Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 177 of 427
Found at i:49140048 original size:15 final size:15
Alignment explanation
Indices: 49140028--49140075 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
49140018 TCAAAGATGG
49140028 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
49140043 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
49140057 GTTTATGGATATAAA
1 GTTTATGGATATGAA
49140072 GTTT
1 GTTT
49140076 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:49140062 original size:14 final size:14
Alignment explanation
Indices: 49140022--49140065 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
49140012 AAGGATTCAA
49140022 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
49140036 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
49140051 AGATGGGTTTATGG
1 AGATGGGTTTATGG
49140065 A
1 A
49140066 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:49140091 original size:29 final size:29
Alignment explanation
Indices: 49140022--49140081 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
49140012 AAGGATTCAA
*
49140022 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
49140051 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
49140080 AG
1 AG
49140082 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:49144140 original size:10 final size:10
Alignment explanation
Indices: 49144125--49144173 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
49144115 ATAAATCACT
49144125 TTTTTTTCAA
1 TTTTTTTCAA
*
49144135 TTTTTTTTAA
1 TTTTTTTCAA
49144145 TTTTTTTCGAA
1 TTTTTTTC-AA
*
49144156 TTTTTTTTGAA
1 -TTTTTTTCAA
49144167 TTTTTTT
1 TTTTTTT
49144174 TAACTTGTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 23 0.68
11 4 0.12
12 7 0.21
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:49144140 original size:11 final size:11
Alignment explanation
Indices: 49144124--49144174 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
49144114 CATAAATCAC
49144124 TTTTTTTTCAA
1 TTTTTTTTCAA
49144135 TTTTTTTT-AA
1 TTTTTTTTCAA
49144145 -TTTTTTTCGAA
1 TTTTTTTTC-AA
*
49144156 TTTTTTTTGAA
1 TTTTTTTTCAA
49144167 TTTTTTTT
1 TTTTTTTT
49144175 AACTTGTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
9 7 0.19
10 2 0.06
11 20 0.56
12 7 0.19
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:49146609 original size:30 final size:30
Alignment explanation
Indices: 49146515--49146610 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
49146505 AGCTCACTCC
49146515 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * * * *
49146545 T-GCTCAGCATCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
49146574 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
49146604 TAGCTCA
1 TAGCTCA
49146611 TTTTAGTTTA
Statistics
Matches: 46, Mismatches: 18, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
29 19 0.41
30 27 0.59
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:49150009 original size:30 final size:29
Alignment explanation
Indices: 49149975--49150070 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
49149965 TAAACTAAAA
49149975 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAG-TTTAGCTCGTGAGCTAAAGT
* * * * * *
49150005 TGAGCTGAGGTTAACTCCTAAGCTGAAGT
1 TGAGCTAAGTTTAGCTCGTGAGCTAAAGT
*
49150034 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAA-GTTTAGCTCGTGAGCT-AAAGT
49150064 TGAGCTA
1 TGAGCTA
49150071 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 22 0.43
30 26 0.51
31 3 0.06
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (29 bp):
TGAGCTAAGTTTAGCTCGTGAGCTAAAGT
Found at i:49150702 original size:19 final size:19
Alignment explanation
Indices: 49150678--49150717 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49150668 AGCTCCCATG
49150678 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
49150697 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
49150716 TA
1 TA
49150718 TCAGCTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:49157598 original size:19 final size:19
Alignment explanation
Indices: 49157574--49157613 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49157564 AGCTCCCATG
49157574 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
49157593 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
49157612 TA
1 TA
49157614 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:49158878 original size:14 final size:14
Alignment explanation
Indices: 49158856--49158903 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
49158846 ACCTAAATAG
* *
49158856 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
49158870 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
49158884 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
49158898 ACCATT
1 ACCATT
49158904 CCGTTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:49158908 original size:14 final size:14
Alignment explanation
Indices: 49158860--49158914 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
49158850 AAATAGACCA
*
49158860 ATTT-GTTCATACC
1 ATTTCGTTCCTACC
*
49158873 ATTTTGTTCCTACC
1 ATTTCGTTCCTACC
*
49158887 CTTTCGTTCCTACC
1 ATTTCGTTCCTACC
* *
49158901 ATTCCGTTCGTACC
1 ATTTCGTTCCTACC
49158915 CCTCTTTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
13 4 0.11
14 31 0.89
ACGTcount: A:0.15, C:0.33, G:0.09, T:0.44
Consensus pattern (14 bp):
ATTTCGTTCCTACC
Found at i:49159262 original size:18 final size:18
Alignment explanation
Indices: 49159204--49159262 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
49159194 AAATTTTAAA
**
49159204 AAAAAGAATGAAAGAAAG
1 AAAAAGAATGTGAGAAAG
*
49159222 TAAAAAGAGAT-TGAGAGCA-
1 -AAAAAGA-ATGTGAGA-AAG
49159241 AAAAAGAATGTGAGAAAG
1 AAAAAGAATGTGAGAAAG
49159259 AAAA
1 AAAA
49159263 GAAAATTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
17 3 0.09
18 16 0.50
19 10 0.31
20 3 0.09
ACGTcount: A:0.64, C:0.02, G:0.24, T:0.10
Consensus pattern (18 bp):
AAAAAGAATGTGAGAAAG
Found at i:49160980 original size:20 final size:20
Alignment explanation
Indices: 49160957--49161008 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
49160947 CAGTTGGCCT
49160957 AGCTCAATTCCAGCCCAACG
1 AGCTCAATTCCAGCCCAACG
* *
49160977 AGCTCAATTCTAGCTCAACG
1 AGCTCAATTCCAGCCCAACG
* *
49160997 AGTTCATTTCCA
1 AGCTCAATTCCA
49161009 TCCTTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (20 bp):
AGCTCAATTCCAGCCCAACG
Found at i:49164849 original size:30 final size:30
Alignment explanation
Indices: 49164815--49164912 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49164805 AGCTCACTCC
49164815 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49164845 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49164875 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49164905 TAGCTCAT
1 TAGCTCAT
