Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 1 of 79
Found at i:1929 original size:31 final size:32
Alignment explanation
Indices: 1853--1929 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
1843 AACCCCTTAA
* *
1853 CCAACGCCGGGATATCCCTGGAATGGGATATAC
1 CCAA-GCCGGGATACCCCTAGAATGGGATATAC
*
1886 CCAAGCCGGGATACCCCTAGAATGGGATATCC
1 CCAAGCCGGGATACCCCTAGAATGGGATATAC
1918 CCAA-CCGGGATA
1 CCAAGCCGGGATA
1930 AGTGCGCTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 8 0.20
32 29 0.71
33 4 0.10
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (32 bp):
CCAAGCCGGGATACCCCTAGAATGGGATATAC
Found at i:1984 original size:21 final size:20
Alignment explanation
Indices: 1956--1999 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 20
1946 CGGCCCAGAC
1956 TCATAAAACAACAGAACCGG
1 TCATAAAACAACAGAACCGG
1976 TCATCAAAACAACAGAACCGG
1 TCAT-AAAACAACAGAACCGG
1997 TCA
1 TCA
2000 GCTAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.48, C:0.27, G:0.14, T:0.11
Consensus pattern (20 bp):
TCATAAAACAACAGAACCGG
Found at i:9024 original size:19 final size:19
Alignment explanation
Indices: 9002--9041 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8992 CAAGATAGGA
9002 TAACTTGTTTCTAATATGT
1 TAACTTGTTTCTAATATGT
9021 TAACTTGTTTCTAATATGT
1 TAACTTGTTTCTAATATGT
9040 TA
1 TA
9042 CCTGTAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (19 bp):
TAACTTGTTTCTAATATGT
Found at i:23121 original size:132 final size:132
Alignment explanation
Indices: 22884--23144 Score: 477
Period size: 132 Copynumber: 2.0 Consensus size: 132
22874 CCGAATTTAG
* *
22884 TTGAATTGAAGAAGAGCAGAACAAAGCAGAGATGGACAAGTTTGCATTGCATGATGATGATGGTG
1 TTGAAATGAAGAAGAGCAGAACAAAGCAGAGATGGACAAGTTTGCACTGCATGATGATGATGGTG
* *
22949 CTAATTCCGCTGCTCTTTTCTTTTTCTTGATTAAACAAACGCACTTCACATTCACGTTGTACATA
66 CTAATTCCGCTGCTCGTTTCTTTTTCTTCATTAAACAAACGCACTTCACATTCACGTTGTACATA
23014 AA
131 AA
*
23016 TTGAAATGAAGAGGAGCAGAACAAAGCAGAGATGGACAAGTTTGCACTGCATGATGATGATGGTG
1 TTGAAATGAAGAAGAGCAGAACAAAGCAGAGATGGACAAGTTTGCACTGCATGATGATGATGGTG
23081 CTAATTCCGCTGCTCGTTTCTTTTTCTTCATTAAACAAACGCACTTCACATTCACGTTGTACAT
66 CTAATTCCGCTGCTCGTTTCTTTTTCTTCATTAAACAAACGCACTTCACATTCACGTTGTACAT
23145 TACACAAAGA
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (132 bp):
TTGAAATGAAGAAGAGCAGAACAAAGCAGAGATGGACAAGTTTGCACTGCATGATGATGATGGTG
CTAATTCCGCTGCTCGTTTCTTTTTCTTCATTAAACAAACGCACTTCACATTCACGTTGTACATA
AA
Found at i:25994 original size:15 final size:15
Alignment explanation
Indices: 25966--26003 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
25956 ACACAACCGG
25966 TAAAAAATAATTTTA
1 TAAAAAATAATTTTA
* *
25981 TAATAAATATTTTTA
1 TAAAAAATAATTTTA
25996 TAAAAAAT
1 TAAAAAAT
26004 TATACTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAAAATAATTTTA
Found at i:35589 original size:77 final size:76
Alignment explanation
Indices: 35484--35694 Score: 332
Period size: 77 Copynumber: 2.7 Consensus size: 76
35474 TATAATTTGA
*
35484 TATACCAATTTGGCTTCGGGCCATGCATATCAGATAAATTGGCTTCAGGCCATGATATTAGCACT
1 TATACCGATTTGGCTTCGGGCCATGCATATCAGATAAATTGGCTTC-GGCCATGATATTAGCACT
35549 TCGGGTGCGATT
65 TCGGGTGCGATT
* * * *
35561 TATATCGATTTGGCTTTGGGACATGCATATCGGATAAATTGGCTTCGGACCATGATATTAGCACT
1 TATACCGATTTGGCTTCGGGCCATGCATATCAGATAAATTGGCTTCGG-CCATGATATTAGCACT
35626 TCGGGTGCGATT
65 TCGGGTGCGATT
* *
35638 TATACCGATTTGGCTTCGGGCCATGCATATCAGATAAATTGGTTTCGGGCCACGATA
1 TATACCGATTTGGCTTCGGGCCATGCATATCAGATAAATTGGCTTC-GGCCATGATA
35695 AATAGTTCTT
Statistics
Matches: 121, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
76 2 0.02
77 117 0.97
78 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (76 bp):
TATACCGATTTGGCTTCGGGCCATGCATATCAGATAAATTGGCTTCGGCCATGATATTAGCACTT
CGGGTGCGATT
Found at i:41029 original size:15 final size:14
Alignment explanation
Indices: 41009--41036 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40999 ATCTCCCCCA
41009 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
41023 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
41037 AACACTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTAGTTTTC
Found at i:46910 original size:3 final size:3
Alignment explanation
Indices: 46895--46945 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
46885 GAAATTGAAG
*
46895 CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
46943 CTT
1 CTT
46946 TTTTTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:46950 original size:1 final size:1
Alignment explanation
Indices: 46944--46977 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
46934 CTTCTTCTTC
46944 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46978 GCATTTTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47181 original size:33 final size:33
Alignment explanation
Indices: 47133--47196 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
47123 CGGGAGTGAG
47133 GGTTTTACGGCTTAGGGGCTTACTATTATTATT
1 GGTTTTACGGCTTAGGGGCTTACTATTATTATT
* * *
47166 GGTTTTAGGGGTTAGGGGGTTACTATTATTA
1 GGTTTTACGGCTTAGGGGCTTACTATTATTA
47197 CTATCATCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.19, C:0.08, G:0.30, T:0.44
Consensus pattern (33 bp):
GGTTTTACGGCTTAGGGGCTTACTATTATTATT
Found at i:54008 original size:15 final size:15
Alignment explanation
Indices: 53988--54018 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53978 TAAATTTAGA
53988 TCAAAATAAATCATG
1 TCAAAATAAATCATG
54003 TCAAAATAAATCATG
1 TCAAAATAAATCATG
54018 T
1 T
54019 AACTACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (15 bp):
TCAAAATAAATCATG
Found at i:64074 original size:12 final size:12
Alignment explanation
Indices: 64057--64083 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
64047 TGCTGCCACC
64057 TCTCTTGCTAGT
1 TCTCTTGCTAGT
64069 TCTCTTGCTAGT
1 TCTCTTGCTAGT
64081 TCT
1 TCT
64084 GTAGAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.26, G:0.15, T:0.52
Consensus pattern (12 bp):
TCTCTTGCTAGT
Found at i:70848 original size:13 final size:14
Alignment explanation
Indices: 70830--70862 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
70820 AATGTTTAAT
70830 AATTTAAATAT-TA
1 AATTTAAATATCTA
*
70843 AATTTAAATTTCTA
1 AATTTAAATATCTA
70857 AATTTA
1 AATTTA
70863 TTTGGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTAAATATCTA
Found at i:74584 original size:51 final size:51
Alignment explanation
Indices: 74529--74650 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
74519 CGGATCACAT
** * * *
74529 TTATCACTTGTTGCTTATCATTGATTAGATAAGCGTAGCTAAAGCTATCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGCGTAGCTAAAGCTACCAC
* * *
74580 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAT
1 TTATCACTTGTCACTTATCACTGATCAGATAAGCGTAGCTAAAGCTACCAC
*
74631 TTATCACTTGTCACTGATCA
1 TTATCACTTGTCACTTATCA
74651 GAAGTACTCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGCGTAGCTAAAGCTACCAC
Found at i:81289 original size:126 final size:125
Alignment explanation
Indices: 80962--81355 Score: 462
Period size: 125 Copynumber: 3.2 Consensus size: 125
80952 GGCCAAGCAA
* *
80962 GAACTACTGTA-AAAAATAGCG-TCTACGTGGGAGC-TTTTTCAGTAATTTTGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAAAGCGATC-ACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCAT
*
81024 CCTGCTTGAAGCGTTTTTTGACACTATTTTTTCAGAATCGTCGTCTCAAAATT-TTTTT-AG
65 CCTGCTTGAAGCGTTTTTTGACACTATTTTTTCA-AATCGTCATCTCAAAATTATTTTTCAG
* * * *
81084 GAACTACTTTAGAAAAAAAAGCGTTCACATGGGAGCTTTTTTCAGTAATTTTGATGATAGTGCAT
1 GAACTACTGTAG-AAAAAAAGCGATCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCAT
* *
81149 CATTCTTGAAGCGTTTTTTGACACTATTTTTTCATAATCGTCATCTCAAAATTATTTTTCAG
65 CCTGCTTGAAGCGTTTTTTGACACTATTTTTTCA-AATCGTCATCTCAAAATTATTTTTCAG
* * * * *
81211 GAACTGCTGTAGAAAAAGAGC-ATC-CATGTTGGAGCTTTTTTTAGTAATTTTGCTGACAATACA
1 GAACTACTGTAGAAAAAAAGCGATCACATG--GGAGCTTTTTTCAGTAATTTTGCTGACAGTGCA
* * * * * *
81274 CCCTGCTTGAAGCG-TTTTTGACATTATCTTTTCAGATCCGTCTTCTCAAAATTAATTTTTCTG
64 TCCTGCTTGAAGCGTTTTTTGACACTATTTTTTCAAAT-CGTCATCTCAAAATT-ATTTTTCAG
* *
81337 AAATTACTGTAGAAAAAAA
1 GAACTACTGTAGAAAAAAA
81356 CAAAATCATT
Statistics
Matches: 232, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
122 10 0.04
124 24 0.10
125 111 0.48
126 75 0.32
127 12 0.05
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAAAGCGATCACATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTTGACACTATTTTTTCAAATCGTCATCTCAAAATTATTTTTCAG
Found at i:81506 original size:34 final size:34
Alignment explanation
Indices: 81462--81550 Score: 128
Period size: 34 Copynumber: 2.6 Consensus size: 34
81452 ATTAAATCCC
*
81462 AATTTCATTTATTTATTTTAAACCCC-AAAACCCT
1 AATTTAATTTATTTATTTTAAACCCCTAAAA-CCT
81496 AATTTAATTTATTTATTTTAAACCCCTAAAACCT
1 AATTTAATTTATTTATTTTAAACCCCTAAAACCT
* *
81530 AGTTTAA-TTAATTATTTTAAA
1 AATTTAATTTATTTATTTTAAA
81551 AACTTTAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 13 0.25
34 34 0.67
35 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.01, T:0.45
Consensus pattern (34 bp):
AATTTAATTTATTTATTTTAAACCCCTAAAACCT
Found at i:81566 original size:25 final size:24
Alignment explanation
