Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008936.1 Hibiscus syriacus cultivar Beakdansim tig00112254_pilon, whole genome shotgun sequence
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: 973811
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:591379 original size:64 final size:64
Alignment explanation
Indices: 591265--591430 Score: 183
Period size: 64 Copynumber: 2.6 Consensus size: 64
591255 TGGCTGTCCA
* ** * * *
591265 AGTGCATCGGTGCACTAGGGTGTGCGTCGGTGCAT-AAATCAGCTTCGATGTTTCAAAATAACCA
1 AGTGCATCGATGCA-TAGTTTGTGCATCAGTGCATAAAATCA-ATTCGATGTTTCAAAATAACCA
591329 G
64 G
* * * * *
591330 GGTGCATCGATGCAT-GTCTTGTGTATCAGTTCATAAAATCAATTCGATGTTTTAAAATAGCCAG
1 AGTGCATCGATGCATAGT-TTGTGCATCAGTGCATAAAATCAATTCGATGTTTCAAAATAACCAG
*
591394 AGTGCATCGATGCATAGTTTGTGCATCGGTGCATAAA
1 AGTGCATCGATGCATAGTTTGTGCATCAGTGCATAAA
591431 TTGCATTCAA
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.75
65 20 0.24
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
AGTGCATCGATGCATAGTTTGTGCATCAGTGCATAAAATCAATTCGATGTTTCAAAATAACCAG
Found at i:593302 original size:59 final size:59
Alignment explanation
Indices: 593210--593385 Score: 253
Period size: 59 Copynumber: 3.0 Consensus size: 59
593200 ACAACACATG
* *
593210 AGGGATCAACATTTTCTTTGCTCGATTCATGACATTTCGAATCAGCGATGCTTCACTCA
1 AGGGATTAACATTTTCTTTGCTCGATTCATGACATTTCGAATCAGCGATGCCTCACTCA
* * ** *
593269 AGGGATTAACATTTTCTTGGCTCGATTCATGACATTTCGAATTAGCGACACCTCACTCG
1 AGGGATTAACATTTTCTTTGCTCGATTCATGACATTTCGAATCAGCGATGCCTCACTCA
* * * *
593328 AGGGATTAACATTTCCTTTGCTCGATTCACGACATTTTGAATCAGCGATGCCTTACTC
1 AGGGATTAACATTTTCTTTGCTCGATTCATGACATTTCGAATCAGCGATGCCTCACTC
593386 GAGAGACCAA
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 102 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (59 bp):
AGGGATTAACATTTTCTTTGCTCGATTCATGACATTTCGAATCAGCGATGCCTCACTCA
Found at i:599523 original size:53 final size:53
Alignment explanation
Indices: 599466--599570 Score: 117
Period size: 53 Copynumber: 2.0 Consensus size: 53
599456 AATATATATC
* *
599466 ATTAATAATATTGTAAT-A-GTTATGTTTAAAATT-AATTACTTAAATTTGAATTA
1 ATTAA-AATATT-TAATAACGTTAT-TTTAAAATTAAATAACTTAAATTTAAATTA
* * *
599519 ATTAAATTATTTATTAACGTTATTTTAAAATTAAATAATTTAAATTTAAATT
1 ATTAAAATATTTAATAACGTTATTTTAAAATTAAATAACTTAAATTTAAATT
599571 TAAATTGAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
51 3 0.07
52 15 0.34
53 26 0.59
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (53 bp):
ATTAAAATATTTAATAACGTTATTTTAAAATTAAATAACTTAAATTTAAATTA
Found at i:599818 original size:21 final size:21
Alignment explanation
Indices: 599744--599818 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
599734 GTTTCCAGAT
* *
599744 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
* *
599765 TCGCAA--CGAATTTGGAATAAA
1 TCGCAATGCGAACTTGGACT--A
* *
599786 TTGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
599807 TCGCAATGCGAA
1 TCGCAATGCGAA
599819 TATGTAAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 9 0.21
21 23 0.55
23 10 0.24
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:599888 original size:51 final size:51
Alignment explanation
Indices: 599823--600002 Score: 159
Period size: 51 Copynumber: 3.3 Consensus size: 51
599813 TGCGAATATG
599823 TAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAA
1 TAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAA
* * *
599874 TAAATCGCAATGCGA-ACTTCGACTA-TCGCAATGCGAACTTG-GACTATCGCAACGAATTTGGA
1 TAAATCGCAATGCGATA-GTCGA--AGT-TC---GCG---TTGCGA-TA--G--TCGAATTTGGA
599936 A
51 A
*
599937 TAAATCGTAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAA
1 TAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAA
*
599988 TAAATCGCAACGCGA
1 TAAATCGCAATGCGA
600003 ACTTCGACTA
Statistics
Matches: 102, Mismatches: 9, Indels: 36
0.69 0.06 0.24
Matches are distributed among these distances:
50 1 0.01
51 43 0.42
52 1 0.01
53 3 0.03
55 5 0.05
56 5 0.05
58 5 0.05
59 5 0.05
61 3 0.03
62 1 0.01
63 29 0.28
64 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (51 bp):
TAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAA
Found at i:599901 original size:21 final size:21
Alignment explanation
Indices: 599877--599925 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
599867 TTTGGAATAA
599877 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
599898 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
599919 ATCGCAA
1 ATCGCAA
599926 CGAATTTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:599934 original size:19 final size:20
Alignment explanation
Indices: 599877--599935 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
599867 TTTGGAATAA
*
599877 ATCGCAATGCGAACTTCGACT
1 ATCGCAA-GCGAACTTGGACT
599898 ATCGCAATGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
*
599919 ATCGCAA-CGAATTTGGA
1 ATCGCAAGCGAACTTGGA
599936 ATAAATCGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.25
21 27 0.75
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAAGCGAACTTGGACT
Found at i:599943 original size:21 final size:20
Alignment explanation
Indices: 599863--599938 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
599853 TTGCGATAGT
*
599863 CGAATTTGGAATAAATCGCAATG
1 CGAACTTGGAAT--ATCGCAA-G
* *
599886 CGAACTTCGACTATCGCAATG
1 CGAACTTGGAATATCGCAA-G
*
599907 CGAACTTGGACTATCGCAA-
1 CGAACTTGGAATATCGCAAG
*
599926 CGAATTTGGAATA
1 CGAACTTGGAATA
599939 AATCGTAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 11 0.23
21 27 0.57
23 9 0.19
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (20 bp):
CGAACTTGGAATATCGCAAG
Found at i:599968 original size:114 final size:112
Alignment explanation
Indices: 599788--600038 Score: 405
Period size: 114 Copynumber: 2.2 Consensus size: 112
599778 GGAATAAATT
*
599788 GCAATACGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCG
1 GCAATGCGAACTTGGACTATCGCAA-GCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCG
*
599853 TTGCGATAGTCGAATTTGGAATAAATCGCAATGCGAACTTCGACTATC
65 TTGCGATAGTCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
* *
599901 GCAATGCGAACTTGGACTATCGCAA-CGAATTTGGAATAAATCGTAATGCGATAGTCGAAGTTCG
1 GCAATGCGAACTTGGACTATCGCAAGCGAATAT-G--TAAATCGCAATGCGATAGTCGAAGTTCG
599965 CGTTGCGATAGTCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
63 CGTTGCGATAGTCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
* *
600015 GCAATGCAAACTTCGACTATCGCA
1 GCAATGCGAACTTGGACTATCGCA
600039 TTGCGATAGT
Statistics
Matches: 129, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
111 6 0.05
112 1 0.01
113 24 0.19
114 98 0.76
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (112 bp):
GCAATGCGAACTTGGACTATCGCAAGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGT
TGCGATAGTCGAATTTGGAATAAATCGCAACGCGAACTTCGACTATC
Found at i:600015 original size:21 final size:21
Alignment explanation
Indices: 599991--600038 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
599981 TTTGGAATAA
*
599991 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCAAACTTCGACT
*
600012 ATCGCAATGCAAACTTCGACT
1 ATCGCAACGCAAACTTCGACT
600033 ATCGCA
1 ATCGCA
600039 TTGCGATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCAAACTTCGACT
Found at i:600058 original size:21 final size:21
Alignment explanation
Indices: 600034--600129 Score: 115
Period size: 21 Copynumber: 4.6 Consensus size: 21
600024 ACTTCGACTA
600034 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
600055 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
*
600078 TCG--TTGCGATAGTCAAAGT
1 TCGCATTGCGATAGTCCAAGT
*
600097 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
600118 TCGCGTTGCGAT
1 TCGCATTGCGAT
600130 TTATTCCAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
19 10 0.16
21 43 0.67
23 11 0.17
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:600083 original size:114 final size:111
Alignment explanation
Indices: 599826--600091 Score: 295
Period size: 114 Copynumber: 2.3 Consensus size: 111
599816 GAATATGTAA
* * *
599826 ATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAATAAATCGCAATGCGAAC
1 ATCGCAATGCGATAGTCCAAATTC-CGTTGCGATAGTCGAATTTGGAATAAATCGCAACGCGAAC
* * * **
599891 TTCGACTATCGCAATGCGAACTTGGACTATCGCAACGAATTTGGAAT
65 TTCGACTATCGCAATGCAAACTTCGACTATCGCAACGAATGTCCAAT
* * *
599938 AAATCGTAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAATAAATCGCAACGCGA
1 --ATCGCAATGCGATAGTCCAAATTC-CGTTGCGATAGTCGAATTTGGAATAAATCGCAACGCGA
*
600003 ACTTCGACTATCGCAATGCAAACTTCGACTATCGCATTGCG-ATAGTCCAAGT
