Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 36 of 356
Found at i:11998015 original size:49 final size:48
Alignment explanation
Indices: 11997942--11998047 Score: 149
Period size: 49 Copynumber: 2.2 Consensus size: 48
11997932 TATGGTCTTA
* *
11997942 CACATATTCATATATCGATACCATAGCCCAACTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATACCATAGCCCAACTAGGGTCTTACACG-AAT
* * *
11997992 TACATATCACATATCGATGCCATAGCCCAGCTAGGGTCTTACACGAAT
1 CACATATCACATATCGATACCATAGCCCAACTAGGGTCTTACACGAAT
11998040 CACATATC
1 CACATATC
11998048 TCACGGATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
48 10 0.20
49 35 0.70
50 5 0.10
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (48 bp):
CACATATCACATATCGATACCATAGCCCAACTAGGGTCTTACACGAAT
Found at i:11998076 original size:46 final size:46
Alignment explanation
Indices: 11998006--11998131 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 46
11997996 TATCACATAT
* * * * * * *
11998006 CGATGCCATAGCCCAGCTAGGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATAACACAC
* * * *
11998052 GGATGCCATATCCCAGATATGGTCTTATATAGTAGCATATAACACAC
1 CGATGCCATATCCCAGATATGGTCTTATA-CGAAGCACATAACACAC
*
11998099 CGATGCCATATCCCAAATATGGTCTTATACGAA
1 CGATGCCATATCCCAGATATGGTCTTATACGAA
11998132 AATCACTTGT
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
46 26 0.41
47 38 0.59
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATAACACAC
Found at i:11998190 original size:31 final size:31
Alignment explanation
Indices: 11998153--11998295 Score: 223
Period size: 31 Copynumber: 4.6 Consensus size: 31
11998143 ACTTGTATTC
*
11998153 GAAGCTACCACTATTCACTGATCAGGTAGCT
1 GAAGCTACCACTTTTCACTGATCAGGTAGCT
* *
11998184 GGAGCTACCATTTTTCACTGATCAGGTAGCT
1 GAAGCTACCACTTTTCACTGATCAGGTAGCT
* *
11998215 GGAGCTACCACTTTTCACTGATCAGGTAGCA
1 GAAGCTACCACTTTTCACTGATCAGGTAGCT
* *
11998246 GAAGCTACCACTTTTCACTGATCTGGTAGCC
1 GAAGCTACCACTTTTCACTGATCAGGTAGCT
11998277 GAAGCTACCACTTTTCACT
1 GAAGCTACCACTTTTCACT
11998296 TGTCATTTGT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAGCTACCACTTTTCACTGATCAGGTAGCT
Found at i:11998385 original size:50 final size:51
Alignment explanation
Indices: 11998271--11998399 Score: 179
Period size: 50 Copynumber: 2.5 Consensus size: 51
11998261 CACTGATCTG
* * *
11998271 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
** * *
11998322 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTTTTTTATCAGATAATT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
*
11998372 GTAGCCAAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
11998400 TGTCATGGTC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 44 0.64
51 25 0.36
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
Found at i:12020308 original size:2 final size:2
Alignment explanation
Indices: 12020303--12020331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12020293 TCTCTGTGTT
12020303 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12020332 GTCTTAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12024446 original size:20 final size:21
Alignment explanation
Indices: 12024413--12024451 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
12024403 GGGACCACTA
12024413 ATGTGGCAAATTAA-TTGCTG
1 ATGTGGCAAATTAACTTGCTG
* *
12024433 ATGTGGCCAGTTAACTTGC
1 ATGTGGCAAATTAACTTGC
12024452 CATGTTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (21 bp):
ATGTGGCAAATTAACTTGCTG
Found at i:12028482 original size:3 final size:3
Alignment explanation
Indices: 12028476--12028528 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
12028466 AGAAGAAGAA
12028476 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
12028524 GAT GA
1 GAT GA
12028529 GGAGGAGGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:12028533 original size:3 final size:3
Alignment explanation
Indices: 12028527--12028594 Score: 73
Period size: 3 Copynumber: 22.7 Consensus size: 3
12028517 TGATGATGAT
* * * *
12028527 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAA GAA GAA GAG GAT GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
* * *
12028575 GAA GAA GAT GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GA
12028595 CGATGACGAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.41, C:0.00, G:0.56, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:12028607 original size:9 final size:9
Alignment explanation
Indices: 12028593--12028654 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 9
12028583 TGAGGAGGAG
12028593 GACGATGAC
1 GACGATGAC
*
12028602 GACGATGAT
1 GACGATGAC
*
12028611 GACGATGAT
1 GACGATGAC
*
12028620 GTC---GAC
1 GACGATGAC
12028626 GACGATGAC
1 GACGATGAC
*
12028635 GACGGTGAC
1 GACGATGAC
*
12028644 GACGGTGAC
1 GACGATGAC
12028653 GA
1 GA
12028655 TGACAATGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 4 0.09
9 41 0.91
ACGTcount: A:0.29, C:0.19, G:0.37, T:0.15
Consensus pattern (9 bp):
GACGATGAC
Found at i:12028613 original size:12 final size:12
Alignment explanation
Indices: 12028596--12028638 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12028586 GGAGGAGGAC
12028596 GATGACGACGAT
1 GATGACGACGAT
*
12028608 GATGACGATGAT
1 GATGACGACGAT
12028620 G-TCGACGACGAT
1 GAT-GACGACGAT
*
12028632 GACGACG
1 GATGACG
12028639 GTGACGACGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.30, C:0.19, G:0.35, T:0.16
Consensus pattern (12 bp):
GATGACGACGAT
Found at i:12028707 original size:3 final size:3
Alignment explanation
Indices: 12028699--12028725 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12028689 GGATCATTTT
12028699 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
12028726 CTCATTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12028891 original size:3 final size:3
Alignment explanation
Indices: 12028885--12028914 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12028875 CATTTTCAAT
12028885 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12028915 CTCACTGTTA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12028915 original size:189 final size:190
Alignment explanation
Indices: 12028699--12029104 Score: 715
Period size: 192 Copynumber: 2.1 Consensus size: 190
12028689 GGATCATTTT
*
12028699 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCATTGTTACAATCACCAAATTCAACAGAAGAAGATG
1 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCACCAAATTCAACAGAAGAAGATG
*
12028764 AAGAACATTCACCAATGGGATCAACACTT-GAAGAAGAAGAAGACTCACCATTGCAATCATCATT
66 AAGAACATTCACCAATGGGATCAACACTTAGAAGAAGAAGAAGACCCACCATTGCAATCATCATT
* *
12028828 GTCAATAGGGGAAGAAGATGAAGAAGAATATTCACAAAGGCAATCATCATTTTCAATAGA
131 GTCAACAGGGGAAGAAGATGAAGAAGAATATTCACAAAGGCAATCATCATTTTCAACAGA
*
12028888 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCATCAAATTCAACAGAAGAAGATG
1 AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCACCAAATTCAACAGAAGAAGATG
* *
12028953 AAGAACATTCACCAGTGGGATCAATACTTGAAGAAGAAGAAGAAGACCCACCATTGCAATCATCA
66 AAGAACATTCACCAATGGGATCAACACTT--AGAAGAAGAAGAAGACCCACCATTGCAATCATCA
*
12029018 TTGTCAACAGGGGAAGAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAACAGA
129 TTGTCAACAGGGGAAGAAGATGAAGAAGAATATTCACAAAGGCAATCATCATTTTCAACAGA
12029080 AGAAGAAGAAGAAGAAGAAGAAGAA
1 AGAAGAAGAAGAAGAAGAAGAAGAA
12029105 AGCAAAAAGA
Statistics
Matches: 206, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
189 90 0.44
192 116 0.56
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (190 bp):
AGAAGAAGAAGAAGAAGAAGAAGAAGACTCACTGTTACAATCACCAAATTCAACAGAAGAAGATG
AAGAACATTCACCAATGGGATCAACACTTAGAAGAAGAAGAAGACCCACCATTGCAATCATCATT
GTCAACAGGGGAAGAAGATGAAGAAGAATATTCACAAAGGCAATCATCATTTTCAACAGA
Found at i:12028929 original size:57 final size:56
Alignment explanation
Indices: 12028793--12028957 Score: 160
Period size: 57 Copynumber: 3.0 Consensus size: 56
12028783 ATCAACACTT
* *
12028793 GAAGAAGAAGAAGACTCACCATTGCAATCATCATTGTCAATAG--G--G-GAAGAA
1 GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAATAGAAGAAGAGAAGAA
* * * **
12028844 GATGAAGAAGAATATTCACAAAGGCAATCATCATTTTCAATAGAAGAAGAAGAAGAA
1 GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAATAGAAGAAG-AGAAGAA
** * ** *
12028901 GAAGAAGAAGAAGACTCACTGTTACAATCATCAAATTCAACAGAAGAAGATGAAGAA
1 GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAATAGAAGAAGA-GAAGAA
12028958 CATTCACCAG
Statistics
Matches: 89, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
51 36 0.40
53 1 0.01
55 1 0.01
56 1 0.01
57 50 0.56
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (56 bp):
GAAGAAGAAGAAGACTCACAATTGCAATCATCATTTTCAATAGAAGAAGAGAAGAA
Found at i:12029043 original size:51 final size:51
Alignment explanation
Indices: 12028982--12029100 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
12028972 ATCAATACTT
* * **
12028982 GAAGAAGAAGAAGAAGACCCACCATTGCAATCATCATTGTCAACAGGGGAA
1 GAAGAAGAAGAAGAAGACCCACAAATGCAATCATCATTGTCAACAGAAGAA
* * ** *
12029033 GAAGATGAAGAAGAATATTCACAAATGCAATCATCATTTTCAACAGAAGAA
1 GAAGAAGAAGAAGAAGACCCACAAATGCAATCATCATTGTCAACAGAAGAA
12029084 GAAGAAGAAGAAGAAGA
1 GAAGAAGAAGAAGAAGA
12029101 AGAAAGCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.15
Consensus pattern (51 bp):
GAAGAAGAAGAAGAAGACCCACAAATGCAATCATCATTGTCAACAGAAGAA
Found at i:12029083 original size:3 final size:3
Alignment explanation
Indices: 12029077--12029104 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12029067 CATTTTCAAC
12029077 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
12029105 AGCAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12031355 original size:19 final size:19
Alignment explanation
Indices: 12031304--12031355 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
12031294 AAATAACAAA
* *
12031304 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTC
* *
12031323 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTC
12031343 AAAATTCAAAATA
1 AAAATTCAAAATA
12031356 TATATAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:12031406 original size:17 final size:17
Alignment explanation
Indices: 12031386--12031439 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
12031376 TATATTTTTT
12031386 AAAAAATTATAAATTTA
1 AAAAAATTATAAATTTA
12031403 AAAAAA--ACTACAATTTA
1 AAAAAATTA-TA-AATTTA
*
12031420 AAAAAATTATAAATTCA
1 AAAAAATTATAAATTTA
12031437 AAA
1 AAA
12031440 TATATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 1 0.03
16 2 0.06
17 26 0.81
18 2 0.06
19 1 0.03
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAATTATAAATTTA
Found at i:12031465 original size:17 final size:17
Alignment explanation
Indices: 12031375--12031465 Score: 66
Period size: 16 Copynumber: 5.6 Consensus size: 17
12031365 ATTCTAATAT
* *
12031375 TTATATTTTTTAAAAAA
1 TTATAATTTTAAAAAAA
*
12031392 TTATAAATTTAAAAAAAA
1 TTAT-AATTTTAAAAAAA
* *
12031410 CTACAA-TTTAAAAAAA
1 TTATAATTTTAAAAAAA
* *
12031426 TTATAA-ATT--CAAAA
1 TTATAATTTTAAAAAAA
*
12031440 -TATATTTTTAAAAAAA
1 TTATAATTTTAAAAAAA
12031456 TTATAATTTT
1 TTATAATTTT
12031466 TTAAGGAGGA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
13 4 0.07
14 6 0.11
16 19 0.35
17 14 0.25
18 12 0.22
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTATAATTTTAAAAAAA
Found at i:12043422 original size:12 final size:11
Alignment explanation
Indices: 12043398--12043427 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
12043388 CATTTTGTTC
12043398 TTTAGTTTCTTT
1 TTTA-TTTCTTT
12043410 TTTATTTCTTT
1 TTTATTTCTTT
12043421 TTTATTT
1 TTTATTT
12043428 TTGTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTATTTCTTT
Found at i:12044580 original size:3 final size:3
Alignment explanation
Indices: 12044572--12044608 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12044562 TTGATTTTAC
12044572 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12044609 TAGTCCCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12051060 original size:43 final size:43
Alignment explanation
Indices: 12051013--12051126 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 43
12051003 CCTTAAACCT
* ***
12051013 CTAAGCAGTAGGGTAACAGGCTGAATTTGT-AGATTTTAACCCC
1 CTAAGCAGTAGGGTAACAGGCTGAATTGGTGA-ACCCTAACCCC
* ** **
12051056 CTAAGCAGTAGGGAAACAGATTGAAGACGGTGAACCCTAACCCC
1 CTAAGCAGTAGGGTAACAGGCTGAA-TTGGTGAACCCTAACCCC
12051100 CTAAGCAGTAGGGTAACAGGCTGAATT
1 CTAAGCAGTAGGGTAACAGGCTGAATT
12051127 ACAAATCACT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
43 22 0.40
44 32 0.58
45 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (43 bp):
CTAAGCAGTAGGGTAACAGGCTGAATTGGTGAACCCTAACCCC
Found at i:12051578 original size:138 final size:138
Alignment explanation
Indices: 12051210--12052258 Score: 1694
Period size: 138 Copynumber: 7.6 Consensus size: 138
12051200 GTAGATCAAC
* *
12051210 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051275 GTTGCAGTGGAACAGATTGAAGCTAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
12051340 TCGAAGTT
131 TCGAAGTT
* * * *
12051348 ACAAGTCTTATCTCCTTGAA-TTGTAGTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
* * *
12051412 GTTGCAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCTCTGAAGTTGCAATAGAGTAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
12051477 TCGAAGTT
131 TCGAAGTT
* * *
12051485 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCATATTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
* *
12051550 GTTGTAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
12051615 TCGAAGTT
131 TCGAAGTT
* *
12051623 ACAAGTCTTATCTCCCTGAAGTTGCATTGGAACAGACTGAAGATAGCAAATCTTATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051688 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
*
12051753 TCAAAGTT
131 TCGAAGTT
* * *
12051761 ACAAGTCTTATCTCCTTGAAGTTGCAGAGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051826 GTT-CAG-GGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
12051889 TCGAAGTT
131 TCGAAGTT
*
12051897 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCATATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
** * *
12051962 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCCAAAGTTGCAATAGAGTAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
12052027 TCGAAGTT
131 TCGAAGTT
* *
12052035 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCATATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12052100 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
12052165 TCGAAGTT
131 TCGAAGTT
* * * * * * *
12052173 ACAAGTCTTATCTCTCTAAAGTTGTAGTAGAGCAGA-TCGAAGTTA-CAAGTCTTATCTCCCTGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAGCAAATCTTATTTCCCTGA
* *
12052236 AGTTGCAGTGGAGCAGACTGAAG
65 AGTTGCAGTGGAACAGATTGAAG
12052259 ATAGTAAATC
Statistics
Matches: 850, Mismatches: 57, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
136 126 0.15
137 174 0.20
138 550 0.65
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (138 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
TCGAAGTT
Found at i:12051773 original size:182 final size:178
Alignment explanation
Indices: 12051210--12052662 Score: 761
Period size: 182 Copynumber: 7.9 Consensus size: 178
12051200 GTAGATCAAC
* * * * * * * * *
12051210 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACTGAAGATAGTAAATCTTATTTTCCTGA
1 ACAAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTC-GAAGTTA-CAAGTCTTATCTCCCTAA
* * * *
12051274 AGTTGCAGTGGAACAGATTGAAGCTAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAG
64 AGTTGCAGTAGAACAGACTGAAG----A-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* * * * * *
12051339 GTCGAAG--TTACAAGTCTTATCTC-CTTGAA-TTGTAGTGGAGCA-GACTGAAGAT
124 ATTGAAGAATTACAA-TCTTATCTCTC-TGAAGTTGCAGTGGAGCAGGGCTAAAGTT
* * * * * * * * *
12051391 AGTAAATCTTAT-TTTCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTC
1 A-CAAGTCTTATCTCT-CTGAAGTTGCAGTAGAGCAGGTCGAAG-T-TA-CA-AG-TCTTATCTC
* * * ** * * *
12051455 TCTGAAGTTGCAATAGAGTAG-GTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
59 CCTAAAGTTGCAGTAGAACAGACT-GAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * * *
12051519 AACTGAAG-A-TAGCAAATCATAT-TTTCCTGAAGTTGTAGTGGAACAGATTGAAGCTAAA-TT
123 GATTGAAGAATTA-C-AATCTTATCTCT-CTGAAGTTGCAGTGGAGCAG---G--GCTAAAGTT
* *
12051579 A-TAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAA
1 ACAAG-TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTAAA
* * * *
12051643 GTTGCATTGGAACAGACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGA
65 GTTGCAGTAGAACAGACTGAAGATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * *
12051708 AGCTAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGGTC-AAAGTT
129 AG---AATTACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGGCTAAAGTT
* * * * * *
12051761 ACAAGTCTTATCTC-CTTGAAGTTGCAG-AGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTG
1 ACAAGTCTTATCTCTC-TGAAGTTGCAGTA-GAGCAGGTCGAAGTTA-CAAGTCTTATCTCCCTA
* * * *
12051824 AAGTT-CAG-GGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTGGAGCA
63 AAGTTGCAGTAGAACAGACTGAAG----A-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * * * *
12051887 GGTCGAAG--TTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACTGAAGAT
123 GATTGAAGAATTACAA-TCTTATCTCTCTGAAGTTGCAGTGGAGCAGGGCTAAAGTT
* * * * * * * *
12051941 AGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTAC-AGATCTTATCTC
1 A-CAAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAG-----TTACAAG-TCTTATCTC
* ** * * *
12052005 TCC-AAAGTTGCAATAGAGTAG-GTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
59 -CCTAAAGTTGCAGTAGAACAGACT-GAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
* * * * * *
12052068 AAACTGAAG-A-TAGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAA-TT
122 AGATTGAAGAATTA-C-AATCTTATCTCTCTGAAGTTGCAGTGGAGCAG---G--GCTAAAGTT
* *
12052129 AC-AGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCTCTAAA
1 ACAAG-TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTAAA
* * * * *
12052193 GTTGTAGTAGAGCAGA-TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA
65 GTTGCAGTAGAACAGACT-GAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * *
12052257 AGATAGTA-AATCTTAT-TTTCCTGAAGTTGCATTGGAACAGATTGAAGCTAAA-TT
129 AGA-ATTACAATCTTATCTCT-CTGAAGTTGCAGTGGAGCAG---G--GCTAAAGTT
* *
12052311 AC-AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTGAA
1 ACAAG-TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTAAA
* * * * *
12052375 GTTGCAGT-GAAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTG
65 GTTGCAGTAGAA-CAGACTGAAGATA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG
* * * * *
12052439 AAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAAGTC-GAAGTT
128 AAG---AATTACA-ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGGCTAAAGTT
* * * * * *
12052493 ATAAGTCTTATCTC-CTTGAAGTTGCAGTGGAGCA-GACTGAAGATAGCAAATCTTATTTCCCTA
1 ACAAGTCTTATCTCTC-TGAAGTTGCAGTAGAGCAGGTC-GAAGTTA-CAAGTCTTATCTCCCTA
** * * * * *
12052556 AAGTTGCAGTAGAGTAGATTGAAGCTAAATTACAGATTTTATCTCTCTGAAGTTGCAGTAGAGCA
63 AAGTTGCAGTAGAACAGACTGAAG----A-TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCA
* * * *
12052621 GGTCGAAG--TTACAAGTTTTATCTCTCTTAAGTTGCAGTGGAG
123 GATTGAAGAATTACAA-TCTTATCTCTCTGAAGTTGCAGTGGAG
12052663 TAGACTGAAG
Statistics
Matches: 1001, Mismatches: 177, Indels: 187
0.73 0.13 0.14
Matches are distributed among these distances:
179 3 0.00
180 36 0.04
181 102 0.10
182 407 0.41
183 173 0.17
184 12 0.01
185 58 0.06
186 42 0.04
187 146 0.15
188 14 0.01
189 8 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (178 bp):
ACAAGTCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTAAAG
TTGCAGTAGAACAGACTGAAGATACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG
AATTACAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGGCTAAAGTT
Found at i:12051989 original size:412 final size:414
Alignment explanation
Indices: 12051210--12052258 Score: 1732
Period size: 412 Copynumber: 2.5 Consensus size: 414
12051200 GTAGATCAAC
* *
12051210 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051275 GTTGCAGTGGAACAGATTGAAGCTAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
* * *
12051340 TCGAAGTTACAAGTCTTATCTCCTTGAA-TTGTAGTGGAGCAGACTGAAGATAGTAAATCTTATT
131 TCGAAGTTACAAGTCTTATCTCCTTGAAGTTGTAGAGGAGCAGATTGAAGATAGCAAATCTTATT
* *
12051404 TTCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCTCTGAAGTTGCAAT
196 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAAT
*
12051469 AGAGTAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAA
261 AGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAA
* * * **
12051534 ATCATATTTTCCTGAAGTTGTAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCTCTGAA
326 ATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCCAAA
*
12051599 GTTGCAGTAGAGCAGGTCGAAGTT
391 GTTGCAATAGAGCAGGTCGAAGTT
* *
12051623 ACAAGTCTTATCTCCCTGAAGTTGCATTGGAACAGACTGAAGATAGCAAATCTTATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051688 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTACAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
* *
12051753 TCAAAGTTACAAGTCTTATCTCCTTGAAGTTGCAGAGGAGCAGATTGAAGATAGCAAATCTTATT
131 TCGAAGTTACAAGTCTTATCTCCTTGAAGTTGTAGAGGAGCAGATTGAAGATAGCAAATCTTATT
*
12051818 TCCCTGAAGTT-CAG-GGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGT
196 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAAT
* *
12051881 GGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAA
261 AGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAA
12051946 ATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCCAAA
326 ATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCCAAA
*
12052011 GTTGCAATAGAGTAGGTCGAAGTT
391 GTTGCAATAGAGCAGGTCGAAGTT
* *
12052035 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCATATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12052100 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
* * * *
12052165 TCGAAGTTACAAGTCTTATCT-CTCTAAAGTTGTAGTA-GAGCAGATCGAAGTTA-CAAGTCTTA
131 TCGAAGTTACAAGTCTTATCTCCT-TGAAGTTGTAG-AGGAGCAGATTGAAGATAGCAAATCTTA
* * *
12052227 TCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
194 TTTCCCTGAAGTTGCAGTGGAACAGATTGAAG
12052259 ATAGTAAATC
Statistics
Matches: 592, Mismatches: 39, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
411 22 0.04
412 361 0.61
413 167 0.28
414 42 0.07
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (414 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGAA
GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
TCGAAGTTACAAGTCTTATCTCCTTGAAGTTGTAGAGGAGCAGATTGAAGATAGCAAATCTTATT
TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAAT
AGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAA
ATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCCAAA
GTTGCAATAGAGCAGGTCGAAGTT
Found at i:12052240 original size:320 final size:320
Alignment explanation
Indices: 12051858--12052579 Score: 1151
Period size: 320 Copynumber: 2.3 Consensus size: 320
12051848 AAATTACAGA
*
12051858 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
12051923 GTGGAGCAGACTGAAGATAGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAA
66 GTGGAGCAGACTGAAGATAGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAA
*
12051988 ATTACAGATCTTATCTCTCCAAAGTTGCAATAGAGTAGGTCGAAGTTACAAGTCTTATCTCCCTG
131 ATTACAGATCTTATCTCTCCAAAGTTGCAATAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTG
* *
12052053 AAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATT
196 AAGTTGCAGTGAAGCAAACTGAAGATAGCAAATCATATTTCCCTAAAGTTGCAGTGGAACAGATT
*
12052118 GAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAG
261 GAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAAGTCGAAGTTACAAG
* * *
12052178 TCTTATCTCTCTAAAGTTGTAGTAGAGCAGATCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
* * * *
12052243 GTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTGAAGTTGCATTGGAACAGATTGAAGCTAA
66 GTGGAGCAGACTGAAGATAGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAA
** * *
12052308 ATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTG
131 ATTACAGATCTTATCTCTCCAAAGTTGCAATAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTG
* * * *
12052373 AAGTTGCAGTGAAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATT
196 AAGTTGCAGTGAAGCAAACTGAAGATAGCAAATCATATTTCCCTAAAGTTGCAGTGGAACAGATT
*
12052438 GAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAAGTCGAAGTTATAAG
261 GAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAAGTCGAAGTTACAAG
* * * *
12052498 TCTTATCTC-CTTGAAGTTGCAGTGGAGCAGA-CTGAAGATAGCAAATCTTATTTCCCTAAAGTT
1 TCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATC-GAAGTTA-CAAGTCTTATCTCCCTGAAGTT
* * *
12052561 GCAGTAGAGTAGATTGAAG
63 GCAGTGGAGCAGACTGAAG
12052580 CTAAATTACA
Statistics
Matches: 368, Mismatches: 31, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
319 2 0.01
320 331 0.90
321 35 0.10
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (320 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTGAAGATAGCAAATCATATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAA
ATTACAGATCTTATCTCTCCAAAGTTGCAATAGAGCAGGTCGAAGTTACAAGTCTTATCTCCCTG
AAGTTGCAGTGAAGCAAACTGAAGATAGCAAATCATATTTCCCTAAAGTTGCAGTGGAACAGATT
GAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAAGTCGAAGTTACAAG
Found at i:12052322 original size:276 final size:279
Alignment explanation
Indices: 12051210--12052620 Score: 1581
Period size: 276 Copynumber: 5.1 Consensus size: 279
12051200 GTAGATCAAC
* * *
12051210 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051275 GTTGCAGTGGAACAGATTGAAGCTAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
* * *
12051340 TCGAAGTTACAAGTCTTATCTCCTTGAA-TTGTAGTGGAGCAGACTGAAGATAGTAAATCTTATT
131 TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATT
* *
12051404 TTCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTATAGATCTTA-TCTCTCTGAAGTTGCAA
196 TCCCTGAAGTTGCAGTGGAACAGATTGAAGC-AAATTACAGATCTTATTCTC-CTGAAGTTGCAA
*
12051468 TAGAGTAGGTCGAAG----TT
259 TAGAGTAGATCGAAGCAAATT
* *
12051485 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCATATTTTCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAA
* *
12051550 GTTGTAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
* *
12051615 TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCATTGGAACAGACTGAAGATAGCAAATCTTATT
131 TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATT
* *
12051680 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTA-TCTCTCTGAAGTTACAG
196 TCCCTGAAGTTGCAGTGGAACAGATTGAAGC-AAATTACAGATCTTATTCTC-CTGAAGTTGCAA
* * *
12051744 TAGAGCAGGTC--A--AAGTT
259 TAGAGTAGATCGAAGCAAATT
* * * *
12051761 ACAAGTCTTATCTCCTTGAAGTTGCAGAGGAGCAGATTGAAGATAGCAAATCTTATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12051826 GTT-CAG-GGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
*
12051889 TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCATATT
131 TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATT
*
12051954 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCC-AAAGTTGCAA
196 TCCCTGAAGTTGCAGTGGAACAGATTGAAGC-AAATTACAGATCTTAT-TCTCCTGAAGTTGCAA
*
12052018 TAGAGTAGGTCGAAG----TT
259 TAGAGTAGATCGAAGCAAATT
*
12052035 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCATATTTCCCTGAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAA
*
12052100 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTTTGAAGTTGCAGTAGAGCAGG
66 GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
* * * * * *
12052165 TCGAAGTTACAAGTCTTATCTCTCTAAAGTTGTAGTAGAGCAGA-TCGAAGTTA-CAAGTCTTAT
131 TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAGCAAATCTTAT
* * * * * * *
12052228 CTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-ATAGTA-A-ATCTTATTTTCCTGAAGTTGCATT
195 TTCCCTGAAGTTGCAGTGGAACAGATTGAAGCAAATTACAGATCTTATTCTCCTGAAGTTGCAAT
* ** *
12052290 GGAACAGATTGAAGCTAAATT
260 AGAGTAGATCGAAGC-AAATT
* * ** * * * *
12052311 AC-AGATCTTATCTCTCTGAAGTTGCAGTAGAGC-AGGTCGAAGTTA-CAAGTCTTATCTCCTTG
1 ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACT-GAAGATAGCAAATCTTATTTCCCTG
* * * * * * *
12052373 AAGTTGCAGT-GAAGCAGACTGAAG--ATAGTA-A-ATCTTAT-TTTCCTAAAGTTGCAGTGGAA
64 AAGTTGCAGTGGAA-CAGATTGAAGCTAAATTACAGATCTTATCTCT-CTGAAGTTGCAGTAGAG
* * ** * * *
12052432 CAGATTGAAGCTAAATTAC-AGATCTTATCTCTTTGAAGTTGCAGTAGAGCA-AGTCGAAGTTA-
127 CAGGTCGAAG-----TTACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATAG
* * * * * * *
12052494 TAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAG---A-TAGCAAATCTTATT-TCCC
185 CAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCAAATTA-CAGATCTTATTCT-CC
* * *
12052554 TAAAGTTGCAGTAGAGTAGATTGAAGCTAAATT
248 TGAAGTTGCAATAGAGTAGATCGAAGC-AAATT
* * *
12052587 AC-AGATTTTATCTCTCTGAAGTTGCAGTAGAGCA
1 ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCA
12052621 GGTCGAAGTT
Statistics
Matches: 1013, Mismatches: 89, Indels: 66
0.87 0.08 0.06
Matches are distributed among these distances:
270 6 0.01
271 53 0.05
272 2 0.00
273 10 0.01
274 251 0.25
275 235 0.23
276 456 0.45
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (279 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTTATTTCCCTGAA
GTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGG
TCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATT
TCCCTGAAGTTGCAGTGGAACAGATTGAAGCAAATTACAGATCTTATTCTCCTGAAGTTGCAATA
GAGTAGATCGAAGCAAATT
Found at i:12052767 original size:49 final size:48
Alignment explanation
Indices: 12051270--12052769 Score: 377
Period size: 44 Copynumber: 32.6 Consensus size: 48
12051260 TCTTATTTTC
* ** * * * *
12051270 CTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAAATCTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* *
12051319 CTGAAGTTGCAGTAGAGCAGGTCGAAGTT--A-CAAG-TCTTATCTC-
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * * * *
12051362 CTTGAA-TTGTAGTGGAGCA-GACTGAAG--ATAGTAA-ATCTTAT-TTT
1 C-TGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* ** * * *
12051406 CCTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCT
1 -CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * *
12051456 CTGAAGTTGCAATAGAGTAGGTCGAAGTT--A-CAAG-TCTTATCTCC
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * ** * ** * *
12051500 CTGAAGTTGCAGTGGAGCA-AACTGAAG--ATAGCAA-ATCATAT-TTT
1 CTGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* * ** * * *
12051544 CCTGAAGTTGTAGTGGAACAGATTGAAGCTAAATTATAGATCTTATCTCT
1 -CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * *
12051594 CTGAAGTTGCAGTAGAGCAGGTCGAAGTT--A-CAAG-TCTTATCTCC
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * ** * * ** * *
12051638 CTGAAGTTGCATTGGAACA-GACTGAAG--ATAGCAA-ATCTTATTTCC
1 CTGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* ** * * *
12051683 CTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * * *
12051732 CTGAAGTTACAGTAGAGCAGGTCAAAGTT--A-CAAG-TCTTATCTC-
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * ** * *
12051775 CTTGAAGTTGCAG-AGGAGCAGATTGAAG--ATAGCAA-ATCTTATTTCC
1 C-TGAAGTTGCAGTA-GAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* ** * * *
12051821 CTGAAGTT-CAG-GGAACAGATTGAAGCTAAATTACAGATCTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * * *
12051868 CTGAAGTTGCAGTGGAGCAGGTCGAAGTT--A-CAAG-TCTTATCTCC
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * ** * * *
12051912 CTGAAGTTGCAGTGGAGCA-GACTGAAG--ATAGCAA-ATCATATTTCC
1 CTGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* ** * * *
12051957 CTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
** * * *
12052006 CCAAAGTTGCAATAGAGTAGGTCGAAGTT--A-CAAG-TCTTATCTCC
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * ** * ** * * *
12052050 CTGAAGTTGCAGTGGAGCA-AACTGAAG--ATAGCAA-ATCATATTTCC
1 CTGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* ** * * *
12052095 CTGAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * *
12052144 TTGAAGTTGCAGTAGAGCAGGTCGAAGTT--A-CAAG-TCTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * * *
12052188 CTAAAGTTGTAGTAGAGCAGATCGAAGTT--A-CAAG-TCTTATCTCC
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * * *
12052232 CTGAAGTTGCAGTGGAGCA-GACTGAAG--ATAGTAA-ATCTTAT-TTT
1 CTGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* * ** * * *
12052276 CCTGAAGTTGCATTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCT
1 -CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* *
12052326 CTGAAGTTGCAGTAGAGCAGGTCGAAGTT--A-CAAG-TCTTATCTC-
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * *
12052369 CTTGAAGTTGCAGT-GAAGCA-GACTGAAG--ATAGTAA-ATCTTAT-TTT
1 C-TGAAGTTGCAGTAG-AGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* * ** * * *
12052414 CCTAAAGTTGCAGTGGAACAGATTGAAGCTAAATTACAGATCTTATCTCT
1 -CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * *
12052464 TTGAAGTTGCAGTAGAGCAAGTCGAAGTT--A-TAAG-TCTTATCTC-
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * ** * *
12052507 CTTGAAGTTGCAGTGGAGCA-GACTGAAG--ATAGCAA-ATCTTATTTCC
1 C-TGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* * * * *
12052553 CTAAAGTTGCAGTAGAGTAGATTGAAGCTAAATTACAGATTTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* * *
12052602 CTGAAGTTGCAGTAGAGCAGGTCGAAGTT--A-CAAG-TTTTATCTCT
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
* * * * * *
12052646 CTTAAGTTGCAGTGGAGTA-GACTGAAG--ATAGTAA-ATCTTAT-TTT
1 CTGAAGTTGCAGTAGAGTAGGTC-GAAGTTAAATTAAGATCTTATCTCT
* * * *
12052690 CCTGAAGTTGCAGTGGAATAGATTGAAGTTAAATTATAGATCTTATCTCT
1 -CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTA-AGATCTTATCTCT
* *
12052740 CTGAAGTTGCAATAGAGCAGGTCGAAGTTA
1 CTGAAGTTGCAGTAGAGTAGGTCGAAGTTA
12052770 CAAGTCTTAT
Statistics
Matches: 1095, Mismatches: 234, Indels: 244
0.70 0.15 0.16
Matches are distributed among these distances:
42 2 0.00
43 47 0.04
44 346 0.32
45 297 0.27
46 18 0.02
47 58 0.05
48 12 0.01
49 305 0.28
50 10 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (48 bp):
CTGAAGTTGCAGTAGAGTAGGTCGAAGTTAAATTAAGATCTTATCTCT
Found at i:12052783 original size:138 final size:138
Alignment explanation
Indices: 12052178--12052782 Score: 987
Period size: 138 Copynumber: 4.4 Consensus size: 138
12052168 AAGTTACAAG
* * * *
12052178 TCTTATCTCTCTAAAGTTGTAGTAGAGCAGATCGAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTGAAGTTGCA
* *
12052243 GTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTGAAGTTGCATTGGAACAGATTGAAGCTAA
66 GTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTGAAGCTAA
12052308 ATTACAGA
131 ATTACAGA
12052316 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTGAAGTTGCA
*
12052381 GTGAAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTGAAGCTAA
66 GTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTGAAGCTAA
12052446 ATTACAGA
131 ATTACAGA
* * *
12052454 TCTTATCTCTTTGAAGTTGCAGTAGAGCAAGTCGAAGTTATAAGTCTTATCTCCTTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTGAAGTTGCA
* * * **
12052519 GTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTTGCAGTAGAGTAGATTGAAGCTAA
66 GTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTGAAGCTAA
12052584 ATTACAGA
131 ATTACAGA
* *
12052592 TTTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTTTTATCTCTCTT-AAGTTGC
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTC-CTTGAAGTTGC
* * * *
12052656 AGTGGAGTAGACTGAAGATAGTAAATCTTATTTTCCTGAAGTTGCAGTGGAATAGATTGAAGTTA
65 AGTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTGAAGCTA
*
12052721 AATTATAGA
130 AATTACAGA
*
12052730 TCTTATCTCTCTGAAGTTGCAATAGAGCAGGTCGAAGTTACAAGTCTTATCTC
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTC
12052783 TTTGTGCTTA
Statistics
Matches: 434, Mismatches: 32, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
138 431 0.99
139 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.32
Consensus pattern (138 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTTACAAGTCTTATCTCCTTGAAGTTGCA
GTGGAGCAGACTGAAGATAGTAAATCTTATTTTCCTAAAGTTGCAGTGGAACAGATTGAAGCTAA
ATTACAGA
Found at i:12061266 original size:29 final size:30
Alignment explanation
Indices: 12061208--12061266 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
12061198 CTAATATAAT
* * *
12061208 TAATTATTTTAATAAAATTCTTTAATATTA
1 TAATTATTTTAATAAAAATCTATAACATTA
12061238 TAATT-TTTTAATAATAAAT-TATAACATTA
1 TAATTATTTTAATAA-AAATCTATAACATTA
12061267 ATGATTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
TAATTATTTTAATAAAAATCTATAACATTA
Found at i:12062715 original size:29 final size:27
Alignment explanation
Indices: 12062640--12062736 Score: 89
Period size: 27 Copynumber: 3.6 Consensus size: 27
12062630 ATACATGGAT
12062640 TCCTCCCAAACACACCAGAATATCCA-A
1 TCCTCCCAAACACACCAGAATAT-CATA
*
12062667 ----CCCAAACACACCCAGAATATTATAAA
1 TCCTCCCAAACACA-CCAGAATATCAT--A
*
12062693 TCCT-CCATAACACACCAGTATATCATA
1 TCCTCCCA-AACACACCAGAATATCATA
12062720 TCCTCCCAAACACACCA
1 TCCTCCCAAACACACCA
12062737 ATAAGGCATT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
23 11 0.19
24 9 0.16
26 1 0.02
27 14 0.25
28 3 0.05
29 13 0.23
30 6 0.11
ACGTcount: A:0.41, C:0.38, G:0.03, T:0.18
Consensus pattern (27 bp):
TCCTCCCAAACACACCAGAATATCATA
Found at i:12063200 original size:15 final size:15
Alignment explanation
Indices: 12063180--12063226 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
12063170 TAATATATAT
12063180 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
12063195 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
12063210 TTCAATCAATATAAA
1 TTCAATCAATATAAA
12063225 TT
1 TT
12063227 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:12064492 original size:22 final size:21
Alignment explanation
Indices: 12064460--12064523 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
12064450 TCCCCTGTTC
*
12064460 TTTTCTATTTCGTTTGCTTTGT
1 TTTTCTATTTCATTT-CTTTGT
*
12064482 TTTTCTTTTTCATTTCTTT-T
1 TTTTCTATTTCATTTCTTTGT
* *
12064502 ATTTC-ATTT-ATTTCTTTAT
1 TTTTCTATTTCATTTCTTTGT
12064521 TTT
1 TTT
12064524 ATTTCTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.22
19 6 0.17
20 5 0.14
21 4 0.11
22 13 0.36
ACGTcount: A:0.09, C:0.12, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTCTATTTCATTTCTTTGT
Found at i:12064526 original size:13 final size:13
Alignment explanation
Indices: 12064508--12064539 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
12064498 TTTTATTTCA
12064508 TTTATTTCTTTAT
1 TTTATTTCTTTAT
12064521 TTTATTTCTTTAT
1 TTTATTTCTTTAT
12064534 TTTATT
1 TTTATT
12064540 ATTAAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTCTTTAT
Found at i:12064564 original size:23 final size:23
Alignment explanation
Indices: 12064534--12064586 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
12064524 ATTTCTTTAT
12064534 TTTATTA-TTAAACTAT-TATAATA
1 TTTATTATTTAAAC-ATGTAT-ATA
*
12064557 TTTATTATTTATACATGTATATA
1 TTTATTATTTAAACATGTATATA
12064580 TTTATTA
1 TTTATTA
12064587 ATACACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTATTATTTAAACATGTATATA
Found at i:12069005 original size:13 final size:14
Alignment explanation
Indices: 12068989--12069024 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
12068979 CAATCTCATA
12068989 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
12069002 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
12069015 TCTC-ATTTCA
1 TCTCAATTTCA
12069025 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:12069014 original size:18 final size:19
Alignment explanation
Indices: 12068976--12069016 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
12068966 TGGTTCATGT
12068976 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
12068995 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
12069013 TTTC
1 TTTC
12069017 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:12069151 original size:23 final size:23
Alignment explanation
Indices: 12069121--12069186 Score: 123
Period size: 23 Copynumber: 2.8 Consensus size: 23
12069111 GTGGATTCCT
12069121 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
12069144 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
12069167 CCCAAACACACCCAGAATAT
1 CCCAAACACA-CCAGAATAT
12069187 TATAAATCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 33 0.79
24 9 0.21
ACGTcount: A:0.47, C:0.39, G:0.05, T:0.09
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:12069231 original size:27 final size:28
Alignment explanation
Indices: 12069117--12069236 Score: 93
Period size: 23 Copynumber: 4.6 Consensus size: 28
12069107 ATACGTGGAT
*
12069117 TCCTCCCAAACACACCAGAATATC-CAA
1 TCCTCCCAAACACACCAGAATATCATAA
*
12069144 ----CCCAAACACACCAGAATATC-CAA
1 TCCTCCCAAACACACCAGAATATCATAA
*
12069167 ----CCCAAACACACCCAGAATATTATAAA
1 TCCTCCCAAACACA-CCAGAATATCAT-AA
*
12069193 TCCT-CCATAACACACCAGTATATCAT-A
1 TCCTCCCA-AACACACCAGAATATCATAA
12069220 TCCTCCCAAACACACCA
1 TCCTCCCAAACACACCA
12069237 ATAAGGCATT
Statistics
Matches: 80, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
23 33 0.41
24 9 0.11
26 2 0.03
27 14 0.17
28 3 0.04
29 13 0.16
30 6 0.08
ACGTcount: A:0.42, C:0.38, G:0.03, T:0.16
Consensus pattern (28 bp):
TCCTCCCAAACACACCAGAATATCATAA
Found at i:12069698 original size:15 final size:15
Alignment explanation
Indices: 12069678--12069724 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
12069668 TAATATATAT
12069678 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
12069693 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
12069708 TTCAATCAATATAAA
1 TTCAATCAATATAAA
12069723 TT
1 TT
12069725 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:12076689 original size:30 final size:32
Alignment explanation
Indices: 12076637--12076699 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
12076627 CTAAGTTTTG
*
12076637 AATCAATCTCAATTTCTTCAAGTGTTTGTATT
1 AATCAATCTCAATTTCTTCAAGTATTTGTATT
*
12076669 AATCAATCTTAA-TT-TTCAAGTATTTGTATT
1 AATCAATCTCAATTTCTTCAAGTATTTGTATT
12076699 A
1 A
12076700 CTCATCCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.55
31 2 0.07
32 11 0.38
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.48
Consensus pattern (32 bp):
AATCAATCTCAATTTCTTCAAGTATTTGTATT
Found at i:12088989 original size:3 final size:3
Alignment explanation
Indices: 12088981--12089176 Score: 392
Period size: 3 Copynumber: 65.3 Consensus size: 3
12088971 CAGACACATA
12088981 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12089029 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12089077 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12089125 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
12089173 TTC T
1 TTC T
12089177 GTGGAATGTT
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 193 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:12094658 original size:30 final size:30
Alignment explanation
Indices: 12094622--12094685 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
12094612 ACTGTTAAAA
12094622 ATTTGTATAGTTAATTATAACCAATGATGG
1 ATTTGTATAGTTAATTATAACCAATGATGG
12094652 ATTTGTATAGTTAATTATAACCAATGATGG
1 ATTTGTATAGTTAATTATAACCAATGATGG
12094682 ATTT
1 ATTT
12094686 AGGGGCGGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
ATTTGTATAGTTAATTATAACCAATGATGG
Found at i:12100618 original size:37 final size:37
Alignment explanation
Indices: 12100563--12100637 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
12100553 AAACCAATCC
12100563 AAACACATTTTATATATTATCTAATACTTAACTTTAA
1 AAACACATTTTATATATTATCTAATACTTAACTTTAA
*
12100600 AAACGCATTTTATATATTATCTAATACTTAACTTTAA
1 AAACACATTTTATATATTATCTAATACTTAACTTTAA
12100637 A
1 A
12100638 CACTTATCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.43
Consensus pattern (37 bp):
AAACACATTTTATATATTATCTAATACTTAACTTTAA
Found at i:12101312 original size:18 final size:18
Alignment explanation
Indices: 12101278--12101337 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
12101268 AATTGGTTAA
* *
12101278 TCAGTAATATTCATTTAT
1 TCAGTAACAGTCATTTAT
* *
12101296 TCAGTATCAGTCGTTTAT
1 TCAGTAACAGTCATTTAT
*
12101314 TCTA-TAACAGTCAATTAT
1 TC-AGTAACAGTCATTTAT
12101332 TCAGTA
1 TCAGTA
12101338 GCAGACAGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (18 bp):
TCAGTAACAGTCATTTAT
Found at i:12101530 original size:54 final size:51
Alignment explanation
Indices: 12101471--12101588 Score: 121
Period size: 51 Copynumber: 2.3 Consensus size: 51
12101461 CCGTAAGAGT
12101471 AACAGTAACAGTAACAGT-AGCAGTACACAAAGTACCTCATCGGAACAAATCCAA
1 AACAGTAACAGTAACAGTCAG--GT--ACAAAGTACCTCATCGGAACAAATCCAA
* * ** * **
12101525 AACAGTAATAGTAATAGTCAGGTACGGAGTACCTCTTCGGAACAAATCCGG
1 AACAGTAACAGTAACAGTCAGGTACAAAGTACCTCATCGGAACAAATCCAA
*
12101576 AACAGTCACAGTA
1 AACAGTAACAGTA
12101589 GTCGACACAT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
51 34 0.63
53 2 0.04
54 16 0.30
55 2 0.04
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (51 bp):
AACAGTAACAGTAACAGTCAGGTACAAAGTACCTCATCGGAACAAATCCAA
Found at i:12101907 original size:3 final size:3
Alignment explanation
Indices: 12101892--12101921 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12101882 ATTCAATACC
*
12101892 ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12101922 CTTACCATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12102621 original size:13 final size:13
Alignment explanation
Indices: 12102603--12102627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12102593 TTCTTTCCTT
12102603 TTTCTTTATTTCA
1 TTTCTTTATTTCA
12102616 TTTCTTTATTTC
1 TTTCTTTATTTC
12102628 TTTTATTTTA
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:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTATTTCA
Found at i:12108992 original size:46 final size:45
Alignment explanation
Indices: 12108967--12109221 Score: 287
Period size: 46 Copynumber: 5.4 Consensus size: 45
12108957 GATCAAGTGA
* * *
12108967 CAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
* * * *
12109012 CAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGA-CAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
*
12109058 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
* *
12109104 CAAGTGACAAGTGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGAC------AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
