Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 20 of 20
Found at i:3091551 original size:25 final size:27
Alignment explanation
Indices: 3091512--3091562 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
3091502 AAAGAAAACA
*
3091512 TTTTTTCATTATTTTTTGAAAGTAAAG
1 TTTTTTCATTATTTTTTAAAAGTAAAG
*
3091539 TTTTTT-ATT-TTTTTTAAAATTAAA
1 TTTTTTCATTATTTTTTAAAAGTAAA
3091563 AATGACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 3 0.14
27 6 0.27
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (27 bp):
TTTTTTCATTATTTTTTAAAAGTAAAG
Found at i:3091738 original size:2 final size:2
Alignment explanation
Indices: 3091679--3091719 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3091669 ATCAAATACT
3091679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3091720 GTACATATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3095103 original size:20 final size:20
Alignment explanation
Indices: 3095078--3095202 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
3095068 TTTTAACTAG
*
3095078 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTGAAAA
3095098 ATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACAT-T--G--AAAA
*
3095123 GATAGAATGTATCGATACATTGAAGA
1 -AT-G--T--ATCGATACATTGAAAA
* * *
3095149 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
3095169 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
3095189 ATATATCGATACAT
1 ATGTATCGATACAT
3095203 CTGGGTACTT
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 55 0.65
21 1 0.01
22 1 0.01
23 1 0.01
24 1 0.01
25 6 0.07
26 5 0.06
27 1 0.01
28 1 0.01
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:3096060 original size:28 final size:28
Alignment explanation
Indices: 3096029--3096090 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
3096019 ATAGTGGTGA
*
3096029 TTTGAAATGATGCCACTGACTTGTGGGC
1 TTTGAAATGATGCCACTGACTTGTGGAC
* *
3096057 TTTGAAATGGTGCCACTGGCTTGTGGAC
1 TTTGAAATGATGCCACTGACTTGTGGAC
3096085 TTTGAA
1 TTTGAA
3096091 GAGATGAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTGAAATGATGCCACTGACTTGTGGAC
Found at i:3097323 original size:13 final size:12
Alignment explanation
Indices: 3097292--3097349 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
3097282 ACCTCTTTCT
3097292 GTTTTTTTTTTG
1 GTTTTTTTTTTG
* *
3097304 CTATTTTTTCTTG
1 GT-TTTTTTTTTG
3097317 GTTTTTTTGTTT-
1 GTTTTTTT-TTTG
3097329 -TTTGTTTTTTT-
1 GTTT-TTTTTTTG
3097340 GTTTTTTTTT
1 GTTTTTTTTT
3097350 ATTTTTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 12 0.32
12 14 0.37
13 12 0.32
ACGTcount: A:0.02, C:0.03, G:0.12, T:0.83
Consensus pattern (12 bp):
GTTTTTTTTTTG
Found at i:3097328 original size:8 final size:8
Alignment explanation
Indices: 3097317--3097347 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3097307 TTTTTTCTTG
3097317 GTTTTTTT
1 GTTTTTTT
3097325 G-TTTTTT
1 GTTTTTTT
3097332 GTTTTTTT
1 GTTTTTTT
3097340 GTTTTTTT
1 GTTTTTTT
3097348 TTATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (8 bp):
GTTTTTTT
Found at i:3097354 original size:15 final size:15
Alignment explanation
Indices: 3097317--3097346 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3097307 TTTTTTCTTG
3097317 GTTTTTTTGTTTTTT
1 GTTTTTTTGTTTTTT
3097332 GTTTTTTTGTTTTTT
1 GTTTTTTTGTTTTTT
3097347 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GTTTTTTTGTTTTTT
Found at i:3103183 original size:52 final size:52
Alignment explanation
Indices: 3103105--3103232 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
3103095 CGAAATATGA
*
3103105 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
3103157 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
3103209 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3103233 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:3103343 original size:33 final size:33
Alignment explanation
Indices: 3103306--3103372 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3103296 AGTAGCTTAA
3103306 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3103339 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3103372 A
1 A
3103373 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3103346 original size:13 final size:13
Alignment explanation
Indices: 3103328--3103352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3103318 CAAAAAAATA
