Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 11 of 172
Found at i:3028806 original size:19 final size:19
Alignment explanation
Indices: 3028769--3028833 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 19
3028759 ATAAAAGTTT
*
3028769 TAAAAAATATATTTAAAAAAA
1 TAAAAAATA-CTTT-AAAAAA
3028790 TAAAAAACT-CTTT-AAAAA
1 TAAAAAA-TACTTTAAAAAA
*
3028808 TAAAAAATATTTTAAAAAA
1 TAAAAAATACTTTAAAAAA
3028827 TATAAAA
1 TA-AAAA
3028834 GATTCTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 1 0.03
18 15 0.39
19 7 0.18
20 7 0.18
21 7 0.18
22 1 0.03
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAAATACTTTAAAAAA
Found at i:3029215 original size:19 final size:19
Alignment explanation
Indices: 3029188--3029224 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3029178 TGAATTTGAG
3029188 AATC-TTTTTATAGTTTTAA
1 AATCATTTTTAT-GTTTTAA
3029207 AATCATTTTTATGTTTTA
1 AATCATTTTTATGTTTTA
3029225 TTTTTTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
AATCATTTTTATGTTTTAA
Found at i:3036504 original size:20 final size:19
Alignment explanation
Indices: 3036475--3036514 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
3036465 TCTTTTCAAG
3036475 TTTCACATCTCATTTCATCA
1 TTTCACATCTCATTTC-TCA
*
3036495 TTTCATATCTCATTTCTCA
1 TTTCACATCTCATTTCTCA
3036514 T
1 T
3036515 AATTCAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTCACATCTCATTTCTCA
Found at i:3036544 original size:27 final size:27
Alignment explanation
Indices: 3036511--3036565 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3036501 ATCTCATTTC
3036511 TCATAATTCAATTCATATTCACAACAA
1 TCATAATTCAATTCATATTCACAACAA
3036538 TCATAATTCAATTCATATTCACAACAA
1 TCATAATTCAATTCATATTCACAACAA
3036565 T
1 T
3036566 ATACTATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.35
Consensus pattern (27 bp):
TCATAATTCAATTCATATTCACAACAA
Found at i:3036576 original size:24 final size:27
Alignment explanation
Indices: 3036511--3036580 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
3036501 ATCTCATTTC
*
3036511 TCATAATTCAATTCATATTCACAACAA
1 TCATAACTCAATTCATATTCACAACAA
*
3036538 TCATAATTCAATTCATATTCACAACAA
1 TCATAACTCAATTCATATTCACAACAA
*
3036565 T-AT-ACT-ATTTCATATT
1 TCATAACTCAATTCATATT
3036581 TCATTTCTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.22
25 2 0.05
26 2 0.05
27 28 0.68
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (27 bp):
TCATAACTCAATTCATATTCACAACAA
Found at i:3037818 original size:3 final size:3
Alignment explanation
Indices: 3037810--3037848 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3037800 TTTTCCTTTC
*
3037810 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3037849 ATAACATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3040338 original size:19 final size:20
Alignment explanation
Indices: 3040298--3040335 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3040288 GAAATAGAAA
*
3040298 AAACTGATTTAAAAAAAAAG
1 AAACCGATTTAAAAAAAAAG
3040318 AAACCGATTTAAAAAAAA
1 AAACCGATTTAAAAAAAA
3040336 GAACAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.08, G:0.08, T:0.18
Consensus pattern (20 bp):
AAACCGATTTAAAAAAAAAG
Found at i:3040346 original size:20 final size:19
Alignment explanation
Indices: 3040303--3040354 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3040293 AGAAAAAACT
**
3040303 GATTTAAAAAAAAAGAAACC
1 GATTT-AAAAAAAAGAAAAA
3040323 GATTTAAAAAAAAGAACAAA
1 GATTTAAAAAAAAGAA-AAA
*
3040343 GATTCAAAAAAA
1 GATTTAAAAAAA
3040355 TAAATTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.67, C:0.08, G:0.10, T:0.15
Consensus pattern (19 bp):
GATTTAAAAAAAAGAAAAA
Found at i:3041116 original size:3 final size:3
Alignment explanation
Indices: 3041108--3041138 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3041098 AAATTTGATG
*
3041108 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3041139 ATTTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:3041144 original size:6 final size:6
Alignment explanation
Indices: 3041135--3041161 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3041125 ATCATTATTA
3041135 TTATAT TTATAT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATAT TTA
3041162 CTTATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:3041144 original size:12 final size:12
Alignment explanation
Indices: 3041108--3041156 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
3041098 AAATTTGATG
3041108 TTATTAT-TATTA
1 TTATTATAT-TTA
3041120 TTATTATCA-TTA
1 TTATTAT-ATTTA
3041132 TTATTATATTTA
1 TTATTATATTTA
3041144 -TATTTATATTTA
1 TTA-TTATATTTA
3041156 T
1 T
3041157 ATTTACTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.09
12 29 0.91
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATTATATTTA
Found at i:3041144 original size:18 final size:17
Alignment explanation
Indices: 3041109--3041161 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 17
3041099 AATTTGATGT
3041109 TATTATTATTAT-TATTA
1 TATTATTATTATAT-TTA
3041126 TCATTATTATTATATTTA
1 T-ATTATTATTATATTTA
3041144 TATT-TATATTTATATTTA
1 TATTAT-TA-TTATATTTA
3041162 CTTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.03
17 6 0.19
18 24 0.75
19 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTATTATATTTA
Found at i:3042547 original size:30 final size:30
Alignment explanation
Indices: 3042494--3042575 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
3042484 GCGTAACCTC
* * * **
3042494 GATATAATTTCAACTTGTTTGAGCAATTCT
1 GATATAATGTCAGCTTGTGTGAGCAACCCT
* *
3042524 GTTATAATGTCAGTTTGTGTGAGCAACCCT
1 GATATAATGTCAGCTTGTGTGAGCAACCCT
*
3042554 GATATACTGTCAGCTTGTGTGA
1 GATATAATGTCAGCTTGTGTGA
3042576 ATATCATATT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.39
Consensus pattern (30 bp):
GATATAATGTCAGCTTGTGTGAGCAACCCT
Found at i:3044778 original size:30 final size:30
Alignment explanation
Indices: 3044744--3044804 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
3044734 CAATTCCAAG
3044744 ACTTGAGACTTTGACAAGCGTATCATGGCC
1 ACTTGAGACTTTGACAAGCGTATCATGGCC
*
3044774 ACTTGAGACTTTGACATGCGTATCATGGCC
1 ACTTGAGACTTTGACAAGCGTATCATGGCC
3044804 A
1 A
3044805 GATCTTTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (30 bp):
ACTTGAGACTTTGACAAGCGTATCATGGCC
Found at i:3048041 original size:15 final size:14
Alignment explanation
Indices: 3048002--3048043 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3047992 TTGATCTATA
3048002 TAATCAAATTTAAC
1 TAATCAAATTTAAC
3048016 TAATTCAAATTTAATTC
1 TAA-TCAAATTTAA--C
3048033 TAATC-AATTTA
1 TAATCAAATTTA
3048044 GTCCAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.12
15 16 0.64
16 2 0.08
17 4 0.16
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATCAAATTTAAC
Found at i:3056817 original size:20 final size:20
Alignment explanation
Indices: 3056794--3056848 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
3056784 GTATGTTCCC
3056794 ATTAACTTATGTTAATTAAG
1 ATTAACTTATGTTAATTAAG
3056814 ATTATGAC-TA-GTTAATTAAG
1 ATTA--ACTTATGTTAATTAAG
3056834 ATTAA-TTAATGTTAA
1 ATTAACTT-ATGTTAA
3056849 AAAAAGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 2 0.07
19 1 0.03
20 23 0.77
21 2 0.07
22 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (20 bp):
ATTAACTTATGTTAATTAAG
Found at i:3061071 original size:17 final size:17
Alignment explanation
Indices: 3061031--3061071 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3061021 TAGAACAATC
*
3061031 CGCCAAACCCTAGAGTT
1 CGCCAAAACCTAGAGTT
* *
3061048 TGTCAAAACCTAGAGTT
1 CGCCAAAACCTAGAGTT
3061065 CGCCAAA
1 CGCCAAA
3061072 TGACGAATCC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (17 bp):
CGCCAAAACCTAGAGTT
Found at i:3067443 original size:21 final size:21
Alignment explanation
Indices: 3067419--3067487 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
3067409 TTAAAATTAT
3067419 TAAAATTATTTTTTTGAAATA
1 TAAAATTATTTTTTTGAAATA
*
3067440 TAAAATTA-----TTAAAATTA
1 TAAAATTATTTTTTTGAAA-TA
* *
3067457 TTATATTATTTTTTTGAAATA
1 TAAAATTATTTTTTTGAAATA
3067478 TAAAATTATT
1 TAAAATTATT
3067488 AAAATATATC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
21 18 0.50
22 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TAAAATTATTTTTTTGAAATA
Found at i:3067474 original size:38 final size:39
Alignment explanation
Indices: 3067409--3067492 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 39
3067399 GTAAATGATT
3067409 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
*
3067448 TTAAAATTATT-ATATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
3067486 TTAAAAT
1 TTAAAAT
3067493 ATATCATTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 33 0.75
39 11 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (39 bp):
TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
Found at i:3067854 original size:23 final size:23
Alignment explanation
Indices: 3067823--3067867 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3067813 AATTGCTTAA
3067823 GGTGATCGAATTTGGGGATTTTG
1 GGTGATCGAATTTGGGGATTTTG
*
3067846 GGTGGTCGAATTTGGGGATTTT
1 GGTGATCGAATTTGGGGATTTT
3067868 ATGTAAGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.04, G:0.40, T:0.40
Consensus pattern (23 bp):
GGTGATCGAATTTGGGGATTTTG
