Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold669
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: 84068
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1047 original size:2 final size:2
Alignment explanation
Indices: 1035--1075 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1025 TTAGAAACGT
*
1035 TA TA AA 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
1076 TGCATTTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2557 original size:22 final size:22
Alignment explanation
Indices: 2515--2557 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2505 AGATAAAAAA
**
2515 AAATCTTATTATCCAAAATTTT
1 AAATCTTATTATAAAAAATTTT
2537 AAATCTTATT-TAAAAACATTT
1 AAATCTTATTATAAAAA-ATTT
2558 CATAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATCTTATTATAAAAAATTTT
Found at i:5621 original size:25 final size:25
Alignment explanation
Indices: 5592--5651 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
5582 TCATTTTATA
5592 CAAATTTTTATTAGGAGGTTTAAGG
1 CAAATTTTTATTAGGAGGTTTAAGG
5617 CAAATTTTTATTAGGAGGTTTAAGG
1 CAAATTTTTATTAGGAGGTTTAAGG
5642 CAAATTTTTA
1 CAAATTTTTA
5652 ATTTAATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (25 bp):
CAAATTTTTATTAGGAGGTTTAAGG
Found at i:6059 original size:18 final size:19
Alignment explanation
Indices: 6031--6067 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6021 CATAAAGAAA
*
6031 CAAATATGACTACTCCTAT
1 CAAATATGACTAATCCTAT
6050 CAAA-ATGACTAATCCTAT
1 CAAATATGACTAATCCTAT
6068 GATTAATCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (19 bp):
CAAATATGACTAATCCTAT
Found at i:8379 original size:25 final size:25
Alignment explanation
Indices: 8350--8409 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
8340 TCATTTTATA
8350 CAAATTTTTATTAGGAGGTTTAAGG
1 CAAATTTTTATTAGGAGGTTTAAGG
8375 CAAATTTTTATTAGGAGGTTTAAGG
1 CAAATTTTTATTAGGAGGTTTAAGG
8400 CAAATTTTTA
1 CAAATTTTTA
8410 ATTTAATACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (25 bp):
CAAATTTTTATTAGGAGGTTTAAGG
Found at i:8817 original size:18 final size:19
Alignment explanation
Indices: 8789--8825 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
8779 CATAAAGAAA
*
8789 CAAATATGACTACTCCTAT
1 CAAATATGACTAATCCTAT
8808 CAAA-ATGACTAATCCTAT
1 CAAATATGACTAATCCTAT
8826 GATTAATCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (19 bp):
CAAATATGACTAATCCTAT
Found at i:10472 original size:13 final size:13
Alignment explanation
Indices: 10454--10501 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
10444 AGTTCCCATG
*
10454 TATCGATATAATA
1 TATCGATACAATA
10467 TATCGATACAATA
1 TATCGATACAATA
* *
10480 TATTGATACAATG
1 TATCGATACAATA
10493 TATCGATAC
1 TATCGATAC
10502 TAAGAACACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:14077 original size:12 final size:12
Alignment explanation
Indices: 14056--14085 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
14046 TACCCAAACT
14056 TTGT-TGGGTCC
1 TTGTGTGGGTCC
14067 TTGTGTGGGTCC
1 TTGTGTGGGTCC
14079 TTGTGTG
1 TTGTGTG
14086 TTAGTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.00, C:0.13, G:0.40, T:0.47
Consensus pattern (12 bp):
TTGTGTGGGTCC
Found at i:16886 original size:52 final size:49
Alignment explanation
Indices: 16760--17841 Score: 653
Period size: 49 Copynumber: 22.9 Consensus size: 49
16750 TCGAAGATGC
* * * * * *
16760 GAAGAATGACAATGTGCTGATTCATGGCCATCGACATTTAGACTTGAAGA-
1 GAAG-ATGCCAATATGCTGATTCAAGGCCAGCGACA-TTGGACTTAAAGAT
* * ** * * *
16810 -AAAATGCCAATGTGCTGAGGCAAGGCTAGCGACATTGGGCTTAGGAATGTT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GAT
* * * * * * *
16861 AAAGATGTCAATATGCTGATTCAAGGTCAACGATATCGGACTTAAAGCT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * *
16910 GAAGATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCATAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* *
16959 GACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT
1 ---GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
*
17011 GAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTA-TTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGG-ACTTAAAGAT
** * * * *
17060 GACAAAGGCGCCAATATGCTGATTCAAGGCCTGTGATATTGGGC-T-----T
1 G---AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17106 ---G-TGCCAATGTGCTAATTCAAGGCCACCAACATTGGTCTTAAAGA-
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17150 CAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGGC-T-----T
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * * *
17193 ----ATGCTAATGTGCTGATTCAAGACCAGCGACATTGGTCTCAGAGA-
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * *
17237 CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17280 ----ATGCCAATGTGCTGATTCAAGGCTAACGACATTGGTCTTAAAGAC
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17325 AAAG-TGCCAATATGCTAATTTAAGGCCAGCGATATTGGGC-T-----T
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * *
17367 ----ATGCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTGAAAGA-
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17411 GAAGGTGCCAATATGTTGATTCAATGCCAGCGATATTGGTCTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * *
17460 GAAGATGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17509 GAAGATGCCAGTGTGCTGATTCAAGGCTAGAGACATTGGTCTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* *
17558 GAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACATAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * *
17607 GACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAA-ACT
1 GA-AGATG--CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-T
* * * *
17659 GAAGATGCCAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGAT
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
** * *
17708 GACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T
1 G---AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * *
17754 ---G-TGCCAATGTGCTAATTCAAGGCCAGTGACATTGGTCTTAAAGA-
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
17798 CAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTA
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
