGAG
12202753 CCGATGAGACACTGGGTGTCAATTTACTATTTCGGATTAAT
1 CCGATGAGACACTGGGTGTCAATTTA-TATTTCGGATT-AT
* * * * *
12202794 TCGATGAGGCACTGGGTGCCAA-TT-TATTTCGGTTTAG
1 CCGATGAGACACTGGGTGTCAATTTATATTTCGGATTAT
* * * *
12202831 CCGATGAGAAATTGGGTGTCAATTTATTACTTCGAATTAT
1 CCGATGAGACACTGGGTGTCAATTTA-TATTTCGGATTAT
*
12202871 CCGATGAGGCACTGGGTG
1 CCGATGAGACACTGGGTG
12202889 CCAAACTGGT
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 18 0.24
38 12 0.16
40 26 0.35
41 19 0.25
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (39 bp):
CCGATGAGACACTGGGTGTCAATTTATATTTCGGATTAT
Found at i:12206455 original size:30 final size:31
Alignment explanation
Indices: 12206387--12206452 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
12206377 AATAATCTAT
* *
12206387 ATTTTTA-TAATTTTTAAGGGATTAAATTAA
1 ATTTTTATTAATTTTTAAGGGATCAAAATAA
12206417 ATTTTTATTAA-TTTTAAGGGATCAAAATACA
1 ATTTTTATTAATTTTTAAGGGATCAAAATA-A
12206448 ATTTT
1 ATTTT
12206453 ATTTTTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (31 bp):
ATTTTTATTAATTTTTAAGGGATCAAAATAA
Found at i:12206861 original size:19 final size:21
Alignment explanation
Indices: 12206816--12206863 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
12206806 CAATTTCATA
*
12206816 AATTTTAAATAAATCAAAATAT
1 AATTTT-AATAAATCAAAAAAT
*
12206838 TATTTTAA-AAAT-AAAAAAT
1 AATTTTAATAAATCAAAAAAT
12206857 AATTTTA
1 AATTTTA
12206864 TAATATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.52
20 4 0.17
21 2 0.09
22 5 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTTTAATAAATCAAAAAAT
Found at i:12217640 original size:21 final size:21
Alignment explanation
Indices: 12217601--12217640 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12217591 GCCCCTCGGT
* * *
12217601 TTTTTTTTTCCATTGTTTTTC
1 TTTTTCTTTCCACTATTTTTC
12217622 TTTTTCTTTCCACTATTTT
1 TTTTTCTTTCCACTATTTT
12217641 ACTTGCTTTT
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:0.07, C:0.17, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTCTTTCCACTATTTTTC
Found at i:12229858 original size:22 final size:22
Alignment explanation
Indices: 12229807--12229858 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
12229797 TTTTATAGTT
*
12229807 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
12229830 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
12229852 ATAATAA
1 ATAATAA
12229859 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:12233213 original size:64 final size:64
Alignment explanation
Indices: 12233112--12233258 Score: 276
Period size: 64 Copynumber: 2.3 Consensus size: 64
12233102 ATGTTATATT
*
12233112 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAGAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAAAAATTTGAGAATTTTAAAATCTTA
*
12233176 AGTTCGAATCCTTTAATTTTGATTGAATTAATAAGGTTAAAAATTTGAGAATTTTAAAATCTTA
1 AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAAAAATTTGAGAATTTTAAAATCTTA
12233240 AGTTCGAATCCTCTAATTT
1 AGTTCGAATCCTCTAATTT
12233259 AAATACTATA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (64 bp):
AGTTCGAATCCTCTAATTTTGATTGAATTAATAAGGTTAAAAATTTGAGAATTTTAAAATCTTA
