Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 137 of 279
Found at i:44263783 original size:13 final size:13
Alignment explanation
Indices: 44263765--44263791 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44263755 CAATAGCCAG
44263765 TTATTTCATTCAA
1 TTATTTCATTCAA
44263778 TTATTTCATTCAA
1 TTATTTCATTCAA
44263791 T
1 T
44263792 GATCCAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTTCATTCAA
Found at i:44264265 original size:6 final size:6
Alignment explanation
Indices: 44264250--44264291 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
44264240 TGGTGGGGGA
* * *
44264250 GGTGGT GGTGGC GGTGGC GGTGGC GGTGGA GGTGGG GGTGGC
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC
44264292 AAAGGCGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.02, C:0.10, G:0.69, T:0.19
Consensus pattern (6 bp):
GGTGGC
Found at i:44264265 original size:12 final size:12
Alignment explanation
Indices: 44264238--44264290 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
44264228 TGGCGGCTTA
* *
44264238 GGTGGTGGGGGA
1 GGTGGTGGTGGC
44264250 GGTGGTGGTGGC
1 GGTGGTGGTGGC
*
44264262 GGTGGCGGTGGC
1 GGTGGTGGTGGC
* *
44264274 GGTGGAGGTGGG
1 GGTGGTGGTGGC
44264286 GGTGG
1 GGTGG
44264291 CAAAGGCGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.04, C:0.06, G:0.72, T:0.19
Consensus pattern (12 bp):
GGTGGTGGTGGC
Found at i:44265859 original size:42 final size:42
Alignment explanation
Indices: 44265752--44265834 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
44265742 AAAAGAAAAG
* *
44265752 AAATTGGTTGACAATGATGAGATTGAACCTTTTTTCCACATT
1 AAATTGATTGACAATGACGAGATTGAACCTTTTTTCCACATT
44265794 AAATTGATTGACAATGACGAGATTGAA-CTTTTTTCCACATT
1 AAATTGATTGACAATGACGAGATTGAACCTTTTTTCCACATT
44265835 TAAAATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 14 0.36
42 25 0.64
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (42 bp):
AAATTGATTGACAATGACGAGATTGAACCTTTTTTCCACATT
Found at i:44271537 original size:15 final size:16
Alignment explanation
Indices: 44271519--44271549 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44271509 TTCAAGAGCA
44271519 AAAGGA-AAACATTTG
1 AAAGGAGAAACATTTG
44271534 AAAGGAGAAACATTTG
1 AAAGGAGAAACATTTG
44271550 CATGGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (16 bp):
AAAGGAGAAACATTTG
Found at i:44280818 original size:6 final size:6
Alignment explanation
Indices: 44280807--44280831 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44280797 ATGTTGGTCC
44280807 ATTAAA ATTAAA ATTAAA ATTAAA A
1 ATTAAA ATTAAA ATTAAA ATTAAA A
44280832 CAGAACATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTAAA
Found at i:44281479 original size:20 final size:21
Alignment explanation
Indices: 44281442--44281481 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44281432 GCAGTGTACC
*
44281442 AAATATTTTTCATTATTTTAA
1 AAATATTTTTCATCATTTTAA
44281463 AAATATTTTT-ATCATTTTA
1 AAATATTTTTCATCATTTTA
44281482 TATCTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATATTTTTCATCATTTTAA
Found at i:44293665 original size:5 final size:6
Alignment explanation
Indices: 44293635--44293663 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
44293625 TCCTTAAATT
44293635 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
44293664 TAGATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:44297652 original size:59 final size:59
Alignment explanation
Indices: 44297581--44297701 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
44297571 AGCTAATTAA
*
44297581 AAATGATAATGGTCCTGCTACTGTTTACACCAGGCGAAACTGCAAGTAATAAAATAAAT
1 AAATGATAATGGTCCTGCTACTGTTTACACCAGGCGAAACTGCAAGTAATAAAAAAAAT
44297640 AAATGATAATGGTCCTGCTACTGTTTACACCAGGCGAAACTGCAAGTAATAAAAAAAAT
1 AAATGATAATGGTCCTGCTACTGTTTACACCAGGCGAAACTGCAAGTAATAAAAAAAAT
44297699 AAA
1 AAA
44297702 GGACTCTTCC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (59 bp):
AAATGATAATGGTCCTGCTACTGTTTACACCAGGCGAAACTGCAAGTAATAAAAAAAAT
Found at i:44303642 original size:114 final size:113
Alignment explanation
Indices: 44303443--44304224 Score: 1305
Period size: 114 Copynumber: 6.9 Consensus size: 113
44303433 CAATAAGCAA
* * *
44303443 TAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAATCCAAAACAATGCAGTTTTGTGAGCTTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTT
44303508 GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
66 GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
44303556 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
44303621 TGTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
65 TGTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
* *
44303670 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACATAATCCAAAACGACGCAGTTTTGTGAGCTTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTT
*
44303735 GTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
66 GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
44303783 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
*
44303848 TGTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
65 TGTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
44303897 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
* *
44303962 TGTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCACGGCTT
65 TGTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
* * ** *
44304011 TAGCGGCGTTTTTGAGATAGCGCTGCAAAAAACCTAATGTAAAACGACGCAGTTTTTGTGAGCTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAG-TTTTGTGAGCTT
* *
44304076 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTT
65 T-GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
* * *
44304126 TAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCCGTTTTGTGAGCTTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTT
* *
44304191 CG-GAGATTTAGCGGCGTTTTTTAGAAAGCGCCGC
66 -GTG-GATTTAGCGGCGTTTTTAAGGAAGCGCCGC
44304225 AAAAAACCTA
Statistics
Matches: 639, Mismatches: 25, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
113 158 0.25
114 391 0.61
115 90 0.14
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (113 bp):
TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTT
GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
Found at i:44303838 original size:227 final size:227
Alignment explanation
Indices: 44303443--44304224 Score: 1316
Period size: 227 Copynumber: 3.4 Consensus size: 227
44303433 CAATAAGCAA
* * * *
44303443 TAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAATCCAAAACAATGCAGTTTTGTGAGCTTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTT
*
44303508 GTGGATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGA
66 GTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGA
44303573 AAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGGATTTAGCGGCGT
131 AAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGGATTTAGCGGCGT
44303638 TTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
196 TTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
*
44303670 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACATAATCCAAAACGACGCAGTTTTGTGAGCTTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTT
44303735 GTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGA
66 GTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGA
*
44303800 AAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGGATTTAGCGGCAT
131 AAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGGATTTAGCGGCGT
44303865 TTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
196 TTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
*
44303897 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTT
*
44303962 TGTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCACGGCTTTAGCGGCGTTTTTGAG
65 TGTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * ** * *
44304027 ATAGCGCTGC-AAAAAACCTAATGTAAAACGACGCAGTTTTTGTGAGCTTTCGGGGATTTAGCGG
130 AAAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAG-TTTTGTGAGCTTT-GTGGATTTAGCGG
*
44304091 CGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTT
193 CGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
* *
44304126 TAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCCGTTTTGTGAGCTTT
1 TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTT
* * *
44304191 CG-GAGATTTAGCGGCGTTTTTTAGAAAGCGCCGC
66 -GTG-GATTTAGCGGCATTTTTAAGGAAGCGCCGC
44304225 AAAAAACCTA
Statistics
Matches: 526, Mismatches: 24, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
227 269 0.51
228 159 0.30
229 98 0.19
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (227 bp):
TAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCAGTTTTGTGAGCTTT
GTGGATTTAGCGGCATTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGA
AAGCGCCGCAAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGGATTTAGCGGCGT
TTTTAAGGAAGCGCCGCTAATGCTCAGGGCTT
Found at i:44304209 original size:73 final size:73
Alignment explanation