Indices: 81538--81590 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 24
81528 CTAGTTTAAT
81538 TAATTATTTT-AAAAACTTTAAACCC
1 TAATT-TTTTAAAAAAC-TTAAACCC
81563 TAATTTTTTAAAAAAACTTAAACCC
1 TAATTTTTT-AAAAAACTTAAACCC
81588 TAA
1 TAA
81591 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 4 0.15
25 16 0.62
26 6 0.23
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (24 bp):
TAATTTTTTAAAAAACTTAAACCC
Found at i:81594 original size:16 final size:16
Alignment explanation
Indices: 81571--81607 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
81561 CCTAATTTTT
*
81571 TAAAAAAACTTAAACCC
1 TAAAAAAA-TAAAACCC
81588 TAAAAAAATAAAACCC
1 TAAAAAAATAAAACCC
81604 TAAA
1 TAAA
81608 TTATTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAAAAATAAAACCC
Found at i:82801 original size:21 final size:21
Alignment explanation
Indices: 82777--82823 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
82767 AATTCAACTA
* *
82777 AAAAAGAGCAAGAAAGACAAG
1 AAAAAGAGAAAGAAAGAAAAG
*
82798 AAAAAGCGAAAGAAAGAAAAG
1 AAAAAGAGAAAGAAAGAAAAG
*
82819 GAAAA
1 AAAAA
82824 CAACGAAGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.70, C:0.06, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAGAAAGAAAAG
Found at i:90745 original size:8 final size:8
Alignment explanation
Indices: 90720--90823 Score: 127
Period size: 8 Copynumber: 13.0 Consensus size: 8
90710 ATGAGCTCAG
*
90720 CTCTCCCT
1 CTCTCTCT
*
90728 CTCCCTCT
1 CTCTCTCT
*
90736 CCCTCTCT
1 CTCTCTCT
*
90744 CCCTCTCT
1 CTCTCTCT
*
90752 CCCTCTCT
1 CTCTCTCT
*
90760 CCCTCTCT
1 CTCTCTCT
*
90768 CTCTCCCT
1 CTCTCTCT
*
90776 CTCTCCCT
1 CTCTCTCT
*
90784 CCCTCTCT
1 CTCTCTCT
90792 CTCTCTCT
1 CTCTCTCT
90800 CTCTCTCT
1 CTCTCTCT
90808 CTCTCTCT
1 CTCTCTCT
90816 CTCTCTCT
1 CTCTCTCT
90824 ATTATATTTA
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 87 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (8 bp):
CTCTCTCT
Found at i:90821 original size:6 final size:6
Alignment explanation
Indices: 90720--90823 Score: 127
Period size: 6 Copynumber: 17.3 Consensus size: 6
90710 ATGAGCTCAG
* * * * * *
90720 CTCTCC CTCTCC CTCTCC CTCTCT CCCTCT CTCCCT CTCTCC CTCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
* * *
90768 CTCTCC CTCTCT CCCTCC CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
1 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
90816 CTCTCT CT
1 CTCTCT CT
90824 ATTATATTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
CTCTCT
Found at i:90878 original size:12 final size:12
Alignment explanation
Indices: 90865--90966 Score: 136
Period size: 12 Copynumber: 8.7 Consensus size: 12
90855 NNNTCCCCCC
*
90865 CTCTCTCTCCCC
1 CTCTCTCTCCCT
*
90877 CTCCCTCTCCCT
1 CTCTCTCTCCCT
90889 CTCTCTCTCCCT
1 CTCTCTCTCCCT
90901 CTCTCTCT--CT
1 CTCTCTCTCCCT
*
90911 CTCCCTCTCCCT
1 CTCTCTCTCCCT
*
90923 CCCTCTCTCCCT
1 CTCTCTCTCCCT
*
90935 CTCTCTCTCTCT
1 CTCTCTCTCCCT
*
90947 CTCTCTCTCTCT
1 CTCTCTCTCCCT
90959 CTCTCTCT
1 CTCTCTCT
90967 ATTAAATTGA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.11
12 71 0.89
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCTCTCCCT
Found at i:90886 original size:6 final size:6
Alignment explanation
Indices: 90869--90966 Score: 94
Period size: 6 Copynumber: 16.7 Consensus size: 6
90859 CCCCCCCTCT
* * *
90869 CTCTCC CCCTCC CTCTCC CTCTCT CTCTCC CTCT-- CTCTCT CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
* * * * *
90915 CTCTCC CTC-CC TCTCTCC CTCTCT CTCTCT CTCTCT CTCTCT CTCTCT
1 CTCTCC CTCTCC -CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
90963 CTCT
1 CTCT
90967 ATTAAATTGA
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
4 4 0.05
5 2 0.02
6 74 0.90
7 2 0.02
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
CTCTCC
Found at i:90894 original size:10 final size:10
Alignment explanation
Indices: 90867--90963 Score: 103
Period size: 10 Copynumber: 9.9 Consensus size: 10
90857 NTCCCCCCCT
*
90867 CTCTCTCCCC
1 CTCTCTCTCC
*
90877 CTCCCTCTCC
1 CTCTCTCTCC
90887 CTCTCTCTCTC
1 CTCTCTCTC-C
90898 C-CTCTCT--
1 CTCTCTCTCC
90905 CTCTCTCTCC
1 CTCTCTCTCC
*
90915 CTCTCCCTCC
1 CTCTCTCTCC
90925 CTCTCTC-CC
1 CTCTCTCTCC
*
90934 TCTCTCTCTCT
1 -CTCTCTCTCC
*
90945 CTCTCTCTCT
1 CTCTCTCTCC
90955 CTCTCTCTC
1 CTCTCTCTC
90964 TCTATTAAAT
Statistics
Matches: 75, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
7 1 0.01
8 6 0.08
9 2 0.03
10 63 0.84
11 3 0.04
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (10 bp):
CTCTCTCTCC
Found at i:90940 original size:4 final size:4
Alignment explanation
Indices: 90865--90966 Score: 123
Period size: 4 Copynumber: 25.5 Consensus size: 4
90855 NNNTCCCCCC
* * * * *
90865 CTCT CTCT CCCC CTCC CTCT CCCT CTCT CTCT CCCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * * *
90913 CCCT CTCC CTCC CTCT CTCC CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
90961 CTCT CT
1 CTCT CT
90967 ATTAAATTGA
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 84 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (4 bp):
CTCT
Found at i:92863 original size:147 final size:147
Alignment explanation
Indices: 92596--92866 Score: 425
Period size: 147 Copynumber: 1.8 Consensus size: 147
92586 TCTTCTCCAT
* * * * *
92596 TTCTTTTCGTTCTTGCTCCTCTAATTTCTGATTCTGCTTCTTTTTCTCTTTCGTCAGGGTATCTG
1 TTCTTGTCGTTCTTGCTCCTCTAATTCCTGATCCTGCTTCTTTTTCTCTTCCGTCAGGGTACCTG
*
92661 CCTCTGCCTGCTTCTTAGCCTTCCATTGCTGTGCCTGTTTACATGCCTTTGTAAATGCACGAGCA
66 CCTCTGCCTGCTTCTTAGCCTTCCATTGCTGTGCCTGTTCACATGCCTTTGTAAATGCACGAGCA
92726 TTCTTGGTGAAGAACAC
131 TTCTTGGTGAAGAACAC
**
92743 TTCTTGTCGTTCTTGCTCCTCTAATTCCTGATCCTGCTTCTTTTTCTCTTCCGTCATTGTACCTG
1 TTCTTGTCGTTCTTGCTCCTCTAATTCCTGATCCTGCTTCTTTTTCTCTTCCGTCAGGGTACCTG
* * * * *
92808 CCTCTGCCTGCTTCTTATCGTTCCCTTGCTGTGCCTGTTCACGTGCCTTTTTAAATGCA
66 CCTCTGCCTGCTTCTTAGCCTTCCATTGCTGTGCCTGTTCACATGCCTTTGTAAATGCA
92867 AGAACATCCT
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
147 111 1.00
ACGTcount: A:0.11, C:0.29, G:0.16, T:0.44
Consensus pattern (147 bp):
TTCTTGTCGTTCTTGCTCCTCTAATTCCTGATCCTGCTTCTTTTTCTCTTCCGTCAGGGTACCTG
CCTCTGCCTGCTTCTTAGCCTTCCATTGCTGTGCCTGTTCACATGCCTTTGTAAATGCACGAGCA
TTCTTGGTGAAGAACAC
Found at i:95406 original size:29 final size:30
Alignment explanation
Indices: 95368--95441 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
95358 ACAACGTGAT
*
95368 AACATAAGTGACTAAAACGTAACAT-TTCA
1 AACATAAGTGACTAAAACGTAACATAGTCA
* *
95397 AACATAAGTGATTAAAATGTAACATGAGTCA
1 AACATAAGTGACTAAAACGTAACAT-AGTCA
*
95428 AACAAAAGTGACTA
1 AACATAAGTGACTA
95442 TTTTAGTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 23 0.61
31 15 0.39
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (30 bp):
AACATAAGTGACTAAAACGTAACATAGTCA
Found at i:95437 original size:31 final size:30
Alignment explanation
Indices: 95343--95438 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 30
95333 CTAACGGCTC
* *
95343 AGTGATTAAAATGTTACA-ACGTGATAACATA
1 AGTGATTAAAATGTAACATA-GTCA-AACATA
* * *
95374 AGTGACTAAAACGTAACAT-TTCAAACATA
1 AGTGATTAAAATGTAACATAGTCAAACATA
*
95403 AGTGATTAAAATGTAACATGAGTCAAACAAA
1 AGTGATTAAAATGTAACAT-AGTCAAACATA
95434 AGTGA
1 AGTGA
95439 CTATTTTAGT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 23 0.43
30 2 0.04
31 28 0.53
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (30 bp):
AGTGATTAAAATGTAACATAGTCAAACATA
Found at i:101185 original size:15 final size:13
Alignment explanation
Indices: 101174--101203 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
101164 AGAAAAAACC
101174 AAAATTGAAAAAA
1 AAAATTGAAAAAA
*
101187 GAAATTGAAAAAA
1 AAAATTGAAAAAA
101200 AAAA
1 AAAA
101204 CCCTCTTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (13 bp):
AAAATTGAAAAAA
Found at i:102061 original size:66 final size:66
Alignment explanation
Indices: 101978--102110 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
101968 GCAAGCTTAT
101978 GTTACATTCTCTCATCCCTCTTGTTTTTTCGTGTTACATGTTGAATTTTATCATGATTTCCTATT
1 GTTACATTCTCTCATCCCTCTTGTTTTTTCGTGTTACATGTTGAATTTTATCATGATTTCCTATT
102043 G
66 G
102044 GTTACATTCTCTCATCCCTCTTGTTTTTTCGTGTTACATGTTGAATTTTATCATGATTTCCTATT
1 GTTACATTCTCTCATCCCTCTTGTTTTTTCGTGTTACATGTTGAATTTTATCATGATTTCCTATT
102109 G
66 G
102110 G
1 G
102111 GTCATTTAGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.17, C:0.20, G:0.13, T:0.51
Consensus pattern (66 bp):
GTTACATTCTCTCATCCCTCTTGTTTTTTCGTGTTACATGTTGAATTTTATCATGATTTCCTATT
G
Found at i:106447 original size:45 final size:45
Alignment explanation
Indices: 106334--106435 Score: 168
Period size: 45 Copynumber: 2.3 Consensus size: 45
106324 ACGTTAGATT
*
106334 AAAAAACAAATTGACATAGTTAAAGAGCAAATTTGCTCTTTGCTC
1 AAAAAACAAATTGACATAGTTAAAGAGCAAATTTGCTCTTTGATC
* * *
106379 AAAAAACAGATTGACATGGTTAAAGGGCAAATTTGCTCTTTGATC
1 AAAAAACAAATTGACATAGTTAAAGAGCAAATTTGCTCTTTGATC
106424 AAAAAACAAATT
1 AAAAAACAAATT
106436 TTTATTGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (45 bp):
AAAAAACAAATTGACATAGTTAAAGAGCAAATTTGCTCTTTGATC
Found at i:108849 original size:18 final size:19
Alignment explanation
