Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 19 of 29
Found at i:2856972 original size:33 final size:35
Alignment explanation
Indices: 2856929--2856998 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
2856919 ATCTTTCTCC
2856929 CTTCCTAAAGCCCACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
2856963 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
2856997 CT
1 CT
2856999 AAGCCCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:2856972 original size:104 final size:102
Alignment explanation
Indices: 2856760--2856977 Score: 235
Period size: 104 Copynumber: 2.1 Consensus size: 102
2856750 TTCCCTTTTT
* ** *
2856760 AAAGCCTACAACTCCGTGGCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCC
* * * **
2856825 GTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
66 CTTCTCAAAGCCCACAACTCCGTGGCAC--TCTTCTTCC
* *
2856864 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA-TCTTTCTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTC
* *
2856928 CCTTC-CTAAAGCCCACACAAGTCGGTGGCAAC-CTTCTTCC
65 CCTTCTC-AAAG-CC-CACAACTCCGTGGC-ACTCTTCTTCC
2856968 AAAGCCCACA
1 AAAGCCCACA
2856978 CAAGTCGGTG
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
103 1 0.01
104 50 0.52
105 31 0.32
106 12 0.12
107 2 0.02
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (102 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCC
CTTCTCAAAGCCCACAACTCCGTGGCACTCTTCTTCC
Found at i:2857117 original size:49 final size:49
Alignment explanation
Indices: 2856998--2857601 Score: 756
Period size: 49 Copynumber: 12.7 Consensus size: 49
2856988 GCAACCCTTC
* * *
2856998 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
2857050 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
2857099 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
2857142 TAAGTCCAATATAGCTGGTCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
2857191 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * * * *
2857234 TAAGTCCAATATCGTTGGCCTTAAATCAGCATATTGGCATCATCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
2857283 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
2857332 TAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACC-TCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
2857380 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
2857429 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
2857477 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
2857520 TAAGTCCAATATAGCTGGCGTTGAATCAG--CA-T---ACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTT
* *
2857566 TAAGTTCAATGTAGCTGGTCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
2857602 ACATCCTTTT
Statistics
Matches: 488, Mismatches: 38, Indels: 54
0.84 0.07 0.09
Matches are distributed among these distances:
37 1 0.00
40 1 0.00
41 2 0.00
43 106 0.22
44 1 0.00
45 2 0.00
46 28 0.06
47 2 0.00
48 93 0.19
49 213 0.44
50 2 0.00
52 37 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:2857400 original size:97 final size:97
Alignment explanation
Indices: 2856998--2857601 Score: 748
Period size: 92 Copynumber: 6.4 Consensus size: 97
2856988 GCAACCCTTC
* * *
2856998 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTCCAATGTA
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGTCCAATGTA
* *
2857063 GCTGGCCTTGACTCAGCACATTGGCACCTTTATCTT
63 GCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
*
2857099 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* * *
2857158 GGTCTTGAATCAGCATATTGGCATCTTCATCTT
66 GGCCTTGAATCAGCACATTGGCA-CCTCATCTT
* * *
2857191 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* * *
2857250 GGCCTTAAATCAGCATATTGGCATCATCATCTT
66 GGCCTTGAATCAGCACATTGGCA-CCTCATCTT
*
2857283 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
2857348 GACCTTGAATCAGCACATTGGCACCTCATCTT
66 GGCCTTGAATCAGCACATTGGCACCTCATCTT
*
2857380 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
*
2857445 GGCCTTGAATCAGCACATTGGCACCTCACCTT
66 GGCCTTGAATCAGCACATTGGCACCTCATCTT
*
2857477 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGCT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* * **
2857536 GGCGTTGAATCAGCATACCTT---TTC-CATCTT
66 GGCCTTGAATCAGC--ACATTGGCACCTCATCTT
* *
2857566 TAAGTTCAATGTAGCTGGTCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
2857602 ACATCCTTTT
Statistics
Matches: 461, Mismatches: 33, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
89 39 0.08
90 1 0.00
91 31 0.07
92 169 0.37
93 6 0.01
94 1 0.00
96 1 0.00
97 141 0.31
98 36 0.08
101 36 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (97 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTCATCTT
Found at i:2857752 original size:49 final size:49
Alignment explanation
Indices: 2857680--2857825 Score: 220
Period size: 49 Copynumber: 2.9 Consensus size: 49
2857670 CTTTTCTCAT
*
2857680 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2857729 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCAC
1 CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2857778 CTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 C--TT-CATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
2857826 ACATCCTTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
49 47 0.54
51 2 0.02
52 38 0.44
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2857815 original size:224 final size:214
Alignment explanation
Indices: 2857474--2857953 Score: 662
Period size: 224 Copynumber: 2.2 Consensus size: 214
2857464 GGCACCTCAC
2857474 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTTAAGTCCAATATAGCTGG
* *
2857538 CGTTGAATCAGCATACCTTTTCCATCTTTAAGTTCAATGTAGCTGGTCTTGAATCAGCACATTGA
66 CCTTGAATCAGCATACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGA
*
2857603 CATCCTTTTTCATCATCTTT-AAGCCTAATATCGTTGGTCGTGAATCAACATATTGG-CATCTTT
131 CATCCTTTTTCATCATCTTTAAAGCC-AATATCGTTGGCCGTGAATCAACATATTGGTCAT-TTT
* *
2857666 ATCACTTTTC-TCATCTTCAT
194 ATCACTCTTCATCATCATCAT
* *
2857686 CTTTAAGTCCAATATAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATA
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--C--CTTTAAGTCCAATATA
2857751 GCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAAT
61 GCTGGCCTTGAATCAGC--AT----ACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAAT
* *
2857816 CAGCACATTGACATCCTTTTTCATCATCTTTAAATCCAATATCGTTGGCCGTGAATCAACGTATT
120 CAGCACATTGACATCCTTTTTCATCATCTTTAAAGCCAATATCGTTGGCCGTGAATCAACATATT
* * *
2857881 GGTCCTTTTATCGCTCTTCATCCTCATCAT
185 GGTCATTTTATCACTCTTCATCATCATCAT
* * * * *
2857911 CTTTAAGTCCAGTGTGGCAGGCCTTGAATCTGCACAATGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
2857954 ACTGCAAGAC
Statistics
Matches: 234, Mismatches: 19, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
212 40 0.17
216 1 0.00
218 32 0.14
220 2 0.01
224 110 0.47
225 49 0.21
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (214 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTTAAGTCCAATATAGCTGG
CCTTGAATCAGCATACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGA
CATCCTTTTTCATCATCTTTAAAGCCAATATCGTTGGCCGTGAATCAACATATTGGTCATTTTAT
CACTCTTCATCATCATCAT
Found at i:2858626 original size:13 final size:13
Alignment explanation
Indices: 2858608--2858632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2858598 ATTACTCAAA
2858608 TGTATCGATACAT
1 TGTATCGATACAT
2858621 TGTATCGATACA
1 TGTATCGATACA
2858633 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2858734 original size:52 final size:52
Alignment explanation
Indices: 2858641--2858764 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
2858631 CACTGATCTT
*
2858641 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2858692 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2858744 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
2858765 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 19 0.28
52 50 0.72
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2860928 original size:27 final size:27
Alignment explanation
Indices: 2860890--2860960 Score: 133
Period size: 27 Copynumber: 2.6 Consensus size: 27
2860880 TTTATTCACC
2860890 GGGGACACTCCAACCCCAATCCTCCGA
1 GGGGACACTCCAACCCCAATCCTCCGA
*
2860917 GGGGACACTCCAACCCCAATCTTCCGA
1 GGGGACACTCCAACCCCAATCCTCCGA
2860944 GGGGACACTCCAACCCC
1 GGGGACACTCCAACCCC
2860961 GTTTTCAACC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.25, C:0.44, G:0.20, T:0.11
Consensus pattern (27 bp):
GGGGACACTCCAACCCCAATCCTCCGA
Found at i:2862096 original size:12 final size:12
Alignment explanation
Indices: 2862079--2862112 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2862069 TTTGGCTGAG
*
2862079 ATGTGGTTGATA
1 ATGTGGTTGACA
*
2862091 ATGTGGTTAACA
1 ATGTGGTTGACA
2862103 ATGTGGTTGA
1 ATGTGGTTGA
2862113 AAGAGAAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.38
Consensus pattern (12 bp):
ATGTGGTTGACA
Found at i:2862689 original size:20 final size:20
Alignment explanation
Indices: 2862666--2862718 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2862656 GTTTGGACCT
**
2862666 TGTATCGATACATTCTTGAA
1 TGTATCGATACATTCTAAAA
*
2862686 TGTATCGATACATTGTAAAA
1 TGTATCGATACATTCTAAAA
2862706 TGTATCGATACAT
1 TGTATCGATACAT
2862719 CTAGGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTCTAAAA
Found at i:2862807 original size:180 final size:180
Alignment explanation
Indices: 2862500--2862878 Score: 713
Period size: 180 Copynumber: 2.1 Consensus size: 180
2862490 GTGCAAATTG
*
2862500 CTTGCATGTATCGATACATTGCAAAATGTATCGATACATCTAGGTAAAAACCCAAAATGTATCGA
1 CTTGAATGTATCGATACATTGCAAAATGTATCGATACATCTAGGTAAAAACCCAAAATGTATCGA
2862565 TACAAAGAAAATTTATTAATACATTCACTTATGTATCAATACATTTACTGTTCATATCGATACAA
66 TACAAAGAAAATTTATTAATACATTCACTTATGTATCAATACATTTACTGTTCATATCGATACAA
*
2862630 ATTGTAAAAATTTAAGATTTTCGATCGTTTGGACCTTGTATCGATACATT
131 ATTGTAAAAATTTAAGATTTTCGATCGTTGGGACCTTGTATCGATACATT
*
2862680 CTTGAATGTATCGATACATTGTAAAATGTATCGATACATCTAGGTAAAAACCCAAAATGTATCGA
1 CTTGAATGTATCGATACATTGCAAAATGTATCGATACATCTAGGTAAAAACCCAAAATGTATCGA
*
2862745 TACAAAGAAAATTTATTGATACATTCACTTATGTATCAATACATTTACTGTTCATATCGATACAA
66 TACAAAGAAAATTTATTAATACATTCACTTATGTATCAATACATTTACTGTTCATATCGATACAA
*
2862810 ATTGTAAAAATTTAAGATTTTCGATTGTTGGGACCTTGTATCGATACATT
