Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 60 of 295
Found at i:17544094 original size:27 final size:27
Alignment explanation
Indices: 17544039--17544118 Score: 144
Period size: 27 Copynumber: 3.0 Consensus size: 27
17544029 ACGGAAAAGA
17544039 AGATTGATGAGGGAGTT-GACCATGTC
1 AGATTGATGAGGGAGTTAGACCATGTC
*
17544065 AGATTGATGAGGGAGTTAGACCATTTC
1 AGATTGATGAGGGAGTTAGACCATGTC
17544092 AGATTGATGAGGGAGTTAGACCATGTC
1 AGATTGATGAGGGAGTTAGACCATGTC
17544119 CAGAGAACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 17 0.33
27 34 0.67
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.28
Consensus pattern (27 bp):
AGATTGATGAGGGAGTTAGACCATGTC
Found at i:17546688 original size:50 final size:50
Alignment explanation
Indices: 17546564--17546913 Score: 409
Period size: 50 Copynumber: 7.0 Consensus size: 50
17546554 GTAACCGAAG
* * * * *
17546564 CTATCTGGTACGCATAGTAGCCTGCATTTAGTACTACACATGCGACC-AA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
* *
17546613 CAATCTGGTACACGTAGTAGCCTGCACTTTGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
* * * * *
17546663 CCATCTGATACACGTAGTAGGCTGCAGTTAGTACTACACACGTGA-TTGAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA
* * * * * * * * *
17546713 GTTGTCGGGTACGCATAGTAGCCTGTACTTAGTACTATACATGCGACCTAA
1 -CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
*
17546764 CTATTTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
* * *
17546814 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACACATGCT-ACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACG-TGACCTAA
* *
17546864 CTATCTGGTACACGTAGTAGCCTACATTTAGTACTACACACGTGACCTAA
1 CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
17546914 AACCATCTTA
Statistics
Matches: 249, Mismatches: 46, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
49 42 0.17
50 171 0.69
51 35 0.14
52 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (50 bp):
CTATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
Found at i:17546811 original size:151 final size:150
Alignment explanation
Indices: 17546570--17546853 Score: 487
Period size: 151 Copynumber: 1.9 Consensus size: 150
17546560 GAAGCTATCT
*
17546570 GGTACGCATAGTAGCCTGCATTTAGTACTACACATGCGACCAACAATCTGGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTACACGTAGTAGCC
* * *
17546635 TGCACTTTGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGGCTGCAGTTAGTACTAC
66 TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
17546700 ACACGTGATTGAAGTTGTCG
131 ACACGTGATTGAAGTTGTCG
* * * *
17546720 GGTACGCATAGTAGCCTGTACTTAGTACTATACATGCGACCTAACTATTTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC-AACAATCTGGTACACGTAGTAGC
17546785 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
65 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
17546850 CACA
130 CACA
17546854 TGCTACCTAA
Statistics
Matches: 125, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
150 38 0.30
151 87 0.70
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (150 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTAC
ACACGTGATTGAAGTTGTCG
Found at i:17550687 original size:5 final size:5
Alignment explanation
Indices: 17550677--17550746 Score: 131
Period size: 5 Copynumber: 13.8 Consensus size: 5
17550667 AATGAATAAG
17550677 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
17550727 TTATA TTATA TTATTA TTAT
1 TTATA TTATA TTA-TA TTAT
17550747 TTTAAAGGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 59 0.92
6 5 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:17551064 original size:49 final size:49
Alignment explanation
Indices: 17550992--17551098 Score: 205
Period size: 49 Copynumber: 2.2 Consensus size: 49
17550982 ATTATTGATA
17550992 TCTCATATCCAAATATCCTTTAATAGAGATTTTGTACTTTTAGTTCCTT
1 TCTCATATCCAAATATCCTTTAATAGAGATTTTGTACTTTTAGTTCCTT
*
17551041 TCTCATATCCAAATATCCTTTAATGGAGATTTTGTACTTTTAGTTCCTT
1 TCTCATATCCAAATATCCTTTAATAGAGATTTTGTACTTTTAGTTCCTT
17551090 TCTCATATC
1 TCTCATATC
17551099 ACTTCACTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 57 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (49 bp):
TCTCATATCCAAATATCCTTTAATAGAGATTTTGTACTTTTAGTTCCTT
Found at i:17554702 original size:17 final size:18
Alignment explanation
Indices: 17554680--17554714 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17554670 GATATGATAC
*
17554680 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
17554697 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
17554715 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:17555058 original size:17 final size:18
Alignment explanation
Indices: 17555005--17555076 Score: 110
Period size: 19 Copynumber: 3.9 Consensus size: 18
17554995 AATCATATCT
17555005 TCTAAGATTGCTTATCATA
1 TCTAAGATTGC-TATCATA
*
17555024 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
17555042 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
17555059 TCTAAGATTGCATATCAT
1 TCTAAGATTGC-TATCAT
17555077 TGAAGATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.33
18 16 0.33
19 17 0.35
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:17555061 original size:35 final size:37
Alignment explanation
Indices: 17554998--17555076 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
17554988 ATTACAAAAT
17554998 CATATC-T-TCTAAGATTGCTTATCATATCTAAGATTG
1 CATATCATATCTAAGATTGC-TATCATATCTAAGATTG
17555034 CA-ATCATATCTAAGATTG-TATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCTATCATATCTAAGATTG
17555069 CATATCAT
1 CATATCAT
17555077 TGAAGATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (37 bp):
CATATCATATCTAAGATTGCTATCATATCTAAGATTG
Found at i:17555074 original size:14 final size:15
Alignment explanation
Indices: 17555019--17555074 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
17555009 AGATTGCTTA
17555019 TCATATCTAAGATTG
1 TCATATCTAAGATTG
17555034 CAATCATATCTAAGATTG
1 ---TCATATCTAAGATTG
17555052 TATCATATCTAAGATTG
1 --TCATATCTAAGATTG
17555069 -CATATC
1 TCATATC
17555075 ATTGAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 6 0.16
17 16 0.43
18 15 0.41
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
TCATATCTAAGATTG
Found at i:17555489 original size:45 final size:45
Alignment explanation
Indices: 17555432--17555700 Score: 267
Period size: 45 Copynumber: 5.9 Consensus size: 45
17555422 CAATATCTAC
* * *
17555432 TATCTTTGATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * *
17555477 TATCTTCAATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGC
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * *
17555522 T-TCTTCAATCTACTCCCCGTCTAATACAGAGATGTCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * * *
17555566 TATCTCCGATTTGCTCCCCATCTAATACAGAGATGTCAAATCTGT
1 TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
* * * * * * * *
17555611 CATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAGATCTGT
1 TATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAAATCTGT
17555656 TAATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
1 T-A--TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
17555701 ATCTTGGATC
Statistics
Matches: 183, Mismatches: 31, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
43 5 0.03
44 45 0.25
45 102 0.56
46 1 0.01
48 19 0.10
49 5 0.03
50 6 0.03
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (45 bp):
TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCTGT
Found at i:17555561 original size:89 final size:89
Alignment explanation
Indices: 17555440--17555609 Score: 250
Period size: 89 Copynumber: 1.9 Consensus size: 89
17555430 ACTATCTTTG
* * * *
17555440 ATCTGCTCCCTGTCTAATACAGAGACGCCAAATCTGTTATCTTCAATCTGCTCCCCGTCTAATAC
1 ATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCCAATCTGCTCCCCATCTAATAC
17555505 AGAGACGCCAAATCTGCTTCTTCA
66 AGAGACGCCAAATCTGCTTCTTCA
* * * *
17555529 ATCTACTCCCCGTCTAATACAGAGATGTCAAATCTGTTATCTCCGATTTGCTCCCCATCTAATAC
1 ATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCCAATCTGCTCCCCATCTAATAC
* *
17555594 AGAGATGTCAAATCTG
66 AGAGACGCCAAATCTG
17555610 TCATCTTGGA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (89 bp):
ATCTACTCCCCGTCTAATACAGAGACGCCAAATCTGTTATCTCCAATCTGCTCCCCATCTAATAC
AGAGACGCCAAATCTGCTTCTTCA
Found at i:17555769 original size:78 final size:78
Alignment explanation
Indices: 17555639--17555856 Score: 328
Period size: 78 Copynumber: 2.8 Consensus size: 78
17555629 ATGTAAACAC
*
17555639 ATGAAGGTCAGATCTGTTAATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGTCAGATCTGCT-ATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
*
17555704 TTGGATCTGCTTCA
65 TTGGATCTACTTCA
* * *
17555718 ATGAAGGTCAGATTTGCTGTGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
*
17555783 TGGATCTATTTCA
66 TGGATCTACTTCA
* * ** *
17555796 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAAATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
17555857 TGTTTCTTCG
Statistics
Matches: 125, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 109 0.87
79 16 0.13
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTACTTCA
Found at i:17556186 original size:220 final size:220
Alignment explanation
Indices: 17555797--17556387 Score: 941
Period size: 220 Copynumber: 2.7 Consensus size: 220
17555787 TCTATTTCAA
* *
17555797 TGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAAATGCCAAATCTGTTT
1 TGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTT
* *
17555862 CTTCGATTTGTTCTTTGACAGTACAGAGATGCCAAATCATCTTAGATCTACTTCAGCGTAAACAC
66 CTTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACAC
* *
17555927 GTGAAAGCCAAATCTGCTATGTCTTTGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTT
131 GTGAAAGCCAAATCTGCTATGTCTTCGATCTGATCCTTGTCAACGCAAGGATGCCAAATCATCTT
*
17555992 GGGTCTACTTCGATGTGAAAACATC
196 GGATCTACTTCGATGTGAAAACATC
* **
17556017 TGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCAAATATGGAGATTTCAAATCTGTTT
1 TGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTT
17556082 CTTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACAC
66 CTTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACAC
17556147 GTGAAAGCCAAATCTGCTATGTCTTCGATCTGATCCTTGTCAACGCAAGGATGCCAAATCATCTT
131 GTGAAAGCCAAATCTGCTATGTCTTCGATCTGATCCTTGTCAACGCAAGGATGCCAAATCATCTT
17556212 GGATCTACTTCGATGTGAAAACATC
196 GGATCTACTTCGATGTGAAAACATC
** * *
17556237 CAAAGGTTAGATCTGCTATGTCTTCGATCTACTCTCCGTCGAATATGGAGATGCCAAATCTGTCT
1 TGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTT
* * * ** * * * *
17556302 CTTCGATTTATTCTCTAACAATACAGAGATGTTAAATCATCTTGGATCCGCTTCAACGTAAACGT
66 CTTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAAC-A
* *
17556367 C-TGAAGGTCAAATCTGCTATG
130 CGTGAAAGCCAAATCTGCTATG
17556388 CTTTAGCTTC
Statistics
Matches: 342, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
220 341 1.00
221 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (220 bp):
TGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTT
CTTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACAC
GTGAAAGCCAAATCTGCTATGTCTTCGATCTGATCCTTGTCAACGCAAGGATGCCAAATCATCTT
GGATCTACTTCGATGTGAAAACATC
Found at i:17566250 original size:17 final size:18
Alignment explanation
Indices: 17566228--17566262 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17566218 GATATGATAC
*
17566228 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
17566245 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
17566263 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:17566552 original size:22 final size:21
Alignment explanation
Indices: 17566517--17566592 Score: 59
Period size: 22 Copynumber: 3.7 Consensus size: 21
17566507 AAAAGGTATC
* * *
17566517 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
17566538 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* * *
17566561 TGCATATCATA--TCTAAGAC
1 TACAAATCATATCTCTAAGAT
17566580 TAC-AATCATATCT
1 TACAAATCATATCT
17566593 AAGATTGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
18 6 0.14
19 9 0.21
20 1 0.02
21 3 0.07
22 15 0.35
23 9 0.21
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:17566577 original size:19 final size:19
Alignment explanation
Indices: 17566553--17566643 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
17566543 AATCATATCT
17566553 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
17566572 TCTAAGACTACA-ATCATA
1 TCTAAGATTGCATATCATA
17566590 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
17566607 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
17566626 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
17566644 TGAAGATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
17 16 0.25
18 14 0.22
19 35 0.54
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:17568139 original size:21 final size:20
Alignment explanation
Indices: 17568107--17568147 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
17568097 ATACATGAGT
17568107 ATTTTGATGTTTAATGATAG
1 ATTTTGATGTTTAATGATAG
*
17568127 ATTTTGAATGTTTGATGATAG
1 ATTTTG-ATGTTTAATGATAG
17568148 TTATACAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (20 bp):
ATTTTGATGTTTAATGATAG
Found at i:17575132 original size:10 final size:10
Alignment explanation
Indices: 17575105--17575164 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
17575095 TGAAATTCTA
17575105 AAAGATAAAT
1 AAAGATAAAT
17575115 ACAA-ATAAAT
1 A-AAGATAAAT
*
17575125 AAAGATAATT
1 AAAGATAAAT
17575135 AAAGATAAAT
1 AAAGATAAAT
*
17575145 AAGGATAAAT
1 AAAGATAAAT
17575155 GAAA-ATAAAT
1 -AAAGATAAAT
17575165 CCTAGAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.05
10 37 0.86
11 4 0.09
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:17575983 original size:96 final size:97
Alignment explanation
Indices: 17575818--17576004 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 97
17575808 ATTCTATTTA
** * * *
17575818 TTTATTTTTACTTAGGAATATATTGAACCTTTTGATGCGAAGAGAGATGACAGCCAAGCACCCCA
1 TTTATTTTTACTTAAAAACATATCGAACCTTTTGAGGCGAAGAGAGATGACAGCCAAGCACCCCA
*
17575883 CCCCGGTTACTCAGCCCAACACATTCCTAATT
66 CCCCGGTTACTCAACCCAACACATTCCTAATT
*
17575915 TTTATTTTT-CTTAAAAACATATCGAACCTTTTGAGGCGAAGAGAGATGACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAAAACATATCGAACCTTTTGAGGCGAAGAGAGATGACAGCCAAGCACCCCA
*
17575979 CCCCGGTTACTTAACCCAACACATTC
66 CCCCGGTTACTCAACCCAACACATTC
17576005 TTAAAAATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 73 0.89
97 9 0.11
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (97 bp):
TTTATTTTTACTTAAAAACATATCGAACCTTTTGAGGCGAAGAGAGATGACAGCCAAGCACCCCA
CCCCGGTTACTCAACCCAACACATTCCTAATT
Found at i:17576071 original size:57 final size:57
Alignment explanation
Indices: 17575983--17576096 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
17575973 ACCTCACCCC
*
17575983 GGTTACTTAACCCAACACATTCTTAAAAATTAATTCTAATTAGCGGAGTTTTACCTA
1 GGTTACTTAACCCAACACATTCTTAAAAATTAATTCCAATTAGCGGAGTTTTACCTA
* * ** *
17576040 GGTTACTTAGCCCAACACATTCTTATAAATTAATTCCGGTTAGCGGTGTTTTACCTA
1 GGTTACTTAACCCAACACATTCTTAAAAATTAATTCCAATTAGCGGAGTTTTACCTA
17576097 ACACATCACA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (57 bp):
GGTTACTTAACCCAACACATTCTTAAAAATTAATTCCAATTAGCGGAGTTTTACCTA
Found at i:17576579 original size:15 final size:15
Alignment explanation
Indices: 17576559--17576588 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17576549 AATTTTATAT
17576559 GGGCAGCAACAACCA
1 GGGCAGCAACAACCA
*
17576574 GGGCAGCAACGACCA
1 GGGCAGCAACAACCA
17576589 AATCAGCATC
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:0.37, C:0.33, G:0.30, T:0.00
Consensus pattern (15 bp):
GGGCAGCAACAACCA
Found at i:17576856 original size:18 final size:15
Alignment explanation
Indices: 17576823--17576863 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
17576813 TTAATATCTG
17576823 AAAATAATAAATAAT
1 AAAATAATAAATAAT
*
17576838 AAAATAAT-AA-GAT
1 AAAATAATAAATAAT
17576851 AAAATAA-AAATAA
1 AAAATAATAAATAA
17576864 AAATTGGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAATAATAAATAAT
Found at i:17582612 original size:23 final size:21
Alignment explanation
Indices: 17582560--17582655 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
17582550 CCTGATCAGT
** * *
17582560 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
17582581 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
17582602 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
17582623 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
17582644 AAATACGACACA
1 --ATACGACACA
17582656 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:17582620 original size:42 final size:43
Alignment explanation
Indices: 17582560--17582665 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
17582550 CCTGATCAGT
*
17582560 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
17582602 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
17582646 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
17582666 GATCAGTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:17586332 original size:10 final size:10
Alignment explanation
Indices: 17586313--17586372 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
17586303 TGAAATTCTA
17586313 AAAGATAAAT
1 AAAGATAAAT
17586323 ACAA-ATAAAT
1 A-AAGATAAAT
*
17586333 AAAGATAATT
1 AAAGATAAAT
17586343 AAAGATAAAT
1 AAAGATAAAT
17586353 AAAGATAAAT
1 AAAGATAAAT
17586363 GAAA-ATAAAT
1 -AAAGATAAAT
17586373 CCTAGAATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:17592207 original size:52 final size:52
Alignment explanation
Indices: 17592129--17592233 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
17592119 TGCAACTTGC
* *
17592129 AAACATCCAAACTCTAAATTGGACAATTAGGAATTAACCTTAAATTCTTCAA
1 AAACATCCAAACTCTAAATTGGACAATTAGGAATCAACCCTAAATTCTTCAA
17592181 AAACATCCAAACTCTAAATTGGACAATTAGGAATCAACCCTAAATTCTTCAA
1 AAACATCCAAACTCTAAATTGGACAATTAGGAATCAACCCTAAATTCTTCAA
17592233 A
1 A
17592234 TAGGAATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.27
Consensus pattern (52 bp):
AAACATCCAAACTCTAAATTGGACAATTAGGAATCAACCCTAAATTCTTCAA
Found at i:17592986 original size:49 final size:48
Alignment explanation
Indices: 17592913--17593007 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 48
17592903 TGTGAGAAAA
*
17592913 ATAATAGATCATTACTCTAGGTAAGACCCTACAGACGTATATCGAAGAG
1 ATAATAGATCATTACTCTAAGTAAGACCCTACAGAC-TATATCGAAGAG
* *
17592962 ATAATAGATCATTACTCTAAGTAAGGCCCTACAGACTATATTGAAG
1 ATAATAGATCATTACTCTAAGTAAGACCCTACAGACTATATCGAAG
17593008 TTGAAATGCG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 9 0.21
49 34 0.79
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (48 bp):
ATAATAGATCATTACTCTAAGTAAGACCCTACAGACTATATCGAAGAG
Found at i:17594669 original size:22 final size:22
Alignment explanation
Indices: 17594630--17594676 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
17594620 AAAAAATAAG
*
17594630 TTAAATTAAAATATTTAAAAAT
1 TTAAATGAAAATATTTAAAAAT
17594652 TTAAATGAGAAATA-TTAAAAAT
1 TTAAATGA-AAATATTTAAAAAT
17594674 TTA
1 TTA
17594677 TTTGAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
TTAAATGAAAATATTTAAAAAT
Found at i:17611389 original size:46 final size:46
Alignment explanation
Indices: 17611313--17611856 Score: 811
Period size: 46 Copynumber: 11.8 Consensus size: 46
17611303 TGATGTCATA
* * * * *
17611313 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGTTGCCATG
** *** *
17611359 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATG
* *
17611406 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
** *
17611452 GTATCTTTCAACCATGGTCTTATTCATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
*
17611498 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* * *
17611544 GTATCTTGCAACCATGGTCTTACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
*
17611590 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGCTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* * *
