Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold242
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: 756895
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:405913 original size:33 final size:33
Alignment explanation
Indices: 405867--405936 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
405857 ATACATTTTG
*
405867 CATTGTATTGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
405900 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACATTGCTCATTGTATCGATA
405933 CATT
1 CATT
405937 TTACAATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTGCTCATTGTATCGATA
Found at i:405936 original size:13 final size:13
Alignment explanation
Indices: 405887--405917 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
405877 ATACATTGCT
405887 CATTGTATCGATA
1 CATTGTATCGATA
405900 CATTGTATCGATA
1 CATTGTATCGATA
405913 CATTG
1 CATTG
405918 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:405965 original size:20 final size:19
Alignment explanation
Indices: 405850--405956 Score: 68
Period size: 20 Copynumber: 5.7 Consensus size: 19
405840 TTTACCCAGA
405850 TGTATCGATACATTTTG-CAT
1 TGTATCGATACA--TTGACAT
* *
405870 TGTATTGATACATTGCTCAT
1 TGTATCGATACATTG-ACAT
405890 TGTATCG----A-T-ACAT
1 TGTATCGATACATTGACAT
*
405903 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTG-ACAT
*
405923 TGTATCGATACATTTTACAAT
1 TGTATCGATACA-TTGAC-AT
405944 T-TATCGATACATT
1 TGTATCGATACATT
405957 CAGACATTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
13 10 0.14
15 1 0.01
16 1 0.01
17 1 0.01
18 4 0.06
19 2 0.03
20 46 0.66
21 5 0.07
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTGACAT
Found at i:408520 original size:51 final size:52
Alignment explanation
Indices: 408465--408581 Score: 143
Period size: 51 Copynumber: 2.3 Consensus size: 52
408455 TTATTTCTGA
*
408465 GGGGATACTCCAACCT-CAATTTTATTT-CTAAAATACC-AATTTTCCACAATC
1 GGGGATACTCCAACCTCCAATTTTATTTAC-AAAACACCGAATTTT-CACAATC
* * *
408516 GGGGATGCTCCAA-CTCCGATTTTATTTACAAAACACCGACTTTTCACAATC
1 GGGGATACTCCAACCTCCAATTTTATTTACAAAACACCGAATTTTCACAATC
*
408567 GGGGATACTCTAACC
1 GGGGATACTCCAACC
408582 CGTTATTTCG
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
50 2 0.04
51 47 0.84
52 7 0.12
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (52 bp):
GGGGATACTCCAACCTCCAATTTTATTTACAAAACACCGAATTTTCACAATC
Found at i:408714 original size:79 final size:78
Alignment explanation
Indices: 408518--408745 Score: 248
Period size: 79 Copynumber: 2.9 Consensus size: 78
408508 CCACAATCGG
* * * * *
408518 GGATGCTCCAACTCCGATTTTATTTAC-AAAACACCGACTTTTCACAATCGGGGATACTCTAA-C
1 GGATACTCCAAC-CCGATTTTATTT-CTAAATCATCGATTTTTCACAATCGGGGATACTCCAACC
*
408581 CCGTTA-TTTCGAGG
64 CCGTTATTTTCGAGA
* * * * * *
408595 GGATACTCTAACCTTGGTTTTATTTCTAACAT-ATCAATTTTTCATAGTCGGGGATACTCCAACC
1 GGATACTCCAACC-CGATTTTATTTCTAA-ATCATCGATTTTTCACAATCGGGGATACTCCAACC
*
408659 CCGTTATTTTTGAGA
64 CCGTTATTTTCGAGA
* *
408674 GGATACTCCAATCCCGATTTTATTTCTAAATCATCGATTTTTCACAATCAGGGATACTCCGACCC
1 GGATACTCCAA-CCCGATTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAACCC
408739 CGTTATT
65 CGTTATT
408746 ATCTCTAAAA
Statistics
Matches: 123, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
76 2 0.02
77 45 0.37
78 10 0.08
79 64 0.52
80 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (78 bp):
GGATACTCCAACCCGATTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAACCCC
GTTATTTTCGAGA
Found at i:411926 original size:11 final size:10
Alignment explanation
Indices: 411905--411951 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
411895 TGTCCTTCGT
411905 AAAAAAAA-A
1 AAAAAAAACA
*
411914 AACAAAAACA
1 AAAAAAAACA
411924 AAAAACAAACA
1 AAAAA-AAACA
*
411935 AAAAAACACA
1 AAAAAAAACA
411945 AAAAAAA
1 AAAAAAA
411952 GAAAAGAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 7 0.22
10 15 0.47
11 10 0.31
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:411926 original size:17 final size:17
Alignment explanation
Indices: 411906--411938 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
411896 GTCCTTCGTA
411906 AAAAAAAAAACAAAAAC
1 AAAAAAAAAACAAAAAC
*
411923 AAAAAACAAACAAAAA
1 AAAAAAAAAACAAAAA
411939 AACACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Found at i:411927 original size:19 final size:19
Alignment explanation
Indices: 411905--411956 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
411895 TGTCCTTCGT
411905 AAAAAAAAAAACAAAAACA-
1 AAAAAAAAAAA-AAAAACAC
*
411924 AAAAACAAACAAAAAAACAC
1 AAAAA-AAAAAAAAAAACAC
411944 AAAAAAAAGAAAA
1 AAAAAAAA-AAAA
411957 GAAGAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.87, C:0.12, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAACAC
Found at i:413040 original size:13 final size:13
Alignment explanation
Indices: 413022--413046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
413012 CATAAAATGT
413022 TGTATCGATACAA
1 TGTATCGATACAA
413035 TGTATCGATACA
1 TGTATCGATACA
413047 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:413044 original size:33 final size:33
Alignment explanation
Indices: 413002--413068 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
412992 TTCAACGATT
413002 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
413035 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
413068 T
1 T
413069 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:413129 original size:13 final size:13
Alignment explanation
Indices: 413111--413135 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
413101 ATTACTCACA
413111 TGTATCGATACAT
1 TGTATCGATACAT
413124 TGTATCGATACA
1 TGTATCGATACA
413136 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:413187 original size:52 final size:53
Alignment explanation
Indices: 413124--413268 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 53
413114 ATCGATACAT
***
413124 TGTATCGATACACTGAT-CTTTGTATCAATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
* *
413176 TGTATCGATACA-TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
* * *
413228 TGTATCGATACACT-ATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAA
413269 CTTTTCATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 3 0.04
52 80 0.95
53 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
Found at i:414164 original size:20 final size:20
Alignment explanation
Indices: 414119--414165 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
414109 GTTAACAACC
*
414119 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
414139 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
414160 CATGTT
1 CATGTT
414166 CAGCACCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.43
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:416941 original size:28 final size:27
Alignment explanation
Indices: 416908--416972 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 27
416898 AACCCACTAG
416908 TCAGTGGCACCTCTTCGAAGTCCACAAA
1 TCAGTGGCACCTCTTCGAAGTCCA-AAA
* * * *
416936 TCAGTGGCATCTTTTTGAAGTCCATAA
1 TCAGTGGCACCTCTTCGAAGTCCAAAA
*
416963 TCGGTGGCAC
1 TCAGTGGCAC
416973 TTGCTGTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 10 0.32
28 21 0.68
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.28
Consensus pattern (27 bp):
TCAGTGGCACCTCTTCGAAGTCCAAAA
Found at i:417190 original size:32 final size:32
Alignment explanation
Indices: 417146--417304 Score: 94
Period size: 32 Copynumber: 5.0 Consensus size: 32
417136 AGTGGAGGAA
*
417146 CCTTCTCTAAAGCCCACATAAGCTAGTGGCAG
1 CCTTCTCTAAAGCCCACACAAGCTAGTGGCAG
* * * *
417178 CCTTCT-TCAAAGCCTACACAAGTTAGTGGTAA
1 CCTTCTCT-AAAGCCCACACAAGCTAGTGGCAG
* *
417210 CACTT-TCTAAAGCCTACACAAG-TCAGTGGCAAC
1 C-CTTCTCTAAAGCCCACACAAGCT-AGTGGC-AG
* * * * * *
417243 CCTT-TTTGAAGCTCGCACGAGCTAGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGCTAGTGGC-AG
* * *
417275 CCTT-TCAAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTCTAAAGCCCACACAAGCTAGTGGCA
417305 TCTCTTTCTA
Statistics
Matches: 100, Mismatches: 21, Indels: 13
0.75 0.16 0.10
Matches are distributed among these distances:
31 3 0.03
32 90 0.90
33 7 0.07
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (32 bp):
CCTTCTCTAAAGCCCACACAAGCTAGTGGCAG
Found at i:417481 original size:52 final size:50
Alignment explanation
Indices: 417408--418391 Score: 287
Period size: 52 Copynumber: 19.9 Consensus size: 50
417398 AGCACATTGG
* *
417408 CACTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTA
1 CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-TTA
* ** * * *
417459 CCACTTTTAAGTCAAATGTCGCTAACGTTGAATTAGCACATTGGCA-CTT-
1 -CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* *
417508 CA-TCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGC-TCATTAGCACCTT-
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCAT-ATTGGCACCTTA
*** * ** *
417557 CA-TCTTTAAGTATGATATCATTGGCCTTGAATCAGCATATTGGCATCTTTA
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CCTTA
* * * * * *
417608 AAATTCCTAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGG---C--A
1 CACTT-TTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * * * *
417654 C-C-TTTAAGTCTAATATCGTTGGCTTTGAATCAGCATAATGGAACCTTTA
1 CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-TTA
* * * * * * *
417703 CCACATTTAAGTCTAATGTCGCTAGCCGTGAATTAGCACATTGGCACC-TC
1 -CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * *
417753 CA-TCTTTATGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTTT
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA--CCTTA
* * ** * * * * * * *
417805 TA-TCTTCAAGTTTAATGTTGCTAG--TTGTAGATCAACACATTGACATTCTTTG
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTG-A-ATCAGCATATTGGCA--CCTTA
* * *
417857 TA-TCTTTAAG-CCTAATATCACTGGCCTTGAATCAGCATATTGGCACCCTTCTCA
