Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2484
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: 85290
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3720 original size:22 final size:24
Alignment explanation
Indices: 3689--3737 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3679 TATTTTTTCC
3689 TTTTTCTC-TTTCTTT-TTCCTTT
1 TTTTTCTCTTTTCTTTCTTCCTTT
* *
3711 TTTTTGTCTTTTCTTTCTTTCTTT
1 TTTTTCTCTTTTCTTTCTTCCTTT
3735 TTT
1 TTT
3738 AGCTGAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 7 0.30
24 9 0.39
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTTCTCTTTTCTTTCTTCCTTT
Found at i:5518 original size:13 final size:13
Alignment explanation
Indices: 5500--5526 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5490 TACAATGAAC
5500 ATGTATCGATACA
1 ATGTATCGATACA
5513 ATGTATCGATACA
1 ATGTATCGATACA
5526 A
1 A
5527 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:7860 original size:22 final size:21
Alignment explanation
Indices: 7827--7876 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
7817 TTTGTTGATG
*
7827 ATTTT-AA-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
7847 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
7868 AATTTGAAG
1 ATTTTGAAG
7877 ATGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:7873 original size:21 final size:22
Alignment explanation
Indices: 7834--7876 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
7824 ATGATTTTAA
* *
7834 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
7856 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
7877 ATGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:10826 original size:13 final size:13
Alignment explanation
Indices: 10808--10832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10798 ATATTGCACA
10808 GTATCGATACATT
1 GTATCGATACATT
10821 GTATCGATACAT
1 GTATCGATACAT
10833 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:10950 original size:13 final size:13
Alignment explanation
Indices: 10932--10957 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10922 TACACACAAG
10932 ATGTATCGATACA
1 ATGTATCGATACA
10945 ATGTATCGATACA
1 ATGTATCGATACA
10958 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10974 original size:33 final size:32
Alignment explanation
Indices: 10914--10977 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
10904 CTTAACTATT
*
10914 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
10946 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
10978 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:20288 original size:52 final size:52
Alignment explanation
Indices: 20210--20338 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
20200 CAAAATATGA
*
20210 AAATTTGCCTGCATGTATCGATACATTTCATATTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
20262 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
20314 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
20339 ATGTATCGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:20344 original size:13 final size:13
Alignment explanation
Indices: 20326--20351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20316 ATTTGCCTGC
20326 ATGTATCGATACA
1 ATGTATCGATACA
20339 ATGTATCGATACA
1 ATGTATCGATACA
20352 GTTGAGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20418 original size:19 final size:19
Alignment explanation
Indices: 20394--20465 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
20384 TAGCTTATAT
20394 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
20413 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
20432 TGTATCGATACAACACTTTA
1 TGTATCGATACAAAAC-TTA
*
20452 TGTATCAATACAAA
1 TGTATCGATACAAA
20466 TCGTTGAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 34 0.69
20 15 0.31
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:21353 original size:52 final size:49
Alignment explanation
Indices: 21276--21904 Score: 689
Period size: 52 Copynumber: 13.1 Consensus size: 49
21266 CTTAGGAATG
* * *
21276 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAA
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
21325 TTAAAGATGACAGAGACGCCAATATGCTGATTCCAA-GCCAGCGATATTGGAC
1 TTAAAGATGA-AG-G-TGCCAATATGCTGATT-CAAGGCCAGCGATATTGGAC
* *
21377 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
21429 TT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGG-C
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGAC
*
21472 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
21522 TTAAAGATGACAGAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGA-AG-G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
21574 TTAAAGATGACAGAGACGCCGATATGCTGATTCAAGGCCAACGATATTGGAC
1 TTAAAGATGA-AG-G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
21626 TT---G--G-AGGTGCCAATGTGCTAATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
21669 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
21718 TT---G--G-AGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
21761 TTAAAGATGAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
21810 TT----A--AAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
21853 TCAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
21902 TTA
1 TTA
21905 GAAGGGTTGC
Statistics
Matches: 498, Mismatches: 44, Indels: 76
0.81 0.07 0.12
Matches are distributed among these distances:
43 141 0.28
44 4 0.01
45 3 0.01
46 3 0.01
47 2 0.00
48 4 0.01
49 133 0.27
50 39 0.08
51 5 0.01
52 157 0.32
53 4 0.01
54 2 0.00
55 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
Found at i:21449 original size:43 final size:44
Alignment explanation
Indices: 21389--21909 Score: 440
Period size: 43 Copynumber: 11.1 Consensus size: 44
21379 AAAGATGACA
* *