63 ACTTCGACTATCGCAATGCAAACTTCGACTATCGCA--ACGAAT-GTCCAA-T
* *
600055 -TCGCATTGCGATTTATTCCAAATT-CGTTGCGATAGTC
1 ATCGCAATGCGA--TAGTCCAAATTCCGTTGCGATAGTC
600092 AAAGTTCGCA
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
114 117 0.88
115 2 0.02
116 13 0.10
117 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (111 bp):
ATCGCAATGCGATAGTCCAAATTCCGTTGCGATAGTCGAATTTGGAATAAATCGCAACGCGAACT
TCGACTATCGCAATGCAAACTTCGACTATCGCAACGAATGTCCAAT
Found at i:600088 original size:135 final size:133
Alignment explanation
Indices: 599947--600247 Score: 381
Period size: 135 Copynumber: 2.2 Consensus size: 133
599937 TAAATCGTAA
* * * *
599947 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAATAAAT-CGCA-ACGCGAACTTCGA
1 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGAAT---TGCG-ATACGCCAAATTCGA
* * *
600010 CTATCGCAATGCAAACTTCGACTATCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCA
62 CTATCGAAACGCAAACTTCGACTATCGCATTGCGATAGTCCAAGTTCGCATTACGATTTATTCCA
600075 AATTCGT
127 AATTCGT
* * ** **
600082 TGCGATAGTCAAAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGACT
1 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGAATTGCGA--TACGCCAAATTCGACT
* * *
600147 ATCGAAACGCGAACTTCGACTATCGCGTTGCGATAGTCCAAGTTTGCATTACGATTTATTCCAAA
64 ATCGAAACGCAAACTTCGACTATCGCATTGCGATAGTCCAAGTTCGCATTACGATTTATTCCAAA
600212 TTCGT
129 TTCGT
*
600217 TGCGATAGTCGAAGTTTGCGTTGCGATAGTC
1 TGCGATAGTCGAAGTTCGCGTTGCGATAGTC
600248 CAAAATCGCA
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
132 2 0.01
133 2 0.01
135 139 0.97
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (133 bp):
TGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGAATTGCGATACGCCAAATTCGACTAT
CGAAACGCAAACTTCGACTATCGCATTGCGATAGTCCAAGTTCGCATTACGATTTATTCCAAATT
CGT
Found at i:600112 original size:63 final size:63
Alignment explanation
Indices: 600034--600250 Score: 231
Period size: 63 Copynumber: 3.3 Consensus size: 63
600024 ACTTCGACTA
600034 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAGT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAGT
* * *
600097 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGACTAT-CGAAACG-CGAA
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG--T-TGCGATA-GTC-AA
*
600160 CTTCGACT
61 -----AGT
* * * *
600168 ATCGCGTTGCGATAGTCCAAGTTTGCATTACGATTTATTCCAAATTCGTTGCGATAGTCGAAGT
1 -TCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAGT
* *
600232 TTGCGTTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
600251 AATCGCAACG
Statistics
Matches: 128, Mismatches: 13, Indels: 26
0.77 0.08 0.16
Matches are distributed among these distances:
63 63 0.49
64 2 0.02
65 6 0.05
66 4 0.03
69 3 0.02
70 6 0.05
71 2 0.02
72 42 0.33
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (63 bp):
TCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCAAAGT
Found at i:600238 original size:21 final size:21
Alignment explanation
Indices: 600171--600250 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
600161 TTCGACTATC
600171 GCGTTGCGATAGTCCAAGTTT
1 GCGTTGCGATAGTCCAAGTTT
* * * *
600192 GCATTACGATTTATTCCAA-ATT
1 GCGTTGCGA--TAGTCCAAGTTT
*
600214 -CGTTGCGATAGTCGAAGTTT
1 GCGTTGCGATAGTCCAAGTTT
600234 GCGTTGCGATAGTCCAA
1 GCGTTGCGATAGTCCAA
600251 AATCGCAACG
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
19 6 0.13
20 2 0.04
21 28 0.62
22 2 0.04
23 7 0.16
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (21 bp):
GCGTTGCGATAGTCCAAGTTT
Found at i:600351 original size:6 final size:6
Alignment explanation
Indices: 600340--600425 Score: 172
Period size: 6 Copynumber: 14.3 Consensus size: 6
600330 GACACGTATT
600340 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
600388 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
600426 GGCGGCGGCG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:601041 original size:21 final size:21
Alignment explanation
Indices: 601014--601096 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
601004 CGTTGCGATT
*
601014 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
601035 TTCGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
*
601054 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
601077 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAATGCGAA
601097 TATGTAAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.17
21 33 0.63
23 10 0.19
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:601075 original size:42 final size:40
Alignment explanation
Indices: 601021--601115 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 40
601011 ATTTTGGACT
* *
601021 ATCGCAACGCGAACTTCGACTATCGCAA-CGAATTTGGAATAA
1 ATCGCAATGCGAACTTCGACTATCGCAAGCGAATAT-G--TAA
*
601063 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTCGACTATCGCAA-GCGAATATGTAA
601104 ATCGCAATGCGA
1 ATCGCAATGCGA
601116 TAGTCGAAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
41 15 0.31
42 26 0.54
43 1 0.02
44 6 0.12
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
ATCGCAATGCGAACTTCGACTATCGCAAGCGAATATGTAA
Found at i:601109 original size:20 final size:20
Alignment explanation
Indices: 601060--601115 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
601050 GAATTTGGAA
601060 TAAATCGCAATGCGAACTTG
1 TAAATCGCAATGCGAACTTG
* *
601080 GACTATCGCAATGCGAA-TATG
1 TA-AATCGCAATGCGAACT-TG
601101 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
601116 TAGTCGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:601172 original size:23 final size:21
Alignment explanation
Indices: 601141--601202 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
601131 TTGCGATAGT
*
601141 CGAATTTGGAATAAATCGCAACG
1 CGAACTTGGAAT--ATCGCAACG
* *
601164 CGAACTTGGACTATCGCAATG
1 CGAACTTGGAATATCGCAACG
*
601185 CGAACTTGGACTATCGCA
1 CGAACTTGGAATATCGCA
601203 TTGCGATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 26 0.72
23 10 0.28
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
CGAACTTGGAATATCGCAACG
Found at i:601207 original size:21 final size:21
Alignment explanation
Indices: 601155--601208 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
601145 TTTGGAATAA
*
601155 ATCGCAACGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
601176 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
*
601197 ATCGCATTGCGA
1 ATCGCAATGCGA
601209 TTTACATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGGACT
Found at i:601243 original size:21 final size:21
Alignment explanation
Indices: 601217--601270 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
601207 GATTTACATA
601217 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
601238 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
601259 TTCGCGTTGCGA
1 TTCGCATTGCGA
601271 ATCTGGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:617629 original size:60 final size:60
Alignment explanation
Indices: 617502--617630 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 60
617492 AGTATAAATG
* * ** **
617502 TATAGTTTGGGATAAAATTGGAATGTTCAAAATGTTTGGGGACCAATTTAGAATGAAGAT
1 TATAGTTTGGGATAAAATTGAAATATTCAAAATGTTTAAGGACCAATTTAGAAACAAGAT
* * **
617562 CAGAGTTTGGAGATAAAATTGAAATATTCAAAA-GTTTAAGGATTAATTTA-AAACAAGAGT
1 TATAGTTTGG-GATAAAATTGAAATATTCAAAATGTTTAAGGACCAATTTAGAAACAAGA-T
617622 TATAGTTTG
1 TATAGTTTG
617631 AGGACATGTG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
59 6 0.11
60 29 0.53
61 20 0.36
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (60 bp):
TATAGTTTGGGATAAAATTGAAATATTCAAAATGTTTAAGGACCAATTTAGAAACAAGAT
Found at i:618959 original size:18 final size:17
Alignment explanation
Indices: 618907--618959 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
618897 AATATGGAAT
*
618907 TAGATTCCAATTCCTGA
1 TAGATTCCAATTCCTCA
*
618924 CAGATT-CAATTCCTTCA
1 TAGATTCCAATTCC-TCA
618941 TAGATTCCAATTCTCTCA
1 TAGATTCCAATTC-CTCA
618959 T
1 T
618960 GTGCCGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 7 0.23
17 12 0.40
18 10 0.33
19 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (17 bp):
TAGATTCCAATTCCTCA
Found at i:632862 original size:165 final size:168
Alignment explanation
Indices: 632590--632922 Score: 645
Period size: 165 Copynumber: 2.0 Consensus size: 168
632580 TTCTTTCTTT
632590 TTGGCTCCTGTACCAGAGGGTTTCAATCTCAACAGTTTCTTTAATGTACTTATCATAACATTGCA
1 TTGGCTCCTGTACCAGAGGGTTTCAATCTCAACAGTTTCTTTAATGTACTTATCATAACATTGCA
632655 CCGAATCCCTCCAAGCTTAACATCTATTTCAGCTCTAACAGGTGAGATTGGCTGAAATGCAACAG
66 CCGAATCCCTCCAAGCTTAACATCTATTTCAGCTCTAACAGGTGAGATTGGCTGAAATGCAACAG
632720 CATTAAAATAAAT-AAC-AG-CCACTGAACCAACTCAA