131 ATTGTAAAAATTTAAGATTTTCGATCGTTGGGACCTTGTATCGATACATT
2862860 CTTGAATGTATCGATACAT
1 CTTGAATGTATCGATACAT
2862879 CTGGACAAAA
Statistics
Matches: 194, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 194 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (180 bp):
CTTGAATGTATCGATACATTGCAAAATGTATCGATACATCTAGGTAAAAACCCAAAATGTATCGA
TACAAAGAAAATTTATTAATACATTCACTTATGTATCAATACATTTACTGTTCATATCGATACAA
ATTGTAAAAATTTAAGATTTTCGATCGTTGGGACCTTGTATCGATACATT
Found at i:2862869 original size:90 final size:90
Alignment explanation
Indices: 2862595--2862878 Score: 263
Period size: 90 Copynumber: 3.2 Consensus size: 90
2862585 ACATTCACTT
* *
2862595 ATGTATCAATACATTTACTGTTCATATCGATACAAATTGTAAAAATTTAAGATTTTCGATCGTTT
1 ATGTATCAATACATTTACTGTTCATATCGATACAAATTGTAAAAATTTAAGATTTTCGATAGTTA
2862660 GGACCTTGTATCGATACATTCTTGA
66 GGACCTTGTATCGATACATTCTTGA
* *** * ** * *** * * *
2862685 ATGTATCGATACATTGTA-AAAT-GTATCGATACATCTAGGTAAAAACCCAAAATGTATCGATAC
1 ATGTATCAATACATT-TACTGTTCATATCGATACAAAT-TGTAAAAATTTAAGAT-TTTCGATAG
** * ** *
2862748 AAAGAAAATT-TATTGATACATTCACTT--
63 TTAGGACCTTGTATCGATACATT--CTTGA
* *
2862775 ATGTATCAATACATTTACTGTTCATATCGATACAAATTGTAAAAATTTAAGATTTTCGATTGTTG
1 ATGTATCAATACATTTACTGTTCATATCGATACAAATTGTAAAAATTTAAGATTTTCGATAGTTA
2862840 GGACCTTGTATCGATACATTCTTGA
66 GGACCTTGTATCGATACATTCTTGA
*
2862865 ATGTATCGATACAT
1 ATGTATCAATACAT
2862879 CTGGACAAAA
Statistics
Matches: 139, Mismatches: 45, Indels: 20
0.68 0.22 0.10
Matches are distributed among these distances:
88 3 0.02
89 23 0.17
90 87 0.63
91 23 0.17
92 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (90 bp):
ATGTATCAATACATTTACTGTTCATATCGATACAAATTGTAAAAATTTAAGATTTTCGATAGTTA
GGACCTTGTATCGATACATTCTTGA
Found at i:2865140 original size:21 final size:21
Alignment explanation
Indices: 2865097--2865140 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2865087 GATGCATTGG
* **
2865097 TTGGATGAAAGAATACATTTT
1 TTGGATGAAAAAATACAACTT
*
2865118 TTGGATGAAAAAATGCAACTT
1 TTGGATGAAAAAATACAACTT
2865139 TT
1 TT
2865141 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
TTGGATGAAAAAATACAACTT
Found at i:2868302 original size:13 final size:13
Alignment explanation
Indices: 2868284--2868309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2868274 AATTTTTTTG
2868284 TGTATCGATACAT
1 TGTATCGATACAT
2868297 TGTATCGATACAT
1 TGTATCGATACAT
2868310 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2872967 original size:15 final size:16
Alignment explanation
Indices: 2872942--2872976 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2872932 ATCAATTTCG
*
2872942 TTTGTAGCTTCTTCAT
1 TTTGTAGCTTCCTCAT
2872958 TTTG-AGCTTCCTCAT
1 TTTGTAGCTTCCTCAT
2872973 TTTG
1 TTTG
2872977 GACATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.54
Consensus pattern (16 bp):
TTTGTAGCTTCCTCAT
Found at i:2874808 original size:21 final size:21
Alignment explanation
Indices: 2874779--2874823 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2874769 AAGTTTTCAT
*
2874779 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2874799 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2874821 TTT
1 TTT
2874824 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2881138 original size:11 final size:10
Alignment explanation
Indices: 2881119--2881156 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
2881109 AATATCGATC
2881119 TTTTTTTCCT
1 TTTTTTTCCT
2881129 TTTTTCTTCCT
1 TTTTT-TTCCT
*
2881140 TTTTTTTTCT
1 TTTTTTTCCT
2881150 TTTTTTT
1 TTTTTTT
2881157 TTCTTTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTCCT
Found at i:2881144 original size:22 final size:21
Alignment explanation
Indices: 2881119--2881163 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2881109 AATATCGATC
*
2881119 TTTTTTTCCTTTTTTCTTCCT
1 TTTTTTTTCTTTTTTCTTCCT
* *
2881140 TTTTTTTTCTTTTTTTTTTCT
1 TTTTTTTTCTTTTTTCTTCCT
2881161 TTT
1 TTT
2881164 CATCTCGACA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTCTTCCT
Found at i:2881157 original size:11 final size:11
Alignment explanation
Indices: 2881119--2881163 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
2881109 AATATCGATC
2881119 TTTTTTTCCTT
1 TTTTTTTCCTT
*
2881130 TTTTCTTCCTT
1 TTTTTTTCCTT
2881141 TTTTTTT-CTT
1 TTTTTTTCCTT
*
2881151 TTTTTTTTCTT
1 TTTTTTTCCTT
2881162 TT
1 TT
2881164 CATCTCGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCCTT
Found at i:2884246 original size:20 final size:20
Alignment explanation
Indices: 2884232--2884271 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2884222 ATTTATATAT
2884232 TAAT-ATTATTTTTTAAATA
1 TAATAATTATTTTTTAAATA
* *
2884251 TAATAATTATATTTAAAATA
1 TAATAATTATTTTTTAAATA
2884271 T
1 T
2884272 TATATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATAATTATTTTTTAAATA
Found at i:2884289 original size:34 final size:32
Alignment explanation
Indices: 2884233--2884296 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 32
2884223 TTTATATATT
2884233 AATATTATTTTTTAAATATAATAATTATATTTAA
1 AATATTATTTTTTAAATATAAT-A-TATATTTAA
**
2884267 AATATTATATTTTTATGT-TAATATATATTT
1 AATATTAT-TTTTTAAATATAATATATATTT
2884297 TATTCTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 7 0.26
33 1 0.04
34 12 0.44
35 7 0.26
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
AATATTATTTTTTAAATATAATATATATTTAA
Found at i:2884585 original size:22 final size:24
Alignment explanation
Indices: 2884549--2884593 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
2884539 AAATAAAAAA
*
2884549 TTAATAAAATAAAATTTTTATAAG
1 TTAATAAAATAAAATTTTAATAAG
2884573 TTAA-AAAAT-AAATTTTAATAA
1 TTAATAAAATAAAATTTTAATAA
2884594 AATAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TTAATAAAATAAAATTTTAATAAG
Found at i:2886182 original size:18 final size:17
Alignment explanation
Indices: 2886149--2886201 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
2886139 AATATTCAAT
2886149 GATAAGAAGCTTGCTAG
1 GATAAGAAGCTTGCTAG
2886166 GATAAGAAGCTTTGCTAG
1 GATAAGAAGC-TTGCTAG
2886184 GATAAGAAGCTTGCTAG
1 GATAAGAAGCTTGCTAG
2886201 G
1 G
2886202 TAGGGAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 18 0.51
18 17 0.49
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (17 bp):
GATAAGAAGCTTGCTAG
Found at i:2896915 original size:2 final size:2
Alignment explanation
Indices: 2896908--2896939 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2896898 TTCAGTTCGG
2896908 AT AT 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 AT AT
2896940 TAATTCTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2898234 original size:3 final size:3
Alignment explanation
Indices: 2898228--2898258 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2898218 ATCAACAACT
2898228 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2898259 ATACAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2899068 original size:2 final size:2
Alignment explanation
Indices: 2899063--2899098 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2899053 TAAGAGGGGC
2899063 AT AT AT AT 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 AT AT AT AT
2899099 GTATTGTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2899285 original size:21 final size:22
Alignment explanation
Indices: 2899239--2899286 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
2899229 AATTTTTTAT
*
2899239 ATTATTAAATTTTAATAAATTG
1 ATTATTAAATTTTAATAAATTA
2899261 ATTATTAAA-TTTAAT-AATATA
1 ATTATTAAATTTTAATAAAT-TA
2899282 ATTAT
1 ATTAT
2899287 ATTTGTTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 12 0.50
22 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATTAAATTTTAATAAATTA
Found at i:2900152 original size:27 final size:28
Alignment explanation
Indices: 2900114--2900170 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 28
2900104 TAAATTAATG
2900114 AATAATAAATAT-AAATAAATAACAAAA
1 AATAATAAATATGAAATAAATAACAAAA
* *
2900141 AATAA-AATATATGGAACTATATAACAAAA
1 AATAATAA-ATAT-GAAATAAATAACAAAA
2900170 A
1 A
2900171 TACGGTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 2 0.08
27 9 0.36
29 14 0.56
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.23
Consensus pattern (28 bp):
AATAATAAATATGAAATAAATAACAAAA
Found at i:2901274 original size:25 final size:25
Alignment explanation
Indices: 2901246--2901328 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
2901236 TTGTTATGAC
2901246 TTAATTAACTTTCCATTTATATAAT
1 TTAATTAACTTTCCATTTATATAAT
* * * * * *
2901271 TTAATCATCTAAAATCAATTGT-TATGAC
1 TTAATTAACT---TTCCATT-TATATAAT
2901299 TTAATTAACTTTCCATTTATATAAT
1 TTAATTAACTTTCCATTTATATAAT
2901324 TTAAT
1 TTAAT
2901329 CACAGTAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 1 0.02
25 22 0.54
28 17 0.41
29 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.48
Consensus pattern (25 bp):
TTAATTAACTTTCCATTTATATAAT
Found at i:2901295 original size:53 final size:53
Alignment explanation
Indices: 2901224--2901330 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
2901214 AATTTCTCTT
2901224 ATCTAAAATCAATTGTTATGACTTAATTAACTTTCCATTTATATAATTTAATC
1 ATCTAAAATCAATTGTTATGACTTAATTAACTTTCCATTTATATAATTTAATC
2901277 ATCTAAAATCAATTGTTATGACTTAATTAACTTTCCATTTATATAATTTAATC
1 ATCTAAAATCAATTGTTATGACTTAATTAACTTTCCATTTATATAATTTAATC
2901330 A
1 A
2901331 CAGTAAATTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.45
Consensus pattern (53 bp):
ATCTAAAATCAATTGTTATGACTTAATTAACTTTCCATTTATATAATTTAATC
Found at i:2902045 original size:2 final size:2
Alignment explanation
Indices: 2902038--2902067 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2902028 ATTCATTTTA
2902038 AT 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 AT
2902068 GGGATTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2903434 original size:15 final size:15
Alignment explanation
Indices: 2903414--2903442 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2903404 GATACTTTAT
2903414 AAAAAGAAGAAAAAA
1 AAAAAGAAGAAAAAA
2903429 AAAAAGAAGAAAAA
1 AAAAAGAAGAAAAA
2903443 GCATTCGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAAAAA
Found at i:2904706 original size:28 final size:28
Alignment explanation
Indices: 2904666--2904720 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2904656 CAAATACCAC
* *
2904666 CCTTTGTATTTATTAAATATGGTGGTTT