3103328 TGTATCGATACAT
1 TGTATCGATACAT
3103341 TGTATCGATACA
1 TGTATCGATACA
3103353 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3104192 original size:43 final size:43
Alignment explanation
Indices: 3104131--3104224 Score: 188
Period size: 43 Copynumber: 2.2 Consensus size: 43
3104121 AGAAAAGTGA
3104131 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCT
1 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCT
3104174 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCT
1 TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCT
3104217 TAAAGATG
1 TAAAGATG
3104225 ATGAAAAAGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (43 bp):
TAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCT
Found at i:3104343 original size:213 final size:212
Alignment explanation
Indices: 3103970--3104394 Score: 816
Period size: 213 Copynumber: 2.0 Consensus size: 212
3103960 GATAAAAGGA
3103970 CCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAA
1 CCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAA
3104035 TATGCGGCTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
66 TATGCGGCTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
3104100 TTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGA
131 TTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGA
3104165 TATTGGGCTTAAAGATG
196 TATTGGGCTTAAAGATG
*
3104182 CCAATATGTTGATTCACGGCCAACGATATTGGGCTT-AAAGATGATGAAAAAGGATAAAAGAGCC
1 CCAATACGTTGATTCACGGCCAACGATATTGGG-TTCAAAGATGA-GAAAAAGGATAAAAGAGCC
3104246 AATATGCGGCTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
64 AATATGCGGCTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
3104311 CATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAAC
129 CATTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAAC
3104376 GATATTGGGCTTAAAGATG
194 GATATTGGGCTTAAAGATG
3104395 AGAAAAAGGA
Statistics
Matches: 210, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
212 40 0.19
213 170 0.81
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (212 bp):
CCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGATAAAAGAGCCAA
TATGCGGCTAGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
TTGGACTTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGA
TATTGGGCTTAAAGATG
Found at i:3104555 original size:49 final size:49
Alignment explanation
Indices: 3104413--3105270 Score: 1137
Period size: 49 Copynumber: 17.6 Consensus size: 49
3104403 GATGTCAACG
* *
3104413 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* * *
3104465 TGCTAATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
3104508 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3104557 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3104600 TGCTGAGTCAAGGCCAGCTACATTGGACTTCAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3104649 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
3104698 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3104747 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
3104796 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
3104848 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3104897 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * * * *
3104946 TGCTGATTCAAGGCCAACTATATTGGGCTTAATGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* *
3104995 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
3105044 TGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3105093 TGCTGAGTCAAGGCCAGCTACATTGGAATTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
3105142 TGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
3105191 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
3105240 TGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTA
3105271 GAAGGGTTGC
Statistics
Matches: 700, Mismatches: 91, Indels: 33
0.85 0.11 0.04
Matches are distributed among these distances:
43 75 0.11
45 1 0.00
47 2 0.00
48 1 0.00
49 547 0.78
50 1 0.00
51 1 0.00
52 72 0.10
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:3104717 original size:98 final size:98
Alignment explanation
Indices: 3104346--3105270 Score: 1334
Period size: 98 Copynumber: 9.4 Consensus size: 98
3104336 AAAAGTGATA
* * * * * *
3104346 AAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TGCCAA
* * *
