Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 48 of 50
Found at i:11282801 original size:42 final size:42
Alignment explanation
Indices: 11282684--11282802 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 42
11282674 TGTTTTGGCT
* *
11282684 AAAACGCCACTATATATTAA-TCTATTGTGGCGTTTGTGGTA
1 AAAACGCCGCTATATATCAACTCTATTGTGGCGTTTGTGGTA
* * * * * *
11282725 TAAACGCCGCTA-ATTTACCACCCTATTGCGGCGTTTGTTGTA
1 AAAACGCCGCTATATAT-CAACTCTATTGTGGCGTTTGTGGTA
* * *
11282767 AAAACGCCGCTATATGTCAACTCTATTATAGCGTTT
1 AAAACGCCGCTATATATCAACTCTATTGTGGCGTTT
11282803 TTACAACAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
40 3 0.05
41 11 0.18
42 43 0.72
43 3 0.05
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (42 bp):
AAAACGCCGCTATATATCAACTCTATTGTGGCGTTTGTGGTA
Found at i:11283561 original size:30 final size:30
Alignment explanation
Indices: 11283527--11283583 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
11283517 ACAAACACTA
*
11283527 AAAAAATTGAGCCTC-TAATAAAAAATATTG
1 AAAAAATTG-GACTCGTAATAAAAAATATTG
* *
11283557 AAAAAGTTGGACTCGTAATAACAAATA
1 AAAAAATTGGACTCGTAATAAAAAATA
11283584 AATATTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.53, C:0.11, G:0.12, T:0.25
Consensus pattern (30 bp):
AAAAAATTGGACTCGTAATAAAAAATATTG
Found at i:11283643 original size:21 final size:21
Alignment explanation
Indices: 11283619--11283658 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11283609 AAAAGTATGT
11283619 CCCTAATAAAAAAAATTGACC
1 CCCTAATAAAAAAAATTGACC
* *
11283640 CCCTAATAATAATAATTGA
1 CCCTAATAAAAAAAATTGA
11283659 AAATAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.20, G:0.05, T:0.25
Consensus pattern (21 bp):
CCCTAATAAAAAAAATTGACC
Found at i:11283829 original size:34 final size:31
Alignment explanation
Indices: 11283759--11283816 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
11283749 AGTTAACCCC
11283759 TAATAATAAATATTAGAAGAAAAAAAACTCA
1 TAATAATAAATATTAGAAGAAAAAAAACTCA
11283790 TAATAATAAATATT-GAA-AAAAAAAACT
1 TAATAATAAATATTAGAAGAAAAAAAACT
11283817 AAATCCTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.37
30 3 0.11
31 14 0.52
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (31 bp):
TAATAATAAATATTAGAAGAAAAAAAACTCA
Found at i:11286174 original size:45 final size:47
Alignment explanation
Indices: 11286123--11286225 Score: 183
Period size: 45 Copynumber: 2.2 Consensus size: 47
11286113 TGTCTGGGCC
*
11286123 TTGTTTATCTAAGGGAGGTTTATGCAATTCCTGGTTGT-G-TAGAAT
1 TTGTTTATCTAAGGGAGGTTTATGCAATACCTGGTTGTGGCTAGAAT
11286168 TTGTTTATCTAAGGGAGGTTTATGCAATACCTGGTTGTGGCTAGAAT
1 TTGTTTATCTAAGGGAGGTTTATGCAATACCTGGTTGTGGCTAGAAT
11286215 TTGTTTATCTA
1 TTGTTTATCTA
11286226 GCCACTGTTA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
45 37 0.67
46 1 0.02
47 17 0.31
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (47 bp):
TTGTTTATCTAAGGGAGGTTTATGCAATACCTGGTTGTGGCTAGAAT
Found at i:11293927 original size:20 final size:20
Alignment explanation
Indices: 11293904--11294003 Score: 119
Period size: 20 Copynumber: 5.0 Consensus size: 20
11293894 GAATATGTAA
* *
11293904 ATCGCAATGTGATTATGACT
1 ATCGCAATGAGATTCTGACT
* *
11293924 ATCGCAACGCGATTCTGACT
1 ATCGCAATGAGATTCTGACT
* *
11293944 ATCTCAATGAGATTCTGATT
1 ATCGCAATGAGATTCTGACT
*
11293964 ATCGCAACGAGATTCTGACT
1 ATCGCAATGAGATTCTGACT
* *
11293984 ATCGCAACGCGATTCTGACT
1 ATCGCAATGAGATTCTGACT
11294004 GACTATCGCG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGCAATGAGATTCTGACT
Found at i:11293952 original size:60 final size:60
Alignment explanation
Indices: 11293880--11294003 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
11293870 GCGATTTTCC
* * *
11293880 GACTATCGCAATGCGAATATG-TAAATCGCAATGTGATTATGACTATCGCAACGCGATTCT
1 GACTATCGCAATGAGAATATGAT-AATCGCAACGAGATTATGACTATCGCAACGCGATTCT
* * * * *
11293940 GACTATCTCAATGAGATTCTGATTATCGCAACGAGATTCTGACTATCGCAACGCGATTCT
1 GACTATCGCAATGAGAATATGATAATCGCAACGAGATTATGACTATCGCAACGCGATTCT
11294000 GACT
1 GACT
11294004 GACTATCGCG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (60 bp):
GACTATCGCAATGAGAATATGATAATCGCAACGAGATTATGACTATCGCAACGCGATTCT
Found at i:11293998 original size:40 final size:40
Alignment explanation
Indices: 11293904--11294003 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
11293894 GAATATGTAA
* * *
11293904 ATCGCAATGTGATTATGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGAGATTCTGACTATCGCAACGAGATTCTGACT
* *
11293944 ATCTCAATGAGATTCTGATTATCGCAACGAGATTCTGACT
1 ATCGCAATGAGATTCTGACTATCGCAACGAGATTCTGACT
* *
11293984 ATCGCAACGCGATTCTGACT
1 ATCGCAATGAGATTCTGACT
11294004 GACTATCGCG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
ATCGCAATGAGATTCTGACTATCGCAACGAGATTCTGACT
Found at i:11294224 original size:22 final size:22
Alignment explanation
Indices: 11294199--11294241 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11294189 GGCGACATCC
11294199 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
11294221 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
11294242 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:11294731 original size:20 final size:20
Alignment explanation
Indices: 11294638--11294733 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
11294628 GTGATTTTAG
11294638 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
* ** *
11294657 TTTCGCATTGCGATAGTCAA
1 TTTCGCGTTGCGATTTTCAT
* **
11294677 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
11294697 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
11294717 TTTCGTGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
11294734 AAGTTTCAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 16 0.24
20 50 0.76
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:11294740 original size:20 final size:20
Alignment explanation
Indices: 11294697--11294740 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
11294687 CGATAGTCAT
* *
11294697 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
11294717 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
11294737 TTTC
1 TTTC
11294741 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:11296968 original size:55 final size:55
Alignment explanation
Indices: 11296900--11297384 Score: 522
Period size: 55 Copynumber: 9.0 Consensus size: 55
11296890 CAAATGACGA
11296900 GTCTGCTCTCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATA-AAACGT
1 GTCTGCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCA-ACAAACGT
* * * *
11296955 GTCTGCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGG
1 GTCTGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGT
* *
11297011 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-ATTCTTCAATAAACAG-
1 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCAACAAAC-GT
* * * * * *
11297066 GTCCGTTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGT
1 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * *
11297117 GT-TCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATA-AAACGG
1 GTCT-GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGT
*
11297172 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
1 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
** *
11297227 GT-TCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGG
1 GTCT-GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * *
11297282 GTCCGCTCTCTATTCCTTC--AGAGTATAGAACTCGAACAATCTTCAACGAACTT
1 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
* * *
11297335 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACG
11297385 AGTTTGCTTC
Statistics
Matches: 371, Mismatches: 39, Indels: 44
0.82 0.09 0.10
Matches are distributed among these distances:
50 1 0.00
51 54 0.15
53 47 0.13
54 2 0.01
55 216 0.58
56 47 0.13
57 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
GTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGT
Found at i:11297204 original size:161 final size:162
Alignment explanation
Indices: 11296937--11297384 Score: 517
Period size: 161 Copynumber: 2.8 Consensus size: 162
11296927 TAAGACTCGA
* *
11296937 ACAATCTTCATA-AAACGTG-TCTGCTCTCTATTCATTCAGAGAGTATA-AGACTTGAACAATCT
1 ACAATCTTCA-ACAAACGTGTTC-GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCT
* * *
11296999 TCAATAAAACGGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-ATTCTTCAATAAA
63 TC-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCAACAAA
* * *
11297063 CAG-GTCCGTTCCCTATTCTTTCAGAGAGTATAGGACT
126 C-GTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
* * *
11297100 -CAATCTTTAACAAACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCA
1 ACAATCTTCAACAAACGTGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA
11297164 TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGT
66 TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGT
* *
11297229 TCGCTCTCTATTCCTTCAGAGAGTATAGAACT
131 CCGCTCCCTATTCCTTCAGAGAGTATAGAACT
** * *
11297261 CGAACAATCTTCATGAAACGGGTCCGCTCTCTATTCCTTC--AGAGTATAGAACTCGAACAATCT
1 ---ACAATCTTCAACAAACGTGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCT
* ** * *
11297324 TCA-ACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACAAAC
63 TCATA-AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
11297384 G
127 G
11297385 AGTTTGCTTC
Statistics
Matches: 250, Mismatches: 25, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
159 16 0.06
160 4 0.02
161 85 0.34
162 52 0.21
163 63 0.25
165 30 0.12
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (162 bp):
ACAATCTTCAACAAACGTGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA
TAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGT
CCGCTCCCTATTCCTTCAGAGAGTATAGAACT
Found at i:11297258 original size:110 final size:110
Alignment explanation
Indices: 11296904--11297369 Score: 596
Period size: 110 Copynumber: 4.3 Consensus size: 110
11296894 TGACGAGTCT
* *
11296904 GCTCTCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAACGTGTCTGCTCTCTA
1 GCTCTCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTA
* * * *
11296967 TTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACG-GGTC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGTGTTC
* * * *
11297014 TGCTCTCTATTCCTTCAGAGAGTATAGAACTCGGAA-ATTCTTCA-ATAAACAGGTCCGTTCCCT