17842 TGCCAATGTG
Statistics
Matches: 804, Mismatches: 153, Indels: 152
0.72 0.14 0.14
Matches are distributed among these distances:
39 148 0.18
40 5 0.01
46 2 0.00
47 10 0.01
48 186 0.23
49 261 0.32
50 8 0.01
51 6 0.01
52 178 0.22
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
Found at i:16944 original size:101 final size:101
Alignment explanation
Indices: 16813--18007 Score: 676
Period size: 87 Copynumber: 12.8 Consensus size: 101
16803 TTGAAGAAAA
** * * * ** *
16813 ATGCCAATGTGCTGAGGCAAGGCTAGCGACATTGGGC-TTAGGAATGTTAAAGATGTCAATATGC
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAG-ATGACAAAGATGCCAATATGC
* *
16877 TGATTCAAGGTCAACGATATCGGACTTAAAGCTGAAG
65 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * *
16914 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCATAAAGATGACGAAGGTGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* *
16979 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAG
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* **
17015 ATGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTATTAAAGATGACAAAGGCGCCAATATGC
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCA-TAAAGATGACAAAGATGCCAATATGC
*** * *
17079 TGATTCAAGGCCTGTGATATTGGGC-T-----T---G
65 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * * * * *
17107 -TGCCAATGTGCTAATTCAAGGCCACCAACATTGGTC-TTAA-A-GAC-AAGGTGCCAATATGTT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* * *
17167 GATTCAAGGCCAGCGATATTGGGC-T-----T----
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * * *
17193 ATGCTAATGTGCTGATTCAAGACCAGCGACATTGGTC-T-CAGA-GAC-AAGGTGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* * *
17254 GATTCAAGGCCAGCGATATTGGGC-T-----T----
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * *
17280 ATGCCAATGTGCTGATTCAAGGCTAACGACATTGGTC-TTAA-A-GACAAAG-TGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* * * * *
17341 AATTTAAGGCCAGCGATATTGGGC-T-----T----
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * *
17367 ATGCCAATGTACTGATTCAAGGCCAGCGACATTGGTC-TGAAAGA-G---AAGGTGCCAATATGT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCAT-AAAGATGACAAAGATGCCAATATGC
* * * *
17427 TGATTCAATGCCAGCGATATTGGTCTTAAAGATGAAG
65 TGATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * * *
17464 ATGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGATG---AAGATGCCAGTGTGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* * * *
17526 GATTCAAGGCTAGA-GACATTGGTCTTAAAGATGAAG
66 GATTCAAGGCCA-ACGATATCGGACTTAAAGATGAAG
* ***
17562 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACATAAAGATGACAAAGGCACCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
*
17627 GATTCAAGGCCAGCGATATCGGACTTAAA-ACTGAAG
66 GATTCAAGGCCAACGATATCGGACTTAAAGA-TGAAG
* * * * **
17663 ATGCCAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* * *
17728 GATTCAAGGCCAGCGATATTGGGC-T-----T---G
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * * *
17755 -TGCCAATGTGCTAATTCAAGGCCAGTGACATTGGTC-TTAA-A-GAC-AAGGTGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
* * * *
17815 AATTCAAGGCCAGCGATATTGGGC-T-----T----
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * * *
17841 ATGCCAATGTGCTGATCCAAGGCCAGCGACATTGGTC-T-TAGA-GAC-AAGGTGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
** * *
17902 GATTCAAGGCCAGTGATATTGGGC-T-----T----
66 GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
* * *
17928 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTC-TTAA-A-GACAAAG-TGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
*
17989 GATTCAAGGCCAGCGATAT
66 GATTCAAGGCCAACGATAT
18008 TGAGCTTATG
Statistics
Matches: 958, Mismatches: 104, Indels: 78
0.84 0.09 0.07
Matches are distributed among these distances:
86 5 0.01
87 443 0.46
88 17 0.02
89 4 0.00
90 6 0.01
91 61 0.06
92 3 0.00
93 1 0.00
95 2 0.00
97 40 0.04
98 88 0.09
100 5 0.01
101 280 0.29
102 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (101 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCATAAAGATGACAAAGATGCCAATATGCT
GATTCAAGGCCAACGATATCGGACTTAAAGATGAAG
Found at i:17202 original size:87 final size:87
Alignment explanation
Indices: 17015--18097 Score: 1266
Period size: 87 Copynumber: 12.0 Consensus size: 87
17005 AAAGATGAAG
* *
17015 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTATTAAAGATGACAAAGGCGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCT
* *
17080 GATTCAAGGCCTGTGATATTGGGCTT
62 GATTCAAGGCCAGCGATATTGGGCTT
* * * * *
17106 GTGCCAATGTGCTAATTCAAGGCCACCAACATTGGTCTTAAAGACAAGGTGCCAATATGTTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
17171 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * *
17193 ATGCTAATGTGCTGATTCAAGACCAGCGACATTGGTCTCAGAGACAAGGTGCCAATATGCTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
17258 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * *
17280 ATGCCAATGTGCTGATTCAAGGCTAACGACATTGGTCTTAAAGACAAAGTGCCAATATGCTAATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
17345 TAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * *
17367 ATGCCAATGTACTGATTCAAGGCCAGCGACATTGGTCTGAAAGAGAAGGTGCCAATATGTTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
17432 CAATGCCAGCGATATTGGTCTTAAAGAT
66 CAAGGCCAGCGATATTGGGC-T-----T
* * * * *
17460 GAAGATGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGATGAAGATGCCAGTGTGC
1 ----ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGC
* * * *
17525 TGATTCAAGGCTAGAGACATTGGTCTTAAAGAT
61 TGATTCAAGGCCAGCGATATTGGGC-T-----T
* * **
17558 GAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACATAAAGATGACAAAGGCACCAATA
1 ----ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC-TTAA-A-GAC-AAGGTGCCAATA
* *
17623 TGCTGATTCAAGGCCAGCGATATCGGACTTAAAACT
58 TGCTGATTCAAGGCCAGCGATATTGGGC-T-----T
* * *
17659 GAAGATGCCAATGTGTTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACAAAGGCGCCAATA
1 ----ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATA
17724 TGCTGATTCAAGGCCAGCGATATTGGGCTT
58 TGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * *
17754 GTGCCAATGTGCTAATTCAAGGCCAGTGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
17819 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* *
17841 ATGCCAATGTGCTGATCCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
17906 CAAGGCCAGTGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* *
17928 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAAGTGCCAATATGCTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
17993 CAAGGCCAGCGATATTGAGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * *
18015 ATGCCAATGTGCTGATTCAAGGCTATCGACATTGGTCTGAAAGACAAGGTGCCAATATGTTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
18080 CAATGCCAGCGATATTGG
66 CAAGGCCAGCGATATTGG
18098 TGTAGACACC
Statistics
Matches: 877, Mismatches: 99, Indels: 36
0.87 0.10 0.04
Matches are distributed among these distances:
87 545 0.62
88 7 0.01
89 2 0.00
90 4 0.00
91 68 0.08
93 1 0.00
95 1 0.00
97 41 0.05
98 80 0.09
99 3 0.00
100 3 0.00
101 122 0.14
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (87 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGGCTT
Found at i:17220 original size:39 final size:39
Alignment explanation
Indices: 17155--17401 Score: 179
Period size: 39 Copynumber: 5.9 Consensus size: 39
17145 AAAGACAAGG
* *
17155 TGCCAATATGTTGATTCAAGGCCAGCGATATTGGGCTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
* * * * *
17194 TGCTAATGTGCTGATTCAAGACCAGCGACATTGGTCTCAGAGACAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCT-------TA
*
17240 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 --TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
* * * *
17281 TGCCAATGTGCTGATTCAAGGCTAACGACATTGGTCTTAAAGACAAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT--------A
* * *
17328 GTGCCAATATGCTAATTTAAGGCCAGCGATATTGGGCTTA
1 -TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
* *
17368 TGCCAATGTACTGATTCAAGGCCAGCGACATTGG
1 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGG
17402 TCTGAAAGAG
Statistics
Matches: 160, Mismatches: 30, Indels: 36
0.71 0.13 0.16
Matches are distributed among these distances:
39 93 0.58
40 1 0.01
41 1 0.01
46 1 0.01
47 1 0.01
48 63 0.39
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (39 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTA
Found at i:17772 original size:39 final size:39
Alignment explanation
Indices: 17717--18037 Score: 219
Period size: 39 Copynumber: 7.5 Consensus size: 39
17707 TGACAAAGGC
17717 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
* * * * *
17756 GCCAATGTGCTAATTCAAGGCCAGTGACATTGGTCTTAAAGACAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT---------GT
* *
17804 GCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTAT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
* * * *
17843 GCCAATGTGCTGATCCAAGGCCAGCGACATTGGTCTTAGAGACAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT---------GT
* *
17891 GCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
* * * *
17930 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAAGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT---------GT
* *
17978 GCCAATATGCTGATTCAAGGCCAGCGATATTGAGCTTAT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
*
18017 GCCAATGTGCTGATTCAAGGC
1 GCCAATATGCTGATTCAAGGC
18038 TATCGACATT
Statistics
Matches: 220, Mismatches: 35, Indels: 54
0.71 0.11 0.17
Matches are distributed among these distances:
39 119 0.54
48 101 0.46
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGT
Found at i:18439 original size:13 final size:13
Alignment explanation
Indices: 18421--18445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18411 CATAAAGTGT
18421 TGTATCGATACAA
1 TGTATCGATACAA
18434 TGTATCGATACA
1 TGTATCGATACA
18446 TATTTTTTTT
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:18527 original size:13 final size:13
Alignment explanation
Indices: 18509--18533 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18499 ATCACTTAAA
18509 TGTATCGATACAT
1 TGTATCGATACAT
18522 TGTATCGATACA
1 TGTATCGATACA
18534 CTGATCTTTG
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:18598 original size:52 final size:52
Alignment explanation
Indices: 18542--18670 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
18532 CACTGATCTT
* *
18542 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
18594 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
18646 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
18671 TCATATTTCG
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:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:21800 original size:49 final size:49
Alignment explanation
Indices: 21726--22576 Score: 759
Period size: 49 Copynumber: 18.2 Consensus size: 49
21716 AGCGCACGTT
*
21726 GCGACAATTGGTTTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
1 GCGAC-ATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
21776 TCGACATTGGTCTTACAGATGAAGATGCCAATGTGTTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * ** * * * *
21825 ACAACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCTAATTCAAGTCTA
1 GCGACATTGGTCTTAAAGATG---AAGATGCCAATGTGCTGATTCAAGGCCA
* * * *
21877 GCGATATTGGGCTT---G-T---G--G-CAATGTGCTAATTCAAGGCTA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * * * *
21916 GCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTAATTCAAGGCTA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
21964 GCGATATTGGGC-T-----T----ATGCCAATGTGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * * * *
22003 GCGACATTGGTCTTAGAGA-CAAGGTGCTAATATGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
** *
22051 GCGATGTTGGGC-T-----T----ATGCCAATGTGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * ** * *
22090 ACGACATTAGTCTTAAAGACAAAG-TGCCAATATGTTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
22138 GCGATATTGAG-CTT----AT---G-T--CAATGTGCTGATTCAAGACTA
1 GCGACATTG-GTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * * * * * *
22177 CCGACATTGGTCTGAGAGA-CAGGGTG-CAATATGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