Indices: 44304124--44304282 Score: 228
Period size: 73 Copynumber: 2.2 Consensus size: 73
44304114 TGCTCAGGGC
* * *
44304124 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAATCCAAAACGACGCCGTTTTGTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
44304189 TTCGGAGA
66 TTCGGAGA
* * * * *
44304197 TTTAGCGGCGTTTTTTAGAAAGCGCCGCAAAAAACCTAAGCCAAAACTACACCTTTTTTTGCGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
*
44304262 TTCGGGGA
66 TTCGGAGA
*
44304270 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
44304283 AATTGATTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCCAAAACGACACCGTTTTGTGAGCT
TTCGGAGA
Found at i:44304667 original size:17 final size:17
Alignment explanation
Indices: 44304636--44304679 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
44304626 TAGGGAGTAT
44304636 TTATGGATT--TAGGGA
1 TTATGGATTAATAGGGA
44304651 TTATGGATTAATAGGGA
1 TTATGGATTAATAGGGA
*
44304668 TTATGGTTTAAT
1 TTATGGATTAAT
44304680 TAAGGGTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 9 0.35
17 17 0.65
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (17 bp):
TTATGGATTAATAGGGA
Found at i:44304983 original size:14 final size:15
Alignment explanation
Indices: 44304953--44304990 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
44304943 CTACTATATA
44304953 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
*
44304968 TATGGA-TTAGGTAT
1 TATGGATTTAGGGAT
44304982 TATGG-TTTA
1 TATGGATTTA
44304991 ATTAAGGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:44305038 original size:15 final size:14
Alignment explanation
Indices: 44305013--44305044 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
44305003 TGGTCGAGAT
44305013 TTAAGGTTTAGGGG
1 TTAAGGTTTAGGGG
44305027 TTAAGAGTTTAGGGG
1 TTAAG-GTTTAGGGG
44305042 TTA
1 TTA
44305045 GACGTTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (14 bp):
TTAAGGTTTAGGGG
Found at i:44305081 original size:29 final size:30
Alignment explanation
Indices: 44305010--44305081 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 30
44305000 CGTTGGTCGA
* *
44305010 GATTTAAGGTTTAGGGGTTAAGAGTTTAGG
1 GATTTAGGGTTTAGGGGCTAAGAGTTTAGG
* * *
44305040 G-GTTAGACG-TTAGTGGCTAAGAG-TTAGG
1 GATTTAG-GGTTTAGGGGCTAAGAGTTTAGG
44305068 GATTTAGGGTTTAG
1 GATTTAGGGTTTAG
44305082 AGTTTTAAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
28 7 0.22
29 23 0.72
30 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.38, T:0.35
Consensus pattern (30 bp):
GATTTAGGGTTTAGGGGCTAAGAGTTTAGG
Found at i:44305551 original size:47 final size:46
Alignment explanation
Indices: 44305486--44305586 Score: 157
Period size: 47 Copynumber: 2.2 Consensus size: 46
44305476 AATAATGAAA
* *
44305486 TAAAAACACTAAACTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAA-ACTAAACTTTTAAATTTATCTAATTTTTATAAATATAACT
*
44305533 TAAAAAACTAAAATTTTTAAATTTATCTAATTTTTATAAATATAACT
1 TAAAAAACT-AAACTTTTAAATTTATCTAATTTTTATAAATATAACT
44305580 TAAAAAA
1 TAAAAAA
44305587 ACCTATGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 3 0.06
47 47 0.94
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (46 bp):
TAAAAAACTAAACTTTTAAATTTATCTAATTTTTATAAATATAACT
Found at i:44308721 original size:14 final size:14
Alignment explanation
Indices: 44308702--44308731 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44308692 ACATAAAGCA
44308702 ACTAACCTTTTCCC
1 ACTAACCTTTTCCC
44308716 ACTAACCTTTTCCC
1 ACTAACCTTTTCCC
44308730 AC
1 AC
44308732 ACCTAATCTG
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:0.23, C:0.43, G:0.00, T:0.33
Consensus pattern (14 bp):
ACTAACCTTTTCCC
Found at i:44309915 original size:15 final size:15
Alignment explanation
Indices: 44309895--44309924 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44309885 GAGTTGAAAG
44309895 TGAAGAAGAAGATGA
1 TGAAGAAGAAGATGA
*
44309910 TGAAGATGAAGATGA
1 TGAAGAAGAAGATGA
44309925 AGATGATCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (15 bp):
TGAAGAAGAAGATGA
Found at i:44310182 original size:16 final size:16
Alignment explanation
Indices: 44310158--44310191 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44310148 TAATACTAAT
*
44310158 TAATTTTTTATATTAA
1 TAATGTTTTATATTAA
*
44310174 TAATGTTTTATTTTAA
1 TAATGTTTTATATTAA
44310190 TA
1 TA
44310192 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TAATGTTTTATATTAA
Found at i:44310370 original size:43 final size:44
Alignment explanation
Indices: 44310267--44310381 Score: 153
Period size: 43 Copynumber: 2.6 Consensus size: 44
44310257 TGTTTTTAGC
* * *
44310267 GGCGTTTGTAATCAAAGCGTCGCTAAAGGTCTTTGATATATAGT
1 GGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCTTTGAGATATAGT
* *
44310311 GGCGTTTGTGGTAAAAGCGTCGCTAAAGGTC-TTGAGCTATAGT
1 GGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCTTTGAGATATAGT
*
44310354 GGCGTTTGTTAG-AAAAGCGCCGCTAAAG
1 GGCGTTTG-TAGTAAAAGCGTCGCTAAAG
44310382 ATCCCAAGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 33 0.52
44 30 0.48
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (44 bp):
GGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCTTTGAGATATAGT
Found at i:44310395 original size:43 final size:43
Alignment explanation
Indices: 44310305--44310425 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
44310295 GTCTTTGATA
* * * ***
44310305 TATAGTGGCGTTTG-TGGTAAAAGCGTCGCTAAAGGTCTTGAGC
1 TATAGTGGCGTTTGTTAG-AAAAGCGCCGCTAAAGATCCCAAGC
*
44310348 TATAGTGGCGTTTGTTAGAAAAGCGCCGCTAAAGATCCCAAGT
1 TATAGTGGCGTTTGTTAGAAAAGCGCCGCTAAAGATCCCAAGC
* * **
44310391 TATAGCGGCGTTTATTTCTAAAAGCGCCGCTAAAG
1 TATAGTGGCGTTT-GTTAGAAAAGCGCCGCTAAAG
44310426 TTTGCGGCGA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 45 0.69
44 20 0.31
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.28
Consensus pattern (43 bp):
TATAGTGGCGTTTGTTAGAAAAGCGCCGCTAAAGATCCCAAGC
Found at i:44312454 original size:5 final size:5
Alignment explanation
Indices: 44312444--44312473 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
44312434 AGTATAAATA
44312444 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
44312474 AAAACAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:44312579 original size:25 final size:25
Alignment explanation
Indices: 44312502--44312588 Score: 68
Period size: 30 Copynumber: 3.3 Consensus size: 25
44312492 GTAAATAAAT
*
44312502 AGAAATAGAAAAAGAAAAAGAAAGCTAA
1 AGAAA-AGAAAAAGAGAAAGAAAG--AA
* * *
44312530 AGCAGAAATGAAACAGGGAAGGAAAGAA
1 AG-A-AAA-GAAAAAGAGAAAGAAAGAA
*
44312558 AGAAAAGAAAAAGAGAAAGAAAG-G
1 AGAAAAGAAAAAGAGAAAGAAAGAA
44312582 AGAAAAG
1 AGAAAAG
44312589 GCTAGGATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
24 7 0.15
25 14 0.29
26 3 0.06
27 1 0.02
28 6 0.12
29 2 0.04
30 15 0.31
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.03
Consensus pattern (25 bp):
AGAAAAGAAAAAGAGAAAGAAAGAA
Found at i:44313447 original size:41 final size:40
Alignment explanation
Indices: 44313402--44313516 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 40
44313392 ACTTCGAGTT
**
44313402 GATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAAGCC
* * *
44313443 GATGAGGCACTGGGTGCCAA-TT-TACTTCGG-TTTAGCC
1 GATGAGACACTGGGTGTCAATTTATACTTCGGATTAAGCC
*
44313480 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTA
1 GATGAGACACTGGGTGTCAATTTA-TACTTCGGATTA
44313517 TCCAATGAGG
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
37 22 0.36
38 10 0.16
40 9 0.15
41 20 0.33
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATACTTCGGATTAAGCC
Found at i:44313525 original size:40 final size:40
Alignment explanation
Indices: 44313402--44313535 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
44313392 ACTTCGAGTT
* *
44313402 GATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATTC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATT-ATCC
* * * *
44313443 GATGAGGCACTGGGTGCCAA--T-TTACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
*
44313480 GATGAGACACTGGGTGTCAATTTATTACTTCGAATTATCC
1 GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
* * *
44313520 AATGAGGCACTAGGTG
1 GATGAGACACTGGGTG
44313536 CCAAAATGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
37 20 0.26
38 10 0.13
39 2 0.03
40 26 0.34
41 18 0.24
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAATTTATTACTTCGGATTATCC
Found at i:44316316 original size:52 final size:52
Alignment explanation
Indices: 44316256--44316360 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
44316246 CTCTTCGAAT
*
44316256 TTGCTTGTACATATAATCTTTATTCTATTAAAAACAACATATATATCTTAGA
1 TTGCTTGTACATATAATCTTTATTCTATTAAAAACAACATATATATATTAGA
*
44316308 TTGCTTGTACATATAATCTTTATTCTATTAAAAACAATATATATATATTAGA
1 TTGCTTGTACATATAATCTTTATTCTATTAAAAACAACATATATATATTAGA
44316360 T
1 T
44316361 ATAAATATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (52 bp):
TTGCTTGTACATATAATCTTTATTCTATTAAAAACAACATATATATATTAGA