21389 AAGGCGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
* *
21432 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGG-CTTAAAAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTT---AG
21479 ATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G
*
21531 ACAGAGACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 A-AG-G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G
* * *
21583 ACAGAGACGCCGATATGCTGATTCAAGGCCAACGATATTGGACTT-G
1 A-AG-G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
* * * *
21629 GAGGTGCCAATGTGCTAATTCAAGGCCAGCTATATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G
*
21678 AAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT-G
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
* * * * *
21721 GAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G
*
21770 AAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
* * * * *
21813 AAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTCAAAGATG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT----TA-G
*
21862 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAG
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
21906 AAGG
1 AAGG
21910 GTTGCCACCG
Statistics
Matches: 404, Mismatches: 43, Indels: 61
0.80 0.08 0.12
Matches are distributed among these distances:
43 142 0.35
44 8 0.02
45 4 0.01
46 2 0.00
47 2 0.00
49 116 0.29
50 36 0.09
51 5 0.01
52 89 0.22
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (44 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAG
Found at i:21504 original size:197 final size:196
Alignment explanation
Indices: 21276--21904 Score: 908
Period size: 197 Copynumber: 3.3 Consensus size: 196
21266 CTTAGGAATG
* * *
21276 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAATTAAAGATGACAGAGA
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAGA
21341 CGCCAATATGCTGATTCCAA-GCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCT
66 CGCCAATATGCTGATT-CAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCT
* *
21405 GATTCAAGGCCAGCGACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAG
130 GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT-G
21470 G-C
194 GAC
*
21472 TTAAAAGATGAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAG
1 TT-AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAG
* * *
21537 ACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAGACGCCGATATGCT
65 ACGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCT
* ** * *
21602 GATTCAAGGCCAACGATATTGGACTTGGAGGTGCCAATGTGCTAATTCAAGGCCAGCTATATTGG
130 GATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGG
21667 AC
195 AC
*
21669 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT---G--G--AG-G-
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAGA
* * * * * * *
21725 TGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTGCTAATATGCTG
66 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
*
21787 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGA
131 ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
21852 C
196 C
* *
21853 TCAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
21905 GAAGGGTTGC
Statistics
Matches: 394, Mismatches: 35, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
184 120 0.30
187 40 0.10
188 1 0.00
189 2 0.01
191 1 0.00
193 1 0.00
196 54 0.14
197 175 0.44
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (196 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAGA
CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
ATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
C
Found at i:21752 original size:92 final size:92
Alignment explanation
Indices: 21539--21899 Score: 560
Period size: 92 Copynumber: 3.9 Consensus size: 92
21529 TGACAGAGAC
* * * * *
21539 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAGAGACGCCGATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA-AG-G-TGCCAATATGCTGA
21604 TTCAAGGCCAACGATATTGGACTTGGAGGT
63 TTCAAGGCCAACGATATTGGACTTGGAGGT
* *
21634 GCCAATGTGCTAATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
21699 AAGGCCAACGATATTGGACTTGGAGGT
66 AAGGCCAACGATATTGGACTTGGAGGT
* *
21726 GCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCTAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
* **
21791 AAGGCCAGCGATATTGGACTTAAAGGT
66 AAGGCCAACGATATTGGACTTGGAGGT
* *
21818 GCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTCAAAGATGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
*
21883 AAGGCCAGCGATATTGG
66 AAGGCCAACGATATTGG
21900 GCTTAGAAGG
Statistics
Matches: 250, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
92 205 0.82
93 1 0.00
94 2 0.01
95 42 0.17
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (92 bp):
GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTC
AAGGCCAACGATATTGGACTTGGAGGT
Found at i:21967 original size:33 final size:33
Alignment explanation
Indices: 21904--21977 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
21894 TATTGGGCTT
* **
21904 AGAAGGGTTGCCACCGACTTGCGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGCGTCAGCTTTAG
* *
21937 AGAATGGTTGCCACCAACTTGTGTCAGCTTT-G
1 AGAAGGGTTGCCACCAACTTGCGTCAGCTTTAG
21969 AAGAAGGGT
1 -AGAAGGGT
21978 GAAAGATGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCAACTTGCGTCAGCTTTAG
Found at i:22029 original size:33 final size:33
Alignment explanation
Indices: 21992--22691 Score: 559
Period size: 33 Copynumber: 21.2 Consensus size: 33
21982 GATGCCACAA
*
21992 AGTTGTGGACTTAAAAAGAACAAGGTGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* **
22025 AGTTGTGGGCTTTAAAGGGAAAAAGAGTGCCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAG-GTGCCACGG
* *
22060 AGTTGTGGGCTTTGAAAAG---AAGGTGCCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGG
* * ** *