1 -GCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCATA-AAACGGGTCCGCTCTCT
* * *
11297077 ATTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTTC
63 ATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTTC
* *
11297121 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
11297186 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTTC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTTC
*
11297231 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* * *
11297296 CCTTC--AGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTTC
* *
11297339 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC
11297370 AATCTTCAAC
Statistics
Matches: 315, Mismatches: 28, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
105 2 0.01
106 77 0.24
107 13 0.04
108 64 0.20
110 88 0.28
111 66 0.21
112 5 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (110 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTTC
Found at i:11297434 original size:36 final size:36
Alignment explanation
Indices: 11297387--11297493 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
11297377 AACAAACGAG
11297387 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGA
*
11297423 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGA
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAG-ATGA
* * * * * *
11297460 ATTGCTTTACTGCTCTTTCATGTAGGCTTAAGAT
1 TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
11297494 TGACCTGTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGA
Found at i:11297476 original size:37 final size:36
Alignment explanation
Indices: 11297388--11297496 Score: 137
Period size: 37 Copynumber: 3.0 Consensus size: 36
11297378 ACAAACGAGT
* *
11297388 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTGAA
11297424 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAG-TTGAA
* * * * *
11297461 TTGCTTTACTGCTCTTTCATGTAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAG-TTGA
11297497 CCTGTTTTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 31 0.48
37 33 0.52
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGTTGAA
Found at i:11298795 original size:18 final size:18
Alignment explanation
Indices: 11298772--11298912 Score: 64
Period size: 18 Copynumber: 7.8 Consensus size: 18
11298762 CCTCCTTTTA
11298772 TTTCTCTTTTTTTTCATT
1 TTTCTCTTTTTTTTCATT
11298790 TTTCTC--TTTTTTCATT
1 TTTCTCTTTTTTTTCATT
* **
11298806 TTTCAT-TTTTTCTTCCCT
1 TTTC-TCTTTTTTTTCATT
*
11298824 TTTCCCTTTTCCCTTTT--TT
1 TTTCTCTTTT---TTTTCATT
* *
11298843 TTT-TTTTTTCTTTTCGTT
1 TTTCTCTTTT-TTTTCATT
**
11298861 TTT-TCCATCATTTTTCATT
1 TTTCT-C-TTTTTTTTCATT
*
11298880 TTTCTC-ATTTTTTCATTT
1 TTTCTCTTTTTTTTCA-TT
*
11298898 TTTCTCTTTTATTTC
1 TTTCTCTTTTTTTTC
11298913 TTCTTCAAGC
Statistics
Matches: 93, Mismatches: 16, Indels: 27
0.68 0.12 0.20
Matches are distributed among these distances:
16 19 0.20
17 8 0.09
18 39 0.42
19 21 0.23
20 3 0.03
21 3 0.03
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (18 bp):
TTTCTCTTTTTTTTCATT
Found at i:11298799 original size:16 final size:16
Alignment explanation
Indices: 11298767--11298809 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
11298757 TGAACCCTCC
* *
11298767 TTTT-ATTTCTCTTTT
1 TTTTCATTTTTCTCTT
11298782 TTTTCATTTTTCTCTT
1 TTTTCATTTTTCTCTT
11298798 TTTTCATTTTTC
1 TTTTCATTTTTC
11298810 ATTTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCATTTTTCTCTT
Found at i:11298889 original size:9 final size:8
Alignment explanation
Indices: 11298871--11298901 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
11298861 TTTTCCATCA
11298871 TTTTTCAT
1 TTTTTCAT
11298879 TTTTCTCAT
1 TTTT-TCAT
11298888 TTTTTCAT
1 TTTTTCAT
11298896 TTTTTC
1 TTTTTC
11298902 TCTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:11308593 original size:45 final size:46
Alignment explanation
Indices: 11308522--11308626 Score: 167
Period size: 45 Copynumber: 2.3 Consensus size: 46
11308512 CCATGCTTTG
11308522 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
* * *
11308569 TTGTTCAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATTC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
11308614 TTATTCAAAAAAT
1 TTATTCAAAAAAT
11308627 GAAAATAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 39 0.72
46 9 0.17
47 6 0.11
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:11315220 original size:28 final size:27
Alignment explanation
Indices: 11315167--11315220 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
11315157 GTACACTTTT
****
11315167 TTTGATTGTTTAATTGATTCTTAAAAG
1 TTTGATTGTTTAATTGATGAGGAAAAG
11315194 TTTGATTTGTTTAATTGATGAGGAAAA
1 TTTGA-TTGTTTAATTGATGAGGAAAA
11315221 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (27 bp):
TTTGATTGTTTAATTGATGAGGAAAAG
Found at i:11315287 original size:14 final size:14
Alignment explanation
Indices: 11315250--11315311 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
11315240 TTGCTTGTTT
*
11315250 AATTGATTTATAAA
1 AATTGATTTGTAAA
11315264 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
11315278 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
11315293 TATTGATGTGTAAA
1 AATTGATTTGTAAA
11315307 TAATT
1 -AATT
11315312 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:11315463 original size:20 final size:20
Alignment explanation
Indices: 11315410--11315463 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
11315400 AGGTACACTT
* **
11315410 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
**
11315430 TCGCAATACGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
11315450 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
11315464 TCAATTCGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.26, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:11315479 original size:19 final size:20
Alignment explanation
Indices: 11315457--11315499 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
11315447 AAATCGCAAC
*
11315457 GCGAAAGTC-AATTCGCATT
1 GCGAAAGTCTAATACGCATT
* *
11315476 GCGATAGTCTAATACGCTTT
1 GCGAAAGTCTAATACGCATT
11315496 GCGA
1 GCGA
11315500 TTTTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (20 bp):
GCGAAAGTCTAATACGCATT
Found at i:11315535 original size:20 final size:20
Alignment explanation
Indices: 11315506--11315762 Score: 270
Period size: 20 Copynumber: 13.4 Consensus size: 20
11315496 GCGATTTTCT
* * *
11315506 CGTTGTGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
11315526 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
11315546 CGTTGCGATACTCAAGTTCG
1 CGTTGCGATAGTCAAATTCG
11315566 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
11315586 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
11315600 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
11315619 CTGTTGCGATAATCAAATTCG
1 C-GTTGCGATAGTCAAATTCG
11315640 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
11315660 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
11315680 CGTTGCGATAGACAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
11315700 CGTTACGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
11315714 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
11315734 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
11315754 CGTTGCGAT
1 CGTTGCGAT
11315763 TTTTGAGTTG
Statistics
Matches: 198, Mismatches: 25, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
14 22 0.11
16 2 0.01
18 1 0.01
19 2 0.01
20 168 0.85
21 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:11315604 original size:74 final size:74
Alignment explanation
Indices: 11315526--11315668 Score: 234
Period size: 74 Copynumber: 1.9 Consensus size: 74
11315516 GTCAAATACC
* * *
11315526 CGTTGCGATAATCAAATTCGC-GTTGCGATACTCAAGTTCGCGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAATCAAA-TAGCTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
11315590 GCGATTTTCT
65 GCGATTTTCT
*
11315600 CGTTGCGATAGTCAAATAGCTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATAGCTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
11315665 CGAT
66 CGAT
11315669 AGACAAATTC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
73 3 0.05
74 61 0.95
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (74 bp):
CGTTGCGATAATCAAATAGCTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CGATTTTCT
Found at i:11315628 original size:54 final size:54
Alignment explanation
Indices: 11315545--11315804 Score: 299
Period size: 54 Copynumber: 4.7 Consensus size: 54
11315535 AATCAAATTC
* *
11315545 GCGTTGCGATACTCAAGTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-T
* * *
11315600 -CGTTGCGATAGTCAAA-TAGCTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTCGC-GTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTT
* * * *
11315659 GCGTTGCGATAGACAAATTCGCGTTGCGATAGACAAATTCACGTTACGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* *
11315713 GCGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * * *
11315767 GAGTTGTGATAATCAAATTCGCGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
11315805 GAATGTGTAA
Statistics
Matches: 172, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
53 3 0.02
54 123 0.72
56 1 0.01
58 1 0.01
60 41 0.24
61 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (54 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:11315629 original size:94 final size:93
Alignment explanation
Indices: 11315464--11315688 Score: 351
Period size: 94 Copynumber: 2.4 Consensus size: 93
11315454 AACGCGAAAG
* * * * *
11315464 TCAATTCGCATTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGTGATAGTCAAATACCCGT
1 TCAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGT
11315529 TGCGATAATCAAATTCGCGTTGCGATAC
66 TGCGATAATCAAATTCGCGTTGCGATAC
* *
11315557 TCAAGTTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCTG
1 TCAA-TTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCG
*
11315622 TTGCGATAATCAAATTCGCGTTGCGATAG
65 TTGCGATAATCAAATTCGCGTTGCGATAC
*
11315651 TCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGAT
1 TC-AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
11315689 AGACAAATTC
Statistics
Matches: 121, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
93 4 0.03
94 115 0.95