Found at i:44317058 original size:20 final size:21
Alignment explanation
Indices: 44317025--44317073 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
44317015 ACCATTACCG
* * *
44317025 TTATTATTATTATTATTAGTA
1 TTATTTTTACTATTATTAGAA
44317046 -TATTTTTACTATTATTAGAA
1 TTATTTTTACTATTATTAGAA
44317066 TTATTTTT
1 TTATTTTT
44317074 TTAGTTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (21 bp):
TTATTTTTACTATTATTAGAA
Found at i:44317644 original size:24 final size:23
Alignment explanation
Indices: 44317602--44317662 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
44317592 TCTAATATGT
* * *
44317602 ATATACTATGTAAATATTTTAATA
1 ATATATTATGTATACATTTT-ATA
* *
44317626 ATATATTATGTATACATTTTTTT
1 ATATATTATGTATACATTTTATA
*
44317649 ATATATTACGTATA
1 ATATATTATGTATA
44317663 TATATCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (23 bp):
ATATATTATGTATACATTTTATA
Found at i:44317677 original size:23 final size:23
Alignment explanation
Indices: 44317626--44317678 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
44317616 TATTTTAATA
* *
44317626 ATATATTATGTATACATTTTTTT
1 ATATATTACGTATACATTCTTTT
*
44317649 ATATATTACGTATATATATCTTTT
1 ATATATTACGTATACAT-TCTTTT
44317673 A-ATATT
1 ATATATT
44317679 GTATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (23 bp):
ATATATTACGTATACATTCTTTT
Found at i:44317941 original size:3 final size:3
Alignment explanation
Indices: 44317933--44317965 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
44317923 CGTTTTATAC
44317933 TAT TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
44317966 CGTTTTCGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.04
3 26 0.93
4 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44317946 original size:15 final size:15
Alignment explanation
Indices: 44317926--44317957 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44317916 TTGTTAACGT
44317926 TTTATACTATTATTA
1 TTTATACTATTATTA
*
44317941 TTTATATTATTATTA
1 TTTATACTATTATTA
44317956 TT
1 TT
44317958 ATTATTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATACTATTATTA
Found at i:44321031 original size:29 final size:29
Alignment explanation
Indices: 44320989--44321049 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
44320979 TATGTCCATA
44320989 TCATTCAAAATTCTTTCTACATAACCTAC
1 TCATTCAAAATTCTTTCTACATAACCTAC
44321018 TCATTCAAAATTCTTTCTACATAACCTAC
1 TCATTCAAAATTCTTTCTACATAACCTAC
44321047 TCA
1 TCA
44321050 AAGCTTTTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (29 bp):
TCATTCAAAATTCTTTCTACATAACCTAC
Found at i:44321247 original size:23 final size:23
Alignment explanation
Indices: 44321215--44321266 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
44321205 CCATGCATCC
44321215 TAACACGTATGCT-ATCCTAAACT
1 TAACACGTATGCTGAT-CTAAACT
* *
44321238 TAACATGTATGCTGATCTAGACT
1 TAACACGTATGCTGATCTAAACT
44321261 TAACAC
1 TAACAC
44321267 ATGCTCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (23 bp):
TAACACGTATGCTGATCTAAACT
Found at i:44331055 original size:28 final size:28
Alignment explanation
Indices: 44331014--44331068 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
44331004 TTTTTTTTGA
* *
44331014 AATTTTCATGAATT-TAATAATTTTAAAG
1 AATTTTCATAAATTAGAAT-ATTTTAAAG
*
44331042 AATTTTTATAAATTAGAATATTTTAAA
1 AATTTTCATAAATTAGAATATTTTAAA
44331069 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
AATTTTCATAAATTAGAATATTTTAAAG
Found at i:44335758 original size:24 final size:26
Alignment explanation
Indices: 44335711--44335759 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
44335701 ATATTAAAAG
*
44335711 ATATATATATATAAAATGTATACATA
1 ATATATATATATAAAATATATACATA
*
44335737 ATATA-ATAT-TAAAATATTTACAT
1 ATATATATATATAAAATATATACAT
44335760 GGTATATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 4 0.19
26 5 0.24
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATATATATATAAAATATATACATA
Found at i:44336362 original size:39 final size:39
Alignment explanation
Indices: 44336278--44336416 Score: 165
Period size: 39 Copynumber: 3.6 Consensus size: 39
44336268 CTCATGCTAC
* * * **
44336278 TTTGTTTTATTATTAATCAAAAAC-AC-TCCCCATGCTAT
1 TTTGTTTTATTGTTAAT-TAAAACTACTTCTCCATAATAT
* *
44336316 TTTGTTTTACTGTTAATTAAAACTATTTCTCCATAATAT
1 TTTGTTTTATTGTTAATTAAAACTACTTCTCCATAATAT
* *
44336355 TTTGTTTTATTGTTAATTAAAACTACTTCTTCATACTAT
1 TTTGTTTTATTGTTAATTAAAACTACTTCTCCATAATAT
*
44336394 TTTGTTTTATTATTAATTAAAAC
1 TTTGTTTTATTGTTAATTAAAAC
44336417 CATACTTTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
37 5 0.06
38 16 0.18
39 66 0.76
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (39 bp):
TTTGTTTTATTGTTAATTAAAACTACTTCTCCATAATAT
Found at i:44336455 original size:22 final size:23
Alignment explanation
Indices: 44336427--44336477 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
44336417 CATACTTTAT
44336427 TTTTTTTATCAT-AAAAAAAACC
1 TTTTTTTATCATAAAAAAAAACC
44336449 TTTTTTTATCATAAAAAAAAACC
1 TTTTTTTATCATAAAAAAAAACC
44336472 TTTTTT
1 TTTTTT
44336478 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTTTATCATAAAAAAAAACC
Found at i:44336487 original size:23 final size:23
Alignment explanation
Indices: 44336439--44336487 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
44336429 TTTTTATCAT
* ** *
44336439 AAAAAAAACCTTTTTTTATCATA
1 AAAAAAAACCTTTTTTAAAAAAA
44336462 AAAAAAAACCTTTTTTAAAAAAA
1 AAAAAAAACCTTTTTTAAAAAAA
44336485 AAA
1 AAA
44336488 CAACAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAAAACCTTTTTTAAAAAAA
Found at i:44338053 original size:21 final size:21
Alignment explanation
Indices: 44338019--44338062 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
44338009 AAATCTCTAC
*
44338019 AATTTCTCCCTAAAGCTCTCA
1 AATTTCTCACTAAAGCTCTCA
* **
44338040 AATTTCTCATTAAATTTCTCA
1 AATTTCTCACTAAAGCTCTCA
44338061 AA
1 AA
44338063 GCTCTTTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTCTCACTAAAGCTCTCA
Found at i:44338258 original size:19 final size:19
Alignment explanation
Indices: 44338236--44338301 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
44338226 AATTTGAATA
44338236 TTATTTAATATTTTTTCAT
1 TTATTTAATATTTTTTCAT
* * **
44338255 TTATTTTA-AGTTTTAAAT
1 TTATTTAATATTTTTTCAT
44338273 ATTATTTAATATTTTTTCAT
1 -TTATTTAATATTTTTTCAT
*
44338293 TTATGTAAT
1 TTATTTAAT
44338302 TTTAATTAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
18 7 0.19
19 22 0.61
20 7 0.19
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTATTTAATATTTTTTCAT
Found at i:44338274 original size:38 final size:38
Alignment explanation
Indices: 44338216--44338296 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
44338206 ATGGTAACGG
*
44338216 TTTATTTTAAAATTTGAATATTATTTAATATTTTTTCA
1 TTTATTTTAAAATTTAAATATTATTTAATATTTTTTCA
**
44338254 TTTATTTTAAGTTTTAAATATTATTTAATATTTTTTCA
1 TTTATTTTAAAATTTAAATATTATTTAATATTTTTTCA
44338292 TTTAT
1 TTTAT
44338297 GTAATTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (38 bp):
TTTATTTTAAAATTTAAATATTATTTAATATTTTTTCA
Found at i:44344358 original size:44 final size:45
Alignment explanation
Indices: 44344308--44344410 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
44344298 TGTCTTTGAC
* * *
44344308 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTATCTCCAAAGCCATATTATAAT
** * * *
44344352 ATGGACTTACATGGCTCAATCCTGTCTCTAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTATCTCCAAAGCCATA-TTATAAT
44344398 ATGGACTTACATG
1 ATGGACTTACATG
44344411 GTTCATTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 31 0.63
46 18 0.37
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTATCTCCAAAGCCATATTATAAT
Found at i:44346324 original size:21 final size:21
Alignment explanation
Indices: 44346300--44346343 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
44346290 TCGGAGTAAT
44346300 CACAATCCCCGCAGAAGCAAC
1 CACAATCCCCGCAGAAGCAAC
* * *
44346321 CACAATCCTCGCCGGAGCAAC
1 CACAATCCCCGCAGAAGCAAC
44346342 CA
1 CA
44346344 AAGAGGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.43, G:0.16, T:0.07
Consensus pattern (21 bp):
CACAATCCCCGCAGAAGCAAC
Found at i:44347986 original size:126 final size:126
Alignment explanation
Indices: 44347711--44348212 Score: 618
Period size: 126 Copynumber: 4.0 Consensus size: 126
44347701 GGCCAATCAT
* ** *** *
44347711 GAACTACTGTAGAAAAAGATCGTCCACG-TAGGAACTTTTTTCACAAATTTTGCTGACATTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTTA-GAGTTTTTTTCTGTAATTTTGCTGACAGTGCAT
* * *
44347775 CCTGTTTGAAGCGTTTTTGACACTATTTGTT-AAAAATATCTTCTCAAAATTATTTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
44347836 GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
* * * * *
44347901 CTGCTTGAAGCGTTTTTTACATTATTTGTTCAGAAACGTCTTCTAAAAATTATTTTTTCAT
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * * *
44347962 AAATTACTGTAGAAAAAGAGCGTCCACGTGGTA-ACTTTTTTCCT-TAATTTTACTGACTGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACGT--TAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCA
* * * * * *
44348025 TCCTACTTGAAGCGTTTTTTACAGTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTTAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * * *
44348088 GAACTACTGTAGAAAATGAGCGTTCACGTGAGAGCTTTTTTT-TGTATTTTTGCTAACAATGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAG-TTTTTTTCTGTAATTTTGCTGACAGTGCAT
* *
44348152 CCTGCTTGAAGTGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCA
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCA
44348213 ACGTACAAAA
Statistics
Matches: 324, Mismatches: 46, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
124 1 0.00
125 84 0.26
126 228 0.70
127 9 0.03
128 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
Found at i:44348204 original size:252 final size:251
Alignment explanation
Indices: 44347715--44348212 Score: 707
Period size: 252 Copynumber: 2.0 Consensus size: 251
44347705 AATCATGAAC
* * **
44347715 TACTGTAGAAAAAGATCGTCCACGTAGGAACTTTTTTCACAAATTTTGCTGACATTGCATCCTGT
1 TACTGTAGAAAAAGAGCGTCCACGTAGGAACTTTTTTCACAAATTTTACTGACATTGCATCCTAC
*
44347780 TTGAAGCGTTTTTGACACTATTTGTTAAAAATATCTTCTCAAAATTATTTTTTCAGGAACTACTG
66 TTGAAGCGTTTTTGACACTATTTGTTAAAAACATCTTCTCAAAATTATTTTTTCAGGAACTACTG
* * *
44347845 TAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCCTGCTTGAA
131 TAGAAAAAGAGCGTCCACGTGAGAGTTTTTTTCTGTAATTTTGCTAACAATGCATCCTGCTTGAA
* * *
44347910 GCGTTTTTTACATTATTTGTTCAGAAACGTCTTCTAAAAATTATTTTTTCATAAAT
196 GCGTTTTTGACACTATTTGTTCAGAAACATCTTCTAAAAATTATTTTTTCATAAAT
*
44347966 TACTGTAGAAAAAGAGCGTCCACGT-GGTAACTTTTTTC-CTTAATTTTACTGAC-TGTGCATCC
1 TACTGTAGAAAAAGAGCGTCCACGTAGG-AACTTTTTTCAC-AAATTTTACTGACAT-TGCATCC
* * * * * *
44348028 TACTTGAAGCGTTTTTTACAGTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTTAGGAACT
63 TACTTGAAGCGTTTTTGACACTATTTGTT-AAAAACATCTTCTCAAAATTATTTTTTCAGGAACT
* * *
44348093 ACTGTAGAAAATGAGCGTTCACGTGAGAGCTTTTTTT-TGTATTTTTGCTAACAATGCATCCTGC
127 ACTGTAGAAAAAGAGCGTCCACGTGAGAG-TTTTTTTCTGTAATTTTGCTAACAATGCATCCTGC
* * *
44348157 TTGAAGTGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCA
191 TTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTAAAAATTATTTTTTCA
44348213 ACGTACAAAA
Statistics
Matches: 218, Mismatches: 24, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
250 4 0.02
251 77 0.35
252 130 0.60
253 7 0.03
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (251 bp):
TACTGTAGAAAAAGAGCGTCCACGTAGGAACTTTTTTCACAAATTTTACTGACATTGCATCCTAC
TTGAAGCGTTTTTGACACTATTTGTTAAAAACATCTTCTCAAAATTATTTTTTCAGGAACTACTG
TAGAAAAAGAGCGTCCACGTGAGAGTTTTTTTCTGTAATTTTGCTAACAATGCATCCTGCTTGAA
GCGTTTTTGACACTATTTGTTCAGAAACATCTTCTAAAAATTATTTTTTCATAAAT
Found at i:44350642 original size:34 final size:34
Alignment explanation
Indices: 44350582--44350653 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
44350572 AAACCCTAAT
*
44350582 TTAATTTATTTAAAACACTAGGACCCTAATTTAC
1 TTAATTTATTTAAAACACTAGAACCCTAATTTAC
*
44350616 TTAATTTATTTAAAA-ACCATA-AACCCTAATTTAT
1 TTAATTTATTTAAAACA-C-TAGAACCCTAATTTAC
44350650 TTAA
1 TTAA
44350654 ATCACTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 1 0.03
34 31 0.91
35 2 0.06
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (34 bp):
TTAATTTATTTAAAACACTAGAACCCTAATTTAC
Found at i:44353554 original size:211 final size:211
Alignment explanation
Indices: 44353190--44353615 Score: 843
Period size: 211 Copynumber: 2.0 Consensus size: 211
44353180 GGAAAGCTTC
*
44353190 ACATTTCATTCACTTCATAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
1 ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
44353255 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
66 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
44353320 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
131 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
44353385 TCTTCTTAGTCAAACA
196 TCTTCTTAGTCAAACA
44353401 ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
1 ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
44353466 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
66 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
44353531 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
131 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
44353596 TCTTCTTAGTCAAACA
196 TCTTCTTAGTCAAACA
44353612 ACAT
1 ACAT
44353616 GATCTAACAT
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 214 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (211 bp):
ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
TCTTCTTAGTCAAACA
Found at i:44360714 original size:12 final size:11
Alignment explanation
Indices: 44360692--44360726 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
44360682 AAAGAGCTAA
44360692 AAATAATTTTT
1 AAATAATTTTT
44360703 AAATATATTTTT
1 AAATA-ATTTTT
*
44360715 AAAAAATTTTT
1 AAATAATTTTT
44360726 A
1 A
44360727 GAGTTAGGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AAATAATTTTT
Found at i:44360800 original size:61 final size:61
Alignment explanation
Indices: 44360721--44360848 Score: 145
Period size: 61 Copynumber: 2.1 Consensus size: 61
44360711 TTTTAAAAAA
* * * * * *
44360721 TTTTTAGAGTTAGGACTAAATTGACATATTTTGTAAATATTGAGGGCCA-AAATTTATTG-AT
1 TTTTTAGAATTAGGACTAAAATGACAAATTTTATAAACATTAAGGG--ATAAATTTATTGAAT
*
44360782 TTTTTAGAATT-GGAACTAAAATGATAAATTTTATAAACATTAAGGGATAAATTTATTGAAT
1 TTTTTAGAATTAGG-ACTAAAATGACAAATTTTATAAACATTAAGGGATAAATTTATTGAAT
44360843 TTTTTA
1 TTTTTA
44360849 TACTTAAGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
59 1 0.02
60 12 0.21
61 44 0.77
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
TTTTTAGAATTAGGACTAAAATGACAAATTTTATAAACATTAAGGGATAAATTTATTGAAT
Found at i:44368225 original size:18 final size:19
Alignment explanation
Indices: 44368202--44368238 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44368192 AAATAAATAT
*
44368202 AATAAAA-CAAGATTTTAA
1 AATAAAATCAACATTTTAA
44368220 AATAAAATCAACATTTTAA
1 AATAAAATCAACATTTTAA
44368239 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAAAATCAACATTTTAA
Found at i:44378290 original size:11 final size:11
Alignment explanation
Indices: 44378266--44378295 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44378256 TAATACTTTT
44378266 ATATTTAA-AA
1 ATATTTAATAA
44378276 ATATTTAATAA
1 ATATTTAATAA
44378287 ATATTTAAT
1 ATATTTAAT
44378296 CTACATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTTAATAA
Found at i:44383266 original size:15 final size:16
Alignment explanation
Indices: 44383246--44383278 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
44383236 TCCAACATGA
44383246 GGCAAATTGTGAG-GG
1 GGCAAATTGTGAGAGG
44383261 GGCAAATTGTGAGAGG
1 GGCAAATTGTGAGAGG
44383277 GG
1 GG
44383279 AGCCCATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.27, C:0.06, G:0.48, T:0.18
Consensus pattern (16 bp):
GGCAAATTGTGAGAGG
Found at i:44393652 original size:7 final size:7
Alignment explanation
Indices: 44393640--44393679 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
44393630 TACTCGTTTC
44393640 GTATTTA
1 GTATTTA
44393647 GTATTTA
1 GTATTTA
*
44393654 ATATTTA
1 GTATTTA
44393661 GTATTTA
1 GTATTTA
44393668 GTATTTA
1 GTATTTA
*
44393675 ATATT
1 GTATT
44393680 ATGTATACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:44393685 original size:21 final size:21
Alignment explanation
Indices: 44393640--44393679 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
44393630 TACTCGTTTC
44393640 GTATTTAGTATTTAATATTTA
1 GTATTTAGTATTTAATATTTA
44393661 GTATTTAGTATTTAATATT
1 GTATTTAGTATTTAATATT
44393680 ATGTATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
GTATTTAGTATTTAATATTTA
Found at i:44394223 original size:30 final size:30
Alignment explanation
Indices: 44394156--44394224 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
44394146 GGATAACGAC
* *
44394156 CCGGGCCCATCAATAATGCCCATACAATCA
1 CCGGGCCCATCAATAACGCCCACACAATCA
* * * *
44394186 GCTGGCCCATCAATAGCGCCCACACAGTCA
1 CCGGGCCCATCAATAACGCCCACACAATCA
44394216 CCGGGCCCA
1 CCGGGCCCA
44394225 ACACTTCAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.41, G:0.19, T:0.13
Consensus pattern (30 bp):
CCGGGCCCATCAATAACGCCCACACAATCA
Found at i:44394792 original size:56 final size:56
Alignment explanation
Indices: 44394731--44394868 Score: 258
Period size: 56 Copynumber: 2.5 Consensus size: 56
44394721 TTCTTTCATT
44394731 TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCGTATTTG
1 TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCGTATTTG
*
44394787 TAATAAAATAAAAGTTGTTTTTAGTATTTTAATTATAATTTACTCTTTCGTATTTG
1 TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCGTATTTG
*
44394843 TAATAAAATAAAAGTTGTTTTGAATA
1 TAATAAAATAAAAGTTGTTTTTAATA
44394869 AGGAAATATT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 79 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (56 bp):
TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCGTATTTG
Found at i:44397878 original size:26 final size:26
Alignment explanation
Indices: 44397829--44397885 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
44397819 CCCGATATAG
*
44397829 GGCTCTTTGTGAGCTTCCCGATTAAA
1 GGCTCTTTGTGAGCTTCCCAATTAAA
* *
44397855 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTTGTGAGCTTCCCAATTAAA
44397881 GGCTC
1 GGCTC
44397886 GCTTGAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCCCAATTAAA
Found at i:44397942 original size:25 final size:25
Alignment explanation
Indices: 44397829--44397997 Score: 114
Period size: 25 Copynumber: 6.8 Consensus size: 25
44397819 CCCGATATAG
* *
44397829 GGCTCTTTGTGAGCTTCCCGATTAAA
1 GGCTCTTTG-GAGCTTCCTGATTAAT
*
44397855 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTTG-GAGCTTCCTGATTAAT
* * *
44397881 GGCTCGCTT-GAACTTCCCGA-TATAT
1 GGCTC-TTTGGAGCTTCCTGATTA-AT
* **
44397906 GGCTATCCGGAGCTTCCTGATTAAT
1 GGCTCTTTGGAGCTTCCTGATTAAT
* *
44397931 GGCTCTTTGGAGCTACCTG-TTATT
1 GGCTCTTTGGAGCTTCCTGATTAAT
**** *
44397955 GGCTCGCAAGAGCTTCCCGATT-AT
1 GGCTCTTTGGAGCTTCCTGATTAAT
44397979 GGCTCTTAT-GAGCTTCCTG
1 GGCTCTT-TGGAGCTTCCTG
44397998 TTATACAGCC
Statistics
Matches: 108, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
24 34 0.31
25 42 0.39
26 30 0.28
27 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCTGATTAAT
Found at i:44397991 original size:24 final size:24
Alignment explanation
Indices: 44397805--44397995 Score: 93
Period size: 25 Copynumber: 7.7 Consensus size: 24
44397795 ACACACTACA
*
44397805 GCTCTTATGAG-TGTCCCGATATAGG
1 GCTCTTATGAGCT-TCCCGAT-TATG
* *
44397830 GCTCTTTGTGAGCTTCCCGATTAAAG
1 GCTC-TTATGAGCTTCCCGATT-ATG
* **
44397856 GCTCTTTGTGAGCTTCCTAATTAATG
1 GCTC-TTATGAGCTTCCCGATT-ATG
* *
44397882 GCTCGCT-TGAACTTCCCGATATATG
1 GCTC-TTATGAGCTTCCCGAT-TATG
* *** *
44397907 GCTATCCGGAGCTTCCTGATTAATG
1 GCTCTTATGAGCTTCCCGATT-ATG
* *
44397932 GCTCTT-TGGAGCTACCTG-TTATTG
1 GCTCTTAT-GAGCTTCCCGATTA-TG
** *
44397956 GCTCGCAAGAGCTTCCCGATTATG
1 GCTCTTATGAGCTTCCCGATTATG
44397980 GCTCTTATGAGCTTCC
1 GCTCTTATGAGCTTCC
44397996 TGTTATACAG
Statistics
Matches: 128, Mismatches: 28, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.01
24 32 0.25
25 50 0.39
26 44 0.34
27 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (24 bp):
GCTCTTATGAGCTTCCCGATTATG
Found at i:44399252 original size:23 final size:23
Alignment explanation
Indices: 44399222--44399268 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
44399212 GTATACTAGG
*
44399222 ACTCTAATTTAATCTAAATAAGA
1 ACTCTAATTTAATCTAAACAAGA
44399245 ACTCTAATTTAATCTAAACAAGA
1 ACTCTAATTTAATCTAAACAAGA
44399268 A
1 A
44399269 GTAGTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (23 bp):
ACTCTAATTTAATCTAAACAAGA
Found at i:44403782 original size:31 final size:31
Alignment explanation
Indices: 44403747--44403827 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
44403737 AAAATTATTG
* *
44403747 TAGTCACTCAT-GTTAGATAAATTGTCAATTT
1 TAGTCACTC-TCGTTAAATAAATTCTCAATTT
* *
44403778 TAGTCACTCTCGTTAAATAAGTTCTTAATTT
1 TAGTCACTCTCGTTAAATAAATTCTCAATTT
44403809 TAGTCACTCTAACGTTAAA
1 TAGTCACTCT--CGTTAAA
44403828 ATGGGTTTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.02
31 35 0.81
33 7 0.16
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (31 bp):
TAGTCACTCTCGTTAAATAAATTCTCAATTT
Found at i:44404021 original size:9 final size:9
Alignment explanation
Indices: 44404007--44404039 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
44403997 AATACAGATT
44404007 AAAAATTTA
1 AAAAATTTA
44404016 AAAAATATT-
1 AAAAAT-TTA
44404025 AAAAATTTA
1 AAAAATTTA
44404034 AAAAAT
1 AAAAAT
44404040 ATATAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.09
9 18 0.82
10 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTTA
Found at i:44404027 original size:18 final size:18
Alignment explanation
Indices: 44404004--44404041 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
44403994 AAAAATACAG
44404004 ATTAAAAATTTAAAAAAT
1 ATTAAAAATTTAAAAAAT
44404022 ATTAAAAATTTAAAAAAT
1 ATTAAAAATTTAAAAAAT
44404040 AT
1 AT
44404042 ATAATTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAAAAATTTAAAAAAT
Found at i:44407591 original size:51 final size:51
Alignment explanation
Indices: 44407521--44407632 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
44407511 AACAAAGGGG
*
44407521 TAAATT-TTATAAAATGAAATATAAAAATAGGCATATATTAAAATTATACA
1 TAAATTATGATAAAATGAAATATAAAAATAGGCATATATTAAAATTATACA
*
44407571 TAAATTATGATAAAATGAAATATAAAAATGGGCATATATTAAAATTATACA
1 TAAATTATGATAAAATGAAATATAAAAATAGGCATATATTAAAATTATACA
44407622 TAAATTATGAT
1 TAAATTATGAT
44407633 TCGTTATTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
50 6 0.10
51 53 0.90
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (51 bp):
TAAATTATGATAAAATGAAATATAAAAATAGGCATATATTAAAATTATACA
Found at i:44417688 original size:29 final size:29
Alignment explanation
Indices: 44417646--44417722 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
44417636 GTAATTAATT
*
44417646 AAAAG-ATTAT-ATTATTTAGTTTTTTAA
1 AAAAGAATTATAATTATTTAATTTTTTAA
44417673 AAAAGAATTATAATTATTTAATTTTTTAA
1 AAAAGAATTATAATTATTTAATTTTTTAA
44417702 AAAAGAATTATAATTATTTAA
1 AAAAGAATTATAATTATTTAA
44417723 ATAATATTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 5 0.11
28 5 0.11
29 37 0.79
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (29 bp):
AAAAGAATTATAATTATTTAATTTTTTAA
Found at i:44427754 original size:62 final size:62
Alignment explanation
Indices: 44427657--44427780 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
44427647 TATTACAAGT
44427657 AAAAGAGTAAAAAAATTTATTAGCACCGAGCCGAGCCGAGCCGTTAACATGGAAGGTAGCCA
1 AAAAGAGTAAAAAAATTTATTAGCACCGAGCCGAGCCGAGCCGTTAACATGGAAGGTAGCCA
*
44427719 AAAAGAGTAAAAAAATTTATTAGCCCCGAGCCGAGCCGAGCCGTTAACATGGAAGGTAGCCA
1 AAAAGAGTAAAAAAATTTATTAGCACCGAGCCGAGCCGAGCCGTTAACATGGAAGGTAGCCA
44427781 GCAGCTGGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (62 bp):
AAAAGAGTAAAAAAATTTATTAGCACCGAGCCGAGCCGAGCCGTTAACATGGAAGGTAGCCA
Found at i:44432241 original size:3 final size:3
Alignment explanation
Indices: 44432233--44432258 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44432223 AAGAATTGCA
44432233 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
44432259 AAGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44432999 original size:30 final size:30
Alignment explanation
Indices: 44432963--44433022 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
44432953 TAAAAATGTA
*
44432963 ATTTTTAAAGGATTAAATTAGAATTTTATC
1 ATTTTTAAAGGATTAAAGTAGAATTTTATC
* *
44432993 ATTTTTAAGGGATTAAAGTATAATTTTATC
1 ATTTTTAAAGGATTAAAGTAGAATTTTATC
44433023 TTTACTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (30 bp):
ATTTTTAAAGGATTAAAGTAGAATTTTATC
Found at i:44434851 original size:13 final size:13
Alignment explanation
Indices: 44434833--44434859 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44434823 AAGGTTTTTC
44434833 TTCAAAATGTTGG
1 TTCAAAATGTTGG
44434846 TTCAAAATGTTGG
1 TTCAAAATGTTGG
44434859 T
1 T
44434860 GTATAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TTCAAAATGTTGG
Found at i:44439318 original size:34 final size:34
Alignment explanation
Indices: 44439280--44439348 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
44439270 CTTTTATTCT
* *
44439280 AGACCTTAAGAGTGAAAACATGGGTCAAATGCTA
1 AGACCATAACAGTGAAAACATGGGTCAAATGCTA
44439314 AGACCATAACAGTGAAAACATGGGTCAAATGCTA
1 AGACCATAACAGTGAAAACATGGGTCAAATGCTA
44439348 A
1 A
44439349 CTTCTACACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (34 bp):
AGACCATAACAGTGAAAACATGGGTCAAATGCTA
Found at i:44460767 original size:27 final size:27
Alignment explanation
Indices: 44460737--44460791 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
44460727 TTACTTGAAA
*
44460737 AATTGGGTAATTTGATGTTCTAAGTTT
1 AATTGGGTAATTTGAGGTTCTAAGTTT
44460764 AATTGGGTAATTTGAGGTTCTAAGTTT
1 AATTGGGTAATTTGAGGTTCTAAGTTT
44460791 A
1 A
44460792 GCGGTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.24, T:0.45
Consensus pattern (27 bp):
AATTGGGTAATTTGAGGTTCTAAGTTT
Found at i:44463827 original size:28 final size:28
Alignment explanation
Indices: 44463795--44463848 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
44463785 AAGATTTTAC
*
44463795 TTTTAACTTTAAAAAAATACT-TTTTATA
1 TTTTAA-TATAAAAAAATACTATTTTATA
*
44463823 TTTTAATATAAAAATATACTATTTTA
1 TTTTAATATAAAAAAATACTATTTTA
44463849 ATTGCATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTTAATATAAAAAAATACTATTTTATA
Found at i:44481103 original size:46 final size:46
Alignment explanation
Indices: 44481050--44481144 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
44481040 ATGATTTCAC
44481050 AGTTGATTTATGTTATAGCCTGTTTAGAAATCATGATTTGGGTAAA
1 AGTTGATTTATGTTATAGCCTGTTTAGAAATCATGATTTGGGTAAA