Found at i:12233910 original size:15 final size:15
Alignment explanation
Indices: 12233890--12233921 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12233880 TGTAAGTTTC
12233890 TTAGAAATAAAATGA
1 TTAGAAATAAAATGA
*
12233905 TTAGAAATAAGATGA
1 TTAGAAATAAAATGA
12233920 TT
1 TT
12233922 GGGGAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (15 bp):
TTAGAAATAAAATGA
Found at i:12236937 original size:21 final size:21
Alignment explanation
Indices: 12236911--12236954 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
12236901 AAATAGAGCT
12236911 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
12236932 TCTTTGAGTCTGCTGTGAGTG
1 TCTTTGAGTCTGCTGTGAGTG
12236953 TC
1 TC
12236955 AATTGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (21 bp):
TCTTTGAGTCTGCTGTGAGTG
Found at i:12249465 original size:44 final size:44
Alignment explanation
Indices: 12249403--12249502 Score: 173
Period size: 44 Copynumber: 2.3 Consensus size: 44
12249393 TATGGATTGA
* *
12249403 GAGAAAACAACACCGATGGTGTTGTTGAGAAAGAATGATAAAGT
1 GAGAAAACGAGACCGATGGTGTTGTTGAGAAAGAATGATAAAGT
*
12249447 GAGAAAACGAGACTGATGGTGTTGTTGAGAAAGAATGATAAAGT
1 GAGAAAACGAGACCGATGGTGTTGTTGAGAAAGAATGATAAAGT
12249491 GAGAAAACGAGA
1 GAGAAAACGAGA
12249503 AAATATGTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.44, C:0.07, G:0.30, T:0.19
Consensus pattern (44 bp):
GAGAAAACGAGACCGATGGTGTTGTTGAGAAAGAATGATAAAGT
Found at i:12249503 original size:22 final size:22
Alignment explanation
Indices: 12249434--12249503 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
12249424 TTGTTGAGAA
12249434 AGAATGATAAAGTGAGAAAACG
1 AGAATGATAAAGTGAGAAAACG
* *** * *
12249456 AGACTGATGGTGTTGTTGAGAA--
1 AGAATGATAAAG-TG-AGAAAACG
12249478 AGAATGATAAAGTGAGAAAACG
1 AGAATGATAAAGTGAGAAAACG
12249500 AGAA
1 AGAA
12249504 AATATGTAAA
Statistics
Matches: 32, Mismatches: 12, Indels: 8
0.62 0.23 0.15
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 20 0.62
23 2 0.06
24 4 0.12
ACGTcount: A:0.47, C:0.04, G:0.30, T:0.19
Consensus pattern (22 bp):
AGAATGATAAAGTGAGAAAACG
Found at i:12249678 original size:24 final size:23
Alignment explanation
Indices: 12249645--12249690 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12249635 TAGGAAAACA
12249645 TTTTCTAAAAAATAAAAGTGATG
1 TTTTCTAAAAAATAAAAGTGATG
12249668 TTTTCTAAAAAATAAAAGTGATG
1 TTTTCTAAAAAATAAAAGTGATG
12249691 AATTAAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (23 bp):
TTTTCTAAAAAATAAAAGTGATG
Found at i:12254388 original size:13 final size:13
Alignment explanation
Indices: 12254344--12254446 Score: 71
Period size: 13 Copynumber: 7.8 Consensus size: 13
12254334 TTTAGCAATA
12254344 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
** * * *
12254357 CAGTGGAAAAATA
1 CTTTTGAAAAGTG
*
12254370 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
12254383 CTTTTGAAAAGTTTG
1 CTTTTGAAAAG--TG
* * **
12254398 GTGTCAAAAAGTG
1 CTTTTGAAAAGTG
* *
12254411 CATTTGAAAAATG
1 CTTTTGAAAAGTG
*
12254424 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
12254437 CTTTTGAAAA
1 CTTTTGAAAA