1 CCTTTATATTTATCAAATATGGTGGTTT
2904694 CCTTTATATTTATCAAATATGGTGGTT
1 CCTTTATATTTATCAAATATGGTGGTT
2904721 ATTTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (28 bp):
CCTTTATATTTATCAAATATGGTGGTTT
Found at i:2904754 original size:24 final size:24
Alignment explanation
Indices: 2904725--2904770 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2904715 GTGGTTATTT
2904725 TTGTTTGTAAAAATTGGTGGCTTG
1 TTGTTTGTAAAAATTGGTGGCTTG
*
2904749 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAATTGGTGGCT
2904771 AATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAATTGGTGGCTTG
Found at i:2909264 original size:28 final size:28
Alignment explanation
Indices: 2909232--2909286 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
2909222 CAAATGCCAC
*
2909232 CCTTTGTATTTGTCAAATATGGTGGTTT
1 CCTTTATATTTGTCAAATATGGTGGTTT
2909260 CCTTTATATTTGTCAAATATGGTGGTT
1 CCTTTATATTTGTCAAATATGGTGGTT
2909287 ATTTTTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (28 bp):
CCTTTATATTTGTCAAATATGGTGGTTT
Found at i:2909327 original size:24 final size:24
Alignment explanation
Indices: 2909291--2909336 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2909281 GTGGTTATTT
2909291 TTGTTTGTAAAAATTGGTGGCTTG
1 TTGTTTGTAAAAATTGGTGGCTTG
*
2909315 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTGTAAAAATTGGTGGCT
2909337 AATTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAATTGGTGGCTTG
Found at i:2911205 original size:15 final size:15
Alignment explanation
Indices: 2911185--2911214 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2911175 ACTTTAGGCA
2911185 ATAAGATTGATATTT
1 ATAAGATTGATATTT
2911200 ATAAGATTGATATTT
1 ATAAGATTGATATTT
2911215 TATAGTTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
ATAAGATTGATATTT
Found at i:2912098 original size:2 final size:2
Alignment explanation
Indices: 2912091--2912120 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2912081 ATTAAAATAC
2912091 AT 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 AT
2912121 TTCACCTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2912403 original size:19 final size:20
Alignment explanation
Indices: 2912376--2912413 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2912366 TAATATTATA
2912376 ATTAGATAATT-ATTGATTG
1 ATTAGATAATTAATTGATTG
*
2912395 ATTATATAATTAATTGATT
1 ATTAGATAATTAATTGATT
2912414 ATATCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTAGATAATTAATTGATTG
Found at i:2913819 original size:8 final size:8
Alignment explanation
Indices: 2913806--2913838 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
2913796 GAAAATTATG
2913806 AAAAAAAT
1 AAAAAAAT
2913814 AAAAAAAT
1 AAAAAAAT
2913822 AAAAAAAT
1 AAAAAAAT
2913830 AAAAAAAT
1 AAAAAAAT
2913838 A
1 A
2913839 CAAACAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:2914338 original size:20 final size:20
Alignment explanation
Indices: 2914313--2914352 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2914303 CCATCGGTGA
2914313 TCGACGA-CTGACGGTGGTCG
1 TCGACGATC-GACGGTGGTCG
*
2914333 TCGACGATCGGCGGTGGTCG
1 TCGACGATCGACGGTGGTCG
2914353 CCGGTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.12, C:0.25, G:0.42, T:0.20
Consensus pattern (20 bp):
TCGACGATCGACGGTGGTCG
Found at i:2916145 original size:27 final size:27
Alignment explanation
Indices: 2916115--2916183 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
2916105 TTTATTCATC
2916115 GGGGATACTCCAACTC-CATTATTCCGA
1 GGGGATACTCCAAC-CACATTATTCCGA
* * *
2916142 GGGGATACTCTAACCATATTCTTCCGA
1 GGGGATACTCCAACCACATTATTCCGA
* *
2916169 GAGGATACTCTAACC
1 GGGGATACTCCAACC
2916184 CCGCTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (27 bp):
GGGGATACTCCAACCACATTATTCCGA
Found at i:2918772 original size:13 final size:13
Alignment explanation
Indices: 2918754--2918783 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2918744 ATACATTGTT
2918754 CATTGTATCAATA
1 CATTGTATCAATA
*
2918767 CATTGTATCGATA
1 CATTGTATCAATA
2918780 CATT
1 CATT
2918784 CGGGTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:2918798 original size:62 final size:63
Alignment explanation
Indices: 2918704--2918832 Score: 215
Period size: 62 Copynumber: 2.1 Consensus size: 63
2918694 ATACATTGTT
*
2918704 CATTATATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTTCATTGTATCAATA
1 CATTATATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTTCAATGTATCAATA
* * *
2918767 CATTGTATCGATACATTC-GGGTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
1 CATTATATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTTCAATGTATCAATA
2918829 CATT
1 CATT
2918833 CAGGCATTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 45 0.73
63 17 0.27
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (63 bp):
CATTATATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTGTTCAATGTATCAATA
Found at i:2920489 original size:19 final size:19
Alignment explanation
Indices: 2920465--2920532 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2920455 AATTCAACGA
2920465 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2920484 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2920499 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2920516 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2920533 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2920503 original size:32 final size:32
Alignment explanation
Indices: 2920467--2920529 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2920457 TTCAACGATT
*
2920467 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2920499 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2920530 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2920504 original size:13 final size:13
Alignment explanation
Indices: 2920486--2920510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2920476 ACATAAGTTT
2920486 TGTATCGATACAA
1 TGTATCGATACAA
2920499 TGTATCGATACA
1 TGTATCGATACA
2920511 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2920590 original size:13 final size:13
Alignment explanation
Indices: 2920572--2920597 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2920562 CATTTTTCTG
2920572 TGTATCGATACAT
1 TGTATCGATACAT
2920585 TGTATCGATACAT
1 TGTATCGATACAT
2920598 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2920594 original size:33 final size:33
Alignment explanation
Indices: 2920552--2920618 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2920542 GCCAAGGAAA
***
2920552 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2920585 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2920618 T
1 T
2920619 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2923022 original size:51 final size:53
Alignment explanation
Indices: 2922958--2923299 Score: 178
Period size: 52 Copynumber: 6.5 Consensus size: 53
2922948 AGTTTCTCAA
* * * *
2922958 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
2923009 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
2923063 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
2923121 TAT-TTC-CAA--GGGGATACTCCAACCCCGGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * * * *
2923170 ATT-TCCTCAATCGGGGATACTCCAA-TCCCGGTTTTATTTTC-AAAACGCCAATT
1 -TTCTTCACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAA-T
* * * *
2923223 TTCCTT--TAATCGGGGATATTCCAACTCCGATTCTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
2923275 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
2923300 CTCGTTATTT
Statistics
Matches: 223, Mismatches: 39, Indels: 57
0.70 0.12 0.18
Matches are distributed among these distances:
49 4 0.02
50 8 0.04
51 33 0.15
52 82 0.37
53 29 0.13
54 34 0.15
55 21 0.09
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:2923102 original size:27 final size:29
Alignment explanation
Indices: 2923072--2923147 Score: 113
Period size: 27 Copynumber: 2.7 Consensus size: 29
2923062 TTTCTTCACA
2923072 ATCGGGGATACTCCAACCCCGTTA-AT-C
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
2923099 ATCGGGGATACTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
2923128 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2923148 GTTTTATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.53
28 19 0.42
29 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATATCC
Found at i:2923319 original size:28 final size:28
Alignment explanation
Indices: 2923283--2923359 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
2923273 ATTTTTCACA
* * *
2923283 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2923311 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
*** *
2923339 CGAGGGGATACTCCAATCCCG
1 ATCGGGGATACTCCAACCCCG
2923360 ATTTTTTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2923332 original size:212 final size:212
Alignment explanation
Indices: 2922965--2923364 Score: 608
Period size: 212 Copynumber: 1.9 Consensus size: 212
2922955 CAATTCTCCA
* *
2922965 CAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
* * *
2923030 CTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCGTT
66 CCAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTT
* *
2923095 AATCATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATCGCTA
131 AATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGATTTTATCGCTA
2923160 AAACACTAATATTTCCT
196 AAACACTAATATTTCCT
* * *
2923177 CAATCGGGGATACTCCAA-TCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGATA
1 CAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATA
* * *
2923241 TTCCAACTCCGATTCTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCG
64 CTCCAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
* * *
2923304 TTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAATCCCGATTTT
129 TTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGATTTT
2923365 TTTTTCTTCT
Statistics
Matches: 169, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
211 29 0.17
212 107 0.63
213 33 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTT
AATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGATTTTATCGCTA
AAACACTAATATTTCCT
Found at i:2935865 original size:15 final size:14
Alignment explanation
Indices: 2935840--2935879 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
2935830 ACCTTCTCTT
