Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 20 of 150
Found at i:5265588 original size:9 final size:9
Alignment explanation
Indices: 5265574--5265686 Score: 97
Period size: 9 Copynumber: 12.6 Consensus size: 9
5265564 TATTTATGTA
5265574 TTATGTAAG
1 TTATGTAAG
5265583 TTATGTAAG
1 TTATGTAAG
*
5265592 TTATGATATG
1 TTATG-TAAG
* * *
5265602 ATATAT-AT
1 TTATGTAAG
5265610 TTATGTAAG
1 TTATGTAAG
*
5265619 TTATGTAAA
1 TTATGTAAG
*
5265628 TTATGCAAG
1 TTATGTAAG
5265637 TTATGTAAG
1 TTATGTAAG
*
5265646 TTATGATATG
1 TTATG-TAAG
* *
5265656 ATATAT-A-
1 TTATGTAAG
5265663 TTAATGTAAG
1 TT-ATGTAAG
5265673 TTATGTAAG
1 TTATGTAAG
5265682 TTATG
1 TTATG
5265687 ATTATCATCT
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
7 1 0.01
8 7 0.09
9 58 0.73
10 14 0.17
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5265614 original size:27 final size:27
Alignment explanation
Indices: 5265583--5265677 Score: 120
Period size: 27 Copynumber: 3.5 Consensus size: 27
5265573 ATTATGTAAG
5265583 TTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGATATGATATATAT
* * ** *
5265610 TTATGTAAGTTATGTAAATTATGCA-AG
1 TTATGTAAGTTATG-ATATGATATATAT
5265637 TTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGATATGATATATAT
*
5265664 TAATGTAAGTTATG
1 TTATGTAAGTTATG
5265678 TAAGTTATGA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
26 6 0.11
27 43 0.78
28 6 0.11
ACGTcount: A:0.37, C:0.01, G:0.17, T:0.45
Consensus pattern (27 bp):
TTATGTAAGTTATGATATGATATATAT
Found at i:5265638 original size:54 final size:54
Alignment explanation
Indices: 5265573--5265686 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 54
5265563 ATATTTATGT
* *
5265573 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
1 ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
5265627 ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
1 ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
*
5265681 GTTATG
1 ATTATG
5265687 ATTATCATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.45
Consensus pattern (54 bp):
ATTATGCAAGTTATGTAAGTTATGATATGATATATATTAATGTAAGTTATGTAA
Found at i:5265715 original size:13 final size:13
Alignment explanation
Indices: 5265697--5265721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5265687 ATTATCATCT
5265697 TTAAATTTTAACA
1 TTAAATTTTAACA
5265710 TTAAATTTTAAC
1 TTAAATTTTAAC
5265722 CCTTTAATTA
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTTTAACA
Found at i:5265988 original size:17 final size:17
Alignment explanation
Indices: 5265966--5265998 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5265956 ACTAACCTTA
5265966 CATGATAAATGAAATTG
1 CATGATAAATGAAATTG
5265983 CATGATAAATGAAATT
1 CATGATAAATGAAATT
5265999 ATATTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (17 bp):
CATGATAAATGAAATTG
Found at i:5266527 original size:43 final size:43
Alignment explanation
Indices: 5266480--5266702 Score: 290
Period size: 43 Copynumber: 5.2 Consensus size: 43
5266470 AAAGAAAAAT
*
5266480 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAC
5266523 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAC
* ** *
5266566 GCCGCTAAAGACCATAACCTTTAGCGGTGCTTCTATCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAC
* * *
5266609 GCCGCTAAAGAACATGACTTTTAGCGACGCTTTTGTCACAAAC
1 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAC
* * * * *
5266652 GCCGCTATAA-AACA-AACCTTTAGCGACGCGTCTCA-CAAAAAC
1 GCCGCTA-AAGACCATGACCTTTAGCGACGC-TTTTATCACAAAC
5266694 GCCGCTAAA
1 GCCGCTAAA
5266703 AACATAACAT
Statistics
Matches: 160, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.01
42 26 0.16
43 130 0.81
44 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAC
Found at i:5266603 original size:86 final size:86
Alignment explanation
Indices: 5266480--5266707 Score: 320
Period size: 86 Copynumber: 2.7 Consensus size: 86
5266470 AAAGAAAAAT
* * *
5266480 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGACCATGACCTTT
1 GCCGCTAAAGACCATAACCTTTAGCGGCGCTTCTATCACAAACGCCGCTAAAGAACATGACCTTT
5266545 AGCGACGCTTTTATCACAAAC
66 AGCGACGCTTTTATCACAAAC
* *
5266566 GCCGCTAAAGACCATAACCTTTAGCGGTGCTTCTATCACAAACGCCGCTAAAGAACATGACTTTT
1 GCCGCTAAAGACCATAACCTTTAGCGGCGCTTCTATCACAAACGCCGCTAAAGAACATGACCTTT
*
5266631 AGCGACGCTTTTGTCACAAAC
66 AGCGACGCTTTTATCACAAAC