* *
12109155 CAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
*
12109201 CAAGAGACAAAGTGATAAGTG
1 CAAGTGAC-AAGTGATAAGTG
12109222 GCTACACTTA
Statistics
Matches: 193, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
44 2 0.01
45 5 0.03
46 142 0.74
51 44 0.23
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
CAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
Found at i:12109137 original size:51 final size:51
Alignment explanation
Indices: 12109066--12109221 Score: 223
Period size: 51 Copynumber: 3.1 Consensus size: 51
12109056 ATCAAGTGAC
*
12109066 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
*
12109117 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
**
12109163 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC-AAGTG
12109215 ATAAGTG
1 A-AAGTG
12109222 GCTACACTTA
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
46 43 0.46
51 44 0.47
52 1 0.01
53 5 0.05
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:12109164 original size:97 final size:97
Alignment explanation
Indices: 12108922--12109221 Score: 394
Period size: 97 Copynumber: 3.1 Consensus size: 97
12108912 ATCAAGTGAT
* ** * *
12108922 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC------AAAGTGATAAGTG
*
12108987 ATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
60 ATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
12109020 AAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
12109085 TCGGCTACACTTATCTGATCAAGTGACAAGTG
66 TCGGCTACACTTATCTGATCAAGTGACAAGTG
*
12109117 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
** *
12109182 TTAGCTACACTTATCTGATCAAGAGACAAAGTG
66 TCGGCTACACTTATCTGATCAAGTGAC-AAGTG
12109215 ATAAGTG
1 A-AAGTG
12109222 GCTACACTTA
Statistics
Matches: 183, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
92 42 0.23
95 1 0.01
96 1 0.01
97 87 0.48
98 47 0.26
99 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
TCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:12109182 original size:143 final size:144
Alignment explanation
Indices: 12108908--12109221 Score: 513
Period size: 143 Copynumber: 2.2 Consensus size: 144
12108898 TTTGAGTACT
* * *
12108908 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
12108973 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGC
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
* *
12109038 TTCGGCTATACTTA
131 TTCAGCTACACTTA
*
12109052 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
12109116 GAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
*
12109181 TTTAGCTACACTTA
131 TTCAGCTACACTTA
*
12109195 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
12109222 GCTACACTTA
Statistics
Matches: 158, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
143 98 0.62
144 60 0.38
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (144 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
TTCAGCTACACTTA
Found at i:12109229 original size:37 final size:37
Alignment explanation
Indices: 12109185--12109294 Score: 195
Period size: 37 Copynumber: 3.0 Consensus size: 37
12109175 GATAGCTTTA
12109185 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
12109222 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
12109259 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
12109295 ATCATACGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 12 0.17
37 58 0.83
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:12110626 original size:58 final size:57
Alignment explanation
Indices: 12110548--12110715 Score: 226
Period size: 49 Copynumber: 3.0 Consensus size: 57
12110538 CATGTGAACA
*
12110548 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGT-AGTGATATG
12110607 TGTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATC-G--GT-A-A--
1 TGTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAGTGATATG
* *
12110657 -GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTA-GTGATATG
12110714 TG
1 TG
12110716 ATTACGTGTA
Statistics
Matches: 97, Mismatches: 3, Indels: 19
0.82 0.03 0.16
Matches are distributed among these distances:
49 43 0.44
50 1 0.01
52 1 0.01
53 3 0.03
54 3 0.03
57 1 0.01
58 40 0.41
59 5 0.05
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34
Consensus pattern (57 bp):
TGTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAGTGATATG
Found at i:12110680 original size:49 final size:49
Alignment explanation
Indices: 12110608--12110750 Score: 241
Period size: 49 Copynumber: 2.9 Consensus size: 49
12110598 AGTGATATGT
*
12110608 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
*
12110657 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* * *
12110706 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCG
12110751 AGAAAACGAA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 89 1.00
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:12113958 original size:46 final size:45
Alignment explanation
Indices: 12113933--12114186 Score: 276
Period size: 46 Copynumber: 5.4 Consensus size: 45
12113923 GATCAAGTGA
* * *
12113933 CAAGTGGA-AAGTGATAAGTAATAGCTTCGGCTATACTTATCTGAT
1 CAAGT-GACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
* * * *
12113978 CAAGTGATAAAGTGATAAGTTATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGA-CAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
*
12114024 CAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
* *
12114070 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGAC-------AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
* *
12114122 CAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
*
12114168 CAAGAGACAAAGTGATAAG
1 CAAGTGAC-AAGTGATAAG
12114187 GCTACACTTA
Statistics
Matches: 191, Mismatches: 9, Indels: 17
0.88 0.04 0.08
Matches are distributed among these distances:
44 2 0.01
45 5 0.03
46 140 0.73
52 44 0.23
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
CAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAT
Found at i:12113994 original size:98 final size:92
Alignment explanation
Indices: 12113940--12114186 Score: 368
Period size: 98 Copynumber: 2.6 Consensus size: 92
12113930 TGACAAGTGG
* * *
12113940 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGCT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCT
12114005 TCGGCTATACTTATCTGATCAAGTGAC
66 TCGGCTATACTTATCTGATCAAGTGAC
12114032 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTG---A-T--AAAGTGATAAGTG
*
12114097 ATAGCTTCGGCTATACTTATCTGATCAAGAGAC
60 ATAGCTTCGGCTATACTTATCTGATCAAGTGAC
** * *
12114130 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTGATAAG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAAGTGATAAG
12114187 GCTACACTTA
Statistics
Matches: 141, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
92 53 0.38
95 2 0.01
96 1 0.01
98 85 0.60
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (92 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCT
TCGGCTATACTTATCTGATCAAGTGAC
Found at i:12114134 original size:144 final size:144
Alignment explanation
Indices: 12113874--12114186 Score: 509
Period size: 144 Copynumber: 2.2 Consensus size: 144
12113864 TTTGAGTACT
* * *
12113874 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * * *
12113939 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTTATAGC
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
* *
12114004 TTCGGCTATACTTA
131 TTCAGCTACACTTA
*
12114018 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
12114083 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
*
12114148 TTTAGCTACACTTA
131 TTCAGCTACACTTA
*
12114162 TCTGATCAAGAGACAAAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
12114187 GCTACACTTA
Statistics
Matches: 156, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 156 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (144 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGC
TTCAGCTACACTTA
Found at i:12114236 original size:37 final size:37
Alignment explanation
Indices: 12114152--12114259 Score: 177
Period size: 35 Copynumber: 3.0 Consensus size: 37
12114142 GATAGCTTTA
12114152 GCTACACTTATCTGATCAAGAGACAAAGTGATAA--G
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
12114187 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
12114224 GCTACACTTATCTGATCAAGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
12114260 ATCATACGTA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 33 0.49
36 12 0.18
37 23 0.34
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:12115289 original size:30 final size:30
Alignment explanation
Indices: 12115255--12115314 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
12115245 ACTTAACAAG
*
12115255 CAAATATCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
12115285 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
12115315 TAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:12116332 original size:34 final size:35
Alignment explanation
Indices: 12116288--12116354 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
12116278 CTGTAAAATG
*
12116288 TTTTCCGTAAAATGAATT-TTGGAAAATATTTTAC
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
* *
12116322 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTT
12116355 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
Found at i:12117768 original size:27 final size:27
Alignment explanation
Indices: 12117706--12117768 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
12117696 AATTCAATAC
* *
12117706 CCAACAATGTTAAAACATAATCAATAT
1 CCAACAATGTCAAAACATAATCAAAAT
* *
12117733 CTAACCAAT-TCAAGACATATATCAAAAT
1 CCAA-CAATGTCAAAACATA-ATCAAAAT
12117761 CCAACAAT
1 CCAACAAT
12117769 CTAAAATCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (27 bp):
CCAACAATGTCAAAACATAATCAAAAT
Found at i:12122039 original size:6 final size:6
Alignment explanation
Indices: 12122028--12122058 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12122018 AATATTTCCC
*
12122028 ACAGAA ACAGAA ACAGAA ACAAAA ACAGAA A
1 ACAGAA ACAGAA ACAGAA ACAGAA ACAGAA A
12122059 ATACAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.71, C:0.16, G:0.13, T:0.00
Consensus pattern (6 bp):
ACAGAA
Found at i:12124327 original size:50 final size:51
Alignment explanation
Indices: 12124247--12124372 Score: 184
Period size: 50 Copynumber: 2.5 Consensus size: 51
12124237 GACCATGGCA
* *
12124247 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCAACACTTATCTAATCAAGGACAAA-TG
*
12124298 A-AAGTGATAAGTGATAGCTTCGGCAACACTTATCTAATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCAACACTTATCTAATCAAGGACAAATG
* *
12124348 ACAAGTGAAAAGTGGTAGCTTCGGC
1 ACAAGTGATAAGTGATAGCTTCGGC
12124373 TACCTGATCA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
50 43 0.63
51 25 0.37
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCAACACTTATCTAATCAAGGACAAATG
Found at i:12124389 original size:31 final size:31
Alignment explanation
Indices: 12124351--12124460 Score: 177
Period size: 31 Copynumber: 3.5 Consensus size: 31
12124341 ACAAATGACA
*
12124351 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
12124382 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
12124413 AGTGAAAAGTGGTAG-TACCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCT-CCGGCTACCTGATC
*
12124444 AGTGAATAGTGGTAGCT
1 AGTGAAAAGTGGTAGCT
12124461 TCGACTACAA
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
30 1 0.01
31 72 0.97
32 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:12124604 original size:46 final size:47