49164913 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49166488 original size:30 final size:30
Alignment explanation
Indices: 49166454--49166551 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49166444 AGCTCACTCC
49166454 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49166484 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49166514 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49166544 TAGCTCAT
1 TAGCTCAT
49166552 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49168126 original size:30 final size:30
Alignment explanation
Indices: 49168092--49168189 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49168082 AGCTCACTCC
49168092 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49168122 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49168152 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49168182 TAGCTCAT
1 TAGCTCAT
49168190 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49169766 original size:30 final size:30
Alignment explanation
Indices: 49169732--49169829 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49169722 AGCTCACTCC
49169732 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49169762 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49169792 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49169822 TAGCTCAT
1 TAGCTCAT
49169830 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49171406 original size:30 final size:30
Alignment explanation
Indices: 49171372--49171469 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49171362 AGCTCACTCC
49171372 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49171402 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49171432 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49171462 TAGCTCAT
1 TAGCTCAT
49171470 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49173073 original size:11 final size:11
Alignment explanation
Indices: 49173059--49173099 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
49173049 GTTAAAAAAA
49173059 AAAAAAAATCG
1 AAAAAAAATCG
49173070 AAAAAAAATTCG
1 AAAAAAAA-TCG
49173082 -AAAAAAATCG
1 AAAAAAAATCG
49173092 AAAAAAAA
1 AAAAAAAA
49173100 AGAAAAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.11
11 22 0.79
12 3 0.11
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:49173075 original size:12 final size:12
Alignment explanation
Indices: 49173058--49173100 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
49173048 AGTTAAAAAA
49173058 AAAAAAAAATCG
1 AAAAAAAAATCG
*
49173070 AAAAAAAATTCG
1 AAAAAAAAATCG
49173082 --AAAAAAATCG
1 AAAAAAAAATCG
49173092 AAAAAAAAA
1 AAAAAAAAA
49173101 GAAAAGAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.09
Consensus pattern (12 bp):
AAAAAAAAATCG
Found at i:49174037 original size:21 final size:20
Alignment explanation
Indices: 49174003--49174070 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
49173993 ACATTCTTGT
49174003 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
49174024 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
49174045 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
49174066 AAAGA
1 AAAGA
49174071 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:49174038 original size:6 final size:5
Alignment explanation
Indices: 49174014--49174070 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49174004 AAGAGAAAAC
*
49174014 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
49174061 AAAGA AAAGA
1 AAAGA AAAGA
49174071 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:49174045 original size:15 final size:14
Alignment explanation
Indices: 49174014--49174070 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
49174004 AAGAGAAAAC
49174014 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
49174030 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
49174045 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
49174061 AAAGAAAAGA
1 AAAGAAAAGA
49174071 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:49174142 original size:11 final size:12
Alignment explanation
Indices: 49174118--49174147 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
49174108 TTGAGAGAAC
49174118 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49174130 TTGAAAAAG-CT
1 TTGAAAAAGCCT
49174141 TTGAAAA
1 TTGAAAA
49174148 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:49174158 original size:12 final size:12
Alignment explanation
Indices: 49174150--49174174 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49174140 TTTGAAAAGC
49174150 AAAAAGAAAATG
1 AAAAAGAAAATG
49174162 AAAAAGAAAATG
1 AAAAAGAAAATG
49174174 A
1 A
49174175 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:49174171 original size:18 final size:18
Alignment explanation
Indices: 49174144--49174199 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
49174134 AAAAGCTTTG
49174144 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
49174163 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
49174181 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
49174198 AA
1 AA
49174200 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:49174186 original size:30 final size:31
Alignment explanation
Indices: 49174150--49174231 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
49174140 TTTGAAAAGC
*
49174150 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
49174180 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
49174210 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
49174232 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:49176475 original size:30 final size:30
Alignment explanation
Indices: 49176441--49176538 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49176431 AGCTCACTCC
49176441 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49176471 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49176501 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49176531 TAGCTCAT
1 TAGCTCAT
49176539 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49180741 original size:29 final size:29
Alignment explanation
Indices: 49180675--49180731 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
49180665 GATTCAAAGA
*
49180675 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
49180704 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
49180732 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:49182862 original size:30 final size:31
Alignment explanation
Indices: 49182828--49182924 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
49182818 AGCTCACTCC
*
49182828 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
49182858 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
49182888 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
49182918 TAGCTCA
1 TAGCTCA