* * * *
5266652 GCCGCTATAA-AACA-AACCTTTAGCGACGCGTCTCA-CAAAAACGCCGCTAAA-AACAT
1 GCCGCTA-AAGACCATAACCTTTAGCGGCGCTTCT-ATCACAAACGCCGCTAAAGAACAT
5266708 AACATTTAAA
Statistics
Matches: 129, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
84 5 0.04
85 31 0.24
86 91 0.71
87 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (86 bp):
GCCGCTAAAGACCATAACCTTTAGCGGCGCTTCTATCACAAACGCCGCTAAAGAACATGACCTTT
AGCGACGCTTTTATCACAAAC
Found at i:5268448 original size:22 final size:22
Alignment explanation
Indices: 5268423--5268480 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
5268413 CCCCTGAATC
5268423 CTTAAACCC-TAA-ATCCTTAACT
1 CTTAAACCCATAACAT-C-TAACT
5268445 CTT-AACCTCATAACATCTAACT
1 CTTAAACC-CATAACATCTAACT
*
5268467 CTTAAACCCCTAAC
1 CTTAAACCCATAAC
5268481 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 4 0.13
22 17 0.55
23 8 0.26
24 2 0.06
ACGTcount: A:0.36, C:0.34, G:0.00, T:0.29
Consensus pattern (22 bp):
CTTAAACCCATAACATCTAACT
Found at i:5268543 original size:22 final size:21
Alignment explanation
Indices: 5268503--5268543 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5268493 AATCCCAACC
*
5268503 CTTAAACCATAATCTCTAATT
1 CTTAAACCATAATCCCTAATT
*
5268524 CTTAAACCCATACTCCCTAA
1 CTTAAA-CCATAATCCCTAA
5268544 ACCTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (21 bp):
CTTAAACCATAATCCCTAATT
Found at i:5268549 original size:22 final size:21
Alignment explanation
Indices: 5268474--5268551 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
5268464 ACTCTTAAAC
* * *
5268474 CCCTAACCCCTAAACCTTCAAT
1 CCCTAAACCTTAAACCAT-AAT
*
5268496 CCC-AACCCTTAAACCATAAT
1 CCCTAAACCTTAAACCATAAT
* ** *
5268516 CTCTAATTCTTAAACCCATACT
1 CCCTAAACCTTAAA-CCATAAT
5268538 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
5268552 ATAGTAACTC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 5 0.11
21 20 0.44
22 20 0.44
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (21 bp):
CCCTAAACCTTAAACCATAAT
Found at i:5268952 original size:41 final size:41
Alignment explanation
Indices: 5268892--5269009 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 41
5268882 TAAAATGTTT
* *
5268892 TTAGCGGCGC-TTTCTCAAAAGCGCTGCTAAAGCCCCTAGCA
1 TTAGCGGCGCTTTTC-CAAAAACGCCGCTAAAGCCCCTAGCA
*
5268933 TTAGCGGCGCTTTTCCAAAAATGCCGCTAAAGCCCCTAGCA
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCTAGCA
5268974 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCC
1 TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCC
5269010 GAAAGGTCAG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 68 0.94
42 4 0.06
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCTAGCA
Found at i:5270699 original size:127 final size:127
Alignment explanation
Indices: 5270408--5270902 Score: 695
Period size: 127 Copynumber: 4.0 Consensus size: 127
5270398 CGTTTGTAGT
* * * **
5270408 GTTTTTTACCTAGCGCCACTATTGCTCGATCTATTGCGGCG-TTTTCACCTAGTACCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCCGCTAATGC
* * *
5270472 CACTAAAGACGCCACTTAAAATGGCGCTGTTTTGTTTAAAGT-AAA------TTTTTACAGC
66 CACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
* * * *
5270527 GTTTTTTACCTAGCGTCGCTAATGTTCTATCTATTGCAGCGTTTTTCACCTAGCGCCGCCAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCCGCTAATGC
* *
5270592 CACTAAAGACGCTACTTAAAATGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
66 CACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
* * *
5270654 GTTTTTTACCTAGCGCCGCTAATGCTTGATCTATTGCGGCGTTTTTCACCTAGTGCCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCCGCTAATGC
* * * * * *
5270719 CATTAAAGACGCCACGTAAAACGGCGTCATTTTGTTTAAAGTAAAATGTTTTTTTGTG--GT
66 CACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
*
5270779 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCATTTTTCACCTAGCGCCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCCGCTAATGC
*
5270844 CACTAAAGATGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGC
66 CACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGC
5270903 TGCATTTTAA
Statistics
Matches: 330, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
119 35 0.11
120 60 0.18
121 3 0.01
125 114 0.35
127 118 0.36
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (127 bp):
GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCCGCTAATGC
CACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
Found at i:5270837 original size:125 final size:125
Alignment explanation
Indices: 5270400--5270898 Score: 686
Period size: 125 Copynumber: 4.0 Consensus size: 125
5270390 AAAATGACCG
* * * * **
5270400 TTTGTAGTGTTTTTTACCTAGCGCCACTATTGCTCGATCTATTGCGGCG-TTTTCACCTAGTACC
1 TTTGTAGCGTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCC
* *
5270464 GCTAATGCCACTAAAGACGCCACTTAAAATGGCGCTGTTTTGTTTAAAGT-AAA----TT
66 GCTAATGCCACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTT
** * * *
5270519 TTTACAGCGTTTTTTACCTAGCGTCGCTAATGTTCTATCTATTGCAGCGTTTTTCACCTAGCGCC
1 TTTGTAGCGTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCC
* * *
5270584 GCCAATGCCACTAAAGACGCTACTTAAAATGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTT
66 GCTAATGCCACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATG--TTTT
* * * *
5270646 TTTGCAGCGTTTTTTACCTAGCGCCGCTAATGCTTGATCTATTGCGGCGTTTTTCACCTAGTGCC
1 TTTGTAGCGTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCC
* * * *
5270711 GCTAATGCCATTAAAGACGCCACGTAAAACGGCGTCATTTTGTTTAAAGTAAAATGTTTT
66 GCTAATGCCACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTT
* * *
5270771 TTTGTGGTGTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCATTTTTCACCTAGCGCC
1 TTTGTAGCGTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCC
*
5270836 GCTAATGCCACTAAAGATGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTT
66 GCTAATGCCACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTT
5270896 TTT
1 TTT
5270899 TTGCTGCATT
Statistics
Matches: 332, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
119 40 0.12
120 60 0.18
121 3 0.01
125 120 0.36
127 109 0.33
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (125 bp):
TTTGTAGCGTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCGTTTTTCACCTAGCGCC
GCTAATGCCACTAAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTT
Found at i:5270847 original size:252 final size:246
Alignment explanation
Indices: 5270408--5270902 Score: 740
Period size: 252 Copynumber: 2.0 Consensus size: 246
5270398 CGTTTGTAGT
*
5270408 GTTTTTTACCTAGCGCCACTATTGCTCGATCTATTGCGGCGTTTTCACCTAGTACCGCTAATGCC
1 GTTTTTTACCTAGCGCCACTAATGCTCGATCTATTGCGGCGTTTTCACCTAGTACCGCTAATGCC
* * *
5270473 ACTAAAGACGCCACTTAAAATGGCGCTGTTTTGTTTAAAGTAAATTTTTACAGCGTTTTTTACCT
66 ACTAAAGACGCCACGTAAAACGGCGCTATTTTGTTTAAAGTAAATTTTTACAGCGTTTTTTACCT
* * * *
5270538 AGCGTCGCTAATGTTCTATCTATTGCAGCGTTTTTCACCTAGCGCCGCCAATGCCACTAAAGACG
131 AGCGCCGCTAATGCTCGATCTATTGCAGCATTTTTCACCTAGCGCCGCCAATGCCACTAAAGACG
* *
5270603 CTACTTAAAATGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
196 CCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
* * *
5270654 GTTTTTTACCTAGCGCCGCTAATGCTTGATCTATTGCGGCGTTTTTCACCTAGTGCCGCTAATGC
1 GTTTTTTACCTAGCGCCACTAATGCTCGATCTATTGCGGCG-TTTTCACCTAGTACCGCTAATGC
* *** *
5270719 CATTAAAGACGCCACGTAAAACGGCG-TCATTTTGTTTAAAGTAAAATGTTTTTTTGTGGTGTTT
65 CACTAAAGACGCCACGTAAAACGGCGCT-ATTTTGTTTAAAGT-AAA----TTTTTACAGCGTTT
*
5270783 TTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCATTTTTCACCTAGCGCCGCTAATGCCACT
124 TTTACCTAGCGCCGCTAATGCTCGATCTATTGCAGCATTTTTCACCTAGCGCCGCCAATGCCACT
*
5270848 AAAGATGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGC
189 AAAGACGCCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGC
5270903 TGCATTTTAA
Statistics
Matches: 222, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
246 39 0.18
247 58 0.26
248 3 0.01
252 122 0.55
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (246 bp):
GTTTTTTACCTAGCGCCACTAATGCTCGATCTATTGCGGCGTTTTCACCTAGTACCGCTAATGCC
ACTAAAGACGCCACGTAAAACGGCGCTATTTTGTTTAAAGTAAATTTTTACAGCGTTTTTTACCT
AGCGCCGCTAATGCTCGATCTATTGCAGCATTTTTCACCTAGCGCCGCCAATGCCACTAAAGACG
CCACTTAAAACGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCAGC
Found at i:5271546 original size:21 final size:21
Alignment explanation
Indices: 5271519--5271649 Score: 104
Period size: 21 Copynumber: 6.1 Consensus size: 21
5271509 CAAAATCCCT
5271519 AACCCTAAAACATAAACACTA
1 AACCCTAAAACATAAACACTA
* **
5271540 AATCCTAAAACCATAAATCTTTA
1 AACCCTAAAA-CATAAA-CACTA
*
5271563 AACCCT-AAACTATAAAAAACTA
1 AACCCTAAAAC-AT-AAACACTA
* *
5271585 AACCCCAAAACATAAACCCTA
1 AACCCTAAAACATAAACACTA
* *