95 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (93 bp):
TCAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGT
TGCGATAATCAAATTCGCGTTGCGATAC
Found at i:11315647 original size:114 final size:114
Alignment explanation
Indices: 11315507--11315762 Score: 363
Period size: 114 Copynumber: 2.2 Consensus size: 114
11315497 CGATTTTCTC
* * * * *
11315507 GTTGTGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGATACTCAAGTTCGCGTTGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATACACAAATTCGCGTTGC
* * *
11315572 GATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATAGTCAAATAGC-T
66 GATAGACAAATTCACGTTACGATTTT-TGCGTTGCGATAGTCAAAT-GCGT
* * *
11315621 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGC
1 GTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATACACAAATTCGCGTTGC
* *
11315686 GATAGACAAATTCACGTTACGATTTTTGCGTTGCGATAGTCATATTCGT
66 GATAGACAAATTCACGTTACGATTTTTGCGTTGCGATAGTCAAATGCGT
11315735 GTTGCGATAGTCAAATTCGCGTTGCGAT
1 GTTGCGATAGTCAAATTCGCGTTGCGAT
11315763 TTTTGAGTTG
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
113 2 0.02
114 124 0.98
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (114 bp):
GTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCGATACACAAATTCGCGTTGC
GATAGACAAATTCACGTTACGATTTTTGCGTTGCGATAGTCAAATGCGT
Found at i:11315719 original size:94 final size:90
Alignment explanation
Indices: 11315526--11315762 Score: 271
Period size: 94 Copynumber: 2.5 Consensus size: 90
11315516 GTCAAATACC
* * *
11315526 CGTTGCGATAATCAAATTCGCGTTGCGATACTCAAGTTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTG
* * *
11315591 CGATTTTCTCGTTGCGATAGTCAAATAG
66 CGATATTCACGTTACGATA-T--AATAG
11315619 CTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
1 C-GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
* *
11315684 GCGATAGACAAATTCACGTTACGAT-T-TTTG
65 GCGAT------ATTCACGTTACGATATAATAG
* * *
11315714 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
11315763 TTTTGAGTTG
Statistics
Matches: 126, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
93 1 0.01
94 110 0.87
95 3 0.02
98 1 0.01
100 11 0.09
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (90 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTG
CGATATTCACGTTACGATATAATAG
Found at i:11315791 original size:74 final size:74
Alignment explanation
Indices: 11315547--11315804 Score: 199
Period size: 74 Copynumber: 3.5 Consensus size: 74
11315537 TCAAATTCGC
* * * *
11315547 GTTGCGATACTCAAGTTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT------TTTCTCGTTGC
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGC
*
11315606 GATAGTCAAATA
66 GATAG--ACA-A
11315618 GCTGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGT
1 ---GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGT
11315683 TGCGATAGACAA
63 TGCGATAGACAA
* * * ** * * * *
11315695 ATTCACG-TTA-CGATTTTTGCGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTT
1 GTT-GCGATAATC-AAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTT
*****
11315758 GCGATTTTTGA
64 GCGATAGACAA
* *
11315769 GTTGTGATAATCAAATTCGCGTTGCGATATTCAAAT
1 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAAT
11315805 GAATGTGTAA
Statistics
Matches: 146, Mismatches: 28, Indels: 20
0.75 0.14 0.10
Matches are distributed among these distances:
73 2 0.01
74 124 0.85
75 3 0.02
77 1 0.01
78 2 0.01
80 14 0.10
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (74 bp):
GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGC
GATAGACAA
Found at i:11316031 original size:140 final size:140
Alignment explanation
Indices: 11315779--11316044 Score: 523
Period size: 140 Copynumber: 1.9 Consensus size: 140
11315769 GTTGTGATAA
*
11315779 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAGC
11315844 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
11315909 CACATAATAG
131 CACATAATAG
11315919 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAGC
11315984 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
11316045 TACAACGTTT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCATAGC
AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAG
Found at i:11318181 original size:14 final size:14
Alignment explanation
Indices: 11318162--11318197 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
11318152 CCCGTGGCTA
11318162 TTTCTTCGGGGACT
1 TTTCTTCGGGGACT
*
11318176 TTTCTTCGGGGATT
1 TTTCTTCGGGGACT
11318190 TCTTCTTC
1 T-TTCTTC
11318198 TTATTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCTTCGGGGACT
Found at i:11318421 original size:24 final size:24
Alignment explanation
Indices: 11318387--11318440 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
11318377 CTGAAACATC
11318387 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
11318411 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
11318435 ATCAAA
1 ATCAAA
11318441 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:11319285 original size:20 final size:20
Alignment explanation
Indices: 11319260--11319327 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
11319250 GAAATTCAGT
* *
11319260 GTTGCGACAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
11319280 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
11319300 ATTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
11319320 ATTGCGAT
1 GTTGCGAT
11319328 TTACATATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:11319334 original size:20 final size:20
Alignment explanation
Indices: 11319294--11319367 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
11319284 CGATAGTCAG
*
11319294 AATCGCATTGCGATAGT-CAT
1 AATCGCATTGCGAT-TTACAT
11319314 AATCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAT
* *
11319334 ATTCGCATTGCAATTTACAT
1 AATCGCATTGCGATTTACAT
*
11319354 ATTCGCATTGCGAT
1 AATCGCATTGCGAT
11319368 AGTCGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAT
Found at i:11320417 original size:300 final size:300
Alignment explanation
Indices: 11319875--11320473 Score: 1117
Period size: 300 Copynumber: 2.0 Consensus size: 300
11319865 CTACTATCTA
* *
11319875 TGCTACTCGAATCTGAGACTTCTAAGAATAACACTCATTCTTTCAACCACTGAAGTAAATTTGTT
1 TGCTACTCGAACCTGAGACTTCTAAGAATAACAATCATTCTTTCAACCACTGAAGTAAATTTGTT
11319940 TTAATCATGATACACTATATATAAACAAATATTCTTAACAATCTTTAATATAAGTGTAAAGTACA
66 TTAATCATGATACACTATATATAAACAAATATTCTTAACAATCTTTAATATAAGTGTAAAGTACA
11320005 CAAATGGTCTCCCATATGACTATTCATATGTTTCAAACTTGTAACTTTTAATAGTAGGGGACTCA
131 CAAATGGTCTCCCATATGACTATTCATATGTTTCAAACTTGTAACTTTTAATAGTAGGGGACTCA
**
11320070 ACAAAGTGGCGCCCCTATAGTCGGAGGTCTATTTGTAAACTTTACCCTTAATTTAAATATTTTTT
196 ACAAAGTGGCGCCCCTATAGTCGGAGAACTATTTGTAAACTTTACCCTTAATTTAAATATTTTTT
11320135 TTGAATCAAGCTAAGGTGATTAAAAAAAGTATATGTTCTC
261 TTGAATCAAGCTAAGGTGATTAAAAAAAGTATATGTTCTC
11320175 TGCTACTCGAACCTGAGACTTCTAAGAATAACAATCATTCTTTCAACCACTGAAGTAAATTTGTT
1 TGCTACTCGAACCTGAGACTTCTAAGAATAACAATCATTCTTTCAACCACTGAAGTAAATTTGTT
* *
11320240 TTAATCATGATACACTATATATAAACAAATATTTTTAACGATCTTTAATATAAGTGTAAAGTACA
66 TTAATCATGATACACTATATATAAACAAATATTCTTAACAATCTTTAATATAAGTGTAAAGTACA
*
11320305 CAAATGGTCTCCCATCTGACTATTCATATGTTTCAAACTTGTAACTTTTAATAGTAGGGGACTCA
131 CAAATGGTCTCCCATATGACTATTCATATGTTTCAAACTTGTAACTTTTAATAGTAGGGGACTCA
*
11320370 ACAAAGTGTCGCCCCTATAGTCGGAGAACTATTTGTAAACTTTACCCTTAATTTAAATATTTTTT
196 ACAAAGTGGCGCCCCTATAGTCGGAGAACTATTTGTAAACTTTACCCTTAATTTAAATATTTTTT
*
11320435 TTGAATCAAGCTAAGGTGATTAAAAGAAGTATATGTTCT
261 TTGAATCAAGCTAAGGTGATTAAAAAAAGTATATGTTCT
11320474 AAATATACTA
Statistics
Matches: 290, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
300 290 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (300 bp):
TGCTACTCGAACCTGAGACTTCTAAGAATAACAATCATTCTTTCAACCACTGAAGTAAATTTGTT
TTAATCATGATACACTATATATAAACAAATATTCTTAACAATCTTTAATATAAGTGTAAAGTACA
CAAATGGTCTCCCATATGACTATTCATATGTTTCAAACTTGTAACTTTTAATAGTAGGGGACTCA
ACAAAGTGGCGCCCCTATAGTCGGAGAACTATTTGTAAACTTTACCCTTAATTTAAATATTTTTT
TTGAATCAAGCTAAGGTGATTAAAAAAAGTATATGTTCTC
Found at i:11321086 original size:32 final size:33
Alignment explanation
Indices: 11321028--11321108 Score: 155
Period size: 32 Copynumber: 2.5 Consensus size: 33
11321018 TGAAAAATGT
11321028 CTCCTTTTGATTATTCTTTTTTTTTTTGAAGAA
1 CTCCTTTTGATTATTCTTTTTTTTTTTGAAGAA
11321061 CTCCTTTTGATTATTC-TTTTTTTTTTGAAGAA
1 CTCCTTTTGATTATTCTTTTTTTTTTTGAAGAA
11321093 CTCCTTTTGATTATTC
1 CTCCTTTTGATTATTC
11321109 AGAATCAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 32 0.67
33 16 0.33
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (33 bp):
CTCCTTTTGATTATTCTTTTTTTTTTTGAAGAA
Found at i:11329927 original size:26 final size:26
Alignment explanation
Indices: 11329877--11329954 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
11329867 AGAAGGCGCG
* * *
11329877 CTAACTAGATCTTCTAGAAACTGCCA
1 CTAACTGGACCTTATAGAAACTGCCA
*
11329903 CTGACTGGACCTTATAGAAACTGCCA
1 CTAACTGGACCTTATAGAAACTGCCA
* *
11329929 TTAACTGGACCTTTTAGAAACTGCCA
1 CTAACTGGACCTTATAGAAACTGCCA
11329955 TGTCAGACCG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (26 bp):
CTAACTGGACCTTATAGAAACTGCCA
Found at i:11329955 original size:26 final size:26
Alignment explanation
Indices: 11329891--11329955 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
11329881 CTAGATCTTC
* *
11329891 TAGAAACTGCCACTGACTGGACCTTA
1 TAGAAACTGCCATTAACTGGACCTTA
*
11329917 TAGAAACTGCCATTAACTGGACCTTT
1 TAGAAACTGCCATTAACTGGACCTTA
11329943 TAGAAACTGCCAT
1 TAGAAACTGCCAT
11329956 GTCAGACCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (26 bp):
TAGAAACTGCCATTAACTGGACCTTA
Found at i:11339201 original size:21 final size:22
Alignment explanation
Indices: 11339176--11339221 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
11339166 GGGTTCGGTA
* *
11339176 AAAAGATATTTAAA-TAATAAT
1 AAAAGAGATTTAAAGTAAAAAT
*
11339197 AAAAGCGATTTAAAGTAAAAAT
1 AAAAGAGATTTAAAGTAAAAAT
11339219 AAA
1 AAA
11339222 GAAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (22 bp):
AAAAGAGATTTAAAGTAAAAAT
Found at i:11340553 original size:24 final size:24
Alignment explanation
Indices: 11340520--11340579 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
11340510 ATGTTCACAA
11340520 ATAAACTCATTTGAAAACTAGTTT
1 ATAAACTCATTTGAAAACTAGTTT