*
44481096 AGTTGATTTATGTTATAGCCTGTTTCGAAATCATGATTTGGGTAAA
1 AGTTGATTTATGTTATAGCCTGTTTAGAAATCATGATTTGGGTAAA
44481142 AGT
1 AGT
44481145 AAATGGATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.41
Consensus pattern (46 bp):
AGTTGATTTATGTTATAGCCTGTTTAGAAATCATGATTTGGGTAAA
Found at i:44504089 original size:32 final size:32
Alignment explanation
Indices: 44504049--44504114 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
44504039 CAATTATAAG
44504049 TTAATTAAGATGAAAACAATACATATGTAATA
1 TTAATTAAGATGAAAACAATACATATGTAATA
44504081 TTAATTAAGATGAAAACAATACATATGTAATA
1 TTAATTAAGATGAAAACAATACATATGTAATA
44504113 TT
1 TT
44504115 GTAAATATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (32 bp):
TTAATTAAGATGAAAACAATACATATGTAATA
Found at i:44507321 original size:24 final size:24
Alignment explanation
Indices: 44507284--44507338 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
44507274 TATTATGATA
** *
44507284 TTTTATTTCTTAAAGGTAATTTTAT
1 TTTTATTTCTTAAAAATAATGTT-T
44507309 TTTTATTTC-TAAAAATAATGTTT
1 TTTTATTTCTTAAAAATAATGTTT
44507332 TTTTATT
1 TTTTATT
44507339 GGATTCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 8 0.30
24 10 0.37
25 9 0.33
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (24 bp):
TTTTATTTCTTAAAAATAATGTTT
Found at i:44507968 original size:18 final size:18
Alignment explanation
Indices: 44507945--44508001 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
44507935 TACGACCGTT
44507945 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
44507963 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
44507981 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
44507999 TAC
1 TAC
44508002 AGTAGTTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:44510284 original size:6 final size:6
Alignment explanation
Indices: 44510273--44510302 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
44510263 AGAATTCTAA
44510273 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
44510303 CAGATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:44511070 original size:24 final size:24
Alignment explanation
Indices: 44511041--44511087 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44511031 CAAAGATGAT
* *
44511041 TCTATTATGGATTAAATTAATTTC
1 TCTATTATGAAATAAATTAATTTC
*
44511065 TCTATTATTAAATAAATTAATTT
1 TCTATTATGAAATAAATTAATTT
44511088 TATCTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.51
Consensus pattern (24 bp):
TCTATTATGAAATAAATTAATTTC
Found at i:44511104 original size:24 final size:24
Alignment explanation
Indices: 44511041--44511104 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
44511031 CAAAGATGAT
** *
44511041 TCTATTATGGATTAAATTAATTTC
1 TCTATTATTAATTAAATTAATTTA
*
44511065 TCTATTATTAAATAAATTAATTTTA
1 TCTATTATTAATTAAATTAA-TTTA
44511090 TCT-TATATT-ATTAAA
1 TCTAT-TATTAATTAAA
44511105 ATGAGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (24 bp):
TCTATTATTAATTAAATTAATTTA
Found at i:44516381 original size:42 final size:43
Alignment explanation
Indices: 44516325--44516412 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 43
44516315 TTAGTATTTA
* * * **
44516325 TTTCTTGTAAAATAATTTATAGGTTAATGTAAAATAAATTATT
1 TTTCTTATAAAATAACTTATAGGTAAAAATAAAATAAATTATT
44516368 TTTCTTAT-AAATAACTTATAGGTAAAAATAAAATAAATTATT
1 TTTCTTATAAAATAACTTATAGGTAAAAATAAAATAAATTATT
44516410 TTT
1 TTT
44516413 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 33 0.82
43 7 0.17
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (43 bp):
TTTCTTATAAAATAACTTATAGGTAAAAATAAAATAAATTATT
Found at i:44516633 original size:16 final size:16
Alignment explanation
Indices: 44516611--44516647 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
44516601 CAATTTTATT
44516611 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
44516628 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
44516643 TAATA
1 TAATA
44516648 TTATTTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:44516731 original size:15 final size:15
Alignment explanation
Indices: 44516666--44516733 Score: 50
Period size: 15 Copynumber: 4.4 Consensus size: 15
44516656 ATATTATTGA
44516666 AAATAT-TTAAT-AT
1 AAATATATTAATAAT
* *
44516679 TAATATTTTAATAAT
1 AAATATATTAATAAT
* *
44516694 AAATGTTTATTACAGTTAT
1 AAA--TATATTA-A-TAAT
44516713 AAATATATTAATAAT
1 AAATATATTAATAAT
44516728 AAATAT
1 AAATAT
44516734 TTTATAGTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
13 5 0.12
14 5 0.12
15 13 0.31
16 1 0.02
17 11 0.26
18 1 0.02
19 6 0.14
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (15 bp):
AAATATATTAATAAT
Found at i:44516745 original size:31 final size:34
Alignment explanation
Indices: 44516680--44516747 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
44516670 ATTTAATATT
* *
44516680 AATATTTTAATAATAAATGTTTATTACAGTTATA
1 AATATATTAATAATAAATGATTATTACAGTTATA
*
44516714 AATATATTAATAATAAAT-ATT-TTATAG-TATA
1 AATATATTAATAATAAATGATTATTACAGTTATA
44516745 AAT
1 AAT
44516748 GTTAAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 5 0.16
33 2 0.06
34 17 0.55
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (34 bp):
AATATATTAATAATAAATGATTATTACAGTTATA
Found at i:44517695 original size:11 final size:11
Alignment explanation
Indices: 44517681--44517728 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
44517671 TAATTAGAAA
*
44517681 ATTATTATTTT
1 ATTAATATTTT
44517692 ATTAATA-TTT
1 ATTAATATTTT
* *
44517702 AATAAGATATTT
1 ATTAATAT-TTT
44517714 ATTAATATTTT
1 ATTAATATTTT
44517725 ATTA
1 ATTA
44517729 TTTTATTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:44517716 original size:30 final size:30
Alignment explanation
Indices: 44517656--44517717 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
44517646 ATGTTGATGA
*
44517656 TATTTTATAATTATTTAATTAGAAAATTAT
1 TATTTTATAATTATTTAATAAGAAAATTAT
* *
44517686 TATTTTATTAA-TATTTAATAAGATATTTAT
1 TATTTTA-TAATTATTTAATAAGAAAATTAT
44517716 TA
1 TA
44517718 ATATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
TATTTTATAATTATTTAATAAGAAAATTAT
Found at i:44517731 original size:30 final size:30
Alignment explanation
Indices: 44517660--44517731 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
44517650 TGATGATATT
* * *
44517660 TTATAATTATTTAATTAGAAAATTATTATT
1 TTATTATTATTTAATAAGAAAATTATTATA
* * *
44517690 TTATTAATATTTAATAAGATATTTATTAATA
1 TTATTATTATTTAATAAGAAAATTATT-ATA
44517721 TT-TTATTATTT
1 TTATTATTATTT
44517732 TATTTAGTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (30 bp):
TTATTATTATTTAATAAGAAAATTATTATA
Found at i:44525602 original size:32 final size:32
Alignment explanation
Indices: 44525566--44525633 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
44525556 TGGCCTCCTT
44525566 TTTTTATTTTATTTTATGTCTTTTCATTTTTG
1 TTTTTATTTTATTTTATGTCTTTTCATTTTTG
44525598 TTTTTATTTTATTTTATGTCTTTTCATTTTTG
1 TTTTTATTTTATTTTATGTCTTTTCATTTTTG
44525630 TTTT
1 TTTT
44525634 ACTTTTCAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (32 bp):
TTTTTATTTTATTTTATGTCTTTTCATTTTTG
Found at i:44530045 original size:15 final size:15
Alignment explanation
Indices: 44530025--44530102 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
44530015 TTTATGGAAA
44530025 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
44530040 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
44530054 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44530070 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44530084 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
44530100 ATC
1 ATC
44530103 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:44530062 original size:30 final size:30
Alignment explanation
Indices: 44530021--44530102 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
44530011 CATATTTATG
*
44530021 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
44530051 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
44530081 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
44530103 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:44534709 original size:15 final size:15
Alignment explanation
Indices: 44534689--44534765 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
44534679 TTTATGGAAA
44534689 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
44534704 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
44534718 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
44534734 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
44534748 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
44534764 AT
1 AT
44534766 TGAGATATTG
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.20
15 28 0.61
16 9 0.20
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:44534718 original size:30 final size:30
Alignment explanation
Indices: 44534682--44534765 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
44534672 ATCCATATTT