131 CATTAAAATAAATAAACAAGCCCACTGAACCAACTCAA
632755 TTGGCTCCTGTACCAGAGGGTTTCAATCTCAACAGTTTCTTTAATGTACTTATCATAACATTGCA
1 TTGGCTCCTGTACCAGAGGGTTTCAATCTCAACAGTTTCTTTAATGTACTTATCATAACATTGCA
632820 CCGAATCCCTCCAAGCTTAACATCTATTTCAGCTCTAACAGGTGAGATTGGCTGAAATGCAACAG
66 CCGAATCCCTCCAAGCTTAACATCTATTTCAGCTCTAACAGGTGAGATTGGCTGAAATGCAACAG
632885 CATTAAAATAAATAAACAAGCCCACTGAACCAACTCAA
131 CATTAAAATAAATAAACAAGCCCACTGAACCAACTCAA
632923 AAAATAAATA
Statistics
Matches: 165, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
165 143 0.87
166 3 0.02
167 2 0.01
168 17 0.10
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (168 bp):
TTGGCTCCTGTACCAGAGGGTTTCAATCTCAACAGTTTCTTTAATGTACTTATCATAACATTGCA
CCGAATCCCTCCAAGCTTAACATCTATTTCAGCTCTAACAGGTGAGATTGGCTGAAATGCAACAG
CATTAAAATAAATAAACAAGCCCACTGAACCAACTCAA
Found at i:639253 original size:18 final size:18
Alignment explanation
Indices: 639230--639268 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
639220 ACGGACTCAA
639230 GATGTCGAAAAACATCAG
1 GATGTCGAAAAACATCAG
639248 GATGTCGAAAAACATCAG
1 GATGTCGAAAAACATCAG
639266 GAT
1 GAT
639269 AGATATTCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (18 bp):
GATGTCGAAAAACATCAG
Found at i:640511 original size:27 final size:27
Alignment explanation
Indices: 640464--640531 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
640454 ATTCCATGGC
* * *
640464 TTAAGGATAATTTAGGTCATTTCATATT
1 TTAAGGGT-ATTTTGGTCATTTCATAAT
640492 TTAAGGGTATTTTGGTCATTTCATAAT
1 TTAAGGGTATTTTGGTCATTTCATAAT
*
640519 TCAAGGGTATTTT
1 TTAAGGGTATTTT
640532 AGTCCTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (27 bp):
TTAAGGGTATTTTGGTCATTTCATAAT
Found at i:641440 original size:24 final size:22
Alignment explanation
Indices: 641413--641462 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
641403 CAAAGACCAG
641413 TCAATGGTCTCGGCTCGGCTCGAC
1 TCAATGGT-TCGGCTCGG-TCGAC
* *
641437 TCAATGGTTTGGCTCGGTCGGC
1 TCAATGGTTCGGCTCGGTCGAC
641459 TCAA
1 TCAA
641463 ACAACTCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 8 0.33
24 8 0.33
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (22 bp):
TCAATGGTTCGGCTCGGTCGAC
Found at i:642036 original size:22 final size:22
Alignment explanation
Indices: 642008--642061 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
641998 GAGGAGCGGC
642008 TAGGGATTTTAGGTTTGGGAAT
1 TAGGGATTTTAGGTTTGGGAAT
* *
642030 TAGGGATTTCATGTTTGGGAAT
1 TAGGGATTTTAGGTTTGGGAAT
642052 TAGGGATTTT
1 TAGGGATTTT
642062 TGGGTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (22 bp):
TAGGGATTTTAGGTTTGGGAAT
Found at i:643708 original size:24 final size:24
Alignment explanation
Indices: 643681--643730 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
643671 GTAAAGAACC
*
643681 AAAATAAACTT-AAATATACCATTA
1 AAAATAAACTTCAAACA-ACCATTA
*
643705 AAAATAAAGTTCAAACAACCATTA
1 AAAATAAACTTCAAACAACCATTA
643729 AA
1 AA
643731 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTCAAACAACCATTA
Found at i:653896 original size:24 final size:24
Alignment explanation
Indices: 653869--653915 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
653859 AAGAACCAAA
*
653869 ATAAACTT-AAATATACCATTAAAC
1 ATAAACTTCAAACA-ACCATTAAAC
*
653893 ATAAAGTTCAAACAACCATTAAA
1 ATAAACTTCAAACAACCATTAAA
653916 TCAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (24 bp):
ATAAACTTCAAACAACCATTAAAC
Found at i:662403 original size:15 final size:15
Alignment explanation
Indices: 662383--662420 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
662373 CTCCAATACT
662383 TCATCATCAAAT-TCA
1 TCATCATC-AATCTCA
662398 TCATCATCAATCTCA
1 TCATCATCAATCTCA
*
662413 TGATCATC
1 TCATCATC
662421 TTGATCTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (15 bp):
TCATCATCAATCTCA
Found at i:668717 original size:27 final size:27
Alignment explanation
Indices: 668679--668730 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
668669 TATTAGATGA
668679 AACAACATTGGAAGACATAGATAGAAC
1 AACAACATTGGAAGACATAGATAGAAC
668706 AACAACATTGGAAGACATAGATAGA
1 AACAACATTGGAAGACATAGATAGA
668731 GCATCCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.15
Consensus pattern (27 bp):
AACAACATTGGAAGACATAGATAGAAC
Found at i:674044 original size:27 final size:27
Alignment explanation
Indices: 674005--674060 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
673995 AATGAACAAG
674005 TCAAGCAAGACTCAACTAACAAACGAC
1 TCAAGCAAGACTCAACTAACAAACGAC
*
674032 TCAAGC-AGAACTCAACTAACTAACGAC
1 TCAAGCAAG-ACTCAACTAACAAACGAC
674059 TC
1 TC
674061 GCTCGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.45, C:0.30, G:0.11, T:0.14
Consensus pattern (27 bp):
TCAAGCAAGACTCAACTAACAAACGAC
Found at i:677626 original size:25 final size:25
Alignment explanation
Indices: 677598--677655 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
677588 ATAAGGTTAT
677598 ATGATATGTTATATATGTGAAATGA
1 ATGATATGTTATATATGTGAAATGA
677623 ATGATATGTTATATATGTGAAATGA
1 ATGATATGTTATATATGTGAAATGA
677648 ATGATATG
1 ATGATATG
677656 AATACATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.40
Consensus pattern (25 bp):
ATGATATGTTATATATGTGAAATGA
Found at i:677977 original size:18 final size:18
Alignment explanation
Indices: 677954--678041 Score: 140
Period size: 18 Copynumber: 4.9 Consensus size: 18
677944 GAGGGTCTAC
*
677954 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGGGACATA
677972 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
677990 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
678008 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
678026 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
678042 AATTCTACGC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:690001 original size:17 final size:17
Alignment explanation
Indices: 689968--690001 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
689958 TTGAATATTT
* *
689968 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
689985 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
690002 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:691612 original size:18 final size:18
Alignment explanation
Indices: 691589--691676 Score: 140
Period size: 18 Copynumber: 4.9 Consensus size: 18
691579 GAGGGTCTAC
691589 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
691607 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
691625 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
691643 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
*
691661 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
691677 AATTCTACGC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:691846 original size:7 final size:7
Alignment explanation
Indices: 691834--691860 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
691824 GTGAAAAGGT
691834 ATATGTG
1 ATATGTG
691841 ATATGTG
1 ATATGTG
691848 ATATGTG
1 ATATGTG
691855 ATATGT
1 ATATGT
691861 ATAAGTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
ATATGTG
Found at i:695793 original size:12 final size:12
Alignment explanation
Indices: 695778--695808 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
695768 GTTATTTAAA
*
695778 CGGGTATCTGGC
1 CGGGTATCGGGC
695790 CGGGTATCGGGC
1 CGGGTATCGGGC
695802 CGGGTAT
1 CGGGTAT
695809 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.45, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:695837 original size:15 final size:15
Alignment explanation
Indices: 695819--695885 Score: 54
Period size: 15 Copynumber: 4.8 Consensus size: 15
695809 ATATATTTAA
695819 ATTAAATATATAAAT
1 ATTAAATATATAAAT
* *
695834 ATTATATATATATAT
1 ATTAAATATATAAAT
695849 ATT-AAT-T-T-AA-
1 ATTAAATATATAAAT
* *
695859 ATTAAATTTATTAAT
1 ATTAAATATATAAAT
*
695874 ATTATATATATA
1 ATTAAATATATA
695886 TATAATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
10 3 0.08
11 4 0.10
12 2 0.05
13 2 0.05
14 4 0.10
15 25 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAAATATATAAAT
Found at i:695857 original size:40 final size:39
Alignment explanation
Indices: 695806--695895 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 39
695796 TCGGGCCGGG
695806 TATATAT-ATTTAAATTAAATATATAAATATTATATATA
1 TATATATAATTTAAATTAAATATATAAATATTATATATA
* *
695844 TATATATTAATTTAAATTAAATTTATTAATATTATATATA
1 TATATA-TAATTTAAATTAAATATATAAATATTATATATA
695884 TATATAATAATT
1 TATAT-ATAATT
695896 ATTTTTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
38 6 0.13
39 1 0.02
40 39 0.83
41 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TATATATAATTTAAATTAAATATATAAATATTATATATA