Found at i:3067887 original size:28 final size:30
Alignment explanation
Indices: 3067856--3067925 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 30
3067846 GGTGGTCGAA
*
3067856 TTTGGGGATTTTATG-TAAGGGTTT-TGAT
1 TTTGGGGATTTTATGTTAAGGATTTCTGAT
*
3067884 TTTGGGGATTTT-TGTTTAGGATTTCTGAT
1 TTTGGGGATTTTATGTTAAGGATTTCTGAT
*
3067913 TTTGGAGATTTTA
1 TTTGGGGATTTTA
3067926 GGGATTGCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 19 0.53
29 15 0.42
ACGTcount: A:0.17, C:0.01, G:0.29, T:0.53
Consensus pattern (30 bp):
TTTGGGGATTTTATGTTAAGGATTTCTGAT
Found at i:3068241 original size:21 final size:19
Alignment explanation
Indices: 3068211--3068266 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
3068201 AATCTTCAAG
*
3068211 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3068230 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
3068251 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
3068267 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3068288 original size:23 final size:22
Alignment explanation
Indices: 3068211--3068289 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 22
3068201 AATCTTCAAG
* *
3068211 GATATACAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
3068233 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
3068251 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
3068273 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
3068290 GATTTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
21 11 0.23
22 8 0.17
23 12 0.25
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:3068511 original size:23 final size:21
Alignment explanation
Indices: 3068485--3068527 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3068475 TGGTTTGTTC
*
3068485 TTATTTTGTTGATCTGTGTATAA
1 TTATTTTATTGAT-T-TGTATAA
3068508 TTATTTTATTGATTTGTATA
1 TTATTTTATTGATTTGTATA
3068528 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.60
Consensus pattern (21 bp):
TTATTTTATTGATTTGTATAA
Found at i:3068906 original size:36 final size:36
Alignment explanation
Indices: 3068831--3068906 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
3068821 CATACATACG
*
3068831 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
3068868 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
3068904 TTT
1 TTT
3068907 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:3069015 original size:68 final size:66
Alignment explanation
Indices: 3068928--3069056 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
3068918 AATTTTATAT
* * * *
3068928 ACATACTTATATATATTTCTTACATATTAAAATATGTATATTTATATATATTATATTTTTTATAA
1 ACATACATATATATATTTCTT--ATATGAAAATATATATATTTATATATATTATAATTTTTATAA
3068993 TTC
64 TTC
* * * * *
3068996 ACATACATATATATTTTTCTTATATGCACATATATATATTTTTATATTTTATAATTTTTAT
1 ACATACATATATATATTTCTTATATGAAAATATATATATTTATATATATTATAATTTTTAT
3069057 CTATTTTCTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
66 33 0.63
68 19 0.37
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (66 bp):
ACATACATATATATATTTCTTATATGAAAATATATATATTTATATATATTATAATTTTTATAATT
C
Found at i:3069030 original size:23 final size:22
Alignment explanation
Indices: 3069000--3069042 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3068990 TAATTCACAT
*
3069000 ACATATATATTTTTCTTATATGC
1 ACATATATATATTT-TTATATGC
3069023 ACATATATATATTTTTATAT
1 ACATATATATATTTTTATAT
3069043 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
ACATATATATATTTTTATATGC
Found at i:3069030 original size:25 final size:25
Alignment explanation
Indices: 3068971--3069038 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
3068961 ATGTATATTT
*
3068971 ATATATATTATATTTTTTATAATTCAC
1 ATATATA-TAT-TTTTTTATAATGCAC
3068998 ATACATATATATTTTTCTTAT-ATGCAC
1 AT--ATATATATTTTT-TTATAATGCAC
3069025 ATATATATATTTTT
1 ATATATATATTTTT
3069039 ATATTTTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
25 12 0.32
27 13 0.35
28 7 0.19
29 5 0.14
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.54
Consensus pattern (25 bp):
ATATATATATTTTTTTATAATGCAC
Found at i:3073659 original size:17 final size:17
Alignment explanation
Indices: 3073637--3073669 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3073627 ATAATTGTCC
*
3073637 GCCAAACCCTAGAGTTT
1 GCCAAAACCTAGAGTTT
3073654 GCCAAAACCTAGAGTT
1 GCCAAAACCTAGAGTT
3073670 CACCAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (17 bp):
GCCAAAACCTAGAGTTT
Found at i:3073675 original size:17 final size:17
Alignment explanation
Indices: 3073638--3073676 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3073628 TAATTGTCCG
* **
3073638 CCAAACCCTAGAGTTTG
1 CCAAAACCTAGAGTTCA
3073655 CCAAAACCTAGAGTTCA
1 CCAAAACCTAGAGTTCA
3073672 CCAAA
1 CCAAA
3073677 TGGCGAACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.31, G:0.13, T:0.18
Consensus pattern (17 bp):
CCAAAACCTAGAGTTCA
Found at i:3078819 original size:15 final size:14
Alignment explanation
Indices: 3078794--3078835 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3078784 CTTTAAAATA
3078794 AATA-ATTTAATTT
1 AATATATTTAATTT
* *
3078807 AATTATTTTTAATAT
1 AA-TATATTTAATTT
3078822 AATATATTTAATTT
1 AATATATTTAATTT
3078836 TAGTTCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 12 0.52
15 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATATATTTAATTT
Found at i:3078971 original size:18 final size:19
Alignment explanation
Indices: 3078934--3078973 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3078924 ACAAATCGCG
3078934 TAACCTTAGGCGATTTTTT
1 TAACCTTAGGCGATTTTTT
3078953 TAACCTTAGGCGATTTTTT
1 TAACCTTAGGCGATTTTTT
3078972 TA
1 TA
3078974 CTCTGAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (19 bp):
TAACCTTAGGCGATTTTTT
Found at i:3079711 original size:64 final size:66
Alignment explanation
Indices: 3079634--3079767 Score: 191
Period size: 64 Copynumber: 2.0 Consensus size: 66
3079624 TCAACTTAGG
* *
3079634 TTCCACAAGTTACGTTAAATTTGATATTAAATGAAAAT-A-CGAGGACCACTAATCTACCATAAT
1 TTCCACAAATTACGTTAAATTTAATATTAAATGAAAATAATCGAGGACCACTAATCTACCATAAT
3079697 T
66 T
* * *
3079698 TTCCACAAATTACGTTAATTTTAATATTAAATGAAAATAAATTTGAGGACCACTAATCTACCATG
1 TTCCACAAATTACGTTAAATTTAATATTAAATGAAAAT-AA-TCGAGGACCACTAATCTACCATA
3079763 ATT
64 ATT
3079766 TT
1 TT
3079768 GGCATAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 35 0.57
66 1 0.02
68 25 0.41
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (66 bp):
TTCCACAAATTACGTTAAATTTAATATTAAATGAAAATAATCGAGGACCACTAATCTACCATAAT
T
Found at i:3081075 original size:29 final size:30
Alignment explanation
Indices: 3081032--3081090 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
3081022 GAATTGGAGC
* *
3081032 AAATCAAAATTTCATATATAAAATTGCACA
1 AAATCAAAAGTTCATATATAAAATTACACA
* *
3081062 AAATC-AAAGTTCATGTATACAATTACACA
1 AAATCAAAAGTTCATATATAAAATTACACA
3081091 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATATATAAAATTACACA
Found at i:3085572 original size:22 final size:21
Alignment explanation
Indices: 3085528--3085578 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
3085518 GTTTTCCTAC
*
3085528 AAAAAT-AA-AATAAAATAGT
1 AAAAATAAATAATAAAATAGG
3085547 AAAAATAAATAATAATAATAGG
1 AAAAATAAATAATAA-AATAGG
*
3085569 AAAATTAAAT
1 AAAAATAAAT
3085579 TTTTTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 2 0.07
21 5 0.19
22 14 0.52
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (21 bp):
AAAAATAAATAATAAAATAGG
Found at i:3089360 original size:30 final size:30
Alignment explanation
Indices: 3089301--3089357 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3089291 TTGGCCCTCC
*
3089301 TTCTTTGCTTCTTTCTTCAATCTAGCCCAA
1 TTCTTTCCTTCTTTCTTCAATCTAGCCCAA
* *
3089331 TTCTTTCCTT-TTTCTTCTATTTAGCCC
1 TTCTTTCCTTCTTTCTTCAATCTAGCCC
3089358 CAAATTGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.12, C:0.30, G:0.05, T:0.53
Consensus pattern (30 bp):
TTCTTTCCTTCTTTCTTCAATCTAGCCCAA
Found at i:3090020 original size:37 final size:37
Alignment explanation
Indices: 3089963--3090089 Score: 106
Period size: 37 Copynumber: 3.6 Consensus size: 37
3089953 TATATTATTA
* *
3089963 TATATTATG-ATTTTAGTAAATTCATA-TAAGAATAAT
1 TATATTAAGAATTTTATTAAATT-ATATTAAGAATAAT
*
3089999 TATATTAAGAATTTTATTAAATTATATTTAATAATAAT
1 TATATTAAGAATTTTATTAAATTATA-TTAAGAATAAT
* * * * *
3090037 TATGTTAA-AATATGATTAAATTAT-TT---ATTATT
1 TATATTAAGAATTTTATTAAATTATATTAAGAATAAT
*
3090069 TATATTAATAATTTTATTAAA
1 TATATTAAGAATTTTATTAAA
3090090 ATTTAATAAC
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
32 11 0.14
33 10 0.13
35 2 0.03
36 11 0.14
37 26 0.34
38 16 0.21
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (37 bp):
TATATTAAGAATTTTATTAAATTATATTAAGAATAAT
Found at i:3090269 original size:45 final size:43
Alignment explanation
Indices: 3090182--3090274 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 43
3090172 ATTACAATAT
*
3090182 CATTCCATTCAACCAAACGCAAGGATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAAC-CAAGAATACTATTACAGTTCTATTC
3090226 CATTCCATTCAACCAAA-CAATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACCAA--GAA-TACTATTACAGTTCTATTC
3090271 CATT
1 CATT
3090275 ATAGCTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 3 0.07