22091 AGTCGCGGACTTTGAAAG--GAAGGTGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* * * *
22122 AGTCGTGGACTTAAAAGGAACAAGGTGCCATGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* *
22155 GGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGG
1 AGTTGTGGAC-TTAAAA-AGAAAAAG-GTGCCACGG
* ** *
22191 AGTTGTGGGCTT-TGAA-AATAAGGTGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* * * *
22222 AGTCGTGGACTTAAAAGGAACAAGGTGCCATGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
*
22255 AGTCGTGGACTTAAAAAG-AAAAGGTGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* * * *
22287 AGTGGTGGGCTTTGAAAAGAAAATGGTGCCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGG
* * *
22321 AGTTGTGGGCTTTAAAAAG--GAAGGTGTCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGG
* * * *
22353 AGTCGTGGACTTAAAAGGAACAAGATGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* * * *
22386 AGTCGTGGACTTAAAAGGAACAAGATGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* ** **
22419 GGTCATGGACTTTGAAAG---AAGGTGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* *
22449 AGTCGTGGACTT-AAAAGGAAAAGGTGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* * *
22481 AGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGG
* * *
22515 AGTTGTGGGCTTTAAAAAG--GAAGGTTCCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGG
** * * *
22547 AGTCATGGACTTAAAAGGAACAAGATGCCACGG
1 AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
* *
22580 AGTTGTGGACTTAAAAGGAATAAAGAGTTCCACGG
1 AGTTGTGGACTTAAAAAGAA-AAAG-GTGCCACGG
*
22615 AGTTGTGGACTTTGAAAAGAAAAAGAGTGCCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAG-GTGCCACGG
* * * *
22650 AGTTGTGGGCTTTGACAAGAAAAAGGTACCACGG
1 AGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGG
22684 AGTTGTGG
1 AGTTGTGG
22692 GCTTTGGAAA
Statistics
Matches: 556, Mismatches: 87, Indels: 47
0.81 0.13 0.07
Matches are distributed among these distances:
29 4 0.01
30 27 0.05
31 75 0.13
32 85 0.15
33 151 0.27
34 103 0.19
35 87 0.16
36 24 0.04
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.20
Consensus pattern (33 bp):
AGTTGTGGACTTAAAAAGAAAAAGGTGCCACGG
Found at i:22217 original size:131 final size:130
Alignment explanation
Indices: 21978--22657 Score: 643
Period size: 131 Copynumber: 5.2 Consensus size: 130
21968 GAAGAAGGGT
* ** * * * * *
21978 GAAAGATGCCACAAAGTTGTGGACTTAAAAAGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAGG
1 GAAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTAAAAG
* * *
22043 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGCGGACTTTGAAA
66 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTCGTGGAC-TTAAAA
22108 G
130 G
* * *
22109 G-AAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCATGGGGTTGTGGACTTTAAAAG
1 GAAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTAAAA-
* *
22173 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAATAAGGTGCCACGGAGTCGTGGACTTAAAA
65 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAA
22238 G
130 G
* * * *
22239 GAACAAGGTGCCATGGAGTCGTGGACTTAAAAAGAA-AAGGTGCCACGGAGTGGTGGGCTTTGAA
1 G-A-AAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTT-AA
* *
22303 AA-GAAAATG-GTGCCACGGAGTTGTGGGCTTTAAAAAGGAAGGTGTCACGGAGTCGTGGACTTA
63 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA-GAAGGTGCCACGGAGTCGTGGACTTA
22366 AAAG
127 AAAG
* * * * *
22370 GAACAAGATGCCACGGAGTCGTGGACTTAAAAGGAACAAGATGCCACGGGGTCATGGACTTTGAA
1 G-A-AAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTAAA
* * * * *
22435 A-G---AAG-GTGCCACGGAGTCGTGGAC-TTAAAAGGAAAAGGTGCCACGGAGTGGTGGGCTTT
64 AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--AGAAGGTGCCACGGAGTCGTGGAC-TT
22494 GAAAAG
126 -AAAAG
* * * * *
22500 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGG---AAGGTTCCACGGAGTCATGGAC-TTAA
1 -GAAAGGTGCCACGGAGTCGTGGAC-TT-AAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTAA
* * * * * *
22561 AAGGAACAAGA-TGCCACGGAGTTGTGGACTTAAAAGGAATAAAGAGTTCCACGGAGTTGTGGAC
63 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA--AA-GAAG-GTGCCACGGAGTCGTGGAC
22625 TTTGAAAAG
124 -TT-AAAAG
* *
22634 AAAAAGAGTGCCACGGAGTTGTGG
1 -GAAAG-GTGCCACGGAGTCGTGG
22658 GCTTTGACAA
Statistics
Matches: 473, Mismatches: 51, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
127 11 0.02
128 58 0.12
129 22 0.05
130 94 0.20
131 155 0.33
132 46 0.10
133 38 0.08
134 32 0.07
135 17 0.04
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (130 bp):
GAAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCCACGGAGTCGTGGACTTTAAAAG
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAG
Found at i:22453 original size:194 final size:197
Alignment explanation
Indices: 21980--22703 Score: 771
Period size: 194 Copynumber: 3.7 Consensus size: 197
21970 AGAAGGGTGA
** * * * *
21980 AAGATGCCACAAAGTTGTGGACTTAAAAAGAACAAGGTGCCACGGAGTTGTGGGCTTT-AAAGGG
1 AAGATGCCACGGAGTTGTGGACTTAAAAGGAACAAGATGCCACGGAGTCGTGGACTTTGAAA-GG
* * * * * *
22044 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG--AAGGTGCCACGGAGTCGCGGACTTTG-A
65 --AAAGAGTGCCACGGAGTCGTGGACTTTAAAAAGAAAAGGTGCCACGGAGTGGTGGGCTTTGAA
* * * * * * *
22106 AAG-GAAGGTGCCACGGAGTCGTGGAC-TT-AAAAGGAACAAGGTGCCATGGGGTTGTGGACTTT
128 AAGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGG---AAGGTGTCACGGAGTCGTGGAC-TT
*
22168 AAAAGGGAAA
189 AAAA-GGAAC
* ** * * *
22178 AAGAGTGCCACGGAGTTGTGGGCTTTGAA--AATAAGGTGCCACGGAGTCGTGGAC-TTAAAAGG
1 AAGA-TGCCACGGAGTTGTGGACTTAAAAGGAACAAGATGCCACGGAGTCGTGGACTTTGAAAGG
*
22240 AACA-AGGTGCCATGGAGTCGTGGAC-TTAAAAAGAAAAGGTGCCACGGAGTGGTGGGCTTTGAA
65 AA-AGA-GTGCCACGGAGTCGTGGACTTTAAAAAGAAAAGGTGCCACGGAGTGGTGGGCTTTGAA
22303 AAGAAAATGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAGGTGTCACGGAGTCGTGGACTTAAA