3104411 CGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
60 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
3104451 AAAATGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAGA--TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
3104510 CTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
3104545 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
3104604 GAGTCAAGGCCAGCTACATTGGACTTCAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
3104637 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3104702 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
3104735 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3104800 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
*
3104834 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTG
* *
3104899 CTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATA
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * * *
3104934 AAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGGCTTAATGGTGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
3104999 GAGTCAAGGCCAGCTACATTGGACTTAAAGATA
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
3105032 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* *
3105097 GAGTCAAGGCCAGCTACATTGGAATTAAAGATA
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
3105130 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3105195 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
3105228 AAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
3105271 GAAGGGTTGC
Statistics
Matches: 777, Mismatches: 32, Indels: 29
0.93 0.04 0.03
Matches are distributed among these distances:
92 126 0.16
94 4 0.01
95 41 0.05
96 5 0.01
98 470 0.60
99 1 0.00
101 94 0.12
103 1 0.00
105 3 0.00
107 32 0.04
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (98 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:3105355 original size:67 final size:68
Alignment explanation
Indices: 3105270--3105645 Score: 611
Period size: 67 Copynumber: 5.6 Consensus size: 68
3105260 TATTGGGCTT
* * *
3105270 AGAAGGG-TTGCCATCGACTTGTGTGGGCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
*
3105333 TGG
66 TAG
3105336 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
3105401 TAG
66 TAG
* * * *
3105404 AGAATGG-TTGCCACCAACTTGTGTGGGCTTTGGCGAAGGGTTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
3105468 TAG
66 TAG
* *
3105471 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
*
3105535 TGG
66 TAG
3105538 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
3105603 TAG
66 TAG
3105606 AGAA-GGTTTGCCACCGACTTGTGTGGGCTTTAGA-AAGGGT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
3105646 GAAAGATGCC
Statistics
Matches: 288, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
66 13 0.05
67 188 0.65
68 87 0.30
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.30
Consensus pattern (68 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
TAG
Found at i:3105357 original size:34 final size:34
Alignment explanation
Indices: 3105270--3105645 Score: 611
Period size: 34 Copynumber: 11.2 Consensus size: 34
3105260 TATTGGGCTT
*
3105270 AGAAGGG-TTGCCATCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
* * *
3105303 AGAATGG-TTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105336 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105370 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
* * *
3105404 AGAATGG-TTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
3105437 CGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105471 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
* * *
3105505 AGAATGG-TTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105538 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105572 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105606 AGAA-GGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105639 A-AAGGGT
1 AGAAGGGT
3105646 GAAAGATGCC
Statistics
Matches: 318, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
32 2 0.01
33 127 0.40
34 189 0.59
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.30
Consensus pattern (34 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:3105452 original size:101 final size:101
Alignment explanation
Indices: 3105270--3105645 Score: 686