17611636 GTATCTTGCAACCATGGTCTTACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
17611682 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
* * *
17611728 GTACCTTTCAACCATGGTCTTACACATTCCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
17611774 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
*
17611820 GTATCTTTCAACCATGGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACACATTTCATATCAG
17611857 ATAGCACACT
Statistics
Matches: 457, Mismatches: 39, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
46 419 0.92
47 38 0.08
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
Found at i:17622669 original size:16 final size:18
Alignment explanation
Indices: 17622634--17622673 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
17622624 TCAGCCGCTG
17622634 CTACCCACGTTTGCCTCCA
1 CTACCCACGTTT-CCTCCA
17622653 CTACCCACG-TT-CTCCA
1 CTACCCACGTTTCCTCCA
17622669 CTACC
1 CTACC
17622674 ATGCGCCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.17, C:0.50, G:0.07, T:0.25
Consensus pattern (18 bp):
CTACCCACGTTTCCTCCA
Found at i:17622932 original size:12 final size:11
Alignment explanation
Indices: 17622917--17622958 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
17622907 TATTTTCGAA
17622917 TCTTTCTTTCTT
1 TCTTTCTTT-TT
17622929 TCTTTCTTTTT
1 TCTTTCTTTTT
*
17622940 TGTTT-TTTTT
1 TCTTTCTTTTT
17622950 TCTCTTCTT
1 TCT-TTCTT
17622959 CCTTTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 7 0.27
11 8 0.31
12 11 0.42
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (11 bp):
TCTTTCTTTTT
Found at i:17623638 original size:3 final size:3
Alignment explanation
Indices: 17623614--17623700 Score: 86
Period size: 3 Copynumber: 28.3 Consensus size: 3
17623604 TAATTAATTA
* ** *
17623614 ATT ATT CTT ATT AATGT ATT ATT ATT ACC ATT ATT ATT ACT ATT ACTT
1 ATT ATT ATT ATT -AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
17623662 -TT ATT TTT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
17623701 CATTTTCTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.03
3 59 0.87
4 6 0.09
5 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:17632993 original size:42 final size:42
Alignment explanation
Indices: 17632871--17632995 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 42
17632861 CATCTATCTG
* *
17632871 AGATA-TCGTGTAAGACCGTGTTTGGGACAGAGGCCTCGATT
1 AGATATTCGTGTAAGACCGTGTCTGGGACAGAGGCATCGATT
* *
17632912 GAGATATTACGTATAAGACCGTGTCTGGGACATCA-GCATCGTATCT
1 -AGATATT-CGTGTAAGACCGTGTCTGGGACA-GAGGCATCG-AT-T
* *
17632958 -GAT-TTCGTGTAAAACCTTGTCTGGGACAGAGGCATCGA
1 AGATATTCGTGTAAGACCGTGTCTGGGACAGAGGCATCGA
17632996 CATTGAATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
41 2 0.03
42 31 0.45
43 3 0.04
44 29 0.42
45 3 0.04
46 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (42 bp):
AGATATTCGTGTAAGACCGTGTCTGGGACAGAGGCATCGATT
Found at i:17650313 original size:24 final size:25
Alignment explanation
Indices: 17650280--17650341 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
17650270 ATAAAAACAT
*
17650280 TACATAAATATATATTGAAAA-TAGA
1 TACAT-AATATATATTGAAAAGCAGA
* * *
17650305 TATATAATA-ATATTTAAAAGCATA
1 TACATAATATATATTGAAAAGCAGA
17650329 TACATAATATATA
1 TACATAATATATA
17650342 CATAACATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 9 0.30
24 14 0.47
25 7 0.23
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (25 bp):
TACATAATATATATTGAAAAGCAGA
Found at i:17650865 original size:11 final size:11
Alignment explanation
Indices: 17650792--17650867 Score: 57
Period size: 11 Copynumber: 6.8 Consensus size: 11
17650782 AAAAATGTCT
17650792 AAATAATAATA
1 AAATAATAATA
*
17650803 AAAT-ATATTAA
1 AAATAATAAT-A
17650814 AAATAATAATA
1 AAATAATAATA
* * *
17650825 CAAGAATAGTA
1 AAATAATAATA
17650836 AAATAGAATAAT-
1 AAAT--AATAATA
* *
17650848 GAATAATATTA
1 AAATAATAATA
17650859 AAATAATAA
1 AAATAATAA
17650868 AGAGTAAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
10 9 0.19
11 27 0.56
12 7 0.15
13 5 0.10
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (11 bp):
AAATAATAATA
Found at i:17653772 original size:13 final size:13
Alignment explanation
Indices: 17653754--17653778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17653744 AAGTGATAAG
17653754 TAAAAAAATTAAC
1 TAAAAAAATTAAC
17653767 TAAAAAAATTAA
1 TAAAAAAATTAA
17653779 AATGTTTATC
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAAATTAAC
Found at i:17658851 original size:174 final size:177
Alignment explanation
Indices: 17658665--17658985 Score: 558
Period size: 179 Copynumber: 1.8 Consensus size: 177
17658655 AAATTAAAAA
**
17658665 AAAAAAACCTTGTTTTGTTAATTCAATTGTGAGTCTAACAATTTTT-TTT-TTAAAA-TTGAGCT
1 AAAAAAACCTTGTTTTGTTAATTCAATTGTGAGTCTAACAATTTTTCTTTAAAAAAATTTGAGCT
17658727 TTAATTTGCTTCATTAATGGCAGTGAACTCAAGCTAATGAAAAATGAATTGATTAATACTAAGAG
66 TTAATTTGCTTCATTAATGGCAGTGAACTCAAGCTAATGAAAAATGAATTGATTAATACTAAGAG
17658792 ATATTAAGTTTTTGGTCATTTGAAGCATAAGAAAAACAATATATTGT
131 ATATTAAGTTTTTGGTCATTTGAAGCATAAGAAAAACAATATATTGT
17658839 AAAAAAACCTTGTTTTGTTAATTCAATTGTGAGTCTAACAATTTTTCTTTAAAAAAAAATTTGAG
1 AAAAAAACCTTGTTTTGTTAATTCAATTGTGAGTCTAACAATTTTTCTTT--AAAAAAATTTGAG
* * *
17658904 CTTTAATTTGCTTCATTAGTGGCAGTGAACTCAAGCTAATGAAAAATGAATTGATTATTATTAAG
64 CTTTAATTTGCTTCATTAATGGCAGTGAACTCAAGCTAATGAAAAATGAATTGATTAATACTAAG
17658969 AGATATTAAGTTTTTGG
129 AGATATTAAGTTTTTGG
17658986 CATAAGAAAA
Statistics
Matches: 137, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
174 46 0.34
175 3 0.02
178 4 0.03
179 84 0.61
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (177 bp):
AAAAAAACCTTGTTTTGTTAATTCAATTGTGAGTCTAACAATTTTTCTTTAAAAAAATTTGAGCT
TTAATTTGCTTCATTAATGGCAGTGAACTCAAGCTAATGAAAAATGAATTGATTAATACTAAGAG
ATATTAAGTTTTTGGTCATTTGAAGCATAAGAAAAACAATATATTGT
Found at i:17662470 original size:13 final size:13
Alignment explanation
Indices: 17662452--17662478 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17662442 GAAGTATGAG
17662452 ATATATTCCTTCT
1 ATATATTCCTTCT
17662465 ATATATTCCTTCT
1 ATATATTCCTTCT
17662478 A
1 A
17662479 AGGCAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTCCTTCT
Found at i:17674819 original size:21 final size:22
Alignment explanation
Indices: 17674781--17674821 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17674771 TTGAATTGGT
17674781 CACACGGGTGTGTTGCCCCTCC
1 CACACGGGTGTGTTGCCCCTCC
17674803 CACACGGGTGT-TTGCCCCT
1 CACACGGGTGTGTTGCCCCT
17674822 GTGGCTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.10, C:0.39, G:0.27, T:0.24
Consensus pattern (22 bp):
CACACGGGTGTGTTGCCCCTCC
Found at i:17680422 original size:15 final size:16
Alignment explanation
Indices: 17680397--17680436 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
17680387 GGTTATAGGG
17680397 ATTTTATTTATTTATT
1 ATTTTATTTATTTATT
17680413 ATTTTA-TTATTTATT
1 ATTTTATTTATTTATT
17680428 -TTTCTATTT
1 ATTT-TATTT
17680437 TCCTTACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 11 0.50
16 8 0.36
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (16 bp):
ATTTTATTTATTTATT
Found at i:17682486 original size:27 final size:27
Alignment explanation
Indices: 17682399--17682488 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
17682389 AGTCTGACAA
* *
17682399 GACAATAAATATAGGGTAGTCCATCGG
1 GACAGTAAACATAGGGTAGTCCATCGG
* * *
17682426 GACAGTAAACATAGGGTAGTCTACCGA
1 GACAGTAAACATAGGGTAGTCCATCGG
* * *
17682453 GACAGTAACCATGGGGTAGTCCGTCGG
1 GACAGTAAACATAGGGTAGTCCATCGG
*
17682480 GATAGTAAA
1 GACAGTAAA
17682489 TACGAGGATT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (27 bp):
GACAGTAAACATAGGGTAGTCCATCGG
Found at i:17686035 original size:31 final size:31
Alignment explanation
Indices: 17686000--17686171 Score: 206
Period size: 31 Copynumber: 5.5 Consensus size: 31
17685990 TTGTAGCCGA
* *
17686000 AGCTACCACTATTCACTGATTAGGTAGCTAG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
* *
17686031 AGCTACCATTTTTCACTGATCAGGTAG-TCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCT-AG
* *
17686062 AGCTACCATTTTTCACTGATCAGTTAGC-AG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
* *
17686092 AAGCTACCACTTTTCACTGATCAGGTAGCAAA
1 -AGCTACCACTTTTCACTGATCAGGTAGCTAG
*
17686124 AGCTACCACTTTTCACTGATCAGGTAGC-CG
1 AGCTACCACTTTTCACTGATCAGGTAGCTAG
*
17686154 AAACTACCACTTTTCACT
1 -AGCTACCACTTTTCACT
17686172 TGTCATTTGT
Statistics
Matches: 124, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
30 2 0.02
31 121 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCTAG
Found at i:17686077 original size:62 final size:62
Alignment explanation
Indices: 17685999--17686171 Score: 233
Period size: 62 Copynumber: 2.8 Consensus size: 62
17685989 CTTGTAGCCG
* * * *
17685999 AAGCTACCACTATTCACTGATTAGGTAGCTAG-AGCTACCATTTTTCACTGATCAGGTAGTC-G
1 AAGCTACCACTTTTCACTGATCAGGTAGC-AGAAGCTACCACTTTTCACTGATCAGGTAG-CAA
* * *
17686061 GAGCTACCATTTTTCACTGATCAGTTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
1 AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
* *
17686123 AAGCTACCACTTTTCACTGATCAGGTAGCCGAAACTACCACTTTTCACT
1 AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
17686172 TGTCATTTGT
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
61 3 0.03
62 94 0.97
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (62 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAA
Found at i:17686110 original size:93 final size:93
Alignment explanation
Indices: 17685993--17686171 Score: 268
Period size: 93 Copynumber: 1.9 Consensus size: 93
17685983 TTATCACTTG
* * * * *
17685993 TAGCCGAAGCTACCACTATTCACTGATTAGGTAGCTAGAGCTACCATTTTTCACTGATCAGGTAG
1 TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
* * * *
17686058 TCGGAGCTACCATTTTTCACTGATCAGT
66 CCGAAACTACCACTTTTCACTGATCAGT
*
17686086 TAGCAGAAGCTACCACTTTTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
1 TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
17686151 CCGAAACTACCACTTTTCACT
66 CCGAAACTACCACTTTTCACT