44 19 0.42
45 23 0.51
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.33
Consensus pattern (43 bp):
CATTCCATTCAACCAAACCAAGAATACTATTACAGTTCTATTC
Found at i:3090283 original size:16 final size:16
Alignment explanation
Indices: 3090256--3090311 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
3090246 TTGAATTACT
*
3090256 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
* *
3090272 ATTATAGCTCTATTCA
1 ATTACAGCTCTATTCC
3090288 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
3090304 ATTACAGC
1 ATTACAGC
3090312 GAACCAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:3090398 original size:21 final size:21
Alignment explanation
Indices: 3090369--3090413 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3090359 CTTTAAAAAT
3090369 ATTAAATTTGTTAAA-CATTAA
1 ATTAAATTTGTTAAACCA-TAA
* *
3090390 ATTATATTTTTTAAACCATAA
1 ATTAAATTTGTTAAACCATAA
3090411 ATT
1 ATT
3090414 TTAACTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTAAATTTGTTAAACCATAA
Found at i:3090829 original size:31 final size:31
Alignment explanation
Indices: 3090786--3090844 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3090776 TTAAAATGTG
*
3090786 TACAATTGAATCAAAATTAAAGTTTCATATA
1 TACAATTGAATCAAAATCAAAGTTTCATATA
* *
3090817 TACATTTGAATCACAATCAAAGTTTCAT
1 TACAATTGAATCAAAATCAAAGTTTCAT
3090845 GTGTATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (31 bp):
TACAATTGAATCAAAATCAAAGTTTCATATA
Found at i:3091928 original size:17 final size:17
Alignment explanation
Indices: 3091906--3091945 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
3091896 AGAGAAAAAC
*
3091906 AAATAAATAAAAATAAA
1 AAATAAAGAAAAATAAA
**
3091923 AAATAAAGCCAAATAAA
1 AAATAAAGAAAAATAAA
3091940 AAATAA
1 AAATAA
3091946 TAGTGAAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
AAATAAAGAAAAATAAA
Found at i:3093642 original size:15 final size:15
Alignment explanation
Indices: 3093619--3093661 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3093609 AAAACGTAGA
*
3093619 TATTAATTTTTAAGT
1 TATTCATTTTTAAGT
**
3093634 TATTCATTTTTATTT
1 TATTCATTTTTAAGT
3093649 TATTTCATTTTTA
1 TA-TTCATTTTTA
3093662 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (15 bp):
TATTCATTTTTAAGT
Found at i:3093651 original size:5 final size:5
Alignment explanation
Indices: 3093641--3093679 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
3093631 AGTTATTCAT
*
3093641 TTTTA TTTTA TTTCA TTTTTA TTTTA TTTT- TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT
3093680 TTATAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.13
5 22 0.73
6 4 0.13
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:3093655 original size:16 final size:16
Alignment explanation
Indices: 3093636--3093679 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
3093626 TTTTAAGTTA
3093636 TTCATTTTTATTTTAT
1 TTCATTTTTATTTTAT
3093652 TTCATTTTTATTTTAT
1 TTCATTTTTATTTTAT
3093668 TT--TTTTTATTTT
1 TTCATTTTTATTTT
3093680 TTATAAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.36
16 18 0.64
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCATTTTTATTTTAT
Found at i:3093683 original size:21 final size:21
Alignment explanation
Indices: 3093641--3093680 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3093631 AGTTATTCAT
3093641 TTTTATTTTATTTCATTTTTA
1 TTTTATTTTATTTCATTTTTA
*
3093662 TTTTATTTT-TTTTATTTTT
1 TTTTATTTTATTTCATTTTT
3093681 TATAAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTATTTTATTTCATTTTTA
Found at i:3106147 original size:42 final size:42
Alignment explanation
Indices: 3106061--3106169 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
3106051 AAAGGACGGC
* **
3106061 TCAAATATTGATTAGAACGGGGCATGAGGTGATCTAAGTGGT
1 TCAAATATTGATTAGAATGGGGCATGAGGTGATCTAAGCAGT
* *
3106103 TCAAAAATTGATCAGAATGGGGCATGAGGTGATCTGAA-CAGT
1 TCAAATATTGATTAGAATGGGGCATGAGGTGATCT-AAGCAGT
* *
3106145 TCAAATTTTGATTAGATTGGGGCAT
1 TCAAATATTGATTAGAATGGGGCAT
3106170 ATGACGATCT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 55 0.96
43 2 0.04
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.29
Consensus pattern (42 bp):
TCAAATATTGATTAGAATGGGGCATGAGGTGATCTAAGCAGT
Found at i:3107294 original size:45 final size:44
Alignment explanation
Indices: 3107254--3107357 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
3107244 CTCCCTGAAT
* * *
3107254 AGCAGTGGAGTAGGTTGAAAAATTACAGATCTTATCTCCCTAAGC
1 AGCAGTGGAGTAGATCG-AAAATGACAGATCTTATCTCCCTAAGC
* *
3107299 AGTAGTGGAGTAGATCGAAGATGACAGATCTTATCTCCCTAAGC
1 AGCAGTGGAGTAGATCGAAAATGACAGATCTTATCTCCCTAAGC
* *
3107343 AGTAGTGGAGCAGAT
1 AGCAGTGGAGTAGAT
3107358 TGAAGCCAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 39 0.74
45 14 0.26
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (44 bp):
AGCAGTGGAGTAGATCGAAAATGACAGATCTTATCTCCCTAAGC
Found at i:3107338 original size:44 final size:44
Alignment explanation
Indices: 3107278--3107362 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
3107268 TTGAAAAATT
*
3107278 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
*
3107322 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
3107363 CCAGTAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (44 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
Found at i:3107676 original size:9 final size:9
Alignment explanation
Indices: 3107662--3107737 Score: 116
Period size: 9 Copynumber: 8.4 Consensus size: 9
3107652 TTTGGTTAAA
*
3107662 AATTAACTG
1 AATTAACCG
3107671 AATTAACCG
1 AATTAACCG
*
3107680 AATTACCCG
1 AATTAACCG
3107689 AATTAACCG
1 AATTAACCG
3107698 AATTAACCG
1 AATTAACCG
*
3107707 AATTAATCG
1 AATTAACCG
*
3107716 AATTACCCG
1 AATTAACCG
3107725 AATTAACCG
1 AATTAACCG
3107734 AATT
1 AATT
3107738 GAATCACTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:3108199 original size:44 final size:44
Alignment explanation
Indices: 3108136--3108427 Score: 206
Period size: 44 Copynumber: 6.7 Consensus size: 44
3108126 ATGAAGAATT
3108136 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
**
3108180 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAA-A--
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
* * ** * * *
3108221 CCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATA
1 ACAG--ATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAGATG
* * ** * * * *
3108267 AAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATC---GCATC
1 ACAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCAAAG-ATG
** * * * * * *
3108310 A-AG-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGGCTGAAAAATT
1 ACAGATCTTATCTCCCT-AAGCAGTAGTGGAGCA-GATCAAAGATG
* *
3108354 ACAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
*
3108398 GCAGATCTTATCTCCCTAAGCAGTAGTGGA
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGA
3108428 TTTCCTTGAA
Statistics
Matches: 201, Mismatches: 34, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
41 30 0.15
42 4 0.02
43 16 0.08
44 124 0.62
45 13 0.06
46 14 0.07
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
Found at i:3108571 original size:195 final size:195
Alignment explanation
Indices: 3108239--3108622 Score: 653
Period size: 195 Copynumber: 2.0 Consensus size: 195
3108229 CCTATCTCCC
*
3108239 TGAAGTTGCAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TGAAGTTGCAGTAGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
* * *
3108304 CGCATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGGCTGAAAAATTACAAATCTTATCTCC
66 CGCATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAAAAATTACAAATCTTATCTCC
*
3108369 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATCTTATCTCCCTAAGCAGTAGTGGATTTCCT
131 CTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAGTGGATTTCCT
* *
3108434 TGAAGTTGCAGTAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TGAAGTTGCAGTAGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
* * * *
3108499 CGTATC-AGTTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCGAAGAATTACAGATCTTATCTC
66 CGCATCAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAAAAATTACAAATCTTATCTC
3108563 CCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAGTGGA
130 CCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAGTGGA
3108623 GCGGATTAAA
Statistics
Matches: 177, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
194 2 0.01
195 175 0.99
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (195 bp):
TGAAGTTGCAGTAGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
CGCATCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCGAAAAATTACAAATCTTATCTCC
CTAAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAGTGGATTTCCT
Found at i:3108609 original size:44 final size:44
Alignment explanation
Indices: 3108528--3108801 Score: 229
Period size: 44 Copynumber: 6.2 Consensus size: 44
3108518 CTGAGGTTGC
* *
3108528 AGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGAAG-ATGACAGATCTTATCTCCCTAAGCAGT
3108573 AGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGT
* * * * * * * ** *
3108617 AGTGGAGCGGAT-TAAAATAAAAGATCTTATCTCTCTGGAGTTGC
1 AGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCT-AAGCAGT
* * * * * *