Alignment explanation
Indices: 12124491--12124609 Score: 168
Period size: 47 Copynumber: 2.6 Consensus size: 47
12124481 ATTTCCGTAC
* * *
12124491 AAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTGTAT
1 AAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTGTAT
* *
12124538 AAGACCATATCTGGGATATGGCATCAGTGAGATATTTGATA-TGTGT
1 AAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTGTAT
* *
12124584 AAGACCATAGCTGGGCTATGGCATCA
1 AAGACCATATCTGGGATATGGCATCA
12124610 TTATGTGAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
46 28 0.43
47 37 0.57
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (47 bp):
AAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACTGTAT
Found at i:12125634 original size:17 final size:15
Alignment explanation
Indices: 12125612--12125670 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 15
12125602 TTAAAAAAAA
12125612 TATTTTATTTATCCATT
1 TATTTTATTT-T-CATT
12125629 TATTTTATTTT-ATT
1 TATTTTATTTTCATT
* *
12125643 AAATTTATTTTTGCATT
1 TATTTTA-TTTT-CATT
12125660 TATTTTATTTT
1 TATTTTATTTT
12125671 ATTACACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 8 0.23
15 4 0.11
16 5 0.14
17 18 0.51
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (15 bp):
TATTTTATTTTCATT
Found at i:12125660 original size:31 final size:31
Alignment explanation
Indices: 12125615--12125674 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
12125605 AAAAAAATAT
12125615 TTTATTTATCCATTTATTTTATTTTATTAAA
1 TTTATTTATCCATTTATTTTATTTTATTAAA
* *
12125646 TTTATTTTTGCATTTATTTTATTTTATTA
1 TTTATTTATCCATTTATTTTATTTTATTA
12125675 CACTTCATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (31 bp):
TTTATTTATCCATTTATTTTATTTTATTAAA
Found at i:12128256 original size:20 final size:20
Alignment explanation
Indices: 12128231--12128272 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12128221 TAAGTATTCA
12128231 TTTATATATATT-TATGTATT
1 TTTATA-ATATTATATGTATT
*
12128251 TTTATAATTTTATATGTATT
1 TTTATAATATTATATGTATT
12128271 TT
1 TT
12128273 ATCGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTATAATATTATATGTATT
Found at i:12128788 original size:12 final size:13
Alignment explanation
Indices: 12128762--12128787 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12128752 AAATTAAATC
12128762 TAAAAAATAATTT
1 TAAAAAATAATTT
12128775 TAAAAAATAATTT
1 TAAAAAATAATTT
12128788 ATTTTTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAATAATTT
Found at i:12129266 original size:15 final size:15
Alignment explanation
Indices: 12129246--12129299 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
12129236 ATACTACAAA
12129246 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
12129261 ATATTTATAATTATAAT
1 ATATTTATTA-T-TAAT
*
12129278 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
12129295 ATATT
1 ATATT
12129300 AATATAGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:12129285 original size:19 final size:19
Alignment explanation
Indices: 12129261--12129297 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12129251 TATTATTAAT
*
12129261 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
12129280 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
12129298 TTAATATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:12129363 original size:16 final size:16
Alignment explanation
Indices: 12129332--12129368 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12129322 ATGTGAATAA
12129332 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
12129348 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
12129364 TATTA
1 TATTA
12129369 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:12129420 original size:22 final size:22
Alignment explanation
Indices: 12129380--12129435 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
12129370 AATAAAATTG
*
12129380 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
12129400 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
12129422 TATTAATAATTTAT
1 AAATAATAAATTAT
12129436 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:12130510 original size:3 final size:3
Alignment explanation
Indices: 12130502--12130547 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
12130492 TAGTTAAAGT
12130502 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
12130548 GAAAGTAGGA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12148336 original size:7 final size:7
Alignment explanation
Indices: 12148324--12148359 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
12148314 GAAGACTAAA
12148324 GGCAAAG
1 GGCAAAG
12148331 GGCAAAG
1 GGCAAAG
*
12148338 GGCAGAG
1 GGCAAAG
12148345 GGCAAAG
1 GGCAAAG
*
12148352 GGAAAAG
1 GGCAAAG
12148359 G
1 G
12148360 CGACAAGGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.47, T:0.00
Consensus pattern (7 bp):
GGCAAAG
Found at i:12152477 original size:44 final size:44
Alignment explanation
Indices: 12152414--12152501 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
12152404 ACAATAATGG
12152414 ATCGTTTCCTCTTCTTTTCTTTTTTTTCTTTTGAACTTTGCATT
1 ATCGTTTCCTCTTCTTTTCTTTTTTTTCTTTTGAACTTTGCATT
12152458 ATCGTTTCCTCTTCTTTTCTTTTTTTTCTTTTGAACTTTGCATT
1 ATCGTTTCCTCTTCTTTTCTTTTTTTTCTTTTGAACTTTGCATT
12152502 TTGCAATGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.09, C:0.20, G:0.07, T:0.64
Consensus pattern (44 bp):
ATCGTTTCCTCTTCTTTTCTTTTTTTTCTTTTGAACTTTGCATT
Found at i:12155450 original size:16 final size:17
Alignment explanation
Indices: 12155429--12155465 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
12155419 ACTGAGATAA
12155429 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
12155445 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
12155463 AAA
1 AAA
12155466 ACTTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:12158348 original size:23 final size:25
Alignment explanation
Indices: 12158322--12158368 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12158312 TATCATTTAT
*
12158322 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
12158345 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
12158369 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:12158689 original size:46 final size:46
Alignment explanation
Indices: 12158629--12158929 Score: 386
Period size: 46 Copynumber: 6.7 Consensus size: 46
12158619 TTTGACGTGA
* * ** * * *
12158629 TGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
12158675 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12158721 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12158767 TGCCATGGTATCTTTCAACCATGATCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12158813 TGTCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
12158851 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
12158897 TGCCATGGTATCTTTCAACCATGGTCTTACACA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA
12158930 GAGGTTGTCA
Statistics
Matches: 227, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
38 32 0.14
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 5 0.02
46 181 0.80
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:12158745 original size:92 final size:88
Alignment explanation
Indices: 12158629--12158977 Score: 408
Period size: 84 Copynumber: 4.0 Consensus size: 88
12158619 TTTGACGTGA
* * ** *
12158629 TGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CA--TTCT-TCAGGTTGCCATGGTATCTTTCAAC
** * *
12158694 CATGGTCTTATTCTTTTCATGTCACGT
62 CATGGTCTTACACATTTCATATCACGT
12158721 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CAT-TC-T-TCAGGTTGCCATGGTATCTTTCAAC
* *
12158786 CATGATCTTACACATTTCATATCAGGT
62 CATGGTCTTACACATTTCATATCACGT
* *
12158813 TGTCATGGTATCTTTCAACCATGGTCTTA-CA--C-ACAGGTTGCCATGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
*
12158874 GTCTTACACATTTCATATCATGT
66 GTCTTACACATTTCATATCACGT
** *
12158897 TGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-AGAGGTTGTCATGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
*
12158958 GTCTTACACAATTCATATCA
66 GTCTTACACATTTCATATCA
12158978 GAGAGCACAC
Statistics
Matches: 234, Mismatches: 21, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
84 126 0.54
87 1 0.00
90 3 0.01
91 2 0.01
92 102 0.44
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (88 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
GTCTTACACATTTCATATCACGT
Found at i:12158859 original size:38 final size:38
Alignment explanation
Indices: 12158808--12158967 Score: 212
Period size: 38 Copynumber: 4.0 Consensus size: 38
12158798 CATTTCATAT
*
12158808 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
12158846 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
*
12158891 TCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
12158930 GAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
12158968 ATTCATATCA
Statistics
Matches: 109, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
38 67 0.61
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 32 0.29
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:12158901 original size:130 final size:122
Alignment explanation
Indices: 12158719--12158967 Score: 390
Period size: 130 Copynumber: 2.0 Consensus size: 122
12158709 TTCATGTCAC
12158719 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
12158784 ACCATGATCTTACACATTTCATATCAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACACAG
66 ACCATGATCTT--ACA---C--A-CAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACACAG
* *
12158849 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
* *
12158914 ACCATGGTCTTACACAGAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
66 ACCATGATCTTACACACAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACA
12158968 ATTCATATCA
Statistics
Matches: 115, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
122 37 0.32
123 1 0.01
125 1 0.01
128 3 0.03
130 73 0.63
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (122 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCA
ACCATGATCTTACACACAGGTTGTCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:12158941 original size:46 final size:46
Alignment explanation
Indices: 12158849--12158967 Score: 146
Period size: 46 Copynumber: 2.8 Consensus size: 46
12158839 TTACACACAG
***
12158849 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACAGAGCATATCAT
12158895 GTTGCCATGGTATCTTTCAACCATGGTCTTACACAGAG--------
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACAGAGCATATCAT
*
12158933 GTTGTCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
12158968 ATTCATATCA
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
38 34 0.49
46 35 0.51
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACAGAGCATATCAT
Found at i:12161269 original size:23 final size:23
Alignment explanation
Indices: 12161239--12161325 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
12161229 GCTTTACTGA
* *
12161239 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
12161262 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
12161283 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
12161305 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
12161326 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:12169824 original size:3 final size:3
Alignment explanation
Indices: 12169816--12169860 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
12169806 TCTCCGTTCC