Indices: 108818--108853 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
108808 TTTTAAGGGA
108818 AAAAATCTAAAAACTAATG
1 AAAAATCTAAAAACTAATG
*
108837 AAAAA-CTACAAACTAAT
1 AAAAATCTAAAAACTAAT
108854 TCTTCAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.64, C:0.14, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAAATCTAAAAACTAATG
Found at i:109807 original size:27 final size:27
Alignment explanation
Indices: 109769--109828 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
109759 ATATTAGAGC
109769 TTGAACTAAGTATCCTCAAATTGAGGT
1 TTGAACTAAGTATCCTCAAATTGAGGT
109796 TTGAACTAAGTATCCTCAAATTGAGGT
1 TTGAACTAAGTATCCTCAAATTGAGGT
109823 TTGAAC
1 TTGAAC
109829 CCTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
TTGAACTAAGTATCCTCAAATTGAGGT
Found at i:117710 original size:24 final size:24
Alignment explanation
Indices: 117683--117728 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
117673 AATGATATAA
117683 TGAAATACATACATATATATATGT
1 TGAAATACATACATATATATATGT
*
117707 TGAAATACATGCATATATATAT
1 TGAAATACATACATATATATAT
117729 ACATATGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (24 bp):
TGAAATACATACATATATATATGT
Found at i:121139 original size:2 final size:2
Alignment explanation
Indices: 121132--121168 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
121122 ATAACCCAAA
121132 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
121169 AATACCTCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:122367 original size:6 final size:6
Alignment explanation
Indices: 122332--122358 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
122322 ATAATAAATA
122332 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
122359 TAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:122522 original size:18 final size:17
Alignment explanation
Indices: 122499--122532 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
122489 TTTATTTTTA
122499 TTTTTAAATTTTAAAATG
1 TTTTT-AATTTTAAAATG
*
122517 TTTTTATTTTTAAAAT
1 TTTTTAATTTTAAAAT
122533 AATTTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTTAATTTTAAAATG
Found at i:131613 original size:32 final size:32
Alignment explanation
Indices: 131577--131640 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
131567 GAAAGGGTTT
131577 TCGGTTGGTATGAATGAGAAGGTTAGTAACAA
1 TCGGTTGGTATGAATGAGAAGGTTAGTAACAA
131609 TCGGTTGGTATGAATGAGAAGGTTAGTAACAA
1 TCGGTTGGTATGAATGAGAAGGTTAGTAACAA
131641 ATTTTAACAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.28
Consensus pattern (32 bp):
TCGGTTGGTATGAATGAGAAGGTTAGTAACAA
Found at i:133312 original size:15 final size:15
Alignment explanation
Indices: 133275--133316 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
133265 AAAGTAATTT
* *
133275 AGAAAAAATGGAAAA
1 AGAAAAAAAGAAAAA
133290 A-AAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
133304 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
133317 GAGAAGTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:147523 original size:24 final size:24
Alignment explanation
Indices: 147496--147544 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
147486 TGCGATCTGA
147496 ACTAACACATTATATGCAGAGCAG
1 ACTAACACATTATATGCAGAGCAG
147520 ACTAACACATTATATGCAGAGCAG
1 ACTAACACATTATATGCAGAGCAG
147544 A
1 A
147545 ATCTATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (24 bp):
ACTAACACATTATATGCAGAGCAG
Found at i:159546 original size:12 final size:12
Alignment explanation
Indices: 159529--159555 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
159519 AACGCTAGAG
159529 ATGTTTGTGTTA
1 ATGTTTGTGTTA
159541 ATGTTTGTGTTA
1 ATGTTTGTGTTA
159553 ATG
1 ATG
159556 GATTGGGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
ATGTTTGTGTTA
Found at i:168564 original size:23 final size:24
Alignment explanation
Indices: 168538--168590 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
168528 ACAAAAATGG
168538 AAATATTAGTT-TTTAT-TTTATCA
1 AAATATTA-TTCTTTATATTTATCA
*
168561 AAAT-TTATTCTTTATATTTTTCA
1 AAATATTATTCTTTATATTTATCA
168584 AAA-ATTA
1 AAATATTA
168591 AAAAAATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 2 0.08
22 8 0.31
23 16 0.62
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.55
Consensus pattern (24 bp):
AAATATTATTCTTTATATTTATCA
Found at i:172249 original size:19 final size:19
Alignment explanation
Indices: 172225--172262 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
172215 AACTTTACCG
172225 CCTATGTATCAAATAACTA
1 CCTATGTATCAAATAACTA
172244 CCTATGTATCAAATAACTA
1 CCTATGTATCAAATAACTA
172263 TCCTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (19 bp):
CCTATGTATCAAATAACTA
Found at i:176570 original size:29 final size:28
Alignment explanation
Indices: 176537--176591 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
176527 ACTAATTATA
* * *
176537 AAATATTATAAAATTATTTTTACTATTTT
1 AAATATAAAAAAATTATATTTA-TATTTT
176566 AAATATAAAAAAATTATATTTATATT
1 AAATATAAAAAAATTATATTTATATT
176592 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
AAATATAAAAAAATTATATTTATATTTT
Found at i:176601 original size:28 final size:29
Alignment explanation
Indices: 176546--176603 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
176536 AAAATATTAT
* ** *
176546 AAAATTATTTTTACTATTTTAAATATAAA
1 AAAATTATATTTACTATTAAAAAAATAAA
176575 AAAATTATATTTA-TATTAAAAAAATAAA
1 AAAATTATATTTACTATTAAAAAAATAAA
176603 A
1 A
176604 CTAATCATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATTATATTTACTATTAAAAAAATAAA
Found at i:179608 original size:24 final size:25
Alignment explanation
Indices: 179571--179622 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
179561 TTAAATTAAT
*
179571 AAAATTATATTTTAA-TTC-ACGTC
1 AAAATTATAATTTAATTTCTACGTC
179594 AAAATATATAATTTAATTTCTACGTC
1 AAAAT-TATAATTTAATTTCTACGTC
179620 AAA
1 AAA
179623 CTTCAATCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 9 0.36
25 3 0.12
26 8 0.32
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAATTATAATTTAATTTCTACGTC
Found at i:183563 original size:677 final size:678
Alignment explanation
Indices: 182258--183615 Score: 2700
Period size: 677 Copynumber: 2.0 Consensus size: 678
182248 GATACTAATC
182258 TATGCTGATAGTTTTTTTTTTTAATAATTATTATTTTTTATGATAAAATATATTATTAAACCAAA
1 TATGCTGATAG-TTTTTTTTTTAATAATTATTATTTTTTATGATAAAATATATTATTAAACCAAA
182323 ATTCCTCATGTGCTATCCTTTGATTGGTATAAAATTTTATATTATTAAACCAAAAAATGGAAACT
65 ATTCCTCATGTGCTATCCTTTGATTGGTATAAAATTTTATATTATTAAACCAAAAAATGGAAACT
182388 ATTAAGGGATATAAATAATTTTTTTAATTAATGACAATGACTTAATTAAGTACAACTTTAACCTA
130 ATTAAGGGATATAAATAATTTTTTTAATTAATGACAATGACTTAATTAAGTACAACTTTAACCTA
182453 TAAAAACTTACGTATATTCTCGTTTAGAGTTAGGGTTTGCTGCAAATCTTAAAAGAGAAAAAATA
195 TAAAAACTTACGTATATTCTCGTTTAGAGTTAGGGTTTGCTGCAAATCTTAAAAGAGAAAAAATA
182518 AGTTAATGGTGACATTTACAGGTCACTAGAACAGTTAATGAACAAAGATTTAAGTAAATAATTTT
260 AGTTAATGGTGACATTTACAGGTCACTAGAACAGTTAATGAACAAAGATTTAAGTAAATAATTTT
182583 ATCAAAAACTCTTATCTGATCACTTAAATCTGTTTTTAATGGTAGGACTTTTATTGTTTTTCATT
325 ATCAAAAACTCTTATCTGATCACTTAAATCTGTTTTTAATGGTAGGACTTTTATTGTTTTTCATT
182648 TTGATAATTAATATTTCAAAAAGAGTTTAAATATTTTTTTAATAAAAATGTTAATTAAAATATCA
390 TTGATAATTAATATTTCAAAAAGAGTTTAAATATTTTTTTAATAAAAATGTTAATTAAAATATCA
182713 ATTTTTTAAAAGATGTTGACATGACAATCCGCATTGCAATCCACATGTATTTTATGCCAACATAT
455 ATTTTTTAAAAGATGTTGACATGACAATCCGCATTGCAATCCACATGTATTTTATGCCAACATAT
182778 AACTGTCTGCCTTATATGTCATGTCAAAAAATAATTTAAAATTTTAAAAATATTCAGAAATAAAA
520 AACTGTCTGCCTTATATGTCATGTCAAAAAATAATTTAAAATTTTAAAAATATTCAGAAATAAAA
182843 AGAATTAAAAAACTCAAAAAAAAGTTCATAAAATTTTTAAAAAATTGAATGAAGTATTCGTGGAT
585 AGAATTAAAAAACTCAAAAAAAAGTTCATAAAATTTTTAAAAAATTGAATGAAGTATTCGTGGAT
182908 TGCCATGTAGGTTGTTGTGTTTAAAAATT
650 TGCCATGTAGGTTGTTGTGTTTAAAAATT
182937 TATGCTGATAG-TTTTTTTTTAATAATTATTATTTTTTATGATAAAATATATTATTAAACCAAAA
1 TATGCTGATAGTTTTTTTTTTAATAATTATTATTTTTTATGATAAAATATATTATTAAACCAAAA
183001 TTCCTCATGTGCTATCCTTTGATTGGTATAAAATTTTATATTATTAAACCAAAAAATGGAAACTA
66 TTCCTCATGTGCTATCCTTTGATTGGTATAAAATTTTATATTATTAAACCAAAAAATGGAAACTA
183066 TTAAGGGATATAAATAATTTTTTTAATTAATGACAATGACTTAATTAAGTACAACTTTAACCTAT
131 TTAAGGGATATAAATAATTTTTTTAATTAATGACAATGACTTAATTAAGTACAACTTTAACCTAT
183131 AAAAACTTACGTATATTCTCGTTTAGAGTTAGGGTTTGCTGCAAATCTTAAAAGAGAAAAAATAA
196 AAAAACTTACGTATATTCTCGTTTAGAGTTAGGGTTTGCTGCAAATCTTAAAAGAGAAAAAATAA
183196 GTTAATGGTGACATTTACAGGTCACTAGAACAGTTAATGAACAAAGATTTAAGTAAATAATTTTA
261 GTTAATGGTGACATTTACAGGTCACTAGAACAGTTAATGAACAAAGATTTAAGTAAATAATTTTA
183261 TCAAAAACTCTTATCTGATCACTTAAATCTGTTTTTAATGGTAGGACTTTTATTGTTTTTCATTT
326 TCAAAAACTCTTATCTGATCACTTAAATCTGTTTTTAATGGTAGGACTTTTATTGTTTTTCATTT
183326 TGATAATTAATATTTCAAAAAGAGTTTAAATATTTTTTTAATAAAAATGTTAATTAAAATATCAA
391 TGATAATTAATATTTCAAAAAGAGTTTAAATATTTTTTTAATAAAAATGTTAATTAAAATATCAA
183391 TTTTTTAAAAGATGTTGACATGACAATCCGCATTGCAATCCACATGTATTTTATGCCAACATATA
456 TTTTTTAAAAGATGTTGACATGACAATCCGCATTGCAATCCACATGTATTTTATGCCAACATATA
183456 ACTGTCTGCCTTATATGTCATGTCAAAAAATAATTTAAAATTTTAAAAATATTCAGAAATAAAAA
521 ACTGTCTGCCTTATATGTCATGTCAAAAAATAATTTAAAATTTTAAAAATATTCAGAAATAAAAA