3108661 AGTAGAGTATATCG--CATCA-AG-TCTTATCTCCCTGAG--GTT
1 AGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAG-T
* *
3108700 ACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGT
1 --AGTGGAGCAGATCGAAG-ATGACAGATCTTATCTCCCTAAGCAGT
* * * *
3108747 AGTGGAGCAGATCTAAGATGGCAGATCTTATCCCCCTAGGCAGT
1 AGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGT
3108791 AGTGGAGCAGA
1 AGTGGAGCAGA
3108802 CTGAAGCCAG
Statistics
Matches: 183, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
38 1 0.01
40 3 0.02
41 21 0.11
42 2 0.01
43 22 0.12
44 85 0.46
45 33 0.18
46 14 0.08
47 1 0.01
48 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (44 bp):
AGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGT
Found at i:3108737 original size:174 final size:174
Alignment explanation
Indices: 3108447--3108798 Score: 607
Period size: 174 Copynumber: 2.0 Consensus size: 174
3108437 AGTTGCAGTA
* *
3108447 GAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGTATCAGTTCTT
1 GAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGTTCTT
*
3108512 ATCTCCCTGAGGTTGCAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGTAGTG
66 ATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGTAGTG
*
3108577 GAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAGTG
131 GAGCAGATCGAAGATGACAGATCTTATCCCCCTAAGCAGTAGTG
* *
3108621 GAGCGGATTAAAATAAAAGATCTTATCTCTCTGGAGTTGCAGTAGAGTATATCGCATCAAG-TCT
1 GAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATC-AGTTCT
3108685 TATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGTAGT
65 TATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGTAGT
* * *
3108750 GGAGCAGATCTAAGATGGCAGATCTTATCCCCCTAGGCAGTAGTG
130 GGAGCAGATCGAAGATGACAGATCTTATCCCCCTAAGCAGTAGTG
3108795 GAGC
1 GAGC
3108799 AGACTGAAGC
Statistics
Matches: 168, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
174 166 0.99
175 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (174 bp):
GAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGTTCTT
ATCTCCCTGAGGTTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGATGACAGATCTTATCCCCCTAAGCAGTAGTG
Found at i:3108866 original size:44 final size:44
Alignment explanation
Indices: 3108434--3108866 Score: 190
Period size: 44 Copynumber: 9.9 Consensus size: 44
3108424 TGGATTTCCT
* * *
3108434 TGAAGTTGCAGTAGAGCGGATTAAAATAA-AGGATCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAAATAACA-GATCTTATCTCCC
* * ** * *
3108478 TGAAGTTGCAGTAGAGTAGA-T--CGTATCAGTTCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCC
* ** *
3108519 TGAGGTTGCAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGA-TTAA-AATAACAGATCTTATCTCCC
** * * * *
3108565 T-AAGCAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGAT-TAAAATAACAGATCTTATCTCCC
** * * * *
3108609 T-AAGCAGTAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTC
1 TGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCC
* * * * *** *
3108652 TGGAGTTGCAGTAGAGTATA-TCGCATCA-AG-TCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCC
* * ** *
3108693 TGAGGTTACAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCC
1 TGAAGTTGCAGTGGAGCAGA-TTAA-AATAACAGATCTTATCTCCC
** * * ** *
3108739 T-AAGCAGTAGTGGAGCAGATCTAAGATGGCAGATCTTATCCCCC
1 TGAAGTTGCAGTGGAGCAGAT-TAAAATAACAGATCTTATCTCCC
* ** * * * ** *
3108783 T-AGGCAGTAGTGGAGCAGACT-GAA-GCCAGTAATCCTATCTCCC
1 TGAAGTTGCAGTGGAGCAGATTAAAATAACAG--ATCTTATCTCCC
* *
3108826 TGAAGTTGCAGTGGAGCGGATTAAAATAATAGATCTTATCT
1 TGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCT
3108867 ATCTGACGTT
Statistics
Matches: 288, Mismatches: 82, Indels: 38
0.71 0.20 0.09
Matches are distributed among these distances:
41 58 0.20
42 4 0.01
43 36 0.12
44 124 0.43
45 36 0.12
46 30 0.10
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGATTAAAATAACAGATCTTATCTCCC
Found at i:3108985 original size:218 final size:217
Alignment explanation
Indices: 3108504--3109001 Score: 490
Period size: 218 Copynumber: 2.3 Consensus size: 217
3108494 TAGATCGTAT
* * * ** *
3108504 CAGTTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACCGAAGAATTACAGATCTTATCTCCCTAAG
1 CAGTT-TTATCTCCCT-AAGTTGCAGTGGAGCAAACTGAAG-ATGGCAGATCTTATCCCCCTAAG
* *
3108569 CAGTAGTGGAGCAGATCGAAGATGACAGATCTTATCTCCCTAAGCAGTAGTGGAGCGGATTAAAA
63 CAGTAGTGGAGCAGATCGAAGATGACAGATCCTATCTCCCTAAGCAGCAGTGGAGCGGATTAAAA
* * * * *
3108634 TAAAAGATCTTATCTCTCTGGAGTTGCAGTAGAGTATATCGCATCAAGTCTTATCTCCCTGAGGT
128 TAAAAGATCTTATCTATCTGGAGTTGCAGTAGAATAGATCGCATCAAGTCTTATCACCCTGAAGT
* * **
3108699 TACAGTGGAGCAGACCGAAGAATTA
193 TACAGCGGAACAGACCGAAGAAGCA
* ** * * *
3108724 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCT-AAGATGGCAGATCTTATCCCCCTAGGC
1 CAG-TTTTATCTCCCTAAGTTGCAGTGGAGCA-AACTGAAGATGGCAGATCTTATCCCCCTAAGC
* **
3108788 AGTAGTGGAGCAGA-CTG-A-A-GCCAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTA
64 AGTAGTGGAGCAGATC-GAAGATGACAG--ATCCTATCTCCCT-AAGCAGCAGTGGAGCGGATTA
* * *
3108849 AAATAATAGATCTTATCTATCT-GACGTTGCTGTAGAAATAGATCGCATC-TGATCTTATCACCC
125 AAATAAAAGATCTTATCTATCTGGA-GTTGCAGTAG-AATAGATCGCATCAAG-TCTTATCACCC
* * *
3108912 TGAAGTTGCAGCGGAACAGATCGAGGAAGCA
187 TGAAGTTACAGCGGAACAGACCGAAGAAGCA
* * * *
3108943 -AGTTTTATCCCCCTAAAGTTGCAGTGGGGCAAACTGAAGATGGCAAATCCTATCTCCCC
1 CAGTTTTATCTCCCT-AAGTTGCAGTGGAGCAAACTGAAGATGGCAGATCTTATC-CCCC
3109002 GACGTTGTAG
Statistics
Matches: 225, Mismatches: 41, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
215 4 0.02
216 1 0.00
217 29 0.13
218 113 0.50
219 63 0.28
220 14 0.06
221 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (217 bp):
CAGTTTTATCTCCCTAAGTTGCAGTGGAGCAAACTGAAGATGGCAGATCTTATCCCCCTAAGCAG
TAGTGGAGCAGATCGAAGATGACAGATCCTATCTCCCTAAGCAGCAGTGGAGCGGATTAAAATAA
AAGATCTTATCTATCTGGAGTTGCAGTAGAATAGATCGCATCAAGTCTTATCACCCTGAAGTTAC
AGCGGAACAGACCGAAGAAGCA
Found at i:3115504 original size:126 final size:123
Alignment explanation
Indices: 3115299--3115609 Score: 347
Period size: 126 Copynumber: 2.5 Consensus size: 123
3115289 AGGCTAAATT
* * * * * * *
3115299 CATTCTTAAAGATCAAGCCTAAAAGGCCTTTGAAG-TGAATCATCAATCCAAGGTCAAGTTTCAA
1 CATTCTTCAAGATCAAG-CTAAAAGACCCTTGAAGCAGAATCATCCATCCAAGATCAAGTCTCAA
* *
3115363 AGACCCTTGGTTAAAAGCTTTCCCCAATCTAGTTACACCAACATAAAAAAAGATAAAAACC
65 AGAACCTTGGATAAAAGCTTTCCCCAATCTAGTTACACCAAC-TAAAAAAAGAT-AAAACC
* *
3115424 CATTCTTCAGGATCAAGTCTAAAAGACCCTTGAAGCAGAATCTTCCATCCAAGATCAAGTCTCAA
1 CATTCTTCAAGATCAAG-CTAAAAGACCCTTGAAGCAGAATCATCCATCCAAGATCAAGTCTCAA
* ** * * * * *
3115489 ATAACCTTGGATAAAAGCTTTTTCCGATTTAGTTGCACCAACTCAAAGAAGATAAAACC
65 AGAACCTTGGATAAAAGCTTTCCCCAATCTAGTTACACCAACTAAAAAAAGATAAAACC
* * * *
3115548 CATTCTTCAATATCAAGCTTAGAAGACCCTTGAAGCAAAATCGTCCATCCCAA-ATCAAGTCT
1 CATTCTTCAAGATCAAGC-TAAAAGACCCTTGAAGCAGAATCATCCAT-CCAAGATCAAGTCT
3115610 TGACAACCTT
Statistics
Matches: 158, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
123 1 0.01
124 56 0.35
125 43 0.27
126 58 0.37
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (123 bp):
CATTCTTCAAGATCAAGCTAAAAGACCCTTGAAGCAGAATCATCCATCCAAGATCAAGTCTCAAA
GAACCTTGGATAAAAGCTTTCCCCAATCTAGTTACACCAACTAAAAAAAGATAAAACC
Found at i:3116542 original size:13 final size:13
Alignment explanation
Indices: 3116526--3116550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3116516 CAAATTTTAA
3116526 ATTTGAATTATTT
1 ATTTGAATTATTT
3116539 ATTTGAATTATT
1 ATTTGAATTATT
3116551 CGAAATTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATTTGAATTATTT
Found at i:3122213 original size:24 final size:24
Alignment explanation
Indices: 3122196--3122252 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
3122186 TGTAGTTGAT
*
3122196 ATTGCATCTGACTTTGTATCTGAA
1 ATTGCATCTGACTTTGTATATGAA
3122220 ATTGCATCTGACTTTGTATATGAA
1 ATTGCATCTGACTTTGTATATGAA
3122244 ATTGCATCT
1 ATTGCATCT
3122253 ATATTTGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (24 bp):
ATTGCATCTGACTTTGTATATGAA
Found at i:3122259 original size:24 final size:24
Alignment explanation
Indices: 3122196--3122260 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
3122186 TGTAGTTGAT
* *
3122196 ATTGCATCTGACTTTGTATCTGAA
1 ATTGCATCTGAATTTGTATATGAA
*
3122220 ATTGCATCTGACTTTGTATATGAA
1 ATTGCATCTGAATTTGTATATGAA
3122244 ATTGCATCT-ATATTTGT
1 ATTGCATCTGA-ATTTGT
3122261 TCTGTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (24 bp):
ATTGCATCTGAATTTGTATATGAA
Found at i:3125824 original size:13 final size:13
Alignment explanation
Indices: 3125806--3125831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3125796 GGTGTTTTCA
3125806 AAAACCATTTGTT
1 AAAACCATTTGTT
3125819 AAAACCATTTGTT
1 AAAACCATTTGTT
3125832 TGCGTAAAGT
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:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AAAACCATTTGTT
Found at i:3148051 original size:17 final size:18
Alignment explanation
Indices: 3148014--3148051 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3148004 TATTTTTTTG
*
3148014 TTAAAAATTTTTTATTAA
1 TTAAAAATTTATTATTAA
*
3148032 TTAAGAATTTATTA-TAA
1 TTAAAAATTTATTATTAA
3148049 TTA
1 TTA
3148052 TCGAACACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TTAAAAATTTATTATTAA
Found at i:3149407 original size:434 final size:421
Alignment explanation
Indices: 3148602--3149423 Score: 1144