*
2935840 CAAAAAAAAAAGAG
1 CAAAAAAAAAAAAG
2935854 CAAAAAAGAAAAAAG
1 CAAAAAA-AAAAAAG
2935869 CAAAAAAAAAA
1 CAAAAAAAAAA
2935880 CAAAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.82, C:0.07, G:0.10, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAG
Found at i:2935876 original size:11 final size:11
Alignment explanation
Indices: 2935857--2935901 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 11
2935847 AAAAGAGCAA
2935857 AAAAGAAAAAAGC
1 AAAA-AAAAAA-C
2935870 AAAAAAAAAAC
1 AAAAAAAAAAC
2935881 AAAAAACAAAAC
1 AAAAAA-AAAAC
2935893 AAAGAAAAA
1 AAA-AAAAA
2935902 GAGAGAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.23
12 16 0.53
13 7 0.23
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:2936969 original size:55 final size:55
Alignment explanation
Indices: 2936885--2937910 Score: 1305
Period size: 55 Copynumber: 18.3 Consensus size: 55
2936875 TCCGCTTTTT
* *
2936885 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2936940 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
2936995 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
2937049 TAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2937105 AGTCCTCAAAGAGCTAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGC-AGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
2937161 AGTCC-CTGAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTC-AAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
2937216 AGTCCTTAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * ** *
2937271 AATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** *
2937326 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
2937387 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGTA--TTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* * * **
2937441 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCATACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** * *
2937496 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* **
2937557 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * **
2937612 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
** *
2937667 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
2937728 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2937783 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
2937838 AGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
2937893 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
2937911 TACACTTTAT
Statistics
Matches: 871, Mismatches: 67, Indels: 66
0.87 0.07 0.07
Matches are distributed among these distances:
53 3 0.00
54 52 0.06
55 596 0.68
56 70 0.08
57 3 0.00
59 3 0.00
60 15 0.02
61 129 0.15
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:2937419 original size:171 final size:171
Alignment explanation
Indices: 2936885--2937855 Score: 1440
Period size: 171 Copynumber: 5.7 Consensus size: 171
2936875 TCCGCTTTTT
* *
2936885 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
2936950 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATG
* * *
2937013 C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
131 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
2937049 TAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCCAGTCCTCAA
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* ** *
2937114 AGAGCTAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC-CTGAAGAGCAGG
65 AGAGC-AGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTC-AAAGAGCAGG
** *
2937178 A--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCC
128 ATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
2937216 AGTCCTTAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
* * *
2937281 GAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGATG
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATG
2937346 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
131 CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2937387 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGTA--TTTCCAGTCCTCA
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCA
* * *
2937449 AAGAGCAGGACACCTTTTAAAGCCCATACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA
64 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA
*
2937514 TGCTTTTTCTTTTCAAAGCCCACACAGGTTGGTGGCACCTTTC
129 TGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* **
2937557 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* *
2937621 AGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGAT
65 AGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGAT
2937686 GCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
130 GCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
2937728 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
**
2937793 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA
2937856 CGCCTCTTAA
Statistics
Matches: 751, Mismatches: 38, Indels: 28
0.92 0.05 0.03
Matches are distributed among these distances:
165 120 0.16
166 146 0.19
167 6 0.01
169 3 0.00
170 167 0.22
171 301 0.40
172 8 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (171 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATG
CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:2938729 original size:19 final size:19
Alignment explanation
Indices: 2938705--2938772 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
2938695 AATTCAACGA
2938705 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2938724 TTTGTATCAATAC--AA--
1 TTTGTATCGATACATAAGT
2938739 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2938756 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2938773 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2938743 original size:32 final size:32
Alignment explanation
Indices: 2938707--2938769 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
2938697 TTCAACGATT
*
2938707 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTATTGTATCAATACAA
*
2938739 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCAATACA
2938770 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCAATACAA
Found at i:2938830 original size:13 final size:13
Alignment explanation
Indices: 2938812--2938837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2938802 CATTTTTCTG
2938812 TGTATCGATACAT
1 TGTATCGATACAT
2938825 TGTATCGATACAT
1 TGTATCGATACAT
2938838 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2938834 original size:33 final size:33
Alignment explanation
Indices: 2938792--2938858 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2938782 GCCAAGGAAA
***
2938792 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2938825 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2938858 T
1 T
2938859 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:2941262 original size:51 final size:53
Alignment explanation
Indices: 2941198--2941539 Score: 178
Period size: 52 Copynumber: 6.5 Consensus size: 53
2941188 AGTTTCTCAA
* * * *
2941198 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
2941249 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
2941303 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * *
2941361 TAT-TTC-CGA--GGGGATACTCCAAC-CCCAGTTTTA--TCGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGA-TTTTATTTC-CAAAAACACCAAT
* * * *
2941410 ATT-TCCTCAATCGGGGATACTCCAA-TCCCGATTTTATTTTC-AAAACGCCAAT
1 -TTCTTCACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAAT
** * * *
2941462 TT-TTCTTTAATCGGGGATATTCCAACTCCGATTCTATTTCCAAAAATACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
2941515 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
2941540 CTCGTTATTT
Statistics
Matches: 222, Mismatches: 42, Indels: 53
0.70 0.13 0.17
Matches are distributed among these distances:
49 4 0.02
50 5 0.02
51 37 0.17
52 76 0.34
53 37 0.17
54 35 0.16
55 17 0.08
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:2941342 original size:27 final size:28
Alignment explanation
Indices: 2941312--2941395 Score: 107
Period size: 27 Copynumber: 3.0 Consensus size: 28
2941302 TTTCTTCACA
2941312 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
2941339 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*** *
2941367 CGAGGGGATACTCCAACCCCAGTTTTATC
1 ATCGGGGATACTCCAACCCC-GTTATATC
2941396 GCTAAAACAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
27 24 0.49
28 19 0.39
29 6 0.12
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:2941559 original size:28 final size:28
Alignment explanation
Indices: 2941523--2941594 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
2941513 ATTTTTCACA
* * *
2941523 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2941551 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2941579 CGAGGGGATACTCCAA
1 ATCGGGGATACTCCAA
2941595 TCCTGATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2941572 original size:212 final size:212
Alignment explanation
Indices: 2941205--2941594 Score: 624
Period size: 212 Copynumber: 1.8 Consensus size: 212
2941195 CAATTCTCCA
* *
2941205 CAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
* * *
2941270 CTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCGTT
66 CCAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTT
*
2941335 AATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATCGCTA
131 AATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCAGTTTTATCGCTA
2941400 AAACACTAATATTTCCT
196 AAACACTAATATTTCCT
* *
2941417 CAATCGGGGATACTCCAA-TCCCGATTTTATTTTCAAAACGCCAATTTTTCTTTAATCGGGGATA
1 CAATCGGGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAA-TTTTCTATAATCGGGGATA
* * *
2941481 TTCCAACTCCGATTCTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCG
64 CTCCAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
*
2941544 TTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAA
129 TTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAA
2941595 TCCTGATTTT
Statistics
Matches: 163, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 29 0.18
212 97 0.60
213 37 0.23
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTCTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCGTT
AATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCAGTTTTATCGCTA
AAACACTAATATTTCCT