183521 GAATTAAAAAACTCAAAAAAAAGTTCATAAAATTTTTAAAAAATTGAATGAAGTATTCGTGGATT
586 GAATTAAAAAACTCAAAAAAAAGTTCATAAAATTTTTAAAAAATTGAATGAAGTATTCGTGGATT
183586 GCCATGTAGGTTGTTGTGTTTAAAAATT
651 GCCATGTAGGTTGTTGTGTTTAAAAATT
183614 TA
1 TA
183616 ACATTTTAGT
Statistics
Matches: 679, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
677 668 0.98
679 11 0.02
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (678 bp):
TATGCTGATAGTTTTTTTTTTAATAATTATTATTTTTTATGATAAAATATATTATTAAACCAAAA
TTCCTCATGTGCTATCCTTTGATTGGTATAAAATTTTATATTATTAAACCAAAAAATGGAAACTA
TTAAGGGATATAAATAATTTTTTTAATTAATGACAATGACTTAATTAAGTACAACTTTAACCTAT
AAAAACTTACGTATATTCTCGTTTAGAGTTAGGGTTTGCTGCAAATCTTAAAAGAGAAAAAATAA
GTTAATGGTGACATTTACAGGTCACTAGAACAGTTAATGAACAAAGATTTAAGTAAATAATTTTA
TCAAAAACTCTTATCTGATCACTTAAATCTGTTTTTAATGGTAGGACTTTTATTGTTTTTCATTT
TGATAATTAATATTTCAAAAAGAGTTTAAATATTTTTTTAATAAAAATGTTAATTAAAATATCAA
TTTTTTAAAAGATGTTGACATGACAATCCGCATTGCAATCCACATGTATTTTATGCCAACATATA
ACTGTCTGCCTTATATGTCATGTCAAAAAATAATTTAAAATTTTAAAAATATTCAGAAATAAAAA
GAATTAAAAAACTCAAAAAAAAGTTCATAAAATTTTTAAAAAATTGAATGAAGTATTCGTGGATT
GCCATGTAGGTTGTTGTGTTTAAAAATT
Found at i:186925 original size:6 final size:7
Alignment explanation
Indices: 186909--186934 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
186899 GGTAGTTGGG
186909 TTTTTCT
1 TTTTTCT
186916 TTTTTCT
1 TTTTTCT
186923 TTTTTCT
1 TTTTTCT
186930 TTTTT
1 TTTTT
186935 TGAGGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:188476 original size:20 final size:20
Alignment explanation
Indices: 188440--188478 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
188430 CACCTTTTTC
*
188440 ATAAAAAAATACTAAATATA
1 ATAAAAAAATACAAAATATA
188460 ATAAGAAAAATA-AAAATAT
1 ATAA-AAAAATACAAAATAT
188479 TATAGACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
ATAAAAAAATACAAAATATA
Found at i:189934 original size:21 final size:21
Alignment explanation
Indices: 189870--189934 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
189860 TTAGCTCTTT
* *
189870 TGAGCTTCTGTTTAACCCTTA
1 TGAGCTTCCGTTCAACCCTTA
* * * *
189891 TGGGTTTTCGTTCAGCTCC-TA
1 TGAGCTTCCGTTCAAC-CCTTA
189912 TGAGCTTCCGTTCAACCCTTA
1 TGAGCTTCCGTTCAACCCTTA
189933 TG
1 TG
189935 GGTTTCTGTT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
TGAGCTTCCGTTCAACCCTTA
Found at i:193850 original size:13 final size:13
Alignment explanation
Indices: 193832--193856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193822 ACCACGAAAC
193832 ATCTAAAACTTGT
1 ATCTAAAACTTGT
193845 ATCTAAAACTTG
1 ATCTAAAACTTG
193857 CACATGGAAA
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
ATCTAAAACTTGT
Found at i:210183 original size:2 final size:2
Alignment explanation
Indices: 210176--210209 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
210166 TGAAGAAGCA
210176 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
210210 GGGGGGGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:219860 original size:30 final size:31
Alignment explanation
Indices: 219814--219872 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
219804 AGGGTTCGAA
219814 ATTAAATCTTATATTTTTA-TAATTTTTAAATG
1 ATTAAATC-TATATTTTTACT-ATTTTTAAATG
219846 ATTAAATC-ATATTTTTACTATTTTTAA
1 ATTAAATCTATATTTTTACTATTTTTAA
219873 GGGGTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 17 0.65
31 1 0.04
32 8 0.31
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (31 bp):
ATTAAATCTATATTTTTACTATTTTTAAATG
Found at i:228433 original size:31 final size:32
Alignment explanation
Indices: 228398--228468 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 32
228388 TTAGGTAAGC
228398 ACTAAAATTTCA-AAATTCAAAAAGTAAAATG
1 ACTAAAATTTCATAAATTCAAAAAGTAAAATG
* *** *
228429 ACTAAAA-TTGATTGGTTCAAAAAGTACAATG
1 ACTAAAATTTCATAAATTCAAAAAGTAAAATG
228460 ACTAAAATT
1 ACTAAAATT
228469 GATCAAATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 3 0.09
31 29 0.88
32 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (32 bp):
ACTAAAATTTCATAAATTCAAAAAGTAAAATG
Found at i:228469 original size:31 final size:31
Alignment explanation
Indices: 228413--228471 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
228403 AATTTCAAAA
228413 TTCAAAAAGTAAAATGACTAAAATTGATTGG
1 TTCAAAAAGTAAAATGACTAAAATTGATTGG
*
228444 TTCAAAAAGTACAATGACTAAAATTGAT
1 TTCAAAAAGTAAAATGACTAAAATTGAT
228472 CAAATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (31 bp):
TTCAAAAAGTAAAATGACTAAAATTGATTGG
Found at i:229137 original size:13 final size:12
Alignment explanation
Indices: 229107--229152 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
229097 TTAAAAAAAT
*
229107 AAAAAATTTAAC
1 AAAAAATTTAAA
**
229119 GTAAAATTTAATA
1 AAAAAATTTAA-A
229132 AAAAAATTTAAA
1 AAAAAATTTAAA
229144 AAAAAATTT
1 AAAAAATTT
229153 TGAAGTTAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
AAAAAATTTAAA
Found at i:229457 original size:10 final size:10
Alignment explanation
Indices: 229442--229470 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
229432 TTTTTGAAAT
229442 TTAAAAATTA
1 TTAAAAATTA
229452 TT-AAAATTA
1 TTAAAAATTA
229461 TTAAAAATTA
1 TTAAAAATTA
229471 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:230342 original size:6 final size:6
Alignment explanation
Indices: 230331--230362 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
230321 CAAAGCAGTG
230331 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
230363 AGAGATCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:230724 original size:30 final size:30
Alignment explanation
Indices: 230680--230742 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
230670 ACTTAACTAG
*
230680 CAAATGCCTCTAAAATAATAACAAATTTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* * *
230710 CAAATGTCTTTAAAATAATAATAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
230740 CAA
1 CAA
230743 TAAAATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:230819 original size:11 final size:11
Alignment explanation
Indices: 230779--230818 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
230769 ACAATAACAA
230779 CAAAATAATAG
1 CAAAATAATAG
*
230790 CAACATAATAG
1 CAAAATAATAG
* *
230801 TAAAATAGTAG
1 CAAAATAATAG
230812 CAAAATA
1 CAAAATA
230819 GAGAGAAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:230827 original size:22 final size:22
Alignment explanation
Indices: 230780--230841 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
230770 CAATAACAAC
* *
230780 AAAATAATAGCAACATAATAGT
1 AAAATAATAGCAAAATAAGAGT
*
230802 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAATAGCAAAATA-AGAGT
*
230824 AAAACAATAAG-AAAATAA
1 AAAATAAT-AGCAAAATAA
230842 TATTAAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 27 0.82
23 5 0.15
ACGTcount: A:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (22 bp):
AAAATAATAGCAAAATAAGAGT
Found at i:240377 original size:95 final size:94
Alignment explanation
Indices: 240153--240420 Score: 423
Period size: 95 Copynumber: 2.8 Consensus size: 94
240143 CCCGCATGCA
*
240153 AATGAAGCTGAAACATCGATTCAAAGTTATATATAC--ATTCAAATTCAATGGAAAATACAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
* *
240216 GTTAAAGAAGGGGAAAAAACCCAAAAATCCC
66 ATTAAAGAA--GAAAAAAACCCAAAAATCCC
**
240247 AATGAAGCTGAAAAGGCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
240312 ATTAAAGAAGAAAAAGAACCCAAAAATCCC
66 ATTAAAGAAGAAAAA-AACCCAAAAATCCC
* * *
240342 AATGAAGCTAAAAAATCGATTCGAAGTTATATATACATATTCAAATTCAATGGAAAACACAGCCG
1 AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
240407 ATTAAAGAAGAAAA
66 ATTAAAGAAGAAAA
240421 TAAAAAAAAC
Statistics
Matches: 161, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
94 38 0.24
95 88 0.55
96 35 0.22
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (94 bp):
AATGAAGCTGAAAAATCGATTCAAAGTTATATATACATATTCAAATTCAATGGAAAATACAGCCG
ATTAAAGAAGAAAAAAACCCAAAAATCCC
Found at i:248526 original size:23 final size:22
Alignment explanation
Indices: 248478--248531 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
248468 TTAAAATTAT
*
248478 TATTTATTTTTTTTATAAACAAA
1 TATTCATTTTTTTTATAAAC-AA
248501 TATTCATTTTTTTTAGTTAAAC-A
1 TATTCATTTTTTTTA--TAAACAA
248524 TATTCATT
1 TATTCATT
248532 ATAAAATCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 23 0.82
25 5 0.18
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTCATTTTTTTTATAAACAA
Found at i:267061 original size:128 final size:129
Alignment explanation
Indices: 266833--267092 Score: 504
Period size: 128 Copynumber: 2.0 Consensus size: 129
266823 AGCGTGAGAC
266833 AAAAAGTAAACTAAACGCACCGCACCCAATCGCCCATCCAAACCCACCCTAAGAAAAGTGAAAGG
1 AAAAAGTAAACTAAACGCACCGCACCCAATCGCCCATCCAAACCCACCCTAAGAAAAGTGAAAGG
266898 GGTAGTGGTTATTGTGATTATTTAGAATTTAATAAGGGATCAAAATACAATTTTATCGTTTTGA
66 GGTAGTGGTTATTGTGATTATTTAGAATTTAATAAGGGATCAAAATACAATTTTATCGTTTTGA
*
266962 AAAAAGTAACCT-AACGCACCGCACCCAATCGCCCATCCAAACCCACCCTAAGAAAAGTGAAAGG
1 AAAAAGTAAACTAAACGCACCGCACCCAATCGCCCATCCAAACCCACCCTAAGAAAAGTGAAAGG
267026 GGTAGTGGTTATTGTGATTATTTAGAATTTAATAAGGGATCAAAATACAATTTTATCGTTTTGA
66 GGTAGTGGTTATTGTGATTATTTAGAATTTAATAAGGGATCAAAATACAATTTTATCGTTTTGA
267090 AAA
1 AAA
