Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 22
Found at i:1801651 original size:31 final size:31
Alignment explanation
Indices: 1801555--1801778 Score: 296
Period size: 31 Copynumber: 7.3 Consensus size: 31
1801545 ATACCTTCTT
*
1801555 AAAGTCCACGACTCAGTGGCATTTTGTC-CC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* *
1801585 AAAGTCCACGACTCAGTAGCATTTTGTC-CC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
*
1801615 AAAGTCCACGACTTAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
*
1801646 AAAGTCCACAACTCAGTGGCAATCTCTTTT-T--
1 AAAGTCCACGACTCAGTGGC-AT-T-TTTTCTCC
*
1801677 AAAGTCCACGACTCAGTGGCATTTTTTCTCT
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
1801708 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
* * *
1801739 AAAGTCCATGACTCAGTGGCATCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATTTTTTCTCC
*
1801770 AAAGCCCAC
1 AAAGTCCAC
1801779 AACTTCGTGG
Statistics
Matches: 174, Mismatches: 13, Indels: 13
0.87 0.06 0.06
Matches are distributed among these distances:
28 4 0.02
29 2 0.01
30 56 0.32
31 104 0.60
32 2 0.01
33 2 0.01
34 4 0.02
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTTTCTCC
Found at i:1801810 original size:37 final size:37
Alignment explanation
Indices: 1801760--1801839 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
1801750 CTCAGTGGCA
1801760 TCTTTTCTTCAAAGCCCACAACT-TCGTGGCACCTTTT
1 TCTTTTCTTCAAAGCCCACAACTCT-GTGGCACCTTTT
* *
1801797 TCTTTTCTTCAAAGCCCACCACTCTGTGGTACCTTTT
1 TCTTTTCTTCAAAGCCCACAACTCTGTGGCACCTTTT
*
1801834 CCTTTT
1 TCTTTT
1801840 AAGTCCACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 38 0.97
38 1 0.03
ACGTcount: A:0.16, C:0.33, G:0.10, T:0.41
Consensus pattern (37 bp):
TCTTTTCTTCAAAGCCCACAACTCTGTGGCACCTTTT
Found at i:1801870 original size:35 final size:36
Alignment explanation
Indices: 1801830--1801900 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1801820 CTGTGGTACC
*
1801830 TTTTCC-TTTTAAGTCCACAACTTCGTGACATCTTT
1 TTTTCCTTTTTAAGTCCACAACTCCGTGACATCTTT
* *
1801865 TTTTCCTTTTTAAGTCCATAACTCCGTGGCATCTTT
1 TTTTCCTTTTTAAGTCCACAACTCCGTGACATCTTT
1801901 CTCCTTTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.18, C:0.25, G:0.10, T:0.46
Consensus pattern (36 bp):
TTTTCCTTTTTAAGTCCACAACTCCGTGACATCTTT
Found at i:1802028 original size:49 final size:48
Alignment explanation
Indices: 1801969--1803217 Score: 1315
Period size: 49 Copynumber: 26.8 Consensus size: 48
1801959 GGCATCTTCT
* * *
1801969 TTTAAGTCCAATGTAGCTGGACTTGAATCAGCACATTGGCATCTTCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
* * *
1802018 TTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
1802067 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* * * * *
1802110 TTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTAGCATCTTCATA
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
*
1802159 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
1802202 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* * * *
1802245 TTTAACTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
* * * *
1802294 TTTAAGTCCAATGTCGCTGGCCTTAAATTAGCACATTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1802337 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
** * * * * * * *
1802386 TTTAAACCCAATGTTGTTGGCCTTGAATCAACACATCGACA-TTCTTC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* * *
1802433 TTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCA---C-T-
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1802476 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCAAATTGGCATCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
** * * * * *
1802525 TTTAAACCCAATGTTGTTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
* *
1802574 TTTAAGTCCAATGTAGCTGGCCTTGAATAAGCACATTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1802617 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCCTCATCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA--CT--TCATC
* * * *
1802669 TTTAAGTCTAATATAGCTGGCCTTGAATCAACATATTGGCACCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1802717 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
* *
1802766 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACCTTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* * *
1802809 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCACC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1802857 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* * *
1802905 TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
* * *
1802954 TTTAAGTCCAATGTAG-TAGCCTTGAATCAGCACCTTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1802996 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
* *
1803045 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACCTTGGCA---C--C
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* * *
1803088 TTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC
*
1803137 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC--CA--
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
* *
1803181 -TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
1803218 ACATCCTTTT
Statistics
Matches: 1025, Mismatches: 122, Indels: 112
0.81 0.10 0.09
Matches are distributed among these distances:
42 16 0.02
43 364 0.36
44 1 0.00
45 3 0.00
46 2 0.00
47 41 0.04
48 150 0.15
49 407 0.40
50 2 0.00
52 39 0.04
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (48 bp):
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACTTCATC
Found at i:1802163 original size:92 final size:88
Alignment explanation
Indices: 1802066--1803217 Score: 1184
Period size: 92 Copynumber: 12.4 Consensus size: 88
1802056 GCACCTTTAT
* * *
1802066 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCAATATCGCTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCTTTAAGTCCAATGTAGCTG
* * *
1802129 GCCTTGAATCAGTATATTAGCATC
66 GCCTTGAATCAGCACATTGGCA-C
* * *
1802153 TTCATATTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCAATAT
1 --C---TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCTTTAAGTCCAATGT
1802216 AGCTGGCCTTGAATCAGCACATTGGCAC
61 AGCTGGCCTTGAATCAGCACATTGGCAC
* * *
1802244 CTTTAACTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC----TCTTTAAGTCCAATGTA
* *
1802309 GCTGGCCTTAAATTAGCACATTGGCAC
62 GCTGGCCTTGAATCAGCACATTGGCAC
* ** *
1802336 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAACCCAATGTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C--C-TCTTTAAGTCCAATGTA
* * * *
1802401 GTTGGCCTTGAATCAACACATCGACATTC
62 GCTGGCCTTGAATCAGCACATTGGCA--C
* * * * * *
1802430 TTCTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCA-CT-TTTAAGTCCAATATCGC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCTTTAAGTCCAATGTAGC
*
1802493 TGGCCTTGAATCAGCAAATTGGCATCTTC
64 TGGCCTTGAATCAGCACATTGGCA----C
** * * *
1802522 ATCTTTAAACCCAATGTTGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC----TCTTTAAGTCCAATG
*
1802587 TAGCTGGCCTTGAATAAGCACATTGGCAC
60 TAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1802616 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCCTCATCATCTTTAAGTCTAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--C-TCTTTAAGTCCAAT
* * *
1802681 ATAGCTGGCCTTGAATCAACATATTGGCACCTC
59 GTAGCTGGCCTTGAATCAGCACATTGGCA---C
* * *
1802714 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C--C-TCTTTAAGTCCAATG
*
1802779 TAGCTGGCCTTGAATCAGCACCTTGGCAC
60 TAGCTGGCCTTGAATCAGCACATTGGCAC
*
1802808 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCACCTTTAAGTCCAATATAG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT---CTTTAAGTCCAATGTAG
*
1802873 CTGGCCTTGAATCAGCATATTGGCACCTC
63 CTGGCCTTGAATCAGCACATTGGCA---C
* * *
1802902 ATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTTATCTTTAAGTCCAATG
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC----TCTTTAAGTCCAATG
* *
1802967 TAG-TAGCCTTGAATCAGCACCTTGGCAC
60 TAGCTGGCCTTGAATCAGCACATTGGCAC
1802995 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC----TCTTTAAGTCCAATGTA
*
1803060 GCTGGCCTTGAATCAGCACCTTGGCAC
62 GCTGGCCTTGAATCAGCACATTGGCAC
*
1803087 CTTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC----TCTTTAAGTCCAATGTA
1803152 GCTGGCCTTGAATCAGCACATTGGCAC
62 GCTGGCCTTGAATCAGCACATTGGCAC
* *
1803179 CATTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTG
1803218 ACATCCTTTT
Statistics
Matches: 926, Mismatches: 89, Indels: 93
0.84 0.08 0.08
Matches are distributed among these distances:
86 37 0.04
87 1 0.00
88 1 0.00
89 3 0.00
90 32 0.03
91 105 0.11
92 461 0.50
93 3 0.00
94 4 0.00
95 40 0.04
96 102 0.11
97 59 0.06
98 39 0.04
100 39 0.04
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (88 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTCTTTAAGTCCAATGTAGCTG
GCCTTGAATCAGCACATTGGCAC
Found at i:1802203 original size:21 final size:21
Alignment explanation
Indices: 1802179--1802246 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1802169 ATGTAGCTGG
1802179 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
1802200 CCTTTAAGTC--CA-ATATAGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
1802222 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
1802243 CCTT
1 CCTT
1802247 TAACTCCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:1803912 original size:19 final size:19
Alignment explanation
Indices: 1803888--1803952 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
1803878 TGTCAACGAT
1803888 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1803907 TTGTAT-GATTC--AA---
1 TTGTATCGATACATAAGTG
1803920 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1803938 TTGTATCGATACATA
1 TTGTATCGATACATA
1803953 TGAAGCTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
12 5 0.14
13 4 0.11
15 2 0.05
16 2 0.05
18 4 0.11
19 20 0.54
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1804012 original size:13 final size:13
Alignment explanation
Indices: 1803994--1804018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1803984 ATTACTCAAA
1803994 TGTATCGATACAT
1 TGTATCGATACAT
1804007 TGTATCGATACA
1 TGTATCGATACA
1804019 CTGATATTTG
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:1804071 original size:52 final size:52
Alignment explanation
Indices: 1804007--1804152 Score: 222
Period size: 52 Copynumber: 2.8 Consensus size: 52
1803997 ATCGATACAT
**
1804007 TGTATCGATACACTGAT-ATTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1804059 TGTATCGATACACTATGAAATGTATGGATACATACAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1804111 TGTATCGATATACTATGAAATGTATCGATACATGTAGGCAAA
1 TGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAA
1804153 ATTTCATATT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACACTATGAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1808588 original size:20 final size:20
Alignment explanation
Indices: 1808541--1808592 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1808531 CTTAACTGTT
*
1808541 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
* *
1808560 TGTACCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1808580 TGTATCGATACAT
1 TGTATCGATACAT
1808593 TGGCTTGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1811983 original size:33 final size:33
Alignment explanation
Indices: 1811941--1812005 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1811931 TACAAGCTAA
* *
1811941 TGTATTGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATTGATACATA-CTTTGGTGTATCGATACAT
1811974 TGTATTGATACATACTTTGGTGTATCGATACA
1 TGTATTGATACATACTTTGGTGTATCGATACA
1812006 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.45
Consensus pattern (33 bp):
TGTATTGATACATACTTTGGTGTATCGATACAT
Found at i:1812707 original size:39 final size:40
Alignment explanation
Indices: 1812632--1812722 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 40
1812622 TTTTCTTTCT
* **
1812632 CCCTTAATTAAAGTAATTTTAACAAGTTTGTACATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTTACACATTCTCC
* * *