* ***
11340544 ATAAATTCATTTGTCGACTAGTTT
1 ATAAACTCATTTGAAAACTAGTTT
*
11340568 ATAAGCTCATTT
1 ATAAACTCATTT
11340580 ACCCATCTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (24 bp):
ATAAACTCATTTGAAAACTAGTTT
Found at i:11347144 original size:29 final size:29
Alignment explanation
Indices: 11347112--11347185 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
11347102 CTAGTGGAAA
*
11347112 TACCTAATTTTCTAATATTCAATGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
*
11347141 TACCTAATTTTCCAATATTCAGTGAGCAT
1 TACCTAATTTTCCAATATTCAATGAGCAT
11347170 TACCTAATTTTCCAAT
1 TACCTAATTTTCCAAT
11347186 TCACAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (29 bp):
TACCTAATTTTCCAATATTCAATGAGCAT
Found at i:11352590 original size:22 final size:22
Alignment explanation
Indices: 11352556--11352654 Score: 117
Period size: 22 Copynumber: 4.2 Consensus size: 22
11352546 AAACATAGAA
* *
11352556 TTAATACTCAATACTAGTGGAT
1 TTAACACTTAATACTAGTGGAT
11352578 TTAACACTTAATACTAGTGGAT
1 TTAACACTTAATACTAGTGGAT
11352600 TTAATACTTAATACTTAATACTAGTGGAT
1 TT-A-AC-----ACTTAATACTAGTGGAT
11352629 TTAACACTTAATACTAGTGGAT
1 TTAACACTTAATACTAGTGGAT
11352651 TTAA
1 TTAA
11352655 TCATGAGCAT
Statistics
Matches: 68, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
22 43 0.63
23 1 0.01
24 2 0.03
27 2 0.03
28 1 0.01
29 19 0.28
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TTAACACTTAATACTAGTGGAT
Found at i:11352605 original size:15 final size:15
Alignment explanation
Indices: 11352585--11352632 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
11352575 GATTTAACAC
11352585 TTAATACTAGTGGAT
1 TTAATACTAGTGGAT
* *
11352600 TTAATACTTAAT--AC
1 TTAATAC-TAGTGGAT
11352614 TTAATACTAGTGGAT
1 TTAATACTAGTGGAT
11352629 TTAA
1 TTAA
11352633 CACTTAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 12 0.46
16 3 0.12
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (15 bp):
TTAATACTAGTGGAT
Found at i:11352620 original size:51 final size:51
Alignment explanation
Indices: 11352556--11352655 Score: 191
Period size: 51 Copynumber: 2.0 Consensus size: 51
11352546 AAACATAGAA
11352556 TTAATACTCAATACTAGTGGATTTAACACTTAATACTAGTGGATTTAATAC
1 TTAATACTCAATACTAGTGGATTTAACACTTAATACTAGTGGATTTAATAC
*
11352607 TTAATACTTAATACTAGTGGATTTAACACTTAATACTAGTGGATTTAAT
1 TTAATACTCAATACTAGTGGATTTAACACTTAATACTAGTGGATTTAAT
11352656 CATGAGCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (51 bp):
TTAATACTCAATACTAGTGGATTTAACACTTAATACTAGTGGATTTAATAC
Found at i:11352640 original size:29 final size:29
Alignment explanation
Indices: 11352578--11352643 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
11352568 ACTAGTGGAT
* *
11352578 TTAACACTTAATACTAGTGGATTTAATAC
1 TTAATACTTAATACTAGTGGATTTAACAC
11352607 TTAATACTTAATACTAGTGGATTTAACAC
1 TTAATACTTAATACTAGTGGATTTAACAC
11352636 TTAATACT
1 TTAATACT
11352644 AGTGGATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (29 bp):
TTAATACTTAATACTAGTGGATTTAACAC
Found at i:11359678 original size:28 final size:29
Alignment explanation
Indices: 11359627--11359681 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
11359617 CAAAAAATAG
*
11359627 TAAAATTTTCATAAAAAATAATAAATTTA
1 TAAAATTTTCATAAAAAAAAATAAATTTA
11359656 TAAAATTTT-A-AAAATAAAAATAAATT
1 TAAAATTTTCATAAAA-AAAAATAAATT
11359682 ATTAATAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 9 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAAATTTTCATAAAAAAAAATAAATTTA
Found at i:11365792 original size:16 final size:16
Alignment explanation
Indices: 11365771--11365804 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11365761 TAATCACTCC
11365771 TAAATT-ATAAAACTTT
1 TAAATTGATAAAA-TTT
11365787 TAAATTGATAAAATTT
1 TAAATTGATAAAATTT
11365803 TA
1 TA
11365805 TGGGAGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATTGATAAAATTT
Found at i:11367778 original size:78 final size:78
Alignment explanation
Indices: 11367649--11367806 Score: 298
Period size: 78 Copynumber: 2.0 Consensus size: 78
11367639 AAATAGTTGC
*
11367649 TAGAATTCAACAAAGCTTACGAGGTAAAAGTCGAGGTTACAACACTTAATGCTTCAAGTTAAAAA
1 TAGAATTCAACAAAGCTTACGACGTAAAAGTCGAGGTTACAACACTTAATGCTTCAAGTTAAAAA
11367714 TAAACACAATATA
66 TAAACACAATATA
*
11367727 TAGAATTCAACAAAGCTTGCGACGTAAAAGTCGAGGTTACAACACTTAATGCTTCAAGTTAAAAA
1 TAGAATTCAACAAAGCTTACGACGTAAAAGTCGAGGTTACAACACTTAATGCTTCAAGTTAAAAA
11367792 TAAACACAATATA
66 TAAACACAATATA
11367805 TA
1 TA
11367807 TGGATAGATA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.25
Consensus pattern (78 bp):
TAGAATTCAACAAAGCTTACGACGTAAAAGTCGAGGTTACAACACTTAATGCTTCAAGTTAAAAA
TAAACACAATATA
Found at i:11368567 original size:41 final size:43
Alignment explanation
Indices: 11368522--11368665 Score: 126
Period size: 41 Copynumber: 3.5 Consensus size: 43
11368512 GTTTTTTGTT
* **
11368522 TAAAAATGCCACTAATGTATGACTAT-TTAGCGGTG-TT-TTGA
1 TAAAAATGCCACTAACGTACAACTATGTT-GCGGTGTTTGTTGA
11368563 TAAAAATGCCACTAACGTACAACTATGTTGCGGTGTTTGTTGA
1 TAAAAATGCCACTAACGTACAACTATGTTGCGGTGTTTGTTGA
* * *
11368606 -AAAAACGCCACTATA-GATTACATCTA--TTGCAGTGTTTG-T-A
1 TAAAAATGCCACTA-ACG--TACAACTATGTTGCGGTGTTTGTTGA
*
11368646 TAAAAATGCCGCTAACGTAC
1 TAAAAATGCCACTAACGTAC
11368666 TATTCTATAT
Statistics
Matches: 87, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
39 3 0.03
40 2 0.02
41 42 0.48
42 28 0.32
43 5 0.06
44 7 0.08
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (43 bp):
TAAAAATGCCACTAACGTACAACTATGTTGCGGTGTTTGTTGA
Found at i:11368738 original size:81 final size:81
Alignment explanation
Indices: 11368608--11368768 Score: 180
Period size: 81 Copynumber: 2.0 Consensus size: 81
11368598 TTTGTTGAAA
* * *** * * * *
11368608 AAACGCCACTATAGATTACATCTATTGCAGTGTTTGTATAAAAATGCCGCTAACGTACTATTCTA
1 AAACGCCACTATAGATGACACCTATTGCAACATTTGTATAAAAACGCCGCTAAAGCACTACTCTA
*
11368673 TATCGGCGTTTGTTGT
66 TAACGGCGTTTGTTGT
* *
11368689 AAACGCCACTATAGATGA-ACCATATTGCAACATTTTTATATAAACGCCGCTAAAGCACTACTCT
1 AAACGCCACTATAGATGACACC-TATTGCAACATTTGTATAAAAACGCCGCTAAAGCACTACTCT
* *
11368753 GTAACGGTGTTTGTTG
65 ATAACGGCGTTTGTTG
11368769 GAAAAATGAC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
80 2 0.03
81 63 0.97
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (81 bp):
AAACGCCACTATAGATGACACCTATTGCAACATTTGTATAAAAACGCCGCTAAAGCACTACTCTA
TAACGGCGTTTGTTGT
Found at i:11370033 original size:21 final size:21
Alignment explanation
Indices: 11370009--11370053 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11369999 ATAGCCTAGA
*
11370009 ATGTTGATGTGATAGTTCACG
1 ATGTTGATGTGATAGTACACG
* *
11370030 ATGTTGTTGTGGTAGTACACG
1 ATGTTGATGTGATAGTACACG
11370051 ATG
1 ATG
11370054 ATGTGATAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (21 bp):
ATGTTGATGTGATAGTACACG
Found at i:11370119 original size:29 final size:28
Alignment explanation
Indices: 11370068--11370123 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
11370058 GATAGATGAA
*
11370068 CCTAATTGATTTTTACTAAGTTTGAGAG
1 CCTAATTGATTTTTACGAAGTTTGAGAG
11370096 CCTAATTGATTTTTTA-GAATGTTTGAGA
1 CCTAATTGA-TTTTTACGAA-GTTTGAGA
11370124 ACTTATTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.45
Consensus pattern (28 bp):
CCTAATTGATTTTTACGAAGTTTGAGAG
Found at i:11372526 original size:12 final size:12
Alignment explanation
Indices: 11372509--11372534 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11372499 TTGCTTTGGC
11372509 AGTATTATTATA
1 AGTATTATTATA
11372521 AGTATTATTATA
1 AGTATTATTATA
11372533 AG
1 AG
11372535 CTGAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (12 bp):
AGTATTATTATA
Found at i:11375837 original size:55 final size:56
Alignment explanation
Indices: 11375717--11375838 Score: 158
Period size: 55 Copynumber: 2.2 Consensus size: 56
11375707 CATAATCCCC
* *
11375717 GTCCTGATTCTGCATTGGCTTAGTCCCTATCATAATTCTGCATGGGCTCTGACCGT
1 GTCCTGATTCTGCATTGGCTAAGTCCCTATCATAATTCTGCATGGGCTCAGACCGT
* * * * *
11375773 ATCCTGATTCTGCA-TGGACTAAGTCCC-ATCTTGATTTTGCATGGGCTCAGACCTT
1 GTCCTGATTCTGCATTGG-CTAAGTCCCTATCATAATTCTGCATGGGCTCAGACCGT
11375828 GTCCTGATTCT
1 GTCCTGATTCT
11375839 ATATGGGCTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
55 36 0.63
56 21 0.37
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.36
Consensus pattern (56 bp):
GTCCTGATTCTGCATTGGCTAAGTCCCTATCATAATTCTGCATGGGCTCAGACCGT
Found at i:11376083 original size:31 final size:31
Alignment explanation
Indices: 11376045--11376106 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
11376035 AAAAAACGCC
11376045 GCAATAGGTATTGATATTTAGCGGCGTTTGT
1 GCAATAGGTATTGATATTTAGCGGCGTTTGT
*
11376076 GCAATAGGTGTTGATATTTAGCGGCGTTTGT
1 GCAATAGGTATTGATATTTAGCGGCGTTTGT
11376107 CATAAAAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.21, C:0.10, G:0.31, T:0.39
Consensus pattern (31 bp):
GCAATAGGTATTGATATTTAGCGGCGTTTGT
Found at i:11376137 original size:43 final size:43
Alignment explanation
Indices: 11376076--11376259 Score: 183
Period size: 43 Copynumber: 4.3 Consensus size: 43
11376066 CGGCGTTTGT
*
11376076 GCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCC
1 GCAATAGGTGTTAATATTTAGCGGCGTTTGTCATAAAAACGCC
* * * *
11376119 GCAATAGGTATTAATATTTACCGACGTTTGTCATAAAAACGTC
1 GCAATAGGTGTTAATATTTAGCGGCGTTTGTCATAAAAACGCC
* * * * *
11376162 GCAATAGGTGTAAATATTTAGCAGCGTTTTTCAGACAAACGCC
1 GCAATAGGTGTTAATATTTAGCGGCGTTTGTCATAAAAACGCC
* * * * * *
11376205 GTAATAGGT-TATGATGTTTAGCGGCGTTTTTCGCT-AAAATGCC
1 GCAATAGGTGT-TAATATTTAGCGGCGTTTGTC-ATAAAAACGCC
*
11376248 GCAGTAGGTGTT
1 GCAATAGGTGTT
11376260 GATGTCTTGC
Statistics
Matches: 113, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
42 1 0.01
43 111 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
GCAATAGGTGTTAATATTTAGCGGCGTTTGTCATAAAAACGCC
Found at i:11376263 original size:43 final size:41
Alignment explanation
Indices: 11376216--11376328 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 41
11376206 TAATAGGTTA
* * *
11376216 TGATGTTTAGCGGCGTTTTTCGCTAAAATGCCGCAGTAGGTGT
1 TGATGTTT-GCGGCGTTTTT-GCTAAAACGCCACAGTAGGTAT
* * *
11376259 TGATGTCTTGCGACATTTTT-TTCACAAACGCCACAGTAGGTAT
1 TGATGT-TTGCGGCGTTTTTGCT-A-AAACGCCACAGTAGGTAT
*
11376302 TGATGTTTTGCGGTGTTTTTGCTAAAA
1 TGATG-TTTGCGGCGTTTTTGCTAAAA
11376329 ACACCGGTAC