17686172 TGTCATTTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (93 bp):
TAGCAGAAGCTACCACTATTCACTGATCAGGTAGCAAAAGCTACCACTTTTCACTGATCAGGTAG
CCGAAACTACCACTTTTCACTGATCAGT
Found at i:17686245 original size:50 final size:51
Alignment explanation
Indices: 17686147--17686275 Score: 197
Period size: 50 Copynumber: 2.5 Consensus size: 51
17686137 CACTGATCAG
* * * * *
17686147 GTAGCCGAAACTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
*
17686198 GTAGCCGAAGCTATTACTTATCACTT-TCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
17686248 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
17686276 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 47 0.67
51 23 0.33
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAGATAAGT
Found at i:17690579 original size:17 final size:17
Alignment explanation
Indices: 17690559--17690592 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17690549 TGTTATTAAA
*
17690559 GGTTAAAATGGTAAAAT
1 GGTTAAAATGATAAAAT
17690576 GGTTAAAATGATAAAAT
1 GGTTAAAATGATAAAAT
17690593 AATTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (17 bp):
GGTTAAAATGATAAAAT
Found at i:17690598 original size:17 final size:17
Alignment explanation
Indices: 17690561--17690601 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17690551 TTATTAAAGG
* **
17690561 TTAAAATGGTAAAATGG
1 TTAAAATGATAAAATAA
17690578 TTAAAATGATAAAATAA
1 TTAAAATGATAAAATAA
17690595 TTAAAAT
1 TTAAAAT
17690602 AAAGCCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (17 bp):
TTAAAATGATAAAATAA
Found at i:17690934 original size:15 final size:17
Alignment explanation
Indices: 17690911--17690942 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17690901 TGAAAATGCA
17690911 AAATGATT-AAATTATG
1 AAATGATTAAAATTATG
17690927 AAAT-ATTAAAATTATG
1 AAATGATTAAAATTATG
17690943 TGGTTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
AAATGATTAAAATTATG
Found at i:17692894 original size:27 final size:26
Alignment explanation
Indices: 17692864--17692915 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
17692854 GGGAAAATCG
17692864 ATAAAGTGGTAATATGTG-AAAGTTATT
1 ATAAAGTGG--ATATGTGCAAAGTTATT
* *
17692891 ATAAGGTGGATATGTGCAAATTTAT
1 ATAAAGTGGATATGTGCAAAGTTAT
17692916 GTTTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (26 bp):
ATAAAGTGGATATGTGCAAAGTTATT
Found at i:17694079 original size:43 final size:43
Alignment explanation
Indices: 17694032--17694113 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
17694022 GTTACCGAGA
*
17694032 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTATGGGACATTGGCATTGTAT
*
17694075 TGTGATTACGTGTAAGACCATGTATGGGACATTGGCATT
1 TGTGATTACATGTAAGACCATGTATGGGACATTGGCATT
17694114 ATTAATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTATGGGACATTGGCATTGTAT
Found at i:17694745 original size:29 final size:29
Alignment explanation
Indices: 17694713--17694771 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
17694703 CGAGATAGAA
17694713 TGGTGAAACCATATGAATTATATCATGTT
1 TGGTGAAACCATATGAATTATATCATGTT
*
17694742 TGGTGAAATCATATGAATTATATCATGTT
1 TGGTGAAACCATATGAATTATATCATGTT
17694771 T
1 T
17694772 TGAGTAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (29 bp):
TGGTGAAACCATATGAATTATATCATGTT
Found at i:17700137 original size:19 final size:20
Alignment explanation
Indices: 17700103--17700142 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17700093 ATATTGAATC
17700103 AAATTAAACTTTCATGCATA
1 AAATTAAACTTTCATGCATA
* *
17700123 AAATTATAC-TTCATGTATA
1 AAATTAAACTTTCATGCATA
17700142 A
1 A
17700143 CATTGTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
AAATTAAACTTTCATGCATA
Found at i:17701317 original size:4 final size:4
Alignment explanation
Indices: 17701308--17701334 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17701298 TCTGATCTCG
17701308 GTTA GTTA GTTA GTTA GTTA GTTA GTT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTT
17701335 GACATATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
GTTA
Found at i:17707152 original size:31 final size:30
Alignment explanation
Indices: 17707117--17707187 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
17707107 ACTAATTAAT
17707117 TTTAAAAAA-TTA-TAAAATGGTCATTAAATTA
1 TTTAAAAAATTTATTAAAAT--T-ATTAAATTA
*
17707148 TTTAAAAAATTTTATTTAAATTATTAAATTA
1 TTTAAAAAA-TTTATTAAAATTATTAAATTA
17707179 TTTAAAAAA
1 TTTAAAAAA
17707188 AATTATTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 27 0.75
32 1 0.03
33 3 0.08
34 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTAAAAAATTTATTAAAATTATTAAATTA
Found at i:17707192 original size:14 final size:14
Alignment explanation
Indices: 17707142--17707197 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
17707132 AATGGTCATT
17707142 AAATTATTTAAAAA
1 AAATTATTTAAAAA
** *
17707156 ATTTTATTTAAATTATT
1 AAATTATTTAAA--A-A
17707173 AAATTATTTAAAAA
1 AAATTATTTAAAAA
17707187 AAATTATTTAA
1 AAATTATTTAA
17707198 TTTATTGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 21 0.64
15 1 0.03
16 1 0.03
17 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATTATTTAAAAA
Found at i:17707194 original size:31 final size:31
Alignment explanation
Indices: 17707139--17707203 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
17707129 TAAAATGGTC
**
17707139 ATTAAATTATTTAAAAAATTTTATTTAAATT
1 ATTAAATTATTTAAAAAAAATTATTTAAATT
*
17707170 ATTAAATTATTTAAAAAAAATTATTTAATTT
1 ATTAAATTATTTAAAAAAAATTATTTAAATT
17707201 ATT
1 ATT
17707204 GGGCTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTAAATTATTTAAAAAAAATTATTTAAATT
Found at i:17708050 original size:22 final size:22
Alignment explanation
Indices: 17708008--17708050 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
17707998 AAAATGATTT
*
17708008 AACAAATAAATTAATCTATAAA
1 AACAAATAAATTAATCAATAAA
*
17708030 AACAATTATAATTAA-CAATAA
1 AACAAATA-AATTAATCAATAA
17708051 CAATAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (22 bp):
AACAAATAAATTAATCAATAAA
Found at i:17709914 original size:20 final size:20
Alignment explanation
Indices: 17709887--17709925 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
17709877 TGTTTATTTT
*
17709887 ATTTCAT-AATTTTTTAAAA
1 ATTTCATAAATATTTTAAAA
17709906 ATTTACATAAATATTTTAAA
1 ATTT-CATAAATATTTTAAA
17709926 TTATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTCATAAATATTTTAAAA
Found at i:17710003 original size:19 final size:19
Alignment explanation
Indices: 17709979--17710017 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17709969 TTTTTTTATA
17709979 TTTTAAAATTTATGAGAAT
1 TTTTAAAATTTATGAGAAT
* *
17709998 TTTTAAATTTTATTAGAAT
1 TTTTAAAATTTATGAGAAT
17710017 T
1 T
17710018 AGGATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTTATGAGAAT
Found at i:17711148 original size:20 final size:22
Alignment explanation
Indices: 17711118--17711158 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17711108 AATAACTTTT
17711118 TAAACAGGGC-ACACGCCCGTA
1 TAAACAGGGCAACACGCCCGTA
17711139 TAAA-AGGGCAACACGCCCGT
1 TAAACAGGGCAACACGCCCGT
17711159 GTGGTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.34, C:0.32, G:0.24, T:0.10
Consensus pattern (22 bp):
TAAACAGGGCAACACGCCCGTA
Found at i:17711319 original size:28 final size:28
Alignment explanation
Indices: 17711282--17711405 Score: 203
Period size: 28 Copynumber: 4.4 Consensus size: 28
17711272 ACAGTCTGAC
17711282 ACACGCCCGTGTCCTTCACACGGCCATG
1 ACACGCCCGTGTCCTTCACACGGCCATG
*
17711310 ACACGTCCGTGTCCTTCACACGGCCATG
1 ACACGCCCGTGTCCTTCACACGGCCATG
** *
17711338 ACACGCCAATGTCCTTCACATGGCCATG
1 ACACGCCCGTGTCCTTCACACGGCCATG
17711366 ACACGCCCGTGTCCTTCACACGGCCATG
1 ACACGCCCGTGTCCTTCACACGGCCATG
*
17711394 ACACGCCTGTGT
1 ACACGCCCGTGT
17711406 TCTAGCCCGT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 87 1.00
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.20
Consensus pattern (28 bp):
ACACGCCCGTGTCCTTCACACGGCCATG
Found at i:17712417 original size:47 final size:46
Alignment explanation
Indices: 17712363--17712629 Score: 224
Period size: 46 Copynumber: 5.7 Consensus size: 46
17712353 GTATAATACT
* * *
17712363 GATGCCATGTCTCAGACATAGTCTTACACTGGCTCATCCATCAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCC-TCAAGCC
* ** ** *
17712410 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTACATATTCGTGTC
1 GATGCCATGTCCCAGACATGGTCTTACACT-G-GC-T-CATCCTCAAGCC
* * * *
17712460 GATGCCATGTCCCAGACATGGTCTTACACTGACACAT-CTCGTAGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCTC-AAGCC
* *
17712506 GATG-CATGTCCTAGACAT-GTCTTACACTGGCTTACAT-CTCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-T-CATCCTC-AAGCC
* *
17712552 AATG-CATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATC--CTCAA-GCC
17712598 GATGCCATGTCCCAGACATGGTCTTACACTGG
1 GATGCCATGTCCCAGACATGGTCTTACACTGG
17712630 ATCTCATAAT
Statistics
Matches: 181, Mismatches: 26, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 13 0.07
45 17 0.09
46 54 0.30
47 42 0.23
48 13 0.07
49 2 0.01
50 36 0.20
51 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCCTCAAGCC
Found at i:17712546 original size:46 final size:48
Alignment explanation
Indices: 17712361--17712673 Score: 221
Period size: 46 Copynumber: 6.7 Consensus size: 48
17712351 GGGTATAATA
* * * *
17712361 CTGATGCCATGTCTCAGACATAGTCTTACACTGGC-TCATCCATC-AAG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATAC-TCGTAG
* *
17712408 -TCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTTACATATTCGT-G
1 CT-GATGCCATGTCCCAGACATGGTCTTACACT-G-GCTT-CATACTCGTAG
* *
17712458 -TCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACAT-CTCGTAG
1 CT-GATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATACTCGTAG
*
17712504 CTGATG-CATGTCCTAGACAT-GTCTTACACTGGCTTACAT-CTCG-AGG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATACTCGTA-G
** * * *
17712550 CCAATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGT-CTC-AATG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATACTCGTA-G
* * * *