12254447 ATTTGAGTGT
Statistics
Matches: 62, Mismatches: 26, Indels: 4
0.67 0.28 0.04
Matches are distributed among these distances:
13 53 0.85
15 9 0.15
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:12254391 original size:26 final size:26
Alignment explanation
Indices: 12254340--12254448 Score: 87
Period size: 26 Copynumber: 4.1 Consensus size: 26
12254330 CTAGTTTAGC
* *
12254340 AATACTTTTGAAAAGTGCAGTGGAAA
1 AATACTTTTGAAAAGTGCATTTGAAA
* *
12254366 AATACTTTTGAGAAGTGCTTTTGAAA
1 AATACTTTTGAAAAGTGCATTTGAAA
* *
12254392 AGT--TTGGTGTCAAAAAGTGCATTTGAAA
1 AATACTT--T-T-GAAAAGTGCATTTGAAA
* * *
12254420 AATGCTTTTGAGAAGTGCTTTTGAAA
1 AATACTTTTGAAAAGTGCATTTGAAA
12254446 AAT
1 AAT
12254449 TTGAGTGTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
24 2 0.03
26 42 0.65
27 2 0.03
28 17 0.26
30 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (26 bp):
AATACTTTTGAAAAGTGCATTTGAAA
Found at i:12254432 original size:54 final size:55
Alignment explanation
Indices: 12254350--12254456 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 55
12254340 AATACTTTTG
*
12254350 AAAAGTGCAGTGGAAAAATACTTTTGAGAAGTGCTTTTGAAAAGTTTG-GTGTCA
1 AAAAGTGCAGTGGAAAAATACTTTTGAGAAGTGCTTTTGAAAAATTTGAGTGTCA
* * *
12254404 AAAAGTGCATTTGAAAAATGCTTTTGAGAAGTGCTTTTGAAAAATTTGAGTGT
1 AAAAGTGCAGTGGAAAAATACTTTTGAGAAGTGCTTTTGAAAAATTTGAGTGT
12254457 TTAGCATTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
54 44 0.92
55 4 0.08
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.34
Consensus pattern (55 bp):
AAAAGTGCAGTGGAAAAATACTTTTGAGAAGTGCTTTTGAAAAATTTGAGTGTCA
Found at i:12276271 original size:17 final size:16
Alignment explanation
Indices: 12276249--12276315 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
12276239 TAAAAAAGAA
*
12276249 TTAATATGTTCAAAATT
1 TTAATATATT-AAAATT
*
12276266 TTAATATATTTAAATATA
1 TTAATATA-TTAAA-ATT
12276284 TTAAGTATATTAAAATT
1 TTAA-TATATTAAAATT
*
12276301 TTAA-ATTTTAAAATT
1 TTAATATATTAAAATT
12276316 GGTTATACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 10 0.23
17 16 0.37
18 13 0.30
19 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (16 bp):
TTAATATATTAAAATT
Found at i:12276361 original size:17 final size:17
Alignment explanation
Indices: 12276335--12276398 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
12276325 CAACATTTTC
*
12276335 TTTAACATATTTAAAAT
1 TTTAATATATTTAAAAT
*
12276352 TTTAATATATTTAAAAAA
1 TTTAATATATTT-AAAAT
*
12276370 TTTAACT-TTTTTAAAAT
1 TTTAA-TATATTTAAAAT
12276387 TTTAAATATATT
1 TTT-AATATATT
12276399 AAATATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 19 0.50
18 18 0.47
19 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATATATTTAAAAT
Found at i:12276441 original size:9 final size:9
Alignment explanation
Indices: 12276422--12276503 Score: 61
Period size: 9 Copynumber: 9.8 Consensus size: 9
12276412 TCTCTTTACC
12276422 TATTAAAATA
1 TATT-AAATA
12276432 TATTAAATA
1 TATTAAATA
12276441 TATTAAA-A
1 TATTAAATA
*
12276449 T-TTCAATA
1 TATTAAATA
*
12276457 TATTTAA-A
1 TATTAAATA
12276465 -A--AAATA
1 TATTAAATA
*
12276471 TATTGAATA
1 TATTAAATA