Found at i:695896 original size:34 final size:34
Alignment explanation
Indices: 695806--695907 Score: 88
Period size: 40 Copynumber: 3.0 Consensus size: 34
695796 TCGGGCCGGG
* * *
695806 TATATATAT-TTA-AATTAAATATATAAATATTATA
1 TATATATATATAATAATTAAATTTATTAATA-T-TA
695840 TATATATATATTAATTTAAATTAAATTTATTAATATTA
1 TATATATATA-TAA--T-AATTAAATTTATTAATATTA
695878 TATATATATATAATAATT--ATTT-TTAATATT
1 TATATATATATAATAATTAAATTTATTAATATT
695908 TATCGGGCCG
Statistics
Matches: 59, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
31 8 0.14
32 4 0.07
34 13 0.22
35 1 0.02
36 2 0.03
37 3 0.05
38 12 0.20
39 1 0.02
40 15 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TATATATATATAATAATTAAATTTATTAATATTA
Found at i:695990 original size:30 final size:30
Alignment explanation
Indices: 695947--696022 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
695937 ACTAAACCCG
*
695947 TCCCCGT-CCCGTTTAACATAAACAGTTTT
1 TCCCCGTCCCCGTTTAACATAAACAATTTT
*
695976 TCCCCGTCCCCGTTTAGCATAAACAATTTT
1 TCCCCGTCCCCGTTTAACATAAACAATTTT
*
696006 TCCTCGTCCCCGTTTAA
1 TCCCCGTCCCCGTTTAA
696023 TTGGTTTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 7 0.17
30 35 0.83
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (30 bp):
TCCCCGTCCCCGTTTAACATAAACAATTTT
Found at i:697869 original size:60 final size:60
Alignment explanation
Indices: 697776--697892 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 60
697766 ACATCTGAAA
*
697776 ATGCTAAGACTCATCTGATGAGGCCAGATCATCCTTATGATTGATCATCCCGGAATCAAT
1 ATGCTAAGACTCATCTGATGAGGCCAGATCATCCTTATGATTGATCATCCCAGAATCAAT
* * *
697836 ATGCTAAGACTCATTTGATGAGG-CTGCATCATCCTTATGCTTGATCATCCCAGAATC
1 ATGCTAAGACTCATCTGATGAGGCCAG-ATCATCCTTATGATTGATCATCCCAGAATC
697893 GACGAGAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 2 0.04
60 50 0.96
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (60 bp):
ATGCTAAGACTCATCTGATGAGGCCAGATCATCCTTATGATTGATCATCCCAGAATCAAT
Found at i:704153 original size:70 final size:67
Alignment explanation
Indices: 704037--704174 Score: 206
Period size: 70 Copynumber: 2.0 Consensus size: 67
704027 TCAATGTACT
* *
704037 CATCGACGCTGAAACTACGTATTAATCACTTGTTGTATAGAATTGACTCTTCATGGTCTACGATG
1 CATCGACACTGAAACTACGTATTAATCACTTGTTGTATAGAATTGACTCTCCATGGTCTACGATG
704102 AG
66 AG
*
704104 CATCGACACTGAAA-TCACGTATTAATTATCACTTGTTGTATAGAATTGACTCTCCATGGTCTAT
1 CATCGACACTGAAACT-ACGTATT-A--ATCACTTGTTGTATAGAATTGACTCTCCATGGTCTAC
704168 GATGAG
62 GATGAG
704174 C
1 C
704175 CGGCCCTGAC
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
66 1 0.02
67 20 0.31
68 1 0.02
70 42 0.66
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (67 bp):
CATCGACACTGAAACTACGTATTAATCACTTGTTGTATAGAATTGACTCTCCATGGTCTACGATG
AG
Found at i:715738 original size:2 final size:2
Alignment explanation
Indices: 715731--715758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
715721 TATATCCAGA
715731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
715759 GTACAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:716785 original size:37 final size:36
Alignment explanation
Indices: 716743--716866 Score: 115
Period size: 37 Copynumber: 3.3 Consensus size: 36
716733 GAAATGTTTG
*
716743 AAACAAATTTTGCCTCG-TTAGAGACAATTTTTCTTAA
1 AAACAAATTTTGCCTCGCTT-GAGACAATTTCTC-TAA
* *
716780 AAACAAATTTTGTCTCGCTTGAGACAATTTCTCTCA
1 AAACAAATTTTGCCTCGCTTGAGACAATTTCTCTAA
*** * * *
716816 AAACAAATTTCATCTTGCTTGAGACATTTGTTCTTTAA
1 AAACAAATTTTGCCTCGCTTGAGACA-AT-TTCTCTAA
716854 AACACAAATTTTG
1 AA-ACAAATTTTG
716867 AAGTTCTTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
36 25 0.35
37 29 0.40
38 10 0.14
39 8 0.11
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGCCTCGCTTGAGACAATTTCTCTAA
Found at i:716836 original size:36 final size:37
Alignment explanation
Indices: 716763--716864 Score: 109
Period size: 36 Copynumber: 2.7 Consensus size: 37
716753 TGCCTCGTTA
* **
716763 GAGACAATTTTTCTTAAAAACAAATTTTGTCTCGCTT
1 GAGACAATTTCTCTTAAAAACAAATTTCATCTCGCTT
* *
716800 GAGACAATTTCTC-TCAAAACAAATTTCATCTTGCTT
1 GAGACAATTTCTCTTAAAAACAAATTTCATCTCGCTT
*
716836 GAGAC-ATTTGTTCTTTAAAACACAAATTT
1 GAGACAATTT-CTC-TTAAAA-ACAAATTT
716865 TGAAGTTCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 4 0.07
36 26 0.48
37 12 0.22
38 4 0.07
39 8 0.15
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (37 bp):
GAGACAATTTCTCTTAAAAACAAATTTCATCTCGCTT
Found at i:717021 original size:36 final size:35
Alignment explanation
Indices: 716900--717156 Score: 111
Period size: 36 Copynumber: 7.6 Consensus size: 35
716890 TTTATAATCT
*
716900 TTGAG-CATGTTTCTCTTGAAACAAATTGTGTCTCTC
1 TTGAGACA-GTTTCCCTTGAAACAAATT-TGTCTCTC
* **
716936 TTGAGACAGTTTCCCTTGAAATAAA---ACCATCT-
1 TTGAGACAGTTTCCCTTGAAACAAATTTGTC-TCTC
* *
716968 TTGAGATC-GTTTACCTTGAAACGAATTTTGTCTCTC
1 TTGAGA-CAGTTTCCCTTGAAAC-AAATTTGTCTCTC
**
717004 TTGAGACAGTTTCCCTTGAAA-AAA---ACCATCT-
1 TTGAGACAGTTTCCCTTGAAACAAATTTGTC-TCTC
* * * *
717035 TTGAGATCA-TTTCCCTTTAAACGAATTTTGCCTATC
1 TTGAGA-CAGTTTCCCTTGAAAC-AAATTTGTCTCTC
* *
717071 TTGAGACAGTTTCTCATGAAACACCAA------TCT-
1 TTGAGACAGTTTCCCTTGAAACA--AATTTGTCTCTC
** *
717101 TTGAGATTGTTTTCCTTGAAACAAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAA-TTTGTCTCTC
* *
717137 TTGAGACAGCTTCTCTTGAA
1 TTGAGACAGTTTCCCTTGAA
717157 TCATCATCTT
Statistics
Matches: 161, Mismatches: 32, Indels: 56
0.65 0.13 0.22
Matches are distributed among these distances:
28 2 0.01
30 18 0.11
31 20 0.12
32 24 0.15
33 8 0.05
34 2 0.01
35 12 0.07
36 72 0.45
37 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (35 bp):
TTGAGACAGTTTCCCTTGAAACAAATTTGTCTCTC
Found at i:717063 original size:67 final size:67
Alignment explanation
Indices: 716896--717156 Score: 330
Period size: 67 Copynumber: 3.9 Consensus size: 67
716886 AAAATTTATA
* *
716896 ATCTTTGAGCAT-GTTTCTCTTGAAACAAATTGTGTCTCTCTTGAGACAGTTTCCCTTGAAATAA
1 ATCTTTGAG-ATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AA
716960 AACC
64 AACC
* *
716964 ATCTTTGAGATCGTTTACCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
1 ATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
717029 CC
66 CC
* * * * * * * *
717031 ATCTTTGAGATCATTTCCCTTTAAACGAATTTTGCCTATCTTGAGACAGTTTCTCATG--AAACA
1 ATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
717094 CC
66 CC
* * * *
717096 AATCTTTGAGATTGTTTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAGCTTCTCTTGAA
1 -ATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAA
717157 TCATCATCTT
Statistics
Matches: 168, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
65 6 0.04
66 49 0.29
67 59 0.35
68 54 0.32
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (67 bp):
ATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAA
CC
Found at i:717242 original size:22 final size:22
Alignment explanation
Indices: 717215--717260 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
717205 CCATCCATCC
717215 TCATCAAGTAGGAACCGTGTCA
1 TCATCAAGTAGGAACCGTGTCA
*
717237 TCATCAAGTAGGAACTGTGTCA
1 TCATCAAGTAGGAACCGTGTCA
717259 TC
1 TC
717261 CCCGACCATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TCATCAAGTAGGAACCGTGTCA
Found at i:717338 original size:43 final size:46
Alignment explanation
Indices: 717265--717392 Score: 140
Period size: 47 Copynumber: 2.8 Consensus size: 46
717255 GTCATCCCCG
**
717265 ACCATACC-TCCTCATCACGTAGGAGTCGTGTCA-CCCCT-AGATA
1 ACCATACCATCCTCATCACGTAGGAACCGTGTCATCCCCTAAGATA
* * *
717308 ACCA-ACCATCCTCATCACGTAGGAACCGTGTTATCATCCTAAAGATG
1 ACCATACCATCCTCATCACGTAGGAACCGTGTCATC-CCCT-AAGATA
* *
717355 A-CATGCCATCCTCATCACGTAGAAACCGTGTCATCCCC
1 ACCATACCATCCTCATCACGTAGGAACCGTGTCATCCCC
717393 GACTAGATCT
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
42 3 0.04
43 26 0.37
44 1 0.01
45 3 0.04
46 4 0.06
47 33 0.47
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (46 bp):
ACCATACCATCCTCATCACGTAGGAACCGTGTCATCCCCTAAGATA
Found at i:720056 original size:20 final size:20
Alignment explanation
Indices: 720031--720072 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
720021 ACATTTTAGG
*
720031 TTGTAACTAAGAATCGATAC
1 TTGTAACCAAGAATCGATAC
*
720051 TTGTAACCAAGGATCGATAC
1 TTGTAACCAAGAATCGATAC
720071 TT
1 TT
720073 TTCGTGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
TTGTAACCAAGAATCGATAC
Found at i:724808 original size:20 final size:20
Alignment explanation
Indices: 724783--724825 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
724773 TCTAAGAGCC
*