17712596 CCGATGCCATGTCCCAGACATGGTCTTACACTGGATCTCATAAT-GTGG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATACTCGTAG
* *
17712644 TTGATG-CATGTCCTAGACAT-GTCTTACACT
1 CTGATGCCATGTCCCAGACATGGTCTTACACT
17712674 AGCACACAAA
Statistics
Matches: 221, Mismatches: 28, Indels: 35
0.78 0.10 0.12
Matches are distributed among these distances:
44 12 0.05
45 18 0.08
46 69 0.31
47 57 0.26
48 23 0.10
49 3 0.01
50 36 0.16
51 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (48 bp):
CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATACTCGTAG
Found at i:17712651 original size:94 final size:97
Alignment explanation
Indices: 17712363--17712676 Score: 302
Period size: 94 Copynumber: 3.3 Consensus size: 97
17712353 GTATAATACT
* * *
17712363 GATGCCATGTCTCAGACATAGTCTTACACTGGCTCATC-CATCAA-GTCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAGACATAGTCTTACACTAGCTC-TCTC-TCAATGCCGATGCCATGTCCCAGA
* *
17712426 CATGGTCTTACACTAGCTCTTACATATTCGT-GTC
64 CATGGTCTTACACTGGCTC-TACATAATCGTGGTC
* * * *
17712460 GATGCCATGTCCCAGACATGGTCTTACACT-GACACATCTCGT--A-GCTGATG-CATGTCCTAG
1 GATGCCATGTCCCAGACATAGTCTTACACTAG-CTC-TCTC-TCAATGCCGATGCCATGTCCCAG
* * *
17712520 ACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCC
63 ACATGGTCTTACACTGGCTCTACATAATCGTGGTC
*
17712552 AATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCCAGAC
1 GATGCCATGTCCCAGACATAGTCTTACACTAGCTCTC-TCTCAATGCCGATGCCATGTCCCAGAC
* *
17712615 ATGGTCTTACACTGGATCT-CATAAT-GTGGTT
65 ATGGTCTTACACTGGCTCTACATAATCGTGGTC
*
17712646 GATG-CATGTCCTAGACAT-GTCTTACACTAGC
1 GATGCCATGTCCCAGACATAGTCTTACACTAGC
17712677 ACACAAATAA
Statistics
Matches: 183, Mismatches: 22, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
89 3 0.02
90 14 0.08
91 19 0.10
92 16 0.09
93 13 0.07
94 61 0.33
95 15 0.08
96 7 0.04
97 33 0.18
98 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (97 bp):
GATGCCATGTCCCAGACATAGTCTTACACTAGCTCTCTCTCAATGCCGATGCCATGTCCCAGACA
TGGTCTTACACTGGCTCTACATAATCGTGGTC
Found at i:17712660 original size:140 final size:141
Alignment explanation
Indices: 17712415--17712673 Score: 375
Period size: 140 Copynumber: 1.8 Consensus size: 141
17712405 AAGTCGATGC
* * *
17712415 CATGTCCCAGACATGGTCTTACACTAGCTCTTACATATTCGTGTCGATGCCATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCTTACATACTCATGCCGATGCCATGTCCCAGACATG
*
17712480 GTCTTACACTGACACATCTCGTAGCTGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCT
66 GTCTTACACTGACACATATCGTAGCTGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCT
17712545 CGAGGCCAATG
131 CGAGGCCAATG
*
17712556 CATGTCCCAGACAT-GTCTTACACTAGCTC-T-CGT-CTCAATGCCGATGCCATGTCCCAGACAT
1 CATGTCCCAGACATGGTCTTACACTAGCTCTTACATACTC-ATGCCGATGCCATGTCCCAGACAT
* * *
17712617 GGTCTTACACTGGATCTCATAAT-GTGGTTGATGCATGTCCTAGACATGTCTTACACT
65 GGTCTTACACT-GA-CACAT-ATCGTAGCTGATGCATGTCCTAGACATGTCTTACACT
17712674 AGCACACAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
137 2 0.02
138 35 0.33
139 3 0.03
140 51 0.48
141 15 0.14
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (141 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCTTACATACTCATGCCGATGCCATGTCCCAGACATG
GTCTTACACTGACACATATCGTAGCTGATGCATGTCCTAGACATGTCTTACACTGGCTTACATCT
CGAGGCCAATG
Found at i:17714333 original size:13 final size:13
Alignment explanation
Indices: 17714296--17714339 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
17714286 AAGATTTAGT
17714296 ATTTATTAGTATA
1 ATTTATTAGTATA
*
17714309 ATATATT--TATA
1 ATTTATTAGTATA
*
17714320 ATTTATTAGCATA
1 ATTTATTAGTATA
17714333 ATTTATT
1 ATTTATT
17714340 TGACCTACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 10 0.38
13 16 0.62
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (13 bp):
ATTTATTAGTATA
Found at i:17715018 original size:25 final size:23
Alignment explanation
Indices: 17714990--17715035 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
17714980 ACGAGCACAA
17714990 AAGTACTAAGAAATCATGAGCACTG
1 AAGTACT-AGAAA-CATGAGCACTG
* *
17715015 AAGTGCTGGAAACATGAGCAC
1 AAGTACTAGAAACATGAGCAC
17715036 ATAAGTATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 4 0.21
25 6 0.32
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (23 bp):
AAGTACTAGAAACATGAGCACTG
Found at i:17715994 original size:31 final size:31
Alignment explanation
Indices: 17715936--17715994 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17715926 TTTAATTTAA
* *
17715936 CCCTTCAACTTTTGAATATTTATTATTTGAC
1 CCCTTCAACTTTTCAATATTTACTATTTGAC
*
17715967 CCCTTC-ACTTTTCACTAGTTTACTATTT
1 CCCTTCAACTTTTCAATA-TTTACTATTT
17715995 AGTCTATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.22, C:0.24, G:0.05, T:0.49
Consensus pattern (31 bp):
CCCTTCAACTTTTCAATATTTACTATTTGAC
Found at i:17718738 original size:32 final size:29
Alignment explanation
Indices: 17718680--17718740 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 29
17718670 TGACTCAAGT
*
17718680 TTTTGATAATTAAAAAAATTAGAAAATAA
1 TTTTGATAATTAAAAAAATTAAAAAATAA
17718709 TTTTGATAATTTAATACAAAATTAAAAAATAA
1 TTTTGATAA-TTAA-A-AAAATTAAAAAATAA
17718741 AATAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 9 0.32
30 4 0.14
31 1 0.04
32 14 0.50
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
TTTTGATAATTAAAAAAATTAAAAAATAA
Found at i:17720513 original size:14 final size:15
Alignment explanation
Indices: 17720491--17720522 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
17720481 GAATTATGTT
17720491 AGTTGTATTATCATA
1 AGTTGTATTATCATA
17720506 AGTT-TATTATCATA
1 AGTTGTATTATCATA
17720520 AGT
1 AGT
17720523 ATAAATCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (15 bp):
AGTTGTATTATCATA
Found at i:17721531 original size:7 final size:6
Alignment explanation
Indices: 17721501--17721532 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
17721491 TTTGCAACCC
17721501 AAGGGG AAGGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
17721533 GAAGAATGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:17737796 original size:20 final size:19
Alignment explanation
Indices: 17737760--17737856 Score: 71
Period size: 19 Copynumber: 5.2 Consensus size: 19
17737750 NNNAATACAA
17737760 TACATAATAACTTACAACT
1 TACATAATAACTTACAACT
*
17737779 TACATAATCAATTTACAACT
1 TACATAAT-AACTTACAACT
* *
17737799 TACA-ACTTAC--ACAA--
1 TACATAATAACTTACAACT
* *
17737813 TACAT-TTAACTTACATAAT
1 TACATAATAACTTACA-ACT
17737832 TACATAATACAACTTACAACT
1 TACATAAT--AACTTACAACT
17737853 TACA
1 TACA
17737857 AACTTACATA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 7 0.12
16 7 0.12
17 1 0.02
18 1 0.02
19 15 0.25
20 15 0.25
21 6 0.10
22 8 0.13
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (19 bp):
TACATAATAACTTACAACT
Found at i:17737798 original size:27 final size:27
Alignment explanation
Indices: 17737768--17737868 Score: 118
Period size: 27 Copynumber: 3.7 Consensus size: 27
17737758 AATACATAAT
17737768 AACTTACAACTTACATAATCAATTTAC
1 AACTTACAACTTACATAATCAATTTAC
*
17737795 AACTTACAACTTACACAAT-ACATTT--
1 AACTTACAACTTACATAATCA-ATTTAC
* *
17737820 AACTTACATAATTACATAATACAACTTAC
1 AACTTACA-ACTTACATAAT-CAATTTAC
17737849 AACTTACAAACTTACATAAT
1 AACTTAC-AACTTACATAAT
17737869 ACATTTAACT
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
25 8 0.13
26 10 0.16
27 25 0.40
28 1 0.02
29 17 0.27
30 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.32
Consensus pattern (27 bp):
AACTTACAACTTACATAATCAATTTAC
Found at i:17737870 original size:55 final size:53
Alignment explanation
Indices: 17737756--17737885 Score: 190
Period size: 55 Copynumber: 2.4 Consensus size: 53
17737746 NNNNNNNAAT
* * *
17737756 ACAATACATAATAACTTACA-ACTTACATAATCAATTTACAACTTACAACTTAC
1 ACAATACAT-TTAACTTACATAATTACATAATCAACTTACAACTTACAACTTAC
17737809 ACAATACATTTAACTTACATAATTACATAATACAACTTACAACTTACAAACTTAC
1 ACAATACATTTAACTTACATAATTACATAAT-CAACTTACAACTTAC-AACTTAC
*
17737864 ATAATACATTTAACTTACATAA
1 ACAATACATTTAACTTACATAA
17737886 CTTAACTAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
52 9 0.13
53 19 0.27
54 14 0.20
55 28 0.40
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.32
Consensus pattern (53 bp):
ACAATACATTTAACTTACATAATTACATAATCAACTTACAACTTACAACTTAC
Found at i:17737871 original size:15 final size:15
Alignment explanation
Indices: 17737831--17737885 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17737821 ACTTACATAA
17737831 TTACATAATAC-AAC
1 TTACATAATACAAAC
*
17737845 TTACA-ACTTACAAAC
1 TTACATA-ATACAAAC
17737860 TTACATAATACATTTAAC
1 TTACATAATACA---AAC
17737878 TTACATAA
1 TTACATAA
17737886 CTTAACTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 1 0.03
14 8 0.24
15 12 0.36
16 1 0.03
18 11 0.33
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
TTACATAATACAAAC
Found at i:17737883 original size:18 final size:18
Alignment explanation
Indices: 17737802--17737885 Score: 68
Period size: 18 Copynumber: 4.6 Consensus size: 18
17737792 TACAACTTAC
*
17737802 AACTTACACAATACATTT
1 AACTTACATAATACATTT
*
17737820 AACTTACATAATTACATAATAC
1 AACTTACATAA-TACAT--T-T
*
17737842 AACTTACA-ACTTACA---
1 AACTTACATA-ATACATTT
17737857 AACTTACATAATACATTT
1 AACTTACATAATACATTT
17737875 AACTTACATAA
1 AACTTACATAA
17737886 CTTAACTAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
15 12 0.23
16 1 0.02
18 21 0.40
19 5 0.09
21 6 0.11
22 8 0.15
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:17737897 original size:9 final size:9
Alignment explanation
Indices: 17737819--17737889 Score: 54
Period size: 7 Copynumber: 8.8 Consensus size: 9
17737809 ACAATACATT
17737819 TAACTTACA
1 TAACTTACA
17737828 TAA-TTACA
1 TAACTTACA
17737836 TAA--TAC-
1 TAACTTACA
17737842 -AACTTAC-
1 TAACTTACA
17737849 -AACTTACA
1 TAACTTACA
17737857 -AACTTACA
1 TAACTTACA
17737865 TAA--TACA
1 TAACTTACA
17737872 TTTAACTTACA
1 --TAACTTACA
17737883 TAACTTA
1 TAACTTA
17737890 ACTAACTTCA
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
5 2 0.04
7 17 0.31
8 16 0.30
9 15 0.28
11 4 0.07
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