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
41 1 0.02
42 4 0.07
43 46 0.84
44 4 0.07
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (41 bp):
TGATGTTTGCGGCGTTTTTGCTAAAACGCCACAGTAGGTAT
Found at i:11376756 original size:21 final size:21
Alignment explanation
Indices: 11376732--11376803 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
11376722 TCTGATATGT
*
11376732 TGCTTCTCTCTGTGCTGCCGC
1 TGCTTCTCTCTGTGCTTCCGC
*
11376753 TGCTTCTCTCTGTGCTTTCGC
1 TGCTTCTCTCTGTGCTTCCGC
* *
11376774 TGCTTCTTTCTCTGCTTCCGC
1 TGCTTCTCTCTGTGCTTCCGC
*
11376795 TGCTGCTCT
1 TGCTTCTCT
11376804 GGCTGCTGCT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.00, C:0.36, G:0.19, T:0.44
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTTCCGC
Found at i:11376789 original size:33 final size:33
Alignment explanation
Indices: 11376752--11376825 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
11376742 TGTGCTGCCG
* * * *
11376752 CTGCTTCTCTCTG-TGCTTTCGCTGCTTCTTTCT
1 CTGCTTC-CGCTGCTGCTCTCGCTGCTGCTCTCT
*
11376785 CTGCTTCCGCTGCTGCTCTGGCTGCTGCTCTCT
1 CTGCTTCCGCTGCTGCTCTCGCTGCTGCTCTCT
11376818 CTGCTTCC
1 CTGCTTCC
11376826 CTTGCTTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.43
Consensus pattern (33 bp):
CTGCTTCCGCTGCTGCTCTCGCTGCTGCTCTCT
Found at i:11379684 original size:41 final size:42
Alignment explanation
Indices: 11379324--11379690 Score: 485
Period size: 42 Copynumber: 8.8 Consensus size: 42
11379314 TTGTAAATAC
*
11379324 AAACGCCACTAAAGTACGAGTC-ATTAGCAGCGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTGTATTCA
* *
11379366 AAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
*
11379408 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA-TAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
* * *
11379449 AAATGCCACTAAAGTACGATTC-ATTAGCAGCGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTGTATTCA
* * *
11379491 AAACGCTACTAAAGTACGAGTCTATAGCGACGTTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
*
11379533 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA-TAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
* * * * *
11379574 AAATGCCACTAAAGTACTAGTCTATAGCGGCATTTATA-TAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
* * * *
11379615 AAATGCTACTAAAGTACGAGTCTTTAGCGGCGTTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
*
11379657 AAACGCCACTAAAGTA-GAGTTTATAGCGGCGTTT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT
11379691 TTGGATACAA
Statistics
Matches: 285, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.00
41 122 0.43
42 160 0.56
43 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (42 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATTCA
Found at i:11379707 original size:42 final size:41
Alignment explanation
Indices: 11379320--11379733 Score: 415
Period size: 42 Copynumber: 10.0 Consensus size: 41
11379310 GCGTTTGTAA
* *
11379320 ATACAAACGCCACTAAAGTACGAGTC-ATTAGCAGCGTTTGT
1 ATACAAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTGC
* *
11379361 ATTCAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGC
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
* *
11379403 ATTCAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
* * * * *
11379445 ATAAAAATGCCACTAAAGTACGATTC-ATTAGCAGCGTTTGT
1 ATACAAACGCCACTAAAGTACGAGTCTA-TAGCGGCGTTTGC
* * *
11379486 ATTCAAAACGCTACTAAAGTACGAGTCTATAGCGACGTTTGC
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
* *
11379528 ATTCAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
* * * * **
11379570 ATAAAAATGCCACTAAAGTACTAGTCTATAGCGGCATTTAT
1 ATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
* * * *
11379611 ATAAAAATGCTACTAAAGTACGAGTCTTTAGCGGCGTTTGC
1 ATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
* * *
11379652 ATTCAAAACGCCACTAAAGTA-GAGTTTATAGCGGCGTTTTTGG
1 ATAC-AAACGCCACTAAAGTACGAGTCTATAGCGGCG--TTTGC
* *
11379695 ATACAAATGCCACAAAATGTTA-GA-TCTATAGCGGCGTTT
1 ATACAAACGCCACTAAA-G-TACGAGTCTATAGCGGCGTTT
11379734 CTAGATACAA
Statistics
Matches: 318, Mismatches: 45, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.00
41 123 0.39
42 169 0.53
43 21 0.07
44 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
ATACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGC
Found at i:11379707 original size:125 final size:125
Alignment explanation
Indices: 11379308--11379690 Score: 592
Period size: 125 Copynumber: 3.1 Consensus size: 125
11379298 TGTAAAATTA
* * *
11379308 CGGCGTTTGTAAATACAAACGCCACTAAAGTACGAGTCATTAGCAGCGTTTGTATTCAAAACGCC
1 CGGCGTTTGT--ATAAAAATGCCACTAAAGTACGAGTCATTAGCAGCGTTTGTATTCAAAACGCT
*
11379373 ACTAAAGTACGAGTCTATAGCGGCATTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAG
64 ACTAAAGTACGAGTCTATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAG
*
11379435 CGGCGTTTGTATAAAAATGCCACTAAAGTACGATTCATTAGCAGCGTTTGTATTCAAAACGCTAC
1 CGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCATTAGCAGCGTTTGTATTCAAAACGCTAC
*
11379500 TAAAGTACGAGTCTATAGCGACGTTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAG
66 TAAAGTACGAGTCTATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAG
* * * * * *
11379560 CGGCGTTTGTATAAAAATGCCACTAAAGTACTAGTC-TATAGCGGCATTTATA-TAAAAATGCTA
1 CGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCAT-TAGCAGCGTTTGTATTCAAAACGCTA
* *
11379623 CTAAAGTACGAGTCTTTAGCGGCGTTTGCATTCAAAACGCCACTAAAGTA-GAGTTTATAG
65 CTAAAGTACGAGTCTATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAG
11379683 CGGCGTTT
1 CGGCGTTT
11379691 TTGGATACAA
Statistics
Matches: 239, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
123 17 0.07
124 58 0.24
125 154 0.64
127 10 0.04
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (125 bp):
CGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCATTAGCAGCGTTTGTATTCAAAACGCTAC
TAAAGTACGAGTCTATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAG
Found at i:11379725 original size:166 final size:167
Alignment explanation
Indices: 11379324--11379733 Score: 519
Period size: 166 Copynumber: 2.5 Consensus size: 167
11379314 TTGTAAATAC
* * *
11379324 AAACGCCACTAAAGTACGAGTC-ATTAGC-AGCGTTTGTATTCAAAACGCCACTAAAGTACGAGT
1 AAACGCCACTAAAGTACGAGTCTA-TAGCGA-CGTTTGCATACAAAACGCCACAAAAGTACGAGT
* * * *
11379387 CTATAGCGGCATTTGCATTCAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA
64 CTATAGCGGCGTTTGCATTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTATATAAAAA
* *
11379452 TGCCACTAAAGTACGATTCATTAGCAGCGTTTGTATTCA
129 TGCCACTAAAGTACGAGTCATTAGCAGCGTTTGCATTCA
* * *
11379491 AAACGCTACTAAAGTACGAGTCTATAGCGACGTTTGCATTCAAAACGCCACTAAAGTACGAGTCT
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGCATACAAAACGCCACAAAAGTACGAGTCT
* * *
11379556 ATAGCGGCGTTTGTA-TAAAAATGCCACTAAAGTACTAGTCTATAGCGGCATTTATATAAAAATG
66 ATAGCGGCGTTTGCATTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTATATAAAAATG
* * *
11379620 CTACTAAAGTACGAGTCTTTAGCGGCGTTTGCATTCA
131 CCACTAAAGTACGAGTCATTAGCAGCGTTTGCATTCA
* * * *
11379657 AAACGCCACTAAAGTA-GAGTTTATAGCGGCGTTTTTGGATAC-AAATGCCACAAAATGTTA-GA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACG--TTTGCATACAAAACGCCACAAAA-G-TACGA
11379719 -TCTATAGCGGCGTTT
62 GTCTATAGCGGCGTTT
11379734 CTAGATACAA
Statistics
Matches: 216, Mismatches: 21, Indels: 13
0.86 0.08 0.05
Matches are distributed among these distances:
165 13 0.06
166 117 0.54
167 82 0.38
168 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (167 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGCATACAAAACGCCACAAAAGTACGAGTCT
ATAGCGGCGTTTGCATTAAAAACGCCACTAAAGTACGAGTCTATAGCGGCATTTATATAAAAATG
CCACTAAAGTACGAGTCATTAGCAGCGTTTGCATTCA
Found at i:11380305 original size:41 final size:42
Alignment explanation
Indices: 11380256--11380416 Score: 188
Period size: 41 Copynumber: 3.9 Consensus size: 42
11380246 TGTTTATACA
* * *
11380256 AAAAAACGCCACTATTGATT-ACATTATTGTGGCGTTTGT-T
1 AAAAAACACCACTATTGATTAACACTATTGCGGCGTTTGTCT
* * * *
11380296 AAAATAACGCCACTATTGATTAAAACTATTGCGGCGTTTTTGT
1 AAAA-AACACCACTATTGATTAACACTATTGCGGCGTTTGTCT
*
11380339 AAAAAA-ACCACTATTGATTAACACTATTGCGGTGTTTGTCT
1 AAAAAACACCACTATTGATTAACACTATTGCGGCGTTTGTCT
*
11380380 -AAAAACACCACTATTTATTATA-ACTATTGCGGCGTTT
1 AAAAAACACCACTATTGATTA-ACACTATTGCGGCGTTT
11380417 TAAGAATAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
40 9 0.09
41 73 0.70
42 18 0.17
43 5 0.05
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (42 bp):
AAAAAACACCACTATTGATTAACACTATTGCGGCGTTTGTCT
Found at i:11380353 original size:82 final size:83
Alignment explanation
Indices: 11380255--11380417 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 83
11380245 GTGTTTATAC
* * *
11380255 AAAAAAACGCCACTATTGATT-ACATTATTGTGGCGTTTGT-TAAAATAACGCCACTATTGATTA
1 AAAAAAAC-CCACTATTGATTAACACTATTGCGGCGTTTGTCT-AAA-AACACCACTATTGATTA
11380318 AAACTATTGCGGCGTTTTTGT
63 AAACTATTGCGGCGTTTTTGT
* * *
11380339 AAAAAAA-CCACTATTGATTAACACTATTGCGGTGTTTGTCTAAAAACACCACTATTTATTATAA
1 AAAAAAACCCACTATTGATTAACACTATTGCGGCGTTTGTCTAAAAACACCACTATTGATTAAAA
11380403 CTATTGCGGCGTTTT
66 CTATTGCGGCGTTTT
11380418 AAGAATAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
82 44 0.62
83 19 0.27
84 8 0.11
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (83 bp):
AAAAAAACCCACTATTGATTAACACTATTGCGGCGTTTGTCTAAAAACACCACTATTGATTAAAA
CTATTGCGGCGTTTTTGT
Found at i:11380467 original size:41 final size:42
Alignment explanation
Indices: 11380403--11380602 Score: 166
Period size: 41 Copynumber: 4.8 Consensus size: 42
11380393 TTTATTATAA
* * *
11380403 CTATTGCGGCGTTT-TAAGAATAAATGCCACTATATGTGT-AT
1 CTATTGCGGCGTTTGT-GGTATAAACGCCACTATATGTGTAAT
*
11380444 CTATTGCGGCGTTTGTGGTATAAACGCCGCTA-AT-T-TACCGAT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTGTA---AT
*
11380486 CTATTGCAGCGTTT-TGGCTA-AAACGCCACTATATGT-TAAT
1 CTATTGCGGCGTTTGTGG-TATAAACGCCACTATATGTGTAAT
* * * * *
11380526 CTATTGCAGCGTTTGTGGTATAAACGCCGCTA-ATTTATCACT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTGT-AAT
* * *
11380568 CTATTGCGGCGTTTGTTGTAAAAACGCCTCTATAT
1 CTATTGCGGCGTTTGTGGTATAAACGCCACTATAT
11380603 TTCAACTCTA
Statistics
Matches: 133, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 23 0.17
41 53 0.40
42 50 0.38
43 5 0.04
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (42 bp):