Period size: 434 Copynumber: 1.9 Consensus size: 421
3148592 AAATCTTATA
* * ** * *
3148602 TATATTTAAAATTTTGATTGATTTGGTGTCAACCATAATCGAGTTCTAACTTAGTTACAAAGTTA
1 TATAGTTAAAATTTTGATTGAGTTAATGACAACCATAATCGAGTTCTAACTCAGTTACAAAGTTA
* * *
3148667 CAAAAAATTTCTTATTTTTACAAAGCAATAGATATTATTTTGAGAGTAATTTCATTTTTTCATAT
66 CAAAAAATCTCTTATTTATACAAAGCAATAGATATTATTTTGAGAGTAATTTCATTTTTTCACAT
* *
3148732 AAAATTTAGAACAAATACTTTTACCTATCGGGAGTTGAACCCAAAACATTATGATTTCAACTAAA
131 AAAATTTAGAACAAATACTTTTACCTAACGGGAGTTAAACCCAAAACATTATGATTTCAACTAAA
* *
3148797 GTAATATAATAACTACCAACTCAATAATGTTAACTAATATTATTATAGTACTTTTGTCTTTTTAT
196 GCAATATAATAACTACCAACTCAATAATGTTAACTAATATTATTATAGTACTTTTATCTTTTTAT
* ** * *
3148862 ATTTTTATATAATCTTTAAATAAAAAATTAAACCCTGCGTGTCCAAAAATTAAAAACATGTTTAA
261 ACTTTTATATAATCTTTAAATAAAAAATTAAACCCCACGTATCCAAAAATCAAAAACATGTTTAA
* ** *
3148927 TAAATTGTATATACAAGCTTTTTACCACTCCACCTATGGTTATTGTTGAATAAATTTTAAAAGAA
326 TAAATTGTATATACAAACTTTTTACCACTCCACCTATGACTATTGTTGAATAAAATTTAAAAGAA
3148992 TTTTTTTTTTACCCAGTGACATAACCTAATG
391 TTTTTTTTTTACCCAGTGACATAACCTAATG
** * *
3149023 TATAGTTAAAATTTTGATTGAGTTAATGACATTCATAATTGAGTTCTAACTCAGTTATAAAGTTA
1 TATAGTTAAAATTTTGATTGAGTTAATGACAACCATAATCGAGTTCTAACTCAGTTACAAAGTTA
* * *
3149088 CCAAAAGTCTCTTATTTATACAAAGCAATAGATATTATTTTGAGGGTAATTTCACCTTTTTT-AC
66 CAAAAAATCTCTTATTTATACAAAGCAATAGATATTATTTTGAGAGTAATTTCA--TTTTTTCAC
*
3149152 ATAAAATTTAGAACAAATACTTTTACTTAACGGGAGTTAAACCCAAAAAGTTACGATAAATTTTA
129 ATAAAATTTAGAACAAATACTTTTACCTAACGGGAGTTAAACCC--AAA---AC-----A--TTA
*
3149217 TGATTTCAACTAAAGCAATATAATAGCTACCAACTCAATAATGTTAACTAATATTATTATAGTAC
182 TGATTTCAACTAAAGCAATATAATAACTACCAACTCAATAATGTTAACTAATATTATTATAGTAC
* *
3149282 TTTTATCTTTTTATACTTTTATATAATTTTTAAATAAAAAATT-AACCACCACGTATTCAAAAAT
247 TTTTATCTTTTTATACTTTTATATAATCTTTAAATAAAAAATTAAACC-CCACGTATCCAAAAAT
* * * * * *
3149346 CGAAAACATGTTTAATAAATTTTATATACAAATTTTTTATCAGTCCACTTATGACTATTGTTGAA
311 CAAAAACATGTTTAATAAATTGTATATACAAACTTTTTACCACTCCACCTATGACTATTGTTGAA
3149411 TAAAATTTAAAAG
376 TAAAATTTAAAAG
3149424 TAAATGTTTT
Statistics
Matches: 347, Mismatches: 39, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
421 104 0.30
422 42 0.12
423 6 0.02
424 3 0.01
427 2 0.01
432 1 0.00
433 4 0.01
434 185 0.53
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (421 bp):
TATAGTTAAAATTTTGATTGAGTTAATGACAACCATAATCGAGTTCTAACTCAGTTACAAAGTTA
CAAAAAATCTCTTATTTATACAAAGCAATAGATATTATTTTGAGAGTAATTTCATTTTTTCACAT
AAAATTTAGAACAAATACTTTTACCTAACGGGAGTTAAACCCAAAACATTATGATTTCAACTAAA
GCAATATAATAACTACCAACTCAATAATGTTAACTAATATTATTATAGTACTTTTATCTTTTTAT
ACTTTTATATAATCTTTAAATAAAAAATTAAACCCCACGTATCCAAAAATCAAAAACATGTTTAA
TAAATTGTATATACAAACTTTTTACCACTCCACCTATGACTATTGTTGAATAAAATTTAAAAGAA
TTTTTTTTTTACCCAGTGACATAACCTAATG
Found at i:3156443 original size:58 final size:58
Alignment explanation
Indices: 3156353--3156465 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
3156343 GTCATAACAA
*
3156353 CATGGTACAAGGTATAAGGTATATGGTCTAAGACCAT-GAATGAAAGATGTAATGGTGG
1 CATGGTACAAGGTATAAGGTATACGGTCTAAGACCATAG-ATGAAAGATGTAATGGTGG
* * * * *
3156411 CATGGTATAATGTATGAGGTATACGGTGTAAGACCATAGATGAAAGATGTTATGG
1 CATGGTACAAGGTATAAGGTATACGGTCTAAGACCATAGATGAAAGATGTAATGG
3156466 CATCCAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
58 47 0.98
59 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.27
Consensus pattern (58 bp):
CATGGTACAAGGTATAAGGTATACGGTCTAAGACCATAGATGAAAGATGTAATGGTGG
Found at i:3157909 original size:19 final size:19
Alignment explanation
Indices: 3157885--3157922 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3157875 ACTAAGTTAA
3157885 TTTGAACTTACAACAGTGT
1 TTTGAACTTACAACAGTGT
3157904 TTTGAACTTACAACAGTGT
1 TTTGAACTTACAACAGTGT
3157923 GGTTGATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
TTTGAACTTACAACAGTGT
Found at i:3161216 original size:17 final size:20
Alignment explanation
Indices: 3161186--3161226 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
3161176 ATCAAATTTT
3161186 AATA-TTTAAGT-AAA-GAA
1 AATAGTTTAAGTAAAATGAA
3161203 AATAGTTTAA-TAAAATGAA
1 AATAGTTTAAGTAAAATGAA
3161222 AATAG
1 AATAG
3161227 AGATAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 8 0.38
19 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (20 bp):
AATAGTTTAAGTAAAATGAA
Found at i:3171396 original size:17 final size:18
Alignment explanation
Indices: 3171363--3171407 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3171353 AAAGGAGGAG
*
3171363 AAGCAAGAAGCAAGAAAC
1 AAGCAAAAAGCAAGAAAC
*
3171381 AAGCAAAAAG-AAGAAAG
1 AAGCAAAAAGCAAGAAAC
3171398 AAGCATAAAA
1 AAGCA-AAAA
3171408 AAAATTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.67, C:0.11, G:0.20, T:0.02
Consensus pattern (18 bp):
AAGCAAAAAGCAAGAAAC
Found at i:3174366 original size:2 final size:2
Alignment explanation
Indices: 3174361--3174434 Score: 50
Period size: 2 Copynumber: 39.5 Consensus size: 2
3174351 TAAAAAAAGC
* * *
3174361 AT AT AT AT AG AT AT A- AA AT A- AT A- AT AT AT AT A- AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
3174399 AT AT TT AA AT A- AT AT AT AT AT AT AG AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3174435 AAATTGAGTG
Statistics
Matches: 54, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
1 5 0.09
2 49 0.91
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (2 bp):
AT
Found at i:3174376 original size:23 final size:22
Alignment explanation
Indices: 3174350--3174397 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3174340 ATATTTACAC
*
3174350 ATAAAAAAAGCATATATATAGAT
1 ATAAAAAAAGAATATATATA-AT
* *
3174373 ATAAAATAATAATATATATAAT
1 ATAAAAAAAGAATATATATAAT
3174395 ATA
1 ATA
3174398 CATATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
ATAAAAAAAGAATATATATAAT
Found at i:3174395 original size:15 final size:16
Alignment explanation
Indices: 3174371--3174422 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
3174361 ATATATATAG
*
3174371 ATATAAAATAATA-AT
1 ATATATAATAATACAT
3174386 ATATATAAT-ATACAT
1 ATATATAATAATACAT
* *
3174401 ATTTA-AATAATATAT
1 ATATATAATAATACAT
3174416 ATATATA
1 ATATATA
3174423 GATATGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.20
15 23 0.77
16 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATAATAATACAT
Found at i:3174571 original size:3 final size:3
Alignment explanation
Indices: 3174563--3174595 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3174553 TAAATAAAAC
3174563 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3174596 GTAAAGATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3177234 original size:12 final size:13
Alignment explanation
Indices: 3177205--3177229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3177195 TAAAAGAGTT
3177205 ATTAATTAAAAAG
1 ATTAATTAAAAAG
3177218 ATTAATTAAAAA
1 ATTAATTAAAAA
3177230 TTTAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:3182003 original size:97 final size:100
Alignment explanation
Indices: 3181801--3182033 Score: 257
Period size: 97 Copynumber: 2.4 Consensus size: 100
3181791 AAACAGATTC
* * *
3181801 CATTGATTCATAAAGGGGTGTGATTG-GACCAAAGGTAAGAATAGTTGCCATTCGGTTCATTGCC
1 CATTGATTCATAAAGGGGTGTGTTTGAG-CCAAAGGCAAGAATAGTT--CA-TCGGTTCATTGCA
* * *
3181865 AATGTGAACTCCATTATGAATCCACCATTACAAGGATTT
62 AATGTGAACTCCATTATAAATCCACCATAACAAGCATTT
*
3181904 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAG-T-A-CTGTTCATTG-AATAT
1 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTTCATCGGTTCATTGCAA-AT
* *
3181965 GTGGACTCCATT-TCAAATCCACCATAACGAGCATTT
65 GTGAACTCCATTAT-AAATCCACCATAACAAGCATTT
* *
3182001 CATTGATTCAGAAA-GGG-GTGTTGGAGCCAAAGG
1 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGG
3182034 TAATAATATT
Statistics
Matches: 116, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
95 15 0.13
96 5 0.04
97 53 0.46
99 1 0.01
102 1 0.01
103 40 0.34
104 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (100 bp):
CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTTCATCGGTTCATTGCAAATG
TGAACTCCATTATAAATCCACCATAACAAGCATTT
Found at i:3186901 original size:3 final size:3
Alignment explanation
Indices: 3186893--3186929 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3186883 GAAATCTTTC
3186893 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3186930 AGAAATAAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3188655 original size:13 final size:14
Alignment explanation
Indices: 3188631--3188663 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3188621 ATGCACATAT
3188631 TAGAATCAAATAAA
1 TAGAATCAAATAAA
*
3188645 TAGAA-CAAATATA
1 TAGAATCAAATAAA
3188658 TAGAAT
1 TAGAAT
3188664 TCTACCCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (14 bp):
TAGAATCAAATAAA
Found at i:3199762 original size:29 final size:30
Alignment explanation
Indices: 3199730--3199795 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
3199720 TAGAGAGTGT
* * *
3199730 ATCAAATTAGTCCCTCTATTATTAAATAG-
1 ATCAAATTAGTCCCTATACTATTAAAAAGA
*
3199759 ATCAATTTAGTCCCTATACTATTAAAAAGA
1 ATCAAATTAGTCCCTATACTATTAAAAAGA
3199789 ATCAAAT
1 ATCAAAT
3199796 AAATCCAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (30 bp):