1812672 CCCTTAA-TAAGGTAATTTTAGCAAATTTACGCATTCTCC
1 CCCTTAATTAAAGTAATTTTAACAAATTTACACATTCTCC
* *
1812711 CCTTTTATTAAA
1 CCCTTAATTAAA
1812723 AAATCTCCCC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
39 31 0.76
40 10 0.24
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.40
Consensus pattern (40 bp):
CCCTTAATTAAAGTAATTTTAACAAATTTACACATTCTCC
Found at i:1820771 original size:13 final size:13
Alignment explanation
Indices: 1820753--1820778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1820743 CAATTTTTTG
1820753 TGTATCGATACAT
1 TGTATCGATACAT
1820766 TGTATCGATACAT
1 TGTATCGATACAT
1820779 ACTTTCGTGT
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:1820775 original size:33 final size:33
Alignment explanation
Indices: 1820733--1820797 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1820723 TACAAGCCAA
* *
1820733 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCGTGTATCGATACAT
1820766 TGTATCGATACATACTTTCGTGTATCGATACA
1 TGTATCGATACATACTTTCGTGTATCGATACA
1820798 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTCGTGTATCGATACAT
Found at i:1825092 original size:18 final size:16
Alignment explanation
Indices: 1825056--1825113 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
1825046 CTTCGATTGC
*
1825056 AAAAAAAA-AAAACATA
1 AAAAAAAACAAAAC-CA
1825072 AAAGAAAAACAATAACCAA
1 AAA-AAAAACAA-AACC-A
*
1825091 AAAAAAAACAAAACGA
1 AAAAAAAACAAAACCA
1825107 AAAAAAA
1 AAAAAAA
1825114 CCTAGCTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 11 0.31
17 8 0.22
18 10 0.28
19 7 0.19
ACGTcount: A:0.83, C:0.10, G:0.03, T:0.03
Consensus pattern (16 bp):
AAAAAAAACAAAACCA
Found at i:1825096 original size:17 final size:17
Alignment explanation
Indices: 1825056--1825113 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1825046 CTTCGATTGC
1825056 AAAAAAAA-AAAA-CATA
1 AAAAAAAACAAAACCA-A
1825072 AAAGAAAAACAATAACCAA
1 AAA-AAAAACAA-AACCAA
*
1825091 AAAAAAAACAAAACGAA
1 AAAAAAAACAAAACCAA
1825108 AAAAAA
1 AAAAAA
1825114 CCTAGCTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 3 0.08
17 16 0.43
18 10 0.27
19 6 0.16
20 2 0.05
ACGTcount: A:0.83, C:0.10, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAAAACAAAACCAA
Found at i:1826180 original size:63 final size:62
Alignment explanation
Indices: 1826097--1827080 Score: 660
Period size: 63 Copynumber: 15.5 Consensus size: 62
1826087 TTCTTTTTTC
* * * *
1826097 TTTTAAAAGCCCATATAAGTTGTTGGCACCTTTTAGTCCTTAAAGAGCTGGACACCTTTTCCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAG-TGGACACCTTTTCCT
* *
1826160 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTT-GTCCTCAAAGAGCAGGACACTTTGCTTTTT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAG-TGGACAC----CTTTTC
1826224 C-
61 CT
* * * * * * * ** *
1826225 TTTTAAAAGCCTATACAAGCTGGTAGCATCTTTTAATTCTCAAAGAGCAGA-ATGCCTTTTCTT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTGGACA--CCTTTTCCT
* * * * *
1826288 TTTTAAAAGCCCACACAAGTTGGTGTCACCTTTTAGTACTCAAAAAGTAGGACATCATTTCCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-GGACACCTTTTCCT
* * * *
1826351 TTTTAAAATCCCACACAAGTTGGTCGCACCTTTTAGTCCTCAAAGAGTAGGATGA-CTTTTCCC
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-GGA-CACCTTTTCCT
* * * * *
1826414 TTTTAAAAGCCTACACAAGCTGGTGGCACTTTTTAGCCCTTAAAGAGTAGGATGC-CCTTTTTCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-GGA--CACC-TTTTC-
*
1826478 TTTT
61 --CT
* * * * * ** * *
1826482 TTTTCAAAA-CCCATC-TATGTTGATGGCACCTTTTAATTCTCAAAGAGCAAGACACTTTCCTTT
1 TTTT-AAAAGCCCA-CACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAG-TGGACACCTT--TTC
*
1826545 TT
61 CT
* * *
1826547 TTTTTAAAGCCCACACAAGTTGGTGGAACCTTTTAGTCCTCAAAGAGCAGGACACC-TTTCC-
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAG-TGGACACCTTTTCCT
* * *
1826608 --CT-----CCCACACAA-TTGGTGGCATCTTTTAGTCCTCAAAGAGTAGGACATCTTTTCCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-GGACACCTTTTCCT
* * * * * * **
1826663 TTTTAAAAGCCCACACAAGTTGGCGGCACATTTTTGTCCTTAAAGAGGAGGACATCTTTTTTT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA-GTGGACACCTTTTCCT
* * ** *
1826726 CTTTTAAAA-CCCTATACAAGTTGGTGGCACCTTTTAGTCCTAAAAGACCAGGATACCTTTTCCT
1 -TTTTAAAAGCCC-ACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA-GTGGACACCTTTTCCT
* * * * *
1826790 TTTTAAAAGCACATACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGTAGGACACATTTTTTTCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-GGACAC--CTTTTCCT
* * ** *
1826855 TTTTAAAAGTCCACACAAGTTGGTGGTACCTTTTAGTCCTCAAAGAGTAGGATGCATTTTCCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT-GGACACCTTTTCCT
* * * * *
1826918 TTTGAAAAGCCCACATAAGCTGGTGGCACCTTTTAGTCCTCAAA-ATGTAGA-ATGTCTTTTTTT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA-GTGGACA---C---CTTT
*
1826981 TTCT
59 TCCT
* * * ** * *
1826985 TTTTAAAAGCCCATAGAAGTTGGTGGCACTCGTTTTTAGTCCTTAAAGAGAAAGACTCATTTT-C
1 TTTTAAAAGCCCACACAAGTTGGTGGCAC-C--TTTTAGTCCTCAAAGAG-TGGACACCTTTTCC
1827049 T
62 T
* *
1827050 TTTTCAAAGCCCACCCAAGTTGGTGGCACCT
1 TTTTAAAAGCCCACACAAGTTGGTGGCACCT
1827081 ATCTACTTCA
Statistics
Matches: 727, Mismatches: 138, Indels: 113
0.74 0.14 0.12
Matches are distributed among these distances:
53 32 0.04
54 14 0.02
57 1 0.00
59 1 0.00
62 38 0.05
63 302 0.42
64 63 0.09
65 161 0.22
66 24 0.03
67 32 0.04
68 35 0.05
69 6 0.01
70 14 0.02
71 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (62 bp):
TTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTGGACACCTTTTCCT
Found at i:1826294 original size:128 final size:128
Alignment explanation
Indices: 1826059--1827080 Score: 885
Period size: 128 Copynumber: 8.0 Consensus size: 128
1826049 AACCTTTTAT
** * *
1826059 CCTTTTAGTCCTCAAAGAGCAGGATGCTTTCTTTTTTCTTTTAAAAGCCCATATAAGTTGTTGGC
1 CCTTTTAGTCCTCAAAGAGCAGGACACTTTC-TTTTTCTTTTAAAAGCCCATACAAGTTGGTGGC
* * **
1826124 ACCTTTTAGTCCTTAAAGAGCTGGACACCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
65 ACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
* * *
1826188 CCTTTT-GTCCTCAAAGAGCAGGACACTTTGCTTTTTCTTTTAAAAGCCTATACAAGCTGGTAGC
1 CCTTTTAGTCCTCAAAGAGCAGGACACTTT-CTTTTTCTTTTAAAAGCCCATACAAGTTGGTGGC
* * * * * *
1826252 ATCTTTTAATTCTCAAAGAGCAGAATGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGTCA
65 ACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
* * * * * * * *
1826316 CCTTTTAGTACTCAAAAAGTAGGACA---TCATTTCCTTTTTAAAATCCCACACAAGTTGGTCGC
1 CCTTTTAGTCCTCAAAGAGCAGGACACTTTCTTTTTC-TTTTAAAAGCCCATACAAGTTGGTGGC
* * * * *
1826378 ACCTTTTAGTCCTCAAAGAGTAGGATGACTTTTCCCTTTTAAAAGCCTACACAAGCTGGTGGCA
65 ACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1826442 CTTTTTAGCCCTTAAAGAGTAGGATGCCCTTTTTCTTTTT-TTTTCAAAA-CCCAT-CTATGTTG
1 CCTTTTAGTCCTCAAAGAGCAGGA--CAC--TTTCTTTTTCTTTT-AAAAGCCCATAC-AAGTTG
* * * * * *
1826504 ATGGCACCTTTTAATTCTCAAAGAGCAAGACACTTTCCTTTT--TTTTTTAAAGCCCACACAAGT
60 GTGGCACCTTTTAGTCCTCAAAGAGC-AG-GA--TGCCTTTTCCTTTTTAAAAGCCCACACAAGT
*
1826567 TGGTGGAA
121 TGGTGGCA
** *
1826575 CCTTTTAGTCCTCAAAGAGCAGGACAC---C--TTTC-CCT-----CCCACACAA-TTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACACTTTCTTTTTCTTTTAAAAGCCCATACAAGTTGGTGGCA
* * *** *
1826628 TCTTTTAGTCCTCAAAGAGTAGGACATCTTTTCCTTTTTAAAAGCCCACACAAGTTGGCGGCA
66 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
* * * *
1826691 CATTTTTGTCCTTAAAGAGGAGGACA-TCTT-TTTTTCTTTTAAAA-CCCTATACAAGTTGGTGG
1 CCTTTTAGTCCTCAAAGAGCAGGACACT-TTCTTTTTCTTTTAAAAGCCC-ATACAAGTTGGTGG
* * * * *
1826753 CACCTTTTAGTCCTAAAAGACCAGGATACCTTTTCCTTTTTAAAAGCACATACAAGTTGGTGGCA
64 CACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
* * * * * *
1826818 CCTTTTAGTCCTCAAAAAGTAGGACACATT-TTTTTCTTTTTAAAAGTCCACACAAGTTGGTGGT
1 CCTTTTAGTCCTCAAAGAGCAGGACACTTTCTTTTTC-TTTTAAAAGCCCATACAAGTTGGTGGC
* * * * *
1826882 ACCTTTTAGTCCTCAAAGAGTAGGATGCATTTTCCTTTTGAAAAGCCCACATAAGCTGGTGGCA
65 ACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
* * ** * *
1826946 CCTTTTAGTCCTCAAA-ATGTAGAATGTCTTTTTTTTTCTTTTTAAAAGCCCATAGAAGTTGGTG
1 CCTTTTAGTCCTCAAAGA-GCAGGA-CACTTTCTTTTTC-TTTTAAAAGCCCATACAAGTTGGTG
* * * * * *
1827010 GCACTCGTTTTTAGTCCTTAAAGAGAAAGACT-CATTTT-CTTTTTCAAAGCCCACCCAAGTTGG
63 GCAC-C--TTTTAGTCCTCAAAGAGCAGGA-TGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGG
1827073 TGGCA
124 TGGCA
1827078 CCT
1 CCT
1827081 ATCTACTTCA
Statistics
Matches: 717, Mismatches: 133, Indels: 83
0.77 0.14 0.09
Matches are distributed among these distances:
114 5 0.01
116 49 0.07
117 2 0.00
118 24 0.03
119 5 0.01
120 5 0.01
121 1 0.00
124 4 0.01
125 8 0.01
126 101 0.14
127 93 0.13
128 206 0.29
129 28 0.04
130 33 0.05
131 37 0.05
132 34 0.05
133 75 0.10
134 1 0.00
135 6 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (128 bp):
CCTTTTAGTCCTCAAAGAGCAGGACACTTTCTTTTTCTTTTAAAAGCCCATACAAGTTGGTGGCA
CCTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAAGCCCACACAAGTTGGTGGCA
Found at i:1826637 original size:53 final size:54
Alignment explanation
Indices: 1826556--1826658 Score: 163
Period size: 53 Copynumber: 1.9 Consensus size: 54
1826546 TTTTTTAAAG
1826556 CCCACACAAGTTGGTGGAACCTTTTAGTCCTCAAAGAGCAGGACACCTTTCCCT
1 CCCACACAAGTTGGTGGAACCTTTTAGTCCTCAAAGAGCAGGACACCTTTCCCT
* * * *
1826610 CCCACACAA-TTGGTGGCATCTTTTAGTCCTCAAAGAGTAGGACATCTTT
1 CCCACACAAGTTGGTGGAACCTTTTAGTCCTCAAAGAGCAGGACACCTTT
1826659 TCCTTTTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 36 0.80
54 9 0.20
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (54 bp):
CCCACACAAGTTGGTGGAACCTTTTAGTCCTCAAAGAGCAGGACACCTTTCCCT
Found at i:1827587 original size:20 final size:19
Alignment explanation
Indices: 1827558--1827598 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
1827548 AACAATGTAA
1827558 ATAATGAATGTATCGATAC
1 ATAATGAATGTATCGATAC
1827577 ATAAGTGAATGTATCGATAC
1 ATAA-TGAATGTATCGATAC
1827597 AT
1 AT
1827599 GTCTAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (19 bp):
ATAATGAATGTATCGATAC
Found at i:1827714 original size:51 final size:52
Alignment explanation
Indices: 1827647--1827759 Score: 138
Period size: 52 Copynumber: 2.2 Consensus size: 52
1827637 TTTTGCATTC
* * *
1827647 ATCGATACATTCTGGG-TTTTAACCTAAATGTATCCATACATTTTTCAATGA
1 ATCGATACATTCTGGGTTTTTAACCCAAATGCATCCATACATTCTTCAATGA
* * ** *
1827698 ATCGATACATTTTGGGTTTTTGACCCAAATGCATTGATACATTCTTCAATGT
1 ATCGATACATTCTGGGTTTTTAACCCAAATGCATCCATACATTCTTCAATGA
*
1827750 ATCAATACAT
1 ATCGATACAT
1827760 GCAAGGTATT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
51 15 0.29
52 37 0.71
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (52 bp):
ATCGATACATTCTGGGTTTTTAACCCAAATGCATCCATACATTCTTCAATGA
Found at i:1830217 original size:52 final size:51
Alignment explanation
Indices: 1830156--1830303 Score: 199
Period size: 52 Copynumber: 2.8 Consensus size: 51
1830146 CATTTCCGAG
* * * *
1830156 GGGATACTCCTATCCCGTTTTTATTTCCAAAATATTGATTTTTTCACTATTA
1 GGGATACTCC-AACCCATTTTTATTTCCAAAATATTAATTTTTTCACCATTA
* *
1830208 GGGATACTCCAACCTTATTTTTATTTCCAAAATATCAATTTTTTCACCATTA
1 GGGATACTCCAACC-CATTTTTATTTCCAAAATATTAATTTTTTCACCATTA
1830260 GGGATACTCCAACCCCATTTTTATTT-CAAAATATTAAATTTTTT
1 GGGATACTCCAA-CCCATTTTTATTTCCAAAATATT-AATTTTTT
1830304 GTCAAGAGGA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 11 0.13
52 72 0.85
53 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (51 bp):
GGGATACTCCAACCCATTTTTATTTCCAAAATATTAATTTTTTCACCATTA
Found at i:1830394 original size:78 final size:78
Alignment explanation
Indices: 1830260--1830689 Score: 364
Period size: 79 Copynumber: 5.4 Consensus size: 78
1830250 TTCACCATTA
* * *** * **
1830260 GGGATACTCCAACCCCATTTTTATTTCAAAATATTAAATTTTTTGTCA-AGAGGATACTCCAGTC
1 GGGATACTCAAACCCCATTTTTATTTCAAAATATT-GATTTTTCACCATCGAGGATACTCCAACC
*
1830324 CTGTTATTTCTGAG
65 CCGTTATTTCTGAG
* * * * * *
1830338 GGGATACTCAAACCTCGTTTTTATTTCAAAATATTGATTTTTCACCATTGACGATACTCTAACAC
1 GGGATACTCAAACCCCATTTTTATTTCAAAATATTGATTTTTCACCATCGAGGATACTCCAACCC
* *
1830403 AGTTATTT-TCGAA
66 CGTTATTTCT-GAG
* * * * *
1830416 GGGATACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCCATC-TCAAGGATACTCCAA