22224 GCGATATTGGTTTTAAAGATGAAGATGCCAATGTGCTGATTCAAAGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
*
22273 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGTTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
22322 GGGACATTGGCCTTAAAGACGAAGATGCCAATGTGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
22371 GCGACATTGGTCTTAAAGACGAAGATGCCAATGTGCTGATTCAAGACCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* * *
22420 GTGACATTGGTCTTAAAGATTAAGATGCCAATGTACTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
**
22469 ATGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
* *
22518 ACGACATTGGTCTTAAAGATGAATATGCCAATGTGCTGATTCAAGGCCA
1 GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
*
22567 GCGATATTGG
1 GCGACATTGG
22577 ATTTAGAAGA
Statistics
Matches: 658, Mismatches: 95, Indels: 97
0.77 0.11 0.11
Matches are distributed among these distances:
38 1 0.00
39 117 0.18
40 3 0.00
41 2 0.00
42 2 0.00
43 1 0.00
44 1 0.00
45 2 0.00
46 1 0.00
47 35 0.05
48 97 0.15
49 361 0.55
50 4 0.01
52 31 0.05
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (49 bp):
GCGACATTGGTCTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCA
Found at i:21917 original size:39 final size:39
Alignment explanation
Indices: 21854--22012 Score: 147
Period size: 39 Copynumber: 3.8 Consensus size: 39
21844 TGACAAAGGC
* *
21854 GCCAATATGCTAATTCAAGTCTAGCGATATTGGGCTTGT
1 GCCAATATGCTAATTCAAGGCTAGCGACATTGGGCTTGT
* * *
21893 GGCAATGTGCTAATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGT
1 GCCAATATGCTAATTCAAGGCTAGCGACATTGGGCTT---------GT
* *
21941 GCCAATATGCTAATTCAAGGCTAGCGATATTGGGCTTAT
1 GCCAATATGCTAATTCAAGGCTAGCGACATTGGGCTTGT
* * *
21980 GCCAATGTGCTGATTCAAGGCCAGCGACATTGG
1 GCCAATATGCTAATTCAAGGCTAGCGACATTGG
22013 TCTTAGAGAC
Statistics
Matches: 97, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
39 62 0.64
48 35 0.36
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (39 bp):
GCCAATATGCTAATTCAAGGCTAGCGACATTGGGCTTGT
Found at i:21973 original size:87 final size:87
Alignment explanation
Indices: 21800--22532 Score: 640
Period size: 87 Copynumber: 8.0 Consensus size: 87
21790 ACAGATGAAG
* * *
21800 ATGCCAATGTGTTGATTCAAGGCCAACAACATTGGTCTTAAAGATGACAAAGGCGCCAATATGCT
1 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCT
* * *
21865 AATTCAAGTCTAGCGATATTGGGCTT
62 GATTCAAGGCCAGCGATATTGGGCTT
* * * * * *
21891 GTGGCAATGTGCTAATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATT
1 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
21956 CAAGGCTAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * *
21978 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCTAATATGCTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
22043 CAAGGCCAGCGATGTTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * *
22065 ATGCCAATGTGCTGATTCAAGGCCAACGACATTAGTCTTAAAGACAAAGTGCCAATATGTTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
22130 CAAGGCCAGCGATATTGAGCTT
66 CAAGGCCAGCGATATTGGGCTT
* * * * * * *
22152 ATGTCAATGTGCTGATTCAAGACTACCGACATTGGTCTGAGAGACAGGGTG-CAATATGCTGATT
1 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* *
22216 CAAGGCCAGCGATATTGGTTTTAAAGATGAAG
66 CAAGGCCAGCGATATTGG-------GCT---T
* * * * * *
22248 ATGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTCTTAAAGATGAAGATGCCAATGTGTTGAT
1 ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGAT
* * *
22313 TCAAGGCCAGGGACATTGGCCTT
65 TCAAGGCCAGCGATATTGGGCTT
* *
22336 AAAGACGAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACGAAGATGCCA
1 ----------ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGAC-AAGGTGCCA
* * * * *
22401 ATGTGCTGATTCAAGACCAGTGACATTGGTCTTAAAGATT
55 ATATGCTGATTCAAGGCCAGCGATATTGG-------GCTT
* * * * *
22441 AAGATGCCAATGTACTGATTCAAGGCCAATGACATTGGTCTTAAAGATGAAGATGCCAATGTGCT
1 ---ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCT
* * *
22506 GATTCAAGGCCAACGACATTGGTCTT
62 GATTCAAGGCCAGCGATATTGGGCTT
22532 A
1 A
22533 AAGATGAATA
Statistics
Matches: 539, Mismatches: 72, Indels: 65
0.80 0.11 0.10
Matches are distributed among these distances:
86 29 0.05
87 239 0.44
88 4 0.01
89 1 0.00
90 2 0.00
91 35 0.06
93 2 0.00
96 37 0.07
97 4 0.01
98 184 0.34
105 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (87 bp):
ATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGGCTT
Found at i:22645 original size:29 final size:30
Alignment explanation
Indices: 22591--22756 Score: 164
Period size: 30 Copynumber: 5.6 Consensus size: 30
22581 AGAAGAAGAC
22591 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTT
1 GCCACCAAC-T-TGTGGGCTTTTGAAAGGGTT
*
22623 G-CACCAACTTGTGTGCTTTTG-AA-GGTT
1 GCCACCAACTTGTGGGCTTTTGAAAGGGTT
*
22650 G-CACCAACTTGTGGGC-TTTGAAAGGGGT
1 GCCACCAACTTGTGGGCTTTTGAAAGGGTT
*** * *
22678 GCCATTGACTTGTAGGCTTTTGAAAGGGGT
1 GCCACCAACTTGTGGGCTTTTGAAAGGGTT
*
22708 GCCACCGACTTGTGGGCTTTTGAAATGGG-T
1 GCCACCAACTTGTGGGCTTTTGAAA-GGGTT
** *
22738 GCCACTGACTTGTAGGCTT
1 GCCACCAACTTGTGGGCTT
22757 AAAAAGAGAA
Statistics
Matches: 117, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
26 4 0.03
27 21 0.18
28 6 0.05
29 22 0.19
30 53 0.45
31 10 0.09
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (30 bp):
GCCACCAACTTGTGGGCTTTTGAAAGGGTT
Found at i:22689 original size:56 final size:60
Alignment explanation
Indices: 22591--22756 Score: 200
Period size: 60 Copynumber: 2.8 Consensus size: 60
22581 AGAAGAAGAC
* ** *
22591 GCCACCAACTTGTGTGGGCTTTTGAAAGGGTTG-CACCAACTTGT-GTGCTTTTG-AA-GGTT
1 GCCACCAAC-T-TGTGGGCTTTTGAAAGGGGTGCCACTGACTTGTAG-GCTTTTGAAAGGGGT
*
22650 G-CACCAACTTGTGGGC-TTTGAAAGGGGTGCCATTGACTTGTAGGCTTTTGAAAGGGGT
1 GCCACCAACTTGTGGGCTTTTGAAAGGGGTGCCACTGACTTGTAGGCTTTTGAAAGGGGT
* *
22708 GCCACCGACTTGTGGGCTTTTGAAATGGGTGCCACTGACTTGTAGGCTT
1 GCCACCAACTTGTGGGCTTTTGAAAGGGGTGCCACTGACTTGTAGGCTT
22757 AAAAAGAGAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
55 12 0.13
56 22 0.24
57 4 0.04
58 11 0.12
59 15 0.16
60 29 0.31
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (60 bp):
GCCACCAACTTGTGGGCTTTTGAAAGGGGTGCCACTGACTTGTAGGCTTTTGAAAGGGGT
Found at i:22848 original size:34 final size:33