128 AAGAAAA-GGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAGGTGTCACGGAGTCGTGGACTTAAA
22368 AGGAAC
192 AGGAAC
* * *
22374 AAGATGCCACGGAGTCGTGGACTTAAAAGGAACAAGATGCCACGGGGTCATGGACTTTGAAA-G-
1 AAGATGCCACGGAGTTGTGGACTTAAAAGGAACAAGATGCCACGGAGTCGTGGACTTTGAAAGGA
*
22437 AAG-GTGCCACGGAGTCGTGGAC-TTAAAAGGAAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAG
66 AAGAGTGCCACGGAGTCGTGGACTTTAAAAAGAAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAG
*
22500 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAGGT-TCCACGGAGTCATGGACTTAAAAG
131 -AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAGGTGT-CACGGAGTCGTGGACTTAAAAG
22564 GAAC
194 GAAC
* * *
22568 AAGATGCCACGGAGTTGTGGACTTAAAAGGAATAAAGAGTTCCACGGAGTTGTGGACTTTGAAAA
1 AAGATGCCACGGAGTTGTGGACTTAAAAGGAA-CAAGA-TGCCACGGAGTCGTGGACTTTG-AAA
* * * * * * *
22633 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGACAAGAAAAAGGTACCACGGAGTTGTGGGCTTTG
63 G-GAAAGAGTGCCACGGAGTCGTGGACTTTAAAAAG-AAAAGGTGCCACGGAGTGGTGGGCTTTG
*
22698 GAAAGA
126 AAAAGA
22704 GATGCCATTA
Statistics
Matches: 450, Mismatches: 50, Indels: 48
0.82 0.09 0.09
Matches are distributed among these distances:
193 1 0.00
194 159 0.35
195 46 0.10
196 54 0.12
197 60 0.13
198 29 0.06
199 37 0.08
200 5 0.01
201 23 0.05
202 6 0.01
203 30 0.07
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (197 bp):
AAGATGCCACGGAGTTGTGGACTTAAAAGGAACAAGATGCCACGGAGTCGTGGACTTTGAAAGGA
AAGAGTGCCACGGAGTCGTGGACTTTAAAAAGAAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAG
AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAGGTGTCACGGAGTCGTGGACTTAAAAGGA
AC
Found at i:31117 original size:52 final size:52
Alignment explanation
Indices: 30969--31097 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
30959 CGAAATATGA
30969 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* * *
31021 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
31073 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
31098 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:31124 original size:13 final size:13
Alignment explanation
Indices: 31106--31130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31096 CAAAGATCAG
31106 TGTATCGATACAA
1 TGTATCGATACAA
31119 TGTATCGATACA
1 TGTATCGATACA
31131 GTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31212 original size:19 final size:20
Alignment explanation
Indices: 31188--31237 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
31178 CGATACATTA
31188 TATCGATACAACAC-TTATG
1 TATCGATACAACACTTTATG
31207 TATCGATACAACACTTTATG
1 TATCGATACAACACTTTATG
31227 TATCGATACAA
1 TATCGATACAA
31238 ATCATTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (20 bp):
TATCGATACAACACTTTATG
Found at i:33955 original size:33 final size:32
Alignment explanation
Indices: 33918--33984 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
33908 ACCCTTAAAA
**
33918 GTATCGATACACCTTCAAATGTATCGATACATT
1 GTATCGATACACCACCAAATGTATCGATAC-TT
* **
33951 GTATCGATCCATGACCAAATGTATCGATACTT
1 GTATCGATACACCACCAAATGTATCGATACTT
33983 GT
1 GT
33985 TAAGAATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (32 bp):
GTATCGATACACCACCAAATGTATCGATACTT
Found at i:34087 original size:20 final size:20
Alignment explanation
Indices: 34044--34095 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
34034 CTTAACTGTT
*
34044 TGTATCGATACA-CACAAGA
1 TGTATCGATACATCACAAAA
*
34063 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
34083 TGTATCGATACAT
1 TGTATCGATACAT
34096 TGGCTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:38616 original size:19 final size:19
Alignment explanation
Indices: 38566--38621 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
38556 CTGCCAGTTT
**
38566 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
38586 CACGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
38605 CATGTATTGATATAATG
1 CATGTATCGATACAATG
38622 TATCGATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:43826 original size:51 final size:54
Alignment explanation
Indices: 43762--44151 Score: 201
Period size: 53 Copynumber: 7.4 Consensus size: 54
43752 AGTTTCTCAA
* * *
43762 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-A-AAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAAT
*
43813 TT-TTCTATAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAAT
* * ** *** * *
43867 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAGCCT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AACAAACACCAA---T
* ** * * * ***
43923 GTTATTTC-TGA-C-GGGATACTCCAAC-CCTGACTTTA-TTTCCA-AAATATTGAT
1 -TT-CTTCACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAACAAACACCAAT
* * * * * *
43974 TT-TTCATAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAC-AACACTAATT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAA-T
* * * *
44026 TTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTT-TA-AAACACCAATT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAA-T
* * * *
44079 TTCCTT--TAATCAGGGATACTCCAACTCCGATTTTATTTCCAA-AAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAAT
*
44131 TT-TTCACAATCGAGGATACTC
1 TTCTTCACAATCGGGGATACTC
44152 TAACCTCGTT
Statistics
Matches: 262, Mismatches: 50, Indels: 53
0.72 0.14 0.15
Matches are distributed among these distances:
48 3 0.01
49 2 0.01
50 7 0.03
51 63 0.24
52 55 0.21
53 69 0.26
54 33 0.13
55 17 0.06
56 4 0.02
57 6 0.02
58 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (54 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAACAAACACCAAT
Found at i:44237 original size:264 final size:263
Alignment explanation
Indices: 43767--44265 Score: 725
Period size: 264 Copynumber: 1.9 Consensus size: 263
43757 CTCAATTCTC
* * * *
43767 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATA
* *