Found at i:2943723 original size:51 final size:51
Alignment explanation
Indices: 2943647--2943766 Score: 132
Period size: 51 Copynumber: 2.4 Consensus size: 51
2943637 TTATTTTCGA
* * * * * * **
2943647 GGGGATACTCCTACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATT
1 GGGGATACTCCAACCCTGACTTTATTTCTAAAACACTAATTTCTCACAAGC
* * *
2943698 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACTAATTTTTCATAAGC
1 GGGGATACTCCAACCCTGACTTTATTTCTAAAACACTAATTTCTCACAAGC
*
2943749 GAGGATACTCCAACCCTG
1 GGGGATACTCCAACCCTG
2943767 TTATTTTCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGACTTTATTTCTAAAACACTAATTTCTCACAAGC
Found at i:2943819 original size:130 final size:130
Alignment explanation
Indices: 2943568--2943822 Score: 324
Period size: 130 Copynumber: 2.0 Consensus size: 130
2943558 TTTTCATCTC
* * * *
2943568 GGGGATACTCCAACCCCGGTTTTATTTCCAAGACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCATAAGCGAGGATACTCCAAT
* * **
2943633 CCCGTTATTTTCGAGGGGATACTCCTACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATT
66 CCCGTTATTTTCGAGGGGATACTCCTACCCCGGCTTTATCTCCAAAATATAAATTTCTCACAATT
* *
2943698 GGGGATACTCCAACCCTGATTTTATTTCTAAAACA-CTAATTTTTCATAAGCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACATC-AATTTTTCATAAGCGAGGATACTCCAA
2943762 -CCCTGTTATTTTCGA-GGGATACTCC-AGCCCC-G-TTGTCATCTCCAAAATATCAAATTTCTC
65 TCCC-GTTATTTTCGAGGGGATACTCCTA-CCCCGGCTT-T-ATCTCCAAAATAT-AAATTTCTC
2943822 A
125 A
2943823 TCGGGAGATG
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
127 2 0.02
128 3 0.03
129 29 0.27
130 75 0.69
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (130 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTTCATAAGCGAGGATACTCCAAT
CCCGTTATTTTCGAGGGGATACTCCTACCCCGGCTTTATCTCCAAAATATAAATTTCTCACAATT
Found at i:2954775 original size:51 final size:52
Alignment explanation
Indices: 2954699--2954826 Score: 231
Period size: 51 Copynumber: 2.5 Consensus size: 52
2954689 CGAAATATGA
2954699 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGG-
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
2954750 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
2954802 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
2954827 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
51 50 0.68
52 24 0.32
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:2954837 original size:52 final size:50
Alignment explanation
Indices: 2954699--2954846 Score: 217
Period size: 51 Copynumber: 2.9 Consensus size: 50
2954689 CGAAATATGA
2954699 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGG
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGG
*
2954750 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGG
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGG
* *
2954801 CAAATTTGCCTACATGTATCGATACA-AAGATCAGTGTATCGATACA
1 -AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
2954847 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
51 52 0.58
52 38 0.42
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (50 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGG
Found at i:2954853 original size:13 final size:13
Alignment explanation
Indices: 2954835--2954859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2954825 CAAAGATCAG
2954835 TGTATCGATACAA
1 TGTATCGATACAA
2954848 TGTATCGATACA
1 TGTATCGATACA
2954860 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2954939 original size:13 final size:13
Alignment explanation
Indices: 2954921--2954945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2954911 ACAAAACTTA
2954921 TGTATCGATACAT
1 TGTATCGATACAT
2954934 TGTATCGATACA
1 TGTATCGATACA
2954946 ATACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2954941 original size:32 final size:33
Alignment explanation
Indices: 2954900--2954965 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
2954890 AGTAGCTTAA
2954900 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
2954932 ATTGTATCGATACAATACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
2954965 A
1 A
2954966 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:2960726 original size:63 final size:62
Alignment explanation
Indices: 2960553--2960956 Score: 476
Period size: 61 Copynumber: 6.5 Consensus size: 62
2960543 CACCCTTGAA
* * * * *
2960553 TCCTTAAATAGTAAGATGCCTTATTCTTTTCAAAGCCCACACAAGTTGGTGGGA-CTCTTTAG
1 TCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT-TTTAG
* *
2960615 TCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTTGAG
1 TCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT-AG
* * * * *
2960676 TCCTTAAAGAGTATGACGCCTTTTTTCTTTTCAAGGCCCACACAAGTTGGTGGCACCCTTTAG
1 TCCTCAAAGAGTAGGATGCC-TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAG
* * * * *
2960739 TCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGCTAGTGGCACCCTTTAG
1 TCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAG
* * *
2960800 TCGTCAAAGAGTAGGATGCCTTTTTCTTTTCGAAGCCCACACAAGTTGGTGACACCTTTCTAG
1 TCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-TAG
* * * * *
2960863 TCCTCAAAGAGTAGGACGCTTTTTTTCTTTTCAAAGCCCACACAAGTTGCTAGCACCTCTTAG
1 TCCTCAAAGAGTAGGATGC-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAG
*
2960926 TCCTCAAAGA-TCAGGATGCTTTTTTTCTTTT
1 TCCTCAAAGAGT-AGGATGC-CTTTTTCTTTT
2960957 TTCCTTTGTC
Statistics
Matches: 295, Mismatches: 39, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
60 3 0.01
61 97 0.33
62 66 0.22
63 91 0.31
64 38 0.13
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (62 bp):
TCCTCAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTTAG
Found at i:2960809 original size:124 final size:122
Alignment explanation
Indices: 2960543--2960935 Score: 459
Period size: 124 Copynumber: 3.2 Consensus size: 122
2960533 TTTTTCCTTT
* * * * * * * *
2960543 CACCCTTGAATCCTTAAATAGTAAGATGCCTTATTCTTTTCAAAGCCCACACAAGTTGGTGGGAC
1 CACCTTTGAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTC-AAGCCCACACAAGTTGGTGGCAC
* * *
2960608 TCTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGG
65 CCTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGCTAGTGG
* * *
2960666 CACTTTTGAGTCCTTAAAGAGTATGACGCCTTTTTTCTTTTCAAGGCCCACACAAGTTGGTGGCA
1 CACCTTTGAGTCCTCAAAGAGTAGGACGCC-TTTTTCTTTTCAA-GCCCACACAAGTTGGTGGCA
2960731 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGCTAGTGG
64 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGCTAGTGG
* * *
2960790 CACCCTTT-AGTCGTCAAAGAGTAGGATGCCTTTTTCTTTTCGAAGCCCACACAAGTTGGTGACA
1 CA-CCTTTGAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTC-AAGCCCACACAAGTTGGTGGCA
* * * * * * *
2960854 CCTTTCTAGTCCTCAAAGAGTAGGACGCTTTTTTTCTTTTCAAAGCCCACACAAG-TTGCTAG
64 CCCTT-TAGTCCTCAAAGAGCAGGATGC-CTTTTCCTTTT-AAAGCCCACACAAGCTAG-TGG
2960916 CACCTCTT-AGTCCTCAAAGA
1 CACCT-TTGAGTCCTCAAAGA
2960936 TCAGGATGCT
Statistics
Matches: 236, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
123 60 0.25
124 127 0.54
125 18 0.08
126 31 0.13
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (122 bp):
CACCTTTGAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTCAAGCCCACACAAGTTGGTGGCACC
CTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGCTAGTGG
Found at i:2961087 original size:41 final size:41
Alignment explanation
Indices: 2960949--2961187 Score: 171
Period size: 41 Copynumber: 5.7 Consensus size: 41
2960939 GGATGCTTTT
* * *
2960949 TTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCA
1 TTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCA
* * *
2960990 TTTCCTTCTTTTCCCTTCCAGTTCTCAAAGAGTAGGATGCAC-TTT-A
1 TTTCC-T-TTTT-CCTT--TGTCCTCAAAGAGCAGGA--CACATTTCA
* * *
2961036 TTCTCC-TTTTCCTTTGTCCTCAAAAAGCAGGGCACATTTAA
1 TT-TCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCA
* * * * ** *
2961077 TTTCCTTTTTCCTTTGTCTTTAAAGGGCATGATGCATTTTA
1 TTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCA
* * *
2961118 TTTCCTTTTTTCCTTTATCCTCAAGGAGCAGGACCCATTTCA
1 TTTCC-TTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCA
* *
2961160 TTCTCC-TTTTCCTTTGTCATTAAAGAGC
1 TT-TCCTTTTTCCTTTGTCCTCAAAGAGC
2961188 TGGATGCCCC
Statistics
Matches: 152, Mismatches: 33, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
39 3 0.02
40 6 0.04
41 69 0.45
42 30 0.20
43 11 0.07
44 8 0.05
46 18 0.12
47 5 0.03
48 2 0.01
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (41 bp):
TTTCCTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCA
Found at i:2961194 original size:83 final size:82
Alignment explanation
Indices: 2960939--2961194 Score: 231
Period size: 83 Copynumber: 3.1 Consensus size: 82
2960929 TCAAAGATCA
* * *
2960939 GGATGC-TTTT-TTT-CTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTT
1 GGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCA-TT-CTCCTTT
* *
2961001 TCCCTTCCAGTTCTCAAAGAG-T
64 T-CCTT--TG-TCTTAAAGAGCT
* * * *
2961023 AGGATGCACTTTATTCTCC--TTTTCCTTTGTCCTCAAAAAGCAGGGCACATTTAATT-TCCTTT
1 -GGATGCATTTTATT-TCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTCTCC-TT
*
2961085 TTCCTTTGTCTTTAAAGGGCAT
63 TTCCTTTGTC-TTAAAGAGC-T
* * *
2961107 -GATGCATTTTATTTCCTTTTTTCCTTTATCCTCAAGGAGCAGGACCCATTTCATTCTCCTTTTC
1 GGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTCTCCTTTTC
2961171 CTTTGTCATTAAAGAGCT
66 CTTTGTC-TTAAAGAGCT
2961189 GGATGC
1 GGATGC
2961195 CCCATTCCTT
Statistics
Matches: 140, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
81 5 0.04
82 20 0.14
83 56 0.40
84 10 0.07
85 10 0.07
86 5 0.04
87 32 0.23
88 1 0.01
89 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.42
Consensus pattern (82 bp):
GGATGCATTTTATTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACATTTCATTCTCCTTTTC
CTTTGTCTTAAAGAGCT
Found at i:2961758 original size:20 final size:20
Alignment explanation
Indices: 2961733--2961819 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
2961723 TTTTCATAAT
2961733 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
2961753 TTGTATCGATACATTCTGGGTTTTACCTA
1 TTGTATCGATACA-T-T--G--TT--C-A
*
2961782 GATGTATCGATACATTGTTCA
1 -TTGTATCGATACATTGTTCA
2961803 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
2961820 ATCAACACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
20 29 0.53
21 2 0.04
22 2 0.04
24 3 0.05
26 3 0.05