724783 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
724803 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
724823 CAT
1 CAT
724826 GTAAGGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:732412 original size:8 final size:9
Alignment explanation
Indices: 732391--732430 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
732381 AGGAGGGAAA
732391 TTTTTTACC
1 TTTTTTACC
732400 TTTTTTACC
1 TTTTTTACC
**
732409 TTTTTTATT
1 TTTTTTACC
732418 TTTTTTA-C
1 TTTTTTACC
732426 TTTTT
1 TTTTT
732431 CTTTAGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTACC
Found at i:735099 original size:20 final size:20
Alignment explanation
Indices: 735074--735116 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
735064 TCTAATAGCC
**
735074 CATTTAGGATTATATAGATG
1 CATTTAGGAGCATATAGATG
*
735094 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
735114 CAT
1 CAT
735117 GTGGTAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:738915 original size:24 final size:23
Alignment explanation
Indices: 738888--738964 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 23
738878 GTTCAGAGAC
**
738888 TATCGATACTACTTTGTGTAGTAG
1 TATCGATACTAC-TTGTAAAGTAG
**
738912 TATCGATA-T-C--GTCCAGTGAG
1 TATCGATACTACTTGTAAAGT-AG
738932 TATCGATACTACTATGTAAAGTAG
1 TATCGATACTACT-TGTAAAGTAG
738956 TATCGATAC
1 TATCGATAC
738965 CTAACATGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
19 5 0.12
20 10 0.23
21 1 0.02
22 2 0.05
23 1 0.02
24 19 0.44
25 5 0.12
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (23 bp):
TATCGATACTACTTGTAAAGTAG
Found at i:741741 original size:95 final size:96
Alignment explanation
Indices: 741577--741769 Score: 336
Period size: 95 Copynumber: 2.0 Consensus size: 96
741567 AGGAATGACT
741577 GAGAGTTTTGAGTTGGGGTTTTTGGCAAAATGATGACATTTTAGGGTTAAATAGCCTAAACCTGT
1 GAGAGTTTTGAGTTGGGGTTTTTGGCAAAATGATGACATTTTAGGGTTAAATAGCCTAAACCTGT
* *
741642 CGAGTAGTATTGGTACTCCTCGAGGAGTATC
66 CGAGTAGTATCGATACTCCTCGAGGAGTATC
*
741673 GAGAGTTTTGAGTTGGGG-TTTTGGCAAAATGATGATATTTTAGGGTTAAATAGCCTAAAACC-G
1 GAGAGTTTTGAGTTGGGGTTTTTGGCAAAATGATGACATTTTAGGGTTAAATAGCCT-AAACCTG
741736 TCGAGTAGTATCGATACTCCTCGAGGAGTATC
65 TCGAGTAGTATCGATACTCCTCGAGGAGTATC
741768 GA
1 GA
741770 TACTTCAAGG
Statistics
Matches: 93, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
95 70 0.75
96 23 0.25
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32
Consensus pattern (96 bp):
GAGAGTTTTGAGTTGGGGTTTTTGGCAAAATGATGACATTTTAGGGTTAAATAGCCTAAACCTGT
CGAGTAGTATCGATACTCCTCGAGGAGTATC
Found at i:741765 original size:20 final size:20
Alignment explanation
Indices: 741736--741773 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
741726 CCTAAAACCG
*
741736 TCGAGTAGTATCGATACTCC
1 TCGAGGAGTATCGATACTCC
741756 TCGAGGAGTATCGATACT
1 TCGAGGAGTATCGATACT
741774 TCAAGGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
TCGAGGAGTATCGATACTCC
Found at i:747718 original size:20 final size:21
Alignment explanation
Indices: 747653--747718 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 21
747643 ATTGTTCAGA
*
747653 GAGTATCGATACTAATTTATGTT
1 GAGTATCGATACTAA-CTATG-T
** *
747676 GTAGTATCGATACTGTCCA-GT
1 G-AGTATCGATACTAACTATGT
747697 GAGTATCGATACT-ACTATGT
1 GAGTATCGATACTAACTATGT
747717 GA
1 GA
747719 ATTAGTATCA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 2 0.06
22 1 0.03
23 2 0.06
24 12 0.34
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (21 bp):
GAGTATCGATACTAACTATGT
Found at i:750920 original size:20 final size:21
Alignment explanation
Indices: 750892--750934 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
750882 TAATCATAAT
750892 AATAATATAATAT-ATATATA
1 AATAATATAATATAATATATA
* *
750912 AATATTATAATGTAATATATA
1 AATAATATAATATAATATATA
750933 AA
1 AA
750935 AAACGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AATAATATAATATAATATATA
Found at i:752016 original size:2 final size:2
Alignment explanation
Indices: 752011--752070 Score: 51
Period size: 2 Copynumber: 32.5 Consensus size: 2
752001 AAAAGAATAA
*
752011 AT AT AT AA AT AT AT -T AT AT AT AT AT AT AT GA- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
*
752051 AG A- AT AT AT -T AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
752071 ATAACGTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
1 6 0.12
2 41 0.85
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:752033 original size:17 final size:17
Alignment explanation
Indices: 752011--752071 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
752001 AAAAGAATAA
752011 ATATATAAATATATTAT
1 ATATATAAATATATTAT
* *
752028 ATATATATATATGAATAT
1 ATATATAAATAT-ATTAT
752046 AT-TATAGAATATATTAT
1 ATATATA-AATATATTAT
752063 ATAATATAA
1 AT-ATATAA
752072 TAACGTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 21 0.58
18 11 0.31
19 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATATAAATATATTAT
Found at i:752044 original size:23 final size:23
Alignment explanation
Indices: 752004--752070 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
751994 GAGAGAAAAA
*
752004 AGAATAAATATATAAATATATTAT
1 AGAATATATATAT-AATATATTAT
*
752028 A-TATATATATATGAATATATTAT
1 AGAATATATATAT-AATATATTAT
752051 AGAATATATTATATAATATA
1 AGAATATA-TATATAATATA
752071 ATAACGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 20 0.54
24 12 0.32
25 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
AGAATATATATATAATATATTAT
Found at i:752047 original size:12 final size:12
Alignment explanation
Indices: 752005--752070 Score: 59
Period size: 12 Copynumber: 5.6 Consensus size: 12
751995 AGAGAAAAAA
*
752005 GAATAAATATAT
1 GAATATATATAT
*
752017 AAATATAT-TAT
1 GAATATATATAT
752028 -ATATATATATAT
1 GA-ATATATATAT
752040 GAATATAT-TAT
1 GAATATATATAT
752051 AGAATATATTATAT
1 -GAATATA-TATAT
752065 -AATATA
1 GAATATA
752071 ATAACGTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
10 1 0.02
11 12 0.26
12 28 0.61
13 2 0.04
14 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (12 bp):
GAATATATATAT
Found at i:752057 original size:35 final size:34
Alignment explanation
Indices: 752005--752070 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
751995 AGAGAAAAAA
752005 GAATAAATATATAAATATATTATATATATATATAT
1 GAATAAATATATAAATATATTATATA-ATATATAT
*
752040 GAATATAT-TATAGAATATATTATATAATATA
1 GAATAAATATATA-AATATATTATATAATATA
752071 ATAACGTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 9 0.31
35 20 0.69
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (34 bp):
GAATAAATATATAAATATATTATATAATATATAT
Found at i:764445 original size:20 final size:19
Alignment explanation
Indices: 764403--764445 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
764393 ATAAAGAAAC
764403 AAAAATAAATAAAAATATGA
1 AAAAATAAATAAAAATA-GA
764423 AAAAATAAATCAATAAATA-A
1 AAAAATAAAT-AA-AAATAGA
764443 AAA
1 AAA
764446 CAAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 14 0.67
21 2 0.10
22 5 0.24
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAATAAATAAAAATAGA
Found at i:764453 original size:24 final size:22
Alignment explanation
Indices: 764389--764455 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 22
764379 ATAACATAAG
764389 ATAAATAAAGAAACAAAAATAAATA
1 ATAAAT-AA-AAAC-AAAATAAATA
**
764414 A-AAATATGAA-AAAATAAATCA
1 ATAAATAAAAACAAAATAAAT-A
764435 ATAAATAAAAACAAGAATAAA
1 ATAAATAAAAACAA-AATAAA
764456 ATAAGATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
20 9 0.26
21 2 0.06
22 9 0.26
23 3 0.09
24 10 0.29
25 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (22 bp):
ATAAATAAAAACAAAATAAATA
Found at i:764500 original size:2 final size:2
Alignment explanation
Indices: 764493--764518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
764483 AAAGAAGATA
764493 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
764519 GTTCATTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:764723 original size:2 final size:2
Alignment explanation
Indices: 764718--764763 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
764708 AGTAATCATA
*
764718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT GT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
764757 AT AT AT A
1 AT AT AT A
764764 AAAAACGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:765858 original size:2 final size:2
Alignment explanation
Indices: 765851--765898 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
765841 AAATATGTAA
765851 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT GA- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