1 CACT-TTTAAGTCC-AATGTCGCTGGCCTTGAATCAGCATATTGGCA-CC-T-T-A
* * *
417911 TCCTTATCATGTTAAAGTCCAATATCGCT-GCCTTGAATCAGCACATTGG---C--A
1 --C--A-C-T-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * *
417962 C-C-TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATAGTGGCACCTTTA
1 CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACC-TTA
* * * * * * *
418011 CCACATTTAAGTCTAATGTCGCTAGCCTTGAATTATCACATTGGCA-CTTT
1 -CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * *
418061 CA-TCTTTAAGTCCAATGTTGCTGCCCTTGTATCAGC-TCATTGGCA-CTTT
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCAT-ATTGGCACCTTA
* * * * * *
418110 CA-TCTTTAAGTGCGATATCACTAGCCTTGAATCAGCATATTGGCATCTTTA
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CCTTA
** * *
418161 -ACATCCCTAAGCCCAATG-CTGCTGGCCTTGAATCAG--T-CT--CA---T-
1 CAC-T-TTTAAGTCCAATGTC-GCTGGCCTTGAATCAGCATATTGGCACCTTA
* * * * * * ** *
418203 --C-TTCAAGTCTAATGTCACTGGCCGTGAATCAGCACATTGACATTTTTCG
1 CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA-CCTT-A
* * * * *
418252 CACCTTTAAGCCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTCTGT
1 CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCT-T-A
* *
418304 CA-TCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGG---C--A
1 CACT-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
* * *
418349 C-C-TTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCA
1 CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
418392 TCTTTATCAC
Statistics
Matches: 692, Mismatches: 165, Indels: 157
0.68 0.16 0.15
Matches are distributed among these distances:
38 22 0.03
39 1 0.00
41 2 0.00
42 16 0.02
43 84 0.12
44 1 0.00
45 2 0.00
46 3 0.00
47 4 0.01
48 34 0.05
49 154 0.22
50 17 0.02
51 15 0.02
52 295 0.43
53 2 0.00
54 3 0.00
56 1 0.00
58 1 0.00
60 19 0.03
61 14 0.02
62 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (50 bp):
CACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTA
Found at i:417525 original size:48 final size:49
Alignment explanation
Indices: 417412--417567 Score: 145
Period size: 48 Copynumber: 3.1 Consensus size: 49
417402 CATTGGCACT
* * ** *
417412 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTACCA-C
1 TTTAAGTCAAATGTCGCTAACCTTGAATCAGCACATTAGCACC-TT--CATC
* * *
417463 TTTTAAGTCAAATGTCGCTAACGTTGAATTAGCACATTGGCA-CTTCATC
1 -TTTAAGTCAAATGTCGCTAACCTTGAATCAGCACATTAGCACCTTCATC
* * ** *
417512 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCTCATTAGCACCTTCATC
1 TTTAAGTCAAATGTCGCTAACCTTGAATCAGCACATTAGCACCTTCATC
417561 TTTAAGT
1 TTTAAGT
417568 ATGATATCAT
Statistics
Matches: 86, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
48 35 0.41
49 15 0.17
50 2 0.02
51 1 0.01
52 33 0.38
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (49 bp):
TTTAAGTCAAATGTCGCTAACCTTGAATCAGCACATTAGCACCTTCATC
Found at i:417689 original size:95 final size:94
Alignment explanation
Indices: 417560--417751 Score: 224
Period size: 95 Copynumber: 2.0 Consensus size: 94
417550 GCACCTTCAT
* * * *
417560 CTTTAAGTATGATATCATTGGCCTTGAATCAGCATATTGGCATCTTTA-AAATTCCTAAGCCCAA
1 CTTTAAGTATAATATCATTGGCCTTGAATCAGCATAATGGAACCTTTACAAATT--TAAGCCCAA
* *
417624 TGTCACTGGCCTTGAATCAGCACATTGGCAC
64 TGTCACTAGCCGTGAATCAGCACATTGGCAC
* * * * * *
417655 CTTTAAGTCTAATATCGTTGGCTTTGAATCAGCATAATGGAACCTTTACCACATTTAAGTCTAAT
1 CTTTAAGTATAATATCATTGGCCTTGAATCAGCATAATGGAACCTTTA-CAAATTTAAGCCCAAT
* *
417720 GTCGCTAGCCGTGAATTAGCACATTGGCAC
65 GTCACTAGCCGTGAATCAGCACATTGGCAC
417750 CT
1 CT
417752 CCATCTTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
95 77 0.95
97 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (94 bp):
CTTTAAGTATAATATCATTGGCCTTGAATCAGCATAATGGAACCTTTACAAATTTAAGCCCAATG
TCACTAGCCGTGAATCAGCACATTGGCAC
Found at i:418004 original size:43 final size:42
Alignment explanation
Indices: 417925--418010 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 42
417915 TATCATGTTA
*
417925 AAGTCCAATATCGCTGCCTTGAATCAGCACATTGGCACCTTT
1 AAGTCCAATATCGCTGCCTTGAATCAGCACAGTGGCACCTTT
* *
417967 AAGTCTAATATCGCTGGCCTTGAATCAGCATAGTGGCACCTTT
1 AAGTCCAATATCGCT-GCCTTGAATCAGCACAGTGGCACCTTT
418010 A
1 A
418011 CCACATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 14 0.35
43 26 0.65
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (42 bp):
AAGTCCAATATCGCTGCCTTGAATCAGCACAGTGGCACCTTT
Found at i:418372 original size:43 final size:43
Alignment explanation
Indices: 418307--418397 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
418297 CCTCTGTCAT
* * *
418307 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
418350 CTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCAT
1 CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
418393 CTTTA
1 CTTTA
418398 TCACTCTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (43 bp):
CTTTAAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:419047 original size:8 final size:8
Alignment explanation
Indices: 419036--419065 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
419026 GAAAAAAATT
419036 AAAAATCAA
1 AAAAATC-A
419045 AAAAATCA
1 AAAAATCA
419053 AAAAATCA
1 AAAAATCA
419061 AAAAA
1 AAAAA
419066 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATCA
Found at i:419048 original size:9 final size:9
Alignment explanation
Indices: 419036--419067 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
419026 GAAAAAAATT
419036 AAAAATCAA
1 AAAAATCAA
419045 AAAAATC-A
1 AAAAATCAA
419053 AAAAATCAA
1 AAAAATCAA
419062 AAAAAT
1 AAAAAT
419068 AATAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATCAA
Found at i:419049 original size:17 final size:17
Alignment explanation
Indices: 419027--419067 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
419017 TTTCAACACG
*
419027 AAAAAAAT-TAAAAATC
1 AAAAAAATCAAAAAATC
419043 AAAAAAATCAAAAAATC
1 AAAAAAATCAAAAAATC
419060 AAAAAAAT
1 AAAAAAAT
419068 AATAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAATCAAAAAATC
Found at i:420682 original size:79 final size:76
Alignment explanation
Indices: 420591--420750 Score: 189
Period size: 77 Copynumber: 2.1 Consensus size: 76
420581 AGAAACAAAT
* *
420591 TCCAACCCCGTTA-TTTGCAAGGGGATACTCCAACCCCGGTTTTACTTCTGA-AACACTGATTTT
1 TCCAACCCCGTTATTTTG-AA-GGGATACTCCAA-CCCGGTTTTACTTC-CATAACA-TCATTTT
* *
420654 TCACCATCAGGGATAC
61 CCACAATCAGGGATAC
* * *
420670 TCCAACCTCGTTATTTTTGAAGGGATACTCTAACCCGGTTTTATTTCCATAACATCATTTTCCAC
1 TCCAACCCCGTTA-TTTTGAAGGGATACTCCAACCCGGTTTTACTTCCATAACATCATTTTCCAC
420735 AATCAGGGATAC
65 AATCAGGGATAC
420747 TCCA
1 TCCA
420751 GTCCCGTCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
77 25 0.35
78 17 0.24
79 23 0.32
80 2 0.03
81 4 0.06
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (76 bp):
TCCAACCCCGTTATTTTGAAGGGATACTCCAACCCGGTTTTACTTCCATAACATCATTTTCCACA
ATCAGGGATAC
Found at i:420772 original size:77 final size:79
Alignment explanation
Indices: 420610--420789 Score: 188
Period size: 77 Copynumber: 2.3 Consensus size: 79
420600 GTTATTTGCA
* * * *
420610 AGGGGATACTCCAACCCCGGTTTTACTTCTGAAACACTGATTTTTCACCATCAGGGATACTCCAA
1 AGGGGATACTCCAACCCCGGTTTTACTTCTCAAACACTCATTTTCCACAATCAGGGATACTCCAA
* * *
420675 CCTCGTTATTTTTG
66 CCTCGTCAATTTAG
* * *
420689 AAGGGATACTCTAA-CCCGGTTTTATTTC-CATAACA-TCATTTTCCACAATCAGGGATACTCCA
1 AGGGGATACTCCAACCCCGGTTTTACTTCTCA-AACACTCATTTTCCACAATCAGGGATACTCCA
*
420751 GTCC-CGTCAATTTAG
65 -ACCTCGTCAATTTAG
* * *
420766 AGGGGATAATCCAATCCCGATTTT
1 AGGGGATACTCCAACCCCGGTTTT
420790 TTATTCCAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
77 44 0.53
78 27 0.33
79 12 0.14
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (79 bp):
AGGGGATACTCCAACCCCGGTTTTACTTCTCAAACACTCATTTTCCACAATCAGGGATACTCCAA
CCTCGTCAATTTAG
Found at i:426696 original size:79 final size:79
Alignment explanation
Indices: 426374--426693 Score: 325
Period size: 79 Copynumber: 4.1 Consensus size: 79
426364 ATGGGGCTGA
* ** *
426374 AGTATCCCCGATTAG-G-AAAATTGGTGTTCCAGAAATAAAATCGGGGTTGGAGTA---CCTCAA
1 AGTATCCCCGATT-GTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTCAG
*
426434 AAATAACAGGGTTGG
65 AAATAACGGGGTTGG
* * * * * * *
426449 AGTA-CCCCTGATTAT-AAAAATCAGTATGTTAAAAATGAAATCGGGGTTGGAGTATCCCCTC-G
1 AGTATCCCC-GATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTCAG
426511 AAAATAACGGGGTTGG
65 -AAATAACGGGGTTGG
* * ** * **
426527 AGTATCCCCGATTGTGAAAAA-TCGATGATTTAGAAATAAGGTCGGGGTTGAAGTATCTCCTTGG
1 AGTATCCCCGATTGTGAAAAATTAG-TGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTCAG
426591 AAATAACGGGGTTGG
65 AAATAACGGGGTTGG
* *
426606 AGTATCCCCAATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCGTCAGA
1 AGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTCAGA
** *
426671 AATAACGGGACTGA
66 AATAACGGGGTTGG
426685 AGTATCCCC
1 AGTATCCCC
426694 AATGAAATAA
Statistics
Matches: 197, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
74 4 0.02
75 38 0.19
78 28 0.14
79 124 0.63
80 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (79 bp):
AGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCTCCTCAGA
AATAACGGGGTTGG
Found at i:426778 original size:108 final size:108
Alignment explanation
Indices: 426651--426881 Score: 347
Period size: 108 Copynumber: 2.1 Consensus size: 108
426641 ATAAAATCGG
* * * *
426651 GGTTGGAGTATCTCGTCAGAAATAACGGGACTGAAGTATCCCCAATGAAATAAC-GGTGTTAGAG
1 GGTTGGAGTATCCCCTCAGAAATAACAGGACTGAAGTATCCCCAATGAAATAACAAG-GTTAGAG
426715 TACCCCCGATTATGAAAAAACAATATTTTTAGATATAAAGCCAA
65 TACCCCCGATTATGAAAAAACAATATTTTTAGATATAAAGCCAA
* * **
426759 GGTTGGAGTATCCCCTCAGAAATAATAGGACTGGAGTATCCCTGATGAAATAACAAGGTTAGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACAGGACTGAAGTATCCCCAATGAAATAACAAGGTTAGAGT
* **
426824 ACCCTCGATTATGAAAAAACAATATTTTTAGATATAAAGCCGG
66 ACCCCCGATTATGAAAAAACAATATTTTTAGATATAAAGCCAA