49182925 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:49185293 original size:30 final size:30
Alignment explanation
Indices: 49185222--49185304 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
49185212 CTTTTGTTTC
* *
49185222 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
49185253 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
49185282 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
49185305 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:49185304 original size:18 final size:18
Alignment explanation
Indices: 49185255--49185310 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
49185245 CACTCTCAAA
* *
49185255 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
49185272 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
49185290 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
49185309 TT
1 TT
49185311 CAAAGACTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:49185311 original size:12 final size:12
Alignment explanation
Indices: 49185280--49185304 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49185270 TTTTTCAATC
49185280 TCATTTTCTTTT
1 TCATTTTCTTTT
49185292 TCATTTTCTTTT
1 TCATTTTCTTTT
49185304 T
1 T
49185305 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:49185322 original size:12 final size:12
Alignment explanation
Indices: 49185307--49185337 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49185297 TTCTTTTTGC
49185307 TTTTCAAAGACT
1 TTTTCAAAGACT
*
49185319 TTTTCAAAGGCT
1 TTTTCAAAGACT
49185331 TTTTCAA
1 TTTTCAA
49185338 GTTCTCTCAA
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:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:49185395 original size:5 final size:5
Alignment explanation
Indices: 49185385--49185441 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49185375 CTCTTGCCTC
*
49185385 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
49185432 TCTTT TCTTT
1 TCTTT TCTTT
49185442 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:49185425 original size:15 final size:14
Alignment explanation
Indices: 49185385--49185441 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
49185375 CTCTTGCCTC
*
49185385 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
49185400 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
49185415 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
49185432 TCTTTTCTTT
1 TCTTTTCTTT
49185442 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:49185442 original size:21 final size:21
Alignment explanation
Indices: 49185385--49185452 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
49185375 CTCTTGCCTC
* *
49185385 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
49185406 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
49185427 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
49185447 CTCTTT
1 -TCTTT
49185453 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:49186380 original size:11 final size:12
Alignment explanation
Indices: 49186364--49186407 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 12
49186354 ACTCTTTTTC
49186364 TTTTTTTCG-AT
1 TTTTTTTCGAAT
49186375 TTTTTTTCGAATTT
1 TTTTTTTCGAA--T
49186389 TTTTTTTCGAAT
1 TTTTTTTCGAAT
49186401 TTTTTTT
1 TTTTTTT
49186408 TAACTTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.30
12 9 0.30
14 12 0.40
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.75
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:49186391 original size:14 final size:14
Alignment explanation
Indices: 49186374--49186408 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
49186364 TTTTTTTCGA
49186374 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
49186388 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
49186402 TTTTTTT
1 TTTTTTT
49186409 AACTTGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:49188132 original size:30 final size:30
Alignment explanation
Indices: 49188045--49188141 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
49188035 TTAAACTAAA
* *
49188045 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * *
49188075 TTGAGCT-AGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
49188104 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
49188134 ATGAGCTA
1 ATGAGCTA
49188142 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 22 0.43
30 29 0.57
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:49191619 original size:30 final size:30
Alignment explanation
Indices: 49191534--49191630 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
49191524 TAAACTAAAA
* *
49191534 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * * *
49191564 TGAGCTGAGATTAAACTCCTAAGCTGATGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
49191594 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
49191623 ATGAGCTA
1 -TGAGCTA
49191631 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:49196459 original size:14 final size:14
Alignment explanation
Indices: 49196420--49196467 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
49196410 GTACGAATGG
*
49196420 AATGGTAGGAACGA
1 AATGGTAGGAACAA
49196434 AA-GAGTAGGAACAA
1 AATG-GTAGGAACAA
*
49196448 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
49196462 ATTGGT
1 AATGGT
49196468 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:49202075 original size:30 final size:30
Alignment explanation
Indices: 49201980--49202076 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
49201970 AGCTCACTCC
* * *
49201980 TAGCTC-ACTTTCAACTCATGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
49202010 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
49202040 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
49202070 TAGCTCA
1 TAGCTCA
49202077 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:49204437 original size:25 final size:27
Alignment explanation
Indices: 49204400--49204452 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
49204390 TCAAACATGC
49204400 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
49204426 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
49204452 A
1 A
49204453 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:49206017 original size:32 final size:32
Alignment explanation
Indices: 49205980--49206044 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
49205970 AATGCTTACC
49205980 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
49206012 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
49206044 A
1 A
49206045 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:49208012 original size:30 final size:30
Alignment explanation
Indices: 49207918--49208005 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
49207908 TAAACTAAAA
* *
49207918 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