12169816 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12169861 GTTGTCTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:12171036 original size:18 final size:19
Alignment explanation
Indices: 12171009--12171044 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12170999 TGTCTCTGTA
12171009 TTTTAATTTTTA-ATTTTT
1 TTTTAATTTTTAGATTTTT
*
12171027 TTTTATTTTTTAGATTTT
1 TTTTAATTTTTAGATTTT
12171045 AATATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTTAATTTTTAGATTTTT
Found at i:12178586 original size:6 final size:6
Alignment explanation
Indices: 12178575--12178605 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12178565 GAACGGGGCC
*
12178575 GAGGGG GAGGGG GAGGGG GAGGGG AAGGGG G
1 GAGGGG GAGGGG GAGGGG GAGGGG GAGGGG G
12178606 GGGAGATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (6 bp):
GAGGGG
Found at i:12189036 original size:33 final size:33
Alignment explanation
Indices: 12188999--12189078 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
12188989 CGTACAATTT
**
12188999 GAAAAGGTTAGGTATACTTTGTGTATACCATAA
1 GAAAAGGAAAGGTATACTTTGTGTATACCATAA
* *
12189032 GAAAAGGAAATGTATACTTTGTGTATACCACT-T
1 GAAAAGGAAAGGTATACTTTGTGTATACCA-TAA
12189065 GAAAAGGAAAGGTA
1 GAAAAGGAAAGGTA
12189079 CACTACATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 40 0.98
34 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (33 bp):
GAAAAGGAAAGGTATACTTTGTGTATACCATAA
Found at i:12189118 original size:65 final size:66
Alignment explanation
Indices: 12189032--12189179 Score: 181
Period size: 65 Copynumber: 2.3 Consensus size: 66
12189022 TATACCATAA
* ** * *
12189032 GAAAAGGAAATGTATACTTTGTGTATACCACTTGAAAAGGAAAGGTACACTACATGTGTA-CACT
1 GAAAAGGGAATGTGCACTTTGTGTATACAAATTGAAAAGGAAAGGTACACTACATGTGTACCACT
12189096 T
66 T
** ** * * *
12189097 GAAAAGGTTATGTGCACTTTGTGTATACAAATTGAAAAGGGTATGTACACTTCGTGTGTACCACT
1 GAAAAGGGAATGTGCACTTTGTGTATACAAATTGAAAAGGAAAGGTACACTACATGTGTACCACT
12189162 T
66 T
12189163 GAAAAGGGAATGTGCAC
1 GAAAAGGGAATGTGCAC
12189180 CTCGGGTGTA
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
65 49 0.71
66 20 0.29
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (66 bp):
GAAAAGGGAATGTGCACTTTGTGTATACAAATTGAAAAGGAAAGGTACACTACATGTGTACCACT
T
Found at i:12189189 original size:33 final size:33
Alignment explanation
Indices: 12189086--12189200 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 33
12189076 GTACACTACA
* *
12189086 TGTGTAC-ACTTGAAAAGGTTATGTGCACTTTG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* * *
12189118 TGTATACAAATTGAAAAGGGTATGTACACTTCG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* * *
12189151 TGTGTACCACTTGAAAAGGGAATGTGCACCTCG
1 TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
* *
12189184 GGTGTACAACTAGAAAA
1 TGTGTACAACTTGAAAA
12189201 AGAAAGGTCC
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
32 6 0.09
33 62 0.91
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (33 bp):
TGTGTACAACTTGAAAAGGGTATGTGCACTTCG
Found at i:12189189 original size:98 final size:99
Alignment explanation
Indices: 12188990--12189200 Score: 232
Period size: 98 Copynumber: 2.1 Consensus size: 99
12188980 TACCCAAATC
* * * *
12188990 GTACAATTTGAAAAGGTTAGGTATACTTTGTGTATACCATAAGAAAAGGAAATGTATACTTTGTG
1 GTACAACTTGAAAAGGTTAGGTACACTTTGTGTATACCATAAGAAAAGGAAATGTACACTTCGTG
*
12189055 TATACCACTTGAAAAGGAAAGGTACACTACATGT
66 TATACCACTTGAAAAGGAAAGGTACACTACAGGT
* * **
12189089 GTAC-ACTTGAAAAGGTTATGTGCACTTTGTGTATA-CA-AATTGAAAAGGGTATGTACACTTCG
1 GTACAACTTGAAAAGGTTAGGTACACTTTGTGTATACCATAA--GAAAAGGAAATGTACACTTCG
* * * * *
12189151 TGTGTACCACTTGAAAAGGGAATGTGCACCT-CGGGT
64 TGTATACCACTTGAAAAGGAAAGGTACA-CTACAGGT
*
12189187 GTACAACTAGAAAA
1 GTACAACTTGAAAA
12189201 AGAAAGGTCC
Statistics
Matches: 93, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
96 2 0.02
97 2 0.02
98 75 0.81
99 14 0.15
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (99 bp):
GTACAACTTGAAAAGGTTAGGTACACTTTGTGTATACCATAAGAAAAGGAAATGTACACTTCGTG
TATACCACTTGAAAAGGAAAGGTACACTACAGGT
Found at i:12189200 original size:66 final size:65
Alignment explanation
Indices: 12189076--12189200 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 65
12189066 AAAAGGAAAG
** * * * *
12189076 GTACACTACATGTGTACACTTGAAAAGGTTATGTGCACTTTGTGTATACAAATTGAAAAGGGTAT
1 GTACACTACATGTGTACACTTGAAAAGGGAATGTGCACCTCGGGTATACAAATAGAAAAGGGTAT
* * * *
12189141 GTACACTTCGTGTGTACCACTTGAAAAGGGAATGTGCACCTCGGGTGTACAACTAGAAAA
1 GTACACTACATGTGTA-CACTTGAAAAGGGAATGTGCACCTCGGGTATACAAATAGAAAA
12189201 AGAAAGGTCC
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
65 14 0.29
66 35 0.71
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (65 bp):
GTACACTACATGTGTACACTTGAAAAGGGAATGTGCACCTCGGGTATACAAATAGAAAAGGGTAT
Found at i:12192406 original size:7 final size:7
Alignment explanation
Indices: 12192396--12192489 Score: 52
Period size: 7 Copynumber: 13.3 Consensus size: 7
12192386 TACTTATGTT
12192396 TTATATA
1 TTATATA
12192403 TTATATTATA
1 -T-TAT-ATA
12192413 TTATATA
1 TTATATA
*
12192420 TAATATA
1 TTATATA
*
12192427 ATA-ATA
1 TTATATA
*
12192433 TAATATA
1 TTATATA
12192440 TTATATA
1 TTATATA
12192447 TTA-ATA
1 TTATATA
*
12192453 CTTAAATA
1 -TTATATA
12192461 TTA-AGT-
1 TTATA-TA
*
12192467 TAATATA
1 TTATATA
*
12192474 ATATATA
1 TTATATA
*
12192481 ATATATA
1 TTATATA
12192488 TT
1 TT
12192490 TTTATATCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
6 11 0.16
7 43 0.63
8 7 0.10
9 4 0.06
10 3 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (7 bp):
TTATATA
Found at i:12192411 original size:19 final size:19
Alignment explanation
Indices: 12192397--12192449 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
12192387 ACTTATGTTT
*
12192397 TATATATTATATTATATTA
1 TATATAATATATTATATTA
* *
12192416 TATATAATATAATAATATAA
1 TATATAATAT-ATTATATTA
*
12192436 TATATTATATATTA
1 TATATAATATATTA
12192450 ATACTTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATAATATATTATATTA
Found at i:12200130 original size:17 final size:18
Alignment explanation
Indices: 12200096--12200131 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12200086 TGAATTTCTA
12200096 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
12200114 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
12200131 T
1 T
12200132 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:12200595 original size:22 final size:20
Alignment explanation
Indices: 12200560--12200600 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
12200550 TCTTGTTTCT
12200560 TTTTAGCTTTGTTTCTTTTG
1 TTTTAGCTTTGTTTCTTTTG
12200580 TTTTATGCTTTTGTTTCTTTT
1 TTTTA-GC-TTTGTTTCTTTT
12200601 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTTAGCTTTGTTTCTTTTG
Found at i:12210177 original size:6 final size:6
Alignment explanation
Indices: 12210166--12210201 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
12210156 AGTCCAAGTG
12210166 GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA
1 GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA
12210202 AGAGTGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
GGAGCA
Found at i:12212046 original size:25 final size:25
Alignment explanation
Indices: 12212012--12212069 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
12212002 TAAAAATAAG
12212012 TAAAAATAATTAATTCTCTGCTTAA
1 TAAAAATAATTAATTCTCTGCTTAA
*
12212037 TAAAAATAATTAATTGTCTGCTTAA
1 TAAAAATAATTAATTCTCTGCTTAA
12212062 TAATAAAT
1 TAA-AAAT
12212070 CAAGATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (25 bp):
TAAAAATAATTAATTCTCTGCTTAA
Found at i:12213021 original size:97 final size:97
Alignment explanation
Indices: 12212838--12213022 Score: 219
Period size: 97 Copynumber: 1.9 Consensus size: 97
12212828 TAACATATAA
* * * * * * *
12212838 ATTTTTAATTTTTTTTAGAATTATTATAACAATTATTATTTATTTTATTTCATTTTTGGGTATTT
1 ATTTTTAATTTTTTTTAGAATAATTACAACAATCACTATTTATTTGATTTCATTTTTGGGCACTT
** *
12212903 GGGTTTGAGTCTTATGCTACAATGTTTCTTTT
66 GGACTTGAGTCTGATGCTACAATGTTTCTTTT
* * *
12212935 ATTTTTTATTTTTTTTGGAATAATTACAATCAA-CACTATTTATTTGGTTTCATTTTTGGGCACT
1 ATTTTTAATTTTTTTTAGAATAATTACAA-CAATCACTATTTATTTGATTTCATTTTTGGGCACT
* *
12212999 TGGACTTGAGTCTGCTGTTACAAT
65 TGGACTTGAGTCTGATGCTACAAT
12213023 AATAATTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
97 69 0.96
98 3 0.04
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (97 bp):
ATTTTTAATTTTTTTTAGAATAATTACAACAATCACTATTTATTTGATTTCATTTTTGGGCACTT
GGACTTGAGTCTGATGCTACAATGTTTCTTTT
Found at i:12213232 original size:9 final size:9
Alignment explanation
Indices: 12213218--12213243 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12213208 TATTTTCTGG
12213218 AATAATTAC
1 AATAATTAC
12213227 AATAATTAC
1 AATAATTAC
12213236 AATAATTA
1 AATAATTA
12213244 AAATCTATTT
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:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (9 bp):
AATAATTAC
Found at i:12213699 original size:89 final size:89
Alignment explanation
Indices: 12213227--12214147 Score: 669
Period size: 88 Copynumber: 10.4 Consensus size: 89
12213217 GAATAATTAC
* * * * * * * *
12213227 AATAATTACAATAATTAAAATCTATTTCATTTCATTTTTGAGGCACTTGGACTTTGAGTTTGCTT
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGAGGCACTTGGGC-TTGAGTCTGGTG
* *
12213292 CTACAATATTTTTTTTATTTTAT-GG
65 CTACAATATATTTTTTATTTT-TCGA
** * *
12213317 AATAATTATAATAA-TAGTTATATATTTCATTTCATTTTTCG-GGCACTTGGGCTTGAGTCTGGC
1 AATAATTATAATAATTA-CAATTTATTTCATTTCA-TTTTCGAGGCACTTGGGCTTGAGTCTGGT
* * * *
12213380 GTTGCAATATTTTTTTTTTAATTTTTCAA
64 GCTACAATA--TATTTTTT-ATTTTTCGA
* * * * *
12213409 AATAATTATAAAAATTACAATTTATATCATTTCATTTTC-ATGGCACTTGGGCTTGAATATGTTG
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGA-GGCACTTGGGCTTGAGTCTGGTG
* * *
12213473 TTGCAATA-ATTTTTCTTATTTTTTGA
65 CTACAATATA-TTTT-TTATTTTTCGA
** * *
12213499 AATAATTATAATAATTACAATTTCCTTCATTTCATTTT-TAGGACACTTGGGCTTGAGTCTGATG
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGAGG-CACTTGGGCTTGAGTCTGGTG
* *
12213563 AC-GCAATA-AGTTTTTATTTTTCGA
65 -CTACAATATATTTTTTATTTTTCGA
* * * *
12213587 AATAGTTATAATAATTACAATTTATTTCATTAT-ATTTTCGAGGCACTAGGGTTTGAGCCTGGTG
1 AATAATTATAATAATTACAATTTATTTCATT-TCATTTTCGAGGCACTTGGGCTTGAGTCTGGTG
*
12213651 CTACAATATATTTTTTATTTTCCGA
65 CTACAATATATTTTTTATTTTTCGA
* * * * *
12213676 AATAATTATAACAATTACCATTTATTTCATTCCATTTTCGAGGCACTTGGGCTTGAATTTGGTGC
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGAGGCACTTGGGCTTGAGTCTGGTGC
* * *
12213741 TACAAGAAATTTATTTTTTAACTTTT-GG
66 TAC----AATATATTTTTT-ATTTTTCGA
* * * * * * *
12213769 AATAATTATAATATTTAC----TA-TTGATTTCATTTTCGAGGAACATAGACTTGAGTCTGGTGT
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGAGGCACTTGGGCTTGAGTCTGGTGC
* * *
12213829 TGCAATA-A--ATTT-TTTTT-GG
66 TACAATATATTTTTTATTTTTCGA
* ** * * * * ***
12213848 AATAATTTTAATTGTTACTATTTATTTCATTTCATTTTTGGGGCACTTGGGCTTGATTCTGAAAC
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGAGGCACTTGGGCTTGAGTCTGGTGC
*
12213913 TACAATA-ATTTTTTATTTTTCGG
66 TACAATATATTTTTTATTTTTCGA
* * * * * * *
12213936 AATAATTATAGTAGTTACCA-TTAGTTTCATTTCATTTTCGGGGCACTTGGGCTTGATTCTAGAG
1 AATAATTATAATAATTACAATTTA-TTTCATTTCATTTTCGAGGCACTTGGGCTTGAGTCTGGTG
12214000 CTACAATA-A--TTTTATTTTTC-A
65 CTACAATATATTTTTTATTTTTCGA
* * * * * * *
12214021 GAATGATTATAATAATTAC-TTTATATTTCATTTCATTTT-TAGGACATTTAGGCTTGAGTTTAG
1 -AATAATTATAATAATTACAATT-TATTTCATTTCATTTTCGAGG-CACTTGGGCTTGAGTCTGG
* *
12214084 TGTTGCAATA-ATTTTTTA-TTTTCTGA
63 TGCTACAATATATTTTTTATTTTTC-GA
* *
12214110 AATAATTATAATAATTACTATTTATTACATTTCATTTT
1 AATAATTATAATAATTACAATTTATTTCATTTCATTTT