426867 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
426882 GATTAAGAAA
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
108 110 0.99
109 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (108 bp):
GGTTGGAGTATCCCCTCAGAAATAACAGGACTGAAGTATCCCCAATGAAATAACAAGGTTAGAGT
ACCCCCGATTATGAAAAAACAATATTTTTAGATATAAAGCCAA
Found at i:429296 original size:13 final size:13
Alignment explanation
Indices: 429278--429303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429268 AACTTCCTAG
429278 ATGTATCGATACA
1 ATGTATCGATACA
429291 ATGTATCGATACA
1 ATGTATCGATACA
429304 TTGAATAATG
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:429382 original size:19 final size:19
Alignment explanation
Indices: 429355--429417 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
429345 AGTGATACAC
429355 TGTATCGATACAACATTTA
1 TGTATCGATACAACATTTA
*
429374 TGTAGCGATAC-AC---TA
1 TGTATCGATACAACATTTA
429389 --TATCGATACAACATTTA
1 TGTATCGATACAACATTTA
429406 TGTATCGATACA
1 TGTATCGATACA
429418 TTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 2 0.06
15 2 0.06
17 2 0.06
18 2 0.06
19 20 0.56
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACATTTA
Found at i:429384 original size:32 final size:32
Alignment explanation
Indices: 429342--429417 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
429332 GCAGTAGCTT
* *
429342 TGTAGTGATACACTGTATCGATACAACATTTA
1 TGTAGCGATACACTATATCGATACAACATTTA
429374 TGTAGCGATACACTATATCGATACAACATTTA
1 TGTAGCGATACACTATATCGATACAACATTTA
*
429406 TGTATCGATACA
1 TGTAGCGATACA
429418 TTTACTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTAGCGATACACTATATCGATACAACATTTA
Found at i:429500 original size:21 final size:22
Alignment explanation
Indices: 429476--429518 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
429466 GTTGGGACCT
*
429476 TGTATCGATACGTTT-GACAAA
1 TGTATCGATACATTTGGACAAA
429497 TGTATCGATACATTTGGACAAA
1 TGTATCGATACATTTGGACAAA
429519 AATGTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (22 bp):
TGTATCGATACATTTGGACAAA
Found at i:430338 original size:13 final size:13
Alignment explanation
Indices: 430320--430345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
430310 CAATTTTTTA
430320 TGTATCGATACAT
1 TGTATCGATACAT
430333 TGTATCGATACAT
1 TGTATCGATACAT
430346 ACTTTGTGTA
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:430362 original size:32 final size:33
Alignment explanation
Indices: 430300--430363 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
430290 TGCAAGCCAA
**
430300 TGTATCGATACAATTTTTTATGTATCGATACAT
1 TGTATCGATACAATACTTTATGTATCGATACAT
* *
430333 TGTATCGATAC-ATACTTTGTGTATTGATACA
1 TGTATCGATACAATACTTTATGTATCGATACA
430364 AGTTTGGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATACTTTATGTATCGATACAT
Found at i:431035 original size:12 final size:12
Alignment explanation
Indices: 431018--431042 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
431008 TAAGGTAATT
431018 TTAGCAAATTTA
1 TTAGCAAATTTA
431030 TTAGCAAATTTA
1 TTAGCAAATTTA
431042 T
1 T
431043 GCATTCTCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTAGCAAATTTA
Found at i:431393 original size:60 final size:57
Alignment explanation
Indices: 431300--431411 Score: 163
Period size: 61 Copynumber: 1.9 Consensus size: 57
431290 AACTAATCTT
* *
431300 AGTCACTAGCTACCGACCTAGGGCGAGTCGATGACG-TGACGCTCGATATTGATCAG
1 AGTCACTAGCTACCGAACTAGGGCGAGTCGATGAAGTTGACGCTCGATATTGATCAG
431356 AGTCACTAGAGCTACTCGAACTAGGGCGAAGTCGATGAAGTTGACGCTCGATATTG
1 AGTCACT--AGCTAC-CGAACTAGGGCG-AGTCGATGAAGTTGACGCTCGATATTG
431412 GTGATGCGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
56 7 0.14
58 6 0.12
59 11 0.22
60 10 0.20
61 15 0.31
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (57 bp):
AGTCACTAGCTACCGAACTAGGGCGAGTCGATGAAGTTGACGCTCGATATTGATCAG
Found at i:432935 original size:13 final size:13
Alignment explanation
Indices: 432917--432941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432907 ATAATCCCCC
432917 TGTATCGATACAG
1 TGTATCGATACAG
432930 TGTATCGATACA
1 TGTATCGATACA
432942 AAGAAAAATG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:439235 original size:20 final size:20
Alignment explanation
Indices: 439189--439262 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
439179 ATCCCAATGA
***
439189 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
439210 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
439230 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
439250 TATGTATCGATAC
1 CATGTATCGATAC
439263 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:440118 original size:40 final size:42
Alignment explanation
Indices: 440074--440173 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
440064 GTCCTACTTT
*
440074 TTGAGGACAAAGGAAAAG-AG-AATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGGAAAAGAAGAAAAGAAA-AGTGTCTTGCTCC
* * * *
440114 TTGAGGACCAAGGAAGAGAAGAAAAGGAAAGTGTCTTGCTTC
1 TTGAGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCTTGCTCC
440156 TTGAGGACAAAGTGAAAA
1 TTGAGGACAAAG-GAAAA
440174 AGAGTACGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
40 16 0.33
41 4 0.08
42 25 0.51
43 4 0.08
ACGTcount: A:0.41, C:0.11, G:0.29, T:0.19
Consensus pattern (42 bp):
TTGAGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCTTGCTCC
Found at i:440476 original size:55 final size:55
Alignment explanation
Indices: 440266--440847 Score: 708
Period size: 55 Copynumber: 10.3 Consensus size: 55
440256 ATAAAGTACA
* * * *
440266 TCCTACTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTT---AA-G--AGGCG
** **
440327 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCATAGAGAAAG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--A-AGAG-GCG
* * * *
440386 ---TGCTCATTGAGGATTGGAAAATGCCACGAATTTGTGTGGGCTTTAAGAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
* * * *
440438 TCCTGTTCTTTGAGGAATGGAGAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
* *
440493 TCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
440548 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
*
440603 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
*
440658 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AA-G---AGGCG
* * *
440718 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAGAGGCG
* ** *
440774 TCTTGCTCTTTGAGGACTAAAAAATGCCACCGACTTGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGCG
440829 TCCTGCTCTTTGAGGACTG
1 TCCTGCTCTTTGAGGACTG
440848 AAAGGTGAAA
Statistics
Matches: 465, Mismatches: 42, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
52 1 0.00
53 4 0.01
54 1 0.00
55 292 0.63
56 69 0.15
58 2 0.00
60 31 0.07
61 63 0.14
62 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGCG
Found at i:455651 original size:13 final size:13
Alignment explanation
Indices: 455633--455658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
455623 TACACAAAGT
455633 ATGTATCGATACA
1 ATGTATCGATACA
455646 ATGTATCGATACA
1 ATGTATCGATACA
455659 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:455656 original size:32 final size:33
Alignment explanation
Indices: 455615--455678 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
455605 TAGCCAAACT
**
455615 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
455647 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
455679 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:459745 original size:15 final size:15
Alignment explanation
Indices: 459725--459764 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
459715 ATAAAAGTGT
*
459725 TCAAAATGAGGAAGC
1 TCAAAATGAAGAAGC
459740 TCAAAATGAAGAAGC
1 TCAAAATGAAGAAGC
*
459755 TCCAAATGAA
1 TCAAAATGAA
459765 ATCGATGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (15 bp):
TCAAAATGAAGAAGC
Found at i:461858 original size:13 final size:13
Alignment explanation
Indices: 461840--461874 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
461830 TTTTCTTTGC
*
461840 ATCGATACATTGT
1 ATCGATACACTGT
461853 ATCGATACACTGT
1 ATCGATACACTGT
461866 ATCGATACA
1 ATCGATACA
461875 AGGGGATTAT
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:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (13 bp):
ATCGATACACTGT
Found at i:462029 original size:20 final size:20
Alignment explanation
Indices: 461986--462031 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
461976 AAATCTTTTG
461986 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
462007 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
462027 CAAAA
1 CAAAA
462032 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:463526 original size:23 final size:21
Alignment explanation
Indices: 463484--463527 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
463474 GTTTGAAGTT
**
463484 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
463505 TTTGCATTGTACTTTGAATTTTA
1 TTTGC-TTG-ACTTTGAATTTTA
463528 ATCTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:464438 original size:12 final size:12
Alignment explanation
Indices: 464421--464445 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
464411 TACACAAAGT
464421 ATGTATCGATAC
1 ATGTATCGATAC
464433 ATGTATCGATAC
1 ATGTATCGATAC
464445 A
1 A
464446 CAAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:464438 original size:31 final size:31
Alignment explanation
Indices: 464403--464465 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
464393 TAGCCAAACT
*
464403 TGTATCGATACAC-AAAGTATGTATCGATACA
1 TGTATCGATACACAAAAAT-TGTATCGATACA
464434 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
464465 T
1 T
464466 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (31 bp):
TGTATCGATACACAAAAATTGTATCGATACA
Found at i:469401 original size:13 final size:13
Alignment explanation