TAACTTACA
Found at i:17743198 original size:20 final size:20
Alignment explanation
Indices: 17743173--17743228 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
17743163 GCAGAGCGGA
*
17743173 AGCGAGGAAGCAGCGACTGC
1 AGCGAGGAAGCAGAGACTGC
* *
17743193 AGCGAGGAAGCGGAGGCTGC
1 AGCGAGGAAGCAGAGACTGC
*
17743213 AGCAAGAGAAGCAGAG
1 AGCGAG-GAAGCAGAG
17743229 CAGAGCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.34, C:0.20, G:0.43, T:0.04
Consensus pattern (20 bp):
AGCGAGGAAGCAGAGACTGC
Found at i:17743342 original size:7 final size:7
Alignment explanation
Indices: 17743327--17743357 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
17743317 CATAAATATT
*
17743327 TTTATCA
1 TTTAACA
17743334 TTTAACA
1 TTTAACA
17743341 TTTAACA
1 TTTAACA
17743348 TTTAACA
1 TTTAACA
17743355 TTT
1 TTT
17743358 TTGCAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (7 bp):
TTTAACA
Found at i:17743600 original size:41 final size:42
Alignment explanation
Indices: 17743547--17743794 Score: 183
Period size: 42 Copynumber: 5.9 Consensus size: 42
17743537 GTTTTTGTAT
* * *
17743547 AAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTG-TA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
* *
17743588 AAAAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAAA
* * ****
17743631 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * ****
17743673 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * * ****
17743715 CTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
** * * *
17743757 CTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTT
17743795 TTTTCTAAGC
Statistics
Matches: 183, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
41 32 0.17
42 118 0.64
43 33 0.18
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (42 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAAA
Found at i:17743838 original size:42 final size:42
Alignment explanation
Indices: 17743636--17743838 Score: 336
Period size: 42 Copynumber: 4.8 Consensus size: 42
17743626 AGAAAAAAAA
* *
17743636 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCC-TAAG
*
17743678 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTCCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
*
17743720 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
*
17743762 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
*
17743804 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
17743839 GTTTGTAAAC
Statistics
Matches: 155, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
42 149 0.96
43 6 0.04
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTCCTAAG
Found at i:17744859 original size:3 final size:3
Alignment explanation
Indices: 17744851--17744878 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17744841 AACAGTAGGT
17744851 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17744879 CAGATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17747849 original size:88 final size:88
Alignment explanation
Indices: 17747745--17747908 Score: 247
Period size: 88 Copynumber: 1.9 Consensus size: 88
17747735 AGAACCTAAG
*
17747745 CACATGAAAACCCAACTTAAAATCAACACTCTCAATAGCCAAAAGGAAAACTGGGGTTTATCTAG
1 CACATGAAAACCCAACTTAAAATCAACACTCTCAAGAGCCAAAAGGAAAACTGGGGTTTATCTAG
*
17747810 GGTTTTTAAAAATCCACCTTAAC
66 GATTTTTAAAAATCCACCTTAAC
* * * * * * *
17747833 CACATGAAAACCCAACTTCAAGTTAGCATTCTCAAGAGCCAAAAGGGAAATTGGGGTTTATCTAG
1 CACATGAAAACCCAACTTAAAATCAACACTCTCAAGAGCCAAAAGGAAAACTGGGGTTTATCTAG
17747898 GATTTTTAAAA
66 GATTTTTAAAA
17747909 TCTTGAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 67 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (88 bp):
CACATGAAAACCCAACTTAAAATCAACACTCTCAAGAGCCAAAAGGAAAACTGGGGTTTATCTAG
GATTTTTAAAAATCCACCTTAAC
Found at i:17748240 original size:43 final size:43
Alignment explanation
Indices: 17748116--17748427 Score: 278
Period size: 43 Copynumber: 7.3 Consensus size: 43
17748106 TTTATGTAAA
* * * * *
17748116 AAAAATGCCGCTAAAGAACATGACATTTAGCGGC-GTTTT-TG
1 AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTCTC
* * * * * **
17748157 AGAAAGCGTCGTTAAAGAACGTGA-ATTTAGTGGTGCTTTTCTC
1 A-AAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTCTC
* * * ** * *
17748200 AAAAACACTGTTAAAGAGGGTAACCTTTAGCGGCAGTTTTCAT-
1 AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTC-TC
* *
17748243 ACAAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCTC
1 AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTCTC
17748286 AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTCAT-
1 AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTC-TC
* * * *
17748329 ACAAACGCCGCTAAAGAACATGACCTTTACCGGCGCTTTTCTC
1 AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTCTC
* * *
17748372 AAAAA-GCCGCTAAAGAAAGTGACCTTTA-CTGGCGCTTTTCTA
1 AAAAACGCCGCTAAAGAACGTGACCTTTAGC-GGCACTTTTCTC
*
17748414 AAAAACGCCACTAA
1 AAAAACGCCGCTAA
17748428 TTTTAGCAGA
Statistics
Matches: 220, Mismatches: 41, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
41 10 0.05
42 75 0.34
43 133 0.60
44 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACGTGACCTTTAGCGGCACTTTTCTC
Found at i:17749212 original size:13 final size:14
Alignment explanation
Indices: 17749186--17749214 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17749176 ACTAACGACG
17749186 AATTAAACCATTAT
1 AATTAAACCATTAT
17749200 AATTAAA-CATTAT
1 AATTAAACCATTAT
17749213 AA
1 AA
17749215 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:17754811 original size:27 final size:27
Alignment explanation
Indices: 17754768--17754825 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
17754758 TCAGTCATTT
* *
17754768 TACACTACAAGCTTATTTCGTTAATTC
1 TACACTACAAGCGTATTTCGATAATTC
* *
17754795 TACACTACAAGGGTATTTCGATAATTT
1 TACACTACAAGCGTATTTCGATAATTC
17754822 TACA
1 TACA
17754826 AATCGGGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (27 bp):
TACACTACAAGCGTATTTCGATAATTC
Found at i:17754835 original size:27 final size:27
Alignment explanation
Indices: 17754804--17754884 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
17754794 CTACACTACA
17754804 AGGGTATTTCGATAATTTTACAAATCG
1 AGGGTATTTCGATAATTTTACAAATCG
* * * *
17754831 GGGGTGTTTCGGTAATTTTACAAATTG
1 AGGGTATTTCGATAATTTTACAAATCG
17754858 AGGGTATTTC-AGTAATTTTACAAATCG
1 AGGGTATTTCGA-TAATTTTACAAATCG
17754885 TTTACAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGATAATTTTACAAATCG
Found at i:17754899 original size:38 final size:38
Alignment explanation
Indices: 17754847--17754921 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
17754837 TTTCGGTAAT
*
17754847 TTTACAAATTGAGGGTATTTCAG-TAATTTTACAAATCG
1 TTTACAAATCGAGGGTATTT-AGATAATTTTACAAATCG
* *
17754885 TTTACAAATCGAGGGTGTTTTGATAATTTTACAAATC
1 TTTACAAATCGAGGGTATTTAGATAATTTTACAAATC
17754922 AGGGATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (38 bp):
TTTACAAATCGAGGGTATTTAGATAATTTTACAAATCG
Found at i:17754915 original size:27 final size:28
Alignment explanation
Indices: 17754885--17755127 Score: 278
Period size: 27 Copynumber: 9.1 Consensus size: 28
17754875 TTACAAATCG
*
17754885 TTTACAAATCGAGGGTGTTTTGA-TAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
17754912 TTTACAAATC-AGGGATATTTTGA-TAAT
1 TTTACAAATCGAGGG-TATTTTGAGTAAT
17754939 TTTACAAATCGAGGGTATTTT-AGTAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
*
17754966 TTTAC-AATTGAGGGTATTTTGA-TAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
* *
17754992 TTTACAATTCG-GGAGTA-TTTCAGTAAT
1 TTTACAAATCGAGG-GTATTTTGAGTAAT
* *
17755019 TTTACAAATTG-GGGTA-TTTCAGTAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
* * *
17755045 TTTATAAATCGAGGGTGTTTCG-GTAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
*
17755072 TTCACAAATCGAGGGTATTTT-AGTAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
*
17755099 TTTACAAATCGAGGATATTTT-AGTAAT
1 TTTACAAATCGAGGGTATTTTGAGTAAT
17755126 TT
1 TT
17755128 CTTTTATTAT
Statistics
Matches: 188, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
26 56 0.30
27 126 0.67
28 6 0.03
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (28 bp):
TTTACAAATCGAGGGTATTTTGAGTAAT
Found at i:17754931 original size:65 final size:65
Alignment explanation
Indices: 17754820--17754949 Score: 183
Period size: 65 Copynumber: 2.0 Consensus size: 65
17754810 TTTCGATAAT
* * *
17754820 TTTACAAATCGGGGGTGTTTCGGTAATTTTACAAATTGAGGGTATTTCAG-TAATTTTACAAATC
1 TTTACAAATCGAGGGTGTTTCGATAATTTTACAAATTCAGGGTATTT-AGATAATTTTACAAATC
17754884 G
65 G
* *
17754885 TTTACAAATCGAGGGTGTTTTGATAATTTTACAAA-TCAGGGATATTTTGATAATTTTACAAATC
1 TTTACAAATCGAGGGTGTTTCGATAATTTTACAAATTCAGGG-TATTTAGATAATTTTACAAATC
17754949 G
65 G
17754950 AGGGTATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
64 6 0.10
65 52 0.90
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (65 bp):
TTTACAAATCGAGGGTGTTTCGATAATTTTACAAATTCAGGGTATTTAGATAATTTTACAAATCG
Found at i:17754964 original size:92 final size:92
Alignment explanation
Indices: 17754804--17755055 Score: 264
Period size: 92 Copynumber: 2.9 Consensus size: 92
17754794 CTACACTACA
* * * * *
17754804 AGGGTATTTCGATAATTTTACAAATCGGGGGTGTTTCGGTAATTTTACAAATTGAGGGTATTTCA
1 AGGGTATTTCGATAATTTTACAAATCAGGGATATTTCGATAATTTTACAAATCGAGGGTATTTCA
17754869 GTAATTTTACAAATCGTTTACAAATCG
66 GTAATTTTACAAATCGTTTACAAATCG
* * * *
17754896 AGGGTGTTTTGATAATTTTACAAATCAGGGATATTTTGATAATTTTACAAATCGAGGGTATTTTA
1 AGGGTATTTCGATAATTTTACAAATCAGGGATATTTCGATAATTTTACAAATCGAGGGTATTTCA
17754961 GTAATTTTAC-AA-----T-----T-G
66 GTAATTTTACAAATCGTTTACAAATCG
* * *
17754976 AGGGTATTTTGATAATTTTACAATTC-GGGAGTATTTC-AGTAATTTTACAAATTG-GGGTATTT
1 AGGGTATTTCGATAATTTTACAAATCAGGGA-TATTTCGA-TAATTTTACAAATCGAGGGTATTT
*
17755038 CAGTAATTTTATAAATCG
64 CAGTAATTTTACAAATCG
17755056 AGGGTGTTTC
Statistics
Matches: 139, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
79 23 0.17
80 46 0.33
81 1 0.01
86 1 0.01
91 2 0.01
92 66 0.47
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.41