*
44534682 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
44534712 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
44534742 TTGGAAAGTCAAAGATATGGGTAT
1 ATGGAAAGTCAAAGATATGGGTAT
44534766 TGAGATATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:44539411 original size:22 final size:21
Alignment explanation
Indices: 44539380--44539438 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
44539370 AAATCAGTTG
44539380 TTTTCTTGTTATTTTCCTACTA
1 TTTTC-TGTTATTTTCCTACTA
* * *
44539402 TTTTGCTGTTGTTTTCTTTCTA
1 TTTT-CTGTTATTTTCCTACTA
44539424 TTTTCTCGTTATTTT
1 TTTTCT-GTTATTTT
44539439 ACTGTTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.68
Consensus pattern (21 bp):
TTTTCTGTTATTTTCCTACTA
Found at i:44539437 original size:33 final size:32
Alignment explanation
Indices: 44539376--44539449 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 32
44539366 AAAAAAATCA
*
44539376 GTTGTTTTCTTGTTATTTTCCTACTATTTTGCT
1 GTTGTTTTCTTGTTATTTTCCTA-TATTTTACT
44539409 GTTGTTTTCTT-TCTATTTTCTCGT-TATTTTACT
1 GTTGTTTTCTTGT-TATTTTC-C-TATATTTTACT
*
44539442 GTTATTTT
1 GTTGTTTT
44539450 ACTATTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
32 1 0.03
33 33 0.92
34 1 0.03
35 1 0.03
ACGTcount: A:0.09, C:0.14, G:0.11, T:0.66
Consensus pattern (32 bp):
GTTGTTTTCTTGTTATTTTCCTATATTTTACT
Found at i:44545341 original size:21 final size:22
Alignment explanation
Indices: 44545312--44545358 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
44545302 CAGAAGGAGT
*
44545312 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
44545334 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
44545355 GAGT
1 GAGT
44545359 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:44549254 original size:2 final size:2
Alignment explanation
Indices: 44549247--44549271 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44549237 TTTACACTTT
44549247 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
44549272 TTTCTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:44550318 original size:18 final size:18
Alignment explanation
Indices: 44550295--44550346 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
44550285 TAAATAGTTT
*
44550295 TTTTATATTTTTTTATTA
1 TTTTATATTTTTTAATTA
*
44550313 TTTTAT-TCTTTTAATTA
1 TTTTATATTTTTTAATTA
*
44550330 TTGTTATATTTTATAAT
1 TT-TTATATTTTTTAAT
44550347 CTCACTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 11 0.39
18 10 0.36
19 7 0.25
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTATATTTTTTAATTA
Found at i:44552447 original size:20 final size:21
Alignment explanation
Indices: 44552402--44552444 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
44552392 ACATCAACAA
44552402 TTTCATCTTAAATTTTAATAT
1 TTTCATCTTAAATTTTAATAT
*
44552423 TTTCAT-TTAAA-TTTAATTT
1 TTTCATCTTAAATTTTAATAT
44552442 TTT
1 TTT
44552445 TCAGATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 5 0.24
21 6 0.29
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTCATCTTAAATTTTAATAT
Found at i:44554706 original size:18 final size:17
Alignment explanation
Indices: 44554685--44554718 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
44554675 TTTAGTCCAT
44554685 ATTCAAAATTTTCAAAAA
1 ATTCAAAATTTT-AAAAA
44554703 ATTCAAAATTTTAAAA
1 ATTCAAAATTTTAAAA
44554719 CTTGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTCAAAATTTTAAAAA
Found at i:44567264 original size:5 final size:5
Alignment explanation
Indices: 44567254--44567281 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
44567244 GATAAATAAA
44567254 AAATT AAATT AAATT AAATT AAATT AAA
1 AAATT AAATT AAATT AAATT AAATT AAA
44567282 AGGTAGTGCA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AAATT
Found at i:44579022 original size:39 final size:39
Alignment explanation
Indices: 44578974--44579062 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
44578964 GCTCTGGTGA
* * *
44578974 GCTTTAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTCCCGTCTAGCACTTATGT
**
44579013 GCTTCAGTTAGTGTTCGGGCTCCCGTCTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTCCCGTCTAGCACTTATGT
*
44579052 GCTTCAATTAG
1 GCTTCAGTTAG
44579063 ACTTTGAGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTCCCGTCTAGCACTTATGT
Found at i:44584577 original size:64 final size:64
Alignment explanation
Indices: 44584493--44584616 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
44584483 TCATTCGTGA
* *
44584493 CACATCTAATTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAGTTATTTGACATAAGCAT
1 CACATCTAATTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
* * * * *
44584557 CACATTTAGTTAGGATCATTTGATTCATTTCAATCATAGCGTCCTAATTATTTGGCATAA
1 CACATCTAATTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAA
44584617 ACATAGTTAC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (64 bp):
CACATCTAATTAGGAGCATTTGATTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:44584798 original size:44 final size:44
Alignment explanation
Indices: 44584736--44585331 Score: 296
Period size: 44 Copynumber: 13.6 Consensus size: 44
44584726 ATTTACAGAT
* *
44584736 CTTAACCCCCTAAGCAGTAGTGAAACAGATCAAAGACGATGGAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
* * * * ** *
44584780 CTTAAACCCCTAGGCAGTAGGGTAACAGGTTGAATTTAC-A--GAT
1 CTTAAACCCCTAAGCAGTAGGGAAACA-GATCAA-AGACGATGGAC
* *
44584823 CTTAACCCCCTAAGCAGTAGTGAAACAGATCAAAGACGATGGAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
* * * * ** *
44584867 CTTAAACCCCTAGGCAGTAGGGTAACAGGTTGAATTTAC-A--GAT
1 CTTAAACCCCTAAGCAGTAGGGAAACA-GATCAA-AGACGATGGAC
* * * *
44584910 CTTAACCCCCTAAGCAGTAAGGAAACAGATCGAAGGCGATGGAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
* * * * ** *** * *
44584954 CTTAAACCCTTAAGCAGTAAGGTAACAGGTTGAA-TTTATAGAT
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
*
44584997 CTT-AACCTCCTAAGCAGTAGGGAAACAGATCGAAGGA-GATGGAC
1 CTTAAACC-CCTAAGCAGTAGGGAAACAGATC-AAAGACGATGGAC
* * * ***
44585041 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGGATTTACAGAT--A-
1 CTTAAACCCCTAAGCAGTAGGGAAACA-GAT-CAAAGAC-GATGGAC
* * * **
44585085 -TTAACCCCCTAAGCAGTAGGGAAATAGATCGAAGGTGATAGG-C
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGAT-GGAC
* * ** * *
44585128 CTTAAAACCCTAAGCAGTAGGGTAACAG-TCTGAATTTAC-A-AGAT
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATC--AA-AGACGATGGAC
* * * *
44585172 CTT-TACCCCTTAAGCAGTAGGGAAACAGATCGAAGCCGATGGGC
1 CTTAAACCCC-TAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
* * * * ** * *
44585216 CTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAATTTAC-A-AGAT
1 CTTAAACCCCTAAGCAGTAGGGAAACA-GATCAA-AGACGATGGAC
* ** *
44585260 CTTAACCCCCTAAGCAGTAGGGAAACAGATTGAAGGCGATGGAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
*
44585304 CTTAAACCCCTAAGCAGTAGGGTAACAG
1 CTTAAACCCCTAAGCAGTAGGGAAACAG
44585332 GCTGAAAATT
Statistics
Matches: 394, Mismatches: 122, Indels: 72
0.67 0.21 0.12
Matches are distributed among these distances:
40 3 0.01
41 3 0.01
42 17 0.04
43 111 0.28
44 221 0.56
45 31 0.08
46 5 0.01
47 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (44 bp):
CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATGGAC
Found at i:44584801 original size:87 final size:87
Alignment explanation
Indices: 44584692--44585337 Score: 972
Period size: 87 Copynumber: 7.4 Consensus size: 87
44584682 AATTCACAAG
*
44584692 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGT
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGG
*
44584757 GAAACAGATCAAAGACGATGGA
66 GAAACAGATCGAAGACGATGGA
* * *
44584779 CCTTAAACCCCTAGGCAGTAGGGTAACAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAGT
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGG
*
44584844 GAAACAGATCAAAGACGATGGA
66 GAAACAGATCGAAGACGATGGA
* * *
44584866 CCTTAAACCCCTAGGCAGTAGGGTAACAGGTTGAATTTACAGATCTTAACCCCCTAAGCAGTAAG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGG
*
44584931 GAAACAGATCGAAGGCGATGGA
66 GAAACAGATCGAAGACGATGGA
* * * * *
44584953 CCTTAAACCCTTAAGCAGTAAGGTAACAGGTTGAATTTATAGATCTTAACCTCCTAAGCAGTAGG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGG
44585018 GAAACAGATCGAAGGA-GATGGA
66 GAAACAGATCGAA-GACGATGGA
* * *
44585040 CCTTAAACCCCTAAGCAGTAGGGTAACAGGTTGGATTTACAGATATTAACCCCCTAAGCAGTAGG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGG
* **
44585105 GAAATAGATCGAAGGTGATAGG-
66 GAAACAGATCGAAGACGAT-GGA
* * * *
44585127 CCTTAAAACCCTAAGCAGTAGGGTAACAGTCTGAATTTACAAGATCTTTACCCCTTAAGCAGTAG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTAC-AGATCTTAACCCCCTAAGCAGTAG
* *
44585192 GGAAACAGATCGAAGCCGATGGG
65 GGAAACAGATCGAAGACGATGGA
*
44585215 CCTTAAAACCCTAAGCAGTAGGGTAACAGGCTGAATTTACAAGATCTTAACCCCCTAAGCAGTAG
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTAC-AGATCTTAACCCCCTAAGCAGTAG
* *
44585280 GGAAACAGATTGAAGGCGATGGA
65 GGAAACAGATCGAAGACGATGGA