5271606 AACCCTAAACCCTAAAC-CTTA
1 AACCCTAAAACATAAACAC-TA
* * *
5271627 AACCTTAAATCATAAACCCTA
1 AACCCTAAAACATAAACACTA
5271648 AA
1 AA
5271650 ATAAAATGAT
Statistics
Matches: 87, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 50 0.57
22 21 0.24
23 15 0.17
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
AACCCTAAAACATAAACACTA
Found at i:5271609 original size:7 final size:7
Alignment explanation
Indices: 5271515--5271649 Score: 74
Period size: 7 Copynumber: 19.0 Consensus size: 7
5271505 TTATCAAAAT
5271515 CCCT-AA
1 CCCTAAA
5271521 CCCTAAA
1 CCCTAAA
* *
5271528 ACATAAA
1 CCCTAAA
*
5271535 CACTAAA
1 CCCTAAA
*
5271542 TCCTAAAA
1 CCCT-AAA
*
5271550 CCATAAA
1 CCCTAAA
**
5271557 TCTTTAAA
1 -CCCTAAA
5271565 CCCTAAA
1 CCCTAAA
**
5271572 CTATAAAA
1 CCCT-AAA
**
5271580 AACTAAA
1 CCCTAAA
*
5271587 CCCCAAA
1 CCCTAAA
* *
5271594 ACATAAA
1 CCCTAAA
5271601 CCCTAAA
1 CCCTAAA
5271608 CCCTAAA
1 CCCTAAA
5271615 CCCTAAA
1 CCCTAAA
*
5271622 CCTTAAA
1 CCCTAAA
*
5271629 CCTTAAA
1 CCCTAAA
* *
5271636 TCATAAA
1 CCCTAAA
5271643 CCCTAAA
1 CCCTAAA
5271650 ATAAAATGAT
Statistics
Matches: 94, Mismatches: 31, Indels: 7
0.71 0.23 0.05
Matches are distributed among these distances:
6 4 0.04
7 76 0.81
8 14 0.15
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:5271734 original size:41 final size:41
Alignment explanation
Indices: 5271675--5271827 Score: 141
Period size: 41 Copynumber: 3.7 Consensus size: 41
5271665 GCGACGTTTT
* * * *
5271675 CGCTACTACTAGATCTTTTGCGGCGTTTATGAT-AAAAACGC
1 CGCTACTAGTTGACCTTTTGCGGCATTT-TGATCAAAAACGC
* * *
5271716 CGCTACTAGTTGACCTTTTGCAGCATTTTTATCATAAACGC
1 CGCTACTAGTTGACCTTTTGCGGCATTTTGATCAAAAACGC
* *
5271757 CGCTACT-GCTTGACCTTTTGCGGCATTTTTATCATAAACGC
1 CGCTACTAG-TTGACCTTTTGCGGCATTTTGATCAAAAACGC
* * *
5271798 CACTA-TAGCTCTAACATTTTGCGGCATTTT
1 CGCTACTAG-T-TGACCTTTTGCGGCATTTT
5271828 CCTATTAGCG
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
40 5 0.05
41 75 0.77
42 17 0.18
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (41 bp):
CGCTACTAGTTGACCTTTTGCGGCATTTTGATCAAAAACGC
Found at i:5273428 original size:17 final size:17
Alignment explanation
Indices: 5273406--5273442 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5273396 AACTCGCTTA
5273406 ATTTTAAATGTTTAACT
1 ATTTTAAATGTTTAACT
*
5273423 ATTTTAAATGTTTAATT
1 ATTTTAAATGTTTAACT
5273440 ATT
1 ATT
5273443 CAATTCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATGTTTAACT
Found at i:5276067 original size:34 final size:34
Alignment explanation
Indices: 5276024--5276089 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
5276014 TAAACTCTGT
5276024 TTATTTATTTCAG-CTAAACACTGATTAGTTTAGA
1 TTATTTATTTCAGTC-AAACACTGATTAGTTTAGA
5276058 TTATTTATTTCAGTCAAACACTGATTAGTTTA
1 TTATTTATTTCAGTCAAACACTGATTAGTTTA
5276090 CAACCTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (34 bp):
TTATTTATTTCAGTCAAACACTGATTAGTTTAGA
Found at i:5280268 original size:5 final size:5
Alignment explanation
Indices: 5280258--5280311 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
5280248 AATGGAAATA
* * * * *
5280258 TTTAT TTTAT TTTAT TTTAT TCTAT TCTATT TTTAA CTTAT TTTCT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT TTTAT
5280309 TTT
1 TTT
5280312 GAAATTAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
5 36 0.90
6 4 0.10
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:5281302 original size:13 final size:13
Alignment explanation
Indices: 5281284--5281309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5281274 AAGTGCGAGC
5281284 CTGTTGAAGACAA
1 CTGTTGAAGACAA
5281297 CTGTTGAAGACAA
1 CTGTTGAAGACAA
5281310 TATGCAAAGA
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:0.23, T:0.23
Consensus pattern (13 bp):
CTGTTGAAGACAA
Found at i:5286759 original size:14 final size:14
Alignment explanation
Indices: 5286740--5286768 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5286730 TAATGTCTAG
5286740 GCTGAGTTTAGAGT
1 GCTGAGTTTAGAGT
5286754 GCTGAGTTTAGAGT
1 GCTGAGTTTAGAGT
5286768 G
1 G
5286769 TTTCACCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.38, T:0.34
Consensus pattern (14 bp):
GCTGAGTTTAGAGT
Found at i:5290906 original size:2 final size:2
Alignment explanation
Indices: 5290884--5290937 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