1 GGGATACTCAAACCCCATTTTTATTT-CAAAATATT--GATTTTTCACCATCGAGGATACTCCAA
*
1830480 CCCCGTT-TATTCCGAG
63 CCCCGTTAT-TTCTGAG
* * * * *
1830496 AGGATACTCTATCCCTATTTTTATTTCCAAAATATCGATTTTTCACCATCGAGGATACTCCAACC
1 GGGATACTCAAACCCCATTTTTATTT-CAAAATATTGATTTTTCACCATCGAGGATACTCCAACC
*
1830561 CCATTATTTCTGAG
65 CCGTTATTTCTGAG
* * * ** * *
1830575 GAGATACTCCAATCCTGTTTTTATTTCTAAATTATCGATTTTTCACCATCGAGGATACTCCAACC
1 GGGATACTCAAACCCCATTTTTATTTC-AAAATATTGATTTTTCACCATCGAGGATACTCCAACC
* * *
1830640 CCATCACTTCTGAG
65 CCGTTATTTCTGAG
* * * *
1830654 GGGATATTCCAACCCCATTTTCACTTTTAAAATATT
1 GGGATACTCAAACCCCATTTTTA-TTTCAAAATATT
1830690 AAAATTTTTC
Statistics
Matches: 283, Mismatches: 58, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
77 9 0.03
78 84 0.30
79 127 0.45
80 55 0.19
81 8 0.03
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (78 bp):
GGGATACTCAAACCCCATTTTTATTTCAAAATATTGATTTTTCACCATCGAGGATACTCCAACCC
CGTTATTTCTGAG
Found at i:1830568 original size:159 final size:156
Alignment explanation
Indices: 1830259--1830601 Score: 385
Period size: 159 Copynumber: 2.2 Consensus size: 156
1830249 TTTCACCATT
* * **
1830259 AGGGATACTCCAACCCCATTTTTATTT-CAAAATATTAAATTTTTTGTCAAGAGGATACTCCAGT
1 AGGGATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTATCTCAAGAGGATACTCCAAC
* * * * * *
1830323 CCTGTTATTTCTGAGGGGATACTCAAACCTCGTTTTTATTTCAAAATATTGATTTTTCACCATTG
66 CCCGTTATTTCCGAGAGGATACTCAAACCTCATTTTTATTTCAAAATATCGATTTTTCACCATCG
*
1830388 ACGATACTCTAACACAGTTATTT-TCG
131 ACGATACTCCAACACAGTTATTTCT-G
1830414 AAGGGATACTCCAACCCCATTTTTATTTCCAAAATATTAAAATTTTCCATCTC-A-AGGATACTC
1 -AGGGATACTCCAACCCCATTTTTATTTCCAAAATATT-AAATTTT--ATCTCAAGAGGATACTC
* *
1830477 CAACCCCGTT-TATTCCGAGAGGATACTCTATCC-CTATTTTTATTTCCAAAATATCGATTTTTC
62 CAACCCCGTTAT-TTCCGAGAGGATACTCAAACCTC-ATTTTTATTT-CAAAATATCGATTTTTC
* *
1830540 ACCATCGAGGATACTCCAACCCCA-TTATTTCTG
124 ACCATCGACGATACTCCAA-CACAGTTATTTCTG
* **
1830573 AGGAGATACTCCAATCCTGTTTTTATTTC
1 AGG-GATACTCCAACCCCATTTTTATTTC
1830602 TAAATTATCG
Statistics
Matches: 159, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
156 27 0.17
157 11 0.07
158 52 0.33
159 62 0.39
160 7 0.04
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (156 bp):
AGGGATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTATCTCAAGAGGATACTCCAAC
CCCGTTATTTCCGAGAGGATACTCAAACCTCATTTTTATTTCAAAATATCGATTTTTCACCATCG
ACGATACTCCAACACAGTTATTTCTG
Found at i:1832508 original size:20 final size:22
Alignment explanation
Indices: 1832483--1832536 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
1832473 TTAGGCTAAT
1832483 TGTATCGATACAATT-CTAGA-
1 TGTATCGATACAATTCCTAGAG
*
1832503 TGTATCGATAC-ATTCCTATATG
1 TGTATCGATACAATTCCTAGA-G
1832525 TGTATCGATACA
1 TGTATCGATACA
1832537 TTTGAAGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.10
20 15 0.52
22 11 0.38
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (22 bp):
TGTATCGATACAATTCCTAGAG
Found at i:1832649 original size:33 final size:33
Alignment explanation
Indices: 1832583--1832649 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1832573 ACTTTCACAT
* *
1832583 AATGTATCGAGACATTGCAATTTGTATCGATAC
1 AATGTATCGAGACATTGCAACTTGTATCAATAC
* * *
1832616 AATGTTTCGATACATTGCAACTTGTATTAATAC
1 AATGTATCGAGACATTGCAACTTGTATCAATAC
1832649 A
1 A
1832650 TCTGCATGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (33 bp):
AATGTATCGAGACATTGCAACTTGTATCAATAC
Found at i:1834386 original size:12 final size:12
Alignment explanation
Indices: 1834371--1834402 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1834361 AAGAAATATG
1834371 AAAAAAAGAGAA
1 AAAAAAAGAGAA
1834383 AAAAAAAGAGAA
1 AAAAAAAGAGAA
*
1834395 AAAGAAAG
1 AAAAAAAG
1834403 GGGATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:1835164 original size:58 final size:59
Alignment explanation
Indices: 1835056--1835170 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 59
1835046 TAGCATTTTT
* **
1835056 CATGCATTTCAGGGTCATTTAGGTTATTTTACATAATCTAGGGAGTATTTAG-AATTGC
1 CATGCATTTCAGGATCATTTAGGTTATTTTACATAATCTAGGGACCATTTAGTAATTGC
* * *
1835114 CATGCATTTTAGGATCATTTCGGTTATTTTATATAATCTAGGGACCATTTAGTAATT
1 CATGCATTTCAGGATCATTTAGGTTATTTTACATAATCTAGGGACCATTTAGTAATT
1835171 TCTAGCATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 46 0.92
59 4 0.08
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (59 bp):
CATGCATTTCAGGATCATTTAGGTTATTTTACATAATCTAGGGACCATTTAGTAATTGC
Found at i:1835232 original size:30 final size:30
Alignment explanation
Indices: 1835197--1835291 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
1835187 CTATTTAGCG
*
1835197 ATTTTCATGCACTTT-GGGATCATTTAGGTT
1 ATTTTCATG-AATTTAGGGATCATTTAGGTT
* * *
1835227 ATTTTCCAT-AATTTAGAGACCATTTA-GTA
1 ATTTT-CATGAATTTAGGGATCATTTAGGTT
* *
1835256 ATGTTCATGTATTTTAGGG-TCATTTAGGTT
1 ATTTTCATG-AATTTAGGGATCATTTAGGTT
1835286 ATTTTC
1 ATTTTC
1835292 CATAATCTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 3 0.06
29 16 0.32
30 28 0.56
31 3 0.06
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (30 bp):
ATTTTCATGAATTTAGGGATCATTTAGGTT
Found at i:1835329 original size:59 final size:58
Alignment explanation
Indices: 1835189--1835341 Score: 150
Period size: 59 Copynumber: 2.6 Consensus size: 58
1835179 ATCAAGGACT
* *
1835189 ATTTAGCGATTTTCATGCACTTT-GGGATCATTTAGGTTATTTTCCATAATTTAGAGACC
1 ATTTAGC-ATTTTCATGCATTTTAGGG-TCATTTAGGTTATTTTCCATAATTAAGAGACC
* * * ***
1835248 ATTTAGTAATGTTCATGTATTTTAGGGTCATTTAGGTTATTTTCCATAATCTAAG-GGTG
1 ATTTAG-CATTTTCATGCATTTTAGGGTCATTTAGGTTATTTTCCATAAT-TAAGAGACC
*
1835307 ATTTAGCATTTTTTATGCATTTTAGGG-CTATTTAG
1 ATTTAGCA-TTTTCATGCATTTTAGGGTC-ATTTAG
1835342 AATATTACAC
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
58 2 0.03
59 69 0.90
60 6 0.08
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (58 bp):
ATTTAGCATTTTCATGCATTTTAGGGTCATTTAGGTTATTTTCCATAATTAAGAGACC
Found at i:1837766 original size:22 final size:21
Alignment explanation
Indices: 1837723--1837763 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1837713 CAAAATTCTT
1837723 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAATACATC
1837745 GTTTTTCA-TCAAAAT-CATC
1 GTTTTTCACTCAAAATACATC
1837764 ATCAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (21 bp):
GTTTTTCACTCAAAATACATC
Found at i:1838066 original size:20 final size:21
Alignment explanation
Indices: 1838027--1838066 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1838017 TTCTAGGCAA
*
1838027 CACCCACCAGGTCGCGACCGG
1 CACCCACCAGGTCGCAACCGG
*
1838048 CACCC-CCAGGTCGTAACCG
1 CACCCACCAGGTCGCAACCG
1838067 AGTAGCCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.20, C:0.47, G:0.25, T:0.07
Consensus pattern (21 bp):
CACCCACCAGGTCGCAACCGG
Found at i:1839524 original size:20 final size:22
Alignment explanation
Indices: 1839494--1839536 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
1839484 TGATTTCCCG
1839494 TTTGAATGTATCGATACA-ATT
1 TTTGAATGTATCGATACATATT
1839515 TTTG-ATGTATCGATACATATT
1 TTTGAATGTATCGATACATATT
1839536 T
1 T
1839537 GAAAATATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (22 bp):
TTTGAATGTATCGATACATATT
Found at i:1839596 original size:20 final size:21
Alignment explanation
Indices: 1839571--1839623 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1839561 TATAAGCCAA
* *
1839571 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
1839591 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
1839611 TGTATCGATACAA
1 TGTATCGATACAA
1839624 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:1839628 original size:19 final size:19
Alignment explanation
Indices: 1839571--1839629 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
1839561 TATAAGCCAA
* *
1839571 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
1839591 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
1839611 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
1839630 CTACTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:1842153 original size:13 final size:13
Alignment explanation
Indices: 1842135--1842169 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1842125 ATAATCCTCC
*
1842135 TGTATCGATACAG
1 TGTATCGATACAA
1842148 TGTATCGATACAA
1 TGTATCGATACAA
1842161 TGTATCGAT
1 TGTATCGAT
1842170 GCAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1848347 original size:20 final size:21
Alignment explanation
Indices: 1848322--1848374 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1848312 TACAAGCCAA
* *
1848322 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
1848342 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
1848362 TGTATCGATACAA
1 TGTATCGATACAA
1848375 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:1848379 original size:19 final size:19
Alignment explanation
Indices: 1848322--1848380 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
1848312 TACAAGCCAA
* *
1848322 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
1848342 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
1848362 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
1848381 CTACTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:1849984 original size:20 final size:21
Alignment explanation
Indices: 1849937--1849990 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
1849927 ATACACATTT
**
1849937 AAATGTATCGATACATGTTGC
1 AAATGTATCGATACATGTACC
*
1849958 ACA-GTATCGATACATG-ACC
1 AAATGTATCGATACATGTACC
1849977 AAATGTATCGATAC
1 AAATGTATCGATAC
1849991 TTGAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (21 bp):
AAATGTATCGATACATGTACC
Found at i:1850082 original size:13 final size:13
Alignment explanation
Indices: 1850064--1850088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1850054 GCACACAGTA
1850064 TGTATCGATACAT
1 TGTATCGATACAT
1850077 TGTATCGATACA
1 TGTATCGATACA
1850089 CCATAAAATG
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:1851292 original size:27 final size:27
Alignment explanation
Indices: 1851244--1851301 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1851234 AAAAAAGTAA
1851244 AAATTTTAAAACTCATAAAATA-AATT
1 AAATTTTAAAACTCATAAAATAGAATT
* **
1851270 AAATTTTCAAAACTGATTTAATATGAATT
1 AAATTTT-AAAACTCATAAAATA-GAATT
1851299 AAA
1 AAA
1851302 CAATAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.27
27 12 0.46
29 7 0.27
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.36
Consensus pattern (27 bp):
AAATTTTAAAACTCATAAAATAGAATT
Found at i:1851550 original size:152 final size:150
Alignment explanation
Indices: 1851098--1851556 Score: 514
Period size: 152 Copynumber: 3.0 Consensus size: 150
1851088 AAAAAGATGC
* * ** *
1851098 AAAACTCATAAAATAAATTGAATCTTCAAAAACCAATTTAATATGAACTT-AATAAAAATATTT-
1 AAAACTCATAAAATAAATTAAATTTTC-AAAACTGATTTAATATGAA-TTAAATAATAATATTTG
* * * * * *
1851161 AATGAATTTTAAAAATTATAAACTCAGAAAAATCCCACAAAAAAATTTACGGAGAAGAAACCTTG
64 AA-GAATTTTAAAAATTATAAACTTAGAAAAATCCTACCAAAAAATTTACGGAGTAGAAAACTTC
* *
1851226 GTATTTTAAAAAAAGTAAAAATTTT
128 GTATTTTGAAAAAA--AAAAATTCT
*
1851251 AAAACTCATAAAATAAATTAAATTTTCAAAACTGATTTAATATGAATTAAACAATAATATTTGAA
1 AAAACTCATAAAATAAATTAAATTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGAA
* * * * *
1851316 GAATTTTAAAAATTATAAACTTAGAAAAATCCTACTAAAAAATTTACGAAGTTA-AAAAATACAT
66 GAATTTTAAAAATTATAAACTTAGAAAAATCCTACCAAAAAATTTACGGAG-TAGAAAACTTCGT
* **
1851380 ATCTTAGTAAAAGGAAAAATTCT
130 AT-TTTG-AAAAAAAAAAATTCT
* *
1851403 AGAA-TCATAAAATAAATTAAAGTTTTTAAAACTGATTTAATATGAATTAAATAATAATATTTGA
1 AAAACTCATAAAATAAATTAAA-TTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGA
* * * * * *
1851467 AGAATTTTTAAAATTACATACTTAGAAATATCTTACCAAAGAAGTTTACGGAGTAGAAAACTTCG
65 AGAATTTTAAAAATTATAAACTTAGAAAAATCCTACCAAA-AAATTTACGGAGTAGAAAACTTCG
1851532 TATTTTGAAAATAAAAAAA-TCT
129 TATTTTGAAAA-AAAAAAATTCT
1851554 AAA
1 AAA
1851557 TGAAAATGAA
Statistics
Matches: 258, Mismatches: 39, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
151 28 0.11
152 177 0.69
153 49 0.19
154 4 0.02