49207948 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
*
49207978 TGAGCTAAGGTTTAGCTCGTGAGATGAA
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
49208006 TATGAGCAAG
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:49211508 original size:15 final size:15
Alignment explanation
Indices: 49211488--49211535 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
49211478 TCAAAGATGG
49211488 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
49211503 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
49211518 -TTTATGGATATAAA
1 GTTTATGGATATGAA
49211532 GTTT
1 GTTT
49211536 TTATAGGATT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:49212248 original size:19 final size:19
Alignment explanation
Indices: 49212224--49212263 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
49212214 AGCTCCCATG
49212224 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
49212243 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
49212262 TA
1 TA
49212264 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:49213527 original size:14 final size:14
Alignment explanation
Indices: 49213505--49213552 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
49213495 ACCTAAACCG
* *
49213505 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
49213519 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
49213533 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
49213547 ACCATT
1 ACCATT
49213553 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:49215963 original size:12 final size:12
Alignment explanation
Indices: 49215946--49215970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49215936 GCCTCGACCA
49215946 CGACCACGGCCT
1 CGACCACGGCCT
49215958 CGACCACGGCCT
1 CGACCACGGCCT
49215970 C
1 C
49215971 TTCCCCGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.52, G:0.24, T:0.08
Consensus pattern (12 bp):
CGACCACGGCCT
Found at i:49217590 original size:26 final size:26
Alignment explanation
Indices: 49217561--49217613 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
49217551 TCAAACATGC
49217561 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGT-AATTTAACTCCTAGGGGT
* * *
49217587 ATTTCGGTAGTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTAACTCCTAGGGGT
49217613 A
1 A
49217614 AAACTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (26 bp):
ATTTAGGTAATTTAACTCCTAGGGGT
Found at i:49219179 original size:32 final size:32
Alignment explanation
Indices: 49219142--49219238 Score: 185
Period size: 32 Copynumber: 3.0 Consensus size: 32
49219132 AATGCTTACC
*
49219142 ATGCCCTTCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
49219174 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
49219206 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
49219238 A
1 A
49219239 AATGCATACA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:49221301 original size:49 final size:49
Alignment explanation
Indices: 49221183--49221410 Score: 271
Period size: 49 Copynumber: 4.6 Consensus size: 49
49221173 AAAACTGTGA
* * * ** *
49221183 TCACGTGTGTAGTACTAATTGTAGGCTACTACGTGTATTAGA-TGGTGAGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GT-TGG
*
49221233 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGG
* * * * *
49221282 TCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAAAAACTG-TGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CC--AGACTGTTGG
*
49221333 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGG
*
49221382 TCGCATGTGTAGTACTAAGTGCAGGCTAC
1 TCACATGTGTAGTACTAAGTGCAGGCTAC
49221411 AATTGTGTAT
Statistics
Matches: 154, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
48 5 0.03
49 64 0.42
50 44 0.29
51 36 0.23
52 5 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (49 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTGG
Found at i:49223007 original size:11 final size:11
Alignment explanation
Indices: 49222959--49223008 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
49222949 GACACCTGCA
49222959 ATTAAACACAT
1 ATTAAACACAT
*
49222970 -TAAAACAAACAT
1 ATTAAAC--ACAT
49222982 ATTAAACACAT
1 ATTAAACACAT
*
49222993 -TTAAACACTT
1 ATTAAACACAT
49223003 ATTAAA
1 ATTAAA
49223009 TACAAAACGC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 14 0.44
11 9 0.28
12 4 0.12
13 5 0.16
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (11 bp):
ATTAAACACAT
Found at i:49223687 original size:17 final size:19
Alignment explanation
Indices: 49223660--49223697 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49223650 TAGAAGTGAA
*
49223660 TGGATAGGTTT-GAATAAG
1 TGGATAGGTTTCAAATAAG
49223678 TGGA-AGGTTTCAAATAAG
1 TGGATAGGTTTCAAATAAG
49223696 TG
1 TG
49223698 TAAGAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.32, T:0.32
Consensus pattern (19 bp):
TGGATAGGTTTCAAATAAG
Found at i:49226603 original size:18 final size:18
Alignment explanation
Indices: 49226558--49226630 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
49226548 ATACTCACTC
49226558 TCTTTTTCAATTT-TCTTT
1 TCTTTTTCAATTTCT-TTT
* **
49226576 TATTGATCAATTTCTTTT
1 TCTTTTTCAATTTCTTTT
*
49226594 TCTTTTTCAATTTTGTTTT
1 TCTTTTTCAA-TTTCTTTT
49226613 TCTTTTCTC-A-TTCTTTT
1 TCTTTT-TCAATTTCTTTT
49226630 T
1 T
49226631 TGCTCTCTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
17 7 0.16
18 20 0.45
19 15 0.34
20 2 0.05
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.70
Consensus pattern (18 bp):
TCTTTTTCAATTTCTTTT
Found at i:49226631 original size:19 final size:19
Alignment explanation
Indices: 49226558--49226618 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 19
49226548 ATACTCACTC
*
49226558 TCTTTTTCAATTTT-CTTT
1 TCTTTTTCAATTTTGTTTT
* ** *
49226576 TATTGATCAA-TTTCTTTT
1 TCTTTTTCAATTTTGTTTT
49226594 TCTTTTTCAATTTTGTTTT
1 TCTTTTTCAATTTTGTTTT
49226613 TCTTTT
1 TCTTTT
49226619 CTCATTCTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
17 3 0.09
18 17 0.52
19 13 0.39
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (19 bp):
TCTTTTTCAATTTTGTTTT
Found at i:49230550 original size:45 final size:48
Alignment explanation
Indices: 49230443--49230552 Score: 149
Period size: 45 Copynumber: 2.4 Consensus size: 48
49230433 GGGAACACCA
* *
49230443 ACCAGCAGC-CTTCAA-GCATTAATCACGTTTCATGCTCCTATTCATGC
1 ACCAGCAGCTCTTTAATGCATTAATCACGTTTCATGCTCC-ACTCATGC
*
49230490 ACCAGCAGCTTTTTAATGCATTAATCACGTTTCATGC-CC-CT-ATGC
1 ACCAGCAGCTCTTTAATGCATTAATCACGTTTCATGCTCCACTCATGC
49230535 ACCAGCAGCTCTTTAATG
1 ACCAGCAGCTCTTTAATG
49230553 TGCCGTCCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
45 21 0.37
46 1 0.02
47 9 0.16
48 6 0.11
49 20 0.35
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (48 bp):
ACCAGCAGCTCTTTAATGCATTAATCACGTTTCATGCTCCACTCATGC
Found at i:49234021 original size:30 final size:30