Indices: 469383--469407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469373 ATAATGCACA
469383 GTATCGATACATT
1 GTATCGATACATT
469396 GTATCGATACAT
1 GTATCGATACAT
469408 GACCACTGTA
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):
GTATCGATACATT
Found at i:469514 original size:13 final size:13
Alignment explanation
Indices: 469496--469520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
469486 ACATACAAGA
469496 TGTATCGATACAC
1 TGTATCGATACAC
469509 TGTATCGATACA
1 TGTATCGATACA
469521 TGACCAAATG
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:469537 original size:33 final size:32
Alignment explanation
Indices: 469477--469540 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
469467 CTTAACTGTT
469477 TGTATCGATACATACAAGATGTATCGATACAC
1 TGTATCGATACATACAAGATGTATCGATACAC
469509 TGTATCGATACATGACCAA-ATGTATCGATACA
1 TGTATCGATACAT-A-CAAGATGTATCGATACA
469541 TTGACTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 13 0.43
33 14 0.47
34 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (32 bp):
TGTATCGATACATACAAGATGTATCGATACAC
Found at i:470543 original size:41 final size:41
Alignment explanation
Indices: 470443--470544 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 41
470433 GTCCCACTTT
* * *
470443 TTGAGGACAAAGG-AAAAGAGAATGAAATAGGTCTTGCTCC
1 TTGAGGACAAAGGAAAAAGAAAAGGAAATAGGTCCTGCTCC
*
470483 TTGAGGACAAAGGAAAAAAGAAAAGGAAA-ATGTCCTGCTCC
1 TTGAGGACAAAGG-AAAAAGAAAAGGAAATAGGTCCTGCTCC
470524 TTGAGGACAAAGTGAAAAAGA
1 TTGAGGACAAAG-GAAAAAGA
470545 GTACGTCTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
40 13 0.24
41 29 0.53
42 13 0.24
ACGTcount: A:0.45, C:0.12, G:0.26, T:0.17
Consensus pattern (41 bp):
TTGAGGACAAAGGAAAAAGAAAAGGAAATAGGTCCTGCTCC
Found at i:470637 original size:42 final size:41
Alignment explanation
Indices: 470574--470828 Score: 217
Period size: 43 Copynumber: 5.9 Consensus size: 41
470564 GATAAAGGAA
*
470574 AAAAGGAAAATGAAA-TGCGTCCTGCTCTTTGAGGACAAAAG
1 AAAAGAAAAAT-AAAGTGCGTCCTGCTCTTTGAGGACAAAAG
470615 AAAGAGAAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
1 AAA-AGAAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
* * * *
470657 AGAAAAAAAGGGAATGAAGTGTGTCCTACTCTTTGAGGACAAAAGGAG
1 A-AAAGAAA---AATAAAGTGCGTCCTGCTCTTTGAGGAC-AAA--AG
* * * *
470705 AAAAGAAGGGAATGGAA-TGTGTCCTGCTCTTTGAGGGCAAAGGAG
1 AAAAGAA--AAAT-AAAGTGCGTCCTGCTCTTTGAGGACAAA--AG
* ** *
470750 AAAAGGAAAATAAAGTGCAACATGCTCTTTGAGGACAAAGAAG
1 AAAAGAAAAATAAAGTGCGTCCTGCTCTTTGAGGAC-AA-AAG
* *
470793 AAAAGGAAAATAAAGTACGTCCTGCTCTTTGAGGAC
1 AAAAGAAAAATAAAGTGCGTCCTGCTCTTTGAGGAC
470829 TAGGTGGTGC
Statistics
Matches: 178, Mismatches: 21, Indels: 28
0.78 0.09 0.12
Matches are distributed among these distances:
41 6 0.03
42 40 0.22
43 55 0.31
44 2 0.01
45 39 0.22
46 25 0.14
47 8 0.04
48 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.19
Consensus pattern (41 bp):
AAAAGAAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
Found at i:470986 original size:61 final size:62
Alignment explanation
Indices: 470812--471362 Score: 606
Period size: 61 Copynumber: 9.0 Consensus size: 62
470802 ATAAAGTACG
** * *
470812 TCCTGCTCTTTGAGGACT-AGGTGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGCCG
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCA
* *
470874 TCCTACTCTTTGAGGACT-AAAGGGTGCCACCAACTTGTGTGAGCTTT-AAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCA
* * * * * *
470935 TCCTGCTCTTTGAGGAC-GAAATGTGCCACCAACTTGTATGGGCTTTAAAAAGAAAAAAGACG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-GAAAAGGCA
* ** ** **
470997 TCCTGCTCTTTGAGGACTG-AGGGTGCCACCAACTCATGTGGGCTTT--AAAGGTGAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCA
* * * * *
471056 TCCTGCTCTTTGAGGACT-AAAGGGTACCACCAACTTATGTGGGCTTTAAAAAGAAAAAAGACA
1 TCCTGCTCTTTGAGGACTGAAA-GGTGCCACCAACTTGTGTGGGCTTTGAAAAG-GAAAAGGCA
* * * *
471119 GTCCTACTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGG-AAAGGCA
1 -TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCA
* * * *
471181 TCCTACTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTAGGCTTTGCAAA-GAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGA-AAAGGCA
*
471242 TCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCA
* * *
471303 TCCTGCTCTCTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGGAAAAG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAG
471363 AAGGAAATAA
Statistics
Matches: 418, Mismatches: 52, Indels: 37
0.82 0.10 0.07
Matches are distributed among these distances:
59 23 0.06
60 56 0.13
61 154 0.37
62 127 0.30
63 13 0.03
64 44 0.11
65 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (62 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGGAAAAGGCA
Found at i:478282 original size:13 final size:13
Alignment explanation
Indices: 478266--478290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
478256 ATTCATCATG
478266 TATCGATACAATA
1 TATCGATACAATA
478279 TATCGATACAAT
1 TATCGATACAAT
478291 GTACCATGTA
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:478288 original size:33 final size:33
Alignment explanation
Indices: 478241--478309 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
478231 CCGTTACAAG
* *
478241 CAATGTATCAATACAAT-TCATCATGTATCGATA
1 CAATATATCAATACAATGT-ACCATGTATCGATA
*
478274 CAATATATCGATACAATGTACCATGTATCGATA
1 CAATATATCAATACAATGTACCATGTATCGATA
478307 CAA
1 CAA
478310 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (33 bp):
CAATATATCAATACAATGTACCATGTATCGATA
Found at i:478382 original size:19 final size:19
Alignment explanation
Indices: 478339--478393 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
478329 TGCCAGTTTT
**
478339 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
478359 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
478378 ATGTATCGATACAATG
1 ATGTATCGATACAATG
478394 TATGGATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:479851 original size:21 final size:21
Alignment explanation
Indices: 479825--479870 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
479815 CTCGAGCGAT
*
479825 TTAATTTATTTAAATTAAAAA
1 TTAATTTAATTAAATTAAAAA
* *
479846 TTAATTTAATTAAATTTAATA
1 TTAATTTAATTAAATTAAAAA
479867 TTAA
1 TTAA
479871 AATCGATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATTTAATTAAATTAAAAA
Found at i:479858 original size:16 final size:17
Alignment explanation
Indices: 479827--479859 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
479817 CGAGCGATTT
*
479827 AATTTATTTAAATTAAA
1 AATTAATTTAAATTAAA
479844 AATTAATTT-AATTAAA
1 AATTAATTTAAATTAAA
479860 TTTAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAATTTAAATTAAA
Found at i:480007 original size:20 final size:21
Alignment explanation
Indices: 479982--480032 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
479972 ATATTTTAAA
479982 ATATTTTATTAAATAT-ATTT
1 ATATTTTATTAAATATAATTT
480002 ATATTTTATTAAATATAATTT
1 ATATTTTATTAAATATAATTT
480023 AAATATTTTA
1 --ATATTTTA
480033 CGTAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.57
21 4 0.14
23 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTTTATTAAATATAATTT
Found at i:480018 original size:14 final size:14
Alignment explanation
Indices: 479952--480006 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
479942 TTTTTTAATT
*
479952 TTAAATATATTTCA
1 TTAAATATATTTTA
*
479966 TTAAGTATA--TT-
1 TTAAATATATTTTA
479977 TTAAA-ATATTTTA
1 TTAAATATATTTTA
479990 TTAAATATATTTATA
1 TTAAATATATTT-TA
480005 TT
1 TT
480007 TTATTAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 3 0.09
13 5 0.15
14 14 0.42
15 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:482751 original size:29 final size:28
Alignment explanation
Indices: 482692--482753 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
482682 AAAAAATTTG
*
482692 ATATTAAATAAGTAAATTTAATATTAAAA
1 ATATTAAATAAGTAAATTT-ATAATAAAA
*
482721 ATATTAAATATAGTAAATTCT-TAATACAA
1 ATATTAAATA-AGTAAATT-TATAATAAAA
482750 ATAT
1 ATAT
482754 GCATTTGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 20 0.69
30 8 0.28
31 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (28 bp):
ATATTAAATAAGTAAATTTATAATAAAA
Found at i:492201 original size:25 final size:25
Alignment explanation
Indices: 492171--492222 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
492161 AATTAATTTT
492171 AATTAAATTAAAAATAATAAAAATA
1 AATTAAATTAAAAATAATAAAAATA
* * *
492196 AATTAAATTAAATATTATAATAATA
1 AATTAAATTAAAAATAATAAAAATA
492221 AA
1 AA
492223 CTTTAAATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AATTAAATTAAAAATAATAAAAATA
Found at i:492292 original size:15 final size:15
Alignment explanation
Indices: 492269--492317 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
492259 CTTAATAATG
492269 ATAATAAATAATTATA
1 ATAA-AAATAATTATA
492285 ATAAAAATAATTAT-
1 ATAAAAATAATTATA
492299 -TAAAAAT-ATTATA
1 ATAAAAATAATTATA
492312 ATAAAA
1 ATAAAA
492318 TATATGTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.16
13 7 0.23
14 5 0.16
15 10 0.32
16 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAAAATAATTATA
Found at i:492320 original size:13 final size:14
Alignment explanation
Indices: 492262--492319 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 14
492252 ATTTAATCTT
*
492262 AATAATGATAAT-A
1 AATAATTATAATAA
492275 AATAATTATAATAAA
1 AATAATTATAAT-AA
*
492290 AATAATTATTA-AA
1 AATAATTATAATAA
492303 AAT-ATTATAATAA
1 AATAATTATAATAA
492316 AATA
1 AATA
492320 TATGTATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 6 0.16
13 21 0.55
15 11 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
AATAATTATAATAA
Found at i:492538 original size:28 final size:29
Alignment explanation
Indices: 492498--492570 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
492488 TTATAATAAT
* *
492498 AAAATCTATATTTATTAGA-TTATTATATA