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.32
Consensus pattern (150 bp):
AAAACTCATAAAATAAATTAAATTTTCAAAACTGATTTAATATGAATTAAATAATAATATTTGAA
GAATTTTAAAAATTATAAACTTAGAAAAATCCTACCAAAAAATTTACGGAGTAGAAAACTTCGTA
TTTTGAAAAAAAAAAATTCT
Found at i:1852382 original size:16 final size:16
Alignment explanation
Indices: 1852348--1852405 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1852338 AACCGACCTA
*
1852348 AACCTGAAATAACTCG
1 AACCTGAAATGACTCG
*
1852364 AA-CTCGAAATGACTTG
1 AACCT-GAAATGACTCG
1852380 AACCTGAAATGA-TCCG
1 AACCTGAAATGACT-CG
*
1852396 AACCCGAAAT
1 AACCTGAAAT
1852406 AACCCAAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 3 0.09
16 30 0.86
17 2 0.06
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (16 bp):
AACCTGAAATGACTCG
Found at i:1852658 original size:15 final size:15
Alignment explanation
Indices: 1852635--1852664 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1852625 GTAAAATAAT
*
1852635 GTAATAATTATATAC
1 GTAACAATTATATAC
1852650 GTAACAATTATATAC
1 GTAACAATTATATAC
1852665 ATGCCTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (15 bp):
GTAACAATTATATAC
Found at i:1853238 original size:53 final size:53
Alignment explanation
Indices: 1853160--1853262 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
1853150 TGAACACGAT
* *
1853160 TTAACCCGAATGTTAAACCCAATTGACCTAAATCCAGAATGACCCGAACCTGA
1 TTAACCCGAATGTTAAACCCAATTGACCCAAATCCAAAATGACCCGAACCTGA
* * * * * *
1853213 TTAATCCGAGTGTTAAACTCGATTGACCCAAGTCCAAAATGACCTGAACC
1 TTAACCCGAATGTTAAACCCAATTGACCCAAATCCAAAATGACCCGAACC
1853263 CAAAATGATC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (53 bp):
TTAACCCGAATGTTAAACCCAATTGACCCAAATCCAAAATGACCCGAACCTGA
Found at i:1853265 original size:16 final size:16
Alignment explanation
Indices: 1853246--1853321 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 16
1853236 TGACCCAAGT
1853246 CCAAAATGACCTGAAC
1 CCAAAATGACCTGAAC
*
1853262 CCAAAATGATCTGAAC
1 CCAAAATGACCTGAAC
* * * **
1853278 TCGAAGTGACCCAAAC
1 CCAAAATGACCTGAAC
* *
1853294 CTAAAATGACATGAAC
1 CCAAAATGACCTGAAC
*
1853310 TCAAAAATGACC
1 -CCAAAATGACC
1853322 CAAAAATTTT
Statistics
Matches: 43, Mismatches: 16, Indels: 1
0.72 0.27 0.02
Matches are distributed among these distances:
16 34 0.79
17 9 0.21
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (16 bp):
CCAAAATGACCTGAAC
Found at i:1853300 original size:32 final size:33
Alignment explanation
Indices: 1853248--1853325 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
1853238 ACCCAAGTCC
**
1853248 AAAATGACCTGAACCCAAAATGATC-TGAACTC-
1 AAAATGACCCAAACCCAAAATGA-CATGAACTCA
* * *
1853280 GAAGTGACCCAAACCTAAAATGACATGAACTCA
1 AAAATGACCCAAACCCAAAATGACATGAACTCA
1853313 AAAATGACCCAAA
1 AAAATGACCCAAA
1853326 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 1 0.03
32 25 0.68
33 11 0.30
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.15
Consensus pattern (33 bp):
AAAATGACCCAAACCCAAAATGACATGAACTCA
Found at i:1853563 original size:78 final size:78
Alignment explanation
Indices: 1853470--1853644 Score: 228
Period size: 78 Copynumber: 2.2 Consensus size: 78
1853460 TGCCCATTAA
* * *
1853470 GGTTACTTTGGTGATATTATATTAACATCAAGGC-TC-TAGGGCCATGTGGGAACTTTCATGTCG
1 GGTTACTTAGGTGATATTATATTAACA-CAA-ACTTCATAGGGCCATGTGGGAACTTTCATATCG
*
1853533 ATACATATCCACTAT
64 ATACATATCCACTAG
* ** *
1853548 GGTTACTTAGGTGATATTATATTAATACAAACTTCATAGGGTTATGTGGGAACTTTCATATTGAT
1 GGTTACTTAGGTGATATTATATTAACACAAACTTCATAGGGCCATGTGGGAACTTTCATATCGAT
* *
1853613 ACATGTCCATTAG
66 ACATATCCACTAG
1853626 GGTTACTTAGGTGATATTA
1 GGTTACTTAGGTGATATTA
1853645 CTTTCATATC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
76 1 0.01
77 5 0.06
78 79 0.93
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (78 bp):
GGTTACTTAGGTGATATTATATTAACACAAACTTCATAGGGCCATGTGGGAACTTTCATATCGAT
ACATATCCACTAG
Found at i:1861717 original size:20 final size:21
Alignment explanation
Indices: 1861690--1861748 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
1861680 GGGTAAAAAG
*
1861690 ATAGAATGTATCGATACATTG
1 ATAGAATGTATCGATACATTC
*
1861711 A-AGAATGTATCGATATATTC
1 ATAGAATGTATCGATACATTC
*
1861731 ATA-CATGTATCGATACAT
1 ATAGAATGTATCGATACAT
1861749 CTGCGTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (21 bp):
ATAGAATGTATCGATACATTC
Found at i:1862222 original size:28 final size:28
Alignment explanation
Indices: 1862181--1862872 Score: 726
Period size: 28 Copynumber: 23.9 Consensus size: 28
1862171 CAATTTTTCT
*
1862181 TGACTTGTGGGCTTTGAAATGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* *
1862209 TGACTTGTGAGC-TTGAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* * *
1862236 TGACTTGTTGGCTTTGAAAGGATGCTAT
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* *
1862264 TGACTTGTAGGCTTTAAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
*
1862292 TGATTTGTGTGGGCTTTGAGAAGGATGCCAC
1 TGA-CT-TGTGGGCTTTGA-AAGGATGCCAC
* *
1862323 TGACTTATGGGCTTTGAAAAGGATGCCAT
1 TGACTTGTGGGCTTTG-AAAGGATGCCAC
*
1862352 TGACTTATGGGCTTTGAAAAGGATGCCAC
1 TGACTTGTGGGCTTTG-AAAGGATGCCAC
* * *
1862381 TAACTTGTGGGCTTTAAAATGGGTTGCCAC
1 TGACTTGTGGGCTTTGAAA--GGATGCCAC
* * *
1862411 CGACTTGTGTGGGCTTTGAAATGGGTTGCCAT
1 TGAC-T-TGTGGGCTTTGAAA--GGATGCCAC
*
1862443 TGACTTGTGTGGGCTTTGAAATGGGTTGCCAC
1 TGAC-T-TGTGGGCTTTGAAA--GGATGCCAC
* * *
1862475 TGACTTGTGTAAGCTTTCAAATAGGTTGCCA-
1 TGACTTGTG--GGCTTT-GAA-AGGATGCCAC
1862506 TCGACTTGTATGGGCTTTGAAAGGATGCCAC
1 T-GACTTG--TGGGCTTTGAAAGGATGCCAC
1862537 TGACTTGTGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * **
1862565 TAACTTGTGCGCTTTAAAAGGGTGCTTC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
1862593 TGACTTGTGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* *
1862621 TGACTTATGGGCTTTGAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
*
1862649 TGACTTGTAGGCTTTGAAAGGATGCCACCCAC
1 TGACTTGTGGGCTTTGAAAGGATG----CCAC
* * *
1862681 TAACTTGTGGGTTTTGAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* *
1862709 TAACTTGTGGGCTTTGAGAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
*
1862737 TGACTTGTGGGCTTTGAAAAGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* * *
1862765 TGACTTGTGTGCTTT-AGAAGGGTGCCAT
1 TGACTTGTGGGCTTTGA-AAGGATGCCAC
1862793 TGACTTGTGGGCTTTGAAAGGATGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
* *
1862821 TGACTTGTGGGCTTTAAAAGGGTGCCAC
1 TGACTTGTGGGCTTTGAAAGGATGCCAC
1862849 TGACTTGTGGGCTTT-AAAGAGATG
1 TGACTTGTGGGCTTTGAAAG-GATG
1862873 AACGTTCTAG
Statistics
Matches: 569, Mismatches: 71, Indels: 48
0.83 0.10 0.07
Matches are distributed among these distances:
27 28 0.05
28 308 0.54
29 63 0.11
30 40 0.07
31 20 0.04
32 105 0.18
33 2 0.00
34 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
TGACTTGTGGGCTTTGAAAGGATGCCAC
Found at i:1862717 original size:172 final size:172
Alignment explanation
Indices: 1862181--1862848 Score: 719
Period size: 172 Copynumber: 3.8 Consensus size: 172
1862171 CAATTTTTCT
* * * * *
1862181 TGACTTGTGGGCTTTGAAATGATGCCACTGACTTGTGAGC-TTGAAAGGGTGCCACTGACTTGTT
1 TGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
* * * * *
1862245 GGCTTTGAAAGGATGCTATTGACTTGTAGGCTTTAAAAGGATGCCACTGATTTGTGTGGGCTTTG
66 GGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGA-CTGTGTAGGCTTT-
* *
1862310 AGAAGGATG----CCACTGACTTATGGGCTTTGAAAAGGATGCCAT
129 AAAAGGATGCCACCCACT-ACTTATGGGCTTTG-AAAGGATGCCAC
* *
1862352 TGACTTATGGGCTTTGAAAAGGATGCCACTAACTTGTGGGCTTTAAAATGGGTTGCCACCGACTT
1 TGACTTGTGGGCTTTG-AAAGGATGCCACTAACTTGTGGGCTTTAAAA-GGG-TGCCACTGAC-T
* *
1862417 GTGTGGGCTTTGAAATGGGTTGCCATTGACTTGTGTGGGCTTTGAAATGGGTTGCCACTGACTTG
62 -TGTGGGCTTTGAAA--GGATGCCATTGAC-T-TGTGGGCTTTGAAA--GGATGCCACTGAC-TG
* * * *
1862482 TGTAAGCTTTCAAATAGGTTGCCATCGACT--TGTATGGGCTTTGAAAGGATGCCAC
119 TGTAGGCTTT-AAA-AGGATGCCACCCACTACT-TATGGGCTTTGAAAGGATGCCAC
* **
1862537 TGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGCGCTTTAAAAGGGTGCTTCTGACTTGTG
1 TGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
* * * *
1862602 GGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTGACT-TGTAGGCTTTGA
66 GGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTGTGTAGGCTTTAA
* * *
1862666 AAGGATGCCACCCACTAACTTGTGGGTTTTGAAAGGGTGCCAC
131 AAGGATGCCACCCACT-ACTTATGGGCTTTGAAAGGATGCCAC
* * * *
1862709 TAACTTGTGGGCTTTGAGAGGATGCCACTGACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGT
1 TGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGT
* * *
1862773 GTGCTTT-AGAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACT-TGTGGGCTTT
65 GGGCTTTGA-AAGGATGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTGTGTAGGCTTT
*
1862836 AAAAGGGTGCCAC
129 AAAAGGATGCCAC
1862849 TGACTTGTGG
Statistics
Matches: 421, Mismatches: 52, Indels: 47
0.81 0.10 0.09
Matches are distributed among these distances:
170 12 0.03
171 18 0.04
172 168 0.40
173 11 0.03
174 15 0.04
175 9 0.02
176 14 0.03
177 14 0.03
178 11 0.03
179 11 0.03
180 15 0.04
181 13 0.03
182 7 0.02
183 26 0.06
184 35 0.08
185 27 0.06
186 11 0.03
188 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (172 bp):
TGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTG
GGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGATGCCACTGACTGTGTAGGCTTTAA
AAGGATGCCACCCACTACTTATGGGCTTTGAAAGGATGCCAC
Found at i:1869988 original size:52 final size:50
Alignment explanation
Indices: 1869927--1870283 Score: 212
Period size: 49 Copynumber: 7.4 Consensus size: 50
1869917 AATTCATGAT
* *
1869927 CAGCAACATTTGACTTGAAGATGAGAAGAATTCCAATGTGCTGATTCAAGGC
1 CAGCAACATTTGACTTAAAGATG-GAAG-ATGCCAATGTGCTGATTCAAGGC
* ** * * * *
1869979 CAGCGACA-TTGGGTTCAGGAATGTTACAGATGCCAATATGCTGATTCAAGGC
1 CAGCAACATTTGACTTAAAG-ATG-GA-AGATGCCAATGTGCTGATTCAAGGC
** * * *
1870031 CAGTGATATTGGACTTAAAGAT-GAAGGTGCCAATGTGCTGATTCAAGGC
1 CAGCAACATTTGACTTAAAGATGGAAGATGCCAATGTGCTGATTCAAGGC
* * *
1870080 CAGCAACATTGGACCT-AA-A--G--G-TGCCAATATGCTGATTCAAGGC
1 CAGCAACATTTGACTTAAAGATGGAAGATGCCAATGTGCTGATTCAAGGC
* * ** * *
1870123 CAGCGATA-TTGAACTTAAAGATAAAAG-TGCCGATGTACTGATTCAAGGC
1 CAGCAACATTTG-ACTTAAAGATGGAAGATGCCAATGTGCTGATTCAAGGC
* ** * *
1870172 CAGCAACATTGGTGTT-AA-A--G--G-TGCCAATATGCTAATTCAAGGC
1 CAGCAACATTTGACTTAAAGATGGAAGATGCCAATGTGCTGATTCAAGGC
* * * * * *
1870215 CAACTATATTGGACTTAAAGAT-GAAGGTGCCAATGTGCTGATTCAAAGC
1 CAGCAACATTTGACTTAAAGATGGAAGATGCCAATGTGCTGATTCAAGGC
*
1870264 CAGCAACATTAGACTTAAAG
1 CAGCAACATTTGACTTAAAG
1870284 GTGCCAATAT
Statistics
Matches: 234, Mismatches: 54, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
42 2 0.01
43 60 0.26
44 5 0.02
45 2 0.01
46 2 0.01
47 2 0.01
48 5 0.02
49 98 0.42
50 3 0.01
51 7 0.03
52 40 0.17
53 8 0.03
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (50 bp):
CAGCAACATTTGACTTAAAGATGGAAGATGCCAATGTGCTGATTCAAGGC
Found at i:1870166 original size:92 final size:92
Alignment explanation
Indices: 1870009--1870323 Score: 486
Period size: 92 Copynumber: 3.4 Consensus size: 92
1869999 ATGTTACAGA
**
1870009 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
*
1870074 CAAGGCCAGCAACATTGGACCTAAAGG
66 CAAGGCCAGCAACATTGGACTTAAAGG
* * * * * *
1870101 TGCCAATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAGATAAAAGTGCCGATGTACTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
**
1870166 CAAGGCCAGCAACATTGGTGTTAAAGG
66 CAAGGCCAGCAACATTGGACTTAAAGG
* *
1870193 TGCCAATATGCTAATTCAAGGCCAACTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
1870258 CAAAGCCAGCAACATTAGACTTAAAGG
66 CAAGGCCAGCAACATTGGACTTAAAGG
*
1870285 TGCCAATATGCCGATTCAAGGCCAACGATATTGGACTTA
1 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA
1870324 GAAAAAGATG
Statistics
Matches: 199, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 199 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (92 bp):
TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATT
CAAGGCCAGCAACATTGGACTTAAAGG
Found at i:1870325 original size:49 final size:49
Alignment explanation
Indices: 1869959--1870323 Score: 282
Period size: 43 Copynumber: 7.8 Consensus size: 49