Alignment explanation
Indices: 49233935--49234032 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
49233925 TTAAACTAAA
* *
49233935 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
49233965 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
49233995 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
49234025 ATGAGCTA
1 ATGAGCTA
49234033 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:49236315 original size:30 final size:30
Alignment explanation
Indices: 49236244--49236326 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
49236234 CTTTTGTTTC
* *
49236244 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
49236275 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
49236304 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
49236327 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:49236326 original size:18 final size:18
Alignment explanation
Indices: 49236277--49236332 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
49236267 CACTCTCAAA
* *
49236277 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
49236294 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
49236312 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
49236331 TT
1 TT
49236333 CAAAGACTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:49236333 original size:12 final size:12
Alignment explanation
Indices: 49236302--49236326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49236292 TTTTTCAATC
49236302 TCATTTTCTTTT
1 TCATTTTCTTTT
49236314 TCATTTTCTTTT
1 TCATTTTCTTTT
49236326 T
1 T
49236327 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:49236344 original size:12 final size:12
Alignment explanation
Indices: 49236329--49236359 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49236319 TTCTTTTTGC
49236329 TTTTCAAAGACT
1 TTTTCAAAGACT
*
49236341 TTTTCAAAGGCT
1 TTTTCAAAGACT
49236353 TTTTCAA
1 TTTTCAA
49236360 GTTCTCTCAA
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:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:49236417 original size:5 final size:5
Alignment explanation
Indices: 49236407--49236463 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49236397 CTCTTGCCTC
*
49236407 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
49236454 TCTTT TCTTT
1 TCTTT TCTTT
49236464 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:49236447 original size:15 final size:14
Alignment explanation
Indices: 49236407--49236463 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
49236397 CTCTTGCCTC
*
49236407 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
49236422 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
49236437 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
49236454 TCTTTTCTTT
1 TCTTTTCTTT
49236464 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:49236464 original size:21 final size:21
Alignment explanation
Indices: 49236407--49236474 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
49236397 CTCTTGCCTC
* *
49236407 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
49236428 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
49236449 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
49236469 CTCTTT
1 -TCTTT
49236475 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:49237407 original size:13 final size:12
Alignment explanation
Indices: 49237391--49237434 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
49237381 TTATTTTTAT
49237391 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
49237404 TTTTTTTTTGGAA
1 TTTTTTTTT-GAA
49237417 TTTTTTTTTG-A
1 TTTTTTTTTGAA
49237428 TTTTTTT
1 TTTTTTT
49237435 AACTTGTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 8 0.27
12 1 0.03
13 21 0.70
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:49242358 original size:30 final size:30
Alignment explanation
Indices: 49242324--49242407 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
49242314 TAAACTAAAA
* *
49242324 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
49242354 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
*
49242384 TGAGC-AAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
49242408 GAATATGAGC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:49242987 original size:11 final size:11
Alignment explanation
Indices: 49242971--49243034 Score: 94
Period size: 11 Copynumber: 5.7 Consensus size: 11
49242961 GTACAAGTAT
49242971 AAAAAAATTC-
1 AAAAAAATTCA
49242981 AAAAAAATTCA
1 AAAAAAATTCA
*
49242992 AAAAAAATTCG
1 AAAAAAATTCA
49243003 AAAAAAATTCA
1 AAAAAAATTCA
49243014 AAAAAAAGTTTCA
1 AAAAAAA--TTCA
49243027 AAAAAAAT
1 AAAAAAAT
49243035 GATTTGTGCA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
10 10 0.20
11 28 0.57
13 11 0.22
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:49243958 original size:9 final size:10
Alignment explanation
Indices: 49243951--49244006 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 10
49243941 AAGAGAAAAT
49243951 AAAGAAAAGA
1 AAAGAAAAGA
*
49243961 AAAGAAAAACA
1 AAAG-AAAAGA
*
49243972 AAAGAAGA-A
1 AAAGAAAAGA
49243981 AAAGAAAATGA
1 AAAGAAAA-GA
49243992 AATA-AAAAGA
1 AA-AGAAAAGA
49244002 AAAGA
1 AAAGA
49244007 GAGGCAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 9 0.24
10 12 0.32
11 16 0.42
12 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:49243961 original size:5 final size:5
Alignment explanation
Indices: 49243951--49244006 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
49243941 AAGAGAAAAT
* *
49243951 AAAGA AAAGA AAAGAA AAACA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA AA-AGA
49243997 AAAGA AAAGA
1 AAAGA AAAGA
49244007 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.10
5 29 0.69
6 8 0.19
7 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:49243983 original size:25 final size:25
Alignment explanation
Indices: 49243955--49244002 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
49243945 GAAAATAAAG
49243955 AAAAGAAAA-GAAAAACAAAAGAAGA
1 AAAAGAAAATGAAAAA-AAAAGAAGA
*
49243980 AAAAGAAAATGAAATAAAAAGAA
1 AAAAGAAAATGAAAAAAAAAGAA
49244003 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (25 bp):
AAAAGAAAATGAAAAAAAAAGAAGA
Found at i:49244086 original size:11 final size:12
Alignment explanation
Indices: 49244054--49244084 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49244044 TTGAGAGAAC
49244054 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49244066 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49244078 TTGAAAA
1 TTGAAAA
49244085 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:49244137 original size:30 final size:31
Alignment explanation
Indices: 49244087--49244157 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
49244077 TTTGAAAAGC
* *