12214148 TGGGTCACTT
Statistics
Matches: 671, Mismatches: 117, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
79 21 0.03
81 3 0.00
83 3 0.00
84 38 0.06
85 2 0.00
86 67 0.10
87 16 0.02
88 198 0.30
89 102 0.15
90 108 0.16
91 21 0.03
92 58 0.09
93 30 0.04
94 4 0.01
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (89 bp):
AATAATTATAATAATTACAATTTATTTCATTTCATTTTCGAGGCACTTGGGCTTGAGTCTGGTGC
TACAATATATTTTTTATTTTTCGA
Found at i:12214198 original size:17 final size:18
Alignment explanation
Indices: 12214156--12214198 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
12214146 TTTGGGTCAC
12214156 TTGAAATTTTTTTCATAT
1 TTGAAATTTTTTTCATAT
* *
12214174 TTG-TATTTTTTT-ATTT
1 TTGAAATTTTTTTCATAT
12214190 TTGAAATTT
1 TTGAAATTT
12214199 CGGTTCTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.29
17 12 0.57
18 3 0.14
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (18 bp):
TTGAAATTTTTTTCATAT
Found at i:12214631 original size:22 final size:21
Alignment explanation
Indices: 12214593--12214641 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
12214583 TTAACGAATT
* *
12214593 AATTTTTAAAAAGAAAACAAG
1 AATTTTTAAAAACAAAACAAA
* *
12214614 AATTTTTAAAACCCAAAATAAA
1 AATTTTTAAAA-ACAAAACAAA
12214636 AATTTT
1 AATTTT
12214642 CATTATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (21 bp):
AATTTTTAAAAACAAAACAAA
Found at i:12215180 original size:21 final size:21
Alignment explanation
Indices: 12215156--12215196 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12215146 AAAAATGATA
*
12215156 TAATTTTA-TTAATTATTAATT
1 TAATATTACTTAA-TATTAATT
12215177 TAATATTACTTAATATTAAT
1 TAATATTACTTAATATTAAT
12215197 ATGTTAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATATTACTTAATATTAATT
Found at i:12216158 original size:28 final size:28
Alignment explanation
Indices: 12216126--12216180 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
12216116 GACGTTGATG
12216126 ATATT-TTATAAT-TATTTAATTAAGATAA
1 ATATTATTATAATAT-TTTAA-TAAGATAA
*
12216154 ATATTATTTTAATATTTTAATAAGATA
1 ATATTATTATAATATTTTAATAAGATA
12216181 TTTTATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 11 0.46
30 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
ATATTATTATAATATTTTAATAAGATAA
Found at i:12216205 original size:11 final size:10
Alignment explanation
Indices: 12216183--12216216 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
12216173 ATAAGATATT
12216183 TTATTATTTA
1 TTATTATTTA
12216193 TTATTATTTTA
1 TTATTA-TTTA
12216204 TTATTAATTTA
1 TTATT-ATTTA
12216215 TT
1 TT
12216217 TAATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 15 0.68
12 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATTATTTA
Found at i:12217901 original size:40 final size:40
Alignment explanation
Indices: 12217853--12217990 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
12217843 ATCGAGAATA
*
12217853 TAAAGTGGATAGGATTCGTTCCTGATTCACTATAAT-ATT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATAATAATT
**
12217892 TCAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATT
1 T-AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAATT
* ** *
12217933 TAAAGT-GACTAGGATTTATTCCTGATTCACTATGGTAACT
1 TAAAGTGGA-TAGGATTTGTTCCTGATTCACTATAATAATT
* *
12217973 TAAGGCGGATAGGATTTG
1 TAAAGTGGATAGGATTTG
12217991 ACCTGAAAAG
Statistics
Matches: 87, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
39 3 0.03
40 78 0.90
41 6 0.07
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTGTTCCTGATTCACTATAATAATT
Found at i:12218046 original size:79 final size:79
Alignment explanation
Indices: 12217955--12218196 Score: 326
Period size: 79 Copynumber: 3.1 Consensus size: 79
12217945 GATTTATTCC
* * *
12217955 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGGTAGTCCTGATTCGCTAC
1 TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTAC
*
12218020 GGTTACATGATATA
66 AGTTACATGATATA
*
12218034 TGATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTAC
1 TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTAC
** *
12218099 AGTTACAAAATACA
66 AGTTACATGATATA
* * * * *
12218113 TGATTTC-TTATGATAACTTAATGTGGGTAGGATTTGACCTGAAAA-GGTAATCCTGGTTCACTA
1 TGA-TTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTA
* *
12218176 CAGTTACATGAGATG
65 CAGTTACATGATATA
12218191 TGATTC
1 TGATTC
12218197 GAGAGAGTGC
Statistics
Matches: 143, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
77 3 0.02
78 29 0.20
79 108 0.76
80 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (79 bp):
TGATTCATTATGGTAACTTAAGGTGGATAGGATTTGACCTGAAAAGGGTAATCCTGATTCGCTAC
AGTTACATGATATA
Found at i:12235818 original size:31 final size:31
Alignment explanation
Indices: 12235780--12235840 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
12235770 AGATGGCTCC
*
12235780 CAGGGATGATTTTCTTCCCAACCTTGTCTCT
1 CAGGGATGATTTTCTTCCCAACCTTATCTCT
12235811 CAGGGATGATTTTCTTCCCAACCTTATCTC
1 CAGGGATGATTTTCTTCCCAACCTTATCTC
12235841 AATTTCTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.38
Consensus pattern (31 bp):
CAGGGATGATTTTCTTCCCAACCTTATCTCT
Found at i:12238403 original size:47 final size:47
Alignment explanation
Indices: 12238333--12238465 Score: 151
Period size: 49 Copynumber: 2.8 Consensus size: 47
12238323 ATGCCGACGT
*
12238333 CATGTTCCAAACATGGTCTTACACTAGCTCTCACATCTAAGTCGATGC
1 CATGTTCCAGACA-GGTCTTACACTAGCTCTCACATCTAAGTCGATGC
* **
12238381 CATGTTCCAGACAGGTCTTACACTGGCTCTCACTTATCTGTGTCGATGC
1 CATGTTCCAGACAGGTCTTACACTAGCTCTCAC--ATCTAAGTCGATGC
* * * *
12238430 CATG-TCTAAGACAGGTTTTACACTAGCACACACATC
1 CATGTTC-CAGACAGGTCTTACACTAGCTCTCACATC
12238466 ACCCAAATGT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 22 0.30
48 14 0.19
49 37 0.51
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (47 bp):
CATGTTCCAGACAGGTCTTACACTAGCTCTCACATCTAAGTCGATGC
Found at i:12248606 original size:200 final size:200
Alignment explanation
Indices: 12248210--12248594 Score: 673
Period size: 200 Copynumber: 1.9 Consensus size: 200
12248200 ACCCCAAATA
*
12248210 AAGTTTCATACCATTCATTCGATCTCCTCACAAATCCCTTGCGAAATTATCATTAGATTACATGA
1 AAGTTTCATACCAGTCATTCGATCTCCTCACAAATCCCTTGCGAAATTATCATTAGATTACATGA
*
12248275 AGTAGATGGGAACCTAAAAAAGGACCATTTGAGCTAAAGTAACTTTTCCTAATAAAGATAATTAT
66 AGTAGATGGAAACCTAAAAAAGGACCATTTGAGCTAAAGTAACTTTTCCTAATAAAGATAATTAT
* *
12248340 TATAACAACTCGTTTTCAATGGTGTCGAAAATAGTAGTTTCAAGACCACAATTCCAACATGTGAG
131 TATAACAACTCGTTTTCAATGCTGTCAAAAATAGTAGTTTCAAGACCACAATTCCAACATGTGAG
12248405 TCCGT
196 TCCGT
* *
12248410 AAGTTTCGTACCAGTCATTCGATCTCCTTACAAATCCCTTGCGAAATTATCATTAGATTACATGA
1 AAGTTTCATACCAGTCATTCGATCTCCTCACAAATCCCTTGCGAAATTATCATTAGATTACATGA
*
12248475 AGTAGATGGAAACCTAAAGAAGGACCGA-TTGAGCTAAAGTAACTTTTCCTAATAAAGATAATTA
66 AGTAGATGGAAACCTAAAAAAGGACC-ATTTGAGCTAAAGTAACTTTTCCTAATAAAGATAATTA
* *
12248539 TTGTAACAACTCGTTTTCAATGCTGTCAAAAATAGTAGTTTCAAGACCATAATTCC
130 TTATAACAACTCGTTTTCAATGCTGTCAAAAATAGTAGTTTCAAGACCACAATTCC
12248595 GATGTGTGAG
Statistics
Matches: 175, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
200 174 0.99
201 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (200 bp):
AAGTTTCATACCAGTCATTCGATCTCCTCACAAATCCCTTGCGAAATTATCATTAGATTACATGA
AGTAGATGGAAACCTAAAAAAGGACCATTTGAGCTAAAGTAACTTTTCCTAATAAAGATAATTAT
TATAACAACTCGTTTTCAATGCTGTCAAAAATAGTAGTTTCAAGACCACAATTCCAACATGTGAG
TCCGT
Found at i:12249083 original size:26 final size:25
Alignment explanation
Indices: 12249034--12249091 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
12249024 GCCACATGGC
*
12249034 ATTCTTTTATACCTCTTTTTTCTTT
1 ATTCTTTTATACCTCTTCTTTCTTT
*
12249059 -TTCTTTTATACATTTCTTCTTTCTTT
1 ATTCTTTTATAC--CTCTTCTTTCTTT
12249085 ATTCTTT
1 ATTCTTT
12249092 CTCCTGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 11 0.39
26 11 0.39
27 6 0.21
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (25 bp):
ATTCTTTTATACCTCTTCTTTCTTT
Found at i:12250171 original size:19 final size:19
Alignment explanation
Indices: 12250137--12250174 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12250127 GTAGACCTAG
**
12250137 AAAAAGAAAATTAAAAAAT
1 AAAAAGAAAAGAAAAAAAT
12250156 AAAAAGAAAAGAAAAAAAT
1 AAAAAGAAAAGAAAAAAAT
12250175 GTATAATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAAAT
Found at i:12255773 original size:22 final size:22
Alignment explanation
Indices: 12255731--12255774 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12255721 AGAGGGAAAA
*
12255731 AAATAAAAAAGAAAATTTTAAT
1 AAATAAAAAAGAAAATATTAAT
*
12255753 AAATTAAAAA-AAAATCATTAAT
1 AAATAAAAAAGAAAAT-ATTAAT
12255775 TTAAATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATAAAAAAGAAAATATTAAT
Found at i:12262375 original size:68 final size:69
Alignment explanation
Indices: 12262242--12262378 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 69
12262232 CTTGCAAAAA
* *
12262242 TGTGAAAAACTAGATAGGCAAAATAAGTACAAGCAATAATGCAAATTAGGTTTCCCGAGACATAG
1 TGTGAAAAACTAGATAGGCAAAATAAGTAAAAGCAATAATACAAATTAGGTTTCCCGAGACATAG
12262307 ACAT
66 ACAT
* * * *
12262311 TGTGAAAAACTAGATAGGCAAAAT-AGTAAAAGCAATGATACAAATTTGGTTTCCTGAGATATAG
1 TGTGAAAAACTAGATAGGCAAAATAAGTAAAAGCAATAATACAAATTAGGTTTCCCGAGACATAG
12262375 ACAT
66 ACAT
12262379 GAAGAAAGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
68 38 0.61
69 24 0.39
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (69 bp):
TGTGAAAAACTAGATAGGCAAAATAAGTAAAAGCAATAATACAAATTAGGTTTCCCGAGACATAG
ACAT
Found at i:12264550 original size:15 final size:15
Alignment explanation
Indices: 12264530--12264558 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12264520 GGAACCCAAA
12264530 TAATCATAAATTATG
1 TAATCATAAATTATG
12264545 TAATCATAAATTAT
1 TAATCATAAATTAT
12264559 CTAAAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (15 bp):
TAATCATAAATTATG
Found at i:12271881 original size:13 final size:13
Alignment explanation
Indices: 12271865--12271930 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
12271855 TTTAAATTAA
12271865 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
12271878 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
* *
12271891 ATTTTTTC-ACAGC
1 A-CTTTTCAAAAGC
*
12271904 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
*
12271917 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
12271930 A
1 A
12271931 TTGTCAAACT
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 5 0.12
13 31 0.77
14 4 0.10
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:12271896 original size:26 final size:27
Alignment explanation
Indices: 12271867--12271938 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 27
12271857 TAAATTAAAC
*
12271867 TTTTCAAAAGCACTTCTCAAAAGTATT
1 TTTTCAAAAGCACTTCTCAAAAGTACT
* *
12271894 TTTTC-ACAGCACTTTTCAAAAGTACT
1 TTTTCAAAAGCACTTCTCAAAAGTACT
*
12271920 TTTT-AAAAGCA-TTGTCAAA
1 TTTTCAAAAGCACTTCTCAAA
12271939 CTAACCCTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 7 0.18
26 27 0.69
27 5 0.13
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (27 bp):
TTTTCAAAAGCACTTCTCAAAAGTACT
Found at i:12272122 original size:27 final size:26
Alignment explanation
Indices: 12272076--12272126 Score: 61
Period size: 27 Copynumber: 1.9 Consensus size: 26
12272066 TAAAAAATTT
12272076 AAAAATATGTTTAATAAATAGAAATAA
1 AAAAATATGTTTAATAAATA-AAATAA
12272103 AAAAAT-TGTTTTCAAT-AATAAAAT
1 AAAAATATG-TTT-AATAAATAAAAT
12272127 TATATATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
26 6 0.27
27 13 0.59
28 3 0.14
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (26 bp):
AAAAATATGTTTAATAAATAAAATAA
Done.