43832 CTCCAACTCCGATTTTATTTTCAACAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAACAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
* * * * * *
43897 TTAATCATCGGGGATACTCCAAGCCTGTTATTTCTGACGGGATACTCCAACCCTGACTTTATTTC
131 TTAATCATCGAGGATACTCCAACCCCGTTACTTCCGACGGGATACTCCAACCCCGACTTTATTTC
**
43962 CAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTACAACACTAATTT
196 CAAAATATTGATTTCACATAATCGGGGATACT-CAACCCCGGTTTTATTGCTACAACACTAATTT
44027 TTTT
260 TTTT
* * *
44031 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTTAAAACACCAATTTTCCTTTAATCAGGGAT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCAGGGAT
* * *
44096 ACTCCAACTCCGATTTTATTTCCAA-AAATACCAATTT-TTCACAATCGAGGATACTCTAACCTC
65 ACTCCAACTCCGATTTTATTTCCAACAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCC
* * *
44159 GTTATTTCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA-T
130 GTTA-ATCATCGAGGATACTCCAACCCCGTTACTTCCGACGGGATACTCCAACCCCGACTTTATT
*
44223 TCTCAAAATATTGATTTCACATAATTGGGGATACTCAACCCCG
194 TC-CAAAATATTGATTTCACATAATCGGGGATACTCAACCCCG
44266 TTATTTTCGA
Statistics
Matches: 208, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
263 38 0.18
264 134 0.64
265 36 0.17
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATA
CTCCAACTCCGATTTTATTTCCAACAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTAATCATCGAGGATACTCCAACCCCGTTACTTCCGACGGGATACTCCAACCCCGACTTTATTTC
CAAAATATTGATTTCACATAATCGGGGATACTCAACCCCGGTTTTATTGCTACAACACTAATTTT
TTT
Found at i:56703 original size:5 final size:5
Alignment explanation
Indices: 56690--56735 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
56680 ACCTTCTCTT
56690 CAAAA -AAAA CAAAA CAAAA CAAAA CAAAA C-AAA -AAAA CAAAA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
56736 GAAAAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 10 0.26
5 28 0.74
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:57818 original size:59 final size:58
Alignment explanation
Indices: 57724--58193 Score: 543
Period size: 55 Copynumber: 8.3 Consensus size: 58
57714 TCCGTTTTTT
57724 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
57783 AATCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
57842 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACCCAAG-T--T-G--CCTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
57895 AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGC-CTTTCTTTT-AAAGCCCACACAAGTTGGTGGCACC-TTC
* *
57956 AGTCCCCAAAGAGCAGGAC-CC---CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * **
58011 AGTCCCCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-C
*
58066 AGTCCTCAAAGAGCAGGACACC--TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTC
* * * *
58121 AATCCTCAAAGAGCAGGACGCCTTTC----AAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
58176 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
58194 TACACTTTAT
Statistics
Matches: 368, Mismatches: 23, Indels: 44
0.85 0.05 0.10
Matches are distributed among these distances:
53 34 0.09
54 15 0.04
55 181 0.49
56 9 0.02
57 3 0.01
58 2 0.01
59 101 0.27
60 3 0.01
61 20 0.05
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (58 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:58044 original size:26 final size:26
Alignment explanation
Indices: 57960--58044 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
57950 CCTTTCAGTC
*
57960 CCCAAAGAGCAGGACCCCTTTCAAAG
1 CCCAAAGAGCAGGACACCTTTCAAAG
** * ***
57986 CCCACACA-AGTTGGTGGCACCTTTCAGTC
1 CCCA-A-AGAG-CAG-GACACCTTTCAAAG
58015 CCCAAAGAGCAGGACACCTTTCAAAG
1 CCCAAAGAGCAGGACACCTTTCAAAG
58041 CCCA
1 CCCA
58045 CACAAGTTGG
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
26 18 0.44
27 5 0.12
28 5 0.12
29 13 0.32
ACGTcount: A:0.31, C:0.35, G:0.19, T:0.15
Consensus pattern (26 bp):
CCCAAAGAGCAGGACACCTTTCAAAG
Found at i:59014 original size:19 final size:18
Alignment explanation
Indices: 58989--59056 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
58979 AATTCAACAA
58989 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
59007 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
59023 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
59039 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
59057 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:59028 original size:13 final size:13
Alignment explanation
Indices: 59010--59034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59000 ACATAAGTGT
59010 TGTATCGATACAA
1 TGTATCGATACAA
59023 TGTATCGATACA
1 TGTATCGATACA
59035 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:59028 original size:32 final size:32
Alignment explanation
Indices: 58991--59053 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
58981 TTCAACAATT
*
58991 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
59023 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
59054 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:59114 original size:13 final size:13
Alignment explanation
Indices: 59096--59121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59086 CATTTTTCTG
59096 TGTATCGATACAT
1 TGTATCGATACAT
59109 TGTATCGATACAT
1 TGTATCGATACAT
59122 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:59118 original size:33 final size:33
Alignment explanation
Indices: 59076--59142 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
59066 GCCAAGGAAA
***
59076 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
59109 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
59142 T
1 T
59143 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:59683 original size:10 final size:10
Alignment explanation
Indices: 59657--59685 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
59647 CTTTAGCAAA
59657 AAAAAAAC-C
1 AAAAAAACAC
59666 AAAAAAACAC
1 AAAAAAACAC