Consensus pattern (92 bp):
AGGGTATTTCGATAATTTTACAAATCAGGGATATTTCGATAATTTTACAAATCGAGGGTATTTCA
GTAATTTTACAAATCGTTTACAAATCG
Found at i:17754993 original size:80 final size:80
Alignment explanation
Indices: 17754885--17755127 Score: 314
Period size: 80 Copynumber: 3.0 Consensus size: 80
17754875 TTACAAATCG
17754885 TTTACAAATCGAGGGTGTTTTGATAATTTTACAAATCAGGGATATTTT-GATAATTTTACAAATC
1 TTTAC-AATCGAGGGTGTTTTGATAATTTTACAAATCAGGGATATTTTAG-TAATTTTACAAATC
17754949 GAGGGTATTTTAGTAAT
64 GAGGGTATTTTAGTAAT
* * * * *
17754966 TTTACAATTGAGGGTATTTTGATAATTTTACAATTC-GGGAGTATTTCAGTAATTTTACAAATTG
1 TTTACAATCGAGGGTGTTTTGATAATTTTACAAATCAGGGA-TATTTTAGTAATTTTACAAATCG
*
17755030 -GGGTATTTCAGTAAT
65 AGGGTATTTTAGTAAT
* * * *
17755045 TTTATAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGG-TATTTTAGTAATTTTACAAATC
1 TTTA-CAATCGAGGGTGTTTTGATAATTTTACAAATC-AGGGATATTTTAGTAATTTTACAAATC
*
17755109 GAGGATATTTTAGTAAT
64 GAGGGTATTTTAGTAAT
17755126 TT
1 TT
17755128 CTTTTATTAT
Statistics
Matches: 139, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
79 22 0.16
80 93 0.67
81 21 0.15
82 3 0.02
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (80 bp):
TTTACAATCGAGGGTGTTTTGATAATTTTACAAATCAGGGATATTTTAGTAATTTTACAAATCGA
GGGTATTTTAGTAAT
Found at i:17755010 original size:53 final size:55
Alignment explanation
Indices: 17754885--17755127 Score: 279
Period size: 53 Copynumber: 4.5 Consensus size: 55
17754875 TTACAAATCG
* * *
17754885 TTTACAAATCGAGGGTGTTT-TGATAATTTTACAAA-TCAGGGATATTTTGA-TAAT
1 TTTACAAATCGAGGGTATTTCAG-TAATTTTACAAATTGAGGG-TATTTTGAGTAAT
*
17754939 TTTACAAATCGAGGGTATTTTAGTAATTTTAC-AATTGAGGGTATTTTGA-TAAT
1 TTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTTGAGTAAT
* *
17754992 TTTACAATTCG-GGAGTATTTCAGTAATTTTACAAATTG-GGGTA-TTTCAGTAAT
1 TTTACAAATCGAGG-GTATTTCAGTAATTTTACAAATTGAGGGTATTTTGAGTAAT
* * * * *
17755045 TTTATAAATCGAGGGTGTTTCGGTAATTTCACAAATCGAGGGTATTTT-AGTAAT
1 TTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTTGAGTAAT
* *
17755099 TTTACAAATCGAGGATATTTTAGTAATTT
1 TTTACAAATCGAGGGTATTTCAGTAATTT
17755128 CTTTTATTAT
Statistics
Matches: 164, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
52 6 0.04
53 79 0.48
54 75 0.46
55 4 0.02
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (55 bp):
TTTACAAATCGAGGGTATTTCAGTAATTTTACAAATTGAGGGTATTTTGAGTAAT
Found at i:17757004 original size:9 final size:9
Alignment explanation
Indices: 17756990--17757080 Score: 68
Period size: 9 Copynumber: 10.4 Consensus size: 9
17756980 TATTTATGTA
17756990 TTATGTAAG
1 TTATGTAAG
*
17756999 TTATGTGAG
1 TTATGTAAG
*
17757008 TTATGTAAA
1 TTATGTAAG
17757017 TTAT-T-A-
1 TTATGTAAG
17757023 -TATGATATA-
1 TTATG-TA-AG
*
17757032 TATATATAAG
1 T-TATGTAAG
17757042 TTAT-TAAG
1 TTATGTAAG
17757050 TTATGTAAG
1 TTATGTAAG
* *
17757059 TTGTGTGAG
1 TTATGTAAG
17757068 TTATGTAAG
1 TTATGTAAG
17757077 TTAT
1 TTAT
17757081 TATATGATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 3 0.05
7 2 0.03
8 9 0.14
9 46 0.70
10 3 0.05
11 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:17758556 original size:21 final size:20
Alignment explanation
Indices: 17758519--17758557 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17758509 ATTTAATTTT
*
17758519 ATAATATAAAATGAAATGAA
1 ATAATATAAAATAAAATGAA
*
17758539 ATAACTATAATATAAAATG
1 ATAA-TATAAAATAAAATG
17758558 TCCCCTACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (20 bp):
ATAATATAAAATAAAATGAA
Found at i:17758667 original size:24 final size:24
Alignment explanation
Indices: 17758635--17758692 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
17758625 AGTATTTTAT
17758635 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
*
17758659 AATATAATATTAATTTTAGTTACA
1 AATATAATATTAATTTTAGATACA
*
17758683 AATATTATAT
1 AATATAATAT
17758693 ACATAGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:17759960 original size:3 final size:3
Alignment explanation
Indices: 17759948--17759995 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
17759938 ATATATTTAC
17759948 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
17759993 TTA
1 TTA
17759996 ATTGAGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17763528 original size:7 final size:6
Alignment explanation
Indices: 17763514--17763577 Score: 56
Period size: 7 Copynumber: 9.3 Consensus size: 6
17763504 AAAATTTACC
17763514 CCTAAA CCTTAAA CCTAATA CCCTAAA CCTTAAA CCCTAAA TCCTAAA
1 CCTAAA CC-TAAA CCTAA-A -CCTAAA CC-TAAA -CCTAAA -CCTAAA
17763562 TCCTAAA CCTTAAA CC
1 -CCTAAA CC-TAAA CC
17763578 CACTTCCATG
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
6 9 0.18
7 35 0.69
8 7 0.14
ACGTcount: A:0.42, C:0.34, G:0.00, T:0.23
Consensus pattern (6 bp):
CCTAAA
Found at i:17763538 original size:21 final size:20
Alignment explanation
Indices: 17763513--17763578 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 20
17763503 CAAAATTTAC
17763513 CCCTAAACCTTAAACCTAATA
1 CCCTAAACCTTAAACCTAA-A
17763534 CCCTAAACCTTAAACCCTAAA
1 CCCTAAACCTTAAA-CCTAAA
*
17763555 TCCTAAATCC-TAAACCTTAAA
1 CCCTAAA-CCTTAAACC-TAAA
17763576 CCC
1 CCC
17763579 ACTTCCATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.05
21 31 0.77
22 7 0.17
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (20 bp):
CCCTAAACCTTAAACCTAAA
Found at i:17763542 original size:14 final size:13
Alignment explanation
Indices: 17763514--17763578 Score: 76
Period size: 14 Copynumber: 4.7 Consensus size: 13
17763504 AAAATTTACC
*
17763514 CCTAAACCTTAAA
1 CCTAAACCCTAAA
17763527 CCTAATACCCTAAA
1 CCTAA-ACCCTAAA
17763541 CCTTAAACCCTAAA
1 CC-TAAACCCTAAA
*
17763555 TCCTAAATCCTAAA
1 -CCTAAACCCTAAA
17763569 CCTTAAACCC
1 CC-TAAACCC
17763579 ACTTCCATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
13 7 0.16
14 33 0.73
15 5 0.11
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (13 bp):
CCTAAACCCTAAA
Found at i:17763746 original size:8 final size:7
Alignment explanation
Indices: 17763734--17763837 Score: 77
Period size: 7 Copynumber: 14.7 Consensus size: 7
17763724 ATAATACTCT
17763734 AACCTTA
1 AACCTTA
17763741 TAACCTTA
1 -AACCTTA
*
17763749 AACCCTA
1 AACCTTA
17763756 AACCTTA
1 AACCTTA
*
17763763 AAGAC-TA
1 AA-CCTTA
17763770 AACCTTAA
1 AACCTT-A
17763778 AACC-TA
1 AACCTTA
*
17763784 AAGCTTA
1 AACCTTA
* *
17763791 AACATCA
1 AACCTTA
*
17763798 AACCTCA
1 AACCTTA
17763805 AACCTTA
1 AACCTTA
**
17763812 AAATTTA
1 AACCTTA
*
17763819 AACCCTA
1 AACCTTA
*
17763826 AACCCTA
1 AACCTTA
17763833 AACCT
1 AACCT
17763838 GAAATCCTAA
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
6 5 0.07
7 58 0.76
8 13 0.17
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (7 bp):
AACCTTA
Found at i:17763757 original size:7 final size:7
Alignment explanation
Indices: 17763742--17763862 Score: 50
Period size: 7 Copynumber: 17.1 Consensus size: 7
17763732 CTAACCTTAT
*
17763742 AACCTTA
1 AACCCTA
17763749 AACCCTA
1 AACCCTA
*
17763756 AACCTTA
1 AACCCTA
**
17763763 AAGACTA
1 AACCCTA
*
17763770 AACCTTA
1 AACCCTA
*
17763777 AAACCTA
1 AACCCTA
* *
17763784 AAGCTTA
1 AACCCTA
*
17763791 AA-CATCA
1 AACCCT-A
17763798 AA-CCTCA
1 AACCCT-A
*
17763805 AACCTTA
1 AACCCTA
***
17763812 AAATTTA
1 AACCCTA
17763819 AACCCTA
1 AACCCTA
17763826 AACCCTA
1 AACCCTA
17763833 AA-CCTGA
1 AACCCT-A
*
17763840 AATCCTA
1 AACCCTA
17763847 AATCCCTA
1 AA-CCCTA
*
17763855 CACCCTA
1 AACCCTA
17763862 A
1 A
17763863 CTAAATTATT
Statistics
Matches: 86, Mismatches: 23, Indels: 10
0.72 0.19 0.08
Matches are distributed among these distances:
6 5 0.06
7 71 0.83
8 10 0.12
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:17763774 original size:28 final size:28
Alignment explanation
Indices: 17763742--17763836 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 28
17763732 CTAACCTTAT
* *
17763742 AACCTTAAACCCTAAACCTTAAAGACTA
1 AACCTTAAACCCTAAAACTTAAACACTA
* *
17763770 AACCTTAAAACCTAAAGCTTAAACA-TCA
1 AACCTTAAACCCTAAAACTTAAACACT-A
* * * *
17763798 AACCTCAAACCTTAAAATTTAAACCCTA
1 AACCTTAAACCCTAAAACTTAAACACTA
*
17763826 AACCCTAAACC
1 AACCTTAAACC
17763837 TGAAATCCTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.02
28 52 0.96
29 1 0.02
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.21
Consensus pattern (28 bp):
AACCTTAAACCCTAAAACTTAAACACTA
Found at i:17764112 original size:29 final size:29
Alignment explanation
Indices: 17764079--17764179 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
17764069 CCTTAGCCCT
17764079 TAAACCCTAAACCCTAACCTTTAAAAC-C
1 TAAACCCTAAACCCTAACCTTTAAAACAC
* *
17764107 ATAAACACTAAGACCTTAAACC-TT-AAACAC
1 -TAAACCCTAA-ACCCT-AACCTTTAAAACAC
* * *
17764137 TAAACCCCAAACAAC-AAACTTTAAAACAC
1 TAAACCCTAAAC-CCTAACCTTTAAAACAC
17764166 TAAACCCTAAACCC
1 TAAACCCTAAACCC
17764180 GAAATAACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
27 3 0.05
28 5 0.09
29 38 0.67
30 7 0.12
31 4 0.07
ACGTcount: A:0.49, C:0.33, G:0.01, T:0.18
Consensus pattern (29 bp):
TAAACCCTAAACCCTAACCTTTAAAACAC
Found at i:17764127 original size:22 final size:21
Alignment explanation
Indices: 17764076--17764142 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
17764066 AATCCTTAGC
* *
17764076 CCTTAAACCCTAAACCCT-AA
1 CCTTAAACCATAAACACTAAA
17764096 CCTTTAAAACCATAAACACTAAGA
1 CC-TT-AAACCATAAACACTAA-A
*
17764120 CCTTAAACCTTAAACACTAAA
1 CCTTAAACCATAAACACTAAA
17764141 CC
1 CC
17764143 CCAAACAACA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.05
21 5 0.12
22 27 0.68
23 3 0.08
24 3 0.08
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (21 bp):
CCTTAAACCATAAACACTAAA
Found at i:17764242 original size:15 final size:14
Alignment explanation
Indices: 17764222--17764284 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
17764212 TAATAACTAT
17764222 TAAACCTTAAACCA
1 TAAACCTTAAACCA
*
17764236 TACAACCCTAAACCA
1 TA-AACCTTAAACCA
* *
17764251 TAGACCTTAAACCT
1 TAAACCTTAAACCA
** *
17764265 TAAATATTAAACCC
1 TAAACCTTAAACCA
17764279 TAAACC
1 TAAACC