12276480 TATTAAA-A
1 TATTAAATA
* *
12276488 TTTTTAATA
1 TATTAAATA
12276497 TATTAAA
1 TATTAAA
12276504 ATTTTAAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
5 2 0.04
6 1 0.02
7 6 0.11
8 11 0.20
9 32 0.57
10 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (9 bp):
TATTAAATA
Found at i:12276480 original size:39 final size:39
Alignment explanation
Indices: 12276426--12276504 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
12276416 TTTACCTATT
12276426 AAAATATATTAAATATATTAAAA-TTTCAATATATTTAAA
1 AAAATATATTAAATATATTAAAATTTTCAATATA-TTAAA
* *
12276465 AAAATATATTGAATATATTAAAATTTTTAATATATTAAA
1 AAAATATATTAAATATATTAAAATTTTCAATATATTAAA
12276504 A
1 A
12276505 TTTTAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 28 0.76
40 9 0.24
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
AAAATATATTAAATATATTAAAATTTTCAATATATTAAA
Found at i:12276498 original size:17 final size:17
Alignment explanation
Indices: 12276422--12276511 Score: 74
Period size: 17 Copynumber: 4.9 Consensus size: 17
12276412 TCTCTTTACC
12276422 TATTAAAATATATTAAATA
1 TATTAAAAT-T-TTAAATA
*
12276441 TATTAAAA-TTTCAATA
1 TATTAAAATTTTAAATA
*
12276457 TATTTAAAAAAATATATTGAATA
1 TA-TT---AAAAT-T-TTAAATA
*
12276480 TATTAAAATTTTTAATA
1 TATTAAAATTTTAAATA
12276497 TATTAAAATTTTAAA
1 TATTAAAATTTTAAA
12276512 ATTGGTTATA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
16 8 0.13
17 23 0.38
18 1 0.02
19 13 0.22
20 4 0.07
22 3 0.05
23 8 0.13
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TATTAAAATTTTAAATA
Found at i:12276577 original size:63 final size:63
Alignment explanation
Indices: 12276493--12276616 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 63
12276483 TAAAATTTTT
* *
12276493 AATATATTAAAATTTTAAAATTGGTTATAATTAACATTTTTTAATATATTT-ATTTTTAAAAA
1 AATATATCAAAATATTAAAATTGGTTATAATTAACATTTTTTAATATATTTAATTTTTAAAAA
* *
12276555 AATATATCAAATATATTAAAATTGGTTATACTTAACCTTTTTTAATATATTTAAATTTTTAA
1 AATATATCAAA-ATATTAAAATTGGTTATAATTAACATTTTTTAATATATTT-AATTTTTAA
12276617 TATATTTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
62 10 0.18
63 37 0.67
65 8 0.15
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (63 bp):
AATATATCAAAATATTAAAATTGGTTATAATTAACATTTTTTAATATATTTAATTTTTAAAAA
Found at i:12276615 original size:17 final size:17
Alignment explanation
Indices: 12276593--12276626 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12276583 TACTTAACCT
12276593 TTTTTAATATATTTAAA
1 TTTTTAATATATTTAAA
12276610 TTTTTAATATATTTAAA
1 TTTTTAATATATTTAAA
12276627 AAAATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATATATTTAAA
Found at i:12276635 original size:35 final size:35
Alignment explanation
Indices: 12276596--12276666 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
12276586 TTAACCTTTT
*
12276596 TTAA-TATATTTAAATTTTTAATATATTTAAAAAAA
1 TTAATTATATTTAAATTTTAAATATA-TTAAAAAAA
* * *
12276631 TTAATTTTTTTTAAATTTTAAATATATTAAGAAAA
1 TTAATTATATTTAAATTTTAAATATATTAAAAAAA
12276666 T
1 T
12276667 CTTTTTTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (35 bp):
TTAATTATATTTAAATTTTAAATATATTAAAAAAA
Done.