Alignment explanation
Indices: 22737--23329 Score: 356
Period size: 27 Copynumber: 19.0 Consensus size: 33
22727 TTGAAATGGG
* * * *
22737 TGCCACTGACTTGTAGG-CTTAAAAAGAGAAAGA
1 TGCCACGGAGTTGT-GGACTTAAAAGGAAAAAGA
* *
22770 TGCCACGGAGTTGTGGACTTAAAAGGAATAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
*
22803 TGCCACGGAGTTTTGGACTTAAAAGGAAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAG-A
* *
22837 TACCACGGAGTTGTGGGCTTAAAAGG-----G-
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* * * *
22864 TCCCACAGAGTTATGGACTTAAAGGGAAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAG-A
*
22898 TGCCACGGAGTTGTGGGCTTAAAAGG-----G-
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
**
22925 TGCCACGGAGTTGTGGGTTTAAAAGG-----G-
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* *
22952 TGCCACAGAGTTGTGGGCTTAAAAGG-----G-
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
*
22979 TGCCACAGAGTTGTGGACTTAAAAGG-----G-
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
23006 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
23039 GTGCCACGGAGTTGTGGACTTAAAAGG-----G-
1 -TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* *
23067 TGCCACAGAGTTGTGGACTTAAAAAGAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGAAAAAGA
* * * *
23101 GTGCCACAGAGTTGTGGGCTTTAAAGGAAATAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* * *
23135 GTGCCACAGAGTTGTGGGCTTTAAAAGGAAAAAGG
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGA
** * *
23170 TGCCACAAAGTTGTGAACTTAAAAAGAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
**
23203 GTGCCATAGAGTTGTGGACTT-AAA--AAAAAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* * * **
23234 TGCCACTGAGTCGTAGACTTTGAA-G-AAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
** * *
23265 TGCCACTAAGTCGTGGACTTGAAA-G-AAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
* * * ** *
23296 TGCTACTGAGTCGTGGACTTTGAAGGAAAGAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
23329 T
1 T
23330 TTGAAGAATT
Statistics
Matches: 472, Mismatches: 58, Indels: 60
0.80 0.10 0.10
Matches are distributed among these distances:
27 142 0.30
28 5 0.01
29 3 0.01
30 16 0.03
31 62 0.13
32 5 0.01
33 77 0.16
34 131 0.28
35 31 0.07
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.21
Consensus pattern (33 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGA
Found at i:22883 original size:61 final size:61
Alignment explanation
Indices: 22707--23227 Score: 287
Period size: 61 Copynumber: 8.4 Consensus size: 61
22697 TTGAAAGGGG
* * * * * * *
22707 TGCCACCGACTTGTGGGCTTTTGAAATGGGTGCCACTGACTTGTAGG-CTTAAAAAGAGAAAG-A
1 TGCCACGGAGTTGTGGGC--TT-AAAAGGGTGCCACAGAGTTGT-GGACTTAAAAGGAAAAAGAA
* * *
22770 TGCCACGGAGTTGTGGACTTAAAAGGAATAAGGTGCCACGGAGTTTTGGACTTAAAAGGAAAAAG
1 TGCCACGGAGTTGTGGGCTTAAAA-G-----GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG
22835 AA
60 AA
* * * *
22837 TACCACGGAGTTGTGGGCTTAAAAGGGTCCCACAGAGTTATGGACTTAAAGGGAAAAAGAA
1 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAA
* **
22898 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGTTTAAAAGG-----G--
1 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAA
*
22952 TGCCACAGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG-----G--
1 TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAA
* *
23006 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGG-----
1 TGCCACGGAGTTGTGGGCTTAAAA-G-----G-GTGCCACAGAGTTGTGGACTTAAAAGGAAAAA
23066 G--
59 GAA
* * * * *
23067 TGCCACAGAGTTGTGGACTTAAAAAGAAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAGGAAAT
1 TGCCACGGAGTTGTGGGCTT-AAAAG------G-GTGCCACAGAGTTGTGGACTTAAAAGGAAAA
*
23132 AGAG
58 AGAA
* * * *
23136 TGCCACAGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACAAAGTTGTGAACTTAAAAAGAAAAA
1 TGCCACGGAGTTGTGGGC-TTAAAA-G-----GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAA
*
23201 GAG
59 GAA
** *
23204 TGCCATAGAGTTGTGGACTTAAAA
1 TGCCACGGAGTTGTGGGCTTAAAA
23228 AAAAGATGCC
Statistics
Matches: 390, Mismatches: 42, Indels: 48
0.81 0.09 0.10
Matches are distributed among these distances:
54 72 0.18
55 1 0.00
56 1 0.00
60 4 0.01
61 128 0.33
62 35 0.09
63 15 0.04
65 2 0.01
66 27 0.07
67 30 0.08
68 45 0.12
69 27 0.07
70 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAA
Found at i:23037 original size:115 final size:117
Alignment explanation
Indices: 22767--23090 Score: 362
Period size: 115 Copynumber: 2.8 Consensus size: 117
22757 AAAAAGAGAA
* *
22767 AGATGCCACGGAGTTGTGGACTTAAAAGGAATAA-GGTGCCACGGAGTTTTGGACTTAAAAGGAA
1 AGATGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG--
* * *
22831 AAAGAATACCACGGAGTTGTGGGCTTAAAAGGGTCCCACAGAGTTATGGACTTAAAGGG
64 ---G--TGCCACAGAGTTGTGGGCTTAAAAGGGTCCCACAGAGTTATGGACTTAAAAGG
* **
22890 AAAAAGAATGCCACGGAGTTGTGGGCTT-------AAAAGGGTGCCACGGAGTTGTGGGTTTAAA
1 ----AG-ATGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTTAAA
* *
22948 AGGGTGCCACAGAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG
61 AGGGTGCCACAGAGTTGTGGGCTTAAAAGGGTCCCACAGAGTTATGGACTTAAAAGG
*
23005 -G-TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGT
1 AGATGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGT
*
23068 GCCACAGAGTTGTGGACTTAAAA
66 GCCACAGAGTTGTGGGCTTAAAA
23091 AGAAAAAAGA
Statistics
Matches: 173, Mismatches: 15, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
108 19 0.11
110 1 0.01
115 102 0.59
117 1 0.01
121 3 0.02
122 25 0.14
127 2 0.01
128 20 0.12
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (117 bp):
AGATGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGT
GCCACAGAGTTGTGGGCTTAAAAGGGTCCCACAGAGTTATGGACTTAAAAGG
Found at i:23099 original size:35 final size:35
Alignment explanation
Indices: 23060--23228 Score: 227
Period size: 34 Copynumber: 4.9 Consensus size: 35
23050 TTGTGGACTT
* *
23060 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGAA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAAGGA
* *
23095 AAAAGAGTGCCACAGAGTTGTGGGCTT-TAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAAGGA
* * *