267093 GTTTCGATAA
Statistics
Matches: 130, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
128 119 0.92
129 11 0.08
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (129 bp):
AAAAAGTAAACTAAACGCACCGCACCCAATCGCCCATCCAAACCCACCCTAAGAAAAGTGAAAGG
GGTAGTGGTTATTGTGATTATTTAGAATTTAATAAGGGATCAAAATACAATTTTATCGTTTTGA
Found at i:276086 original size:6 final size:6
Alignment explanation
Indices: 276075--276158 Score: 159
Period size: 6 Copynumber: 14.0 Consensus size: 6
276065 TCCCACCATT
276075 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA CATATA CATATA
*
276123 CATATA CATATA GATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA
276159 GTGATGTTGT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 76 1.00
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:280146 original size:7 final size:8
Alignment explanation
Indices: 280129--280154 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
280119 CTACCCATAG
280129 TTTTTATT
1 TTTTTATT
280137 TTTTTATT
1 TTTTTATT
280145 TTTTTATT
1 TTTTTATT
280153 TT
1 TT
280155 AAAGGGTTGG
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:281625 original size:94 final size:94
Alignment explanation
Indices: 281455--281626 Score: 211
Period size: 94 Copynumber: 1.8 Consensus size: 94
281445 TAATTTGATA
* ** *
281455 AGTTACAATCAATTGCAATCACATTTTCACATAATTAACCACATAAAAAGGTTTTCAATTACCTT
1 AGTTACAATCAATTACAATCACATTCCCACATAATTAACCACATAAAAAGATTTTCAATTACCTT
* *
281520 TATAATAGTTGAGGTATTCAATTATCTTG
66 CACAATAGTTGAGGTATTCAATTATCTTG
* ** * *
281549 AGTTACAATCAATTATAATCGTATTCCCACATAATTAGCCACATAAAATA-ATTTTCAATTATCT
1 AGTTACAATCAATTACAATCACATTCCCACATAATTAACCACATAAAA-AGATTTTCAATTACCT
* *
281613 TCACGATGGTTGAG
65 TCACAATAGTTGAG
281627 ATAAAGTTTG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
94 63 0.98
95 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (94 bp):
AGTTACAATCAATTACAATCACATTCCCACATAATTAACCACATAAAAAGATTTTCAATTACCTT
CACAATAGTTGAGGTATTCAATTATCTTG
Found at i:282316 original size:29 final size:33
Alignment explanation
Indices: 282262--282334 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
282252 TTAAAACTAC
* *
282262 ACATGAACTTTAGATTGTTGTGCAATT-TA-AT
1 ACATAAACTTTAGATTGTAGTGCAATTATACAT
282293 ACATAAACTTTA-ATT-TAGTGCAATTATACAT
1 ACATAAACTTTAGATTGTAGTGCAATTATACAT
*
282324 ATA-AAACTTTA
1 ACATAAACTTTA
282335 TTGCGGTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 9 0.24
30 13 0.35
31 15 0.41
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.40
Consensus pattern (33 bp):
ACATAAACTTTAGATTGTAGTGCAATTATACAT
Found at i:288704 original size:16 final size:17
Alignment explanation
Indices: 288683--288717 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
288673 ATTATACTAG
*
288683 TAGTCAC-CCAACTATT
1 TAGTCACTCAAACTATT
288699 TAGTCACTCAAACTATT
1 TAGTCACTCAAACTATT
288716 TA
1 TA
288718 ATTTTGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (17 bp):
TAGTCACTCAAACTATT
Found at i:295331 original size:15 final size:16
Alignment explanation
Indices: 295311--295340 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
295301 TCTACTGTAA
295311 TTTTAT-CTTTTTTAG
1 TTTTATACTTTTTTAG
295326 TTTTATACTTTTTTA
1 TTTTATACTTTTTTA
295341 AAATTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTATACTTTTTTAG
Found at i:300164 original size:9 final size:9
Alignment explanation
Indices: 300147--300183 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
300137 TGAGTTTTTG
300147 AATTCGAAT
1 AATTCGAAT
*
300156 AACTCGAAT
1 AATTCGAAT
*
300165 AATTCAAAT
1 AATTCGAAT
300174 AATTCGAAT
1 AATTCGAAT
300183 A
1 A
300184 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:300415 original size:30 final size:31
Alignment explanation
Indices: 300367--300426 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
300357 AAACATTTTA
* * *
300367 TTTTCCCCCACAATTTTTATTTCC-TCCCAC
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
*
300397 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTATTCCCTTCCCA
300427 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.43
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATTCCCTTCCCAC
Found at i:301015 original size:5 final size:5
Alignment explanation
Indices: 301005--301030 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
300995 GAACAAATAT
301005 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
301031 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:305710 original size:81 final size:81
Alignment explanation
Indices: 305602--305763 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 81
305592 TTTGCTTAAT
* * * * * * *
305602 GTACCTTTTTGAATTTGTGATAGATTTTCAGTGGG-AATTTATTG-ATATTCTTTGTCACTTACT
1 GTACATTTTTGAATTTGTAATAAATTTTCAGTGGGAAAATT-TTGCAGA-TCTTTATCACATACT
305665 TGTGTATCTTGGCTGTTG
64 TGTGTATCTTGGCTGTTG
* * *
305683 GTACATTTTTTAATTTGTAATAAATTTTCAGTGGGAAAATTTTGCAGATGTTTATCACATGCTTG
1 GTACATTTTTGAATTTGTAATAAATTTTCAGTGGGAAAATTTTGCAGATCTTTATCACATACTTG
305748 TGTATCTTGGCTGTTG
66 TGTATCTTGGCTGTTG
305764 ACTTCAGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 63 0.91
82 6 0.09
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (81 bp):
GTACATTTTTGAATTTGTAATAAATTTTCAGTGGGAAAATTTTGCAGATCTTTATCACATACTTG
TGTATCTTGGCTGTTG
Found at i:313485 original size:18 final size:18
Alignment explanation
Indices: 313454--313488 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
313444 TTTCAGCAGC
**
313454 AAAGATTTCGACTTTGGG
1 AAAGATTTAAACTTTGGG
313472 AAAGATTTAAACTTTGG
1 AAAGATTTAAACTTTGG
313489 ATGAGTGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (18 bp):
AAAGATTTAAACTTTGGG
Found at i:313567 original size:25 final size:26
Alignment explanation
Indices: 313532--313581 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
313522 AACGATGTCA
* *
313532 TTTTCATTTTTTTTTTCAGATTTTTT
1 TTTTCATTTTTCTTTTCAGAATTTTT
313558 TTTTCA-TTTTCTTTTCAGAATTTT
1 TTTTCATTTTTCTTTTCAGAATTTT
313582 AGAACATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTCATTTTTCTTTTCAGAATTTTT
Found at i:313572 original size:14 final size:12
Alignment explanation
Indices: 313532--313572 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 12
313522 AACGATGTCA
313532 TTTTCATTTTTT
1 TTTTCATTTTTT
313544 TTTTCAGATTTTTT
1 TTTTC--ATTTTTT
313558 TTTTCATTTTCTT
1 TTTTCATTTT-TT
313571 TT
1 TT
313573 CAGAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.38
13 4 0.15
14 12 0.46
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTCATTTTTT
Found at i:314977 original size:15 final size:16
Alignment explanation
Indices: 314959--314991 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
314949 TAAATACAAA
314959 ATAAAATAAAA-TTAC
1 ATAAAATAAAAGTTAC
*
314974 ATAATATAAAAGTTAC
1 ATAAAATAAAAGTTAC
314990 AT
1 AT
314992 TATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAAAATAAAAGTTAC
Found at i:314991 original size:16 final size:15
Alignment explanation
Indices: 314959--315000 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
314949 TAAATACAAA
*
314959 ATAAAATAAAATTAC
1 ATAATATAAAATTAC
314974 ATAATATAAAAGTTAC
1 ATAATATAAAA-TTAC
*
314990 ATTATATAAAA
1 ATAATATAAAA
315001 ATTAAATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAATATAAAATTAC
Found at i:315408 original size:27 final size:27
Alignment explanation
Indices: 315367--315439 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
315357 AATTACCCAT
315367 TGGCGCCTCCCTATGAGGCACTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
* *
315394 TGGCGCCTCCTTATGAGACACTTTTAA
1 TGGCGCCTCCCTATGAGGCACTTTTAA
*
315421 TGGTGCCTCCCTATGAGGC
1 TGGCGCCTCCCTATGAGGC
315440 GCCACCCGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.30
Consensus pattern (27 bp):
TGGCGCCTCCCTATGAGGCACTTTTAA
Found at i:326793 original size:14 final size:14
Alignment explanation
Indices: 326774--326803 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
326764 CATGATTTTC
326774 TTTGTACTCCAACA
1 TTTGTACTCCAACA
326788 TTTGTACTCCAACA
1 TTTGTACTCCAACA
326802 TT
1 TT
326804 GAAAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (14 bp):
TTTGTACTCCAACA
Found at i:328857 original size:17 final size:15
Alignment explanation
Indices: 328824--328864 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
328814 TCAAAAAATA
328824 ATATAATTAAATTTT
1 ATATAATTAAATTTT
328839 ATATGAATTAAATTTT
1 ATAT-AATTAAATTTT
*
328855 -TATTATTAAA
1 ATATAATTAAA
328865 GAATCAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATATAATTAAATTTT
Found at i:328894 original size:19 final size:20
Alignment explanation
Indices: 328855--328896 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
328845 ATTAAATTTT
* *
328855 TATTATTAAAGAATCAATAA
1 TATTAATAAAGAATAAATAA
328875 TATTAATAAA-AATAAATAA
1 TATTAATAAAGAATAAATAA
328894 TAT
1 TAT
328897 AATCAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TATTAATAAAGAATAAATAA
Found at i:333076 original size:19 final size:19
Alignment explanation
Indices: 333053--333096 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
333043 GGCAGTAAGG
333053 AAAAATGGAGATGAACA-ATT