5290874 TTGTTAAATC
* *
5290884 TA TA TC TA TA TA -A TC TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5290924 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
5290938 AAGAAGAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5291817 original size:12 final size:12
Alignment explanation
Indices: 5291800--5291824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5291790 TAATTTTCAA
5291800 AAATAAATATAT
1 AAATAAATATAT
5291812 AAATAAATATAT
1 AAATAAATATAT
5291824 A
1 A
5291825 TTATATATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:5293408 original size:26 final size:26
Alignment explanation
Indices: 5293377--5293428 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5293367 AAAATTTGTG
5293377 GTTATTTTGTTTTTTATGTTGCCGTC
1 GTTATTTTGTTTTTTATGTTGCCGTC
5293403 GTTATTTTGTTTTTTATGTTGCCGTC
1 GTTATTTTGTTTTTTATGTTGCCGTC
5293429 TTAGTCATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.08, C:0.12, G:0.19, T:0.62
Consensus pattern (26 bp):
GTTATTTTGTTTTTTATGTTGCCGTC
Found at i:5298051 original size:33 final size:33
Alignment explanation
Indices: 5297942--5298051 Score: 89
Period size: 33 Copynumber: 3.3 Consensus size: 33
5297932 AATTGACGGA
* *
5297942 TAAGACCATA-ACTGGGTTATGGCACTATGAACG
1 TAAGACCATAGA-TGGGCTATGGCATTATGAACG
* * * * * * *
5297975 TAAGACCATGGTTGGACCATGCCAGTGT-TTATATG
1 TAAGACCATAGATGGGCTATGGCA-T-TATGA-ACG
5298010 TAAGACCATAGATGGGCTATGGCATTATGAACG
1 TAAGACCATAGATGGGCTATGGCATTATGAACG
5298043 TAAGACCAT
1 TAAGACCAT
5298052 GGTTGGTTCA
Statistics
Matches: 56, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
33 29 0.52
34 5 0.09
35 22 0.39
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (33 bp):
TAAGACCATAGATGGGCTATGGCATTATGAACG
Found at i:5298051 original size:68 final size:68
Alignment explanation
Indices: 5297942--5298119 Score: 225
Period size: 68 Copynumber: 2.6 Consensus size: 68
5297932 AATTGACGGA
* * * *
5297942 TAAGACCATA-ACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGCCAGTGTTTA
1 TAAGACCATAGA-TGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCAAATGTTTA
5298006 TATG
65 TATG
** *
5298010 TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGTTCATGGAAATGTTTAT
1 TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCAAATGTTTAT
5298075 ATG
66 ATG
* * * *
5298078 TAAGACTATAGCTAGGCTATGGCATTCTG-ACGATAAGACCAT
1 TAAGACCATAGATGGGCTATGGCATTATGAACG-TAAGACCAT
5298120 AACTGGGTTA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
67 3 0.03
68 93 0.96
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (68 bp):
TAAGACCATAGATGGGCTATGGCATTATGAACGTAAGACCATGGTTGGACCATGCAAATGTTTAT
ATG
Found at i:5301871 original size:43 final size:42
Alignment explanation
Indices: 5301791--5301953 Score: 157
Period size: 43 Copynumber: 3.8 Consensus size: 42
5301781 CAAAAGTTCG
* * * *
5301791 TACAATGCCAACGTCCCAGACATGGTCTTTCATGTAATCAAA
1 TACAATGCCAATGTCCCAGAAATGGTCTTACACGTAATCAAA
* * * * * *
5301833 TAACGATGTCACTGTCCCAGATAGGGTCTTACACGTAATCATA
1 T-ACAATGCCAATGTCCCAGAAATGGTCTTACACGTAATCAAA
*
5301876 TACAATGCCAATGTCCTAGAAATGGTCTTACACGTAAATCTTAAA
1 TACAATGCCAATGTCCCAGAAATGGTCTTACACGT-AATC--AAA
* * *
5301921 T-CGATGCCAACGTCCCAGACATGGTCTTACACG
1 TACAATGCCAATGTCCCAGAAATGGTCTTACACG
5301954 ATATCACATT
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 29 0.30
43 37 0.38
44 28 0.29
45 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGAAATGGTCTTACACGTAATCAAA
Found at i:5305645 original size:33 final size:32
Alignment explanation
Indices: 5305600--5305760 Score: 133
Period size: 33 Copynumber: 4.8 Consensus size: 32
5305590 TAGTGTTTAT
*
5305600 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGTTATGGCATTCTG
* * *
5305632 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGGGTTATGGCATTCTG
* * * * * * * *
5305665 AACGTAAGATCATGGTTGGATCATGGCAATGTTTAT
1 -ATGTAAGACCATAGCTGGGTTATGGC-AT-TCT-G
* *
5305701 ATGTAAGACCATAGTTGGGTTATGACATTCTG
1 ATGTAAGACCATAGCTGGGTTATGGCATTCTG
*
5305733 ATGATAAGACCATAACTGGGTTATGGCA
1 ATG-TAAGACCATAGCTGGGTTATGGCA
5305761 CTATGAATGT
Statistics
Matches: 98, Mismatches: 25, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
32 6 0.06
33 65 0.66
34 5 0.05
35 22 0.22
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGTTATGGCATTCTG
Found at i:5305708 original size:101 final size:101
Alignment explanation
Indices: 5305533--5305772 Score: 390
Period size: 101 Copynumber: 2.4 Consensus size: 101
5305523 TGAATTAACG
* * * *
5305533 GATAAGACCATAACTGGTTTATGGCACTATGAACGTAAGACCATGGTTGGGCCATGGTAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
*
5305598 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
* *
5305634 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGATCATGGTTGGATCATGGCAATGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
* *
5305699 ATATGTAAGACCATAGTTGGGTTATGACATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
*
5305735 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
5305773 AGGATGAAGT
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 129 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
ATATGTAAGACCATAGCTGGGCTATGACATTCTGAT
Found at i:5310741 original size:25 final size:25
Alignment explanation
Indices: 5310703--5310778 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
5310693 GAACACACCA
* *
5310703 TAGCTCGTAAGAGCATCCCGTTATT
1 TAGCTCTTATGAGCATCCCGTTATT
* *
5310728 TAGCTCTTATGAGCATCCCGATATA
1 TAGCTCTTATGAGCATCCCGTTATT
* * *
5310753 TGGCTCTCT-TGAGCTTCCTGTTATT
1 TAGCTCT-TATGAGCATCCCGTTATT
5310778 T
1 T
5310779 GGCTTTCACG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
25 40 0.98
26 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (25 bp):
TAGCTCTTATGAGCATCCCGTTATT
Found at i:5310781 original size:25 final size:25
Alignment explanation
Indices: 5310713--5310782 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
5310703 TAGCTCGTAA
*
5310713 GAGCATCCCGTTATTTAGCTCTTAT
1 GAGCATCCCGTTATTTGGCTCTTAT
* *
5310738 GAGCATCCCGATATATGGCTCTCT-T
1 GAGCATCCCGTTATTTGGCTCT-TAT
* *
5310763 GAGCTTCCTGTTATTTGGCT
1 GAGCATCCCGTTATTTGGCT
5310783 TTCACGAGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (25 bp):
GAGCATCCCGTTATTTGGCTCTTAT
Found at i:5310805 original size:25 final size:25
Alignment explanation
Indices: 5310784--5310869 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 25
5310774 TATTTGGCTT
*
5310784 TCACGAGCTTCTCGATAATTGGTTC
1 TCACGAGCTTCCCGATAATTGGTTC
* **
5310809 TCATGAGCTTCCCGATTAA-TGACTC
1 TCACGAGCTTCCCGA-TAATTGGTTC
*
5310834 TC-CGAAGCTTCCCGAT-ATTGGCTC
1 TCACG-AGCTTCCCGATAATTGGTTC
* *
5310858 GCATGAGCTTCC
1 TCACGAGCTTCC
5310870 TAATTATGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.02
24 15 0.31
25 30 0.61
26 3 0.06
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (25 bp):
TCACGAGCTTCCCGATAATTGGTTC
Found at i:5310879 original size:24 final size:24
Alignment explanation
Indices: 5310852--5310932 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 24
5310842 TTCCCGATAT
5310852 TGGCTCGCATGAGCTTCCTAATTA
1 TGGCTCGCATGAGCTTCCTAATTA
** * *
5310876 TGGCTCTTATGAGCTTTCCGTTA-CA
1 TGGCTCGCATGAGC-TTCC-TAATTA
* * *
5310901 TGGCTCACATGAGCTTCCCATTTCA
1 TGGCTCGCATGAGCTTCCTAATT-A
5310926 TGGCTCG
1 TGGCTCG
5310933 AAAAAGCTTC
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
24 16 0.38
25 24 0.57
26 2 0.05
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (24 bp):
TGGCTCGCATGAGCTTCCTAATTA
Found at i:5310903 original size:25 final size:25
Alignment explanation
Indices: 5310875--5310931 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
5310865 CTTCCTAATT
** * *
5310875 ATGGCTCTTATGAGCTTTCCGTTAC
1 ATGGCTCACATGAGCTTCCCATTAC
*
5310900 ATGGCTCACATGAGCTTCCCATTTC
1 ATGGCTCACATGAGCTTCCCATTAC
5310925 ATGGCTC
1 ATGGCTC
5310932 GAAAAAGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCATTAC
Found at i:5314137 original size:50 final size:50
Alignment explanation
Indices: 5314030--5314142 Score: 127
Period size: 50 Copynumber: 2.3 Consensus size: 50
5314020 TGATAGGTAT
* * * * **
5314030 CACGTAAGACCATGTCTAGGACATGACGTTGGTACTGAGATGAGAGGTCC
1 CACGTAAGACCATGTCTAGGACATGACATGGGCACCGAGATGAGAACTCC
* * * *
5314080 CCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAACTCT
1 CACGTAAGACCATGTCTAGGACATGACATGGGCACCGAGATGAGAACTCC
*
5314130 CATGTAAGACCAT
1 CACGTAAGACCAT
5314143 ATTTGGGATA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (50 bp):
CACGTAAGACCATGTCTAGGACATGACATGGGCACCGAGATGAGAACTCC
Found at i:5314440 original size:20 final size:20
Alignment explanation