Period size: 101 Copynumber: 3.7 Consensus size: 101
3105260 TATTGGGCTT
*
3105270 AGAAGGG-TTGCCATCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
3105334 GGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
66 GGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105370 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
*
3105435 GGCGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
66 GGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
3105471 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
3105536 GGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
66 GGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
3105572 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAA-GGTTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTT
*
3105636 TAGA-AAGGGT
65 TGGAGAAGGGT
3105646 GAAAGATGCC
Statistics
Matches: 269, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
100 15 0.06
101 254 0.94
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.30
Consensus pattern (101 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTT
GGAGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:3105744 original size:107 final size:101
Alignment explanation
Indices: 3105627--3105916 Score: 279
Period size: 107 Copynumber: 2.8 Consensus size: 101
3105617 CACCGACTTG
* * * *
3105627 TGTGGGCTTTAGAAAGGGTGAAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCAC
1 TGTGGGCTTTA-AAA-GG-AAAAGGTGCCACGAAGTTGTGGACTTTAAAAAGAAAAAAGTGCCAC
3105691 GGAGTTGTGGGCTTT-AAAAGGGAAAAAAAGAGTGCCACAAAGT
63 GGAGTTGTGGGCTTTGAAAA--G--AAAAAG-GTGCCACAAAGT
* * * *
3105734 TGTGGGCTTTAAAAAGAAAAAGTGTGCCAC-AGAGTTGTGGGCTTTAAGATGAAAAAAGTGCCAC
1 TGTGGGCTTT-AAAAGGAAAAG-GTGCCACGA-AGTTGTGGACTTTAAAAAGAAAAAAGTGCCAC
* **
3105798 GGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
63 GGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAAAGT
* * *
3105837 TGTGGGCTTT-AAAGGAAAAGGTGCCACGAAGTTGTGGGCTTT--GAAGAAAAAA-TGCCACTGA
1 TGTGGGCTTTAAAAGGAAAAGGTGCCACGAAGTTGTGGACTTTAAAAAGAAAAAAGTGCCACGGA
* * *
3105898 GTCGTGGACTTTGAGAAGA
66 GTTGTGGGCTTTGAAAAGA
3105917 GATTGCCACT
Statistics
Matches: 160, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
97 24 0.15
98 9 0.06
100 20 0.12
101 10 0.06
103 20 0.12
104 5 0.03
105 5 0.03
106 17 0.11
107 45 0.28
108 5 0.03
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (101 bp):
TGTGGGCTTTAAAAGGAAAAGGTGCCACGAAGTTGTGGACTTTAAAAAGAAAAAAGTGCCACGGA
GTTGTGGGCTTTGAAAAGAAAAAGGTGCCACAAAGT
Found at i:3105761 original size:35 final size:34
Alignment explanation
Indices: 3105647--3105878 Score: 263
Period size: 34 Copynumber: 6.8 Consensus size: 34
3105637 AGAAAGGGTG
* * *
3105647 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
3105680 CAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAA---AGAA
**
3105717 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* * *
3105752 AAAGTGTGCCACAGAGTTGTGGGCTTTAAGATGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
3105787 AAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
* *
3105821 GAAGGTGCCACGGAGTTGTGGGCTTT--AAAGGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
*
3105853 AAAGGTGCCACGAAGTTGTGGGCTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
3105879 GAAGAAAAAA
Statistics
Matches: 171, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
32 29 0.17
33 19 0.11
34 56 0.33
35 37 0.22
37 6 0.04
38 24 0.14
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
Found at i:3105803 original size:34 final size:34
Alignment explanation
Indices: 3105647--3105909 Score: 241
Period size: 34 Copynumber: 7.7 Consensus size: 34
3105637 AGAAAGGGTG
* * *
3105647 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAAC
1 AAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* *
3105681 AAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAA
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAA---AGAAA
**
3105718 AAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAA
1 AA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * * *
3105753 AAGTGTGCCACAGAGTTGTGGGCTTTAAGATGAAA
1 AA-AGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* *
3105788 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* *
3105822 AAGGTGCCACGGAGTTGTGGGCTTT--AAAGGAA
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * *
3105854 AAGGTGCCACGAAGTTGTGGGCTTT--GAAGAAA
1 AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
* * *
3105886 AAA-TGCCACTGAGTCGTGGACTTT
1 AAAGTGCCACGGAGTTGTGGGCTTT
3105910 GAGAAGAGAT
Statistics
Matches: 194, Mismatches: 30, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
31 17 0.09
32 36 0.19
33 16 0.08
34 59 0.30
35 37 0.19
37 5 0.03
38 24 0.12
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (34 bp):
AAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAA
Found at i:3106988 original size:8 final size:8
Alignment explanation
Indices: 3106972--3107005 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3106962 AGATTTTCTG
*
3106972 TTTTGTTT
1 TTTTCTTT
3106980 TTTTCTTT
1 TTTTCTTT
3106988 TTTTCTTT
1 TTTTCTTT
3106996 TTTT-TTT
1 TTTTCTTT
3107003 TTT
1 TTT
3107006 GTGTTTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (8 bp):
TTTTCTTT
Found at i:3106990 original size:15 final size:16
Alignment explanation
Indices: 3106965--3107007 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
3106955 CTCACCGAGA
*
3106965 TTTTCTGTTTTGT-TT
1 TTTTCTTTTTTGTCTT
3106980 TTTTCTTTTTT-TCTT
1 TTTTCTTTTTTGTCTT
*
3106995 TTTTTTTTTTTGT
1 TTTTCTTTTTTGT
3107008 GTTTGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (16 bp):
TTTTCTTTTTTGTCTT
Found at i:3107286 original size:18 final size:17
Alignment explanation
Indices: 3107247--3107286 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3107237 TTGCCTTTGC
3107247 ACTTTTTTTTTTGTTTT
1 ACTTTTTTTTTTGTTTT
*
3107264 -GTTTTTTTTTTGTGTTT
1 ACTTTTTTTTTTGT-TTT
3107281 ACTTTT
1 ACTTTT
3107287 GACTGTTCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 12 0.63
17 3 0.16
18 4 0.21
ACGTcount: A:0.05, C:0.05, G:0.10, T:0.80
Consensus pattern (17 bp):
ACTTTTTTTTTTGTTTT
Found at i:3114273 original size:52 final size:52
Alignment explanation
Indices: 3114195--3114322 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
3114185 CGAAATATGA
*
3114195 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
3114247 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
3114299 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
3114323 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:3114433 original size:33 final size:33
Alignment explanation
Indices: 3114396--3114462 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3114386 AGTAGCTTAA
3114396 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3114429 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3114462 A
1 A
3114463 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3114436 original size:13 final size:13
Alignment explanation
Indices: 3114418--3114442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3114408 CAAAAAAATA
3114418 TGTATCGATACAT
1 TGTATCGATACAT
3114431 TGTATCGATACA
1 TGTATCGATACA
3114443 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3115595 original size:32 final size:32
Alignment explanation
Indices: 3115540--3115640 Score: 157
Period size: 32 Copynumber: 3.1 Consensus size: 32
3115530 TTCAACGATT
*
3115540 TGTATTGATACATAAAGTGTTGTATCGATACAT
1 TGTATTGATACAT-AAGTGTTGTATCGATACAA
3115573 TGTATTGATACATAAGTGTTGTATCGATACAA
1 TGTATTGATACATAAGTGTTGTATCGATACAA
* * *
3115605 TATATCGATACATAAGTTTTGTATCGATACAA
1 TGTATTGATACATAAGTGTTGTATCGATACAA
3115637 TGTA
1 TGTA
3115641 AGCTACTGCA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTATTGATACATAAGTGTTGTATCGATACAA
Found at i:3115631 original size:19 final size:18
Alignment explanation
Indices: 3115538--3115635 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 18
3115528 ATTTCAACGA
*
3115538 TTTGTATTGATACATAAAG
1 TTTGTATCGATACAT-AAG
3115557 TGTTGTATCGATAC---A-
1 T-TTGTATCGATACATAAG
*
3115572 -TTGTATTGATACATAAG
1 TTTGTATCGATACATAAG
3115589 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
*
3115605 --TATATCGATACATAAG
1 TTTGTATCGATACATAAG
3115621 TTTTGTATCGATACA
1 -TTTGTATCGATACA
3115636 ATGTAAGCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 26
0.66 0.05 0.28
Matches are distributed among these distances:
13 21 0.34
15 2 0.03
16 2 0.03
17 2 0.03
19 23 0.38
20 11 0.18
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:3115695 original size:13 final size:13
Alignment explanation