1869949 GAGAAGAATT
* * * * * *
1869959 CCAATGTGCTGATTCAAGGCCAGCGACATTGG-GTTCAGGAATGTTACAGATG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A--AA-GATAAAGGTG
* *
1870011 CCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
* * * *
1870060 CCAATGTGCTGATTCAAGGCCAGCAACATTGGAC------CTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
* *
1870103 CCAATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAGATAAAAGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
* * * * * *
1870152 CCGATGTACTGATTCAAGGCCAGCAACATTGG---T---GTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
* * * *
1870195 CCAATATGCTAATTCAAGGCCAACTATATTGGACTTAAAGATGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
* * * * *
1870244 CCAATGTGCTGATTCAAAGCCAGCAACATTAGAC-T-----TAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
* *
1870287 CCAATATGCCGATTCAAGGCCAACGATATTGGACTTA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1870324 GAAAAAGATG
Statistics
Matches: 246, Mismatches: 52, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
43 104 0.42
44 1 0.00
46 2 0.01
48 1 0.00
49 104 0.42
50 2 0.01
52 30 0.12
53 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (49 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTG
Found at i:1870378 original size:28 final size:29
Alignment explanation
Indices: 1870345--1870638 Score: 338
Period size: 28 Copynumber: 10.3 Consensus size: 29
1870335 CACCAACTCG
*
1870345 TGTGGGCTTTTG-AAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1870373 TGTGGGC-TTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
* * *
1870401 TATGGGCTTCTG-AAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1870429 TATGGGC-TTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * *
1870457 TGTGAGC-TTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1870485 TGTGTGCTTCTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1870513 TGTGGGC-TTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
1870541 TGTGGGCTTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
*
1870570 TGTGGGCTTTTGAAAGGGGTGCCACTGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* *
1870600 TGTGGGCTTTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1870629 TGTGGGCTTT
1 TGTGGGCTTT
1870639 GGAAGGTGAG
Statistics
Matches: 235, Mismatches: 20, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
27 14 0.06
28 124 0.53
29 72 0.31
30 25 0.11
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:1870415 original size:56 final size:56
Alignment explanation
Indices: 1870345--1870645 Score: 378
Period size: 56 Copynumber: 5.3 Consensus size: 56
1870335 CACCAACTCG
1870345 TGTGGGCTTTTG-AAGGTTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGC-TTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * *
1870401 TATGGGCTTCTG-AAGGTTGCCACTAACTTATGGGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTT-TGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
* * * *
1870457 TGTGAGCTTTGAAAAGATGCCACTAACTTGTGTGCTTCTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTT-TGAAAAGG-TGCCACTGACT
*
1870513 TGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGTTGCCACTAACTTGTGGGC-TTTGAAAAGGTGCCACTGACT
* * *
1870570 TGTGGGCTTTTGAAAGGGGTGCCACTGACTTGTGGGCTTTTAAAAGGATGCCACTGACT
1 TGTGGGC-TTTGAAA-GGTTGCCACTAACTTGTGGGCTTTGAAAAGG-TGCCACTGACT
*
1870629 TGTGGGCTTTGGAAGGT
1 TGTGGGCTTTGAAAGGT
1870646 GAGGAATGTC
Statistics
Matches: 216, Mismatches: 17, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
55 7 0.03
56 117 0.54
57 31 0.14
58 25 0.12
59 36 0.17
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGTTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACT
Found at i:1870494 original size:84 final size:84
Alignment explanation
Indices: 1870345--1870639 Score: 412
Period size: 84 Copynumber: 3.5 Consensus size: 84
1870335 CACCAACTCG
* * * *
1870345 TGTGGGCTTTTG-AAGGTTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTATGGGCT
1 TGTGGGC-TTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCT
*
1870409 TCTGAAGGTTGCCACTAACT
65 TCTGAAGGTTGCCACTGACT
* * * * *
1870429 TATGGGCTTTGAAAAGATGCCACTGACTTGTGAGCTTTGAAAAGATGCCACTAACTTGTGTGCTT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
1870494 CTGAAGGTTGCCACTGACT
66 CTGAAGGTTGCCACTGACT
*
1870513 TGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGGTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGC-TTTGAAAAGGTGCCACTGACTTGTGGGCT
* *
1870578 TTTGAAAGGGGTGCCACTGACT
65 TCTG-AA-GGTTGCCACTGACT
*
1870600 TGTGGGCTTTTAAAAGGATGCCACTGACTTGTGGGCTTTG
1 TGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTG
1870640 GAAGGTGAGG
Statistics
Matches: 186, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
83 4 0.02
84 101 0.54
85 29 0.16
86 2 0.01
87 31 0.17
88 19 0.10
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (84 bp):
TGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTT
CTGAAGGTTGCCACTGACT
Found at i:1871046 original size:37 final size:37
Alignment explanation
Indices: 1871004--1871125 Score: 244
Period size: 37 Copynumber: 3.3 Consensus size: 37
1870994 AAAGATGAAG
1871004 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1871041 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1871078 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1871115 CACAAATGCAT
1 CACAAATGCAT
1871126 GATTGTGGCA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 85 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
Found at i:1880415 original size:20 final size:20
Alignment explanation
Indices: 1880392--1880429 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1880382 GTCAAGTGCC
1880392 TCATGGCATGCTTAGGAATT
1 TCATGGCATGCTTAGGAATT
1880412 TCATGGCATGCTTAGGAA
1 TCATGGCATGCTTAGGAA
1880430 AAATATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (20 bp):
TCATGGCATGCTTAGGAATT
Found at i:1885141 original size:33 final size:33
Alignment explanation
Indices: 1885089--1885151 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1885079 TATCAATACA
*
1885089 TGAATAGTGATGAACAGTGATTTTATCGATGCG
1 TGAACAGTGATGAACAGTGATTTTATCGATGCG
*
1885122 TGAACAGTGTTGAACAGTGATTTTATCGAT
1 TGAACAGTGATGAACAGTGATTTTATCGAT
1885152 ACTATTCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (33 bp):
TGAACAGTGATGAACAGTGATTTTATCGATGCG
Found at i:1893612 original size:10 final size:10
Alignment explanation
Indices: 1893599--1893626 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1893589 TGTTTCTTTT
1893599 GGGAGCTATA
1 GGGAGCTATA
1893609 GGGAGCTATA
1 GGGAGCTATA
1893619 GGGAGCTA
1 GGGAGCTA
1893627 CGGGAATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.43, T:0.18
Consensus pattern (10 bp):
GGGAGCTATA
Found at i:1897802 original size:20 final size:19
Alignment explanation
Indices: 1897779--1897834 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1897769 ATACACATTT
*
1897779 AAATGTATCGATACATGACC
1 AAATGTATCGATACATGA-A
*
1897799 AAATGTATCGATACTTGAA
1 AAATGTATCGATACATGAA
1897818 ATAGATGTATCGATACA
1 A-A-ATGTATCGATACA
1897835 GGTCATTGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 18 0.58
21 12 0.39
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (19 bp):
AAATGTATCGATACATGAA
Found at i:1897889 original size:17 final size:17
Alignment explanation
Indices: 1897867--1897901 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1897857 TAGCCAAACT
1897867 TGTATCGACACATAGTA
1 TGTATCGACACATAGTA
* *
1897884 TGTATCGATACATTGTA
1 TGTATCGACACATAGTA
1897901 T
1 T
1897902 CGATACACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (17 bp):
TGTATCGACACATAGTA
Found at i:1897900 original size:13 final size:13
Alignment explanation
Indices: 1897884--1897908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1897874 ACACATAGTA
1897884 TGTATCGATACAT
1 TGTATCGATACAT
1897897 TGTATCGATACA
1 TGTATCGATACA
1897909 CCATAAAATG
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:1902997 original size:314 final size:314
Alignment explanation
Indices: 1902428--1903043 Score: 1205
Period size: 314 Copynumber: 2.0 Consensus size: 314
1902418 CACCCGTAGC
1902428 TAGGATAGAAGCCGTTAGAATATTACTAGCCTTTGCATGTTTCTATGATTTTAAGTTATATCAAA
1 TAGGATAGAAGCCGTTAGAATATTACTAGCCTTTGCATGTTTCTATGATTTTAAGTTATATCAAA
*
1902493 TGGATGTTAAAAGTGCGTTTTTAAATGGTTTTATAAACGAGGAGGTTTATGTCGAACAACCTCCA
66 TGGATGTTAAAAGTGCGTTTTTAAATGGTTTTATAAACGAAGAGGTTTATGTCGAACAACCTCCA
1902558 GGTTTTGAAAATCCATTATTTCCAAATCATGTGTTTAAACTTTCAAAAGCTTTGTATGGTTTAAA
131 GGTTTTGAAAATCCATTATTTCCAAATCATGTGTTTAAACTTTCAAAAGCTTTGTATGGTTTAAA
*
1902623 ACAAGCTCCTCAAGCTTGGTATGAAAGGCTTTCAAAGTTTTTGACTGAAAAAGGTTTTAATAGCG
196 ACAAGCTCCTCAAGCTTGGTATGAAAGGCTTTCAAAGTTTTTGACTGAAAAAGGTTTTAATAGAG
1902688 GAAATATGGATAAAACCCTTTTCGTTAAATCAAAAGAAAAAGTGCGTTTTAAGT
261 GAAATATGGATAAAACCCTTTTCGTTAAATCAAAAGAAAAAGTGCGTTTTAAGT
1902742 TAGGATAGAAGCCGTTAGAATATTACTAGCCTTTGCATGTTTCTATGATTTTAAGTTATATCAAA
1 TAGGATAGAAGCCGTTAGAATATTACTAGCCTTTGCATGTTTCTATGATTTTAAGTTATATCAAA
1902807 TGGATGTTAAAAGTGCGTTTTTAAATGGTTTTATAAACGAAGAGGTTTATGTCGAACAACCTCCA
66 TGGATGTTAAAAGTGCGTTTTTAAATGGTTTTATAAACGAAGAGGTTTATGTCGAACAACCTCCA
*
1902872 GGTTTTGAAAATCCATTATTTCCAAATTATGTGTTTAAACTTTCAAAAGCTTTGTATGGTTTAAA
131 GGTTTTGAAAATCCATTATTTCCAAATCATGTGTTTAAACTTTCAAAAGCTTTGTATGGTTTAAA
1902937 ACAAGCTCCTCAAGCTTGGTATGAAAGGCTTTCAAAGTTTTTGACTGAAAAAGGTTTTAATAGAG
196 ACAAGCTCCTCAAGCTTGGTATGAAAGGCTTTCAAAGTTTTTGACTGAAAAAGGTTTTAATAGAG
1903002 GAAATATGGATAAAACCCTTTTCGTTAAATCAAAAGAAAAAG
261 GAAATATGGATAAAACCCTTTTCGTTAAATCAAAAGAAAAAG
1903044 ATATTTTGAT
Statistics
Matches: 299, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
314 299 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.35
Consensus pattern (314 bp):
TAGGATAGAAGCCGTTAGAATATTACTAGCCTTTGCATGTTTCTATGATTTTAAGTTATATCAAA
TGGATGTTAAAAGTGCGTTTTTAAATGGTTTTATAAACGAAGAGGTTTATGTCGAACAACCTCCA
GGTTTTGAAAATCCATTATTTCCAAATCATGTGTTTAAACTTTCAAAAGCTTTGTATGGTTTAAA
ACAAGCTCCTCAAGCTTGGTATGAAAGGCTTTCAAAGTTTTTGACTGAAAAAGGTTTTAATAGAG
GAAATATGGATAAAACCCTTTTCGTTAAATCAAAAGAAAAAGTGCGTTTTAAGT
Found at i:1904166 original size:8 final size:8
Alignment explanation
Indices: 1904153--1904178 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1904143 ATTTGATTAA
1904153 ATTTTGTG
1 ATTTTGTG
1904161 ATTTTGTG
1 ATTTTGTG
1904169 ATTTTGTG
1 ATTTTGTG
1904177 AT
1 AT
1904179 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1904399 original size:13 final size:13
Alignment explanation
Indices: 1904380--1904418 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1904370 ACAGAGAATG
1904380 CTGTATCGATACA
1 CTGTATCGATACA
*
1904393 TTGTATCGATACA
1 CTGTATCGATACA
*
1904406 CTATATCGATACA
1 CTGTATCGATACA
1904419 AGAGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:1904591 original size:22 final size:21
Alignment explanation
Indices: 1904547--1904589 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1904537 CAAAACTCTT
1904547 ATTTTTCACTTCAAAATACATC
1 ATTTTTCAC-TCAAAATACATC
1904569 ATTTTTCA-TCAAAAT-CATC
1 ATTTTTCACTCAAAATACATC
1904588 AT
1 AT
1904590 CAAAAACAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
22 8 0.38
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTTCACTCAAAATACATC
Found at i:1904885 original size:20 final size:21
Alignment explanation
Indices: 1904850--1904891 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1904840 CTCTTAGGCA
*
1904850 GCACCCACCAGATCGCGACCG
1 GCACCCACCAGATCGCAACCG
*
1904871 GCACCC-CCAGGTCGCAACCG
1 GCACCCACCAGATCGCAACCG
1904891 G
1 G
1904892 GCAGCCCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.21, C:0.48, G:0.26, T:0.05
Consensus pattern (21 bp):
GCACCCACCAGATCGCAACCG
Found at i:1906942 original size:20 final size:20
Alignment explanation
Indices: 1906895--1906970 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
1906885 ATACACATTT
* *
1906895 AAATGTATCGATATATGTCGC
1 AAATGTATCGATACATGAC-C
*
1906916 ACA-GTATCGATACATGACC
1 AAATGTATCGATACATGACC
* *
1906935 AAATGTATCGATACTTGA-A