1 AAAATATA-ATTTATTACATTTATTATATA
492527 AAAATATAATTTA-TACATTTATTATATA
1 AAAATATAATTTATTACATTTATTATATA
*
492555 ATAATA-AATTTTATTA
1 AAAATATAA-TTTATTA
492571 TACATATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.13
28 24 0.63
29 9 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (29 bp):
AAAATATAATTTATTACATTTATTATATA
Found at i:494401 original size:12 final size:11
Alignment explanation
Indices: 494379--494454 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
494369 AGAGAAAGAA
*
494379 GAGAGAGGAGG
1 GAGATAGGAGG
494390 GATGATAGGAGG
1 GA-GATAGGAGG
*
494402 AGAGACAGGA--
1 -GAGATAGGAGG
*
494412 GAGATAGTA--
1 GAGATAGGAGG
494421 GAGATAGGAGG
1 GAGATAGGAGG
494432 GATGATAGGAGG
1 GA-GATAGGAGG
*
494444 AGAGACAGGAG
1 -GAGATAGGAG
494455 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:494411 original size:24 final size:24
Alignment explanation
Indices: 494378--494463 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
494368 AAGAGAAAGA
*
494378 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
494402 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
494420 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
494444 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
494464 AGAGAGGATG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:494430 original size:42 final size:42
Alignment explanation
Indices: 494369--494487 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
494359 TAGCCCTCAA
* *
494369 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
494411 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
494453 AGAGATAATAGAGAGAGGATGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
494488 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:500173 original size:77 final size:79
Alignment explanation
Indices: 500063--500214 Score: 195
Period size: 78 Copynumber: 1.9 Consensus size: 79
500053 TTAAAGAGGT
* * * *
500063 AAAAGAAAAAAATGTGAAAGGGTGATTATTTTT-GGATGGGTTTAAAAAGTAA-TTGCATTGGCG
1 AAAAGAAAAAAAGGTGAAAGGGTGATTATTTTTGGGATGAGTAT-AAAAGTAACTT-CATTGGAG
500126 -AAAGTGGGCTGTGAC
64 AAAAGTGGGCTGTGAC
* * *
500141 AAAAGAAAAAACGGTGAAA-GTTGATTATTTTTGGGTTGAGTATAAAAGTAACTTCATTGGAGAA
1 AAAAGAAAAAAAGGTGAAAGGGTGATTATTTTTGGGATGAGTATAAAAGTAACTTCATTGGAGAA
500205 AAGTGGGCTG
66 AAGTGGGCTG
500215 GTATTTTTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
77 27 0.42
78 37 0.58
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.28
Consensus pattern (79 bp):
AAAAGAAAAAAAGGTGAAAGGGTGATTATTTTTGGGATGAGTATAAAAGTAACTTCATTGGAGAA
AAGTGGGCTGTGAC
Found at i:500311 original size:9 final size:9
Alignment explanation
Indices: 500299--500333 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
500289 TATTAAAAAT
500299 ATTTTTATA
1 ATTTTTATA
500308 ATTTTTATA
1 ATTTTTATA
500317 ATTTTTATA
1 ATTTTTATA
500326 ATATTTTA
1 AT-TTTTA
500334 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTATA
Found at i:500551 original size:14 final size:15
Alignment explanation
Indices: 500524--500559 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
500514 ATTTTAAATT
*
500524 ATTAAATTTAAAAAA
1 ATTAAAATTAAAAAA
500539 ATTAAAATT-AAAAA
1 ATTAAAATTAAAAAA
500553 ATTAAAA
1 ATTAAAA
500560 ATAGTAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATTAAAAAA
Found at i:501246 original size:21 final size:21
Alignment explanation
Indices: 501207--501247 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
501197 CTTATTAAAA
*
501207 ATATTTTATATTAATATTTAT
1 ATATTTTAAATTAATATTTAT
501228 ATATTTTAAAATTAA-ATTTA
1 ATATTTT-AAATTAATATTTA
501248 AATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATTTTAAATTAATATTTAT
Found at i:504146 original size:18 final size:18
Alignment explanation
Indices: 504112--504161 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
504102 ATTATATGTC
504112 AAAATAATTTCTA-ATATCA
1 AAAAT-ATTT-TAGATATCA
*
504131 AAAATGTTTTAGATATCA
1 AAAATATTTTAGATATCA
504149 AAAATATTTTAGA
1 AAAATATTTTAGA
504162 GACAAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 21 0.75
19 5 0.18
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AAAATATTTTAGATATCA
Found at i:504384 original size:33 final size:33
Alignment explanation
Indices: 504311--504390 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
504301 TACACACCCA
*
504311 GATGTATCGATACATTATACTGATACATATTGT
1 GATGTATCGATACATTATACTGATACAAATTGT
*
504344 GAAGTATCGATACATTATA-TCGATACAAATTGCT
1 GATGTATCGATACATTATACT-GATACAAATTG-T
*
504378 -TTGTATCGATACA
1 GATGTATCGATACA
504391 CCATAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 39 0.95
34 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (33 bp):
GATGTATCGATACATTATACTGATACAAATTGT
Found at i:506897 original size:17 final size:17
Alignment explanation
Indices: 506877--506910 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
506867 TAGCCTAAAC
* *
506877 AACCAATAAACCTAGAA
1 AACCAAGAAAACTAGAA
506894 AACCAAGAAAACTAGAA
1 AACCAAGAAAACTAGAA
506911 GAATTCTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.21, G:0.09, T:0.09
Consensus pattern (17 bp):
AACCAAGAAAACTAGAA
Found at i:510278 original size:158 final size:156
Alignment explanation
Indices: 509998--510384 Score: 530
Period size: 158 Copynumber: 2.5 Consensus size: 156
509988 TTCAACCCCA
* * * * *
509998 ATTTTATTTTCAAAACACCCATTTTCCACCATTGGGGATACTCCAACCCTGTTATTTTCGAGGGG
1 ATTTTATTTCCAAAACAACCATTTTCCACCATTGAGGATACTCCAACCC-CTTATTTTCGAAGGG
510063 ATACTCCAATCCCGGCTGTATTTCTAAAACATCAATTTTCCATAATCGGGGATACTCCAACCTCA
65 ATACTCCAATCCCGGCTGTATTTCTAAAACATCAATTTTCCATAATCGGGGATACTCCAACCTCA
510128 TTATTTTTGAAGGGATACTCCAA-CCCTG
130 TT-TTTTTGAAGGGATACTCCAATCCC-G
* * * *
510156 ATTTTATTTCCAAAATAACCATTTTCCACTATCGAGGATATTCCAATCCCCTTATTTTCGAAGGG
1 ATTTTATTTCCAAAACAACCATTTTCCACCATTGAGGATACTCCAA-CCCCTTATTTTCGAAGGG
* * *
510221 ATACTTCAA-CCCTGGCTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCTC
65 ATACTCCAATCCC-GGCTGTATTTCTAAAACATCAATTTTCCATAATCGGGGATACTCCAACCTC
510285 ATTTTTTTGAAGGGATACTCCAATCCCG
129 ATTTTTTTGAAGGGATACTCCAATCCCG
* * * *
510313 GTTTTATTTCCAAAACATCAATTTTCCACCATTGAGGGTACTCCAACCCCGTTATTCTT-GAGAG
1 ATTTTATTTCCAAAACAACCATTTTCCACCATTGAGGATACTCCAACCCC-TTATT-TTCGA-AG
510377 GG-TACTCC
63 GGATACTCC
510385 GACTCCGTTT
Statistics
Matches: 202, Mismatches: 21, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
156 4 0.02
157 74 0.37
158 121 0.60
159 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (156 bp):
ATTTTATTTCCAAAACAACCATTTTCCACCATTGAGGATACTCCAACCCCTTATTTTCGAAGGGA
TACTCCAATCCCGGCTGTATTTCTAAAACATCAATTTTCCATAATCGGGGATACTCCAACCTCAT
TTTTTTGAAGGGATACTCCAATCCCG
Found at i:510328 original size:78 final size:78
Alignment explanation
Indices: 509999--510406 Score: 380
Period size: 79 Copynumber: 5.2 Consensus size: 78
509989 TCAACCCCAA
* * * ** * * * *
509999 TTTTATTTTCAAAACACCCATTTTCCACCATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGA
1 TTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAACCC-ATTATTTTTGAAGGGA
510064 TACTCCAATCCC-GG
65 TACTCCAA-CCCTGG
* * *
510078 CTGTATTTCTAAAACATCAATTTTCCATAATCGGGGATACTCCAACCTCATTATTTTTGAAGGGA
1 TTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAACC-CATTATTTTTGAAGGGA
*
510143 TACTCCAACCCTGA
65 TACTCCAACCCTGG
* * * * * * *
510157 TTTTATTTCCAAAATAACCATTTTCCACT-ATCGAGGATATTCCAATCCCCTTATTTTCGAAGGG
1 TTTTATTTCCAAAACATCAATTTTCCA-TAATCGGGGATACTCCAA-CCCATTATTTTTGAAGGG
*
510221 ATACTTCAACCCTGG
64 ATACTCCAACCCTGG
* * *
510236 CTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACCTCATT-TTTTTGAAGGGA
1 TTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAACC-CATTATTTTTGAAGGGA
510300 TACTCCAATCCC-GG
65 TACTCCAA-CCCTGG
** * * *
510314 TTTTATTTCCAAAACATCAATTTTCCACCATTGAGGG-TACTCCAACCCCGTTATTCTTGAGAGG
1 TTTTATTTCCAAAACATCAATTTTCCATAATCG-GGGATACTCCAA-CCCATTATTTTTGA-AGG
* *
510378 G-TACTCCGACTCC-GT
63 GATACTCCAAC-CCTGG
*
510393 TTTTATCTCCAAAA
1 TTTTATTTCCAAAA
510407 TATTAAAATT
Statistics
Matches: 270, Mismatches: 47, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
78 65 0.24
79 197 0.73
80 8 0.03
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
TTTTATTTCCAAAACATCAATTTTCCATAATCGGGGATACTCCAACCCATTATTTTTGAAGGGAT
ACTCCAACCCTGG
Found at i:510506 original size:11 final size:12
Alignment explanation
Indices: 510469--510501 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
510459 TTCTAACCCT
510469 ATTTCTTTTTGA
1 ATTTCTTTTTGA
510481 ATTTCTTTTTGA
1 ATTTCTTTTTGA
510493 ATTTCTTTT
1 ATTTCTTTT
510502 AAATTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.70
Consensus pattern (12 bp):
ATTTCTTTTTGA
Found at i:516727 original size:62 final size:62
Alignment explanation
Indices: 516555--517429 Score: 923
Period size: 62 Copynumber: 14.0 Consensus size: 62
516545 TCTAGTCTTT
* * * *
516555 AAAGAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGACACCCTTTAGTCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * ** * * *
516617 AAAAAGTAGGACACC-TTGCCTTTTTAAAGCCCACACAAATTGGTGGCACCTTTTAGTTCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* ** *
516678 AAAGAGCAGGACACCTTTTTCTTTTTAAAGCCTGCACGAGTTGGTGGCACCTTTTAGTCTTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * * *
516740 AAAGAACAGGATGCCTTTTTC-TTTTAAAGCCCACACGAGCTGGTGGCACATTTTAGTCCTT
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * *
516801 AAAGAGCAGGGCACC-TTTTCTTTTTTAAAGCCCACACGAGCTGGTGGCACGCTGGTGGCACATT
1 AAAGAGCAGGACGCCTTTTTC-TTTTTAAAGCCCACACGA----GT-------TGGTGGCACCTT
*
516865 TTAGTCCTT
54 TTAGTCCTC
* * ** * ** *
516874 AAAGAGCATGACGCCTTTTCCTTTTTAAAGCTTACACGAGCTGGTGGCATTTTTTAGTCTTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * * *
516936 AAAGAGCAGGGCACCTTTTTC-TTTTAAAGCTCACATGAGTTAGTGGCACCTTTTAGTCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