17764285 CAAAAATAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:17764273 original size:50 final size:49
Alignment explanation
Indices: 17764189--17764284 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 49
17764179 CGAAATAACA
* *
17764189 AACCCTAAACCATAAACTTAACATAATAACTATTAAACCTTAAACCATAC
1 AACCCTAAACCATAAACTTAACAT-ATAAATATTAAACCCTAAACCATAC
* *
17764239 AACCCTAAACCATAGACCTTAAACCT-TAAATATTAAACCCTAAACC
1 AACCCTAAACCATA-AACTT-AACATATAAATATTAAACCCTAAACC
17764285 CAAAAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 32 0.80
51 4 0.10
52 4 0.10
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.23
Consensus pattern (49 bp):
AACCCTAAACCATAAACTTAACATATAAATATTAAACCCTAAACCATAC
Found at i:17764285 original size:7 final size:7
Alignment explanation
Indices: 17764221--17764284 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
17764211 ATAATAACTA
17764221 TTAAACC
1 TTAAACC
17764228 TTAAACC
1 TTAAACC
*
17764235 ATACAACC
1 TTA-AACC
*
17764243 CTAAACC
1 TTAAACC
* *
17764250 ATAGACC
1 TTAAACC
17764257 TTAAACC
1 TTAAACC
**
17764264 TTAAATA
1 TTAAACC
17764271 TTAAACC
1 TTAAACC
*
17764278 CTAAACC
1 TTAAACC
17764285 CAAAAATAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (7 bp):
TTAAACC
Found at i:17764475 original size:21 final size:21
Alignment explanation
Indices: 17764408--17764482 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
17764398 GGTTTAGGGT
*
17764408 TTTAGGGTTTATAGA-TTAATG
1 TTTAGGGTTTA-AGATTTAAGG
* * * * *
17764429 TTTAGGGTCTATGTTTTTAGAA
1 TTTAGGGTTTAAGATTTAAG-G
17764451 TTTAGGGTTTAAGATTTAAGG
1 TTTAGGGTTTAAGATTTAAGG
17764472 TTTAGGGTTTA
1 TTTAGGGTTTA
17764483 GATAAAGCCA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 1 0.02
21 24 0.59
22 16 0.39
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAAGATTTAAGG
Found at i:17764933 original size:41 final size:41
Alignment explanation
Indices: 17764765--17765135 Score: 313
Period size: 41 Copynumber: 9.1 Consensus size: 41
17764755 TTTTACGGTA
* * * *
17764765 TTTGGACCAAAAACGTCGCTATATA-TCAACTTTTT-GTAGCA
1 TTTGGACCAAAAACGCCGCTAT-TACTC-AGTTTTTAGTGGCG
* * * **
17764806 TTTGGACCAGAAATGCCGCTATTGCTCAGTTTTTAGCAGCG
1 TTTGGACCAAAAACGCCGCTATTACTCAGTTTTTAGTGGCG
** * *
17764847 TTTGGACCAAAAACATCGCTA-TAGTTTAG-TTTTAGTGGCG
1 TTTGGACCAAAAACGCCGCTATTA-CTCAGTTTTTAGTGGCG
* * * *
17764887 TTTGGACCAGAAACGGCGCTATTACCCAGTTTTTAGTGGCA
1 TTTGGACCAAAAACGCCGCTATTACTCAGTTTTTAGTGGCG
* * * * *
17764928 TTTGGAACAAAAACGCCGATA-TAGATAAGTTTTTAGTGGTG
1 TTTGGACCAAAAACGCCGCTATTA-CTCAGTTTTTAGTGGCG
* * * *
17764969 TTTGGACCAGAAACGCCGCTATTGCTCAATTTTTAGAGGCG
1 TTTGGACCAAAAACGCCGCTATTACTCAGTTTTTAGTGGCG
* *
17765010 TTTGGAACAAAAATGCCGCTA-TAGCTCAGTTTTTAGTGGCG
1 TTTGGACCAAAAACGCCGCTATTA-CTCAGTTTTTAGTGGCG
* * ** * *
17765051 TTTGGATCAGAAACGCAACTATTGCTCAGTTTTTGGTGGCG
1 TTTGGACCAAAAACGCCGCTATTACTCAGTTTTTAGTGGCG
* * * *
17765092 TTTGGAACAAAAACGCCGCTATTGCTCAGTTTTTTGCGGCG
1 TTTGGACCAAAAACGCCGCTATTACTCAGTTTTTAGTGGCG
17765133 TTT
1 TTT
17765136 TATTGCAAAT
Statistics
Matches: 261, Mismatches: 60, Indels: 18
0.77 0.18 0.05
Matches are distributed among these distances:
40 40 0.15
41 219 0.84
42 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (41 bp):
TTTGGACCAAAAACGCCGCTATTACTCAGTTTTTAGTGGCG
Found at i:17765119 original size:82 final size:82
Alignment explanation
Indices: 17764765--17765135 Score: 422
Period size: 82 Copynumber: 4.5 Consensus size: 82
17764755 TTTTACGGTA
* * ** * * * *
17764765 TTTGGACCAAAAACGTCGCTATATATCAACTTTTT-GTAGCATTTGGACCAGAAATGCCGCTATT
1 TTTGGAACAAAAACGCCGCTATAGCTC-AGTTTTTAGTGGCGTTTGGACCAGAAACGCCGCTATT
**
17764829 GCTCAGTTTTTAGCAGCG
65 GCTCAGTTTTTAGTGGCG
* ** * * * *
17764847 TTTGGACCAAAAACATCGCTATAGTTTAG-TTTTAGTGGCGTTTGGACCAGAAACGGCGCTATTA
1 TTTGGAACAAAAACGCCGCTATAGCTCAGTTTTTAGTGGCGTTTGGACCAGAAACGCCGCTATTG
* *
17764911 CCCAGTTTTTAGTGGCA
66 CTCAGTTTTTAGTGGCG
* * * *
17764928 TTTGGAACAAAAACGCCGATATAGATAAGTTTTTAGTGGTGTTTGGACCAGAAACGCCGCTATTG
1 TTTGGAACAAAAACGCCGCTATAGCTCAGTTTTTAGTGGCGTTTGGACCAGAAACGCCGCTATTG
* *
17764993 CTCAATTTTTAGAGGCG
66 CTCAGTTTTTAGTGGCG
* * **
17765010 TTTGGAACAAAAATGCCGCTATAGCTCAGTTTTTAGTGGCGTTTGGATCAGAAACGCAACTATTG
1 TTTGGAACAAAAACGCCGCTATAGCTCAGTTTTTAGTGGCGTTTGGACCAGAAACGCCGCTATTG
*
17765075 CTCAGTTTTTGGTGGCG
66 CTCAGTTTTTAGTGGCG
* * *
17765092 TTTGGAACAAAAACGCCGCTATTGCTCAGTTTTTTGCGGCGTTT
1 TTTGGAACAAAAACGCCGCTATAGCTCAGTTTTTAGTGGCGTTT
17765136 TATTGCAAAT
Statistics
Matches: 245, Mismatches: 42, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
80 4 0.02
81 62 0.25
82 179 0.73
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (82 bp):
TTTGGAACAAAAACGCCGCTATAGCTCAGTTTTTAGTGGCGTTTGGACCAGAAACGCCGCTATTG
CTCAGTTTTTAGTGGCG
Found at i:17765485 original size:22 final size:22
Alignment explanation
Indices: 17765447--17765492 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17765437 AATAGAAAAT
*
17765447 AAAGAAAAAAAATGAAAAGTTA
1 AAAGAAAAAAAATGAAAAATTA
*
17765469 AAAGAACATAAAA-GAAAAATTA
1 AAAGAA-AAAAAATGAAAAATTA
17765491 AA
1 AA
17765493 TTGCACAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.74, C:0.02, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAGAAAAAAAATGAAAAATTA
Found at i:17773804 original size:20 final size:20
Alignment explanation
Indices: 17773767--17773805 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17773757 AAGTTACTAA
*
17773767 AACAAAAAATGAATTAAAAT
1 AACAAAAAATGAACTAAAAT
* *
17773787 AACATAAAATGACCTAAAA
1 AACAAAAAATGAACTAAAA
17773806 GCTGTTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.18
Consensus pattern (20 bp):
AACAAAAAATGAACTAAAAT
Found at i:17774861 original size:11 final size:11
Alignment explanation
Indices: 17774847--17774933 Score: 63
Period size: 10 Copynumber: 7.8 Consensus size: 11
17774837 ATAATAAGAT
17774847 TAAAAAATATA
1 TAAAAAATATA
*
17774858 TAAAAAAAATAAA
1 T--AAAAAATATA
* *
17774871 AAAAAAAAATA
1 TAAAAAATATA
17774882 TAAAATATATATA
1 TAAAA-A-ATATA
*
17774895 TAAATAATATA
1 TAAAAAATATA
*
17774906 -AAAAAAAATA
1 TAAAAAATATA
*
17774916 T-AAAAAT-GA
1 TAAAAAATATA
17774925 TAAAAAATA
1 TAAAAAATA
17774934 CAAAAAAACA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
9 2 0.03
10 19 0.33
11 18 0.31
12 2 0.03
13 17 0.29
ACGTcount: A:0.76, C:0.00, G:0.01, T:0.23
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:17774864 original size:13 final size:12
Alignment explanation
Indices: 17774848--17774921 Score: 71
Period size: 13 Copynumber: 6.2 Consensus size: 12
17774838 TAATAAGATT
17774848 AAAAAATATATAA
1 AAAAAATATA-AA
17774861 AAAAAATA-AAA
1 AAAAAATATAAA
* *
17774872 AAAAAAAAT-AT
1 AAAAAATATAAA
* *
17774883 AAAATATATATAT
1 AAAAAATATA-AA
*
17774896 AAATAATATAAA
1 AAAAAATATAAA
17774908 AAAAAATATAAA
1 AAAAAATATAAA
17774920 AA
1 AA
17774922 TGATAAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
11 17 0.34
12 15 0.30
13 18 0.36
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAAATATAAA
Found at i:17774974 original size:11 final size:11
Alignment explanation
Indices: 17774863--17775113 Score: 53
Period size: 10 Copynumber: 22.0 Consensus size: 11
17774853 ATATATAAAA
*
17774863 AAAATAA-AAA
1 AAAATAATAAT
*
17774873 AAAAAAAT-AT
1 AAAATAATAAT
17774883 AAAAT-ATATAT
1 AAAATAATA-AT
17774894 ATAAATAAT-AT
1 A-AAATAATAAT
*
17774905 AAAA-AAAAAT
1 AAAATAATAAT
*
17774915 ATAAA-AATGAT
1 A-AAATAATAAT
17774926 AAAA-AATACA-
1 AAAATAATA-AT
* *
17774936 AAAA-AACAAA
1 AAAATAATAAT
17774946 AAAATGGAA-AAT
1 AAAAT--AATAAT
*
17774958 ATAATAATAAT
1 AAAATAATAAT
17774969 AAAATATATATAT
1 AAAATA-ATA-AT
17774982 AAAATATATACAT
1 AAAATA-ATA-AT
* *
17774995 ACTAATATTTAAT
1 A-AAATA-ATAAT
* *
17775008 ACAATAATAAG
1 AAAATAATAAT
*
17775019 GAAAT-ATAA-
1 AAAATAATAAT
17775028 AAAATACATACAT
1 AAAATA-ATA-AT
* *
17775041 GAAATAGTATAAA
1 AAAATA--ATAAT
17775054 AAAATAATATAT
1 AAAATAATA-AT
17775066 AACTAATAAT-AT
1 AA--AATAATAAT
17775078 ACAATATATATATAT
1 A-AA-ATA-ATA-AT
* *
17775093 GAAATAACAAT
1 AAAATAATAAT
17775104 AAAAT-ATAAT
1 AAAATAATAAT
17775114 GAATAGTATG
Statistics
Matches: 183, Mismatches: 29, Indels: 58
0.68 0.11 0.21
Matches are distributed among these distances:
9 9 0.05
10 44 0.24
11 42 0.23
12 29 0.16
13 39 0.21
14 18 0.10
15 2 0.01
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:17774985 original size:13 final size:14
Alignment explanation
Indices: 17774953--17774991 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 14
17774943 AAAAAAATGG
17774953 AAAATATAATAATAAT
1 AAAATAT-AT-ATAAT
17774969 AAAATATATAT-AT
1 AAAATATATATAAT
17774982 AAAATATATA
1 AAAATATATA
17774992 CATACTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.52
14 2 0.09
15 2 0.09
16 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATATATAAT
Found at i:17775481 original size:14 final size:15
Alignment explanation
Indices: 17775462--17775491 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17775452 ATTTATAACA
17775462 ATAAT-ACTAGAAAT
1 ATAATAACTAGAAAT
17775476 ATAATAACTAGAAAT
1 ATAATAACTAGAAAT
17775491 A
1 A
17775492 ACAATACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
ATAATAACTAGAAAT
Found at i:17790294 original size:30 final size:31
Alignment explanation
Indices: 17790250--17790307 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
17790240 TAAAATGGTC
**
17790250 ATTAAATTATTTAAAAAATTTTATTTAAATT
1 ATTAAATTATTTAAAAAAAATTATTTAAATT
17790281 ATTAAATTA-TTAAAAAAAATTATTTAA
1 ATTAAATTATTTAAAAAAAATTATTTAA
17790308 TATTGGCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTAAATTATTTAAAAAAAATTATTTAAATT
Found at i:17791150 original size:22 final size:22
Alignment explanation
Indices: 17791108--17791150 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
17791098 AAAATGATTT
*
17791108 AACAAATAAATTAATCTATAAA
1 AACAAATAAATTAATCAATAAA
*
17791130 AACAATTATAATTAA-CAATAA
1 AACAAATA-AATTAATCAATAA
17791151 CAATAACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (22 bp):
AACAAATAAATTAATCAATAAA
Done.