CTATTGCGGCGTTTGTGGTATAAACGCCACTATATGTGTAAT
Found at i:11380498 original size:42 final size:41
Alignment explanation
Indices: 11380442--11380619 Score: 188
Period size: 42 Copynumber: 4.3 Consensus size: 41
11380432 CTATATGTGT
*
11380442 ATCTATTGCGGCGTTTGTGGTATAAACGCCGCTA-ATTTACC
1 ATCTATTGCAGCGTTTGTGGTATAAACGCCGCTATATTTA-C
*
11380483 GATCTATTGCAGCGTTT-TGGCTA-AAACGCCACTATATGTTA-
1 -ATCTATTGCAGCGTTTGTGG-TATAAACGCCGCTATAT-TTAC
11380524 ATCTATTGCAGCGTTTGTGGTATAAACGCCGCTA-ATTTATC
1 ATCTATTGCAGCGTTTGTGGTATAAACGCCGCTATATTTA-C
* * * *
11380565 ACTCTATTGCGGCGTTTGTTGTAAAAACGCCTCTATATTT-C
1 A-TCTATTGCAGCGTTTGTGGTATAAACGCCGCTATATTTAC
11380606 AACTCTATTGCAGC
1 -A-TCTATTGCAGC
11380620 ATTTTTACAA
Statistics
Matches: 118, Mismatches: 8, Indels: 20
0.81 0.05 0.14
Matches are distributed among these distances:
39 3 0.03
40 20 0.17
41 28 0.24
42 60 0.51
43 7 0.06
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (41 bp):
ATCTATTGCAGCGTTTGTGGTATAAACGCCGCTATATTTAC
Found at i:11380515 original size:82 final size:82
Alignment explanation
Indices: 11380428--11380619 Score: 257
Period size: 82 Copynumber: 2.3 Consensus size: 82
11380418 AAGAATAAAT
*
11380428 GCCACTATATGTGT-ATCTATTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACCGA-TCTATT
1 GCCACTATATGT-TAATCTATTGCAGCGTTTGTGGTATAAACGCCGCTAATTTACC-ACTCTATT
11380491 GCAGCGTTTTGGCTAAAAC
64 GCAGCGTTTTGGCTAAAAC
*
11380510 GCCACTATATGTTAATCTATTGCAGCGTTTGTGGTATAAACGCCGCTAATTTATCACTCTATTGC
1 GCCACTATATGTTAATCTATTGCAGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGC
* *
11380575 GGCGTTTGTTG-TAAAAAC
66 AGCGTTT-TGGCT-AAAAC
*
11380593 GCCTCTATAT-TTCAACTCTATTGCAGC
1 GCCACTATATGTT-AA-TCTATTGCAGC
11380620 ATTTTTACAA
Statistics
Matches: 99, Mismatches: 5, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
81 2 0.02
82 68 0.69
83 18 0.18
84 11 0.11
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (82 bp):
GCCACTATATGTTAATCTATTGCAGCGTTTGTGGTATAAACGCCGCTAATTTACCACTCTATTGC
AGCGTTTTGGCTAAAAC
Found at i:11385360 original size:20 final size:20
Alignment explanation
Indices: 11385294--11385363 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
11385284 TTGGTACTAG
* *
11385294 TATTGTTCCTCCAATACTGG
1 TATTGTTCATCCAATACTGA
*
11385314 TATTGTTCTTCCTACA-ACATCGA
1 TATTGTTCATCC-A-ATAC-T-GA
*
11385337 TATTGTTCATCCAGTACTGA
1 TATTGTTCATCCAATACTGA
11385357 TATTGTT
1 TATTGTT
11385364 ATTATAGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 20 0.49
21 4 0.10
22 5 0.12
23 12 0.29
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (20 bp):
TATTGTTCATCCAATACTGA
Found at i:11388048 original size:10 final size:10
Alignment explanation
Indices: 11388027--11388067 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
11388017 CTTCATAACT
*
11388027 TATATATATA
1 TATATATGTA
*
11388037 TATATGTGTA
1 TATATATGTA
11388047 TATATATGTA
1 TATATATGTA
*
11388057 TGTATATGTA
1 TATATATGTA
11388067 T
1 T
11388068 CTTGTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (10 bp):
TATATATGTA
Found at i:11388050 original size:16 final size:16
Alignment explanation
Indices: 11388029--11388059 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11388019 TCATAACTTA
11388029 TATATATATATATGTG
1 TATATATATATATGTG
*
11388045 TATATATATGTATGT
1 TATATATATATATGT
11388060 ATATGTATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
TATATATATATATGTG
Found at i:11393362 original size:31 final size:31
Alignment explanation
Indices: 11393324--11393408 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
11393314 ATATATGGTG
*
11393324 ATCGAACTGCATTAGATGCATCAATGTTTTA
1 ATCGAACTGCATTAGATGCATCAATATTTTA
*
11393355 ATCGAACTGCATTAGATGCATCAATATTTTG
1 ATCGAACTGCATTAGATGCATCAATATTTTA
11393386 ATCGAACTGCATTAGATGCATCA
1 ATCGAACTGCATTAGATGCATCA
11393409 GTGTCTTGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (31 bp):
ATCGAACTGCATTAGATGCATCAATATTTTA
Found at i:11394841 original size:17 final size:17
Alignment explanation
Indices: 11394819--11394853 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11394809 AAGATTTAAC
11394819 TTATAAAA-CTACGTAAA
1 TTATAAAATC-ACGTAAA
11394836 TTATAAAATCACGTAAA
1 TTATAAAATCACGTAAA
11394853 T
1 T
11394854 ATTATCCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
TTATAAAATCACGTAAA
Found at i:11395027 original size:29 final size:29
Alignment explanation
Indices: 11394928--11395030 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 29
11394918 TACAAGAAAG
* *
11394928 CTTAATATTTTAAAATTATTAAATAAATA
1 CTTAATATTTTAAAATAATTAAATTAATA
* * *
11394957 -TCTAATCTTTTCGAATATATTTAAA-TAATAA
1 CT-TAATATTTT--AAAATAATTAAATTAAT-A
* * *
11394988 CATATTTTTTTAAAATAATTAAATTAATA
1 CTTAATATTTTAAAATAATTAAATTAATA
11395017 CTTAATATTTTAAA
1 CTTAATATTTTAAA
11395031 TCTACTCGAA
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
28 1 0.02
29 30 0.55
30 7 0.13
31 17 0.31
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.47
Consensus pattern (29 bp):
CTTAATATTTTAAAATAATTAAATTAATA
Found at i:11396411 original size:21 final size:21
Alignment explanation
Indices: 11396385--11396426 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11396375 GCGATTTAAA
* *
11396385 ACCGTCGCGGGTGTTATTGCG
1 ACCGTCGCGGGCGCTATTGCG
11396406 ACCGTCGCGGGCGCTATTGCG
1 ACCGTCGCGGGCGCTATTGCG
11396427 GTTGTAGCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.24
Consensus pattern (21 bp):
ACCGTCGCGGGCGCTATTGCG
Found at i:11398177 original size:34 final size:34
Alignment explanation
Indices: 11398106--11398202 Score: 96
Period size: 33 Copynumber: 2.9 Consensus size: 34
11398096 GTCACTAACC
* *
11398106 TACTAACATTCTAACA--TTTATCTTATTGTTCGA
1 TACTAACATTC-AAAATTTTTATTTTATTGTTCGA
11398139 -ACTAACATTCAAAATTTTTATTTTATTTGTTC-A
1 TACTAACATTCAAAATTTTTATTTTA-TTGTTCGA
* *
11398172 TACTAACATAC-TAATTTTTATTTTTATTGTT
1 TACTAACATTCAAAATTTTTA-TTTTATTGTT
11398203 ATTATTAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 3 0.05
32 10 0.18
33 22 0.40
34 20 0.36
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.52
Consensus pattern (34 bp):
TACTAACATTCAAAATTTTTATTTTATTGTTCGA
Found at i:11398761 original size:2 final size:2
Alignment explanation
Indices: 11398754--11398781 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11398744 TTTTACTCGA
11398754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11398782 TAACCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11398800 original size:22 final size:24
Alignment explanation
Indices: 11398775--11398828 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
11398765 TATATATATA
* * *
11398775 TATATATTAA-CCTTAT-TTTTTT
1 TATATATAAATCCTCATATTTTGT
11398797 TATATATAAATCCTCATATTTTGT
1 TATATATAAATCCTCATATTTTGT
11398821 TATATATA
1 TATATATA
11398829 GAAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 9 0.33
23 5 0.19
24 13 0.48
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATATAAATCCTCATATTTTGT
Found at i:11398990 original size:26 final size:26
Alignment explanation
Indices: 11398955--11399016 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
11398945 TGTTTTTACA
11398955 TTTT-TTTTATTTTATCTCA-TTCTAT
1 TTTTATTTTATTTTATCTCATTTC-AT
*
11398980 TTTTATTTTATTTTATTTCATTTCAT
1 TTTTATTTTATTTTATCTCATTTCAT
11399006 TTTTATCTTTA
1 TTTTAT-TTTA
11399017 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 4 0.12
26 22 0.67
27 7 0.21
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATTTTATTTTATCTCATTTCAT
Found at i:11401211 original size:20 final size:20
Alignment explanation
Indices: 11401186--11401231 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11401176 TTGGGATCAA
*
11401186 CATTTTTGCATTTGCATTTG
1 CATTTTCGCATTTGCATTTG
**
11401206 CATTTTCGTTTTTGCATTTG
1 CATTTTCGCATTTGCATTTG
11401226 CATTTT
1 CATTTT
11401232 GTTTTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.13, C:0.15, G:0.13, T:0.59
Consensus pattern (20 bp):
CATTTTCGCATTTGCATTTG
Found at i:11401238 original size:20 final size:20
Alignment explanation
Indices: 11401196--11401237 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
11401186 CATTTTTGCA
11401196 TTTGCATTTGCATTTTCGTT
1 TTTGCATTTGCATTTTCGTT
11401216 TTTGCATTTGCATTTT-GTT
1 TTTGCATTTGCATTTTCGTT
11401235 TTT
1 TTT
11401238 TTTATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (20 bp):
TTTGCATTTGCATTTTCGTT
Found at i:11404399 original size:25 final size:25
Alignment explanation
Indices: 11404370--11404418 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
11404360 TTTTTCAAAT
*
11404370 TTTTTATTAAACATTTTTCAAAATGC
1 TTTTAATT-AACATTTTTCAAAATGC
* *
11404396 TTTTAATTGATATTTTTCAAAAT
1 TTTTAATTAACATTTTTCAAAAT
11404419 TTTGAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTAATTAACATTTTTCAAAATGC
Found at i:11407119 original size:122 final size:122
Alignment explanation
Indices: 11406895--11407302 Score: 378
Period size: 122 Copynumber: 3.3 Consensus size: 122
11406885 TTCTAGAACA
* ** *
11406895 TCTTTAACACCAAATTATCTCCAGATTGACTTGATTTCCTCAATGAGAAGGAAAAACGTTATCTT
1 TCTTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGGAAAAACGTTATCTT
* * * * *
11406960 CAAGGAACAATTTATCTTAAAACGGCCATATCACTTCAACTTGGATGAACAGTGTTG
66 AAAGGAACAATTTATCTTAAAACGGCCAAATCACTTCAACATGGATGAACAGAGTCG
*
11407017 TCTTCAACACCAAATTATTTCCAGATTGACCCGATTTCCTCAACGAGAA-GAAACAAC-TTAATC
1 TCTTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGGAAA-AACGTT-ATC
* * *
11407080 TTAAATGAACAATTTATC-TAAAAGCGGCCAAATCCCTTCAACATGGATGAGCAGAGTCG
64 TTAAAGGAACAATTTATCTTAAAA-CGGCCAAATCACTTCAACATGGATGAACAGAGTCG
* * * * * * * * * **
11407139 TCTTCAATACCAAATTATCTCCATATTAACCCAACTTCCTCAGCAAGAAGGAACATCGACATCTT
1 TCTTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGGAAAAACGTTATCTT
* * * * * * * * * *
11407204 -CAGCAAACAATTTA-CTTGAAAGCGGCTAGAA-CTCTTCAACACGAATTAGCAGAGTCA
66 AAAG-GAACAATTTATCTT-AAAACGGCCA-AATCACTTCAACATGGATGAACAGAGTCG
** * *
11407261 TCTTCAACACCGTATTATCTCCGGATTAACCCGATTTCCTCA
1 TCTTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCA
11407303 TCACGAAGGA
Statistics
Matches: 235, Mismatches: 42, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
121 13 0.06
122 214 0.91
123 8 0.03
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (122 bp):
TCTTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACGAGAAGGAAAAACGTTATCTT
AAAGGAACAATTTATCTTAAAACGGCCAAATCACTTCAACATGGATGAACAGAGTCG
Found at i:11411081 original size:15 final size:15
Alignment explanation
Indices: 11411063--11411092 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11411053 ACCATATAAG
*
11411063 ATATATGTATATATT
1 ATATAAGTATATATT
11411078 ATATAAGTATATATT
1 ATATAAGTATATATT
11411093 TGTTCATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
ATATAAGTATATATT
Found at i:11411477 original size:17 final size:19
Alignment explanation
Indices: 11411445--11411488 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
11411435 TAAATGCCCT
11411445 ATATTTATTGAATAAA-ATA
1 ATATTT-TTGAATAAATATA
11411464 ATATTTTT-AATAAATATA
1 ATATTTTTGAATAAATATA
*
11411482 TTATTTT
1 ATATTTT
11411489 AGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 11 0.48
19 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATTTTTGAATAAATATA
Found at i:11412747 original size:12 final size:12
Alignment explanation
Indices: 11412730--11412763 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
11412720 AATAACGAAT
11412730 AAAAAAATTTCA
1 AAAAAAATTTCA
11412742 AAAAAAATTTCA
1 AAAAAAATTTCA
*
11412754 AAAAACATTT
1 AAAAAAATTT
11412764 AGTCATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAAAATTTCA
Found at i:11413644 original size:19 final size:19
Alignment explanation
Indices: 11413607--11413651 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11413597 ACTTTTTTCA
11413607 TTATA-TTTTTAGAAAATT
1 TTATATTTTTTAGAAAATT
* *
11413625 TTATATTTTTTGGAATATT
1 TTATATTTTTTAGAAAATT
*
11413644 TTAAATTT
1 TTATATTT
11413652 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (19 bp):
TTATATTTTTTAGAAAATT
Found at i:11414872 original size:13 final size:13
Alignment explanation
Indices: 11414854--11414878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11414844 GATGTTTTTC
11414854 AATATTTTTAAGT
1 AATATTTTTAAGT
11414867 AATATTTTTAAG
1 AATATTTTTAAG
11414879 AAAAAATAAA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AATATTTTTAAGT
Found at i:11415834 original size:26 final size:27
Alignment explanation
Indices: 11415805--11415855 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
11415795 TAATGTAAAA
*
11415805 AAAGTCAACTAAA-TCAAACAAAGATG
1 AAAGTCAACTAAATTAAAACAAAGATG
* *
11415831 AAAGTTAATTAAATTAAAACAAAGA
1 AAAGTCAACTAAATTAAAACAAAGA
11415856 AAGTAAAGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (27 bp):
AAAGTCAACTAAATTAAAACAAAGATG
Found at i:11417107 original size:3 final size:3
Alignment explanation
Indices: 11417075--11417142 Score: 54
Period size: 3 Copynumber: 22.3 Consensus size: 3
11417065 TTTGGACCAA
*
11417075 AAT AAA AAT AAT AAAT AA- AAT AAAT AAAT AAT AAT -AT AAT AAAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT -AAT -AAT AAT AAT AAT AAT -AAT AAT
11417122 AAT -AT AAT AAAT AAT AA- AAT A
1 AAT AAT AAT -AAT AAT AAT AAT A
11417143 CATGAAAATG
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
2 8 0.15
3 31 0.56
4 16 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:11417117 original size:15 final size:15
Alignment explanation
Indices: 11417074--11417138 Score: 102
Period size: 15 Copynumber: 4.6 Consensus size: 15
11417064 ATTTGGACCA
11417074 AAATAA-AA-ATAAT
1 AAATAATAATATAAT
11417087 AAATAA-AATA-AAT
1 AAATAATAATATAAT
11417100 AAATAATAATATAAT
1 AAATAATAATATAAT
11417115 AAATAATAATATAAT
1 AAATAATAATATAAT
11417130 AAATAATAA
1 AAATAATAA
11417139 AATACATGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
13 17 0.35
14 5 0.10
15 27 0.55
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAATAATATAAT
Found at i:11417203 original size:37 final size:37
Alignment explanation
Indices: 11417162--11417556 Score: 433
Period size: 37 Copynumber: 10.8 Consensus size: 37
11417152 GTTTTTTTAA
* * *
11417162 AAAATATTTTTAAAAATTATATATTATAAATATTTTC
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
* *
11417199 AAAATGTTTTCAAAAACTATATATTATATATTTTTTTC
1 AAAATATTTTCAAAAACTATATATTATATA-TATTTTC
11417237 AAAATATTTTCAAAAACTATATATTATATAT-TTTT-
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
* *
11417272 AAAATGTTTTAAAAAACTATATATTATATATATTTTC
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
* *
11417309 AAAACATTTTCAAAAACTATATATTATATATATTTTT
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
* * *
11417346 AAAATGTTTTCAAAAACTAAATATTATGTATATTTTC
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
* *
11417383 AAAACATTTTCAAAAA--ATATA-TGT-TATA---T-
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
*
11417412 ---ATATTTTCAAAAACTATATATTATATATATGTTTTT
1 AAAATATTTTCAAAAACTATATATTATATATA--TTTTC
*
11417448 AAAATGTTTTCAAAAACTATATATTATATATATTTTC
1 AAAATATTTTCAAAAACTATATATTATATATATTTTC
*
11417485 AAAATATTTTTTTAAAAACTATATATTATATATATGTTTTC
1 AAAATA--TTTTCAAAAACTATATATTATATATA--TTTTC
*
11417526 AAAAT-TTTATAAAAAAAACTATATA-TATATA
1 AAAATATTT-T--CAAAAACTATATATTATATA
11417557 CTAAAAAAAA
Statistics
Matches: 307, Mismatches: 28, Indels: 43
0.81 0.07 0.11
Matches are distributed among these distances:
26 12 0.04
28 5 0.02
29 2 0.01
30 5 0.02
33 4 0.01
34 2 0.01
35 34 0.11
36 8 0.03
37 115 0.37
38 38 0.12
39 54 0.18
40 6 0.02
41 22 0.07
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (37 bp):
AAAATATTTTCAAAAACTATATATTATATATATTTTC
Found at i:11417451 original size:28 final size:26
Alignment explanation
Indices: 11417388--11417441 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
11417378 TTTTCAAAAC
*
11417388 ATTTTCAAAAAATATATGTTATATAT
1 ATTTTCAAAAAATATATATTATATAT
*
11417414 ATTTTCAAAAACTATATATTATATAT
1 ATTTTCAAAAAATATATATTATATAT
11417440 AT
1 AT
11417442 GTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTTTCAAAAAATATATATTATATAT
Found at i:11422714 original size:34 final size:35
Alignment explanation
Indices: 11422676--11422745 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
11422666 GAATGAAACG
*
11422676 AAGTACTAAACGAAA-AAAATTGAATTCAAAAGAA
1 AAGTACAAAACGAAAGAAAATTGAATTCAAAAGAA
* *
11422710 AAGTACAAAATGAAAGAAAATTGAGTTCAAAAGAA
1 AAGTACAAAACGAAAGAAAATTGAATTCAAAAGAA
11422745 A
1 A
11422746 TAAGAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 13 0.41
35 19 0.59
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.17
Consensus pattern (35 bp):
AAGTACAAAACGAAAGAAAATTGAATTCAAAAGAA
Found at i:11424990 original size:45 final size:45
Alignment explanation
Indices: 11424940--11425194 Score: 332
Period size: 45 Copynumber: 5.6 Consensus size: 45
11424930 TGTATTAAAT
*
11424940 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTGA
* * * *
11424985 AATGCATATGGGTGCGTTATTGGCATGAAAGGATGTCATTATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTGA
* * * *
11425030 AATGCATATGGGTGCATTATTGTCATGAAAGGATGACATATTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTGA
*
11425075 AATGCATATGGGTGCATTATTGGCATAAAAAGATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTGA
* *** *
11425120 AATGCATATGGGTGCATTATTGGCATTAAAAGATTTTATAAATGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTG-A
**
11425166 AATGCATAAT-GGTGCATTATAAGCATGAA
1 AATGCAT-ATGGGTGCATTATTGGCATGAA
11425195 TGGATGTTAT
Statistics
Matches: 186, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
45 160 0.86
46 24 0.13
47 2 0.01
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAAGATGCCATAATTGA
Found at i:11425006 original size:23 final size:23
Alignment explanation
Indices: 11424940--11425141 Score: 107
Period size: 22 Copynumber: 9.0 Consensus size: 23
11424930 TGTATTAAAT
*
11424940 AATGCATATGGGTGCATTATTGG
1 AATGCATATGGGTGCATTATTGA
* * * *
11424963 CATG-AAAT-GATGCCATAATTGA
1 AATGCATATGGGTG-CATTATTGA
* *
11424985 AATGCATATGGGTGCGTTATTGG
1 AATGCATATGGGTGCATTATTGA
* * *
11425008 CATG-A-AAGGATGTCATTATTGA
1 AATGCATATGGGTG-CATTATTGA
*
11425030 AATGCATATGGGTGCATTATTGT
1 AATGCATATGGGTGCATTATTGA
* * *
11425053 CATG-A-AAGGATGACA-TATTTGA
1 AATGCATATGGGTG-CATTA-TTGA
*
11425075 AATGCATATGGGTGCATTATTGG
1 AATGCATATGGGTGCATTATTGA
* * ** * *
11425098 CAT--AAAAAGATGCCATAATTGA
1 AATGCATATGGGTG-CATTATTGA
11425120 AATGCATATGGGTGCATTATTG
1 AATGCATATGGGTGCATTATTG
11425142 GCATTAAAAG
Statistics
Matches: 124, Mismatches: 41, Indels: 28
0.64 0.21 0.15
Matches are distributed among these distances:
21 20 0.16
22 42 0.34
23 42 0.34
24 20 0.16
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (23 bp):
AATGCATATGGGTGCATTATTGA
Found at i:11433140 original size:15 final size:15
Alignment explanation
Indices: 11433122--11433153 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
11433112 AATAAAAGAA
11433122 AATAAAATAAATAAT
1 AATAAAATAAATAAT
*
11433137 AATATAATAAATAAT
1 AATAAAATAAATAAT
11433152 AA
1 AA
11433154 AATGCATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AATAAAATAAATAAT
Found at i:11433205 original size:25 final size:26
Alignment explanation
Indices: 11433177--11433231 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
11433167 TTTTTTAAAA
**
11433177 ATATTTTCAAAATTTATATATTAT-T
1 ATATTTTCAAAAACTATATATTATAT
*
11433202 ATATTTTGAAAAACTATATATTATAT
1 ATATTTTCAAAAACTATATATTATAT
11433228 ATAT
1 ATAT
11433232 GTTTTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATTTTCAAAAACTATATATTATAT
Found at i:11433300 original size:38 final size:38
Alignment explanation
Indices: 11433205--11433384 Score: 193
Period size: 38 Copynumber: 4.6 Consensus size: 38
11433195 TATTATTATA
* *
11433205 TTTTGAAAAACTATATATTATATATATGTTTTTAAAAT-G
1 TTTTTAAAAACTATATATTATATATA--TTTTTAAAATAT
*
11433244 TTTTCAAAAACTATATATTATATATATTTTTAAAATAT
1 TTTTTAAAAACTATATATTATATATATTTTTAAAATAT
* * *
11433282 TTTTTAAAAACTATATATTATACATATTTTTGAAACGTTT
1 TTTTTAAAAACTATATATTATATATATTTTT-AAA-ATAT
* **
11433322 TTTTTAAAAAAACTATATAATATATATATGTTTTTTAA-AT
1 TTTTT--AAAAACTATATATTATATATAT-TTTTAAAATAT
*
11433362 TTTATAAAAACTATATATTATAT
1 TTTTTAAAAACTATATATTATAT
11433385 CTTATATATA
Statistics
Matches: 121, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
37 10 0.08
38 46 0.38
39 28 0.23
40 12 0.10
42 21 0.17
43 4 0.03
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (38 bp):
TTTTTAAAAACTATATATTATATATATTTTTAAAATAT
Found at i:11444744 original size:31 final size:31