23129 AATAGAGTGCCACAGAGTTGTGGGCTTTAAAAGGA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAAGGA
* *
23164 AAAAG-GTGCCACAAAGTTGTGAACTTAAAAA-GA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAAGGA
*
23197 AAAAGAGTGCCATAGAGTTGTGGACTTAAAAA
1 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAA
23229 AAAGATGCCA
Statistics
Matches: 118, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
33 7 0.06
34 76 0.64
35 35 0.30
ACGTcount: A:0.41, C:0.11, G:0.28, T:0.20
Consensus pattern (35 bp):
AAAAGAGTGCCACAGAGTTGTGGACTTAAAAAGGA
Found at i:23296 original size:31 final size:31
Alignment explanation
Indices: 23164--23329 Score: 140
Period size: 31 Copynumber: 5.2 Consensus size: 31
23154 TTTAAAAGGA
* * * * *
23164 AAAAGGTGCCACAAAGTTGTGAACTTAAAAAG
1 AAAAGATGCCACTAAGTCGTGGACTT-GAAAG
* *
23196 AAAAAGAGTGCCA-TAGAGTTGTGGACTT-AAAA
1 -AAAAGA-TGCCACTA-AGTCGTGGACTTGAAAG
* *
23228 AAAAGATGCCACTGAGTCGTAGACTTTG-AAG
1 AAAAGATGCCACTAAGTCGTGGAC-TTGAAAG
23259 AAAAGATGCCACTAAGTCGTGGACTTGAAAG
1 AAAAGATGCCACTAAGTCGTGGACTTGAAAG
* * *
23290 AAAAGATGCTACTGAGTCGTGGACTTTGAAGG
1 AAAAGATGCCACTAAGTCGTGGAC-TTGAAAG
23322 AAAGAGAT
1 AAA-AGAT
23330 TTGAAGAATT
Statistics
Matches: 112, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
30 16 0.14
31 58 0.52
32 12 0.11
33 10 0.09
34 16 0.14
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (31 bp):
AAAAGATGCCACTAAGTCGTGGACTTGAAAG
Found at i:23296 original size:62 final size:62
Alignment explanation
Indices: 23197--23327 Score: 185
Period size: 62 Copynumber: 2.1 Consensus size: 62
23187 CTTAAAAAGA
*
23197 AAAAGAGTGCCATAGAGTTGTGGACTTAAAAAAAAGATGCCACTGAGTCGTAGACTTTGAAG
1 AAAAGAGTGCCATAGAGTCGTGGACTTAAAAAAAAGATGCCACTGAGTCGTAGACTTTGAAG
* * *
23259 AAAAGA-TGCCACTA-AGTCGTGGACTTGAAAGAAAAGATGCTACTGAGTCGTGGACTTTGAAG
1 AAAAGAGTGCCA-TAGAGTCGTGGACTT-AAAAAAAAGATGCCACTGAGTCGTAGACTTTGAAG
*
23321 GAAAGAG
1 AAAAGAG
23328 ATTTGAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 16 0.26
62 45 0.74
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.21
Consensus pattern (62 bp):
AAAAGAGTGCCATAGAGTCGTGGACTTAAAAAAAAGATGCCACTGAGTCGTAGACTTTGAAG
Found at i:23448 original size:8 final size:8
Alignment explanation
Indices: 23424--23461 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
23414 GATGCAAATA
23424 ATGATGTT
1 ATGATGTT
23432 ATCGATGTT
1 AT-GATGTT
23441 ATGATGTT
1 ATGATGTT
*
23449 ATGATGTC
1 ATGATGTT
23457 ATGAT
1 ATGAT
23462 TATAGCACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
8 20 0.71
9 8 0.29
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (8 bp):
ATGATGTT
Found at i:24536 original size:6 final size:6
Alignment explanation
Indices: 24527--24581 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
24517 CTTTGAACTC
*
24527 TTTTT- TTTTTG TTTTTG TTTTTG TTTTT- TTTTGTG TTGTTTT TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT-TG TT-TTTG TTTTTG
*
24575 TGTTTG T
1 TTTTTG T
24582 ACTTTTGAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
5 9 0.21
6 27 0.63
7 5 0.12
8 2 0.05
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:24556 original size:15 final size:14
Alignment explanation
Indices: 24527--24573 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
24517 CTTTGAACTC
24527 TTTTTTTTTTG--T
1 TTTTTTTTTTGTTT
*
24539 TTTTGTTTTTGTTT
1 TTTTTTTTTTGTTT
*
24553 TTTTTTGTGTTGTTT
1 TTTTTT-TTTTGTTT
24568 TTTTTT
1 TTTTTT
24574 GTGTTTGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 10 0.34
14 6 0.21
15 13 0.45
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TTTTTTTTTTGTTT
Found at i:24557 original size:27 final size:27
Alignment explanation
Indices: 24527--24579 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
24517 CTTTGAACTC
24527 TTTTTTT-T-TTGTTTTTGTTTT-TGTT
1 TTTTTTTGTGTTGTTTTT-TTTTGTGTT
24552 TTTTTTTGTGTTGTTTTTTTTTGTGTT
1 TTTTTTTGTGTTGTTTTTTTTTGTGTT
24579 T
1 T
24580 GTACTTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.28
26 5 0.20
27 13 0.52
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (27 bp):
TTTTTTTGTGTTGTTTTTTTTTGTGTT
Found at i:24587 original size:16 final size:16
Alignment explanation
Indices: 24533--24581 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 16
24523 ACTCTTTTTT
*
24533 TTTTGTTTTTGTTTTTG
1 TTTT-TTTTTGTGTTTG
24550 TTTTTTTTTGTG-TTG
1 TTTTTTTTTGTGTTTG
24565 TTTTTTTTTGTGTTTG
1 TTTTTTTTTGTGTTTG
24581 T
1 T
24582 ACTTTTGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 15 0.50
16 11 0.37
17 4 0.13
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTGTGTTTG
Found at i:31596 original size:13 final size:13
Alignment explanation
Indices: 31578--31602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31568 TACAAAGATC
31578 AATGTATCGATAT
1 AATGTATCGATAT
31591 AATGTATCGATA
1 AATGTATCGATA
31603 CATTGAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:31601 original size:33 final size:33
Alignment explanation
Indices: 31559--31622 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
31549 TCATTCCCAG
31559 ATGTATCGATACAAAG-ATCAATGTATCGATATA
1 ATGTATCGATACAAAGAAT-AATGTATCGATATA
**
31592 ATGTATCGATACATTGAATAATGTATCGATA
1 ATGTATCGATACAAAGAATAATGTATCGATA
31623 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATATA
Found at i:31614 original size:20 final size:20
Alignment explanation
Indices: 31589--31626 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
31579 ATGTATCGAT
31589 ATAATGTATCGATACATTGA
1 ATAATGTATCGATACATTGA
31609 ATAATGTATCGATACATT
1 ATAATGTATCGATACATT
31627 TCCTTGGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAATGTATCGATACATTGA
Found at i:32173 original size:3 final size:3
Alignment explanation
Indices: 32159--32201 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
32149 AGTCAACTTT
* * *
32159 TCA TCG TCA TCA TCA TCA TCA TTA TCA TCA TCT TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
32202 TGATGGTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:33799 original size:20 final size:20
Alignment explanation
Indices: 33774--33828 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
33764 GTTGGGCTCA
* * *