Indices: 3115677--3115701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3115667 ACTACCCAAA
3115677 TGTATCGATACAT
1 TGTATCGATACAT
3115690 TGTATCGATACA
1 TGTATCGATACA
3115702 CCGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3115753 original size:52 final size:50
Alignment explanation
Indices: 3115690--3115838 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 50
3115680 ATCGATACAT
* * *
3115690 TGTATCGATACACCGATCTTTGTATCGATACATGCAGGTAAATTTGCCCAAA
1 TGTATCGATACA-CTAT-TATGTATCGATACATGCAGGCAAATTTGCCCAAA
* *
3115742 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGTCCAAA
1 TGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAAA
3115794 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAAATTT
3115839 TCATATTTCG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 3 0.03
52 84 0.97
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (50 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAAA
Found at i:3125472 original size:41 final size:41
Alignment explanation
Indices: 3125427--3125504 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3125417 TAATTATGAG
*
3125427 TATTTAAATTCTCACGTTATTTTGATTATATTATCTATTAA
1 TATTTAAATTCTCACATTATTTTGATTATATTATCTATTAA
* * * * *
3125468 TATTTGAATTCTCATATTCTTTTGGTTTTATTATCTA
1 TATTTAAATTCTCACATTATTTTGATTATATTATCTA
3125505 GTTGAGAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.56
Consensus pattern (41 bp):
TATTTAAATTCTCACATTATTTTGATTATATTATCTATTAA
Found at i:3126370 original size:14 final size:14
Alignment explanation
Indices: 3126337--3126384 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3126327 TAATATACTA
*
3126337 AAAATAATAAAAAT
1 AAAATAATAATAAT
* *
3126351 ATAATATTACATAA-
1 AAAATAATA-ATAAT
3126365 AAAATAATAATAAT
1 AAAATAATAATAAT
3126379 AAAATA
1 AAAATA
3126385 CAAGCTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 4 0.15
14 20 0.74
15 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:3126371 original size:17 final size:17
Alignment explanation
Indices: 3126339--3126382 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3126329 ATATACTAAA
3126339 AATAATAAAAATATAAT
1 AATAATAAAAATATAAT
*
3126356 ATTACATAAAAA-ATAAT
1 AATA-ATAAAAATATAAT
3126373 AATAATAAAA
1 AATAATAAAA
3126383 TACAAGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 11 0.46
18 7 0.29
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAAAAATATAAT
Found at i:3126443 original size:14 final size:14
Alignment explanation
Indices: 3126394--3126446 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3126384 ACAAGCTCAA
3126394 ATATATTAAAATTT
1 ATATATTAAAATTT
* *
3126408 ATATA--AATTATTA
1 ATATATTAA-AATTT
*
3126421 ATATTTTAAAATTT
1 ATATATTAAAATTT
3126435 ATATATTAAAAT
1 ATATATTAAAAT
3126447 ATCTTAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 2 0.07
13 7 0.23
14 19 0.63
15 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:3126834 original size:18 final size:19
Alignment explanation
Indices: 3126811--3126846 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3126801 AATTTTAAAT
3126811 TTAAATATAATA-TATTTA
1 TTAAATATAATATTATTTA
*
3126829 TTAAATATTATATTATTT
1 TTAAATATAATATTATTT
3126847 TTTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAATATAATATTATTTA
Found at i:3127687 original size:19 final size:20
Alignment explanation
Indices: 3127649--3127687 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3127639 TTAATTTTTT
*
3127649 ATATTATTATTATATTTAAA
1 ATATTATTATTATATATAAA
*
3127669 ATATT-TTATTTTATATAAA
1 ATATTATTATTATATATAAA
3127688 TTTTGATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTATTATTATATATAAA
Found at i:3128424 original size:19 final size:20
Alignment explanation
Indices: 3128400--3128437 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3128390 CTGTATTCAC
3128400 TTATTTTTAAAA-ATTATAA
1 TTATTTTTAAAATATTATAA
3128419 TTATTTTTAAAATATTATA
1 TTATTTTTAAAATATTATA
3128438 TATTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTTTTAAAATATTATAA
Found at i:3128441 original size:18 final size:18
Alignment explanation
Indices: 3128401--3128473 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
3128391 TGTATTCACT
3128401 TATTTTTAAAA-ATTATAA
1 TATTTTTAAAATATTAT-A
3128419 TTATTTTTAAAATATTATA
1 -TATTTTTAAAATATTATA
* *
3128438 TATTTATATAAATTTTA-A
1 TATTTTTA-AAATATTATA
* *
3128456 TATATTAAAAAT-TTATA