Indices: 5314415--5314453 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5314405 TGAGTTGTTT
5314415 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
5314435 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
5314454 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:5314726 original size:17 final size:17
Alignment explanation
Indices: 5314704--5314736 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5314694 ATAGAAAGTC
5314704 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5314721 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
5314737 AAATCTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5319320 original size:17 final size:17
Alignment explanation
Indices: 5319298--5319347 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
5319288 ATAGAAAGTC
5319298 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
5319315 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
5319332 AAAGATATGAGTATCA
1 AAAGATATGGGTATCA
5319348 AAATCTGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5321886 original size:146 final size:146
Alignment explanation
Indices: 5321622--5321901 Score: 560
Period size: 146 Copynumber: 1.9 Consensus size: 146
5321612 CAAGACTCAA
5321622 AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
1 AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
5321687 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
66 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
5321752 CCACTAAGTATGTCTT
131 CCACTAAGTATGTCTT
5321768 AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
1 AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
5321833 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
66 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
5321898 CCAC
131 CCAC
5321902 ATGTGTATAT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 134 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (146 bp):
AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
CCACTAAGTATGTCTT
Found at i:5327921 original size:22 final size:23
Alignment explanation
Indices: 5327868--5327923 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
5327858 CCCGTTTTTA
* * *
5327868 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
5327891 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
5327913 ATTAAAATTAA
1 ATTAAAATTAA
5327924 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:5327936 original size:16 final size:16
Alignment explanation
Indices: 5327899--5327938 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5327889 TTAATAAAAT
* *
5327899 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5327915 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5327931 TAAAATTA
1 TAAAATTA
5327939 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5328023 original size:9 final size:9
Alignment explanation
Indices: 5328011--5328047 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
5328001 TTTATCAAAT
5328011 TATTAATTG
1 TATTAATTG
5328020 TATTAATTG
1 TATTAATTG
5328029 TATTAATTG
1 TATTAATTG
5328038 TATTAATTG
1 TATTAATTG
5328047 T
1 T
5328048 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:5328184 original size:22 final size:24
Alignment explanation
Indices: 5328144--5328187 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5328134 AAATAAACTT
5328144 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
5328168 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
5328188 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:5342928 original size:43 final size:43
Alignment explanation
Indices: 5342875--5342961 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
5342865 AACAAGACGA
* *
5342875 TCGCCTTCATCTTTAGACAAAGTTGATGACCTAATCATTGGTG
1 TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
5342918 TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
1 TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
5342961 T
1 T
5342962 GTGGACACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (43 bp):
TCGCCCTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
Found at i:5347787 original size:22 final size:23
Alignment explanation
Indices: 5347762--5347804 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5347752 TAGATTTTAA
5347762 TAAATTTTATAAA-A-AGATAAAT
1 TAAATTTT-TAAATAGAGATAAAT