28 2 0.04
29 2 0.04
30 12 0.22
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:2961856 original size:62 final size:63
Alignment explanation
Indices: 2961751--2961879 Score: 179
Period size: 62 Copynumber: 2.1 Consensus size: 63
2961741 ATACATTGTT
* * * * * *
2961751 CATTGTATCGATACATTCTGGGTTTTACCTAGATGTATCGATACATTGTTCATTGTATCGATA
1 CATTGTATCAACACATTCTGGGTTTTACCCAGAAGTATCGATACATTGTTCAATATATCGATA
* *
2961814 CATTGTATCAACACATTC-GGGTTTTACCCAGAAGTATTGATACATTTTTCAATATATCGATA
1 CATTGTATCAACACATTCTGGGTTTTACCCAGAAGTATCGATACATTGTTCAATATATCGATA
2961876 CATT
1 CATT
2961880 CAAGCATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 42 0.72
63 16 0.28
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (63 bp):
CATTGTATCAACACATTCTGGGTTTTACCCAGAAGTATCGATACATTGTTCAATATATCGATA
Found at i:2962866 original size:20 final size:21
Alignment explanation
Indices: 2962841--2962894 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2962831 GTTACAAGCT
*
2962841 ATGTATCGATACAATT-CATC
1 ATGTATCGATACAATTGCACC
* *
2962861 ATGTATCAATAC-ATTGTACC
1 ATGTATCGATACAATTGCACC
2962881 ATGTATCGATACAA
1 ATGTATCGATACAA
2962895 ACAGTGGTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACAATTGCACC
Found at i:2962967 original size:19 final size:19
Alignment explanation
Indices: 2962924--2962978 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
2962914 TACCAATCTT
**
2962924 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
2962944 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
2962963 ATGTATCGATACAATG
1 ATGTATCGATACAATG
2962979 TATCGATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:2962981 original size:13 final size:13
Alignment explanation
Indices: 2962963--2962989 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2962953 TACAATGAAC
2962963 ATGTATCGATACA
1 ATGTATCGATACA
2962976 ATGTATCGATACA
1 ATGTATCGATACA
2962989 A
1 A
2962990 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2963575 original size:21 final size:22
Alignment explanation
Indices: 2963531--2963579 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2963521 AATTTTCATT
*
2963531 TTTCTCCCCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
* *
2963553 TTTCTCCCCTTTAATCGAA-AA
1 TTTCTCCCCCTTAATCAAAGAA
2963574 TTTCTC
1 TTTCTC
2963580 AAAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.41
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:2964065 original size:13 final size:13
Alignment explanation
Indices: 2964047--2964072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2964037 TACACAAAGT
2964047 ATGTATCGATACA
1 ATGTATCGATACA
2964060 ATGTATCGATACA
1 ATGTATCGATACA
2964073 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2964070 original size:32 final size:33
Alignment explanation
Indices: 2964029--2964092 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2964019 TAGCCAAACT
**
2964029 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2964061 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2964093 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2966699 original size:13 final size:12
Alignment explanation
Indices: 2966678--2966730 Score: 79
Period size: 12 Copynumber: 4.2 Consensus size: 12
2966668 AAATAGTACC
2966678 CAATATATCGATA
1 CAAT-TATCGATA
2966691 CAATGTATCGATA
1 CAAT-TATCGATA
2966704 CAATTATCGATA
1 CAATTATCGATA
*
2966716 CAATTATCTATA
1 CAATTATCGATA
2966728 CAA
1 CAA
2966731 GGAATACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
12 22 0.58
13 16 0.42
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (12 bp):
CAATTATCGATA
Found at i:2966711 original size:25 final size:25
Alignment explanation
Indices: 2966678--2966730 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
2966668 AAATAGTACC
2966678 CAATATATCGATACAATGTATCGATA
1 CAATATATCGATACAAT-TATCGATA
*
2966704 CAAT-TATCGATACAATTATCTATA
1 CAATATATCGATACAATTATCGATA
2966728 CAA
1 CAA
2966731 GGAATACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 10 0.38
25 12 0.46
26 4 0.15
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (25 bp):
CAATATATCGATACAATTATCGATA
Found at i:2972937 original size:13 final size:13
Alignment explanation
Indices: 2972919--2972949 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2972909 ATAATTCATC
2972919 ATGTATTGATACA
1 ATGTATTGATACA
2972932 ATGTATTGATACA
1 ATGTATTGATACA
*
2972945 TTGTA
1 ATGTA
2972950 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:2973033 original size:13 final size:13
Alignment explanation
Indices: 2973015--2973041 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2973005 ACAATTGTCC
2973015 ATGTATCGATACA
1 ATGTATCGATACA
2973028 ATGTATCGATACA
1 ATGTATCGATACA
2973041 A
1 A
2973042 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2975850 original size:20 final size:20
Alignment explanation
Indices: 2975825--2975878 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2975815 TTTACCCAGA
*
2975825 TGTATCGATACATTTTTCAT
1 TGTATCGATACATTTTGCAT
2975845 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTTGCAT
2975865 TGTATCGATACATT
1 TGTATCGATACATT
2975879 CAGGCATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATTTTGCAT
Found at i:2978358 original size:28 final size:28
Alignment explanation
Indices: 2978325--2978396 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
2978315 TTTCACAATT
*
2978325 GGGGATACTCCAACCTCGTTATTTCATC-A
1 GGGGATACTCCAACCCCGTTATTT--TCGA
2978354 -GGGATACTCCAACCCCGTTATTTTCGA
1 GGGGATACTCCAACCCCGTTATTTTCGA
2978381 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
2978397 TGGCTTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 2 0.05
27 1 0.03
28 37 0.93
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTTCGA
Found at i:2978474 original size:28 final size:28
Alignment explanation
Indices: 2978431--2978506 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
2978421 TTTTTTCATA
* *
2978431 ATCGGGGGTACCCCAACCCCATTATTTC
1 ATCGGGGATACTCCAACCCCATTATTTC
* *
2978459 ATCGGGGATACTCCAATCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCATTATTTC
*** *
2978487 CGAGGGGATGCTCCAACCCC
1 ATCGGGGATACTCCAACCCC
2978507 GATTTTATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATTTC
Found at i:2978566 original size:109 final size:106
Alignment explanation
Indices: 2978276--2978560 Score: 331
Period size: 109 Copynumber: 2.6 Consensus size: 106
2978266 CCGCAATCGA
* *
2978276 GGATACTCCAACTCCGACTTTATTTCCAAA-ACACTAATTTTTCACAATTGGGGATACTCCAACC
1 GGATACTCCAACCCCGACTTTATTTCTAAATAC-C-AATTTTTCACAATTGGGGATACTCCAACC
*
2978340 TCG-TTATTTCATCAGGGATACTCCAACCCCGTTATTTTCGAGG
64 -CGATTATTTCATCAGGGATACTCCAACCCCGTTATTTCCGAGG
* * * ** * * * * *
2978383 GGATACTCCAACCCTGGCTTTATATCTAAAAATATTGATTTTTTCATAATCGGGGGTACCCCAAC
1 GGATACTCCAACCCCGACTTTATTTCT--AAATA-CCAATTTTTCACAATTGGGGATACTCCAAC
* * *
2978448 CCCATTATTTCATCGGGGATACTCCAATCCCGTTATTTCCGAGG
63 CCGATTATTTCATCAGGGATACTCCAACCCCGTTATTTCCGAGG
* *
2978492 GGATGCTCCAACCCCGATTTTATTTCTAAATACCAATTTTTCACAATTGGGGATACTCCAACTCC
1 GGATACTCCAACCCCGACTTTATTTCTAAATACCAATTTTTCACAATTGGGGATACTCCAAC-CC
2978557 GATT
65 GATT
2978561 TTATTTTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
106 23 0.16
107 32 0.22
108 1 0.01
109 86 0.60
110 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (106 bp):
GGATACTCCAACCCCGACTTTATTTCTAAATACCAATTTTTCACAATTGGGGATACTCCAACCCG
ATTATTTCATCAGGGATACTCCAACCCCGTTATTTCCGAGG
Found at i:2978808 original size:79 final size:79
Alignment explanation
Indices: 2978629--2978812 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 79
2978619 CTAAATCATT
* * * * * *
2978629 GATTTTTCACAATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCCGATTTT
1 GATTTTCCATAATCGGAGATACTCCAACCTCATAATTTCCGAGGGGATACTCCAACCCCGATTTT
* *
2978694 ATTTTCAAAATACT
66 ATTTTCAAAACACC
* * *
2978708 GATTTTCTATAATC-AAGGATACTCCAACCTTATAATTTCCGAGGGGATACTCCAACCCCGATTT
1 GATTTTCCATAATCGGA-GATACTCCAACCTCATAATTTCCGAGGGGATACTCCAACCCCGATTT
**
2978772 TA-TTTCTGGAACACC
65 TATTTTC-AAAACACC
2978787 GATTTTCCATAATCGGAGATACTCCA
1 GATTTTCCATAATCGGAGATACTCCA
2978813 GCCCCGTTGT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
78 4 0.05
79 82 0.94
80 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (79 bp):
GATTTTCCATAATCGGAGATACTCCAACCTCATAATTTCCGAGGGGATACTCCAACCCCGATTTT
ATTTTCAAAACACC
Found at i:2980900 original size:12 final size:12
Alignment explanation
Indices: 2980883--2980913 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2980873 TATTTTGAGG
2980883 TGTTTATTTATT
1 TGTTTATTTATT
2980895 TGTTTATTTATT
1 TGTTTATTTATT
*
2980907 TATTTAT
1 TGTTTAT
2980914 AGTCACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
TGTTTATTTATT
Found at i:2991232 original size:8 final size:8
Alignment explanation
Indices: 2991221--2991256 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
2991211 AAAAAACAAC
2991221 AAAAAAGA
1 AAAAAAGA
2991229 AAAAAAGA
1 AAAAAAGA
2991237 AAAAAAGA
1 AAAAAAGA
2991245 AAGAAAAGA
1 AA-AAAAGA
2991254 AAA
1 AAA
2991257 GAACTTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2992361 original size:39 final size:39
Alignment explanation
Indices: 2992287--2992363 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
2992277 AAGTTGGTGG
*
2992287 CACCTTCTAGTCCTCAAAGAGCAAGACGCTCTCTCCTTT
1 CACCTTCTAGTCCTCAAAGAGCAAGACCCTCTCTCCTTT
* * *
2992326 CACCTTTTAGTCCTCAAAGAGTAGGACACCT-TCTCCTT
1 CACCTTCTAGTCCTCAAAGAGCAAGAC-CCTCTCTCCTT
2992364 CAAAGCCCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (39 bp):
CACCTTCTAGTCCTCAAAGAGCAAGACCCTCTCTCCTTT
Found at i:2992399 original size:99 final size:100
Alignment explanation
Indices: 2992218--2992408 Score: 278
Period size: 99 Copynumber: 1.9 Consensus size: 100
2992208 ATCTAAACTT
* ** * * *
2992218 TCTCCTTTCACTTTTCAGTCTTCAAAAAGTAGGACGTCTTTTCCTTTTAAACCCCACACAAGTTG
1 TCTCCTTTCACTTTTCAGTCCTCAAAAAGTAGGACACCTTCTCCTTTCAAACCCCACAAAAGTTG
2992283 GTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCTC
66 GTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCTC
* *
2992318 TCTCCTTTCACCTTTT-AGTCCTCAAAGAGTAGGACACCTTCTCC-TTCAAAGCCCACAAAAGTT
1 TCTCCTTTCA-CTTTTCAGTCCTCAAAAAGTAGGACACCTTCTCCTTTCAAACCCCACAAAAGTT
*
2992381 GGTGGCACCTTTTAGTCCTCAAAGAGCA
65 GGTGGCACCTTCTAGTCCTCAAAGAGCA