ATCAAATTAGTCCCTATACTATTAAAAAGA
Found at i:3200875 original size:20 final size:20
Alignment explanation
Indices: 3200838--3200896 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
3200828 AATTTATCAA
*
3200838 AAATTTAATATTTAA-AAACT
1 AAATTTAAT-TTTAATAAAAT
*
3200858 AAATTTCA-TTTAATAAAAT
1 AAATTTAATTTTAATAAAAT
*
3200877 ATATTTAATTTTAATAAAAT
1 AAATTTAATTTTAATAAAAT
3200897 TTAATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.15
19 10 0.30
20 18 0.55
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTTAATTTTAATAAAAT
Found at i:3200906 original size:20 final size:20
Alignment explanation
Indices: 3200866--3200906 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3200856 CTAAATTTCA
* *
3200866 TTTAATAAAATATATTTAAT
1 TTTAATAAAATATAATAAAT
*
3200886 TTTAATAAAATTTAATAAAT
1 TTTAATAAAATATAATAAAT
3200906 T
1 T
3200907 GTTATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAATAAAATATAATAAAT
Found at i:3206421 original size:4 final size:4
Alignment explanation
Indices: 3206405--3206469 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
3206395 GGTGTTCGAT
* *
3206405 TTTA TTTA CTTA TTTA -TTA TTTA GTTT- TTTA TTTT TATTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA T-TTA TTTA TTTA
3206452 TTTA -TTA TTT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA
3206470 AAATATAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
3 15 0.30
4 29 0.58
5 6 0.12
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3206426 original size:7 final size:7
Alignment explanation
Indices: 3206406--3206469 Score: 85
Period size: 7 Copynumber: 9.0 Consensus size: 7
3206396 GTGTTCGATT
3206406 TTATTTA
1 TTATTTA
3206413 CTTATTTA
1 -TTATTTA
3206421 TTATTTA
1 TTATTTA
*
3206428 GTTTTTTA
1 -TTATTTA
3206436 TT-TTTA
1 TTATTTA
3206442 TTATTTA
1 TTATTTA
3206449 TTATTTA
1 TTATTTA
*
3206456 TTATTTT
1 TTATTTA
3206463 TTATTTA
1 TTATTTA
3206470 AAATATAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
6 6 0.12
7 32 0.63
8 13 0.25
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:3211528 original size:34 final size:32
Alignment explanation
Indices: 3211490--3211594 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 32
3211480 AGCACACTGT
*
3211490 ATGCTCAAGTGAGCCATTCCAACCAGCACACCAA
1 ATGCTCAA--GAGCCAATCCAACCAGCACACCAA
*
3211524 ATGCTCGCAAGAGCCAATCCATCCAGCACACCAA
1 ATGCT--CAAGAGCCAATCCAACCAGCACACCAA
* ** *
3211558 ATGCTCGTAAGAGCAAATCCATTCAGCATACCAA
1 ATGCTC--AAGAGCCAATCCAACCAGCACACCAA
3211592 ATG
1 ATG
3211595 ATTTATACTG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
32 1 0.02
34 58 0.94
36 3 0.05
ACGTcount: A:0.36, C:0.32, G:0.15, T:0.16
Consensus pattern (32 bp):
ATGCTCAAGAGCCAATCCAACCAGCACACCAA
Found at i:3228432 original size:31 final size:31
Alignment explanation
Indices: 3228396--3228459 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
3228386 CTTAGATAAT
3228396 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
3228427 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
3228458 TT
1 TT
3228460 GTAATTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:3229032 original size:21 final size:20
Alignment explanation
Indices: 3229002--3229049 Score: 87
Period size: 21 Copynumber: 2.4 Consensus size: 20
3228992 AAAAAAACAG
3229002 AAAAAAGCAAAAAGCGCAAA
1 AAAAAAGCAAAAAGCGCAAA
3229022 AAAAGAAGCAAAAAGCGCAAA
1 AAAA-AAGCAAAAAGCGCAAA
3229043 AAAAAAG
1 AAAAAAG
3229050 TTGCCTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.71, C:0.12, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAGCAAAAAGCGCAAA
Found at i:3230248 original size:36 final size:36
Alignment explanation
Indices: 3230201--3230386 Score: 246
Period size: 36 Copynumber: 4.9 Consensus size: 36
3230191 GCTAGGCTAC
*
3230201 CACTTATCACTTTGTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
3230237 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTTTCACTTGATCAGAT-A----AG-T-A---TAA
* *
3230283 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
*
3230319 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
3230355 CACTTATCACTTTTTCACTTGATCAGATAAGT
1 CACTTATCACTTTTTCACTTGATCAGATAAGT
3230387 GTAGCTAAAG
Statistics
Matches: 136, Mismatches: 4, Indels: 20
0.85 0.03 0.12
Matches are distributed among these distances:
36 96 0.71
37 1 0.01
39 1 0.01
40 1 0.01
41 4 0.03
42 1 0.01
43 1 0.01
45 1 0.01
46 30 0.22
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
Found at i:3230296 original size:82 final size:81
Alignment explanation
Indices: 3230175--3230355 Score: 326
Period size: 82 Copynumber: 2.2 Consensus size: 81
3230165 CACTTGTCCC
*
3230175 TGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAACAC
1 TGATCAGATAAGTGTAGCTAGGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTATAACAC
3230240 TTATCACTTTTTCACT
66 TTATCACTTTTTCACT
*
3230256 TGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTATAGCA
1 TGATCAGATAAGTGTAGCT-AGGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTATAACA
3230321 CTTATCACTTTTTCACT
65 CTTATCACTTTTTCACT
*
3230338 TGATCAGATAAGTATAGC
1 TGATCAGATAAGTGTAGC
3230356 ACTTATCACT
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 19 0.20
82 77 0.80
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (81 bp):
TGATCAGATAAGTGTAGCTAGGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTATAACAC
TTATCACTTTTTCACT
Found at i:3230373 original size:118 final size:118
Alignment explanation
Indices: 3230201--3230423 Score: 392
Period size: 118 Copynumber: 1.9 Consensus size: 118
3230191 GCTAGGCTAC
3230201 CACTTATCACTTTGTCACTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
* *
3230266 AGTGTAGCTAAGGCTAACACTTATCACTTTGTCACTTGATCAGATAAGTATAG
66 AGTGTAGCTAAAGCTAACACTTATCACTTTATCACTTGATCAGATAAGTATAG
* *
3230319 CACTTATCACTTTTTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
* *
3230384 AGTGTAGCTAAAGCTACCACTTATCACTTTATCTCTTGAT
66 AGTGTAGCTAAAGCTAACACTTATCACTTTATCACTTGAT
3230424 TAGAAGTACG
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 99 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (118 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAACACTTATCACTTTATCACTTGATCAGATAAGTATAG
Found at i:3237421 original size:5 final size:5
Alignment explanation
Indices: 3237411--3237444 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3237401 ACCCATTACT
3237411 TCATA TCATA TCATA TCATA TCATA T-ATA T-ATA T
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA T
3237445 ATAACAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (5 bp):
TCATA
Found at i:3242434 original size:131 final size:132
Alignment explanation
Indices: 3242277--3242571 Score: 466
Period size: 133 Copynumber: 2.2 Consensus size: 132
3242267 TATTTTTTAT
* *
3242277 CCTGCTCCACTGCAACTTTAGGGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAA
1 CCTGCTCCACTGTAACTTCAGGGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAA
* ** * *
3242342 GGAG-GAGATTTTTAGCTTCGATCTACTCTTCTGCAACTTTAAGGAGATAAGAATTGGTAATTTC
66 GGAGAGAGATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTCGTAACTTC
3242406 AA
131 AA
* * * * *
3242408 CCTGCTCTACTGTAACTTCAGGGAGATAAGGATTGTGGTTTCGATCTGCTCTAATGTAATTTTAG
1 CCTGCTCCACTGTAACTTCAGGGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAA
3242473 GGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTCGTAACTT
66 GGAG-AGAGATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTCGTAACTT
3242538 CAA
130 CAA
3242541 CCTGCTCCACTGTAACTTCAGGGAGATAAGG
1 CCTGCTCCACTGTAACTTCAGGGAGATAAGG
3242572 TTTGCAACTT
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
131 62 0.42
133 87 0.58
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (132 bp):
CCTGCTCCACTGTAACTTCAGGGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAA
GGAGAGAGATTTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTCGTAACTTC
AA
Found at i:3242621 original size:96 final size:96
Alignment explanation
Indices: 3242484--3242666 Score: 224
Period size: 96 Copynumber: 1.9 Consensus size: 96
3242474 GAGAAGAGAT
* * * * *
3242484 TTGTAGCTTCGATCTACTCCGCTGCAACTTTAAGGAGATAAGAATTCG-TAACTTCAACCTGCTC
1 TTGTAGCTTCAATCTACTCCGCTACAACTTCAAGGAAATAAG-ATGCGCTAACTTCAACCTGCTC
* ** *
3242548 CACTGTAACTTCAGGGAGATAAGGTTTGCAAC
65 AACTACAACATCAGGGAGATAAGGTTTGCAAC
* * * **
3242580 TTGTAGCTTCAATCTATTCCGCTACAACTTCAGGGAAATAAGATGCGCTATCTTCAGTCTGCTCA
1 TTGTAGCTTCAATCTACTCCGCTACAACTTCAAGGAAATAAGATGCGCTAACTTCAACCTGCTCA
3242645 ACTACAACATCAGGGAGATAAG
66 ACTACAACATCAGGGAGATAAG
3242667 ACTAGTAACT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 4 0.06
96 68 0.94
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (96 bp):
TTGTAGCTTCAATCTACTCCGCTACAACTTCAAGGAAATAAGATGCGCTAACTTCAACCTGCTCA
ACTACAACATCAGGGAGATAAGGTTTGCAAC
Found at i:3250950 original size:53 final size:53
Alignment explanation
Indices: 3250884--3250998 Score: 176
Period size: 53 Copynumber: 2.2 Consensus size: 53
3250874 AAATGAGGAT
* * *
3250884 ACACGGCCGTGTCCTAACCCATGTCCGTGCCCGTGTAACTCTCTGACTTGGTC
1 ACACGGCCATGTCCTAACCCATGTCCATGCCCGTGTAACTCTCTAACTTGGTC
* * *
3250937 ACACGGTCATGTCCTAGCCCATGTCCATGCCCGTGTAACTCTCTAACTTGGTT
1 ACACGGCCATGTCCTAACCCATGTCCATGCCCGTGTAACTCTCTAACTTGGTC