1 AAATGTATCGATACATGACC
1906954 ATAGATGTATCGATACA
1 A-A-ATGTATCGATACA
1906971 GGTCATTGGC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.09
20 27 0.60
21 14 0.31
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (20 bp):
AAATGTATCGATACATGACC
Found at i:1913658 original size:166 final size:162
Alignment explanation
Indices: 1913425--1913810 Score: 412
Period size: 166 Copynumber: 2.4 Consensus size: 162
1913415 CGATATCGGG
* * * * * * * *
1913425 CTTAAAGATGAGAAGAATGTTAAAGGTGCGAATGTGCTAATTTAAGGTCAATGACATTGGACTTA
1 CTTAAA-ATGAAAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTA
* * * *
1913490 AAGATGACAAAGGCGCTATTATGTTGGTTCAAGGCCAACGATATTAGACTTAAGAAAGAAAAAAG
65 AAGATGACAAAGGCGCTAATATGTTGATTCAAGGCCAACAACATTAGACTT--G-AAGAAAAAAG
* *
1913555 -TACCATTTGTGCTGATTCAAGGCCAACGACATTGGA
127 TTACCA-ATGTGCTAATTCAAGGCCAACGACATTGGA
* *
1913591 CTTAAAAATGAAAAGAATGATAAAGGTGCCAATATGCTGATTCAGGGCCAATGATATTGGGCTTA
1 CTT-AAAATGAAAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTA
* * * * ** *
1913656 AAGATGACAAAGGTGCTAATGTGTTGATTGAAGGCCAACAACATTGGACTTGAAGATGAAAGTTG
65 AAGATGACAAAGGCGCTAATATGTTGATTCAAGGCCAACAACATTAGACTTGAAGAAAAAAGTTA
**
1913721 CCAATGTGCTAATTCAAGGCCAGTGACATTGGA
130 CCAATGTGCTAATTCAAGGCCAACGACATTGGA
* *
1913754 C-T----T--AAAGAA-GACAAAGGTGCTAATATGCTGATTCAAGGCCAATGATATTGGACTTAA
1 CTTAAAATGAAAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAA
1913811 GAAAGAAAAA
Statistics
Matches: 189, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
154 44 0.23
155 6 0.03
157 1 0.01
162 1 0.01
163 35 0.19
164 5 0.03
166 94 0.50
167 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (162 bp):
CTTAAAATGAAAAGAATGATAAAGGTGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAA
AGATGACAAAGGCGCTAATATGTTGATTCAAGGCCAACAACATTAGACTTGAAGAAAAAAGTTAC
CAATGTGCTAATTCAAGGCCAACGACATTGGA
Found at i:1913793 original size:102 final size:103
Alignment explanation
Indices: 1913616--1913861 Score: 298
Period size: 102 Copynumber: 2.4 Consensus size: 103
1913606 AATGATAAAG
* * * * * * *
1913616 GTGCCAATATGCTGATTCAGGGCCAATGATATTGGGCTTAAAGATGACAAAGGTGCTAATGTGTT
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAGAAGACAAAGGTGCTAATATGCT
* **
1913681 GATTGAAGGCCAACAACATTGGACTT-G-AAGATGAAA
66 GATTCAAGGCCAACAACATTGGACTTAGAAAGAAAAAA
* *
1913717 GTTGCCAATGTGCTAATTCAAGGCCAGTGACATTGGACTTAAAGAAGACAAAGGTGCTAATATGC
1 G-TGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAGAAGACAAAGGTGCTAATATGC
** *
1913782 TGATTCAAGGCCAATGATATTGGACTTAAGAAAGAAAAAA
65 TGATTCAAGGCCAACAACATTGGACTT-AGAAAGAAAAAA
* * *
1913822 GTGCCAATGTGCTGATTCAAGGCAAATTACAGTGGACTTA
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTA
1913862 GAAAAGATAG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
101 1 0.01
102 77 0.64
104 35 0.29
105 8 0.07
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (103 bp):
GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAGAAGACAAAGGTGCTAATATGCT
GATTCAAGGCCAACAACATTGGACTTAGAAAGAAAAAA
Found at i:1913868 original size:52 final size:51
Alignment explanation
Indices: 1913450--1913868 Score: 266
Period size: 52 Copynumber: 7.9 Consensus size: 51
1913440 AATGTTAAAG
* * * * * * *
1913450 GTGCGAATGTGCTAATTTAAGGTCAATGACATTGGACTTAAAGATGACAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAA-AAGAAAAAA
* * * * * * * * *
1913502 GCGCTATTATGTTGGTTCAAGGCCAACGATATTAGACTTAAGAAAGAAAAAA
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAA-AAAGAAAAAA
* * *
1913554 GTACCATTTGTGCTGATTCAAGGCCAACGACATTGGACTTAAAAATGAAAAGAATGATAAA
1 GTGCCA-ATGTGCTGATTCAAGGCCAATGACATTGGACTT----A--AAAAGAA--A-AAA
* * * * * * *
1913615 GGTGCCAATATGCTGATTCAGGGCCAATGATATTGGGCTTAAAGATGACAAAG
1 -GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAA-AAGAAAAAA
* * * ** * **
1913668 GTGCTAATGTGTTGATTGAAGGCCAACAACATTGGACTT--GAAGATGAAA
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAAAGAAAAAA
* * * *
1913717 GTTGCCAATGTGCTAATTCAAGGCCAGTGACATTGGACTTAAAGAAGACAAAG
1 G-TGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAA-AAGAAAAAA
* * *
1913770 GTGCTAATATGCTGATTCAAGGCCAATGATATTGGACTTAAGAAAGAAAAAA
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAA-AAAGAAAAAA
* * *
1913822 GTGCCAATGTGCTGATTCAAGGCAAATTACAGTGGACTTAGAAAAGA
1 GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTA-AAAAGA
1913869 TAGTTTGACA
Statistics
Matches: 277, Mismatches: 71, Indels: 38
0.72 0.18 0.10
Matches are distributed among these distances:
49 6 0.02
50 31 0.11
52 149 0.54
53 40 0.14
54 1 0.00
55 2 0.01
56 3 0.01
57 2 0.01
58 6 0.02
59 1 0.00
60 1 0.00
61 30 0.11
62 5 0.02
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (51 bp):
GTGCCAATGTGCTGATTCAAGGCCAATGACATTGGACTTAAAAAGAAAAAA
Found at i:1913965 original size:31 final size:31
Alignment explanation
Indices: 1913930--1914360 Score: 271
Period size: 31 Copynumber: 13.7 Consensus size: 31
1913920 GAAAGAGACA
*
1913930 CCACCAACTTGTGTGAGCTTTTGAAAGGTTG
1 CCACCAACTTGTGTGGGCTTTTGAAAGGTTG
* * * *
1913961 CCACCAGCTTATATGGGC-ATTGAGAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTTGA-AA-GGTTG
* * *
1913993 CCACTAACTTCTGTGGGC-TTTGAGAAGGGGTG
1 CCACCAACTTGTGTGGGCTTTTGA-AA-GGTTG
* * * ** *
1914025 CCATCGACTTGTGTGGCCTTGAGAAAGGGTG
1 CCACCAACTTGTGTGGGCTTTTGAAAGGTTG
** * * *
1914056 CCATTAACTTGTGTAGGC-TTTAAAAGGGTTA
1 CCACCAACTTGTGTGGGCTTTTGAAA-GGTTG
* * * * *
1914087 CCACCAGCTTGTGTAGGCTTTAAGAAGGGGTG
1 CCACCAACTTGTGTGGGCTTT-TGAAAGGTTG
* *
1914119 CCACCGACTTGTGTAGGCTTTTGAAGAGGTTG
1 CCACCAACTTGTGTGGGCTTTTGAA-AGGTTG
* * * ** *
1914151 CCACCGACTTGTGTCGGCTTTAGAGGGGTTA
1 CCACCAACTTGTGTGGGCTTTTGAAAGGTTG
* * * **
1914182 CCACCGACTTGTGTCGGCTTTAGAGGGGTTG
1 CCACCAACTTGTGTGGGCTTTTGAAAGGTTG
** * *
1914213 CCACTGACTTGTGCGGGCTTTGAGAAAGGTTG
1 CCACCAACTTGTGTGGGCTTT-TGAAAGGTTG
*
1914245 CCACCAAATTGTGTGGGC-TTTGAAGAGGTTG
1 CCACCAACTTGTGTGGGCTTTTGAA-AGGTTG
* *
1914276 CCACCGACTTGTGCGGGC-TTTGAATAGGTTG
1 CCACCAACTTGTGTGGGCTTTTGAA-AGGTTG
* * * *
1914307 CCACCAACATGTGTGGGCTTTAAGAGGAGGGTG
1 CCACCAACTTGTGTGGGCTTT-TGA-AAGGTTG
1914340 CCACCAACTCT-TGTGGGCTTT
1 CCACCAACT-TGTGTGGGCTTT
1914361 GAGAGGGTTG
Statistics
Matches: 320, Mismatches: 67, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
30 11 0.03
31 158 0.49
32 120 0.38
33 30 0.09
34 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.32, T:0.29
Consensus pattern (31 bp):
CCACCAACTTGTGTGGGCTTTTGAAAGGTTG
Found at i:1913993 original size:32 final size:32
Alignment explanation
Indices: 1913956--1914027 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1913946 GCTTTTGAAA
*
1913956 GGTTGCCACCAGCTTATATGGGCATTGAGAAG
1 GGTTGCCACCAACTTATATGGGCATTGAGAAG
* * * *
1913988 GGTTGCCACTAACTTCTGTGGGCTTTGAGAAG
1 GGTTGCCACCAACTTATATGGGCATTGAGAAG
*
1914020 GGGTGCCA
1 GGTTGCCA
1914028 TCGACTTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.26
Consensus pattern (32 bp):
GGTTGCCACCAACTTATATGGGCATTGAGAAG
Found at i:1914047 original size:63 final size:62
Alignment explanation
Indices: 1913930--1914370 Score: 314
Period size: 63 Copynumber: 7.0 Consensus size: 62
1913920 GAAAGAGACA
* * * * * * *
1913930 CCACCAACTTGTGTGAGCTTTTGAA-AGGTTGCCACCAGCTTATATGGGCATTGAGAAGGGTTG
1 CCACCAACTTGTGTGGGCTTTAGAAGAGGGTGCCACGA-CTTGTGT-GGCTTTGAGAAGGGTTG
* * *
1913993 CCACTAACTTCTGTGGGCTTTGAGAAG-GGGTGCCATCGACTTGTGTGGCCTTGAGAAAGGG-TG
1 CCACCAACTTGTGTGGGCTTT-AGAAGAGGGTGCCA-CGACTTGTGTGGCTTTGAG-AAGGGTTG
** * * * * *
1914056 CCATTAACTTGTGTAGGCTTTA-AA-AGGGTTACCACCAGCTTGTGTAGGCTTTAAGAAGGGGTG
1 CCACCAACTTGTGTGGGCTTTAGAAGAGGG-TGCCACGA-CTTGTGT-GGCTTTGAGAAGGGTTG
* * * * * *
1914119 CCACCGACTTGTGTAGGCTTTTGAAGAGGTTGCCACCGACTTGTGTCGGCTTT-AGAGGGGTTA
1 CCACCAACTTGTGTGGGCTTTAGAAGAGGGTGCCA-CGACTTGTGT-GGCTTTGAGAAGGGTTG
* * * *
1914182 CCACCGACTTGTGTCGGCTTTAG-AG-GGGTTGCCACTGACTTGTGCGGGCTTTGAGAAAGGTTG
1 CCACCAACTTGTGTGGGCTTTAGAAGAGGG-TGCCAC-GACTTGTG-TGGCTTTGAGAAGGGTTG
* * *
1914245 CCACCAAATTGTGTGGGCTTT-GAAGAGGTTGCCACCGACTTGTGCGGGCTTTGA-ATA-GGTTG
1 CCACCAACTTGTGTGGGCTTTAGAAGAGGGTGCCA-CGACTTGTG-TGGCTTTGAGA-AGGGTTG
* * *
1914307 CCACCAACATGTGTGGGCTTTAAGAGGAGGGTGCCACCAACTCT-TGTGGGCTTTGAG-AGGGTT
1 CCACCAACTTGTGTGGGCTTT-AGAAGAGGGTGCCA-CGACT-TGTGT-GGCTTTGAGAAGGGTT
1914370 G
62 G
1914371 GCACTGAGTT
Statistics
Matches: 308, Mismatches: 44, Indels: 51
0.76 0.11 0.13
Matches are distributed among these distances:
61 10 0.03
62 64 0.21
63 153 0.50
64 73 0.24
65 8 0.03
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.28
Consensus pattern (62 bp):
CCACCAACTTGTGTGGGCTTTAGAAGAGGGTGCCACGACTTGTGTGGCTTTGAGAAGGGTTG
Found at i:1914160 original size:126 final size:125
Alignment explanation
Indices: 1913929--1914370 Score: 386
Period size: 126 Copynumber: 3.5 Consensus size: 125
1913919 AGAAAGAGAC
* * * *
1913929 ACCACCAACTTGTGTGAGCTTTTGAAA-GGTTGCCACCAGCTTATATGGGCATTGAGAAGGGTTG
1 ACCACCAACTTGTGTG-GC-TTTAAAAGGGTTGCCACCAGCTTGTGTGGGCTTTGAGAAGGGTTG
* * * * *
1913993 CCACTAACTTCTGTGGGCTTTGAGAAG-GGGTGCCATCGACTTGTGT-GGCCTTGAGAAAGGG-T
64 CCACCAACTTGTGTGGGCTTT-TGAAGAGGTTGCCACCGACTTGTGTCGG-CTTGAG-AAGGGTT
* ** * * * *
1914055 GCCATTAACTTGTGTAGGCTTTAAAAGGGTTACCACCAGCTTGTGTAGGCTTTAAGAAGGGGTGC
1 ACCACCAACTTGTGT-GGCTTTAAAAGGGTTGCCACCAGCTTGTGTGGGCTTTGAGAAGGGTTGC
* * * *
1914120 CACCGACTTGTGTAGGCTTTTGAAGAGGTTGCCACCGACTTGTGTCGGCTTTAGAGGGGTT
65 CACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTCGGCTTGAGAAGGGTT
* * * * * *
1914181 ACCACCGACTTGTGTCGGCTTTAGAGGGGTTGCCA-CTGACTTGTGCGGGCTTTGAGAAAGGTTG
1 ACCACCAACTTGTGT-GGCTTTAAAAGGGTTGCCACCAG-CTTGTGTGGGCTTTGAGAAGGGTTG
*
1914245 CCACCAAATTGTGTGGGC-TTTGAAGAGGTTGCCACCGACTTGTG-CGGGCTTTGA-ATA-GGTT
64 CCACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTC-GGC-TTGAGA-AGGGTT
* * *
1914306 GCCACCAACATGTGTGGGCTTTAAGAGGAGGG-TGCCACCAACTCT-TGTGGGCTTTGAG-AGGG
1 ACCACCAACTTGTGT-GGCTTTAA-A--AGGGTTGCCACCAGCT-TGTGTGGGCTTTGAGAAGGG
1914368 TTG
61 TTG
1914371 GCACTGAGTT
Statistics
Matches: 253, Mismatches: 49, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
124 1 0.00
125 69 0.27
126 156 0.62
127 22 0.09
128 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.28
Consensus pattern (125 bp):
ACCACCAACTTGTGTGGCTTTAAAAGGGTTGCCACCAGCTTGTGTGGGCTTTGAGAAGGGTTGCC
ACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCGACTTGTGTCGGCTTGAGAAGGGTT
Found at i:1914280 original size:94 final size:95
Alignment explanation
Indices: 1913930--1914366 Score: 344
Period size: 94 Copynumber: 4.6 Consensus size: 95
1913920 GAAAGAGACA
* * * * * * * *
1913930 CCACCAACTTGTGTGAGCTTT-TGAAAGGTTGCCACCAGCTTATATGGGCATTG-AGAAGGGTTG
1 CCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAAG-A-GGTTA
** * * *
1913993 CCACTAACTTCTGTGGGCTTTGAGAAGGGGTG
64 CCACCGACTTGTGTCGGCTTTAAGAAGGGGTG
* * * ** * *
1914025 CCATCGACTTGTGT-GGCCTTGAGAAAGGGTGCCATTAACTTGTGTAGGCTTT-AAAAGGGTTAC
1 CCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGA-GGTTAC
*
1914088 CACC-AGCTTGTGTAGGCTTTAAGAAGGGGTG
65 CACCGA-CTTGTGTCGGCTTTAAGAAGGGGTG
* * * * *
1914119 CCACCGACTTGTGTAGGCTTTTGA-AGAGGTTGCCACCGACTTGTGTCGGCTTT-AGAGGGGTTA
1 CCACCGACTTGTGTGGGC-TTTGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGA-AGAGGTTA
1914182 CCACCGACTTGTGTCGGCTTT-AG-AGGGGTTG
64 CCACCGACTTGTGTCGGCTTTAAGAAGGGG-TG
* * * *
1914213 CCACTGACTTGTGCGGGCTTTGAGAAAGGTTGCCACCAAATTGTGTGGGCTTTGAAGAGGTTGCC
1 CCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAGGTTACC
* *
1914278 ACCGACTTGTG-CGGGCTTT--GAATAGGTTG
66 ACCGACTTGTGTC-GGCTTTAAGAA-GGGGTG
* * * * *
1914307 CCACCAACATGTGTGGGCTTTAAGAGGAGGGTGCCACCAACTCT-TGTGGGCTTTG-AGAGG
1 CCACCGACTTGTGTGGGCTTTGAGA-AAGGTTGCCACCAACT-TGTGTGGGCTTTGAAGAGG
1914367 GTTGGCACTG
Statistics
Matches: 278, Mismatches: 49, Indels: 31
0.78 0.14 0.09
Matches are distributed among these distances:
93 13 0.05
94 146 0.53
95 112 0.40
96 7 0.03
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.28
Consensus pattern (95 bp):
CCACCGACTTGTGTGGGCTTTGAGAAAGGTTGCCACCAACTTGTGTGGGCTTTGAAGAGGTTACC
ACCGACTTGTGTCGGCTTTAAGAAGGGGTG