49244087 AAAAAGAAA-ATGAGATTGAAAAAG-AGAATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAAG-ATG
49244117 -AAAAGAAATTTGAGAGTGAAAAAGAAGATG
1 AAAAAGAAATTTGAGAGTGAAAAAGAAGATG
49244147 AAAAAGAAATT
1 AAAAAGAAATT
49244158 GAAACAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 8 0.22
30 16 0.44
31 12 0.33
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (31 bp):
AAAAAGAAATTTGAGAGTGAAAAAGAAGATG
Found at i:49246428 original size:30 final size:30
Alignment explanation
Indices: 49246394--49246491 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49246384 AGCTCACTCC
49246394 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49246424 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49246454 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49246484 TAGCTCAT
1 TAGCTCAT
49246492 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49249614 original size:13 final size:14
Alignment explanation
Indices: 49249596--49249628 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
49249586 CAAAAACAAC
49249596 TTAATAAG-CTTAA
1 TTAATAAGACTTAA
49249609 TTAAT-AGACTTAA
1 TTAATAAGACTTAA
49249622 TTAATAA
1 TTAATAA
49249629 ACACATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 15 0.83
14 1 0.06
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (14 bp):
TTAATAAGACTTAA
Found at i:49253042 original size:10 final size:10
Alignment explanation
Indices: 49253029--49253063 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
49253019 AAGCTCGATT
49253029 GAGCTCAAAC
1 GAGCTCAAAC
*
49253039 GAGCTGAAAC
1 GAGCTCAAAC
*
49253049 GAGCTCAAAT
1 GAGCTCAAAC
49253059 GAGCT
1 GAGCT
49253064 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:49253072 original size:20 final size:20
Alignment explanation
Indices: 49253026--49253073 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
49253016 AGTAAGCTCG
49253026 ATTGAGCTCAAACGAGCTGA
1 ATTGAGCTCAAACGAGCTGA
** *
49253046 AACGAGCTCAAATGAGCTGA
1 ATTGAGCTCAAACGAGCTGA
*
49253066 GTTGAGCT
1 ATTGAGCT
49253074 GGACGGATCT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
ATTGAGCTCAAACGAGCTGA
Found at i:49254690 original size:18 final size:19
Alignment explanation
Indices: 49254667--49254705 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49254657 TTTATCTCAA
*
49254667 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
49254685 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
49254704 TT
1 TT
49254706 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:49254744 original size:18 final size:18
Alignment explanation
Indices: 49254723--49254766 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
49254713 AAACTCTTTT
49254723 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
49254741 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
49254759 TCAATCTC
1 TCATTCTC
49254767 AATCTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.55
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:49254751 original size:30 final size:30
Alignment explanation
Indices: 49254717--49254784 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
49254707 TCTCTCAAAC
* ** *
49254717 TCTTTTTCATTCTCTTTTTCAATCTCATTT
1 TCTTTTTCACTCTCAATCTCAATCTCATTT
*
49254747 TCTTTTTCACTCTCAATCTCAATCTCTTTT
1 TCTTTTTCACTCTCAATCTCAATCTCATTT
49254777 TCTTTTTC
1 TCTTTTTC
49254785 TTTCATTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.60
Consensus pattern (30 bp):
TCTTTTTCACTCTCAATCTCAATCTCATTT
Found at i:49254762 original size:24 final size:24
Alignment explanation
Indices: 49254698--49254779 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
49254688 CTTGTTCACA
* *
49254698 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCATT
* * * *
49254722 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCATT
* *
49254746 TTCTTTTTCACTCTCAATCTCAAT
1 TTCTTTTTCTCTCTCAATCTCATT
*
49254770 CTCTTTTTCT
1 TTCTTTTTCT
49254780 TTTTCTTTCA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.57
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCATT
Found at i:49254838 original size:42 final size:42
Alignment explanation
Indices: 49254782--49254878 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
49254772 CTTTTTCTTT
* * * *
49254782 TTCTTTCA-TTTCTTTGTTTCTTTTCTTGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
49254823 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
49254865 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
49254879 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:49255235 original size:10 final size:10
Alignment explanation
Indices: 49255220--49255246 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49255210 TACTCCTTCA
49255220 AGCTCAAATC
1 AGCTCAAATC
49255230 AGCTCAAATC
1 AGCTCAAATC
49255240 AGCTCAA
1 AGCTCAA
49255247 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:49259039 original size:13 final size:13
Alignment explanation
Indices: 49259023--49259047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49259013 AAAAATATCC
49259023 AAGAAAAGAAAAA
1 AAGAAAAGAAAAA
49259036 AAGAAAAGAAAA
1 AAGAAAAGAAAA
49259048 TCGAGAAAAT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAA
Found at i:49262022 original size:10 final size:10
Alignment explanation
Indices: 49262007--49262033 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49261997 TACTCCTTCA
49262007 AGCTCAAATC
1 AGCTCAAATC
49262017 AGCTCAAATC
1 AGCTCAAATC
49262027 AGCTCAA
1 AGCTCAA
49262034 CTTCAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:49264947 original size:30 final size:30
Alignment explanation
Indices: 49264862--49264958 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
49264852 TAAACTAAAA
* *
49264862 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
49264892 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
49264922 TGAGCTAAGTTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
49264951 ATGAGCTA
1 -TGAGCTA
49264959 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:49267138 original size:30 final size:30
Alignment explanation
Indices: 49267067--49267149 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
49267057 CTTTTCTTTC
* *
49267067 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
49267098 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
49267127 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
49267150 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.12, C:0.22, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:49267167 original size:12 final size:12
Alignment explanation
Indices: 49267152--49267182 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49267142 TTCTTTTTGC
49267152 TTTTCAAAGGCT
1 TTTTCAAAGGCT
49267164 TTTTCAAAGGCT
1 TTTTCAAAGGCT
49267176 TTTTCAA
1 TTTTCAA
49267183 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:49267296 original size:21 final size:20