1 AAAAA-GGAGATGAA-AGATT
*
333073 AAAAAGTAGATGAAAGATT
1 AAAAAGGAGATGAAAGATT
333092 AAAAA
1 AAAAA
333097 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.73
20 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.18, T:0.18
Consensus pattern (19 bp):
AAAAAGGAGATGAAAGATT
Found at i:337834 original size:28 final size:30
Alignment explanation
Indices: 337774--337836 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
337764 GAAAATTAAA
* *
337774 TTTTTTATGTTCTTTTAACTTTCTCTTTTTC
1 TTTTTTA-GTTCTTTTAACTTTCTCTCTCTC
*
337805 TTTTTTA-TTCTTTTAGC-TTCTCTCTCTC
1 TTTTTTAGTTCTTTTAACTTTCTCTCTCTC
337833 TTTT
1 TTTT
337837 CCTCCCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.45
29 9 0.31
31 7 0.24
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (30 bp):
TTTTTTAGTTCTTTTAACTTTCTCTCTCTC
Found at i:341437 original size:646 final size:647
Alignment explanation
Indices: 340196--341488 Score: 2579
Period size: 646 Copynumber: 2.0 Consensus size: 647
340186 ATTAAATCTC
340196 GAATCGAAGCATAATAAAAGGATGAAATTGAAATATGATCATTTTCTTATAACGAAGAAGTAAGA
1 GAATCGAAGCATAATAAAAGGATGAAATTGAAATATGATCATTTTCTTATAACGAAGAAGTAAGA
340261 CAATAAACACGGTTTATTGATTTTTAAACACAAGATAGCCACGTGTTGGAAAACAATTAATTTTC
66 CAATAAACACGGTTTATTGATTTTTAAACACAAGATAGCCACGTGTTGGAAAACAATTAATTTTC
340326 ATGAAATTAATCTTAAAATTCAAATTAAATTATGTGATTATTTTTTATATCGAAATATATAATTT
131 ATGAAATTAATCTTAAAATTCAAATTAAATTATGTGATTATTTTTTATATCGAAATATATAATTT
340391 TCACTAAATATAATTACCATTTTAAATTTAAAAAATAAAAGTGACCAATCAAACTCACATATCGT
196 TCACTAAATATAATTACCATTTTAAATTTAAAAAATAAAAGTGACCAATCAAACTCACATATCGT
340456 ATTAAACATAAAATTTTGAAAGCAGCTGTTTGATTATTTATGTATGTATGACTTAGTTGTTTGGA
261 ATTAAACATAAAATTTTGAAAGCAGCTGTTTGATTATTTATGTATGTATGACTTAGTTGTTTGGA
340521 TAATCTTATGTTGGTCATGTGATTCATGTTTTCCGAAGAGATAAGAACAGAGAATAAACAATTTA
326 TAATCTTATGTTGGTCATGTGATTCATGTTTTCCGAAGAGATAAGAACAGAGAATAAACAATTTA
340586 AATGCAAGAACATAAAATAAAAAAAATAAAAAACCAAACATTTTTATATGTATGTTGGAAAACAT
391 AATGCAAGAACATAAAATAAAAAAAATAAAAAACCAAACATTTTTATATGTATGTTGGAAAACAT
340651 GCTTAAAAGACAACTTATTCTAAACTGCTACCAACCTTTTCTTTGAGAAAGGAAGTTTATATGAT
456 GCTTAAAAGACAACTTATTCTAAACTGCTACCAACCTTTTCTTTGAGAAAGGAAGTTTATATGAT
340716 GTAAAGTAATAAATTTATAAAAATAAATGTGATCCGGTTAATCGGTAATGTCAATTCAATCCAGT
521 GTAAAGTAATAAATTTATAAAAATAAATGTGATCCGGTTAATCGGTAATGTCAATTCAATCCAGT
340781 TTTTAAATGGTAACTAGATTATGGTATACATACGATGTGGGTGAAAATATTATGTATCAAAT
586 TTTTAAATGGTAACTAGATTATGGTATACATACGATGTGGGTGAAAATATTATGTATCAAAT
340843 GAATCGAAGC-TAATAAAAGGATGAAATTGAAATATGATCATTTTCTTATAACGAAGAAGTAAGA
1 GAATCGAAGCATAATAAAAGGATGAAATTGAAATATGATCATTTTCTTATAACGAAGAAGTAAGA
340907 CAATAAACACGGTTTATTGATTTTTAAACACAAGATAGCCACGTGTTGGAAAACAATTAATTTTC
66 CAATAAACACGGTTTATTGATTTTTAAACACAAGATAGCCACGTGTTGGAAAACAATTAATTTTC
340972 ATGAAATTAATCTTAAAATTCAAATTAAATTATGTGATTATTTTTTATATCGAAATATATAATTT
131 ATGAAATTAATCTTAAAATTCAAATTAAATTATGTGATTATTTTTTATATCGAAATATATAATTT
341037 TCACTAAATATAATTACCATTTTAAATTTAAAAAATAAAAGTGACCAATCAAACTCACATATCGT
196 TCACTAAATATAATTACCATTTTAAATTTAAAAAATAAAAGTGACCAATCAAACTCACATATCGT
341102 ATTAAACATAAAATTTTGAAAGCAGCTGTTTGATTATTTATGTATGTATGACTTAGTTGTTTGGA
261 ATTAAACATAAAATTTTGAAAGCAGCTGTTTGATTATTTATGTATGTATGACTTAGTTGTTTGGA
341167 TAATCTTATGTTGGTCATGTGATTCATGTTTTCCGAAGAGATAAGAACAGAGAATAAACAATTTA
326 TAATCTTATGTTGGTCATGTGATTCATGTTTTCCGAAGAGATAAGAACAGAGAATAAACAATTTA
341232 AATGCAAGAACATAAAATAAAAAAAATAAAAAACCAAACATTTTTATATGTATGTTGGAAAACAT
391 AATGCAAGAACATAAAATAAAAAAAATAAAAAACCAAACATTTTTATATGTATGTTGGAAAACAT
341297 GCTTAAAAGACAACTTATTCTAAACTGCTACCAACCTTTTCTTTGAGAAAGGAAGTTTATATGAT
456 GCTTAAAAGACAACTTATTCTAAACTGCTACCAACCTTTTCTTTGAGAAAGGAAGTTTATATGAT
341362 GTAAAGTAATAAATTTATAAAAATAAATGTGATCCGGTTAATCGGTAATGTCAATTCAATCCAGT
521 GTAAAGTAATAAATTTATAAAAATAAATGTGATCCGGTTAATCGGTAATGTCAATTCAATCCAGT
341427 TTTTAAATGGTAACTAGATTATGGTATACATACGATGTGGGTGAAAATATTATGTATCAAAT
586 TTTTAAATGGTAACTAGATTATGGTATACATACGATGTGGGTGAAAATATTATGTATCAAAT
341489 TCATAAAAAA
Statistics
Matches: 646, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
646 636 0.98
647 10 0.02
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (647 bp):
GAATCGAAGCATAATAAAAGGATGAAATTGAAATATGATCATTTTCTTATAACGAAGAAGTAAGA
CAATAAACACGGTTTATTGATTTTTAAACACAAGATAGCCACGTGTTGGAAAACAATTAATTTTC
ATGAAATTAATCTTAAAATTCAAATTAAATTATGTGATTATTTTTTATATCGAAATATATAATTT
TCACTAAATATAATTACCATTTTAAATTTAAAAAATAAAAGTGACCAATCAAACTCACATATCGT
ATTAAACATAAAATTTTGAAAGCAGCTGTTTGATTATTTATGTATGTATGACTTAGTTGTTTGGA
TAATCTTATGTTGGTCATGTGATTCATGTTTTCCGAAGAGATAAGAACAGAGAATAAACAATTTA
AATGCAAGAACATAAAATAAAAAAAATAAAAAACCAAACATTTTTATATGTATGTTGGAAAACAT
GCTTAAAAGACAACTTATTCTAAACTGCTACCAACCTTTTCTTTGAGAAAGGAAGTTTATATGAT
GTAAAGTAATAAATTTATAAAAATAAATGTGATCCGGTTAATCGGTAATGTCAATTCAATCCAGT
TTTTAAATGGTAACTAGATTATGGTATACATACGATGTGGGTGAAAATATTATGTATCAAAT
Found at i:344285 original size:5 final size:5
Alignment explanation
Indices: 344275--344302 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
344265 AAACTCTTAT
344275 CACTC CACTC CACTC CACTC CACTC CAC
1 CACTC CACTC CACTC CACTC CACTC CAC
344303 AATAGCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.61, G:0.00, T:0.18
Consensus pattern (5 bp):
CACTC
Found at i:350442 original size:19 final size:19
Alignment explanation
Indices: 350418--350456 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
350408 TGGTTAATGT
*
350418 TATAAGTTTTTAGAGGAAA
1 TATAAGTTTTTAGACGAAA
350437 TATAAGTTTTTAGACGAAA
1 TATAAGTTTTTAGACGAAA
350456 T
1 T
350457 TGTTTAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (19 bp):
TATAAGTTTTTAGACGAAA
Found at i:358719 original size:18 final size:18
Alignment explanation
Indices: 358684--358722 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
358674 GGACATGGAG
* *
358684 GTGGTGGTGGTAGTGGTA
1 GTGGTGGTGGGAGAGGTA
*
358702 GTGGTGGTGGGGGAGGTA
1 GTGGTGGTGGGAGAGGTA
358720 GTG
1 GTG
358723 CAGGTGGACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.62, T:0.28
Consensus pattern (18 bp):
GTGGTGGTGGGAGAGGTA
Found at i:358840 original size:135 final size:127
Alignment explanation
Indices: 358659--359206 Score: 422
Period size: 123 Copynumber: 4.3 Consensus size: 127
358649 TGGTAGCGGG
* * * * * *
358659 TATGGAGAAGCCGGTGGACATGGAGGTGGTGGTGGTAGTGGTAGTGGTGGTGGGGGAGGTAGTGC
1 TATGGAGGAGCCGGTGGACATGGAGGTGGTGCTGGTGGTGGCAATGGTGGTGGAGGAGG-AGTGC
**
358724 AGGTGGACATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTGGTGAAGGAGGTGGAGCTGGTG
65 A-GT-G-CA-GGTGGT---GCTTCTGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTG
358789 GTGGT
123 GTGGT
* *
358794 TATGGAGGAGCCGGTGGACAAGGAGGTGGTGCTGGTGGTGGC-A--GTGGTAGAGGAGGA--GCT
1 TATGGAGGAGCCGGTGGACATGGAGGTGGTGCTGGTGGTGGCAATGGTGGTGGAGGAGGAGTGC-
* * *
358854 AGTGCAGGTGGTGCTTCTGGGTATGGCAATGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGGT
65 AGTGCAGGTGGTGCTTCTGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGT
* * * *
358917 TATGGAGGAGCTGGTGGACATGGAGGTGGTGCTGGTGGCGGTAA---TGGTGGAGGCGGA--GCT
1 TATGGAGGAGCCGGTGGACATGGAGGTGGTGCTGGTGGTGGCAATGGTGGTGGAGGAGGAGTGC-
* *
358977 AGTGCAGGTGGTGCTTCTGGGTATGGCAGTGGAGGTGG-CAACGGAGGTGGAGCTGGTAGTGGTG
65 AGTGCAGGTGGTGCTTCTGGATATGGCAGTGGAGGTGGTGAA-GGAGGTGGAGCT-G--GTGGT-
*
359041 GCGGC
125 --GGT
* *** * *
359046 TATGAAGGAGCTAATGGACACGGA----G-G-TGGTGGTGGCAATGGTGGTGGAGGAGCTAGTGC
1 TATGGAGGAGCCGGTGGACATGGAGGTGGTGCTGGTGGTGGCAATGGTGGTGGAGGAG-GAGTGC
* *
359105 AGGTGGATATGGTGGTGGAGCTTCTGGATATGGAAGTGGAGGTGGTGAAGGAGGTGGAGC-----
65 A-GT-G-CA-GGTGGT---GCTTCTGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTG
*
359165 -TGGA
123 GTGGT
** *
359169 TATGGAGGAGCTAGTGGACATGGAGGTGGTGGTGGTGG
1 TATGGAGGAGCCGGTGGACATGGAGGTGGTGCTGGTGG
359207 CGGGAGTGGT
Statistics
Matches: 346, Mismatches: 38, Indels: 64
0.77 0.08 0.14
Matches are distributed among these distances:
122 2 0.01
123 180 0.52
124 3 0.01
125 1 0.00
126 22 0.06
127 4 0.01
128 3 0.01
129 36 0.10
130 2 0.01
131 2 0.01
132 17 0.05
135 72 0.21
136 2 0.01
ACGTcount: A:0.18, C:0.08, G:0.51, T:0.22
Consensus pattern (127 bp):
TATGGAGGAGCCGGTGGACATGGAGGTGGTGCTGGTGGTGGCAATGGTGGTGGAGGAGGAGTGCA
GTGCAGGTGGTGCTTCTGGATATGGCAGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGT
Found at i:358870 original size:123 final size:122
Alignment explanation
Indices: 358737--359039 Score: 453
Period size: 123 Copynumber: 2.5 Consensus size: 122
358727 TGGACATGGT
* * **
358737 GGTGGAGCTTCTGGATATGGTGGTGGAGGTGGTGAAGGAGGTGGAGCTGGTGGTGGTTATGGAGG
1 GGTGGTGCTTCTGGGTATGGCAGTGGAGGTGG-GAAGGAGGTGGAGCTGGTGGTGGTTATGGAGG
* *
358802 AGCCGGTGGACAAGGAGGTGGTGCTGGTGGTGGCAGTGGTAGAGGAGGAGCTAGTGCA
65 AGCCGGTGGACAAGGAGGTGGTGCTGGTGGCGGCAATGGTAGAGGAGGAGCTAGTGCA
*
358860 GGTGGTGCTTCTGGGTATGGCAATGGAGGTGGCGAAGGAGGTGGAGCTGGTGGTGGTTATGGAGG
1 GGTGGTGCTTCTGGGTATGGCAGTGGAGGTGG-GAAGGAGGTGGAGCTGGTGGTGGTTATGGAGG
* * * * *
358925 AGCTGGTGGACATGGAGGTGGTGCTGGTGGCGGTAATGGTGGAGGCGGAGCTAGTGCA
65 AGCCGGTGGACAAGGAGGTGGTGCTGGTGGCGGCAATGGTAGAGGAGGAGCTAGTGCA
* *
358983 GGTGGTGCTTCTGGGTATGGCAGTGGAGGTGGCAACGGAGGTGGAGCTGGTAGTGGT
1 GGTGGTGCTTCTGGGTATGGCAGTGGAGGTGGGAA-GGAGGTGGAGCTGGTGGTGGT