2992409 GGACACCTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
99 43 0.53
100 33 0.41
101 5 0.06
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (100 bp):
TCTCCTTTCACTTTTCAGTCCTCAAAAAGTAGGACACCTTCTCCTTTCAAACCCCACAAAAGTTG
GTGGCACCTTCTAGTCCTCAAAGAGCAAGACGCTC
Found at i:2992546 original size:61 final size:61
Alignment explanation
Indices: 2992326--2992970 Score: 658
Period size: 61 Copynumber: 10.7 Consensus size: 61
2992316 TCTCTCCTTT
* * * * *
2992326 CACCTTTTAGTCCTCAAAGAGTAGGACACC-TTCTC-CTTCAAAGCCCACAAAAGTTGGTGG
1 CACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * *
2992386 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTATTCAAAGCCTACACAAGTTGGTGG
1 CACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * *
2992448 CACCTTTTAGTCCTCCAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGG
1 CACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * *
2992510 CACCTTTAGTCCTCAAAGAGCATGACGCCTTTTTCTTTTCAAAGCCTACACTAGTTGGTGG
1 CACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * * * *
2992571 AACTTTTAGTTCTCAAAGAGCAGGACACCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGG
1 CACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* *
2992632 CACCTTCTGGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGG
1 CACCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* *
2992693 CA-TTTTCCAGTCCTCAAAGAGCAGGACG-C-----C-TTTCAAAGCCCACACAAGTTGGTGA
1 CACCTTT--AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * * * * * * *
2992748 CA-TTTTCCAGTCCTCAAAAAGCAGGATG-CTTTCTCCTTT-AAAGACCACTCGAGTTGGTGG
1 CACCTTT--AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * * *
2992808 CACCTTCCAGTCCTCAAAGAGCAGGATG-CTTTCTT-TTTGCAAAGCCCATACAAGTTGGTGG
1 CACCTT-TAGTCCTCAAAGAGCAGGACGCCTTT-TTCTTTTCAAAGCCCACACAAGTTGGTGG
** * * * *
2992869 CACCTTTCAGTCCTCAAAGAGCAAAATGCC-TTTTCTTTTCAAAGCTCACACGAGTTGGTGA
1 CACCTTT-AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
* * * *
2992930 CACTTTTTAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTC
1 CAC-CTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTC
2992971 TCCTTTGTCC
Statistics
Matches: 502, Mismatches: 62, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
54 3 0.01
55 48 0.10
59 1 0.00
60 79 0.16
61 245 0.49
62 126 0.25
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (61 bp):
CACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGG
Found at i:2992901 original size:115 final size:110
Alignment explanation
Indices: 2992669--2992901 Score: 236
Period size: 115 Copynumber: 2.0 Consensus size: 110
2992659 GCCTTTTCCT
* **
2992669 TTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCC
1 TTTAAAGACCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCC
* **
2992734 ACACAAGTTGGTGACATTTTCCAGTCCTCAAAAAGCAGGATGCTTTCTCC
66 ACACAAGTTGGTGACACTTTCCAGTCCTCAAAAAGCAAAATG-----TCC
* * *
2992784 TTTAAAGACCACTCGAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCA
1 TTTAAAGACCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGC---C--TTT-CA
* * *
2992849 AAGCCCATACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAAAATG-CC
60 AAGCCCACACAAGTTGGTGACA-CTTTCCAGTCCTCAAAAAGCAAAATGTCC
2992899 TTT
1 TTT
2992902 TCTTTTCAAA
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
115 52 0.53
118 1 0.01
120 3 0.03
121 40 0.40
122 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (110 bp):
TTTAAAGACCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCC
ACACAAGTTGGTGACACTTTCCAGTCCTCAAAAAGCAAAATGTCC
Found at i:2993073 original size:42 final size:42
Alignment explanation
Indices: 2992960--2993096 Score: 138
Period size: 42 Copynumber: 3.2 Consensus size: 42
2992950 GTAGGACGTC
** *
2992960 TTTTCCT-TTTCTCCTTTGTCCTCAAAGAGCATAACACATTTCA
1 TTTTCCTATTTCT--TTTGTCCTCAAAGAGCAGGACGCATTTCA
*
2993003 TTCCCTT-CT-TTTCCCTTTTGTCCTCAAAGAGTAGGACGCACTTT-A
1 TT---TTCCTATTT--CTTTTGTCCTCAAAGAGCAGGACGCA-TTTCA
2993048 TTTTCCTATTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCA
1 TTTTCCTATTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCA
2993090 TTTTCCT
1 TTTTCCT
2993097 TTTTTCCTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
41 3 0.04
42 35 0.44
43 4 0.05
44 3 0.04
45 28 0.35
46 5 0.06
47 2 0.03
ACGTcount: A:0.20, C:0.27, G:0.11, T:0.42
Consensus pattern (42 bp):
TTTTCCTATTTCTTTTGTCCTCAAAGAGCAGGACGCATTTCA
Found at i:2993848 original size:20 final size:20
Alignment explanation
Indices: 2993823--2993909 Score: 115
Period size: 20 Copynumber: 4.3 Consensus size: 20
2993813 ACTTACATCA
2993823 ATACATTGTT-CATTGTATCG
1 ATACATT-TTACATTGTATCG
*
2993843 ATACATTTTGCATTGTATCG
1 ATACATTTTACATTGTATCG
*
2993863 ATACATTGCT-CATTGTATCG
1 ATACATT-TTACATTGTATCG
*
2993883 ATACATTTTACAATGTATCG
1 ATACATTTTACATTGTATCG
2993903 ATACATT
1 ATACATT
2993910 CAGGCATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.05
20 57 0.93
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (20 bp):
ATACATTTTACATTGTATCG
Found at i:2993867 original size:40 final size:40
Alignment explanation
Indices: 2993823--2993909 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
2993813 ACTTACATCA
* * *
2993823 ATACATTGTTCATTGTATCGATACATTTTGCATTGTATCG
1 ATACATTGCTCATTGTATCGATACATTTTACAATGTATCG
2993863 ATACATTGCTCATTGTATCGATACATTTTACAATGTATCG
1 ATACATTGCTCATTGTATCGATACATTTTACAATGTATCG
2993903 ATACATT
1 ATACATT
2993910 CAGGCATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (40 bp):
ATACATTGCTCATTGTATCGATACATTTTACAATGTATCG
Found at i:2997475 original size:27 final size:28
Alignment explanation
Indices: 2997366--2997803 Score: 417
Period size: 27 Copynumber: 16.0 Consensus size: 28
2997356 TGACCTCTTC
* *
2997366 AAAGTCCACGA-TTCAGTGGCATTTCTTTT
1 AAAGTCCACAACTTC-GTGGCA-TCCTTTT
* * * *
2997395 CAAAGTTCACAACTCCGTGGTATCTTTTT
1 -AAAGTCCACAACTTCGTGGCATCCTTTT
*
2997424 AAAATCCACAACTT--TGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* *
2997450 AAAGTTCACAACTTCGTGGCATCTTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
**
2997478 AAA-TCCACAACTTCGTAACATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
** * *
2997505 -AAGTTTATAAC-TCTGTGGCATCTTTTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
2997532 AAAGTCCACAACTTCGTGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
*
2997560 -AAGTCCATAAC-TCTGTGGCATCC-TTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
2997586 AAAGTCCACAAC-TCTGTGGCATCCTTTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
*
2997614 AAAGTCCACAAC-TCCTGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* * *
2997641 -AAGTCTATAACTCCGTGGCAT-CTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* * *
2997667 TAAGTCCACAAC-TCTATGGCATCATTTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
*
2997695 -AAGTCCACAA-TTCTGTGGCATTCTTTT
1 AAAGTCCACAACTTC-GTGGCATCCTTTT
* *
2997722 AAAGTCTACAACTCCGTGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
* *
2997750 -AAGTCTACAACTCCGTGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
*
2997777 -AAGTCCACAACTCCGTGGCATCCTTTT
1 AAAGTCCACAACTTCGTGGCATCCTTTT
2997804 TAACCCCTAA
Statistics
Matches: 344, Mismatches: 47, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
26 46 0.13
27 186 0.54
28 87 0.25
29 9 0.03
30 14 0.04
31 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (28 bp):
AAAGTCCACAACTTCGTGGCATCCTTTT
Found at i:2997524 original size:82 final size:82
Alignment explanation
Indices: 2997366--2997806 Score: 466
Period size: 82 Copynumber: 5.4 Consensus size: 82
2997356 TGACCTCTTC
* * * * * *
2997366 AAAGTCCACGA-TTCAGTGGCATTTCTTTTCAAAGTTCACAACTCCGTGGTATCTTTTTAAAATC
1 AAAGTCCACAACTTC-GTGGCA--TCTTTTTAAA-TCCACAACTCCGTGGCATCCTTTT-AAGTC
2997430 CACAACT-T-TGGCATCCTTTT
61 CACAACTCTGTGGCATCCTTTT
* * ** ** *
2997450 AAAGTTCACAACTTCGTGGCATCTTTTTAAATCCACAACTTCGTAACATCCTTTTAAGTTTATAA
1 AAAGTCCACAACTTCGTGGCATCTTTTTAAATCCACAACTCCGTGGCATCCTTTTAAGTCCACAA
*
2997515 CTCTGTGGCATCTTTTT
66 CTCTGTGGCATCCTTTT
* * * * *
2997532 AAAGTCCACAACTTCGTGGCATCCTTTTAAGTCCATAACTCTGTGGCATCCTTTAAAGTCCACAA
1 AAAGTCCACAACTTCGTGGCATCTTTTTAAATCCACAACTCCGTGGCATCCTTTTAAGTCCACAA
2997597 CTCTGTGGCATCCTTTT
66 CTCTGTGGCATCCTTTT
* * * * * *
2997614 AAAGTCCACAAC-TCCTGGCATCCTTTTAAGTCTATAACTCCGTGGCATCTTTTTAAGTCCACAA
1 AAAGTCCACAACTTCGTGGCATCTTTTTAAATCCACAACTCCGTGGCATCCTTTTAAGTCCACAA
* *
2997678 CTCTATGGCATCATTTT
66 CTCTGTGGCATCCTTTT
* *
2997695 -AAGTCCACAA-TTCTGTGGCAT-TCTTTTAAAGTCTACAACTCCGTGGCATCCTTTTAAGTCTA
1 AAAGTCCACAACTTC-GTGGCATCT-TTTTAAA-TCCACAACTCCGTGGCATCCTTTTAAGTCCA
*
2997757 CAACTCCGTGGCATCCTTTT
63 CAACTCTGTGGCATCCTTTT
*
2997777 -AAGTCCACAACTCCGTGGCATCCTTTTTAA
1 AAAGTCCACAACTTCGTGGCAT-CTTTTTAA
2997807 CCCCTAAGTT
Statistics
Matches: 303, Mismatches: 44, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
80 20 0.07
81 93 0.31
82 163 0.54
83 8 0.03
84 16 0.05
85 3 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (82 bp):
AAAGTCCACAACTTCGTGGCATCTTTTTAAATCCACAACTCCGTGGCATCCTTTTAAGTCCACAA
CTCTGTGGCATCCTTTT
Found at i:2997849 original size:28 final size:28
Alignment explanation
Indices: 2997812--2998321 Score: 436
Period size: 28 Copynumber: 18.2 Consensus size: 28
2997802 TTTAACCCCT
* *
2997812 AAGTTAGTGGCACCCTTCCAAAGCCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* ***
2997840 AAGTTAGTGGCACCCCTTTCAAAGTTTAC
1 AAGTCAGTGGCA-CCCTTTCAAAGCCCAC
* * * *
2997869 AAATCAATGGCATCCTTTCAAAGTCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
** * * *
2997897 AAACCGGTGGCACCTTTTCGAAGGCCCAC
1 AAGTCAGTGGCACCCTTTC-AAAGCCCAC
* *
2997926 AAGTCAGTGGCTCCCTTTCAAAGCCTAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* * *
2997954 AAGTCAGTGGCATCCTTTTAAAGTCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* * *
2997982 AAGTCAATGGCATCTTTTCAAAGCCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
** **
2998010 AAGTCAGTGGCA-TTTTTTTAAGCCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* * *
2998037 AAGTTAGTAGCACCCTTTTCAAAGCCCAT
1 AAGTCAGTGGCACCC-TTTCAAAGCCCAC
* *
2998066 AAGTTAGTGGCACCCTTTCAAAGCCTAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
*
2998094 AAGTCAGTGGCATCACCTTTCAAAGCCCAT
1 AAGTCAGTGGCA-C-CCTTTCAAAGCCCAC
* ** *
2998124 AAGTCAATGGCACATTTTCAAAGCCCAT
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* * *