765891 AT A- AT AT A
1 AT AT AT AT A
765899 ATAACATTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 36 0.88
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:767404 original size:19 final size:18
Alignment explanation
Indices: 767364--767404 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
767354 GTACGGTAGC
**
767364 ACATAAAACAAAGTTTAA
1 ACATAAAACAAAGTAGAA
767382 ACATAAAACAAAGTAAGAA
1 ACATAAAACAAAGT-AGAA
767401 ACAT
1 ACAT
767405 TTAATCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.17
Consensus pattern (18 bp):
ACATAAAACAAAGTAGAA
Found at i:775222 original size:9 final size:8
Alignment explanation
Indices: 775202--775350 Score: 68
Period size: 8 Copynumber: 17.5 Consensus size: 8
775192 AATGCTAAAT
775202 ATAAAAATA
1 ATAAAAA-A
775211 ATAAACAAA
1 ATAAA-AAA
775220 ATAAGAAAA
1 ATAA-AAAA
775229 ATAAAAAA
1 ATAAAAAA
775237 ATAAAATAA
1 ATAAAA-AA
* *
775246 ATAATATA
1 ATAAAAAA
**
775254 AGGAAAAA
1 ATAAAAAA
*
775262 ATAAAATA
1 ATAAAAAA
*
775270 GTAAAATAA
1 ATAAAA-AA
775279 ATAAACATAAA
1 AT-AA-A-AAA
775290 ATAAAACAA
1 ATAAAA-AA
**
775299 A-AAAATG
1 ATAAAAAA
*
775306 ATTAAAAA
1 ATAAAAAA
* *
775314 ATAAGAAT
1 ATAAAAAA
775322 A-AAAAAA
1 ATAAAAAA
*
775329 AGAAAAAGA
1 ATAAAAA-A
*
775338 AAACAAAAA
1 ATA-AAAAA
775347 ATAA
1 ATAA
775351 GATAAGAATA
Statistics
Matches: 104, Mismatches: 24, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.06
8 45 0.43
9 36 0.35
10 11 0.11
11 5 0.05
12 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:775228 original size:8 final size:9
Alignment explanation
Indices: 775202--775249 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
775192 AATGCTAAAT
*
775202 ATAAAAATA
1 ATAAAAAAA
*
775211 ATAAACAAA
1 ATAAAAAAA
*
775220 ATAAGAAAA
1 ATAAAAAAA
775229 AT-AAAAAA
1 ATAAAAAAA
*
775237 ATAAAATAA
1 ATAAAAAAA
775246 ATAA
1 ATAA
775250 TATAAGGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:775231 original size:29 final size:31
Alignment explanation
Indices: 775198--775267 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
775188 AGAAAATGCT
775198 AAATATAAAAAT-AATAAACAAAATAA-GAA
1 AAATATAAAAATAAATAAACAAAATAAGGAA
* * *
775227 AAATAAAAAAATAAAATAAATAATATAAGGAA
1 AAATATAAAAAT-AAATAAACAAAATAAGGAA
775259 AAA-ATAAAA
1 AAATATAAAA
775268 TAGTAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 11 0.32
31 17 0.50
32 6 0.18
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (31 bp):
AAATATAAAAATAAATAAACAAAATAAGGAA
Found at i:775239 original size:17 final size:18
Alignment explanation
Indices: 775205--775249 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
775195 GCTAAATATA
775205 AAAAT-AATAAACAAAAT
1 AAAATAAATAAACAAAAT
775222 AAGAA-AAATAAA-AAAAT
1 AA-AATAAATAAACAAAAT
775239 AAAATAAATAA
1 AAAATAAATAA
775250 TATAAGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 15 0.60
18 8 0.32
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAATAAACAAAAT
Found at i:775244 original size:13 final size:13
Alignment explanation
Indices: 775226--775328 Score: 63
Period size: 13 Copynumber: 7.9 Consensus size: 13
775216 CAAAATAAGA
775226 AAAATAAAAAAAT
1 AAAATAAAAAAAT
*
775239 AAAAT-AAATAAT
1 AAAATAAAAAAAT
* **
775251 ATAAGGAAAAAAT
1 AAAATAAAAAAAT
**
775264 AAAATAGTAAAAT
1 AAAATAAAAAAAT
*
775277 -AAAT--AAACAT
1 AAAATAAAAAAAT
775287 AAAATAAAACAAA-
1 AAAATAAAA-AAAT
775300 AAAATGATTAAAAAAT
1 AAAAT-A--AAAAAAT
775316 AAGAATAAAAAAA
1 AA-AATAAAAAAA
775329 AGAAAAAGAA
Statistics
Matches: 68, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
10 4 0.06
11 4 0.06
12 13 0.19
13 26 0.38
14 9 0.13
15 3 0.04
16 6 0.09
17 3 0.04
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:775352 original size:15 final size:16
Alignment explanation
Indices: 775309--775355 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
775299 AAAAATGATT
775309 AAAAAATAAGAATAAAA
1 AAAAAATAAG-ATAAAA
* *
775326 AAAAGAAAAAGA-AAAC
1 AAAA-AATAAGATAAAA
775342 AAAAAATAAGATAA
1 AAAAAATAAGATAA
775356 GAATAAGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.24
16 9 0.36
17 5 0.20
18 5 0.20
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.09
Consensus pattern (16 bp):
AAAAAATAAGATAAAA
Found at i:775588 original size:3 final size:3
Alignment explanation
Indices: 775582--775628 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
775572 AATGATGATG
775582 ATA ATA ATA ATA ATA ATA ATA TATA A-A TATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA
775628 A
1 A
775629 AAACAAAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.02
3 36 0.88
4 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:775613 original size:22 final size:21
Alignment explanation
Indices: 775588--775629 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
775578 GATGATAATA
775588 ATAATAATAATAATATATAAAT
1 ATAATAATAATAATA-ATAAAT
775610 ATAATAATAATAATAATAAA
1 ATAATAATAATAATAATAAA
775630 AACAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAATAATAATAATAAAT
Found at i:777607 original size:60 final size:61
Alignment explanation
Indices: 777521--777684 Score: 181
Period size: 65 Copynumber: 2.7 Consensus size: 61
777511 GAAGTTGAGC
* * * * *
777521 TTTGAATTGGAT-TCCTTCGTTGTGAAGTTGAAATCCAA-GGGCT-GTTTCACCAAATTGGT
1 TTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATGAG-TAGTTTCACCAAATTGGA
* * *
777580 TTTGAGTTGGATATCCTTTATGGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCATCAAATTGGA
1 TTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAA---TGAGT-AGTTTCACCAAATTGGA
*
777645 TTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
1 TTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAAT
777685 CTCGAGTAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
59 11 0.12
60 23 0.26
62 1 0.01
63 1 0.01
64 2 0.02
65 50 0.57
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (61 bp):
TTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATGAGTAGTTTCACCAAATTGGA
Found at i:777652 original size:65 final size:65
Alignment explanation
Indices: 777564--777693 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 65
777554 TCCAAGGGCT
* * * *
777564 GTTTCACCAAATTGGTTTTGAGTTGGATATCCTTTATGGTGAAGTTGAAATCCAATCTTGAGTAA
1 GTTTCACCAAATTGGATTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTCGAGTAA
* *
777629 GTTTCATCAAATTGGATTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTCGAGTAA
1 GTTTCACCAAATTGGATTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTCGAGTAA
777694 ATTGTGTCGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (65 bp):
GTTTCACCAAATTGGATTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTCGAGTAA
Found at i:777782 original size:64 final size:64
Alignment explanation
Indices: 777707--778001 Score: 423
Period size: 64 Copynumber: 4.6 Consensus size: 64
777697 GTGTCGCTTC
* *
777707 GAGTCCAATATCCTTCGCTGTGAATTTGAAATTAACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * *
777771 GAGTCCAATATCCTTCGCTGAGAAGTTGAAATTAACTCTGAATGAAACT-GAGAAGTTATTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGA-AAGTTGTTTGTT
* *
777835 GAGTCTAAAATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
** * * * * *
777899 GAACCCAATATCATTTC-TTGTGAAGTTAAAATTGACTATAAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATC-CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
777963 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
778002 AAAAGCTGCA
Statistics
Matches: 204, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
63 5 0.02
64 194 0.95
65 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:787855 original size:22 final size:22
Alignment explanation
Indices: 787829--787885 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
787819 TTGGTGCAGA
*
787829 GGGAATCGATACCCACTTGAAG
1 GGGAATCGATACCCACCTGAAG
* * * *
787851 GGGAACCGATTCCCCCCTGTAG
1 GGGAATCGATACCCACCTGAAG
*
787873 GGGAATTGATACC
1 GGGAATCGATACC
787886 TCTGGAGGTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCACCTGAAG
Found at i:793705 original size:11 final size:11
Alignment explanation
Indices: 793689--793763 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
793679 ATGGTAAAAT
793689 AAATAAACAAA
1 AAATAAACAAA
793700 AAATAAAACAAAA
1 AAAT-AAAC-AAA
* *
793713 AAATGAATAAA
1 AAATAAACAAA
*
793724 AAATAAAAATAA
1 AAATAAACA-AA
*
793736 AAAGAAA-AGAA
1 AAATAAACA-AA
*
793747 AAAAAAACAAA
1 AAATAAACAAA
793758 AAATAA
1 AAATAA
793764 GATAATAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
11 30 0.58
12 15 0.29
13 7 0.13
ACGTcount: A:0.83, C:0.04, G:0.04, T:0.09