1 TATTTTTAAAATATTATA
3128473 T
1 T
3128474 TATATAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.07
17 6 0.13
18 13 0.28
19 19 0.41
20 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTTAAAATATTATA
Found at i:3128458 original size:20 final size:19
Alignment explanation
Indices: 3128405--3128469 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 19
3128395 TTCACTTATT
*
3128405 TTTA-AAAATTATAAT-TA
1 TTTATAAAATTTTAATATA
* *
3128422 TTTTTAAAATATT-ATATA
1 TTTATAAAATTTTAATATA
3128440 TTTATATAAATTTTAATATA
1 TTTATA-AAATTTTAATATA
3128460 -TTA-AAAATTT
1 TTTATAAAATTT
3128470 ATATTATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 11 0.28
18 14 0.36
19 9 0.23
20 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATAAAATTTTAATATA
Found at i:3128477 original size:18 final size:18
Alignment explanation
Indices: 3128406--3128478 Score: 55
Period size: 17 Copynumber: 4.1 Consensus size: 18
3128396 TCACTTATTT
*
3128406 TTAAAAA-TTATAATTATTT
1 TTAAAAATTTAT-ATTA-TA
3128425 TTAAAATATTATATATT-TA
1 TTAAAA-ATT-TATATTATA
* *
3128444 -TATAAATTT-TAATATA
1 TTAAAAATTTATATTATA
3128460 TTAAAAATTTATATTATA
1 TTAAAAATTTATATTATA
3128478 T
1 T
3128479 AAATTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
15 3 0.07
16 3 0.07
17 11 0.26
18 11 0.26
19 7 0.16
20 1 0.02
21 4 0.09
22 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAAAATTTATATTATA
Found at i:3128486 original size:16 final size:16
Alignment explanation
Indices: 3128436--3128486 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3128426 TAAAATATTA
3128436 TATATTTATATAAATTT
1 TATA-TTATATAAATTT
*
3128453 TA-A-TATATTAAAAATT
1 TATATTATA-T-AAATTT
3128469 TATATTATATAAATTT
1 TATATTATATAAATTT
3128485 TA
1 TA
3128487 AAACACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 15 0.54
17 4 0.14
18 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:3128505 original size:33 final size:32
Alignment explanation
Indices: 3128431--3128505 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 32
3128421 ATTTTTAAAA
* *
3128431 TATTATA-TAT-TTATATAAATTTTAATATAT
1 TATTATATTATATTATATAAATTTTAAAACAT
* *
3128461 TA-AAAATTTATATTATATAAATTTTAAAACACT
1 TATTATA-TTATATTATATAAATTTTAAAACA-T
3128494 TATTATATTATA
1 TATTATATTATA
3128506 ATCTTTTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 3 0.09
32 17 0.50
33 8 0.24
34 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (32 bp):
TATTATATTATATTATATAAATTTTAAAACAT
Found at i:3128573 original size:57 final size:57
Alignment explanation
Indices: 3128501--3128615 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3128491 ACTTATTATA
*
3128501 TTATAATCTTTTTAATTTATATAATATTATTAAAACTTATCTAGCACATAATTTTTG
1 TTATAATCTTCTTAATTTATATAATATTATTAAAACTTATCTAGCACATAATTTTTG
* *
3128558 TTATAGTCTTCTTAATTTGTATAATATTATTAAAACTTATCTAGCACATAATTTTTG
1 TTATAATCTTCTTAATTTATATAATATTATTAAAACTTATCTAGCACATAATTTTTG
3128615 T
1 T
3128616 GGGAAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (57 bp):
TTATAATCTTCTTAATTTATATAATATTATTAAAACTTATCTAGCACATAATTTTTG
Found at i:3128917 original size:2 final size:2
Alignment explanation
Indices: 3128910--3128934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3128900 ATTAATAATT
3128910 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3128935 CACCAATCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3129696 original size:18 final size:18
Alignment explanation
Indices: 3129656--3129705 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3129646 TCAAGTTCCG
3129656 GATTTTTTAAATTTATGA
1 GATTTTTTAAATTTATGA
* *
3129674 AATTTTATTCAATTTA-GA
1 GATTTT-TTAAATTTATGA
*
3129692 GATTTTTGAAATTT
1 GATTTTTTAAATTT
3129706 TATCCCAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 6 0.23
18 12 0.46
19 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (18 bp):
GATTTTTTAAATTTATGA
Found at i:3129715 original size:28 final size:27
Alignment explanation
Indices: 3129666--3129727 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
3129656 GATTTTTTAA
* * *
3129666 ATTTATGAAATTTTATTCAATTTAGAG
1 ATTTTTGAAATTTTATCCAATTTAAAG
3129693 ATTTTTGAAATTTTATCCCAATTTAAAG
1 ATTTTTGAAATTTTAT-CCAATTTAAAG
*
3129721 ACTTTTG
1 ATTTTTG
3129728 GATCTTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (27 bp):
ATTTTTGAAATTTTATCCAATTTAAAG
Done.