2998152 AAGTCAGTGGCATCTTTTCAAAGCCCAT
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* * ** * *
2998180 AAGTCGGTGGCA-TCTTTTTATGCCCAT
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
*
2998207 AGGTCAGTGGCA-CCTTTCAAAGCCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* * *
2998234 AAGTTAGTGACA-CCTTTCAAAACCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* *
2998261 AAATCAGTGGCA-CCTTTCAAATCCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
* ** *
2998288 AAGTCAGTGCCACTTTTTCAAGGCCCAC
1 AAGTCAGTGGCACCCTTTCAAAGCCCAC
2998316 AAGTCA
1 AAGTCA
2998322 ATAGCAACTC
Statistics
Matches: 392, Mismatches: 83, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
27 108 0.28
28 192 0.49
29 68 0.17
30 24 0.06
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
AAGTCAGTGGCACCCTTTCAAAGCCCAC
Found at i:2997945 original size:85 final size:85
Alignment explanation
Indices: 2997819--2998191 Score: 268
Period size: 86 Copynumber: 4.4 Consensus size: 85
2997809 CCTAAGTTAG
* * * **
2997819 TGGCACCCTTCCAAAGCCCACAAGTTAGTGGCACCCCTTTCAAAGTTTACAAATCAATGGCATCC
1 TGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCTACAAATCAATGGCATCC
**
2997884 TTTCAAAGTCCACAAACCGG
66 TTTCAAAGTCCACAAACCAA
* * * *
2997904 TGGCACCTTTTCGAAGGCCCACAAGTCAGTGGC-TCCCTTTCAAAGCCTACAAGTCAGTGGCATC
1 TGGCACCTTTTC-AAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCTACAAATCAATGGCATC
* **
2997968 CTTTTAAAGTCCACAAGTCAA
65 CTTTCAAAGTCCACAAACCAA
* ** ** * * * * * *
2997989 TGGCATCTTTTCAAAGCCCACAAGTCAGTGGCA--TTTTTTTAAGCCCACAAGTTAGTAGCACCC
1 TGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCTACAAATCAATGGCATCC
* * *** *
2998052 TTTTCAAAGCCCATAAGTTAG
66 -TTTCAAAGTCCACAAACCAA
* * * * * *
2998073 TGGCACCCTTTCAAAGCCTACAAGTCAGTGGCATCACCTTTCAAAGCCCATAAGTCAATGGCA-C
1 TGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-CCCCTTTCAAAGCCTACAAATCAATGGCATC
* * * ** *
2998137 ATTTTCAAAGCCCATAAGTCAG
65 -CTTTCAAAGTCCACAAACCAA
* * *
2998159 TGGCATCTTTTCAAAGCCCATAAGTCGGTGGCA
1 TGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA
2998192 TCTTTTTATG
Statistics
Matches: 234, Mismatches: 47, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
83 22 0.09
84 64 0.27
85 63 0.27
86 66 0.28
87 19 0.08
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (85 bp):
TGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCCTTTCAAAGCCTACAAATCAATGGCATCC
TTTCAAAGTCCACAAACCAA
Found at i:2998034 original size:27 final size:27
Alignment explanation
Indices: 2997812--2998408 Score: 370
Period size: 28 Copynumber: 21.0 Consensus size: 27
2997802 TTTAACCCCT
* * *
2997812 AAGTTAGTGGCACCCTTCCAAAGCCCAC
1 AAGTCAGTGGCA-TCTTTCAAAGCCCAC
* * ***
2997840 AAGTTAGTGGCACCCCTTTCAAAGTTTAC
1 AAGTCAGTGGCA--TCTTTCAAAGCCCAC
* * *
2997869 AAATCAATGGCATCCTTTCAAAGTCCAC
1 AAGTCAGTGGCAT-CTTTCAAAGCCCAC
** * * *
2997897 AAACCGGTGGCACCTTTTCGAAGGCCCAC
1 AAGTCAGTGGCATC-TTTC-AAAGCCCAC
*
2997926 AAGTCAGTGGC-TCCCTTTCAAAGCCTAC
1 AAGTCAGTGGCAT--CTTTCAAAGCCCAC
* *
2997954 AAGTCAGTGGCATCCTTTTAAAGTCCAC
1 AAGTCAGTGGCAT-CTTTCAAAGCCCAC
*
2997982 AAGTCAATGGCATCTTTTCAAAGCCCAC
1 AAGTCAGTGGCATC-TTTCAAAGCCCAC
* **
2998010 AAGTCAGTGGCATTTTTTTAAGCCCAC
1 AAGTCAGTGGCATCTTTCAAAGCCCAC
* * * *
2998037 AAGTTAGTAGCACCCTTTTCAAAGCCCAT
1 AAGTCAGTGGCA-TC-TTTCAAAGCCCAC
* * *
2998066 AAGTTAGTGGCACCCTTTCAAAGCCTAC
1 AAGTCAGTGGCA-TCTTTCAAAGCCCAC
*
2998094 AAGTCAGTGGCATCACCTTTCAAAGCCCAT
1 AAGTCAGTGGCAT---CTTTCAAAGCCCAC
* *
2998124 AAGTCAATGGCA-CATTTTCAAAGCCCAT
1 AAGTCAGTGGCATC--TTTCAAAGCCCAC
*
2998152 AAGTCAGTGGCATCTTTTCAAAGCCCAT
1 AAGTCAGTGGCATC-TTTCAAAGCCCAC
* ** * *
2998180 AAGTCGGTGGCATCTTTTTATGCCCAT
1 AAGTCAGTGGCATCTTTCAAAGCCCAC
* *
2998207 AGGTCAGTGGCACCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCTTTCAAAGCCCAC
* * * *
2998234 AAGTTAGTGACACCTTTCAAAACCCAC
1 AAGTCAGTGGCATCTTTCAAAGCCCAC
* * *
2998261 AAATCAGTGGCACCTTTCAAATCCCAC
1 AAGTCAGTGGCATCTTTCAAAGCCCAC
* * *
2998288 AAGTCAGTGCCACTTTTTCAAGGCCCAC
1 AAGTCAGTGGCA-TCTTTCAAAGCCCAC
* * * *
2998316 AAGTCAATAGCAACTCTTTTTAAGGCCCAC
1 AAGTCAGTGGC-A-TC-TTTCAAAGCCCAC
** *
2998346 ATAAGTTGGTGGCAACTCACTTCAAAGCCCACAC
1 --AAGTCAGTGGC-A-TC-TTTCAAAG-CC-CAC
*
2998380 AAGTCAATGGCATCATTTCAAAGCCCAC
1 AAGTCAGTGGCATC-TTTCAAAGCCCAC
2998408 A
1 A
2998409 CAAGTTGGTG
Statistics
Matches: 456, Mismatches: 90, Indels: 46
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.00
27 109 0.24
28 198 0.43
29 71 0.16
30 46 0.10
31 1 0.00
32 25 0.05
33 2 0.00
34 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (27 bp):
AAGTCAGTGGCATCTTTCAAAGCCCAC
Found at i:2998343 original size:30 final size:28
Alignment explanation
Indices: 2998283--2998346 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
2998273 CCTTTCAAAT
* *
2998283 CCCACAAGTCAGTGCCACTTTTTCAAGG
1 CCCACAAGTCAATGCAACTTTTTCAAGG
*
2998311 CCCACAAGTCAATAGCAACTCTTTTTAAGG
1 CCCACAAGTCAAT-GCAACT-TTTTCAAGG
2998341 CCCACA
1 CCCACA
2998347 TAAGTTGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.39
29 5 0.16
30 14 0.45
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.23
Consensus pattern (28 bp):
CCCACAAGTCAATGCAACTTTTTCAAGG
Found at i:2998376 original size:32 final size:32
Alignment explanation
Indices: 2998340--2998423 Score: 109
Period size: 30 Copynumber: 2.7 Consensus size: 32
2998330 TCTTTTTAAG
*
2998340 GCCCACATAAGTTGGTGGCAACTCACTTCAAA
1 GCCCACACAAGTTGGTGGCAACTCACTTCAAA
*** *
2998372 GCCCACACAAGTCAATGGC-A-TCATTTCAAA
1 GCCCACACAAGTTGGTGGCAACTCACTTCAAA
2998402 GCCCACACAAGTTGGTGGCAAC
1 GCCCACACAAGTTGGTGGCAAC
2998424 CCTTCTAAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 25 0.60
31 2 0.05
32 15 0.36
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (32 bp):
GCCCACACAAGTTGGTGGCAACTCACTTCAAA
Found at i:3001337 original size:27 final size:27
Alignment explanation
Indices: 3001284--3001337 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3001274 TCATCGGGGA
* *
3001284 TAACCCCATTATTCTGAAGGGACACTC
1 TAACCCCATTATTCCGAAAGGACACTC
* *
3001311 TAACCCCATTCTTCCGAAAGGATACTC
1 TAACCCCATTATTCCGAAAGGACACTC
3001338 CAACTTCGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.26
Consensus pattern (27 bp):
TAACCCCATTATTCCGAAAGGACACTC
Found at i:3002599 original size:6 final size:6
Alignment explanation
Indices: 3002588--3002621 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3002578 ATATAATCGT
3002588 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
3002622 CAATACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:3003029 original size:42 final size:41
Alignment explanation
Indices: 3002951--3003030 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 41
3002941 GAGTCCGTCT
* * *
3002951 AAACTTGTTTGACTCAAACTGATTTGAGCCTGAAATAGGTC
1 AAACTTGTTTAACTCAAACTGATTTAAACCTGAAATAGGTC
* * *
3002992 AAACTTGTCTTAAGTCAAACTGATTTAAATCTTAAATAG
1 AAACTTGT-TTAACTCAAACTGATTTAAACCTGAAATAG
3003031 CTGAAATTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 8 0.25
42 24 0.75
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (41 bp):
AAACTTGTTTAACTCAAACTGATTTAAACCTGAAATAGGTC
Found at i:3003212 original size:16 final size:16
Alignment explanation
Indices: 3003129--3003216 Score: 67
Period size: 16 Copynumber: 5.5 Consensus size: 16
3003119 AAATTATTCG
*
3003129 AATTCGAAAAT-ATTT
1 AATTTGAAAATAATTT
*
3003144 AAGCTT-AAAATAATTT
1 AA-TTTGAAAATAATTT
*
3003160 AATTTG-AAATGAATCTA
1 AATTTGAAAAT-AAT-TT
* *
3003177 AATTTG-AAATAGTCTG
1 AATTTGAAAATAAT-TT
3003193 AATTTGAAAATAATTT
1 AATTTGAAAATAATTT
3003209 AATTTGAA
1 AATTTGAA
3003217 CTTGCTTGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.22
16 29 0.49
17 17 0.29
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.39
Consensus pattern (16 bp):
AATTTGAAAATAATTT
Found at i:3003579 original size:17 final size:17
Alignment explanation
Indices: 3003549--3003581 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3003539 TATATGACAC
3003549 GTAATTATTGATTTATT
1 GTAATTATTGATTTATT
3003566 GTAA-TATTGCATTTAT
1 GTAATTATTG-ATTTAT
3003582 GAATTCGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (17 bp):
GTAATTATTGATTTATT
Found at i:3007993 original size:2 final size:2
Alignment explanation
Indices: 3007981--3008015 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3007971 ATCAAAGTGA
*
3007981 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3008016 AGAGTTATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3008330 original size:40 final size:40
Alignment explanation
Indices: 3008285--3008369 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
3008275 TATATTAAAA
3008285 ATTTACTAACAATAATTAATCAATAAATTTTATTTATGTT
1 ATTTACTAACAATAATTAATCAATAAATTTTATTTATGTT
* *
3008325 ATTTACTCATAATAATTAATCAATAAATTTTATTTATGTT
1 ATTTACTAACAATAATTAATCAATAAATTTTATTTATGTT
3008365 ATTTA
1 ATTTA
3008370 AAATTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (40 bp):
ATTTACTAACAATAATTAATCAATAAATTTTATTTATGTT
Found at i:3011728 original size:20 final size:20
Alignment explanation
Indices: 3011703--3011748 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3011693 ATTTAACCCA
* *
3011703 AATGTATCGATACATTGCTC
1 AATGTATCAATACATTACTC
*
3011723 AATGTATCAATACATTATTC
1 AATGTATCAATACATTACTC
3011743 AATGTA
1 AATGTA
3011749 CCGTTACATG
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:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (20 bp):
AATGTATCAATACATTACTC
Found at i:3016189 original size:20 final size:19
Alignment explanation
Indices: 3016143--3016199 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
3016133 CTATATCGAT
*
3016143 ACATTGTATTGATACATGT
1 ACATTGTATTGATACATGG
* *
3016162 TCATTGTATCGATACATGG
1 ACATTGTATTGATACATGG
3016181 ACAATTGTATTGATACATG
1 AC-ATTGTATTGATACATG
3016200 AGATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
ACATTGTATTGATACATGG
Found at i:3016254 original size:20 final size:20
Alignment explanation
Indices: 3016229--3016281 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3016219 TACCACTATT
*
3016229 TGTATCGATACATGGT-ACAA
1 TGTATCGATACATGATGA-AA
*
3016249 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAA
3016269 TGTATCGATACAT
1 TGTATCGATACAT
3016282 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Done.