44585303 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAA
1 CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAA
44585338 AATTCTAGAT
Statistics
Matches: 516, Mismatches: 38, Indels: 9
0.92 0.07 0.02
Matches are distributed among these distances:
86 1 0.00
87 358 0.69
88 157 0.30
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (87 bp):
CCTTAAACCCCTAAGCAGTAGGGTAACAGGCTGAATTTACAGATCTTAACCCCCTAAGCAGTAGG
GAAACAGATCGAAGACGATGGA
Found at i:44586589 original size:15 final size:14
Alignment explanation
Indices: 44586569--44586598 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
44586559 TTTGTCATAC
44586569 TTATATATATGTATA
1 TTATATATAT-TATA
44586584 TTATATATATTATA
1 TTATATATATTATA
44586598 T
1 T
44586599 AGTATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TTATATATATTATA
Found at i:44586931 original size:17 final size:17
Alignment explanation
Indices: 44586909--44586971 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
44586899 TTAAATATTG
44586909 TATTTTTATTATGTATA
1 TATTTTTATTATGTATA
* * *
44586926 TATTTTTAATACGGATA
1 TATTTTTATTATGTATA
*
44586943 CATTTTTTATTACTCGTATA
1 TA-TTTTTATTA-T-GTATA
44586963 TATATTTTA
1 TAT-TTTTA
44586972 ATATTGTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 15 0.44
18 8 0.24
19 1 0.03
20 10 0.29
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (17 bp):
TATTTTTATTATGTATA
Found at i:44586983 original size:35 final size:33
Alignment explanation
Indices: 44586894--44586984 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 33
44586884 TACTGTGTAA
44586894 ATATTTTAAATATTGTA-TTTTTATTATGTATAT
1 ATATTTT-AATATTGTATTTTTTATTATGTATAT
**
44586927 AT-TTTTAATACGGATACATTTTTTATTACTCGTATAT
1 ATATTTTAATATTG-T--ATTTTTTATTA-T-GTATAT
44586964 ATATTTTAATATTGTATTTTT
1 ATATTTTAATATTGTATTTTT
44586985 ATTGTTATGC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 2 0.04
34 1 0.02
35 15 0.32
36 1 0.02
37 9 0.19
38 9 0.19
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (33 bp):
ATATTTTAATATTGTATTTTTTATTATGTATAT
Found at i:44587056 original size:24 final size:24
Alignment explanation
Indices: 44587010--44587056 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
44587000 CTTTAATACT
* *
44587010 ATATCATTTTTATTTTTATTTTTC
1 ATATCATTCTTATGTTTATTTTTC
44587034 ATATCA-TCTTATGTTTATGTTTT
1 ATATCATTCTTATGTTTAT-TTTT
44587057 TCAAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.04, T:0.66
Consensus pattern (24 bp):
ATATCATTCTTATGTTTATTTTTC
Found at i:44587269 original size:3 final size:3
Alignment explanation
Indices: 44587256--44587367 Score: 70
Period size: 3 Copynumber: 37.3 Consensus size: 3
44587246 TTCCTATCCT
* * * *
44587256 TTA TATA TTA TTA TTG TTA TTAA TGTA -CA TTA TTA TTA TCA AT- TTA
1 TTA T-TA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA TTA TTA
* * * *
44587302 CTA TTAA TT- TTA TTT TTA TTA TTA CTA CTA -TA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
44587346 TCA TTA TCA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
44587368 CATATTTATA
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
2 6 0.07
3 68 0.81
4 9 0.11
5 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:44587351 original size:29 final size:28
Alignment explanation
Indices: 44587284--44587352 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
44587274 ATTAATGTAC
* *
44587284 ATTATTATTATCAAT-TTACTATTAATT
1 ATTATTATTATCATTATTACTACTAATT
44587311 -TTATT-TT-T-ATTATTACTACTATATT
1 ATTATTATTATCATTATTACTACTA-ATT
44587336 ATTATTATTATCATTAT
1 ATTATTATTATCATTAT
44587353 CATTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
23 2 0.06
24 9 0.26
25 5 0.15
26 10 0.29
27 2 0.06
28 1 0.03
29 5 0.15
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATTATTATCATTATTACTACTAATT
Found at i:44587577 original size:3 final size:3
Alignment explanation
Indices: 44587569--44587622 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
44587559 TATCTCTAAC
44587569 TAT TAT TAT TAT T-T TA- TAT ATAT TAT TAT CTA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT
*
44587613 TAC TAT TAT T
1 TAT TAT TAT T
44587623 CTTTATTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 33 0.75
4 5 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:44595807 original size:53 final size:53
Alignment explanation
Indices: 44595651--44595816 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
44595641 GACGAAAAAT
* **
44595651 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
44595703 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
44595756 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
44595810 TATGTGA
1 -ATGTGA
44595817 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:44598525 original size:19 final size:18
Alignment explanation
Indices: 44598487--44598533 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
44598477 GACATGTGGC
44598487 AAAAATAATAAAAA--AT
1 AAAAATAATAAAAATTAT
44598503 AAAAATTAATAAAAATTAT
1 AAAAA-TAATAAAAATTAT
*
44598522 AAAAATATTAAA
1 AAAAATAATAAA
44598534 TTTTAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 5 0.19
17 9 0.33
18 6 0.22
19 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAATAAAAATTAT
Found at i:44598545 original size:28 final size:29
Alignment explanation
Indices: 44598487--44598581 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 29
44598477 GACATGTGGC
* *
44598487 AAAAATAATAAAAA--ATAAAA-ATTAAT
1 AAAAATTATAAAAATCATAAAATTTTAAT
*
44598513 AAAAATTATAAAAAT-ATTAAATTTTAATT
1 AAAAATTATAAAAATCATAAAATTTTAA-T
*
44598542 AAAAA-TACAAAAATCATAAAATTTT-AT
1 AAAAATTATAAAAATCATAAAATTTTAAT
*
44598569 AAAAATTGTAAAA
1 AAAAATTATAAAA
44598582 TTTTATAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
26 13 0.23
27 11 0.19
28 18 0.32
29 15 0.26
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (29 bp):
AAAAATTATAAAAATCATAAAATTTTAAT
Found at i:44598589 original size:29 final size:28
Alignment explanation
Indices: 44598569--44598639 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
44598559 AAAATTTTAT
*
44598569 AAAAATTGTAAAATTTTATAAAAATCGTA
1 AAAAATTATAAAATTTTAT-AAAATCGTA
* **
44598598 AGAAATTATAAAATTTTATAAAGGCGTA
1 AAAAATTATAAAATTTTATAAAATCGTA
*
44598626 AGAAAAGTATAAAA
1 A-AAAATTATAAAA
44598640 AATGTAAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 8 0.23
29 27 0.77
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (28 bp):
AAAAATTATAAAATTTTATAAAATCGTA
Found at i:44598598 original size:19 final size:19
Alignment explanation
Indices: 44598550--44598598 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
44598540 TTAAAAATAC
*
44598550 AAAAATCATAAAATTTTAT
1 AAAAATCGTAAAATTTTAT
*
44598569 AAAAATTGTAAAATTTTAT
1 AAAAATCGTAAAATTTTAT
44598588 AAAAATCGTAA
1 AAAAATCGTAA
44598599 GAAATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAAATCGTAAAATTTTAT
Found at i:44598606 original size:19 final size:19
Alignment explanation
Indices: 44598550--44598610 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
44598540 TTAAAAATAC
* *
44598550 AAAAATCATAAAATTTTAT
1 AAAAATCGTAAAATATTAT
* *
44598569 AAAAATTGTAAAATTTTAT
1 AAAAATCGTAAAATATTAT
44598588 AAAAATCGTAAGAA-ATTAT
1 AAAAATCGTAA-AATATTAT
44598607 AAAA
1 AAAA
44598611 TTTTATAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 35 0.95
20 2 0.05
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAAATCGTAAAATATTAT
Found at i:44598886 original size:20 final size:20
Alignment explanation
Indices: 44598850--44598893 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
44598840 GTTAAATGGT
44598850 ATTTTTTTATGCATTTA-AA
1 ATTTTTTTATGCATTTATAA
44598869 ATTTTTTTATG-ATTTTTATAA
1 ATTTTTTTATGCA--TTTATAA
44598890 ATTT
1 ATTT
44598894 AGTTTCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.05
19 11 0.50
20 4 0.18
21 6 0.27
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (20 bp):
ATTTTTTTATGCATTTATAA
Found at i:44602150 original size:21 final size:20
Alignment explanation
Indices: 44602109--44602153 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
44602099 ACACACAGTC
*
44602109 AATGTTGGTCAATGCCAATT
1 AATGTTGGTCAACGCCAATT
* *
44602129 AATGATTGGTCAACGTCGATT
1 AATG-TTGGTCAACGCCAATT
44602150 AATG
1 AATG
44602154 GCCGATCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (20 bp):
AATGTTGGTCAACGCCAATT
Found at i:44602231 original size:32 final size:35
Alignment explanation
Indices: 44602172--44602240 Score: 99
Period size: 32 Copynumber: 2.1 Consensus size: 35
44602162 AAGTAAACAA
44602172 TATTTTTTAATATTAAATATTTAATATTGTAATTT
1 TATTTTTTAATATTAAATATTTAATATTGTAATTT
* *
44602207 TATTTTTTAAT-TT-AA-ATTTAATATTTTTATTT
1 TATTTTTTAATATTAAATATTTAATATTGTAATTT
44602239 TA
1 TA
44602241 AATAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 17 0.53
33 2 0.06
34 2 0.06
35 11 0.34
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (35 bp):
TATTTTTTAATATTAAATATTTAATATTGTAATTT
Done.