Consensus pattern (11 bp):
AAATAAACAAA
Found at i:793723 original size:17 final size:17
Alignment explanation
Indices: 793701--793733 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
793691 ATAAACAAAA
793701 AATAAAACAA-AAAAATG
1 AATAAAA-AATAAAAATG
793718 AATAAAAAATAAAAAT
1 AATAAAAAATAAAAAT
793734 AAAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (17 bp):
AATAAAAAATAAAAATG
Found at i:793724 original size:24 final size:22
Alignment explanation
Indices: 793697--793760 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 22
793687 ATAAATAAAC
793697 AAAAAATAAAACAAAAAAATGAA
1 AAAAAATAAAACAAAAAAA-GAA
*
793720 TAAAAAATAAAA-ATAAAAAGAA
1 -AAAAAATAAAACAAAAAAAGAA
*
793742 AAGAAAAAAAAACAAAAAA
1 AA-AAAATAAAACAAAAAA
793761 TAAGATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 11 0.31
23 11 0.31
24 11 0.31
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (22 bp):
AAAAAATAAAACAAAAAAAGAA
Found at i:793765 original size:25 final size:24
Alignment explanation
Indices: 793697--793774 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
793687 ATAAATAAAC
*
793697 AAAAAATAAAACAAAAAAATG--AAT
1 AAAAAATAAAA-AAAAAAA-GAAAAG
*
793721 AAAAAATAAAAATAAAAAGAAAAG
1 AAAAAATAAAAAAAAAAAGAAAAG
* *
793745 AAAAAA-AAACAAAAAATAAGATAAT
1 AAAAAATAAA-AAAAAA-AAGAAAAG
793770 AAAAA
1 AAAAA
793775 TATATATACA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 9 0.20
24 24 0.53
25 11 0.24
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (24 bp):
AAAAAATAAAAAAAAAAAGAAAAG
Found at i:793773 original size:21 final size:21
Alignment explanation
Indices: 793700--793774 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
793690 AATAAACAAA
* *
793700 AAATAAAACAAAAAAATGAATAAA
1 AAATAAAA-ACAAAAA-GAA-AAG
*
793724 AAATAAAAATAAAAAGAAAAG
1 AAATAAAAACAAAAAGAAAAG
* *
793745 AAAAAAAAACAAAAA-ATAAG
1 AAATAAAAACAAAAAGAAAAG
793765 ATAATAAAAA
1 A-AATAAAAA
793775 TATATATACA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.11
21 22 0.50
22 3 0.07
23 6 0.14
24 8 0.18
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.11
Consensus pattern (21 bp):
AAATAAAAACAAAAAGAAAAG
Found at i:793979 original size:3 final size:3
Alignment explanation
Indices: 793967--794031 Score: 87
Period size: 3 Copynumber: 21.3 Consensus size: 3
793957 ATAAAAAAAC
* *
793967 ATA ATG ATA ATA ATA ATA ATA ATA ATA A-A TATA TACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA
794013 ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
794032 ATACAAAAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.02
3 51 0.91
4 4 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:797810 original size:38 final size:38
Alignment explanation
Indices: 797768--797881 Score: 219
Period size: 38 Copynumber: 3.0 Consensus size: 38
797758 ACAGTACTGA
*
797768 TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATTAGT
1 TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATCAGT
797806 TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATCAGT
1 TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATCAGT
797844 TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATCAGT
1 TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATCAGT
797882 ATCGATACTG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 75 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (38 bp):
TACTTCAAGGCAAAACTAGTTTGAATTCGAGGATCAGT
Found at i:798632 original size:23 final size:23
Alignment explanation
Indices: 798602--798646 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
798592 GTCGAGGGTT
*
798602 CTATATGGTCATTCAGTACAAAA
1 CTATATGGTCATTCAGGACAAAA
*
798625 CTATATGGTCTTTCAGGACAAA
1 CTATATGGTCATTCAGGACAAA
798647 TATGTGGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (23 bp):
CTATATGGTCATTCAGGACAAAA
Found at i:811491 original size:19 final size:18
Alignment explanation
Indices: 811463--811498 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
811453 TGGAGGGGCA
811463 TTAAGGTTTAAGTAGAAT
1 TTAAGGTTTAAGTAGAAT
811481 TTAATGGTTTAAGTAGAA
1 TTAA-GGTTTAAGTAGAA
811499 AAGTCTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (18 bp):
TTAAGGTTTAAGTAGAAT
Found at i:812400 original size:18 final size:17
Alignment explanation
Indices: 812361--812401 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
812351 GAATTCCAGA
812361 ATACCAAAATGGTAACG
1 ATACCAAAATGGTAACG
* *
812378 GTACCAAAATGGGTATCG
1 ATACCAAAAT-GGTAACG
812396 ATACCA
1 ATACCA
812402 TAAAAGGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (17 bp):
ATACCAAAATGGTAACG
Found at i:813011 original size:23 final size:23
Alignment explanation
Indices: 812981--813062 Score: 146
Period size: 23 Copynumber: 3.6 Consensus size: 23
812971 GTCGAGGGTT
812981 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
813004 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
813027 CTATGTGGTCCTTCGGGAAAAAA
1 CTATGTGGTCCTTCGGGACAAAA
*
813050 CTATATGGTCCTT
1 CTATGTGGTCCTT
813063 AGTTACAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:813071 original size:46 final size:45
Alignment explanation
Indices: 812981--813086 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 45
812971 GTCGAGGGTT
* * *
812981 CTATGTGGTCCTTCGGGACAAAACTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGGGAC-AAA
**
813027 CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGTTACAAA
1 CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGGGACAAA
813072 -TATGTGG-CACTTCGG
1 CTATGTGGTC-CTTCGG
813087 TGCAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 13 0.24
45 3 0.06
46 37 0.69
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (45 bp):
CTATGTGGTCCTTCGGGAAAAAACTATATGGTCCTTAGGGACAAA
Found at i:813869 original size:20 final size:21
Alignment explanation
Indices: 813829--813877 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
813819 ATTCTCTTCA
*
813829 TGAAAAGATTAAATCCTTTCG
1 TGAAAAGGTTAAATCCTTTCG
*
813850 TGAAAAGGTTAACT-CTTTCG
1 TGAAAAGGTTAAATCCTTTCG
813870 TGAAAAGG
1 TGAAAAGG
813878 ATAAGTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (21 bp):
TGAAAAGGTTAAATCCTTTCG
Found at i:814312 original size:19 final size:19
Alignment explanation
Indices: 814290--814327 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
814280 TTATTTTATT
814290 ATTA-TTATTTTATTTAGAA
1 ATTAGTTATTTTA-TTAGAA
814309 ATTAGTTATTTTATTAGAA
1 ATTAGTTATTTTATTAGAA
814328 CACTTGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTAGTTATTTTATTAGAA
Found at i:818112 original size:20 final size:21
Alignment explanation
Indices: 818067--818112 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
818057 AATTTATTTA
*
818067 TTTTA-CTATTTTCTTTTTCT
1 TTTTATCTATTTTATTTTTCT
**
818087 AGTTATCTA-TTTATTTTTCT
1 TTTTATCTATTTTATTTTTCT
818107 TTTTAT
1 TTTTAT
818113 TTTTAGGTAC
Statistics
Matches: 20, Mismatches: 5, Indels: 2
0.74 0.19 0.07
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTATCTATTTTATTTTTCT
Found at i:818672 original size:19 final size:20
Alignment explanation
Indices: 818650--818689 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
818640 ATAGAGAGAA
818650 ACACAG-AAAAAGGGGGAGG
1 ACACAGAAAAAAGGGGGAGG
818669 ACACAGAAAAAAGGGGGAGG
1 ACACAGAAAAAAGGGGGAGG
818689 A
1 A
818690 AAAACAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.40, T:0.00
Consensus pattern (20 bp):
ACACAGAAAAAAGGGGGAGG
Found at i:818698 original size:20 final size:20
Alignment explanation
Indices: 818656--818700 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
818646 AGAAACACAG
* * *
818656 AAAAAGGGGGAGGACACAGA
1 AAAAAGGGGGAGGAAAAACA
818676 AAAAAGGGGGAGGAAAAACA
1 AAAAAGGGGGAGGAAAAACA
818696 AAAAA
1 AAAAA
818701 AATGAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.07, G:0.33, T:0.00
Consensus pattern (20 bp):
AAAAAGGGGGAGGAAAAACA
Found at i:818717 original size:17 final size:17
Alignment explanation
Indices: 818688--818734 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
818678 AAAGGGGGAG
*
818688 GAAAAACAA-AAAAAAT
1 GAAAAAAAATAAAAAAT
818704 GAAAAAAAATAAAAAAT
1 GAAAAAAAATAAAAAAT
818721 GAAAAAAATATAAA
1 GAAAAAAA-ATAAA
818735 GGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 8 0.29
17 15 0.54
18 5 0.18
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.11
Consensus pattern (17 bp):
GAAAAAAAATAAAAAAT
Found at i:818739 original size:15 final size:16
Alignment explanation
Indices: 818686--818744 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
818676 AAAAAGGGGG
818686 AGGAAAAACAA-AAAAA