** * * * * *
516997 AAAGAATAGGACGCCTTTTCCTTTTTAAAGCCCATATGAGTTAGTGGCATCTTTTTAGTCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA-CCTTTTAGTCCTC
* * * * *
517060 AAAGAGCAAGACGTC-TTTCCTTTTTAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTT
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * * *
517121 AAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTAGTGGCACCCTTTAGTCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * *
517183 AAAGAGTAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTTGTCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * * * *
517245 AAAGAGTAGGACGTCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGGCACCCTTTAGCCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * * * *
517307 AAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCCACATGAGTTAGTGGCACCCTTTAGTCCTC
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
* * * * *
517369 AAAGAGTATGACGCATTTTTCCTTTTAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCT
1 AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCT
517430 TAAGGAGAAG
Statistics
Matches: 685, Mismatches: 110, Indels: 36
0.82 0.13 0.04
Matches are distributed among these distances:
60 5 0.01
61 170 0.25
62 432 0.63
63 23 0.03
66 1 0.00
69 1 0.00
73 49 0.07
74 4 0.01
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (62 bp):
AAAGAGCAGGACGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTC
Found at i:516899 original size:73 final size:73
Alignment explanation
Indices: 516778--516922 Score: 236
Period size: 73 Copynumber: 2.0 Consensus size: 73
516768 GCCCACACGA
* *
516778 GCTGGTGGCACATTTTAGTCCTTAAAGAGCAGGGCACCTTTTCTTTTTTAAAGCCCACACGAGCT
1 GCTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACGAGCT
516843 GGTGGCAC
66 GGTGGCAC
* * **
516851 GCTGGTGGCACATTTTAGTCCTTAAAGAGCATGACGCCTTTTCCTTTTTAAAGCTTACACGAGCT
1 GCTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACGAGCT
516916 GGTGGCA
66 GGTGGCA
516923 TTTTTTAGTC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.30
Consensus pattern (73 bp):
GCTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACACGAGCT
GGTGGCAC
Found at i:517580 original size:42 final size:42
Alignment explanation
Indices: 517461--517818 Score: 228
Period size: 42 Copynumber: 8.6 Consensus size: 42
517451 TATTTCCTTA
* *
517461 TTTTCTCTTTGTCCTCAAAGAGCAGAACACACTTTATT-TCCTT
1 TTTTC-CTTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCC-T
* * * *
517504 CTTTTCTCTTTTATCCTCAAAGAGCATGATGCACTTTATTTTCCT
1 -TTTTC-C-TTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCCT
* *
517549 TTTTCATTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCTT
1 TTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCCT
* * * *
517591 TTTTCCTTTGTCCTCAAAGAGCAAGATGCA-TTTCGTTCTCTT
1 TTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTCTCCT
* * * ** *
517633 TTTTCTTTTATCCTCAAAGAGCAAGACATACTTCATT-TCCTT
1 TTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCC-T
* * *
517675 TTTTCCTTTATCCTCAAA-A--AGTA-GGA-TTTA--CT-CT
1 TTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCCT
* * * * *
517709 TTTGCACTTTGTCCTCAAGGAGCAGGA--CACTTTCCTTTTTCTT
1 TTTTC-CTTTGTCCTCAAAGAGCAGGACGCACTTT--ATTCTCCT
* *
517752 TTTTCCTTTGTCCTCAAGGAACAGGAC-CTA-TTTCATTCT-C-
1 TTTTCCTTTGTCCTCAAAGAGCAGGACGC-ACTTT-ATTCTCCT
*
517792 TTTTCGTTTGTCCTCAAAGAGCAGGAC
1 TTTTCCTTTGTCCTCAAAGAGCAGGAC
517819 AACCCCTTCC
Statistics
Matches: 251, Mismatches: 45, Indels: 40
0.75 0.13 0.12
Matches are distributed among these distances:
34 5 0.02
35 12 0.05
36 2 0.01
37 4 0.02
38 7 0.03
39 2 0.01
40 24 0.10
41 6 0.02
42 135 0.54
43 11 0.04
44 13 0.05
45 27 0.11
46 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTCTCCT
Found at i:517636 original size:84 final size:81
Alignment explanation
Indices: 517468--517819 Score: 299
Period size: 84 Copynumber: 4.3 Consensus size: 81
517458 TTATTTTCTC
* *
517468 TTTGTCCTCAAAGAGCAGAACACACTTTATTTCCTTCTTTTCTCTTTTATCCTCAAAGAGCATGA
1 TTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTT-TTTTC-C-TTTATCCTCAAAGAGCAAGA
*
517533 TGCACTTTATTTTCCTTTTTCA
63 -GCA-TTTATTCT-CTTTTTCA
* *
517555 TTTGTCCTCAAAGAGCAGGACGCACTTTA-TTCTCTTTTTTCCTTTGTCCTCAAAGAGCAAGATG
1 TTTGTCCTCAAAGAGCAGGACACACTTTATTTC-CTTTTTTCCTTTATCCTCAAAGAGCAAGA-G
* *
517619 CATTTCGTTCTCTTTTTTCT
64 CATTT-ATTCTC-TTTTTCA
* * * * * *
517639 TTTATCCTCAAAGAGCAAGACATACTTCATTTCCTTTTTTCCTTTATCCTCAAAAAG-TAG-G-A
1 TTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTTCCTTTATCCTCAAAGAGCAAGAGCA
*
517701 TTTA--CTCTTTTGCA
66 TTTATTCTCTTTTTCA
* * * * * * *
517715 CTTTGTCCTCAAGGAGCAGG--ACACTTTCCTTTTTCTTTTTTCCTTTGTCCTCAAGGAACAGGA
1 -TTTGTCCTCAAAGAGCAGGACACACTTT--ATTTCCTTTTTTCCTTTATCCTCAAAGAGCAAGA
* *
517778 CCTATTTCATTCTC-TTTTCG
63 GC-ATTT-ATTCTCTTTTTCA
517798 TTTGTCCTCAAAGAGCAGGACA
1 TTTGTCCTCAAAGAGCAGGACA
517820 ACCCCTTCCA
Statistics
Matches: 214, Mismatches: 35, Indels: 35
0.75 0.12 0.12
Matches are distributed among these distances:
75 5 0.02
76 5 0.02
77 42 0.20
78 1 0.00
80 4 0.02
81 5 0.02
82 19 0.09
83 10 0.05
84 81 0.38
85 4 0.02
86 8 0.04
87 30 0.14
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.41
Consensus pattern (81 bp):
TTTGTCCTCAAAGAGCAGGACACACTTTATTTCCTTTTTTCCTTTATCCTCAAAGAGCAAGAGCA
TTTATTCTCTTTTTCA
Found at i:517807 original size:40 final size:41
Alignment explanation
Indices: 517705--517819 Score: 126
Period size: 40 Copynumber: 2.8 Consensus size: 41
517695 GTAGGATTTA
**
517705 CTCTTTTGCACTTTGTCCTCAAGGAGCAGGACACTTTCCTTTTT
1 CTCTTTT-C-CTTTGTCCTCAAGGAGCAGGACACTTT-CTCATT
* *
517749 CTTTTTTCCTTTGTCCTCAAGGAACAGGAC-CTATT-TCATT
1 CTCTTTTCCTTTGTCCTCAAGGAGCAGGACACT-TTCTCATT
* *
517789 CTCTTTTCGTTTGTCCTCAAAGAGCAGGACA
1 CTCTTTTCCTTTGTCCTCAAGGAGCAGGACA
517820 ACCCCTTCCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 29 0.48
41 2 0.03
42 23 0.38
43 1 0.02
44 6 0.10
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (41 bp):
CTCTTTTCCTTTGTCCTCAAGGAGCAGGACACTTTCTCATT
Found at i:520879 original size:79 final size:78
Alignment explanation
Indices: 520749--521097 Score: 364
Period size: 79 Copynumber: 4.4 Consensus size: 78
520739 TTCATAAAAA
* * * *
520749 TTTTCAACTATCGAGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTAT
1 TTTTC-ACAATCGGGGATACTCCAA-CCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTAT
* *
520814 TTCTAAAATATCGAT
64 TTCCAAAACATCGAT
* * *
520829 TTTTCATAATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATT
1 TTTTCACAATCGGGGATACTCCAACC-CGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATT
* *
520894 TCCAAAACACCCAT
65 TCCAAAACATCGAT
* * * *
520908 TTTTCACCATCGGAGATACTTCAACCTCGTTATTTCTTC--GGGGATACTTCAACCCCGGTTTTA
1 TTTTCACAATCGGGGATACTCCAACC-CGTTA-TT-TTCGAGGGGATACTCCAACCCCGGTTTTA
*
520971 TTTCTAAAACATCGAT
63 TTTCCAAAACATCGAT
* * * * * *
520987 TTTTTATAATCGGGGATACTCCAAACCC-AT-TTTTCGAAGAGATACTCCAACCCTGGTTTTATT
1 TTTTCACAATCGGGGATACTCC-AACCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATT
*
521050 TCCAAAACATTGAT
65 TCCAAAACATCGAT
* * *
521064 TTTTCACCATTGAGGATACTCCAACCCTGTTATT
1 TTTTCACAATCGGGGATACTCCAACCC-GTTATT
521098 CCTGAAGGGG
Statistics
Matches: 221, Mismatches: 39, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
75 3 0.01
76 7 0.03
77 51 0.23
78 4 0.02
79 142 0.64
80 11 0.05
81 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (78 bp):
TTTTCACAATCGGGGATACTCCAACCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTT
CCAAAACATCGAT
Found at i:521127 original size:156 final size:157
Alignment explanation
Indices: 520749--521119 Score: 448
Period size: 156 Copynumber: 2.4 Consensus size: 157
520739 TTCATAAAAA
* * * * *
520749 TTTTCAACTATCGAGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTAT
1 TTTTC-ACCATCGAGGATACTCCAACCCTGTTATTCT-GAGGGGATACTCCAACCCCGGTTTTAT
* * * *
520814 TTCTAAAATATCGATTTTTCATAATCGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCC
64 TTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCTCGATATTTTCGAAGAGATACTCC
520879 AACCCTGATTTTATTTCCAAAACACCCAT
129 AACCCTGATTTTATTTCCAAAACACCCAT
* ** *
520908 TTTTCACCATCG-GAGATACTTCAA-CCTCGTTATTTCTTCGGGGATACTTCAACCCCGGTTTTA
1 TTTTCACCATCGAG-GATACTCCAACCCT-GTTA-TTCTGAGGGGATACTCCAACCCCGGTTTTA
*
520971 TTTCTAAAACATCGATTTTTTATAATCGGGGATACTCCAAACC-C-AT-TTTTCGAAGAGATACT
63 TTTCTAAAACATCGATTTTTCATAATCGGGGATACTCC-AACCTCGATATTTTCGAAGAGATACT
* ***
521033 CCAACCCTGGTTTTATTTCCAAAACATTGAT
127 CCAACCCTGATTTTATTTCCAAAACACCCAT
* *
521064 TTTTCACCATTGAGGATACTCCAACCCTGTTATTCCTGAAGGGG-TACTCCGACCCC
1 TTTTCACCATCGAGGATACTCCAACCCTGTTATT-CTG-AGGGGATACTCCAACCCC
521120 ATTTTTATCT
Statistics
Matches: 180, Mismatches: 24, Indels: 19
0.81 0.11 0.09
Matches are distributed among these distances:
155 2 0.01
156 77 0.43
157 12 0.07
158 77 0.43
159 12 0.07
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (157 bp):
TTTTCACCATCGAGGATACTCCAACCCTGTTATTCTGAGGGGATACTCCAACCCCGGTTTTATTT
CTAAAACATCGATTTTTCATAATCGGGGATACTCCAACCTCGATATTTTCGAAGAGATACTCCAA
CCCTGATTTTATTTCCAAAACACCCAT
Found at i:525791 original size:95 final size:95
Alignment explanation
Indices: 525670--525858 Score: 233
Period size: 95 Copynumber: 2.0 Consensus size: 95
525660 TTGAAAAATG
* * *
525670 GGGTTGGAGTATCCCTTCGAAGGAATGGGGCTGGGGTGT-CCTCGACAAAAATAATTTAGGTAAA
1 GGGTTAGAGTATCCCTTCGAAGGAAT-GGACTGGAGTGTCCCT-GACAAAAATAATTTAGGTAAA
* * *
525734 AGT-AAACATGATCTTGATAAGTTTAAAAACA
64 AGTAAAAAAAGATCTTGACAAGTTTAAAAACA
* * *
525765 GGGTTAGAGTATTCCC-TCGGAA-GAATGGATTGGAGTGTCCCTGATAATAATAATTTAGGTAAA
1 GGGTTAGAGTA-TCCCTTC-GAAGGAATGGACTGGAGTGTCCCTGACAAAAATAATTTAGGTAAA
525828 AGTAAAAAAAGATCTTGACAAGTTTAAAAAC
64 AGTAAAAAAAGATCTTGACAAGTTTAAAAAC
525859 GAGATTGGAG
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