359040 GGCGGCTATG
Statistics
Matches: 163, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
122 2 0.01
123 161 0.99
ACGTcount: A:0.17, C:0.09, G:0.51, T:0.23
Consensus pattern (122 bp):
GGTGGTGCTTCTGGGTATGGCAGTGGAGGTGGGAAGGAGGTGGAGCTGGTGGTGGTTATGGAGGA
GCCGGTGGACAAGGAGGTGGTGCTGGTGGCGGCAATGGTAGAGGAGGAGCTAGTGCA
Found at i:359351 original size:12 final size:12
Alignment explanation
Indices: 359299--359355 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
359289 GGAGGTGTTA
* *
359299 GTGGTGGTGCAA
1 GTGGTGGTGGAG
*
359311 GTGGTGGTGGTG
1 GTGGTGGTGGAG
* **
359323 GTGGTGGCGGCT
1 GTGGTGGTGGAG
*
359335 CTGGTGGTGGAG
1 GTGGTGGTGGAG
359347 GTGGTGGTG
1 GTGGTGGTG
359356 CATATGGTGC
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.05, C:0.07, G:0.60, T:0.28
Consensus pattern (12 bp):
GTGGTGGTGGAG
Found at i:359363 original size:24 final size:24
Alignment explanation
Indices: 359299--359373 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
359289 GGAGGTGTTA
*
359299 GTGGTGGTGCA-AGTGGTGGTGGTG
1 GTGGTGGTGCATA-TGGTGGTGGAG
* *
359323 GTGGTGGCGGC-TCTGGTGGTGGAG
1 GTGGTGG-TGCATATGGTGGTGGAG
*
359347 GTGGTGGTGCATATGGTGCTGGAG
1 GTGGTGGTGCATATGGTGGTGGAG
359371 GTG
1 GTG
359374 CAAATGAGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.08, C:0.08, G:0.56, T:0.28
Consensus pattern (24 bp):
GTGGTGGTGCATATGGTGGTGGAG
Found at i:359942 original size:26 final size:26
Alignment explanation
Indices: 359913--359967 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
359903 AACAAATGTA
* **
359913 TAATAATATTAAATTGTTTTTTTAAG
1 TAATAATATTAAATTATTTGATTAAG
*
359939 TAATAATATTATATTATTTGATTAAG
1 TAATAATATTAAATTATTTGATTAAG
359965 TAA
1 TAA
359968 ACAATTGTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (26 bp):
TAATAATATTAAATTATTTGATTAAG
Found at i:365510 original size:19 final size:20
Alignment explanation
Indices: 365486--365523 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
365476 ATGCAATGTC
365486 ATATAT-AAATTTTAATTTT
1 ATATATGAAATTTTAATTTT
*
365505 ATATATGAAATTTTTATTT
1 ATATATGAAATTTTAATTT
365524 AATTCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
ATATATGAAATTTTAATTTT
Found at i:367629 original size:135 final size:135
Alignment explanation
Indices: 367449--368179 Score: 1061
Period size: 135 Copynumber: 5.3 Consensus size: 135
367439 GAGGTGGCAA
* * *
367449 TGGTGGTGGTGGAGCTAGTGCAGGTGGATATGGCGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
1 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
*
367514 GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGGGTATGGAGGAGCGGGTGGA-ATTGGAGGTGGTGG
66 GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGGGTATGGAGGAGCAGGTGGACA-TGGAGGTGGTGG
367578 TGGTAG
130 TGGTAG
* *
367584 TGGTGGTGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGCGGTGGAGGTG
1 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
* * * * * *
367649 GCGAAGGAGGTGGAGCTGGTGGTGCCGGTGGAG-CTGGTGGTGCAGGTGGACATGGAGGTGGTGG
66 GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGG-GTATGGAGGAGCAGGTGGACATGGAGGTGGTGG
367713 TGGTAG
130 TGGTAG
* *
367719 TGGTGGCGGCGGAGCTAGTACAGGTGGATACGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
1 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
367784 GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGGGTATGGAGGAGCAGGTGGACATGGAGGTGGTGGT
66 GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGGGTATGGAGGAGCAGGTGGACATGGAGGTGGTGGT
367849 GGTAG
131 GGTAG
* *
367854 TGGTGGCGGTGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGCGGTGGAGGTG
1 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
* * * *
367919 GCGAAGGAGGTGGAACTGGTGGTGCCGGGGGGTATGGAGGAGCAGGTGGACATGGAGGTGGTGGT
66 GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGGGTATGGAGGAGCAGGTGGACATGGA------GGT
367984 GGTGGTGGTAG
125 GGTGGTGGTAG
367995 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
1 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
*
368060 GTGAAGGAGGCGGAGCTGGTGGTGCTGGTGGTGCTGGCGGGTATGGAGGAGCCGGTGGACATGGA
66 GTGAAGGAGGCGGAGCTGGTGGTGC--------C-GGCGGGTATGGAGGAGCAGGTGGACATGGA
*
368125 GGTGGTGGTGGAAG
122 GGTGGTGGTGGTAG
* * * *
368139 TGGTGGTGGAGGAGCAAGTGCAGGAGGATATGGTGGTGGAG
1 TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAG
368180 GGGCACATGC
Statistics
Matches: 538, Mismatches: 40, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
134 1 0.00
135 357 0.66
136 2 0.00
141 99 0.18
144 50 0.09
149 1 0.00
150 28 0.05
ACGTcount: A:0.15, C:0.09, G:0.53, T:0.22
Consensus pattern (135 bp):
TGGTGGCGGCGGAGCTAGTGCAGGTGGATATGGTGGTGGAGCTTCTGGATATGGTGGTGGAGGTG
GTGAAGGAGGCGGAGCTGGTGGTGCCGGCGGGTATGGAGGAGCAGGTGGACATGGAGGTGGTGGT
GGTAG
Found at i:367708 original size:18 final size:18
Alignment explanation
Indices: 367656--367698 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
367646 GTGGCGAAGG
367656 AGGTGGAGCTGGTGGTGC
1 AGGTGGAGCTGGTGGTGC
*
367674 CGGTGGAGCTGGTGGTGC
1 AGGTGGAGCTGGTGGTGC
367692 AGGTGGA
1 AGGTGGA
367699 CATGGAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.56, T:0.21
Consensus pattern (18 bp):
AGGTGGAGCTGGTGGTGC
Found at i:368136 original size:12 final size:12
Alignment explanation
Indices: 368121--368150 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
368111 CCGGTGGACA
368121 TGGAGGTGGTGG
1 TGGAGGTGGTGG
*
368133 TGGAAGTGGTGG
1 TGGAGGTGGTGG
368145 TGGAGG
1 TGGAGG
368151 AGCAAGTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.63, T:0.23
Consensus pattern (12 bp):
TGGAGGTGGTGG
Found at i:368173 original size:30 final size:30
Alignment explanation
Indices: 368139--368209 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
368129 GTGGTGGAAG
368139 TGGTGGTGGAGGAGCA-AGTGCAGGAGGATA
1 TGGTGGTGGAGGAGCACA-TGCAGGAGGATA
* *
368169 TGGTGGTGGAGGGGCACATGCAGGTGGATA
1 TGGTGGTGGAGGAGCACATGCAGGAGGATA
368199 TGGTGGTGGAG
1 TGGTGGTGGAG
368210 AAGGAGCTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.07, G:0.52, T:0.20
Consensus pattern (30 bp):
TGGTGGTGGAGGAGCACATGCAGGAGGATA
Found at i:368274 original size:24 final size:24
Alignment explanation
Indices: 368229--368285 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
368219 GAGGAGGTTT
368229 TGGTGGTGCAGGCGGTCATGGTGG
1 TGGTGGTGCAGGCGGTCATGGTGG
* *
368253 TGGTGGTGGAGGTGGTTC-TGGTGG
1 TGGTGGTGCAGGCGG-TCATGGTGG
*
368277 TGGAGGTGC
1 TGGTGGTGC
368286 TGGTGTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.07, C:0.09, G:0.56, T:0.28
Consensus pattern (24 bp):
TGGTGGTGCAGGCGGTCATGGTGG
Found at i:374001 original size:15 final size:15
Alignment explanation
Indices: 373963--373995 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
373953 TTTATACTTT
373963 ATTAATT-TTAAAAA
1 ATTAATTATTAAAAA
*
373977 GTTAATTATTAAAAA
1 ATTAATTATTAAAAA
373992 ATTA
1 ATTA
373996 CATATTGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAATTATTAAAAA
Found at i:378190 original size:145 final size:145
Alignment explanation
Indices: 377920--378192 Score: 465
Period size: 145 Copynumber: 1.9 Consensus size: 145
377910 TACACATATA
* * * *
377920 CATATAGGATTCACATGGCTGCAAATCATACCATCAACAATAGCACATTTAGGAAAAGAATCATC
1 CATATAGGATTCACATGGCTGCAAATCATACCACCAACAACAACACATTTACGAAAAGAATCATC
**
377985 TATCCCTCATATCCTTCATGTCCATGACATGGTTAGAATTATGTTGCATTGCAATATACGTACAT
66 TATCCCTCATATCCTTCATGTCCATGACATAATTAGAATTATGTTGCATTGCAATATACGTACAT
378050 ATATACATACAGATT
131 ATATACATACAGATT
*
378065 CATATAGGATTCACTTGGCTGCAAATCATACCACCAACAACAACACATTTACGAAAAGAATCATC
1 CATATAGGATTCACATGGCTGCAAATCATACCACCAACAACAACACATTTACGAAAAGAATCATC
* *
378130 TATCCCTCATATCCTTCATGTCCATGACATAATTAGAATTATGTTGCATTGCGATGTACGTAC
66 TATCCCTCATATCCTTCATGTCCATGACATAATTAGAATTATGTTGCATTGCAATATACGTAC
378193 TTGTACACAT
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
145 119 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (145 bp):
CATATAGGATTCACATGGCTGCAAATCATACCACCAACAACAACACATTTACGAAAAGAATCATC
TATCCCTCATATCCTTCATGTCCATGACATAATTAGAATTATGTTGCATTGCAATATACGTACAT
ATATACATACAGATT
Found at i:378251 original size:6 final size:6
Alignment explanation
Indices: 378196--378235 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
378186 TACGTACTTG
*
378196 TACACA TACACA TACACA TACACA TACACA TACATA TACA
1 TACACA TACACA TACACA TACACA TACACA TACACA TACA
378236 AGTATATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (6 bp):
TACACA
Found at i:380962 original size:6 final size:6
Alignment explanation
Indices: 380951--381031 Score: 148
Period size: 6 Copynumber: 13.8 Consensus size: 6
380941 AGTTATATAA
380951 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
380999 TGTATG TGTATG TG--TG TGTATG TGTATG TGTAT
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTAT
381032 CCTCTTATTT
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.05
6 69 0.95
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (6 bp):
TGTATG
Found at i:380980 original size:67 final size:65
Alignment explanation
Indices: 380773--380980 Score: 262
Period size: 67 Copynumber: 3.2 Consensus size: 65
380763 TGTATACGTA
* * * * * *