33774 ATGTATCGATATATTTTATC
1 ATGTATCGATACAATTCATC
*
33794 ATGTATCAATACAATTCATC
1 ATGTATCGATACAATTCATC
*
33814 ATGTATCGTTACAAT
1 ATGTATCGATACAAT
33829 GTATCGATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:36762 original size:22 final size:22
Alignment explanation
Indices: 36736--36814 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
36726 TTTCGTTACC
36736 ATGTTATTAATAATTTACTAAT
1 ATGTTATTAATAATTTACTAAT
* **
36758 ATGTTATTAATAA-TTATTTGT
1 ATGTTATTAATAATTTACTAAT
*
36779 ATGTTATCAATAATTTACTAAT
1 ATGTTATTAATAATTTACTAAT
*
36801 ATATTA-TAA-AATTT
1 ATGTTATTAATAATTT
36815 TTAATATATG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.11
21 19 0.40
22 23 0.49
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (22 bp):
ATGTTATTAATAATTTACTAAT
Found at i:36825 original size:43 final size:43
Alignment explanation
Indices: 36736--36855 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
36726 TTTCGTTACC
* * *
36736 ATGTTATTAATAATTTACTAATATGTTATTAATAATTATTTGT
1 ATGTTATCAATAATTTACTAATATATTATTAATAATTATTTAT
*
36779 ATGTTATCAATAATTTACTAATATATTA-TAA-AATTTTTAATAT
1 ATGTTATCAATAATTTACTAATATATTATTAATAATTATT--TAT
* * * * * *
36822 ATGTTGTTAAAAAGTTATTACTATATTATTAATA
1 ATGTTATCAATAATTTACTAATATATTATTAATA
36856 TTTTACTCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
41 6 0.10
42 3 0.05
43 50 0.79
44 3 0.05
45 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (43 bp):
ATGTTATCAATAATTTACTAATATATTATTAATAATTATTTAT
Found at i:37383 original size:15 final size:15
Alignment explanation
Indices: 37363--37393 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37353 TACTGAATTT
37363 TAAATAATTTCATAA
1 TAAATAATTTCATAA
*
37378 TAAATAATTTTATAA
1 TAAATAATTTCATAA
37393 T
1 T
37394 GTAGATAATT
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATAATTTCATAA
Found at i:41125 original size:13 final size:13
Alignment explanation
Indices: 41107--41132 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41097 TACAGCAAGT
41107 ATGTATCGATACA
1 ATGTATCGATACA
41120 ATGTATCGATACA
1 ATGTATCGATACA
41133 CAAAAAATTG
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:43186 original size:15 final size:15
Alignment explanation
Indices: 43166--43196 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43156 TAAAAATGTC
*
43166 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
43181 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
43196 C
1 C
43197 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:45294 original size:13 final size:13
Alignment explanation
Indices: 45276--45301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45266 ACATTTTTCT
45276 TTGTATCGATACA
1 TTGTATCGATACA
45289 TTGTATCGATACA
1 TTGTATCGATACA
45302 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:45446 original size:21 final size:20
Alignment explanation
Indices: 45422--45468 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
45412 AAATCTTTTG
*
45422 CAAAATGCTT-GTTTTTCACTT
1 CAAAATACTTCGTTTTTCA--T
*
45443 CAAATTACTTCGTTTTTCAT
1 CAAAATACTTCGTTTTTCAT
45463 CAAAAT
1 CAAAAT
45469 CAGCATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 8 0.36
22 8 0.36
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (20 bp):
CAAAATACTTCGTTTTTCAT
Found at i:47867 original size:13 final size:13
Alignment explanation
Indices: 47849--47874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47839 TACAGCAAGT
47849 ATGTATCGATACA
1 ATGTATCGATACA
47862 ATGTATCGATACA
1 ATGTATCGATACA
47875 CAAAAAATTG
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:50626 original size:22 final size:22
Alignment explanation
Indices: 50578--50629 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
50568 GTTATTAAAA
* * **
50578 TTTTACTATTGTGCTATTGATC
1 TTTTATTATTGTGATATCAATC
*
50600 ATTTATTATTGTGATATCAATC
1 TTTTATTATTGTGATATCAATC
50622 TTTTATTA
1 TTTTATTA
50630 GTATTATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTTATTATTGTGATATCAATC
Found at i:50972 original size:15 final size:14
Alignment explanation
Indices: 50952--50992 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
50942 TTGATTAATC
50952 AAATTTTAATTGCTT
1 AAATTTTAATT-CTT
*
50967 AAATTTTAAAATCTT
1 AAATTTT-AATTCTT
50982 AAATTTTAATT
1 AAATTTTAATT
50993 TTTTCTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 3 0.13
15 17 0.74
16 3 0.13
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (14 bp):
AAATTTTAATTCTT
Found at i:51882 original size:21 final size:22
Alignment explanation
Indices: 51838--51890 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
51828 TAAATTTTAA
51838 TAAATTAATAAAATTATAAATT
1 TAAATTAATAAAATTATAAATT
*
51860 TAAA-TAA-AAAATGTATTAATT
1 TAAATTAATAAAAT-TATAAATT
*
51881 TAACTTAATA
1 TAAATTAATA
51891 TTCACAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 5 0.19
21 13 0.50
22 7 0.27
23 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATTAATAAAATTATAAATT
Found at i:52191 original size:102 final size:106
Alignment explanation
Indices: 52007--52304 Score: 274
Period size: 102 Copynumber: 2.8 Consensus size: 106
51997 TTTTATTTTT
* *
52007 ACTTTATTTTTAAATAATTAGTTTATTTAAATTTAAATAAATTAATAAAAATTACATATTTAGAT
1 ACTTTATTTTTAAATAATTAGTTAATTTAAATTTAAAT-AATTAATAAAAATTACATATTTAAAT
52072 AGGAAAAGTTTATTAATTTTAAAATCATTTAATATCATGTGG
65 AGGAAAAGTTTATTAATTTTAAAATCATTTAATATCATGTGG
* * * *
52114 ACTTTATTTTTAAATATTTA-TTAATTTAAATTTAAAT-A-TACTAATAATTATATA-TTAAATA
1 ACTTTATTTTTAAATAATTAGTTAATTTAAATTTAAATAATTAATAAAAATTACATATTTAAATA
* * * * *
52175 -GAAGAATTTTATTAATTTTAAAGT-AGATTAATATTACGT--
66 GGAA-AAGTTTATTAATTTTAAAATCA-TTTAATATCATGTGG
* *** * *
52214 AATTT-TTTTTTTTTACATATAGTTTATTTAAATTTAAAATCAATTAAT-AAAATTACGTATTTA
1 ACTTTATTTTTAAATA-AT-TAGTTAATTTAAATTT-AAAT-AATTAATAAAAATTACATATTTA
* * * *
52277 AATAAGACATGTTTGTTAATTTTAAAAT
62 AATAGGAAAAGTTTATTAATTTTAAAAT
52305 TTTAAATTGA
Statistics
Matches: 154, Mismatches: 26, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
99 7 0.05
100 5 0.03
101 6 0.04
102 46 0.30
103 17 0.11
104 1 0.01
105 9 0.06
106 42 0.27
107 21 0.14
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (106 bp):