3250990 ACACGGCCA
1 ACACGGCCA
3250999 AGTCACACGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.18, C:0.35, G:0.21, T:0.26
Consensus pattern (53 bp):
ACACGGCCATGTCCTAACCCATGTCCATGCCCGTGTAACTCTCTAACTTGGTC
Found at i:3251966 original size:52 final size:52
Alignment explanation
Indices: 3251903--3252008 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
3251893 AAACACAAAG
*
3251903 TAAGCATTTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACATTGCCAA
1 TAAGCAATTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACATTGCCAA
*
3251955 TAAGCAATTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACCTTGCCAA
1 TAAGCAATTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACATTGCCAA
3252007 TA
1 TA
3252009 TAATATATAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (52 bp):
TAAGCAATTCATGCTTAGTAAGTTCGTAACACATACAGTCTAACATTGCCAA
Found at i:3258548 original size:14 final size:14
Alignment explanation
Indices: 3258529--3258556 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3258519 AAGGAGGGGG
3258529 AAAATCAGTGTAAA
1 AAAATCAGTGTAAA
3258543 AAAATCAGTGTAAA
1 AAAATCAGTGTAAA
3258557 GAGGACGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
AAAATCAGTGTAAA
Found at i:3268168 original size:27 final size:27
Alignment explanation
Indices: 3267884--3268281 Score: 395
Period size: 27 Copynumber: 14.8 Consensus size: 27
3267874 ACCTTCGAAA
* ** *
3267884 GGTAAAATGAACAAAATA-CCCTCTATG
1 GGTAAAATGACCGTAATACCCCTGTA-G
* * * * *
3267911 GGTAAAATAACTGAAATGCCCCTATAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* *
3267938 GGTAAAATGACCGAAATACCCCCGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* * * * *
3267965 GGTAGAAT-ACCGAAATACCCTTATAT
1 GGTAAAATGACCGTAATACCCCTGTAG
* * *
3267991 GGTAAAATAACAGTAATACCTCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* * *
3268018 GGTAAAATAACCGTAATACCCCTATAA
1 GGTAAAATGACCGTAATACCCCTGTAG
*
3268045 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* * * *
3268072 GGTAAAATGATCGTAATGCCTCTATAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* *
3268099 GGTAAAATGACCATAATACCCCGGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* *
3268126 GGTAAAATAACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
** * *
3268153 GGTAAAATGATTGTAATACACCTGTAA
1 GGTAAAATGACCGTAATACCCCTGTAG
*
3268180 GGTAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* * * *
3268207 GATAAAATAATCGTAATACCCTTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
* *
3268234 GATAAAATGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATACCCCTGTAG
3268261 GGTAAAATGACCGTAATACCC
1 GGTAAAATGACCGTAATACCC
3268282 TCGAGGTCAA
Statistics
Matches: 303, Mismatches: 66, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
26 21 0.07
27 276 0.91
28 6 0.02
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCCTGTAG
Found at i:3268327 original size:23 final size:24
Alignment explanation
Indices: 3268301--3268356 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
3268291 AATGATTGAA
3268301 TTGTCTGTGGTT-AAATGACTAAT
1 TTGTCTGTGGTTGAAATGACTAAT
* * ** *
3268324 TTGTCTTTGTTTGGTATGACTGAT
1 TTGTCTGTGGTTGAAATGACTAAT
3268348 TTGTCTGTG
1 TTGTCTGTG
3268357 ATTTGAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (24 bp):
TTGTCTGTGGTTGAAATGACTAAT
Found at i:3268527 original size:26 final size:25
Alignment explanation
Indices: 3268488--3268540 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
3268478 TTGGCCACAT
3268488 ATACTATACTGGCAACTTTGCTGCG
1 ATACTATACTGGCAACTTTGCTGCG
* *
3268513 ATACTACTGCTGGCAGCTTTGCTGCG
1 ATACTA-TACTGGCAACTTTGCTGCG
3268539 AT
1 AT
3268541 GCCACTGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.32
Consensus pattern (25 bp):
ATACTATACTGGCAACTTTGCTGCG
Found at i:3268547 original size:26 final size:26
Alignment explanation
Indices: 3268496--3268547 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3268486 ATATACTATA
*
3268496 CTGGCAACTTTGCTGCGATACTACTG
1 CTGGCAACTTTGCTGCGATACCACTG
* *
3268522 CTGGCAGCTTTGCTGCGATGCCACTG
1 CTGGCAACTTTGCTGCGATACCACTG
3268548 ATGGATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (26 bp):
CTGGCAACTTTGCTGCGATACCACTG
Found at i:3268589 original size:32 final size:32
Alignment explanation
Indices: 3268544--3268745 Score: 289
Period size: 32 Copynumber: 6.3 Consensus size: 32
3268534 CTGCGATGCC
* * *
3268544 ACTGATGGATTTGTGCCAATCATATTACCATT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
3268576 ACTGATGGCTTTGTGCCGATCATATTACCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
*
3268608 ACTGATGGCTTTGTTCCGATCATATTACCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* *
3268640 ACTGATGGCTTTATGCC-ATCATATTATCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* * *
3268671 ATTGATGGCTTTGTACCGATCATATTACCATT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
* * *
3268703 ACTAATGTCTTTGTACCGATCATATTACCGTT
1 ACTGATGGCTTTGTGCCGATCATATTACCGTT
3268735 ACTGATGGCTT
1 ACTGATGGCTT
3268746 GTAGCCATTC
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
31 27 0.18
32 124 0.82
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (32 bp):
ACTGATGGCTTTGTGCCGATCATATTACCGTT
Found at i:3268715 original size:95 final size:95
Alignment explanation
Indices: 3268544--3268753 Score: 305
Period size: 95 Copynumber: 2.2 Consensus size: 95
3268534 CTGCGATGCC
* * * *
3268544 ACTGATGGATTTGTGCCAATCATATTACCATTACTGATGGCTTTGTGCCGATCATATTACCGTTA
1 ACTGATGGCTTTATGCC-ATCATATTACCATTACTGATGGCTTTGTACCGATCATATTACCATTA
* *
3268609 CTGATGGCTTTGTTCCGATCATATTACCGTT
65 CTAATGGCTTTGTACCGATCATATTACCGTT
* * *
3268640 ACTGATGGCTTTATGCCATCATATTATCGTTATTGATGGCTTTGTACCGATCATATTACCATTAC
1 ACTGATGGCTTTATGCCATCATATTACCATTACTGATGGCTTTGTACCGATCATATTACCATTAC
*
3268705 TAATGTCTTTGTACCGATCATATTACCGTT
66 TAATGGCTTTGTACCGATCATATTACCGTT
3268735 ACTGATGGCTTGTA-GCCAT
1 ACTGATGGCTT-TATGCCAT
3268754 TCTGTTTATA
Statistics
Matches: 103, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
95 86 0.83
96 17 0.17
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (95 bp):
ACTGATGGCTTTATGCCATCATATTACCATTACTGATGGCTTTGTACCGATCATATTACCATTAC
TAATGGCTTTGTACCGATCATATTACCGTT
Found at i:3268772 original size:22 final size:21
Alignment explanation
Indices: 3268742--3268798 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
3268732 GTTACTGATG
3268742 GCTTGTAGCCATTCTGTTTATA
1 GCTT-TAGCCATTCTGTTTATA
* * *
3268764 GCTTATAGCTATCCTGTTTATG
1 GCTT-TAGCCATTCTGTTTATA
3268786 GCTGTTAGCCATT
1 GCT-TTAGCCATT
3268799 TTGACTACTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (21 bp):
GCTTTAGCCATTCTGTTTATA
Found at i:3269238 original size:14 final size:14
Alignment explanation
Indices: 3269215--3269244 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3269205 AAAAGTATTT
*
3269215 TAAAATTAAAAAAA
1 TAAAAATAAAAAAA
3269229 TAAAAATAAAAAAA
1 TAAAAATAAAAAAA
3269243 TA
1 TA
3269245 TATTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:3269249 original size:35 final size:33
Alignment explanation
Indices: 3269158--3269249 Score: 94
Period size: 35 Copynumber: 2.7 Consensus size: 33
3269148 CCTATTTTTT
* *
3269158 AATAAACATTAAAAAATTATTTTAAAAATAAAA
1 AATAAAAATAAAAAAATTATTTTAAAAATAAAA
** * *
3269191 AATAAAAATATTTTAAAAGTATTTTAAAATTAAAAA
1 AATAAAAATA--AAAAAATTATTTTAAAAAT-AAAA
3269227 AATAAAAATAAAAAAATATATTT
1 AATAAAAATAAAAAAAT-TATTT
3269250 ATTATATTCG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
33 8 0.17
34 4 0.09
35 20 0.43
36 14 0.30
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (33 bp):
AATAAAAATAAAAAAATTATTTTAAAAATAAAA
Found at i:3280624 original size:15 final size:15
Alignment explanation
Indices: 3280604--3280637 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3280594 ACCTGAACCA
3280604 ATTTTTTAA-AATTTT
1 ATTTTTTAATAA-TTT
3280619 ATTTTTTAATAATTT
1 ATTTTTTAATAATTT
3280634 ATTT
1 ATTT
3280638 GCTTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTTAATAATTT
Found at i:3280927 original size:29 final size:28
Alignment explanation
Indices: 3280878--3280932 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3280868 CTTTTTATAA
* *
3280878 TTTTTATTTAAAAAATTAAAATTTTATG
1 TTTTTATTTAAAAAATAAAAAATTTATG
*
3280906 TTTTTATTTAAAATATAAAAAAATTTA
1 TTTTTATTTAAAAAAT-AAAAAATTTA
3280933 AAAATTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTTTATTTAAAAAATAAAAAATTTATG
Found at i:3282708 original size:22 final size:22
Alignment explanation
Indices: 3282680--3282729 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
3282670 TACACACTTT
3282680 TTCATGCCATTTTTAACTAAAA
1 TTCATGCCATTTTTAACTAAAA
* *
3282702 TTCATGCCCTTTTTAACTCAAA
1 TTCATGCCATTTTTAACTAAAA
3282724 TTCATG
1 TTCATG
3282730 TAGTTTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.42
Consensus pattern (22 bp):
TTCATGCCATTTTTAACTAAAA
Found at i:3290310 original size:41 final size:41
Alignment explanation
Indices: 3290264--3290347 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
3290254 GGGTCAAATT
3290264 AGTCAATTTTGTATACAAAACCTATATTAGCAGACAAGAGA
1 AGTCAATTTTGTATACAAAACCTATATTAGCAGACAAGAGA
*
3290305 AGTCAATTTTGTATACAAAACCTATATTAGCGGACAAGAGA
1 AGTCAATTTTGTATACAAAACCTATATTAGCAGACAAGAGA
3290346 AG