59676 AAAAAAACAC
1 AAAAAAACAC
59686 TATTCCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAC
Found at i:61607 original size:27 final size:28
Alignment explanation
Indices: 61577--61652 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
61567 TTTCTTCACA
61577 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* * *
61604 ATCGGGGATACTCTAACCCCATTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
61632 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
61653 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:61799 original size:106 final size:103
Alignment explanation
Indices: 61460--61858 Score: 267
Period size: 105 Copynumber: 3.8 Consensus size: 103
61450 TTGAGTTTCT
* * * * * * *
61460 CAATTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCTATA
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTC-ACA
* *
61523 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAGAAACAC
65 ATCGGGGATACTCCAACCCCGACTTTATTTCC-A-AAACAC
* * * * * * *
61564 CAATTTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCTAAC-CCCAT
1 CAATTT-TCCATAATCGGGGATACTCCAACCCCGATTTTAT-TTC---CA-A---AAACACCAAT
** * *
61626 TATTTC-TGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATAT
57 T-TTTCACAATCGGGGATACTCCAACCCCGACTTTATTTCCAAAACAC
** * * * * * *
61671 TGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTACAACACTAATTTTTTTTCA
1 CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAA---TTTTTCA
** *
61735 CAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC
63 CAATCGGGGATACTCCAACCCCGACTTTATTTCCAAAACAC
* * *
61776 CAATTTTCCTTTAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACA
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACA
*
61841 ATCGAGGATACTCCAACC
65 ATCGGGGATACTCCAACC
61859 TCGTTATTTC
Statistics
Matches: 226, Mismatches: 46, Indels: 46
0.71 0.14 0.14
Matches are distributed among these distances:
99 3 0.01
100 2 0.01
102 5 0.02
103 7 0.03
104 32 0.14
105 61 0.27
106 53 0.23
107 19 0.08
108 4 0.02
109 28 0.12
111 4 0.02
112 4 0.02
113 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAA
TCGGGGATACTCCAACCCCGACTTTATTTCCAAAACAC
Found at i:61815 original size:52 final size:53
Alignment explanation
Indices: 61471--61858 Score: 210
Period size: 54 Copynumber: 7.4 Consensus size: 53
61461 AATTCTCCAC
* * * * *
61471 AATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAATTTT-CTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTTT
* *
61522 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAGAAACACCAA-TTT-CTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAA-AAACACCAATTTTCCTT--T
* * *** * * * ** *
61576 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCTAA--CCCCATT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACACCAATTTTCCTTT
* * * *** * *
61627 ATTTCTGAGGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGATTTTTC-AT
1 A-ATC---GGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTTT
* * * * * *
61682 AATCGGGGATACTCCAACCCCGGTTTTA-TTGCTACAACACTAATTTT-TTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTTT
* *
61733 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTTT
1 ---AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTTT
* * * **
61788 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTTT
*
61840 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
61859 TCGTTATTTC
Statistics
Matches: 258, Mismatches: 56, Indels: 45
0.72 0.16 0.13
Matches are distributed among these distances:
50 3 0.01
51 65 0.25
52 57 0.22
53 33 0.13
54 67 0.26
55 26 0.10
56 3 0.01
57 4 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTCCTTT
Found at i:61877 original size:28 final size:28
Alignment explanation
Indices: 61841--61917 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
61831 ATTTTTCACA
* * *
61841 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
61869 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
61897 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
61918 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:61941 original size:265 final size:265
Alignment explanation
Indices: 61468--61968 Score: 810
Period size: 265 Copynumber: 1.9 Consensus size: 265
61458 CTCAATTCTC
* * *
61468 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATA
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
*
61533 CTCCAACTCCGATTTTATTTCCAAGAAACACCAATTTCTTCACAATCGGGGATACTCCAACCCCG
66 CTCCAACTCCGATTTTATTTCCAAGAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
* * *
61598 TTAATCATCGGGGATACTCTAACCCCATTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTC
131 TTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGACTTTATTTC
*
61663 CAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTACAACACTAATTT
196 CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTACAACACTAATTT
61728 TTTTT
261 TTTTT
* *
61733 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGAT
* *
61798 ACTCTAACTCCGATTTTATTTCCAA-AAACACCAATTT-TTCACAATCGAGGATACTCCAACCTC
65 ACTCCAACTCCGATTTTATTTCCAAGAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCC
* * *
61861 GTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA-T
130 GTTA-ATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
*
61925 TCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
194 TCC-AAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
61969 TTATTTTCGA
Statistics
Matches: 217, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
264 32 0.15
265 148 0.68
266 37 0.17
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (265 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAGAAACACCAATTTCTTCACAATCGAGGATACTCCAACCCCG
TTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGACTTTATTTC
CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTACAACACTAATTT
TTTTT
Found at i:62012 original size:79 final size:80
Alignment explanation
Indices: 61872--62026 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 80
61862 TTATTTCATC
* *
61872 GGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATT
1 GGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCTAAAATATT
*
61937 -GATTTCTCATAATT
66 AAATTTCTCATAATT
* * *
61951 GGGGATACTCCAACCCCGTTATTTTCGAGGGAACACTCCAACCCC-GTTATTATCTCC-AAAATA
1 GGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGGCT-TTAT-TCCTAAAATA
62014 TTAAATTTCTCAT
64 TTAAATTTCTCAT
62027 CGGGAAATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
78 2 0.03
79 53 0.79
80 12 0.18
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCTAAAATATT
AAATTTCTCATAATT
Found at i:64370 original size:22 final size:21
Alignment explanation
Indices: 64329--64374 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
64319 TTCAGAATAG
64329 ATTTTATTTTATTAATATTTTT
1 ATTTTATTTTA-TAATATTTTT
*
64351 ATTTTAATTTTA-AATA-ATTT
1 ATTTT-ATTTTATAATATTTTT
64371 ATTT
1 ATTT
64375 AAAGATATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 5 0.23
23 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTATAATATTTTT
Found at i:64617 original size:17 final size:17
Alignment explanation
Indices: 64590--64631 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
64580 AATTATTATT
*
64590 TAATAAATTTTAATTTAA
1 TAATTAATTTTAA-TTAA
*
64608 -AATTAATTTTTATTAA
1 TAATTAATTTTAATTAA
64624 TAATTAAT
1 TAATTAAT
64632 AAAATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTAATTTTAATTAA
Found at i:66706 original size:19 final size:20
Alignment explanation
Indices: 66682--66732 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
66672 AATAAGAAAT
66682 TTTTATTATAAAATT-TATA
1 TTTTATTATAAAATTATATA
* *
66701 TTTTATAATATAATTATATA
1 TTTTATTATAAAATTATATA
*
66721 TATT-TTATAAAA
1 TTTTATTATAAAA
66733 ACAGTTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTATTATAAAATTATATA
Found at i:67564 original size:13 final size:13
Alignment explanation
Indices: 67546--67571 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67536 CAATTTTTTG
67546 TGTATCGATACAT
1 TGTATCGATACAT
67559 TGTATCGATACAT
1 TGTATCGATACAT
67572 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:67636 original size:21 final size:21
Alignment explanation
Indices: 67610--67685 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
67600 CTGCCAAGAA
*
67610 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
67631 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
67651 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
67672 ATGTATCGATACAT
1 ATGTATCGATACAT
67686 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:67656 original size:20 final size:20
Alignment explanation
Indices: 67631--67703 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
67621 CATCTTTTTT
67631 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
67651 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
67672 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
67692 ATGTATCGATAC
1 ATGTATCGATAC
67704 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:67667 original size:41 final size:41
Alignment explanation
Indices: 67610--67703 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
67600 CTGCCAAGAA
*
67610 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
67651 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
67692 ATGTATCGATAC
1 ATGTATCGATAC
67704 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:68362 original size:33 final size:33
Alignment explanation
Indices: 68321--68385 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
68311 TCCCCCGTTT
68321 AAAAAAAATCTCCCCCTTAATCAAGTAATTCAA
1 AAAAAAAATCTCCCCCTTAATCAAGTAATTCAA
68354 AAAAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAAAATCTCCCCCTTAATCAAGTAATTCA
68386 TATCAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.48, C:0.25, G:0.03, T:0.25
Consensus pattern (33 bp):
AAAAAAAATCTCCCCCTTAATCAAGTAATTCAA
Found at i:70197 original size:13 final size:13
Alignment explanation
Indices: 70179--70217 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
70169 ATAATCACCC
*
70179 TGTATCGATACAG
1 TGTATCGATACAA
70192 TGTATCGATACAA
1 TGTATCGATACAA
70205 TGTATCGATACAA
1 TGTATCGATACAA
70218 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:70228 original size:20 final size:20
Alignment explanation
Indices: 70203--70281 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
70193 GTATCGATAC
70203 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
70223 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
70248 AATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
70267 ACATGTATCGATACA
1 A-ATGTATCGATACA
70282 TTTTGGACAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.04
20 26 0.54
21 3 0.06
23 3 0.06
25 14 0.29
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:72315 original size:15 final size:15
Alignment explanation
Indices: 72295--72325 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
72285 ATTTCGTTTG
*
72295 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
72310 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
72325 G
1 G
72326 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:76399 original size:13 final size:13
Alignment explanation
Indices: 76381--76406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76371 CAATTTTTTG
76381 TGTATCGATACAT
1 TGTATCGATACAT
76394 TGTATCGATACAT
1 TGTATCGATACAT
76407 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:76471 original size:21 final size:21
Alignment explanation
Indices: 76445--76520 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
76435 CTGCCAAGAA