380773 TGTATGTGTATTCTCTCATTTGTATAACTACTAGCCGTAAGTTATATAATGGAGATGTATGTCTA
1 TGTATGTGTATGCTCTTATTTGTGTAACTACTGGCCTTAAGTTATATAAT-GAG-TGTATGTGTA
380838 TG
64 TG
* * *
380840 TGTGTGTGTATTCTCTTATTTGTGTAACTACTGTTCCTTAAGTTATAT-A--A-TGTATGTGTAT
1 TGTATGTGTATGCTCTTATTTGTGTAACTACTG-GCCTTAAGTTATATAATGAGTGTATGTGTAT
380901 G
65 G
380902 TGTATGTGTATGCTCTTATTTGTGTAACTACTGGCCTTAAGTTATATAATGTATGTGTATGTGTA
1 TGTATGTGTATGCTCTTATTTGTGTAACTACTGGCCTTAAGTTATATAATG-A-GTGTATGTGTA
380967 TG
64 TG
380969 TGTATGTGTATG
1 TGTATGTGTATG
380981 TGTATGTGTA
Statistics
Matches: 124, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
61 13 0.10
62 43 0.35
64 1 0.01
65 1 0.01
67 54 0.44
68 12 0.10
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (65 bp):
TGTATGTGTATGCTCTTATTTGTGTAACTACTGGCCTTAAGTTATATAATGAGTGTATGTGTATG
Found at i:383299 original size:142 final size:142
Alignment explanation
Indices: 383043--383327 Score: 570
Period size: 142 Copynumber: 2.0 Consensus size: 142
383033 GTGGTGTGAT
383043 CGGATCACCCTGAAAATAATTTTTGGTCTGCGAATTTTAAGAAAAATAGGTTCGGGAGTCAGTTA
1 CGGATCACCCTGAAAATAATTTTTGGTCTGCGAATTTTAAGAAAAATAGGTTCGGGAGTCAGTTA
383108 CGCACGAGGAAGGGTTGGCACCCTCGTAACGCCCAAAATTGGTACCCAATTGATCGTTTAATGTC
66 CGCACGAGGAAGGGTTGGCACCCTCGTAACGCCCAAAATTGGTACCCAATTGATCGTTTAATGTC
383173 TTAGTATCAAAA
131 TTAGTATCAAAA
383185 CGGATCACCCTGAAAATAATTTTTGGTCTGCGAATTTTAAGAAAAATAGGTTCGGGAGTCAGTTA
1 CGGATCACCCTGAAAATAATTTTTGGTCTGCGAATTTTAAGAAAAATAGGTTCGGGAGTCAGTTA
383250 CGCACGAGGAAGGGTTGGCACCCTCGTAACGCCCAAAATTGGTACCCAATTGATCGTTTAATGTC
66 CGCACGAGGAAGGGTTGGCACCCTCGTAACGCCCAAAATTGGTACCCAATTGATCGTTTAATGTC
383315 TTAGTATCAAAA
131 TTAGTATCAAAA
383327 C
1 C
383328 TTTGAAAAGA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 143 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (142 bp):
CGGATCACCCTGAAAATAATTTTTGGTCTGCGAATTTTAAGAAAAATAGGTTCGGGAGTCAGTTA
CGCACGAGGAAGGGTTGGCACCCTCGTAACGCCCAAAATTGGTACCCAATTGATCGTTTAATGTC
TTAGTATCAAAA
Found at i:396124 original size:31 final size:31
Alignment explanation
Indices: 396089--396149 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
396079 AGCCTGGTGA
* *
396089 CTTAAATGAAAATTTTTGAATAGTTCAATGG
1 CTTAAATGAAAATTTTTAAATAATTCAATGG
396120 CTTAAATGAAAATTTTTAAATAATTCAATG
1 CTTAAATGAAAATTTTTAAATAATTCAATG
396150 ACCATATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (31 bp):
CTTAAATGAAAATTTTTAAATAATTCAATGG
Found at i:397261 original size:29 final size:28
Alignment explanation
Indices: 397198--397262 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
397188 TGAATTAAAA
* *
397198 TAAAATAAATTTGAATAAATTAACAATAT
1 TAAAAT-AAGTTGAATAAATTAAAAATAT
* *
397227 TGAAATAAGTTGAAATAAATTAAAAATGT
1 TAAAATAAGTTG-AATAAATTAAAAATAT
397256 TAAAATA
1 TAAAATA
397263 TTTGAAAGAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (28 bp):
TAAAATAAGTTGAATAAATTAAAAATAT
Found at i:397616 original size:19 final size:19
Alignment explanation
Indices: 397571--397618 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
397561 TCAAAATAAT
* *
397571 AATATATT-ATAATATTGA
1 AATATATTAATAAAATTAA
397589 AATAGTATTAATAAAATTAA
1 AATA-TATTAATAAAATTAA
397609 AATATATTAA
1 AATATATTAA
397619 ACTTAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 4 0.15
19 10 0.38
20 12 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
AATATATTAATAAAATTAA
Found at i:398575 original size:25 final size:24
Alignment explanation
Indices: 398523--398575 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
398513 TCAAAAGAAA
*
398523 TCTGTCCTTTTTTTTGCTGTCGATT
1 TCTGCCCTTTTTTTTGCTGTCGA-T
398548 TCTGCCCTTTTTGTTTGCTTGTCG-T
1 TCTGCCCTTTTT-TTTGC-TGTCGAT
398573 TCT
1 TCT
398576 TACAGGTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 15 0.60
26 5 0.20
27 5 0.20
ACGTcount: A:0.02, C:0.23, G:0.17, T:0.58
Consensus pattern (24 bp):
TCTGCCCTTTTTTTTGCTGTCGAT
Found at i:408186 original size:94 final size:94
Alignment explanation
Indices: 408021--408195 Score: 246
Period size: 94 Copynumber: 1.8 Consensus size: 94
408011 GATACGCGGA
408021 TCTGTCACCCCGAGTTGCCTAGCAACAATGATGCTATACATGTACATACTACAACCTCGGGTTGC
1 TCTGTCACCCCGAGTTGCC-A-CAACAATGATGCTATACATGTACATACTACAACCTCGGGTTGC
408086 CCGACAACGATGGTTTCCACATTTTGATTAT
64 CCGACAACGATGGTTTCCACATTTTGATTAT
* * * *
408117 TCTGTCACCCCGGGTTGCC-CAAGAATGATGACTTTACATGTACA-ATCTACCACCTCGGGTTGC
1 TCTGTCACCCCGAGTTGCCACAACAATGATG-CTATACATGTACATA-CTACAACCTCGGGTTGC
* *
408180 CTGACAATGATGGTTT
64 CCGACAACGATGGTTT
408196 TCAATCAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
93 11 0.15
94 42 0.59
96 18 0.25
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (94 bp):
TCTGTCACCCCGAGTTGCCACAACAATGATGCTATACATGTACATACTACAACCTCGGGTTGCCC
GACAACGATGGTTTCCACATTTTGATTAT
Found at i:411855 original size:20 final size:19
Alignment explanation
Indices: 411832--411870 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
411822 ATTTAAGTTT
411832 TTAACAAATAATGAAATATA
1 TTAAC-AATAATGAAATATA
* *
411852 TTAACATTATTGAAATATA
1 TTAACAATAATGAAATATA
411871 AATATATCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
TTAACAATAATGAAATATA
Found at i:412607 original size:3 final size:3
Alignment explanation
Indices: 412599--412941 Score: 679
Period size: 3 Copynumber: 114.7 Consensus size: 3
412589 AAAAAAGGCA
412599 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412647 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412695 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412743 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412791 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412839 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412887 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
412935 -AT AAT AA
1 AAT AAT AA
412942 AAGTCCATGT
Statistics
Matches: 339, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.01
3 337 0.99
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:418336 original size:5 final size:5
Alignment explanation
Indices: 418326--418375 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
418316 ACTATTCATA
418326 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
418376 TATGGTAGGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:419678 original size:11 final size:12
Alignment explanation
Indices: 419653--419677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
419643 AAAATTAGAG
419653 AATAGGTTAAAA
1 AATAGGTTAAAA
419665 AATAGGTTAAAA
1 AATAGGTTAAAA
419677 A
1 A
419678 TTATAAAATA
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:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (12 bp):
AATAGGTTAAAA
Found at i:428260 original size:20 final size:21
Alignment explanation
Indices: 428235--428275 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
428225 TCTTATACAT
*
428235 TTAAGATAAT-TCATCTCAAA
1 TTAAGATAATCTCATATCAAA
*
428255 TTAAGATGATCTCATATCAAA
1 TTAAGATAATCTCATATCAAA
428276 ACTTTACCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (21 bp):
TTAAGATAATCTCATATCAAA
Found at i:428559 original size:25 final size:23
Alignment explanation
Indices: 428521--428635 Score: 86
Period size: 23 Copynumber: 4.8 Consensus size: 23
428511 AATAATAGGT
* *
428521 AGCTCCGAAGAGCCATTAATCTGGA
1 AGCTCCGGAGAGCCA-T-ATCGGGA
*
428546 AGCTCCGGATAGCCATATCGGGA
1 AGCTCCGGAGAGCCATATCGGGA
* ** *
428569 AGTTCAAGCGAGCCATATCGGGA
1 AGCTCCGGAGAGCCATATCGGGA
* *
428592 AGCTCTGGAGAGCCATTAATCAGGA
1 AGCTCCGGAGAGCCA-T-ATCGGGA
* *
428617 AGCTGACGAAGAGCCATAT
1 AGCT-CCGGAGAGCCATAT
428636 AATGGGACGC
Statistics
Matches: 71, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
23 35 0.49
24 4 0.06
25 24 0.34
26 8 0.11
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (23 bp):
AGCTCCGGAGAGCCATATCGGGA
Found at i:429958 original size:12 final size:13
Alignment explanation
Indices: 429933--429961 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
429923 ACAAACCCAT
429933 AATATACAAAACA
1 AATATACAAAACA
429946 AATATAC-AAACA
1 AATATACAAAACA
429958 AATA
1 AATA
429962 ATATTAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (13 bp):
AATATACAAAACA
Found at i:430107 original size:30 final size:30
Alignment explanation
Indices: 430073--430165 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 30
430063 ATGTACATCA
*
430073 ATATAAAAATTAAAAGATATATATATATAT
1 ATATAAAAATTAAAAGATATGTATATATAT
* * *
430103 ATATATATATT-AAAG-TATGCATATATAT
1 ATATAAAAATTAAAAGATATGTATATATAT
* * * * * *
430131 TTATGAAAGTTAAAAAATATGTACATAAAT
1 ATATAAAAATTAAAAGATATGTATATATAT
430161 ATATA
1 ATATA
430166 GACATGTATA
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
28 17 0.37
29 7 0.15
30 22 0.48
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (30 bp):
ATATAAAAATTAAAAGATATGTATATATAT
Found at i:430520 original size:13 final size:13
Alignment explanation
Indices: 430502--430526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430492 AAATATGTAC
430502 ATATATATTATAT
1 ATATATATTATAT
430515 ATATATATTATA
1 ATATATATTATA
430527 AAAATGTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATATTATAT
Done.