94 31 0.38
95 43 0.53
96 7 0.09
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (95 bp):
GGGTTAGAGTATCCCTTCGAAGGAATGGACTGGAGTGTCCCTGACAAAAATAATTTAGGTAAAAG
TAAAAAAAGATCTTGACAAGTTTAAAAACA
Found at i:525875 original size:94 final size:97
Alignment explanation
Indices: 525719--525920 Score: 247
Period size: 95 Copynumber: 2.1 Consensus size: 97
525709 CCTCGACAAA
* * * * *
525719 AATAATTTAGGTAAAAGTAAACATGATCTTGATAAGTTTAAAAACAGGGTTAGAGTATTCCC-TC
1 AATAATTTAGGTAAAAGTAAAAAAGATCTTGACAAGTTTAAAAACAGGATTAGAGTAGTCCCTTC
* *
525783 GGAAGAAT-GGATTGGAGTGTCCCTGAT-AAT
66 GGAAGAATGGGATTGGAGTATCCCCGATGAAT
*
525813 AATAATTTAGGTAAAAGTAAAAAAAGATCTTGACAAGTTTAAAAAC-GAGATTGGAGT-GTCCCT
1 AATAATTTAGGTAAAAGT-AAAAAAGATCTTGACAAGTTTAAAAACAG-GATTAGAGTAGTCCCT
* *
525876 TCGGAATAATGGGGTTGGAGTATCCCCGATGAAT
64 TCGGAAGAATGGGATTGGAGTATCCCCGATGAAT
525910 AA-AATTT-GGTA
1 AATAATTTAGGTA
525921 TTTTTTTATG
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
94 23 0.25
95 44 0.47
96 21 0.23
97 5 0.05
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (97 bp):
AATAATTTAGGTAAAAGTAAAAAAGATCTTGACAAGTTTAAAAACAGGATTAGAGTAGTCCCTTC
GGAAGAATGGGATTGGAGTATCCCCGATGAAT
Found at i:527185 original size:21 final size:20
Alignment explanation
Indices: 527152--527192 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
527142 GAGGTGTTGG
527152 ACATACTAAAAATGCATGAA
1 ACATACTAAAAATGCATGAA
* *
527172 ACATAGCTCAAAATGTATGAA
1 ACATA-CTAAAAATGCATGAA
527193 CATGGGCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (20 bp):
ACATACTAAAAATGCATGAA
Found at i:528796 original size:13 final size:13
Alignment explanation
Indices: 528778--528803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
528768 CAATTTTTTG
528778 TGTATCGATACAT
1 TGTATCGATACAT
528791 TGTATCGATACAT
1 TGTATCGATACAT
528804 ACTTTGGTGT
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:528800 original size:33 final size:33
Alignment explanation
Indices: 528758--528822 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
528748 TACAAGCCAA
* *
528758 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
528791 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
528823 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:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:530929 original size:21 final size:20
Alignment explanation
Indices: 530900--530942 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
530890 GGCTAGTATG
*
530900 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
530921 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
530941 GG
1 GG
530943 TGGTGCTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:531401 original size:13 final size:13
Alignment explanation
Indices: 531383--531421 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
531373 ATAATCCCCC
*
531383 TGTATCGATACAG
1 TGTATCGATACAA
531396 TGTATCGATACAA
1 TGTATCGATACAA
531409 TGTATCGATACAA
1 TGTATCGATACAA
531422 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:542561 original size:20 final size:20
Alignment explanation
Indices: 542475--542589 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 20
542465 AAAAAGATAG
* *
542475 AATGTTTCGATACATTGA-A
1 AATGTATCGATACATTCATA
* *
542494 GAACGTATCAATACATTCATA
1 -AATGTATCGATACATTCATA
* *
542515 CATGTATCGATACATTGA-A
1 AATGTATCGATACATTCATA
*
542534 GAACGTATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
542555 CATGTATTGATACATTGAAA
1 AATGTATCGATACATTCATA
*
542575 AATATATCGATACAT
1 AATGTATCGATACAT
542590 CTGGGTAAAA
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
19 1 0.01
20 70 0.96
21 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:542583 original size:40 final size:40
Alignment explanation
Indices: 542476--542589 Score: 174
Period size: 40 Copynumber: 2.9 Consensus size: 40
542466 AAAAGATAGA
* *
542476 ATGTTTCGATACATTGAAGAACGTATCAATACATTCATAC
1 ATGTATCGATACATTGAAGAACGTATCGATACATTCATAC
542516 ATGTATCGATACATTGAAGAACGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAGAACGTATCGATACATTCATAC
* * **
542556 ATGTATTGATACATTGAAAAATATATCGATACAT
1 ATGTATCGATACATTGAAGAACGTATCGATACAT
542590 CTGGGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (40 bp):
ATGTATCGATACATTGAAGAACGTATCGATACATTCATAC
Found at i:542651 original size:19 final size:20
Alignment explanation
Indices: 542606--542655 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
542596 AAAAAGATAG
*
542606 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
542626 CATGTATCGATA-ATTGAAA
1 AATGTATCGATACATTCAAA
542645 AATGTATCGAT
1 AATGTATCGAT
542656 GCATCTAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:542667 original size:70 final size:71
Alignment explanation
Indices: 542533--542690 Score: 255
Period size: 70 Copynumber: 2.2 Consensus size: 71
542523 GATACATTGA
* * *
542533 AGAACGTATCGATACATTCATACATGTATTGATACATTGAAAAATATATCGATACATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAA
*
542598 AAAGAT
66 AAAGAC
* *
542604 AGAATGTATCGATACATTCATACATGTATCGATA-ATTGAAAAATGTATCGATGCATCTAGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAA
542668 AAAGAC
66 AAAGAC
542674 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
542691 CTGGGTAAAA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 49 0.60
71 32 0.40
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (71 bp):
AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAA
AAAGAC
Found at i:542683 original size:31 final size:31
Alignment explanation
Indices: 542643--542721 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
542633 CGATAATTGA
*
542643 AAAATGTATCGATGCATCTAGGTAAAAAGAC
1 AAAATGTATCGATACATCTAGGTAAAAAGAC
* *
542674 AGAATGTATCGATACATCTGGGTAAAAAGAC
1 AAAATGTATCGATACATCTAGGTAAAAAGAC
542705 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
542722 TCATACATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (31 bp):
AAAATGTATCGATACATCTAGGTAAAAAGAC
Found at i:542733 original size:20 final size:20
Alignment explanation
Indices: 542705--542780 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
542695 GTAAAAAGAC
*
542705 AAAATGTATCGATACATTCA
1 AAAATGTATCGATACACTCA
* * *
542725 TACATGTATCGATACACTGA
1 AAAATGTATCGATACACTCA
**
542745 AAAATGTATCGATACACGAA
1 AAAATGTATCGATACACTCA
*
542765 AAAATGTATCAATACA
1 AAAATGTATCGATACA
542781 TCTAGGTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (20 bp):
AAAATGTATCGATACACTCA
Found at i:542772 original size:40 final size:40
Alignment explanation
Indices: 542705--542780 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
542695 GTAAAAAGAC
*** * * *
542705 AAAATGTATCGATACATTCATACATGTATCGATACACTGA
1 AAAATGTATCGATACACGAAAAAATGTATCAATACACTGA
542745 AAAATGTATCGATACACGAAAAAATGTATCAATACA
1 AAAATGTATCGATACACGAAAAAATGTATCAATACA
542781 TCTAGGTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (40 bp):
AAAATGTATCGATACACGAAAAAATGTATCAATACACTGA
Found at i:543733 original size:32 final size:32
Alignment explanation
Indices: 543688--543751 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
543678 GTTTTTTTTA
*
543688 AAAAAAAGGTGCCA-CTAACTTGTGTGGGCTTT
1 AAAAAAAGGTGCCATC-AACTTATGTGGGCTTT
* * *
543720 AAAAAGAGTTGCCATCGACTTATGTGGGCTTT
1 AAAAAAAGGTGCCATCAACTTATGTGGGCTTT
543752 GAAAGGGTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (32 bp):
AAAAAAAGGTGCCATCAACTTATGTGGGCTTT
Found at i:543780 original size:28 final size:28
Alignment explanation
Indices: 543742--544067 Score: 429
Period size: 28 Copynumber: 11.5 Consensus size: 28
543732 CATCGACTTA
*
543742 TGTGGGCTTTGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
543770 TGTGGGCTTTGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
543798 TGTGGGCTTTGAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAAGGG--TGCCACTGACT
*
543828 TGTGGGCTTTGAAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
543856 TGTTGGCTTTGGAAGGGTATGCCACTAACT
1 TGTGGGCTTTGAAAGGG--TGCCACTGACT
543886 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
543914 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
543942 TATGGTCTTTTG-AAGAGATGCCACTGACT
1 TGTGGGC-TTTGAAAG-GGTGCCACTGACT
* * *
543971 TGTGGGCTTTGAAAAGATGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
543999 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
544027 TGTGGGCTTTGAAAAGATGCCACTGACC
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
544055 TGTGAGCTTTGAA
1 TGTGGGCTTTGAA
544068 GATATGAACA
Statistics
Matches: 266, Mismatches: 25, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
28 191 0.72
29 24 0.09
30 51 0.19
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:543828 original size:58 final size:56
Alignment explanation
Indices: 543692--544067 Score: 441
Period size: 58 Copynumber: 6.5 Consensus size: 56
543682 TTTTTAAAAA
* * * *
543692 AAAGG-TGCCACTAACTTGTGTGGGCTTTAAAAAGAGTTGCCATCGACTTATGTGGGCTTTG
1 AAAGGATGCCACTGAC-T-TGTGGGCTTT-GAAAG-GGTGCCACCGAC-T-TGTGGGCTTTG
* *
543753 AAAGGGTGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG
*
543809 AAAGGGTATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTTGGCTTTGG
1 AAA-GG-ATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTT-G
* * *
543868 AAGGGTATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGG-ATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG
* * * *
543925 AAAGGATGCCACTGACTTATGGTCTTTTG-AAGAGATGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGC-TTTGAAAG-GGTGCCACCGACTTGTGGGCTTTG
* * **
543982 AAAAGATGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG
* * *
544038 AAAAGATGCCACTGACCTGTGAGCTTTGAA
1 AAAGGATGCCACTGACTTGTGGGCTTTGAA
544068 GATATGAACA
Statistics
Matches: 282, Mismatches: 26, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
56 86 0.30
57 58 0.21