Found at i:1914393 original size:125 final size:125
Alignment explanation
Indices: 1914087--1914364 Score: 285
Period size: 125 Copynumber: 2.2 Consensus size: 125
1914077 AAAAGGGTTA
* ** * * * * *
1914087 CCACCAGCTTGTGTAGGCTTTAAGAAGGGGTGCCACCGACTTGTGT-AGGCTTTTGAAGAGGTTG
1 CCACCAACTTGTGCGGGCTTTGAGAAAGGTTGCCACCAAATTGTGTGA-G-TTTTGAAGAGGTTG
* * * *
1914151 CCACCGACTTGTGTCGGCTTTAGAGGGGTTACCACCGACTTGTGTCGGCTTTAGAGGGGTTG
64 CCACCGACTTGTGTCGGCTTTAGAGAGGTTACCACCAACATGTGTCGGCTTTAGAGGGGGTG
** * *
1914213 CCACTGACTTGTGCGGGCTTTGAGAAAGGTTGCCACCAAATTGTGTGGGCTTTGAAGAGGTTGCC
1 CCACCAACTTGTGCGGGCTTTGAGAAAGGTTGCCACCAAATTGTGTGAGTTTTGAAGAGGTTGCC
* * *
1914278 ACCGACTTGTG-CGGGCTTT-GAATAGGTTGCCACCAACATGTGTGGGCTTTAAGAGGAGGGTG
66 ACCGACTTGTGTC-GGCTTTAG-AGAGGTTACCACCAACATGTGTCGGCTTT-AGAGG-GGGTG
*
1914340 CCACCAACTCT-TGTGGGCTTTGAGA
1 CCACCAACT-TGTGCGGGCTTTGAGA
1914365 GGGTTGGCAC
Statistics
Matches: 124, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
124 2 0.02
125 55 0.44
126 42 0.34
127 24 0.19
128 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.28
Consensus pattern (125 bp):
CCACCAACTTGTGCGGGCTTTGAGAAAGGTTGCCACCAAATTGTGTGAGTTTTGAAGAGGTTGCC
ACCGACTTGTGTCGGCTTTAGAGAGGTTACCACCAACATGTGTCGGCTTTAGAGGGGGTG
Found at i:1917537 original size:238 final size:238
Alignment explanation
Indices: 1917119--1917586 Score: 918
Period size: 238 Copynumber: 2.0 Consensus size: 238
1917109 GCTCAAAACA
*
1917119 AATACAAATGAGCTTTCGAAAATAATAATGAATACAAAAGCTCTTGAAAATGAGAAAACAAATCA
1 AATACAAATGAGCTTTCGAAAATAATAATGAATACAAAAGCTCTTAAAAATGAGAAAACAAATCA
1917184 AACTTTGAATGCTTTGATCTCTTGATGTTTCTTGGTTGGTTCTCATGCATTTCAGCTGTTAGAAA
66 AACTTTGAATGCTTTGATCTCTTGATGTTTCTTGGTTGGTTCTCATGCATTTCAGCTGTTAGAAA
1917249 CTCAAATTTATAGGCTTGAATGCTGACATACTCGTTGGAAGGTTGAATGATTGTGTTTCTAGCCG
131 CTCAAATTTATAGGCTTGAATGCTGACATACTCGTTGGAAGGTTGAATGATTGTGTTTCTAGCCG
*
1917314 TTGTTGACTTGTTTGGTGCTTGTTTCAATGCATTCAAGCTTTG
196 TTGTTCACTTGTTTGGTGCTTGTTTCAATGCATTCAAGCTTTG
1917357 AATACAAATGAGCTTTCGAAAATAATAATGAATACAAAAGCTCTTAAAAATGAGAAAACAAATCA
1 AATACAAATGAGCTTTCGAAAATAATAATGAATACAAAAGCTCTTAAAAATGAGAAAACAAATCA
1917422 AACTTTGAATGCTTTGATCTCTTGATGTTTCTTGGTTGGTTCTCATGCATTTCAGCTGTTAGAAA
66 AACTTTGAATGCTTTGATCTCTTGATGTTTCTTGGTTGGTTCTCATGCATTTCAGCTGTTAGAAA
1917487 CTCAAATTTATAGGCTTGAATGCTGACATACTCGTTGGAAGGTTGAATGATTGTGTTTCTAGCCG
131 CTCAAATTTATAGGCTTGAATGCTGACATACTCGTTGGAAGGTTGAATGATTGTGTTTCTAGCCG
1917552 TTGTTCACTTGTTTGGTGCTTGTTTCAATGCATTC
196 TTGTTCACTTGTTTGGTGCTTGTTTCAATGCATTC
1917587 CCATAGCCAT
Statistics
Matches: 228, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
238 228 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (238 bp):
AATACAAATGAGCTTTCGAAAATAATAATGAATACAAAAGCTCTTAAAAATGAGAAAACAAATCA
AACTTTGAATGCTTTGATCTCTTGATGTTTCTTGGTTGGTTCTCATGCATTTCAGCTGTTAGAAA
CTCAAATTTATAGGCTTGAATGCTGACATACTCGTTGGAAGGTTGAATGATTGTGTTTCTAGCCG
TTGTTCACTTGTTTGGTGCTTGTTTCAATGCATTCAAGCTTTG
Found at i:1917692 original size:20 final size:20
Alignment explanation
Indices: 1917667--1917821 Score: 86
Period size: 20 Copynumber: 7.7 Consensus size: 20
1917657 GTTAGAAACA
1917667 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
*
1917687 ATGTATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCATC
* *
1917707 ATGTATCGATACAA-ACAGTGGT
1 ATGTATCGATACAATTCA-T--C
* * * *
1917729 AGGGTAGCTGCTACCAGTT--TC
1 A-TGTATC-GATA-CAATTCATC
* *
1917750 ATGTATCGATACAAATCTTC
1 ATGTATCGATACAATTCATC
* *
1917770 GTGTATCGATACAA-TGATC
1 ATGTATCGATACAATTCATC
** *
1917789 ATGTATCGATACAAAGCATA
1 ATGTATCGATACAATTCATC
1917809 ATGTATCGATACA
1 ATGTATCGATACA
1917822 TCTAGGTGTT
Statistics
Matches: 101, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
18 3 0.03
19 20 0.20
20 65 0.64
21 2 0.02
22 1 0.01
23 5 0.05
24 3 0.03
25 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:1917852 original size:20 final size:20
Alignment explanation
Indices: 1917812--1917852 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1917802 AAGCATAATG
*
1917812 TATCGATACATCTAGGTGTT
1 TATCGATACATCAAGGTGTT
1917832 TATCGATACATTCAAGG-GTT
1 TATCGATACA-TCAAGGTGTT
1917852 T
1 T
1917853 TGACCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (20 bp):
TATCGATACATCAAGGTGTT
Found at i:1931696 original size:20 final size:20
Alignment explanation
Indices: 1931599--1931695 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
1931589 AAATTTGCGT
* *
1931599 GAATATATCGATACATTAAA
1 GAATGTATCGATACATTGAA
1931619 GAATGTATCGATACATTGAA
1 GAATGTATCGATACATTGAA
1931639 GAATGTATCGATACATTGAA
1 GAATGTATCGATACATTGAA
*
1931659 GAATGTATCGATACATTTAA
1 GAATGTATCGATACATTGAA
*
1931679 GAATGTATCAATACATT
1 GAATGTATCGATACATT
1931696 TGGGTCAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (20 bp):
GAATGTATCGATACATTGAA
Found at i:1933503 original size:20 final size:20
Alignment explanation
Indices: 1933478--1933590 Score: 95
Period size: 20 Copynumber: 5.5 Consensus size: 20
1933468 ACCTATATGC
1933478 ATCGATACATTTTTCAATGT
1 ATCGATACATTTTTCAATGT
*** *
1933498 ATCGATACATGGATGAATGT
1 ATCGATACATTTTTCAATGT
* *
1933518 ATCGATGCATTCTTCAATGT
1 ATCGATACATTTTTCAATGT
* *
1933538 ATCGTTTA-ATTTTAACTAGATGT
1 ATCG-ATACATTTT-TC-A-ATGT
1933561 ATCGATACATTGTTT-AATGT
1 ATCGATACATT-TTTCAATGT
1933581 ATCGATACAT
1 ATCGATACAT
1933591 CTAGTTAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
20 53 0.74
21 3 0.04
22 3 0.04
23 11 0.15
24 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (20 bp):
ATCGATACATTTTTCAATGT
Found at i:1941209 original size:15 final size:15
Alignment explanation
Indices: 1941189--1941233 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1941179 ATTCCACCAA
1941189 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
1941204 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
1941219 ACCCACCACAAAATC
1 ATCCACCACAAAATC
1941234 GTCGATACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:1947207 original size:9 final size:9
Alignment explanation
Indices: 1947193--1947290 Score: 63
Period size: 9 Copynumber: 10.0 Consensus size: 9
1947183 TCTTTCGTAC
1947193 CAAAAAAAA
1 CAAAAAAAA
*
1947202 CAAAAAAAC
1 CAAAAAAAA
1947211 CAAAAAACTAA
1 CAAAAAA--AA
1947222 -AAACAAAAA
1 CAAA-AAAAA
*
1947231 AATAGAAAAAA
1 CA-A-AAAAAA
1947242 CAGAAAAAAA
1 CA-AAAAAAA
1947252 CAAACAAAAA
1 CAAA-AAAAA
*
1947262 CAAACAAAA
1 CAAAAAAAA
* *
1947271 GAACTAACAAA
1 CAA--AAAAAA
1947282 CAAAAAAAA
1 CAAAAAAAA
1947291 AGGGTCTAGA
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
9 30 0.43
10 21 0.30
11 18 0.26
12 1 0.01
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1947208 original size:8 final size:8
Alignment explanation
Indices: 1947195--1947289 Score: 70
Period size: 8 Copynumber: 11.9 Consensus size: 8
1947185 TTTCGTACCA
1947195 AAAAAAAC
1 AAAAAAAC
1947203 AAAAAAAC
1 AAAAAAAC
*
1947211 CAAAAAAC
1 AAAAAAAC
*
1947219 -TAAAAAC
1 AAAAAAAC
*
1947226 AAAAAAAT
1 AAAAAAAC
1947234 AGAAAAAAC
1 A-AAAAAAC
1947243 AGAAAAAA-
1 A-AAAAAAC
*
1947251 ACAAACAA-
1 A-AAAAAAC
*
1947259 AAACAAAC
1 AAAAAAAC
*
1947267 AAAAGAAC
1 AAAAAAAC
* *
1947275 TAACAAAC
1 AAAAAAAC
1947283 AAAAAAA
1 AAAAAAA
1947290 AAGGGTCTAG
Statistics
Matches: 68, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
7 10 0.15
8 44 0.65
9 14 0.21
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1947209 original size:10 final size:10
Alignment explanation
Indices: 1947194--1947291 Score: 53
Period size: 10 Copynumber: 9.8 Consensus size: 10
1947184 CTTTCGTACC
1947194 AAAAAAAAC-
1 AAAAAAAACA
*
1947203 AAAAAAACCA
1 AAAAAAAACA
1947213 AAAAACTAAA-A
1 AAAAA--AAACA
*
1947224 ACAAAAAAA-T
1 A-AAAAAAACA
*
1947234 AGAAAAAACA
1 AAAAAAAACA
*
1947244 GAAAAAAACA
1 AAAAAAAACA
*
1947254 AACAAAAACA
1 AAAAAAAACA
1947264 AACAAAAGAAC-
1 AA-AAAA-AACA
* *
1947275 -TAACAAACA
1 AAAAAAAACA
1947284 AAAAAAAA
1 AAAAAAAA
1947292 GGGTCTAGAT
Statistics
Matches: 66, Mismatches: 14, Indels: 17
0.68 0.14 0.18
Matches are distributed among these distances:
8 3 0.05
9 17 0.26
10 32 0.48
11 5 0.08
12 9 0.14
ACGTcount: A:0.81, C:0.13, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1948537 original size:28 final size:28
Alignment explanation
Indices: 1948497--1948829 Score: 285
Period size: 28 Copynumber: 11.7 Consensus size: 28
1948487 CTAGAACGTT
* *
1948497 CATCTCTTCAAAGCCCACAGGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* ** * *
1948525 CATCTCTTCAAAGAAAACAAAAGTTAGTGG
1 CATCTTTTCAAAG--CCCACAAGTCAGTGG
* *
1948555 CATCTCTTCAAAGCCAACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1948583 CATCTTTTCCAAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* *
1948611 CACCTTTTCAAAGCCCACAAGTTAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
*
1948639 CA-CTTTTTCAAAGCCCACAAGTCAGTAG
1 CATC-TTTTCAAAGCCCACAAGTCAGTGG
* * *
1948667 TATTTTTTCATAGCCCACAAGTCAGTGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
1948695 CACCTTTTCAAAGCCTACAAATCAATGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * * *
1948723 CACCTTCTCAAAGCCCACAAATCAGAGG
1 CATCTTTTCAAAGCCCACAAGTCAGTGG
* * *
1948751 CACCTTCTCAAAGGTCC-CAAGTCAGTGG
1 CATCTTTTCAAA-GCCCACAAGTCAGTGG
* *
1948779 CTTCCTTTT-AAAGCCTGCACAAGTCGGTGG
1 CAT-CTTTTCAAAGCC--CACAAGTCAGTGG
* *
1948809 CAACTTTCTCTAAAACCCACA
1 CATCTTT-TC-AAAGCCCACA
1948830 CAAGTTGGTG
Statistics
Matches: 249, Mismatches: 44, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
27 3 0.01
28 190 0.76
29 12 0.05
30 39 0.16
32 5 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
CATCTTTTCAAAGCCCACAAGTCAGTGG
Found at i:1948857 original size:30 final size:32
Alignment explanation
Indices: 1948796--1948857 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1948786 TTAAAGCCTG
**
1948796 CACAAGTCGGTGGCAACTTTCTCTAAAACCCA
1 CACAAGTCGGTGGCAACCCTCTCTAAAACCCA
*
1948828 CACAAGTTGGTGGCAACCCT-TCT-AAACCCA
1 CACAAGTCGGTGGCAACCCTCTCTAAAACCCA
1948858 ATGTCGCTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 3 0.11
32 17 0.63
ACGTcount: A:0.31, C:0.32, G:0.16, T:0.21
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCTCTCTAAAACCCA
Found at i:1949722 original size:20 final size:20
Alignment explanation
Indices: 1949699--1949736 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1949689 TACATGGATG
1949699 AATGTATCAATACATTCTTC
1 AATGTATCAATACATTCTTC
*
1949719 AATGTATCGATACATTCT
1 AATGTATCAATACATTCT
1949737 ACCTAGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
AATGTATCAATACATTCTTC
Found at i:1952958 original size:57 final size:56
Alignment explanation
Indices: 1952865--1953013 Score: 217
Period size: 57 Copynumber: 2.6 Consensus size: 56
1952855 AACAACTGAT
* * * *
1952865 AAGGATGCCACTAACTTGTGGGCTTTAAAAAGGATGCCACTGACTTGTGGGCTTTGA
1 AAGGATGCCACTGACTTGTGGGCTTTGAAGA-GATGCCACTAACTTGTGGGCTTTGA
* **
1952922 AATGATGCCACTGACTTGTGGTTTTTTGAAGAGATGCCACTAACTTGTGGGCTTTGA
1 AAGGATGCCACTGACTTGTGG-GCTTTGAAGAGATGCCACTAACTTGTGGGCTTTGA
1952979 AAGGATGCCACTGACTTGTGGGCTTTGAAGAGATG
1 AAGGATGCCACTGACTTGTGGGCTTTGAAGAGATG
1953014 AACGTTCTAG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
56 12 0.15
57 63 0.78
58 6 0.07
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (56 bp):
AAGGATGCCACTGACTTGTGGGCTTTGAAGAGATGCCACTAACTTGTGGGCTTTGA
Found at i:1953013 original size:28 final size:28
Alignment explanation
Indices: 1952865--1953007 Score: 198
Period size: 28 Copynumber: 5.0 Consensus size: 28
1952855 AACAACTGAT
* *
1952865 AAGGATGCCACTAACTTGTGGGCTTTAAA
1 AAGGATGCCACTGACTTGTGGGCTTT-GA
1952894 AAGGATGCCACTGACTTGTGGGCTTTGA
1 AAGGATGCCACTGACTTGTGGGCTTTGA
* **
1952922 AATGATGCCACTGACTTGTGGTTTTTTG-
1 AAGGATGCCACTGACTTGTGG-GCTTTGA
*
1952950 AAGAGATGCCACTAACTTGTGGGCTTTGA
1 AAG-GATGCCACTGACTTGTGGGCTTTGA
1952979 AAGGATGCCACTGACTTGTGGGCTTTGA
1 AAGGATGCCACTGACTTGTGGGCTTTGA
1953007 A
1 A
1953008 GAGATGAACG
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
28 52 0.51
29 49 0.49
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (28 bp):
AAGGATGCCACTGACTTGTGGGCTTTGA
Found at i:1954220 original size:1 final size:1