ACTTTATTTTTAAATAATTAGTTAATTTAAATTTAAATAATTAATAAAAATTACATATTTAAATA
GGAAAAGTTTATTAATTTTAAAATCATTTAATATCATGTGG
Found at i:52417 original size:228 final size:228
Alignment explanation
Indices: 52129--52570 Score: 622
Period size: 228 Copynumber: 1.9 Consensus size: 228
52119 ATTTTTAAAT
* *
52129 ATTTATTAATTTAAATTTAAATATACTAATAATTATATATTAAATAGAAGAATTTTATTAATTTT
1 ATTTATTAACTTAAATTTAAATATACTAATAATTATATATTAAATAAAAGAATTTTATTAATTTT
* * ** * *
52194 AAAGTAGATTAATATTACGT-AATTTTTTTTTTTTACATATAGTTTATTTAAATTTAAAATCAAT
66 AAAGTAGATTAATA-TACGTGAATTCTATTTTTAAACATATAATTTATTTAAATTTAAAATAAAT
* * * *
52258 TAATAAAATTACGTATTTAAATAAGACATGTTTGTTAATTTTA-AAATTTTAAATTGATATTT-C
130 GAATAAAATTACATATTTAAATAAGACATGTTTGCTAATCTTAGAAATTTTAAATTGATATTTAC
52321 TTTGTTTATTTTTAATACTTTTAAAATATTAATA
195 TTTGTTTATTTTTAATACTTTTAAAATATTAATA
* *
52355 ATTTATTAACTTAAATTTAAATTTATTAATAAATTACCTAT-TTAAATAAAAGAATTTTATTAAT
1 ATTTATTAACTTAAATTTAAATATACTAAT-AATTA--TATATTAAATAAAAGAATTTTATTAAT
* * *
52419 TTTAAAGTAGATTAATATATGTGAATTCTATTTTTAAACATTTAATTTATTTTAATTTAAAATAA
63 TTTAAAGTAGATTAATATACGTGAATTCTATTTTTAAACATATAATTTATTTAAATTTAAAATAA
* * * *
52484 ATGAATAAAATTACATATTTAAATAGGATATGTTTGCTAATCTTAGAATTTTTAAATTGATGTTT
128 ATGAATAAAATTACATATTTAAATAAGACATGTTTGCTAATCTTAGAAATTTTAAATTGATATTT
*
52549 ATTTTGTTTATTTTTAATACTT
193 ACTTTGTTTATTTTTAATACTT
52571 CTGAAGTTTA
Statistics
Matches: 188, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
226 27 0.14
227 9 0.05
228 112 0.60
229 20 0.11
230 20 0.11
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (228 bp):
ATTTATTAACTTAAATTTAAATATACTAATAATTATATATTAAATAAAAGAATTTTATTAATTTT
AAAGTAGATTAATATACGTGAATTCTATTTTTAAACATATAATTTATTTAAATTTAAAATAAATG
AATAAAATTACATATTTAAATAAGACATGTTTGCTAATCTTAGAAATTTTAAATTGATATTTACT
TTGTTTATTTTTAATACTTTTAAAATATTAATA
Found at i:56523 original size:23 final size:22
Alignment explanation
Indices: 56496--56558 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
56486 ATATAATAAA
56496 AAAAATTATTTTAA-ATTAAATTAT
1 AAAAA-TATTTTAATA-TAAA-TAT
*
56520 AAAAATATATTAATATAAATAT
1 AAAAATATTTTAATATAAATAT
56542 AAAAATATTTTTAATAT
1 AAAAATA-TTTTAATAT
56559 TTTTTAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 10 0.29
23 19 0.54
24 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAATATTTTAATATAAATAT
Found at i:57144 original size:13 final size:12
Alignment explanation
Indices: 57124--57158 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
57114 TAAAATTTAT
57124 ATATATATATTA
1 ATATATATATTA
57136 ATATCATATATTA
1 ATAT-ATATATTA
57149 ATATA-ATATT
1 ATATATATATT
57159 TTAGATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.23
12 5 0.23
13 12 0.55
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATATATTA
Found at i:58294 original size:11 final size:11
Alignment explanation
Indices: 58267--58320 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
58257 AAATTTCATA
*
58267 ATTTATATTTT
1 ATTTATATTAT
58278 ATTTTATATTAT
1 A-TTTATATTAT
58290 ATTTATATTAT
1 ATTTATATTAT
* *
58301 TTTTATGTTAT
1 ATTTATATTAT
*
58312 AATTATATT
1 ATTTATATT
58321 TAAAATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
11 26 0.72
12 10 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:58295 original size:6 final size:6
Alignment explanation
Indices: 58267--58322 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
58257 AAATTTCATA
58267 ATTTAT ATTT-T ATTT-T ATATTAT ATTTAT A-TTAT -TTT-T ATGTTAT
1 ATTTAT ATTTAT ATTTAT AT-TTAT ATTTAT ATTTAT ATTTAT AT-TTAT
*
58312 AATTAT ATTTA
1 ATTTAT ATTTA
58323 AAATATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
4 1 0.02
5 15 0.36
6 21 0.50
7 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (6 bp):
ATTTAT
Found at i:58311 original size:22 final size:23
Alignment explanation
Indices: 58267--58320 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
58257 AAATTTCATA
*
58267 ATTTATATTTTATTTTATATTAT
1 ATTTATATTATATTTTATATTAT
*
58290 ATTTATATTAT-TTTTATGTTAT
1 ATTTATATTATATTTTATATTAT
*
58312 AATTATATT
1 ATTTATATT
58321 TAAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTATATTATATTTTATATTAT
Found at i:58333 original size:28 final size:27
Alignment explanation
Indices: 58270--58333 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
58260 TTTCATAATT
* * *
58270 TATATTTTATTTTATATTATATTTATAT
1 TATA-TTTATGTTATATTATATTTAAAA
*
58298 TATTTTTATGTTATAATTATATTTAAAA
1 TATATTTATGTTAT-ATTATATTTAAAA
58326 TATATTTA
1 TATATTTA
58334 AAAATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TATATTTATGTTATATTATATTTAAAA
Found at i:58363 original size:29 final size:30
Alignment explanation
Indices: 58324--58384 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
58314 TTATATTTAA
*
58324 AATATATTTAAAAATATTTTTATA-AATTTT
1 AATATATTTAAAAAT-TTATTATATAATTTT
58354 AATATA-TTAAAAATTTATTATATAATTTT
1 AATATATTTAAAAATTTATTATATAATTTT
58383 AA
1 AA
58385 AATTTATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.24
29 16 0.55
30 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
AATATATTTAAAAATTTATTATATAATTTT
Found at i:61206 original size:18 final size:18
Alignment explanation
Indices: 61183--61219 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
61173 ATGATTAAAT
61183 TTGTGGATTGAAATATGA
1 TTGTGGATTGAAATATGA
61201 TTGTGGATTGAAATATGA
1 TTGTGGATTGAAATATGA
61219 T
1 T
61220 AGTTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.41
Consensus pattern (18 bp):
TTGTGGATTGAAATATGA
Found at i:71555 original size:61 final size:61
Alignment explanation
Indices: 71486--71608 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
71476 GATTTTGTAA
*
71486 GAACTAGAAAAAAAAAAGACAAAAACTATTTCTTCAAGGTGATCTGCTGAATCTTACCAAG
1 GAACTAGAAAAAAAAAAGACAAAAACTATTTCTTCAAGGTGATCTACTGAATCTTACCAAG
*
71547 GAACTAGAAAAAAAAAAGATAAAAACTATTTCTTCAAGGTGATCTACTGAATCTTACCAAG
1 GAACTAGAAAAAAAAAAGACAAAAACTATTTCTTCAAGGTGATCTACTGAATCTTACCAAG
71608 G
1 G
71609 TTTTGATGTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (61 bp):
GAACTAGAAAAAAAAAAGACAAAAACTATTTCTTCAAGGTGATCTACTGAATCTTACCAAG
Done.