58 107 0.38
59 7 0.02
60 10 0.04
61 6 0.02
62 8 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (56 bp):
AAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG
Found at i:543847 original size:86 final size:85
Alignment explanation
Indices: 543742--544067 Score: 442
Period size: 86 Copynumber: 3.8 Consensus size: 85
543732 CATCGACTTA
* *
543742 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
543807 TGAAAGGGTATGCCACTGACT
66 TGAAAGGG-ATGCCACTGACT
* * *
543828 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTTGGCTTTGGAAGGGTATGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTT-GAAAGG-ATGCCACTGACTTGTGGGC
543893 TTTGAAAGGG-TGCCACTGACT
64 TTTGAAAGGGATGCCACTGACT
* * * *
543914 TGTGGGCTTTGAAAGGATGCCACTGACTTATGGTCTTTTG-AAGAGATGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGC-TTTGAAAG-GATGCCACTGACTTGTGGGC
* *
543978 TTTGAAA-AGATGCCATTGACT
64 TTTGAAAGGGATGCCACTGACT
** * * *
543999 TGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGATGCCACTGACCTGTGAGCTT
1 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
544064 TGAA
66 TGAA
544068 GATATGAACA
Statistics
Matches: 213, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
84 29 0.14
85 70 0.33
86 80 0.38
87 8 0.04
88 26 0.12
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAAGGGATGCCACTGACT
Found at i:545324 original size:1 final size:1
Alignment explanation
Indices: 545313--545413 Score: 58
Period size: 1 Copynumber: 101.0 Consensus size: 1
545303 TCTAGACCCC
* ** * ** * * * * *
545313 TTTTTTGTTTTTTTGGTTTTTTTTTTGTTTTTGGTTTTTTTCTGTTTTTTTCTGTTTTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * *
545378 TTTTTCTTGGTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
545414 GGTACGAAAG
Statistics
Matches: 74, Mismatches: 26, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (1 bp):
T
Found at i:545333 original size:10 final size:10
Alignment explanation
Indices: 545320--545416 Score: 98
Period size: 10 Copynumber: 10.0 Consensus size: 10
545310 CCCTTTTTTG
545320 TTTTTTTGGT
1 TTTTTTTGGT
545330 TTTTTTT--T
1 TTTTTTTGGT
*
545338 TGTTTTTGGT
1 TTTTTTTGGT
545348 TTTTTTCT-GT
1 TTTTTT-TGGT
545358 TTTTTTCT-GT
1 TTTTTT-TGGT
*
545368 TTTTTTTGTT
1 TTTTTTTGGT
545378 TTTTTCTTGG-
1 TTTTT-TTGGT
545388 TTTTTTT-GT
1 TTTTTTTGGT
*
545397 TTTTTTTTGT
1 TTTTTTTGGT
545407 TTTTTTTGGT
1 TTTTTTTGGT
545417 ACGAAAGATG
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
8 8 0.11
9 10 0.13
10 53 0.71
11 4 0.05
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.82
Consensus pattern (10 bp):
TTTTTTTGGT
Found at i:545337 original size:19 final size:18
Alignment explanation
Indices: 545313--545413 Score: 114
Period size: 18 Copynumber: 5.3 Consensus size: 18
545303 TCTAGACCCC
*
545313 TTTTTTGTTTTTTTGGTT
1 TTTTTTTTTTTTTTGGTT
*
545331 TTTTTTTTGTTTTTGGTT
1 TTTTTTTTTTTTTTGGTT
*
545349 TTTTTCTGTTTTTTTCTGTTT
1 TTTTT-T-TTTTTTT-TGGTT
545370 TTTTTGTTTTTTTCTTGGTT
1 TTTTT-TTTTTTT-TTGGTT
545390 TTTTTGTTTTTTTTT-GTT
1 TTTTT-TTTTTTTTTGGTT
545408 TTTTTT
1 TTTTTT
545414 GGTACGAAAG
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.01
18 29 0.40
19 3 0.04
20 29 0.40
21 11 0.15
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTTTTGGTT
Found at i:545338 original size:20 final size:20
Alignment explanation
Indices: 545313--545413 Score: 106
Period size: 21 Copynumber: 5.2 Consensus size: 20
545303 TCTAGACCCC
545313 TTTTTTGTTTTTTTGGTTTT
1 TTTTTTGTTTTTTTGGTTTT
545333 TTTTTTG--TTTTTGG-TTT
1 TTTTTTGTTTTTTTGGTTTT
* *
545350 TTTTCTGTTTTTTTCTGTTTT
1 TTTTTTGTTTTTTT-GGTTTT
545371 TTTTGTT-TTTTTCTTGGTTTT
1 TTTT-TTGTTTTT-TTGGTTTT
*
545392 TTTGTT-TTTTTTT-GTTTT
1 TTTTTTGTTTTTTTGGTTTT
545410 TTTT
1 TTTT
545414 GGTACGAAAG
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
17 9 0.13
18 15 0.22
19 7 0.10
20 15 0.22
21 20 0.29
22 3 0.04
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (20 bp):
TTTTTTGTTTTTTTGGTTTT
Found at i:545414 original size:19 final size:19
Alignment explanation
Indices: 545313--545414 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
545303 TCTAGACCCC
*
545313 TTTTTTG-TTTTTTTGGTT
1 TTTTTTGTTTTTTTTTGTT
* *
545331 TTTTTT-TTGTTTTTGGTT
1 TTTTTTGTTTTTTTTTGTT
*
545349 TTTTTCTGTTTTTTTCTGTT
1 TTTTT-TGTTTTTTTTTGTT
*
545369 TTTTTTGTTTTTTTCTTGGT
1 TTTTTTGTTTTTTT-TTGTT
545389 TTTTTTGTTTTTTTTTGTT
1 TTTTTTGTTTTTTTTTGTT
545408 TTTTTTG
1 TTTTTTG
545415 GTACGAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
18 21 0.29
19 21 0.29
20 31 0.42
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.83
Consensus pattern (19 bp):
TTTTTTGTTTTTTTTTGTT
Found at i:548693 original size:13 final size:13
Alignment explanation
Indices: 548675--548699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
548665 CATTTTATGG
548675 TGTATCGATACAA
1 TGTATCGATACAA
548688 TGTATCGATACA
1 TGTATCGATACA
548700 TATTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:548715 original size:32 final size:33
Alignment explanation
Indices: 548652--548719 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
548642 CGTTACAAGC
*
548652 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATATTATGGTGTATCGATA
*
548685 CAATGTATCGATACATATTGT-GTGTATCGATA
1 CAATGTATCGATACATATTATGGTGTATCGATA
548717 CAA
1 CAA
548720 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTATGGTGTATCGATA
Found at i:548788 original size:20 final size:21
Alignment explanation
Indices: 548741--548791 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
548731 ACCAATGACC
**
548741 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
548762 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
548782 TGTATCGATA
1 TGTATCGATA
548792 TAATGTATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:549399 original size:22 final size:21
Alignment explanation
Indices: 549357--549400 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
549347 TTTTCTTTTC
*
549357 TCTCCCCCTTAATCAAAAATT
1 TCTCCCCCTTAATAAAAAATT
*
549378 TCTCCCCCTTAGTAAAATAATT
1 TCTCCCCCTTAATAAAA-AATT
549400 T
1 T
549401 GACAATTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.32, C:0.30, G:0.02, T:0.36
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:550625 original size:13 final size:13
Alignment explanation
Indices: 550607--550631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
550597 ACTGAAGCAA
550607 TGTATCGATACAT
1 TGTATCGATACAT
550620 TGTATCGATACA
1 TGTATCGATACA
550632 ATCTGGAAAA
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:554128 original size:13 final size:13
Alignment explanation
Indices: 554110--554134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
554100 CATTTTATGG
554110 TGTATCGATACAA
1 TGTATCGATACAA
554123 TGTATCGATACA
1 TGTATCGATACA
554135 TGCTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:554150 original size:32 final size:33
Alignment explanation
Indices: 554087--554154 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
554077 CGTTACAAGC
**
554087 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATGCTATGGTGTATCGATA
*
554120 CAATGTATCGATACATGCTGT-GTGTATCGATA
1 CAATGTATCGATACATGCTATGGTGTATCGATA
554152 CAA
1 CAA
554155 ATTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATGCTATGGTGTATCGATA
Found at i:554223 original size:20 final size:21
Alignment explanation
Indices: 554176--554228 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
554166 GGAAATGACC
**
554176 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
554197 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
554217 TGTATCGATACA
1 TGTATCGATACA
554229 ATGAATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:554238 original size:13 final size:14
Alignment explanation
Indices: 554220--554249 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
554210 TTGGTCATGT
554220 ATCGATACAATG-A
1 ATCGATACAATGCA
554233 ATCGATACAATGCA
1 ATCGATACAATGCA
554247 ATC
1 ATC
554250 TGTATCGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (14 bp):
ATCGATACAATGCA
Found at i:566094 original size:20 final size:20
Alignment explanation
Indices: 566050--566124 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
566040 AAAAAGACAG
* * * *
566050 AATGTATCAATACGTTGAAG
1 AATGTATCGATACATTCAAA
* *
566070 AATGTATCGATGCATTCATA
1 AATGTATCGATACATTCAAA
* * *
566090 CATGTTTCGATACATTGAAA
1 AATGTATCGATACATTCAAA
566110 AATGTATCGATACAT
1 AATGTATCGATACAT
566125 CTGGGTAAAA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:566143 original size:71 final size:71
Alignment explanation
Indices: 566068--566277 Score: 341
Period size: 71 Copynumber: 3.0 Consensus size: 71
566058 AATACGTTGA
* *
566068 AGAATGTATCGATGCATTCATACATGTTTCGATACATTGAAAAATGTATCGATACATCTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
566133 AAAGAC
66 AAAGAC
* * *
566139 AGAATGTATCGATACATTCATACATGTATCGATACATTAAAAAATTTATCGATACATTTGGGTAA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
566204 AAAGAC
66 AAAGAC
* *
566210 AAAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCAATACA-CATGGGTA
1 AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATC-TGGGTA
566274 AAAA
65 AAAA
566278 TGTGACTTTT
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
71 128 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (71 bp):
AGAATGTATCGATACATTCATACATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAA
AAAGAC
Found at i:566167 original size:20 final size:20
Alignment explanation
Indices: 566141--566196 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
566131 AAAAAGACAG
* *
566141 AATGTATCGATACATTCATA
1 AATGTATCGATACATTAAAA
*
566161 CATGTATCGATACATTAAAA
1 AATGTATCGATACATTAAAA
*
566181 AATTTATCGATACATT
1 AATGTATCGATACATT
566197 TGGGTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Done.