Alignment explanation
Indices: 49267243--49267297 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
49267233 TTTCTTTTTA
49267243 TTTTATTTTCT-TTTTCTTC
1 TTTTATTTTCTCTTTTCTTC
*
49267262 TTTTGCTTTT-TCTTTTCTTC
1 TTTT-ATTTTCTCTTTTCTTC
49267282 TCTTTATTTTCTCTTT
1 T-TTTATTTTCTCTTT
49267298 ACAAGAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 5 0.17
20 17 0.57
21 8 0.27
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTATTTTCTCTTTTCTTC
Found at i:49268217 original size:11 final size:10
Alignment explanation
Indices: 49268201--49268254 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 10
49268191 TTAAACACTT
49268201 TTTTTTTTAGA
1 TTTTTTTTA-A
49268212 TTTTTTTTGAAA
1 TTTTTTTT--AA
*
49268224 TTTTTTTGAA
1 TTTTTTTTAA
49268234 TTTTTTTTCTAA
1 -TTTTTTT-TAA
49268246 TTTTTTTTA
1 TTTTTTTTA
49268255 CTTGTATAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 4 0.11
11 22 0.59
12 10 0.27
13 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.74
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:49268217 original size:12 final size:11
Alignment explanation
Indices: 49268200--49268253 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 11
49268190 ATTAAACACT
*
49268200 TTTTTTTTTAGA
1 TTTTTTTTGA-A
49268212 TTTTTTTTGAA
1 TTTTTTTTGAA
*
49268223 ATTTTTTTGAA
1 TTTTTTTTGAA
*
49268234 TTTTTTTTCTAA
1 TTTTTTTT-GAA
49268246 TTTTTTTT
1 TTTTTTTT
49268254 ACTTGTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:49268230 original size:22 final size:22
Alignment explanation
Indices: 49268201--49268252 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
49268191 TTAAACACTT
* *
49268201 TTTTTTTTAGATTTTTTTTGAAA
1 TTTTTTTGA-ATTTTTTTTCAAA
*
49268224 TTTTTTTGAATTTTTTTTCTAA
1 TTTTTTTGAATTTTTTTTCAAA
49268246 TTTTTTT
1 TTTTTTT
49268253 TACTTGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (22 bp):
TTTTTTTGAATTTTTTTTCAAA
Found at i:49270001 original size:30 final size:30
Alignment explanation
Indices: 49269916--49270012 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
49269906 TAAACTAAAA
* *
49269916 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
49269946 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
49269976 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
49270005 ATGAGCTA
1 -TGAGCTA
49270013 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:49273132 original size:11 final size:11
Alignment explanation
Indices: 49273112--49273151 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
49273102 AAGTTTTCAC
49273112 TTCA-ATTTTT
1 TTCAGATTTTT
49273122 TTCAGATTTTT
1 TTCAGATTTTT
*
49273133 TTCAAATTTTT
1 TTCAGATTTTT
49273144 TTCCAGAT
1 TT-CAGAT
49273152 CCTACTTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 4 0.15
11 18 0.69
12 4 0.15
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (11 bp):
TTCAGATTTTT
Found at i:49273349 original size:14 final size:14
Alignment explanation
Indices: 49273330--49273360 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
49273320 TGGATAGTTG
49273330 AAGAAAGGCTAAGA
1 AAGAAAGGCTAAGA
*
49273344 AAGAAAGGTTAAGA
1 AAGAAAGGCTAAGA
49273358 AAG
1 AAG
49273361 GTTCAAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (14 bp):
AAGAAAGGCTAAGA
Found at i:49276294 original size:15 final size:15
Alignment explanation
Indices: 49276274--49276304 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
49276264 TCTCTTTGTG
49276274 GACCTTGAGGAGTCC
1 GACCTTGAGGAGTCC
49276289 GACCTTGAGGAGTCC
1 GACCTTGAGGAGTCC
49276304 G
1 G
49276305 CTCTCGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19
Consensus pattern (15 bp):
GACCTTGAGGAGTCC
Found at i:49278536 original size:30 final size:30
Alignment explanation
Indices: 49278502--49278559 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
49278492 TGAGCTAAAC
* *
49278502 CGAGCTCACCCCTAGCTCA-TATTCAGCTCA
1 CGAGCTAAACCCTAGCTCAGT-TTCAGCTCA
*
49278532 CGAGCTAAACCTTAGCTCAGTTTCAGCT
1 CGAGCTAAACCCTAGCTCAGTTTCAGCT
49278560 TAGGAGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (30 bp):
CGAGCTAAACCCTAGCTCAGTTTCAGCTCA
Found at i:49283542 original size:13 final size:13
Alignment explanation
Indices: 49283524--49283552 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49283514 CGGCTAACCT
49283524 ACATAATTAAATA
1 ACATAATTAAATA
49283537 ACATAATTAAATA
1 ACATAATTAAATA
49283550 ACA
1 ACA
49283553 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:49287031 original size:17 final size:16
Alignment explanation
Indices: 49286996--49287031 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
49286986 ATTACAACTT
*
49286996 GAATTTTTTTTAATTC
1 GAATTTTTTTTAATAC
49287012 GAATTTTTTTTAACTAC
1 GAATTTTTTTTAA-TAC
49287029 GAA
1 GAA
49287032 CCTATTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
GAATTTTTTTTAATAC
Found at i:49288136 original size:13 final size:13
Alignment explanation
Indices: 49288118--49288146 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49288108 CGGCTAACCT
49288118 ACATAATTAAATA
1 ACATAATTAAATA
49288131 ACATAATTAAATA
1 ACATAATTAAATA
49288144 ACA
1 ACA
49288147 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:49291621 original size:17 final size:16
Alignment explanation
Indices: 49291586--49291621 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
49291576 ATTACAACTT
*
49291586 GAATTTTTTTTAATTC
1 GAATTTTTTTTAATAC
49291602 GAATTTTTTTTAACTAC
1 GAATTTTTTTTAA-TAC
49291619 GAA
1 GAA
49291622 CCTATTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
GAATTTTTTTTAATAC
Found at i:49292725 original size:13 final size:13
Alignment explanation
Indices: 49292707--49292735 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
49292697 CGGCTAACCT
49292707 ACATAATTAAATA
1 ACATAATTAAATA
49292720 ACATAATTAAATA
1 ACATAATTAAATA
49292733 ACA
1 ACA
49292736 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:49292991 original size:10 final size:10
Alignment explanation
Indices: 49292958--49293003 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
49292948 AAAAAGGAAT
49292958 GAGCTGAAAC
1 GAGCTGAAAC
49292968 GAGCT-AAATTC
1 GAGCTGAAA--C
49292979 GAGCTGAAAC
1 GAGCTGAAAC
*
49292989 GAGCTAAAAC
1 GAGCTGAAAC
49292999 GAGCT
1 GAGCT
49293004 CAAGTGAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.09
10 20 0.62
11 6 0.19
12 3 0.09
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:49305395 original size:30 final size:30
Alignment explanation
Indices: 49305343--49305427 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
49305333 TTCTTTTGTT
* *
49305343 TCAATTTCTTTTTCA-ACTTCTTTTTCACTC
1 TCAATTTCTTTTTCATTC-TCTTTTTCAATC
49305373 TCAAATTTC-TTTTCATTCTCTTTTTCAATC
1 TC-AATTTCTTTTTCATTCTCTTTTTCAATC
* *
49305403 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCATTCTCTTTTT
49305428 GCTTTTCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.10
30 36 0.75
31 7 0.15
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.62
Consensus pattern (30 bp):
TCAATTTCTTTTTCATTCTCTTTTTCAATC
Found at i:49305427 original size:18 final size:18
Alignment explanation
Indices: 49305378--49305433 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
49305368 CACTCTCAAA
*
49305378 TTTC-TTTTCATTCTCTT
1 TTTCATTTTCATTTTCTT
* *
49305395 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
49305413 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
49305432 TT
1 TT
49305434 CAAAGGCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 4 0.13
18 22 0.71
19 5 0.16
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:49305434 original size:12 final size:12
Alignment explanation
Indices: 49305403--49305427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49305393 TTTTTCAATC
49305403 TCATTTTCTTTT
1 TCATTTTCTTTT
49305415 TCATTTTCTTTT
1 TCATTTTCTTTT
49305427 T
1 T
49305428 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:49305519 original size:5 final size:5
Alignment explanation
Indices: 49305509--49305563 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
49305499 CTCTTGCGTC
* * *
49305509 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT T-TTT TCTTTT TCTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT TC-TTT TCTTT TCTTT
49305559 TCTTT
1 TCTTT
49305564 GTTTTCTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
4 6 0.14
5 27 0.64
6 9 0.21
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.82
Consensus pattern (5 bp):
TCTTT
Found at i:49305536 original size:6 final size:6
Alignment explanation
Indices: 49305527--49305563 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
49305517 TTTTATTTTG
49305527 TTTTCT TTTTCTT TTTTCT TTTTC- TTTTC- TTTTCT TT
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TT
49305564 GTTTTCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:49305545 original size:13 final size:13
Alignment explanation
Indices: 49305527--49305554 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
49305517 TTTTATTTTG
49305527 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
49305540 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
49305553 TT
1 TT
49305555 CTTTTCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:49306470 original size:29 final size:29
Alignment explanation
Indices: 49306404--49306460 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
49306394 GATTCAAAGA
*
49306404 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
49306433 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
49306461 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:49307460 original size:14 final size:14
Alignment explanation
Indices: 49307418--49307462 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
49307408 TTAAAGAAGC
49307418 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
49307432 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
49307445 AACTCATTTAATTA
1 AACTCATTAAATTA
49307459 AACT
1 AACT
49307463 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:49310986 original size:16 final size:17
Alignment explanation
Indices: 49310967--49311000 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
49310957 TTGTTTGAAA
49310967 TTTTTTTTC-TTTTTTT
1 TTTTTTTTCGTTTTTTT
49310983 TTTTTTTTCGTTTTTTT
1 TTTTTTTTCGTTTTTTT
49311000 T
1 T
49311001 GAAACTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (17 bp):
TTTTTTTTCGTTTTTTT
Found at i:49311248 original size:28 final size:28
Alignment explanation
Indices: 49311216--49311271 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
49311206 GATTCAAAGA
*
49311216 TGGGTTTATGGATATGAAGTTTATGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
*
49311244 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
49311272 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (28 bp):
TGGGTTTATGGATATAAAGTTTATGTAG
Found at i:49312283 original size:14 final size:14
Alignment explanation
Indices: 49312241--49312285 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
49312231 TTAAAGAAGC
49312241 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
49312255 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
49312268 AACTCATTTAATTA
1 AACTCATTAAATTA
49312282 AACT
1 AACT
49312286 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:49312868 original size:11 final size:11
Alignment explanation
Indices: 49312852--49312901 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
49312842 ATAAAACACC
49312852 TTTTTTCAGATT
1 TTTTTTCAGA-T
*
49312864 TTTTTTCAAAT
1 TTTTTTCAGAT
*
49312875 TTTTTTGA-AT
1 TTTTTTCAGAT
49312885 TTTTTTC-GAAT
1 TTTTTTCAG-AT
49312896 TTTTTT
1 TTTTTT
49312902 AACTTGTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
10 8 0.24
11 16 0.48
12 9 0.27
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTTTTCAGAT
Found at i:49312869 original size:12 final size:12
Alignment explanation
Indices: 49312852--49312901 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
49312842 ATAAAACACC
*
49312852 TTTTTTCAGATT
1 TTTTTTCAAATT
49312864 TTTTTTCAAA-T
1 TTTTTTCAAATT
*
49312875 TTTTTT-GAA-T
1 TTTTTTCAAATT
*
49312885 TTTTTTCGAATT
1 TTTTTTCAAATT
49312897 TTTTT
1 TTTTT
49312902 AACTTGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 9 0.26
11 10 0.29
12 15 0.44
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (12 bp):
TTTTTTCAAATT
Found at i:49313251 original size:30 final size:30
Alignment explanation
Indices: 49313217--49313314 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49313207 AGCTCACTCC
49313217 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49313247 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49313277 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49313307 TAGCTCAT
1 TAGCTCAT
49313315 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:49314753 original size:14 final size:14
Alignment explanation
Indices: 49314734--49314778 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
49314724 AACTCATCTT
*
49314734 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
49314748 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
49314761 AATTTAATTTAATG
1 AGTTTAATTTAATG
49314775 AGTT
1 AGTT
49314779 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:49320766 original size:29 final size:29
Alignment explanation
Indices: 49320697--49320756 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
49320687 AAGGATTCAA
* *
49320697 AGATGGGTTTGTGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
49320726 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
49320755 AG
1 AG
49320757 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Done.