*
76445 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
76466 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
76486 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
76507 ATGTATCGATACAT
1 ATGTATCGATACAT
76521 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:76491 original size:20 final size:20
Alignment explanation
Indices: 76466--76538 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
76456 CATCTTTTTT
76466 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
76486 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
76507 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
76527 ATGTATCGATAC
1 ATGTATCGATAC
76539 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:76502 original size:41 final size:41
Alignment explanation
Indices: 76445--76538 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
76435 CTGCCAAGAA
*
76445 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
76486 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
76527 ATGTATCGATAC
1 ATGTATCGATAC
76539 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:76936 original size:2 final size:2
Alignment explanation
Indices: 76931--76963 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
76921 AGATCTGGAT
*
76931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76964 GAAAGGCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:77247 original size:18 final size:18
Alignment explanation
Indices: 77198--77250 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
77188 TAAATTTTAA
*
77198 ATTTTATTATTTATGTATTT
1 ATTTTATAATTTA--TATTT
77218 ATTTTA-AATTTATATTT
1 ATTTTATAATTTATATTT
*
77235 TTTTTATAATTTATAT
1 ATTTTATAATTTATAT
77251 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.33
18 9 0.30
19 5 0.17
20 6 0.20
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTTATAATTTATATTT
Found at i:77972 original size:28 final size:28
Alignment explanation
Indices: 77941--77995 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
77931 AAAAAAAAAT
* * *
77941 TTAAATTTATTTTTAATTTAATTATATA
1 TTAAATTTAATATTAATATAATTATATA
*
77969 TTAATTTTAATATTAATATAATTATAT
1 TTAAATTTAATATTAATATAATTATAT
77996 TATGAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTAAATTTAATATTAATATAATTATATA
Found at i:79954 original size:3 final size:3
Alignment explanation
Indices: 79946--79987 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
79936 TGGCTTCCCC
* * *
79946 TAT TAT TAT TAT TAT TGT TAT TAT TAT T-T TAT AAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
79988 CAAGTTGCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:81717 original size:2 final size:2
Alignment explanation
Indices: 81710--81750 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
81700 AGCTGTTAGT
81710 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
81751 GTGTTAGTCC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:82308 original size:93 final size:94
Alignment explanation
Indices: 82193--82377 Score: 318
Period size: 93 Copynumber: 2.0 Consensus size: 94
82183 GCAACTTGAG
*
82193 TGTTAACATTTTTGGTTGAAAATATTTGCAAGTTGTTCCTGCATATTCCA-TTGCTCATCAGTAA
1 TGTTAACATTTTTGGTTGAAAATATTTGCAAGTTGTTCCTGCATATTCCATTTGCTAATCAGTAA
* *
82257 CTACTTATTCTTTTCACCAGATATATAAA
66 CTACTTAGTATTTTCACCAGATATATAAA
82286 TGTTAACATTTTTGGTTGAAAATATTTGCAAGTTGTTCCTGCATATTCCATTTGCTAATCAGTAA
1 TGTTAACATTTTTGGTTGAAAATATTTGCAAGTTGTTCCTGCATATTCCATTTGCTAATCAGTAA
* *
82351 CTACTTAGTATTTTCACCGGATCTATA
66 CTACTTAGTATTTTCACCAGATATATA
82378 GATCCGATTA
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
93 50 0.58
94 36 0.42
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (94 bp):
TGTTAACATTTTTGGTTGAAAATATTTGCAAGTTGTTCCTGCATATTCCATTTGCTAATCAGTAA
CTACTTAGTATTTTCACCAGATATATAAA
Found at i:84250 original size:22 final size:22
Alignment explanation
Indices: 84225--84301 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 22
84215 TATATTTTGA
84225 TATATATATATATATATTATAT
1 TATATATATATATATATTATAT
* *
84247 TATAGTGATATGTACATATTAT-T
1 TATA-T-ATATATATATATTATAT
*
84270 ATAGTCATATGTATATATTATTATAGT
1 -TA-T-ATATATATATA-TATTATA-T
84297 TATAT
1 TATAT
84302 GTACATACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 4 0.10
23 2 0.05
24 23 0.55
25 9 0.21
26 3 0.07
27 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (22 bp):
TATATATATATATATATTATAT
Found at i:84302 original size:22 final size:22
Alignment explanation
Indices: 84229--84304 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
84219 TTTTGATATA
*
84229 TATATATATATATTATATTATAGT
1 TATATGTATATA-T-TATTATAGT
* *
84253 GATATGTACATATTATTATAGT
1 TATATGTATATATTATTATAGT
*
84275 CATATGTATATATTATTATAGT
1 TATATGTATATATTATTATAGT
84297 TATATGTA
1 TATATGTA
84305 CATACAACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 36 0.78
23 1 0.02
24 9 0.20
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (22 bp):
TATATGTATATATTATTATAGT
Found at i:84774 original size:22 final size:22
Alignment explanation
Indices: 84725--84774 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
84715 TAAATTTATG
* *
84725 ATATGTACATACTATTATAGTG
1 ATATGTAAATACTATTATAGTC
*
84747 AGATGTAAATACTATTATAGTC
1 ATATGTAAATACTATTATAGTC
84769 ATATGT
1 ATATGT
84775 GCATATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (22 bp):
ATATGTAAATACTATTATAGTC
Found at i:84874 original size:22 final size:23
Alignment explanation
Indices: 84849--84895 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
84839 ATATTTTTGG
84849 AGGGGTT-G-GTTCCTTAATGAAA
1 AGGGGTTAGTGTT-CTTAATGAAA
*
84871 A-GGGTTAGTGTTCTTTATGAAA
1 AGGGGTTAGTGTTCTTAATGAAA
84893 AGG
1 AGG
84896 TTAGATCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.34
Consensus pattern (23 bp):
AGGGGTTAGTGTTCTTAATGAAA
Done.