1 AG
3290348 ACATTAGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (41 bp):
AGTCAATTTTGTATACAAAACCTATATTAGCAGACAAGAGA
Found at i:3290598 original size:51 final size:51
Alignment explanation
Indices: 3290538--3290640 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
3290528 TTTAAACTGG
*
3290538 CCCATAGACGTTCGATTGGTTTCACCTCTTGCATGAATATCACAGCATCAA
1 CCCATAGACGTTCGATTAGTTTCACCTCTTGCATGAATATCACAGCATCAA
3290589 CCCATAGACGTTCGATTAGTTTCACCTCTTGCATGAATATCACAGCATCAA
1 CCCATAGACGTTCGATTAGTTTCACCTCTTGCATGAATATCACAGCATCAA
3290640 C
1 C
3290641 TTTAATAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (51 bp):
CCCATAGACGTTCGATTAGTTTCACCTCTTGCATGAATATCACAGCATCAA
Found at i:3294098 original size:23 final size:22
Alignment explanation
Indices: 3294043--3294126 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
3294033 CGTCACATAA
3294043 GTGCCTGAA-ACGACACACGAG
1 GTGCCTGAATACGACACACGAG
*
3294064 GTGCCT-AATACGACACACGGG
1 GTGCCTGAATACGACACACGAG
** *
3294085 GTGCCTGAATTACGACACATAAA
1 GTGCCTGAA-TACGACACACGAG
3294108 GTGCCTGATATACGACACA
1 GTGCCTGA-ATACGACACA
3294127 TAAAGTGCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 2 0.04
21 23 0.43
22 2 0.04
23 26 0.48
24 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (22 bp):
GTGCCTGAATACGACACACGAG
Found at i:3294112 original size:44 final size:44
Alignment explanation
Indices: 3294043--3294126 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
3294033 CGTCACATAA
* *
3294043 GTGCCTGAAACGACACACGAGGTGCCT-A-ATACGACACACGGG
1 GTGCCTGAAACGACACACAAAGTGCCTGATATACGACACACGGG
*
3294085 GTGCCTGAATTACGACACATAAAGTGCCTGATATACGACACA
1 GTGCCTGAA--ACGACACACAAAGTGCCTGATATACGACACA
3294127 TAAAGTGCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 9 0.26
44 15 0.43
45 1 0.03
46 10 0.29
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (44 bp):
GTGCCTGAAACGACACACAAAGTGCCTGATATACGACACACGGG
Found at i:3294127 original size:23 final size:22
Alignment explanation
Indices: 3294030--3294134 Score: 99
Period size: 23 Copynumber: 4.8 Consensus size: 22
3294020 CCTGATCAAT
*
3294030 ATACGTCACAT-AAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
** *
3294051 A-ACGACACACGAGGTGCCT-A
1 ATACGACACATAAAGTGCCTGA
****
3294071 ATACGACACACGGGGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
3294093 ATTACGACACATAAAGTGCCTGA
1 A-TACGACACATAAAGTGCCTGA
3294116 TATACGACACATAAAGTGC
1 -ATACGACACATAAAGTGC
3294135 TTGATCGGCA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.13
21 25 0.35
22 2 0.03
23 34 0.48
24 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:3294496 original size:26 final size:25
Alignment explanation
Indices: 3294465--3294514 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3294455 TAGTTCAATA
3294465 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
3294491 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
3294515 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:3295323 original size:11 final size:11
Alignment explanation
Indices: 3295303--3295337 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
3295293 AAAACCCTAG
3295303 TTTTTCCTTTTC
1 TTTTT-CTTTTC
3295315 TTTTTCTTTTC
1 TTTTTCTTTTC
3295326 TTCTTTCTTTTC
1 TT-TTTCTTTTC
3295338 CCCTGTTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:3299325 original size:34 final size:32
Alignment explanation
Indices: 3299243--3299331 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 32
3299233 GTATATGTTT
*
3299243 TATATATTTCCAAATTGATTTAAATATAGATA
1 TATATATTGCCAAATTGATTTAAATATAGATA
* * * **
3299275 TATACATTGTCGAATTGATTTGCATAT-GTATACA
1 TATATATTGCCAAATTGATTTAAATATAG-AT--A
3299309 TATATATTGCCAAATTGATTTAA
1 TATATATTGCCAAATTGATTTAA
3299332 GCATTGGATG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
31 1 0.02
32 23 0.53
34 19 0.44
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (32 bp):
TATATATTGCCAAATTGATTTAAATATAGATA
Found at i:3299600 original size:43 final size:42
Alignment explanation
Indices: 3299455--3299600 Score: 129
Period size: 43 Copynumber: 3.5 Consensus size: 42
3299445 TGTGATTTCG
** *
3299455 TGTAAGACCATGTCTGGGACATTGGCATCGA-A-GTGAAAAAA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATG-GTTAACA
* * *
3299496 TGTGTAAGACCATGTCTGGGACATTGGCATGGTATATGATT--CG
1 --TGTAAGACCATGTCTGGGACATTGGCATCG-ATATGGTTAACA
* * *
3299539 TATAAGACCCTGTCTGGGACAGTGGCATCGATATGCGTTAACA
1 TGTAAGACCATGTCTGGGACATTGGCATCGATATG-GTTAACA
*
3299582 TGTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
3299601 TATGACATTG
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
40 5 0.06
41 28 0.34
43 46 0.56
44 1 0.01
45 1 0.01
46 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGGTTAACA
Found at i:3301653 original size:21 final size:20
Alignment explanation
Indices: 3301602--3301653 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3301592 TCTAATCATC
*
3301602 AACCTTAAACCTTAAAACTA
1 AACCCTAAACCTTAAAACTA
* *
3301622 ACCCCTAAACCTTAAACATTA
1 AACCCTAAACCTTAAA-ACTA
*
3301643 AACCCTCAACC
1 AACCCTAAACC
3301654 CTAAGTTCTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCCTAAACCTTAAAACTA
Found at i:3302410 original size:43 final size:42
Alignment explanation
Indices: 3302339--3302542 Score: 282
Period size: 43 Copynumber: 4.7 Consensus size: 42
3302329 ACGCCGCTAA
* * *
3302339 CTTTTGCGGCGCTTTATCCACAAGCGCCGCTAAAGGTAATGTT
1 CTTTAGCGGCGCTTT-TTCACAAACGCCGCTAAAGGTAATGTT
* *
3302382 CTTTAGCGGCGCTTTATTCATAAACGCCGCGAAAGGTAATGTT
1 CTTTAGCGGCGCTTT-TTCACAAACGCCGCTAAAGGTAATGTT
* *
3302425 CTTTAGCGGCGGTTTTTTCACAAGCGCCGCTAAAGGTAATGTT
1 CTTTAGCGGC-GCTTTTTCACAAACGCCGCTAAAGGTAATGTT
* *
3302468 CTTTAGCGGCGCATTTTTCACAAACGCCGCTAAATGTCATGTT
1 CTTTAGCGGCGC-TTTTTCACAAACGCCGCTAAAGGTAATGTT
3302511 CTTTAGCGGCGCTTTTCTCACAAACGCCGCTA
1 CTTTAGCGGCGCTTTT-TCACAAACGCCGCTA
3302543 TTGTTTTGTG
Statistics
Matches: 145, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
42 5 0.03
43 136 0.94
44 4 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTTCACAAACGCCGCTAAAGGTAATGTT
Found at i:3302569 original size:44 final size:44
Alignment explanation
Indices: 3302339--3302587 Score: 228
Period size: 43 Copynumber: 5.8 Consensus size: 44
3302329 ACGCCGCTAA
* * * *
3302339 CTTTTGCGGCGC-TTTATC-CACAAGCGCCGCTAAAGGTAATGTT
1 CTTTAGCGGCGCATTT-TCTCACAAACGCCGCTAAATGTCATGTT
* * * *
3302382 CTTTAGCGGCGC-TTTAT-TCATAAACGCCGCGAAAGGTAATGTT
1 CTTTAGCGGCGCATTT-TCTCACAAACGCCGCTAAATGTCATGTT
* * * * *
3302425 CTTTAGCGGCG-GTTTTTTCACAAGCGCCGCTAAAGGTAATGTT
1 CTTTAGCGGCGCATTTTCTCACAAACGCCGCTAAATGTCATGTT
3302468 CTTTAGCGGCGCATTTT-TCACAAACGCCGCTAAATGTCATGTT
1 CTTTAGCGGCGCATTTTCTCACAAACGCCGCTAAATGTCATGTT
* **
3302511 CTTTAGCGGCGC-TTTTCTCACAAACGCCGCT-ATTGTTTTGTGAT
1 CTTTAGCGGCGCATTTTCTCACAAACGCCGCTAAATGTCATGT--T
* * *
3302555 CTTTAGCGGTGCTTTTTCTCA-AAACGCCACTAA
1 CTTTAGCGGCGCATTTTCTCACAAACGCCGCTAA
3302588 TTTTAGGATT
Statistics
Matches: 181, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
42 12 0.07
43 135 0.75
44 25 0.14
45 9 0.05
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (44 bp):
CTTTAGCGGCGCATTTTCTCACAAACGCCGCTAAATGTCATGTT
Found at i:3304718 original size:25 final size:26
Alignment explanation
Indices: 3304667--3304728 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 26
3304657 TTTTATAATG
* *
3304667 ATTAAGTTATGTAAATAATATGAGTT
1 ATTAAGTTATGCAAATAATATAAGTT
*
3304693 ATTAAGTTATGCATAT-ATATAAGTT
1 ATTAAGTTATGCAAATAATATAAGTT
3304718 ATTAAGTTATG
1 ATTAAGTTATG
3304729 TAAGTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (26 bp):
ATTAAGTTATGCAAATAATATAAGTT
Found at i:3304732 original size:17 final size:17
Alignment explanation
Indices: 3304667--3304738 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
3304657 TTTTATAATG
* *
3304667 ATTAAGTTATGTAAATA
1 ATTAAGTTATGTAAGTT
*
3304684 ATATGAGTTAT-TAAGTT
1 AT-TAAGTTATGTAAGTT
** *
3304701 ATGCA-TATATATAAGTT
1 ATTAAGT-TATGTAAGTT
3304718 ATTAAGTTATGTAAGTT
1 ATTAAGTTATGTAAGTT
3304735 ATTA
1 ATTA
3304739 TGTGAGTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (17 bp):
ATTAAGTTATGTAAGTT
Found at i:3304909 original size:9 final size:9
Alignment explanation
Indices: 3304896--3304943 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
3304886 TATATATGTA
*
3304896 TTATGTAAA
1 TTATGTAAG
*
3304905 TTATGTGAG
1 TTATGTAAG
*
3304914 TTGT-TAAG
1 TTATGTAAG
3304922 TTATGTAAG
1 TTATGTAAG
3304931 TTATGTAAG
1 TTATGTAAG
3304940 TTAT
1 TTAT
3304944 TATGTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
8 6 0.18
9 27 0.82
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3307460 original size:17 final size:16
Alignment explanation
Indices: 3307409--3307478 Score: 74
Period size: 17 Copynumber: 4.5 Consensus size: 16
3307399 TAAAAATTAA
3307409 TAACCCCTAAAT-CCC
1 TAACCCCTAAATCCCC
* * *
3307424 AAATCCCT-AA-CCCA
1 TAACCCCTAAATCCCC
3307438 TAACCCCTAAATCCCC
1 TAACCCCTAAATCCCC
*
3307454 TTAACCCTTAAATCCCC
1 -TAACCCCTAAATCCCC
3307471 TAACCCCT
1 TAACCCCT
3307479 CAACCACAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 10 0.23
15 8 0.19
16 10 0.23
17 15 0.35
ACGTcount: A:0.33, C:0.46, G:0.00, T:0.21
Consensus pattern (16 bp):
TAACCCCTAAATCCCC
Done.