1 AGGAAAAA-AATAAAAA
*
818702 ATGAAAAAAAATAAAAA
1 A-GGAAAAAAATAAAAA
* *
818719 ATGAAAAAAAT-ATAA
1 AGGAAAAAAATAAAAA
*
818734 AGGAAATAAAT
1 AGGAAAAAAAT
818745 GCTTGAATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.34
16 11 0.31
17 12 0.34
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (16 bp):
AGGAAAAAAATAAAAA
Found at i:819629 original size:19 final size:19
Alignment explanation
Indices: 819605--819649 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
819595 TTTGAAGTTA
819605 TACTTTTCTTTCATCT-TTT
1 TACTTTTCTTTCAT-TATTT
819624 TACTTTTCTTTCATTATTT
1 TACTTTTCTTTCATTATTT
819643 T-CTTTTC
1 TACTTTTC
819650 ACAATGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (19 bp):
TACTTTTCTTTCATTATTT
Found at i:821624 original size:39 final size:38
Alignment explanation
Indices: 821575--821653 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
821565 ACCTTTTAGA
*
821575 TTTACGATTTTTAGTTTGATATT-TTTTATTAATTTTTTAT
1 TTTACGATTTTTAGTTT-A-ATTATTTTATT-ATTATTTAT
821615 TTTA-GATTTTTAGTTTAATTATTTTATTATTATTTAT
1 TTTACGATTTTTAGTTTAATTATTTTATTATTATTTAT
821652 TT
1 TT
821654 AATAATTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 13 0.35
38 8 0.22
39 12 0.32
40 4 0.11
ACGTcount: A:0.24, C:0.01, G:0.06, T:0.68
Consensus pattern (38 bp):
TTTACGATTTTTAGTTTAATTATTTTATTATTATTTAT
Found at i:821625 original size:26 final size:26
Alignment explanation
Indices: 821582--821642 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
821572 AGATTTACGA
* *
821582 TTTTTAGTTTGATATTTT-TTATTAAT
1 TTTTTATTTTGATATTTTAGT-TTAAT
821608 TTTTTATTTTAGAT-TTTTAGTTTAAT
1 TTTTTATTTT-GATATTTTAGTTTAAT
821634 TATTTTATT
1 T-TTTTATT
821643 ATTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (26 bp):
TTTTTATTTTGATATTTTAGTTTAAT
Found at i:821651 original size:15 final size:16
Alignment explanation
Indices: 821633--821673 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
821623 TTTAGTTTAA
821633 TTATTTTATTATTA-T
1 TTATTTTATTATTAGT
* *
821648 TTATTTAATAATTAGT
1 TTATTTTATTATTAGT
821664 TT-TTTTATTA
1 TTATTTTATTA
821674 ACTATTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTATTTTATTATTAGT
Found at i:826022 original size:20 final size:22
Alignment explanation
Indices: 825997--826051 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
825987 TAATGTAGGT
825997 ATCGATGCACTCT-AC-AGTGC
1 ATCGATGCACTCTAACGAGTGC
*
826017 ATCGATGCATCCTTTAACGAGTGC
1 ATCGATGCA--CTCTAACGAGTGC
826041 ATCGATGCACT
1 ATCGATGCACT
826052 ACTTATGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.30
22 5 0.17
23 2 0.07
24 14 0.47
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.27
Consensus pattern (22 bp):
ATCGATGCACTCTAACGAGTGC
Found at i:833236 original size:52 final size:52
Alignment explanation
Indices: 833158--833261 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
833148 ATTATAATAT
* *
833158 CCTTGTAATTAGTTTTAATCCCCCAACTCTAGGCTAGTTTCTTATTTCTGTG
1 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
833210 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
1 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
833262 TGCCCAATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.42
Consensus pattern (52 bp):
CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
Found at i:834117 original size:52 final size:52
Alignment explanation
Indices: 834055--834154 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
834045 TGGGCAAATA
834055 GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATGCATG
1 GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATGCATG
* * *
834107 GAAATAGGAAACTAGCCTAGAGTTGGGGGATTGCAACTAATTACAATG
1 GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATG
834155 ATGTTATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (52 bp):
GAAATAGGAAACTAGCCTAGAGTTGAGGGATTACAACTAATTAAAATGCATG
Found at i:837462 original size:9 final size:9
Alignment explanation
Indices: 837452--837484 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
837442 TTCCATAAAT
*
837452 CACATATAT
1 CACATATAC
837461 CACATATAC
1 CACATATAC
837470 CACATATAC
1 CACATATAC
837479 CACATA
1 CACATA
837485 ACATAATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.24
Consensus pattern (9 bp):
CACATATAC
Found at i:840345 original size:12 final size:12
Alignment explanation
Indices: 840328--840352 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
840318 ATGCAAACCC
840328 TTATCATATTCA
1 TTATCATATTCA
840340 TTATCATATTCA
1 TTATCATATTCA
840352 T
1 T
840353 ACTCTTTCTT
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATCATATTCA
Found at i:841839 original size:32 final size:30
Alignment explanation
Indices: 841758--841851 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 30
841748 CCGAAGGACC
* *
841758 ACTATCCATATGTTCCGAAGAACATAGGTA
1 ACTATCCATATGTCCCGAAGGACATAGGTA
* * *
841788 ACTGTACATATGTCTCGAAGGACATAGGTA
1 ACTATCCATATGTCCCGAAGGACATAGGTA
841818 ATCCTATCCATATGTCCCGAAGGACATAGGTA
1 A--CTATCCATATGTCCCGAAGGACATAGGTA
841850 AC
1 AC
841852 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 27 0.50
32 27 0.50
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (30 bp):
ACTATCCATATGTCCCGAAGGACATAGGTA
Found at i:843913 original size:64 final size:64
Alignment explanation
Indices: 843839--843967 Score: 249
Period size: 64 Copynumber: 2.0 Consensus size: 64
843829 CTTCTCCAAT
843839 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
1 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
*
843903 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTTTATTCATTCTTCACTCAGG
1 TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
843967 T
1 T
843968 GACACTAGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.36
Consensus pattern (64 bp):
TCCTCATTGAGTCTGGGTTCACAAACTCTCATGCAGACACTTCTCTATTCATTCTTCACTCAGG
Found at i:848642 original size:24 final size:24
Alignment explanation
Indices: 848610--848684 Score: 118
Period size: 24 Copynumber: 3.2 Consensus size: 24
848600 TTATGAACGC
*
848610 TAAACGAACATATTCCTGAACATA
1 TAAACGAACATGTTCCTGAACATA
848634 TAAACGAACATGTTCCTGAACATA
1 TAAACGAACATGTTCCTGAACATA
848658 TAAACGAACATGTTCGC-GAACA-A
1 TAAACGAACATGTTC-CTGAACATA
848681 TAAA
1 TAAA
848685 TAAACGAAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
23 5 0.10
24 43 0.88
25 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (24 bp):
TAAACGAACATGTTCCTGAACATA
Found at i:849272 original size:28 final size:29
Alignment explanation
Indices: 849237--849294 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
849227 AGTCAACGAG
849237 AATAAATATTAATTG-AAAATCAGATCAA
1 AATAAATATTAATTGAAAAATCAGATCAA
849265 AATAAATATTAATTGAAAAATCAGATCAA
1 AATAAATATTAATTGAAAAATCAGATCAA
849294 A
1 A
849295 TCTATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAAATATTAATTGAAAAATCAGATCAA
Found at i:850923 original size:2 final size:2
Alignment explanation
Indices: 850916--850965 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
850906 TTGATTTTGA
850916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
850958 AT AT AT AT
1 AT AT AT AT
850966 GCAGGTTTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:853995 original size:75 final size:75
Alignment explanation
Indices: 853859--854040 Score: 231
Period size: 75 Copynumber: 2.4 Consensus size: 75
853849 TTTAATCGGT
* * * * * * *
853859 TAAAATAAAATAGGCGCTACCTATTATGTTAAATTACCTACCGGTTTATTTGAATGTTACTAACA
1 TAAAATAAAATAGGTGCTACCTATTAAGTTAAAATACCGACCGGTTTATTTAAAGGCTACTAACA
*
853924 ATGTAAACGG
66 ATGTAAACGA
* * * * * *
853934 TAAAATAAAATAGGTGTTACCTATTACGTTAAAATATCGACTGGTTTGTTTAAAGGCTACTAATA
1 TAAAATAAAATAGGTGCTACCTATTAAGTTAAAATACCGACCGGTTTATTTAAAGGCTACTAACA
853999 ATGTAAACGA
66 ATGTAAACGA
854009 TAAAA-AAAATAGGTGCTACCTATTAAGTTAAA
1 TAAAATAAAATAGGTGCTACCTATTAAGTTAAA
854041 TAAGTGTTAC
Statistics
Matches: 92, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
74 25 0.27
75 67 0.73
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATAGGTGCTACCTATTAAGTTAAAATACCGACCGGTTTATTTAAAGGCTACTAACA
ATGTAAACGA
Found at i:854055 original size:23 final size:23
Alignment explanation
Indices: 854015--854063 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
854005 ACGATAAAAA
* *
854015 AAATAGGTGCTACCTATTAAGTT
1 AAATAAGTGCTACATATTAAGTT
* *
854038 AAATAAGTGTTACATATTATGTT
1 AAATAAGTGCTACATATTAAGTT
854061 AAA
1 AAA
854064 CTAGCTACTT
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:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (23 bp):
AAATAAGTGCTACATATTAAGTT
Done.