Alignment explanation
Indices: 1954201--1954263 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
1954191 TCTAGACCTC
* * * * * * * *
1954201 TTTTTTGTTTGTTTGTTTTTTTGTTTGTTTTTTTTCTTTTTTTTGTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1954264 GTACGAAGGA
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (1 bp):
T
Found at i:1954220 original size:16 final size:14
Alignment explanation
Indices: 1954201--1954263 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
1954191 TCTAGACCTC
1954201 TTTTTTGTTTGTTTGT
1 TTTTTTGTTT-TTT-T
1954217 TTTTTTGTTTGTTTT
1 TTTTTTGTTT-TTTT
*
1954232 TTTTCTT-TTTTTTG
1 TTTT-TTGTTTTTTT
1954246 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
1954260 TTTT
1 TTTT
1954264 GTACGAAGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.05
14 17 0.40
15 8 0.19
16 16 0.37
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (14 bp):
TTTTTTGTTTTTTT
Found at i:1954225 original size:12 final size:12
Alignment explanation
Indices: 1954203--1954265 Score: 65
Period size: 12 Copynumber: 5.1 Consensus size: 12
1954193 TAGACCTCTT
1954203 TTTTGTTTGTTTG
1 TTTT-TTTGTTTG
1954216 TTTTTTTGTTTG
1 TTTTTTTGTTTG
*
1954228 TTTTTTT-TCTTT
1 TTTTTTTGT-TTG
*
1954240 TTTTTGTTTTTTG
1 TTTTT-TTGTTTG
*
1954253 TTTTTTTTTTTG
1 TTTTTTTGTTTG
1954265 T
1 T
1954266 ACGAAGGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
11 1 0.02
12 30 0.67
13 13 0.29
14 1 0.02
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTTG
Found at i:1954244 original size:22 final size:20
Alignment explanation
Indices: 1954201--1954263 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
1954191 TCTAGACCTC
1954201 TTTTTTGTTTGTTTG-TTTTT
1 TTTTTTGTTT-TTTGTTTTTT
* *
1954221 TTGTTTG-TTTTT-TTTCTT
1 TTTTTTGTTTTTTGTTTTTT
1954239 TTTTTTGTTTTTTGTTTTTT
1 TTTTTTGTTTTTTGTTTTTT
1954259 TTTTT
1 TTTTT
1954264 GTACGAAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 13 0.36
19 7 0.19
20 16 0.44
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (20 bp):
TTTTTTGTTTTTTGTTTTTT
Found at i:1964700 original size:20 final size:20
Alignment explanation
Indices: 1964675--1964728 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1964665 GTTAGAAGCA
*
1964675 ATGTATTGATACAAT-TCATC
1 ATGTATTGATACAATAT-ACC
1964695 ATGTATTGATACAATATACC
1 ATGTATTGATACAATATACC
1964715 ATGTATTGATACAA
1 ATGTATTGATACAA
1964729 ACAATGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATTGATACAATATACC
Found at i:1964783 original size:21 final size:19
Alignment explanation
Indices: 1964757--1964830 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 19
1964747 CTGCCAATTT
**
1964757 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1964778 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1964797 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1964818 -ATGTATCGATACA
1 CATGTATCGATACA
1964831 TCTCGGTATG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.38
20 14 0.29
21 16 0.33
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1968902 original size:18 final size:18
Alignment explanation
Indices: 1968870--1968904 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1968860 TTGTTTCTAT
1968870 TTCTTCTCTTTTTTTTTC
1 TTCTTCTCTTTTTTTTTC
1968888 TTCTT-TCTTTCTTTTTT
1 TTCTTCTCTTT-TTTTTT
1968905 TTAGTTGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTTCTCTTTTTTTTTC
Found at i:1969809 original size:21 final size:22
Alignment explanation
Indices: 1969775--1969815 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1969765 AAAATGAAGA
*
1969775 AAATAAAATTTAAAAATCACTT
1 AAATAAAATATAAAAATCACTT
*
1969797 AAATAAAA-ATAAAATTCAC
1 AAATAAAATATAAAAATCAC
1969816 AAGCATAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAAATATAAAAATCACTT
Found at i:1976900 original size:20 final size:20
Alignment explanation
Indices: 1976875--1976927 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1976865 GTTGGGCTCA
*
1976875 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATTCACC
*
1976895 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
1976915 ATGTATCGATACA
1 ATGTATCGATACA
1976928 CTGTATTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1977025 original size:13 final size:13
Alignment explanation
Indices: 1977007--1977031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1976997 TACTATGAAC
1977007 ATGTATCGATACA
1 ATGTATCGATACA
1977020 ATGTATCGATAC
1 ATGTATCGATAC
1977032 TAAGCAATAT
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):
ATGTATCGATACA
Found at i:1977030 original size:32 final size:33
Alignment explanation
Indices: 1976989--1977052 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1976979 TATTTCAAAT
*
1976989 TGTATCGATACTATG-AACATGTATCGATACAA
1 TGTATCGATACTAAGCAACATGTATCGATACAA
*
1977021 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATGTATCGATACA
1977053 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATGTATCGATACAA
Found at i:1979804 original size:33 final size:34
Alignment explanation
Indices: 1979758--1979834 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
1979748 CGATACTCGG
* * * *
1979758 TATCGATATAATGTGTCGATACTAAGAAC-TCTC
1 TATCGATACAATGTATCAATACTAAGAACTTCTA
*
1979791 TATCGATACAATGTATCAATACTAAGAACTTTTA
1 TATCGATACAATGTATCAATACTAAGAACTTCTA
1979825 TATCGATACA
1 TATCGATACA
1979835 TCTGGGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 26 0.68
34 12 0.32
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (34 bp):
TATCGATACAATGTATCAATACTAAGAACTTCTA
Found at i:1980286 original size:20 final size:20
Alignment explanation
Indices: 1980261--1980314 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1980251 GTTAGAGTTA
*
1980261 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATTCACC
*
1980281 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
*
1980301 ATGTATCGAGACAA
1 ATGTATCGATACAA
1980315 AGTGAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1980398 original size:13 final size:13
Alignment explanation
Indices: 1980380--1980405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1980370 TACTATGAAC
1980380 ATGTATCGATACA
1 ATGTATCGATACA
1980393 ATGTATCGATACA
1 ATGTATCGATACA
1980406 TTTGGGTGTA
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:1982167 original size:26 final size:26
Alignment explanation
Indices: 1982136--1982198 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
1982126 CTTAATTCAT
1982136 ACTTGAATGATCTTTAAATCCTAGGA
1 ACTTGAATGATCTTTAAATCCTAGGA
*
1982162 ACTTGAATAATCTTTAAATCCTAGGA
1 ACTTGAATGATCTTTAAATCCTAGGA
1982188 ACTTGAATGAT
1 ACTTGAATGAT
1982199 TTTGCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (26 bp):
ACTTGAATGATCTTTAAATCCTAGGA
Found at i:1982411 original size:47 final size:47
Alignment explanation
Indices: 1982276--1982423 Score: 163
Period size: 47 Copynumber: 3.1 Consensus size: 47
1982266 TTTTATATTG
* * ** *
1982276 ATACAATGCACAATGCATTAATACATTTGGGTTTTTTCAAAATGTATCA
1 ATACAATGCAAAATGTATCGATACATTTGGG--TTTTCAAATTGTATCA
* * * *
1982325 ATACAATGCAAAATGTATCGATACATCTAGTTTTTCAAATTGTATCG
1 ATACAATGCAAAATGTATCGATACATTTGGGTTTTCAAATTGTATCA
* *
1982372 ATACAATG-AATAATGTATCGATACATTTGGGTTTCCAAATTGCATCA
1 ATACAATGCAA-AATGTATCGATACATTTGGGTTTTCAAATTGTATCA
1982419 ATACA
1 ATACA
1982424 CTCATTAATG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
46 2 0.02
47 57 0.69
49 24 0.29
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (47 bp):
ATACAATGCAAAATGTATCGATACATTTGGGTTTTCAAATTGTATCA
Found at i:1983955 original size:20 final size:20
Alignment explanation
Indices: 1983926--1983987 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
1983916 TCGATAACAA
*
1983926 TTCAAAGTATCGATACATGT
1 TTCAATGTATCGATACATGT
*
1983946 TTCAATGTATCGATACATGA
1 TTCAATGTATCGATACATGT
***
1983966 AAAATATGTATCGATACATGT
1 TTCA-ATGTATCGATACATGT
1983987 T
1 T
1983988 ATTGGGATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
TTCAATGTATCGATACATGT
Found at i:1984052 original size:13 final size:13
Alignment explanation
Indices: 1984034--1984059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1984024 TACACCAAGT
1984034 ATGTATCGATACA
1 ATGTATCGATACA
1984047 ATGTATCGATACA
1 ATGTATCGATACA
1984060 TCAGAAAAAT
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:1990214 original size:13 final size:13
Alignment explanation
Indices: 1990196--1990233 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1990186 CATGTTTCTG
*
1990196 TGTATCGATACAT
1 TGTATCGATACAC
1990209 TGTATCGATACAC
1 TGTATCGATACAC
*
1990222 TGTATTGATACA
1 TGTATCGATACA
1990234 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1992798 original size:13 final size:13
Alignment explanation
Indices: 1992780--1992805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1992770 TACACCAAGT
1992780 ATGTATCGATACA
1 ATGTATCGATACA
1992793 ATGTATCGATACA
1 ATGTATCGATACA
1992806 TTGGCTTGTA
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:1995128 original size:19 final size:17
Alignment explanation
Indices: 1995080--1995131 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
1995070 TACTGCCAGC
1995080 TTCATGTATCGATACAA
1 TTCATGTATCGATACAA
1995097 TTCACTGTGTATCGATACCAA
1 TTCA---TGTATCGATA-CAA
1995118 TATCATGTATCGAT
1 T-TCATGTATCGAT
1995132 GCAAAGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
19 9 0.30
20 10 0.33
21 4 0.13
22 3 0.10
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (17 bp):
TTCATGTATCGATACAA
Found at i:1995782 original size:20 final size:20
Alignment explanation
Indices: 1995754--1995794 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1995744 TAATTTATAA
*
1995754 CTCCCCCTTAATAAAACATTT
1 CTCCCCTTTAATAAAA-ATTT
1995775 CTCCCCTTTAATAAAAATTT
1 CTCCCCTTTAATAAAAATTT
1995795 AATGCTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (20 bp):
CTCCCCTTTAATAAAAATTT
Found at i:1997382 original size:21 final size:21
Alignment explanation
Indices: 1997349--1997389 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1997339 CTAAGTAAAA
1997349 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1997370 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1997390 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1997454 original size:20 final size:19
Alignment explanation
Indices: 1997429--1997499 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1997419 ACCCTGAAAA
1997429 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
1997449 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
1997468 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
1997489 GTATCGATACA
1 GTATCGATACA
1997500 TTGGAAGTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:1997575 original size:21 final size:22
Alignment explanation
Indices: 1997545--1997595 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
1997535 ACTATTCATT
1997545 ACTGTTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
1997567 ACT-TTCATGTATCGATACATC
1 ACTGTTCATGTATCGATACATC
1997588 ACTGTTCA
1 ACTGTTCA
1997596 CACTGTTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.75
22 7 0.25
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (22 bp):
ACTGTTCATGTATCGATACATC
Found at i:1998821 original size:11 final size:10
Alignment explanation
Indices: 1998791--1998821 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1998781 GATTTTTGGG
1998791 AGGATTAAAA
1 AGGATTAAAA
1998801 AGGATTAAAA
1 AGGATTAAAA
*
1998811 AGGCTTAAAA
1 AGGATTAAAA
1998821 A
1 A
1998822 TGTGGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.19, T:0.19
Consensus pattern (10 bp):
AGGATTAAAA
Found at i:2008639 original size:20 final size:20
Alignment explanation
Indices: 2008614--2008655 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2008604 TTTTTGCTAT
*
2008614 AAGCTAAGTTGATAAAACCA
1 AAGCTAAATTGATAAAACCA
2008634 AAGCTAAATTGATAAAACCA
1 AAGCTAAATTGATAAAACCA
2008654 AA
1 AA
2008656 TTTATGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.12, T:0.19
Consensus pattern (20 bp):
AAGCTAAATTGATAAAACCA
Done.