Alignment explanation
Indices: 11444678--11444736 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
11444668 AATTTAAGGT
* *
11444678 AAAATGGTTTTTGGACTTGAATTGTATTTAC
1 AAAATGGTATTTGGACTTGAATTGAATTTAC
11444709 AAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAATGGTATTTGGACTTGAATTGAATTTA
11444737 TTCAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 11 0.42
31 5 0.19
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (31 bp):
AAAATGGTATTTGGACTTGAATTGAATTTAC
Found at i:11444978 original size:21 final size:21
Alignment explanation
Indices: 11444952--11444993 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11444942 ATTTGAATAT
*
11444952 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11444973 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
11444994 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:11446604 original size:17 final size:16
Alignment explanation
Indices: 11446578--11446609 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
11446568 TACCATTATG
11446578 TATTTTCGTATTTTAC
1 TATTTTCGTATTTTAC
11446594 TATTATTCGTATTTTA
1 TATT-TTCGTATTTTA
11446610 TTTACTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.22, C:0.09, G:0.06, T:0.62
Consensus pattern (16 bp):
TATTTTCGTATTTTAC
Found at i:11447910 original size:32 final size:32
Alignment explanation
Indices: 11447869--11447931 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
11447859 GCCAATCTAA
* * *
11447869 GGGAGTACCTTAGGGCTTTAGAGCCTACCCAG
1 GGGAGTACCTTAGGGCCTAAAAGCCTACCCAG
*
11447901 GGGAGTACCTTGGGGCCTAAAAGCCTACCCA
1 GGGAGTACCTTAGGGCCTAAAAGCCTACCCA
11447932 AGGGTCATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.19
Consensus pattern (32 bp):
GGGAGTACCTTAGGGCCTAAAAGCCTACCCAG
Found at i:11452721 original size:19 final size:20
Alignment explanation
Indices: 11452689--11452727 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
11452679 ATAAAATGAT
*
11452689 TGGAATAAATAAAAAATAAA
1 TGGAATAAAGAAAAAATAAA
*
11452709 TGGAAT-AAGAAAACATAAA
1 TGGAATAAAGAAAAAATAAA
11452728 ATAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.18
Consensus pattern (20 bp):
TGGAATAAAGAAAAAATAAA
Found at i:11452841 original size:22 final size:24
Alignment explanation
Indices: 11452790--11452842 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
11452780 TTAAATATTT
11452790 AAATAAATAATAAAATAACAATTG
1 AAATAAATAATAAAATAACAATTG
*
11452814 -ATTAAA-AATAAAATAA-ACA-TG
1 AAATAAATAATAAAATAACA-ATTG
11452835 AAATAAAT
1 AAATAAAT
11452843 TAAATAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
21 3 0.12
22 16 0.67
23 5 0.21
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
AAATAAATAATAAAATAACAATTG
Found at i:11461616 original size:20 final size:20
Alignment explanation
Indices: 11461591--11461684 Score: 104
Period size: 20 Copynumber: 4.6 Consensus size: 20
11461581 AACTTGGACT
11461591 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
**
11461611 ATCGCAATGCG-ATAGTCGTCT
1 ATCGCAATGCGAATA-T-GTAA
11461632 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
11461652 ATCGCAATGCG-ATA-GTCAA
1 ATCGCAATGCGAATATGT-AA
11461671 CTATCGCAATGCGA
1 --ATCGCAATGCGA
11461685 TAGTCAACTA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.03
19 8 0.13
20 25 0.40
21 25 0.40
22 3 0.05
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:11461616 original size:41 final size:41
Alignment explanation
Indices: 11461587--11461684 Score: 178
Period size: 41 Copynumber: 2.4 Consensus size: 41
11461577 TGCGAACTTG
11461587 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
11461628 GTCTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
*
11461669 AACTATCGCAATGCGA
1 GACTATCGCAATGCGA
11461685 TAGTCAACTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (41 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:11461637 original size:21 final size:21
Alignment explanation
Indices: 11461589--11461700 Score: 106
Period size: 21 Copynumber: 5.4 Consensus size: 21
11461579 CGAACTTGGA
11461589 CTATCGCAATGCGAATA-T-GT
1 CTATCGCAATGCG-ATAGTCGT
**
11461609 AAATCGCAATGCGATAGTCGT
1 CTATCGCAATGCGATAGTCGT
11461630 CTATCGCAATGCGAATA-T-GT
1 CTATCGCAATGCG-ATAGTCGT
** **
11461650 AAATCGCAATGCGATAGTCAA
1 CTATCGCAATGCGATAGTCGT
**
11461671 CTATCGCAATGCGATAGTCAA
1 CTATCGCAATGCGATAGTCGT
11461692 CTATCGCAA
1 CTATCGCAA
11461701 CGACTGGTTG
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
19 6 0.08
20 26 0.34
21 42 0.55
22 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (21 bp):
CTATCGCAATGCGATAGTCGT
Found at i:11461821 original size:5 final size:6
Alignment explanation
Indices: 11461782--11461818 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
11461772 GACACGTATT
*
11461782 ACCAAG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
11461819 CGAGACGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:11462343 original size:12 final size:12
Alignment explanation
Indices: 11462322--11462361 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
11462312 TCTCGTCTCG
*
11462322 GGTC-GGGTCGG
1 GGTCGGGGTCGC
11462333 GGTCGGGGTCGC
1 GGTCGGGGTCGC
*
11462345 GGTCGCGGTCGC
1 GGTCGGGGTCGC
11462357 GGTCG
1 GGTCG
11462362 TGGTAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.00, C:0.25, G:0.57, T:0.17
Consensus pattern (12 bp):
GGTCGGGGTCGC
Found at i:11462354 original size:18 final size:17
Alignment explanation
Indices: 11462321--11462361 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
11462311 GTCTCGTCTC
*
11462321 GGGTCGGGTCGGGGTCG
1 GGGTCGGGTCGCGGTCG
11462338 GGGTCGCGGTCGCGGTCG
1 GGGTCG-GGTCGCGGTCG
*
11462356 CGGTCG
1 GGGTCG
11462362 TGGTAATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.00, C:0.24, G:0.59, T:0.17
Consensus pattern (17 bp):
GGGTCGGGTCGCGGTCG
Found at i:11462484 original size:21 final size:21
Alignment explanation
Indices: 11462458--11462583 Score: 139
Period size: 21 Copynumber: 5.8 Consensus size: 21
11462448 ATTTTGGACT
*
11462458 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
11462479 ATCGCAACGCGAACTTGGAAAAA
1 ATCGCAA--CGAACTTGGAATAA
*
11462502 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
11462523 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
11462544 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
11462565 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
11462584 CTATCGCAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
19 10 0.11
21 40 0.45
23 38 0.43
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:11462561 original size:42 final size:42
Alignment explanation
Indices: 11462451--11462592 Score: 230
Period size: 42 Copynumber: 3.3 Consensus size: 42
11462441 CGTTGTGATT
11462451 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
**
11462493 TTGGAAAAAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGG--ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
11462537 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
11462579 TTGGACTATCGCAA
1 TTGGACTATCGCAA
11462593 TGCGATAGTC
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
42 52 0.57
44 39 0.43
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:11462589 original size:21 final size:20
Alignment explanation
Indices: 11462451--11462597 Score: 102
Period size: 21 Copynumber: 6.9 Consensus size: 20
11462441 CGTTGTGATT
* *
11462451 TTGGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
11462470 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* *
11462493 TTGGAAAAAATCGCAA-CGAAT
1 TTGG--AATATCGCAAGCGAAC
11462514 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* *
11462537 TTCGACTATCGCAA-CGAAC
1 TTGGAATATCGCAAGCGAAC
11462556 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
*
11462579 TTGGACTATCGCAATGCGA
1 TTGGAATATCGCAA-GCGA
11462598 TAGTCGAAGT
Statistics
Matches: 102, Mismatches: 12, Indels: 26
0.73 0.09 0.19
Matches are distributed among these distances:
19 18 0.18
21 47 0.46
23 35 0.34
25 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (20 bp):
TTGGAATATCGCAAGCGAAC
Found at i:11463070 original size:23 final size:21
Alignment explanation
Indices: 11463044--11463086 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11463034 CTTCACTGTT
*
11463044 TTTTCGCATTTTATACATCAAAC
1 TTTT-GCATTTT-TACAGCAAAC
*
11463067 TTTTGTATTTTTACAGCAAA
1 TTTTGCATTTTTACAGCAAA
11463087 GAATCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTTGCATTTTTACAGCAAAC
Found at i:11463398 original size:3 final size:3
Alignment explanation
Indices: 11463390--11463448 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
11463380 TAAAAAGTAC
* * * *
11463390 TAA TAA TAA TAC TTA TAA TTAA -AA TTA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
11463435 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
11463449 CTATACAGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:11468595 original size:31 final size:30
Alignment explanation
Indices: 11468534--11468639 Score: 119
Period size: 31 Copynumber: 3.6 Consensus size: 30
11468524 CCTTTTCATT
11468534 TAAGTACCTAAAGTATTGTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTGTTTTGGTCAAAA
* *
11468564 TAAGTACCTAAATTTATCT-TTTTTGTCAAAA
1 TAAGTACCTAAA-GTAT-TGTTTTGGTCAAAA
* * *
11468595 TAAGTACTTAAAGTATT-TTAT-GTTAAAA
1 TAAGTACCTAAAGTATTGTTTTGGTCAAAA
*
11468623 TAGGTACCTAAAGTATT
1 TAAGTACCTAAAGTATT
11468640 CAAACCTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 21 0.32
29 4 0.06
30 15 0.23
31 25 0.38
32 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTGTTTTGGTCAAAA
Found at i:11468623 original size:28 final size:28
Alignment explanation
Indices: 11468534--11468639 Score: 122
Period size: 28 Copynumber: 3.6 Consensus size: 28
11468524 CCTTTTCATT
11468534 TAAGTACCTAAAGTATTGTTTTGGTCAAAA
1 TAAGTACCTAAAGTATT-TTTT-GTCAAAA
*
11468564 TAAGTACCTAAATTTATCTTTTTTGTCAAAA
1 TAAGTACCTAAA-GTA--TTTTTTGTCAAAA
* * *
11468595 TAAGTACTTAAAGTATTTTATGTTAAAA
1 TAAGTACCTAAAGTATTTTTTGTCAAAA
*
11468623 TAGGTACCTAAAGTATT
1 TAAGTACCTAAAGTATT
11468640 CAAACCTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
28 26 0.39
30 14 0.21
31 20 0.30
32 4 0.06
33 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTTGTCAAAA
Done.