5347784 TAAATTTTTAAATAGAGATAA
1 TAAATTTTTAAATAGAGATAA
5347805 TTTTTAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
TAAATTTTTAAATAGAGATAAAT
Found at i:5349118 original size:14 final size:12
Alignment explanation
Indices: 5349073--5349143 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 12
5349063 CTTAACAAAT
5349073 ATTTTAATTA-A
1 ATTTTAATTATA
*
5349084 ATATTTAATAATAA
1 AT-TTTAATTAT-A
5349098 ATTTTAATTGATA
1 ATTTTAATT-ATA
5349111 ATTCTTAAATTATTA
1 ATT-TT-AATTA-TA
*
5349126 TTTTTAATTTATA
1 ATTTTAA-TTATA
5349139 ATTTT
1 ATTTT
5349144 GATTGGTACA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 2 0.04
12 7 0.15
13 18 0.38
14 13 0.27
15 8 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (12 bp):
ATTTTAATTATA
Found at i:5356971 original size:20 final size:21
Alignment explanation
Indices: 5356920--5356971 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
5356910 TAAAGTTTTC
* *
5356920 AAAAATATTATAAAAATTATTT
1 AAAAATA-TATTAAAATTATTA
*
5356942 AAAAA-GTATTAAAATTA-TA
1 AAAAATATATTAAAATTATTA
5356961 AAAAATATATT
1 AAAAATATATT
5356972 TTTAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
22 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAATATATTAAAATTATTA
Found at i:5362730 original size:2 final size:2
Alignment explanation
Indices: 5362725--5362753 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5362715 TGAAACCAAA
5362725 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5362754 AAGAAACAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5364312 original size:3 final size:3
Alignment explanation
Indices: 5364306--5364357 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
5364296 CGTTGTTGCA
* *
5364306 CTT CTT CTT CTT CTT TTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
5364354 CTT C
1 CTT C
5364358 GGTCTTCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:5369971 original size:12 final size:12
Alignment explanation
Indices: 5369956--5369981 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5369946 TGGCACACGG
5369956 CCTAACACAAGC
1 CCTAACACAAGC
5369968 CCTAACACAAGC
1 CCTAACACAAGC
5369980 CC
1 CC
5369982 GTGTGACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.46, G:0.08, T:0.08
Consensus pattern (12 bp):
CCTAACACAAGC
Found at i:5371235 original size:23 final size:23
Alignment explanation
Indices: 5371185--5371229 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5371175 CGACATTTTT
*
5371185 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
5371208 TGTAATACCCCGAAAATTACTA
1 TGTAATACCCCGAAAATTACTA
5371230 TAGTAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:5374995 original size:6 final size:6
Alignment explanation
Indices: 5374976--5375020 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
5374966 TCTAAATGAA
*
5374976 TTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TCCATT TT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTCATT TT
5375021 GAGAAAACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCATT
Found at i:5375071 original size:6 final size:6
Alignment explanation
Indices: 5375060--5375089 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5375050 CCATTTTATC
*
5375060 CATTTT CATTTT CCTTTT CATTTT CATTTT
1 CATTTT CATTTT CATTTT CATTTT CATTTT
5375090 GGAGAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (6 bp):
CATTTT
Found at i:5378878 original size:36 final size:36
Alignment explanation
Indices: 5378837--5379027 Score: 229
Period size: 36 Copynumber: 5.0 Consensus size: 36
5378827 GGTAGCTTTA
5378837 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
5378873 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
5378918 AGCTACACTTATCTAATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
5378955 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
5378991 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
5379027 G
1 G
5379028 GTAGCTTAGC
Statistics
Matches: 135, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
36 98 0.73
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 29 0.21
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:5378938 original size:82 final size:82
Alignment explanation
Indices: 5378801--5378991 Score: 328
Period size: 82 Copynumber: 2.3 Consensus size: 82
5378791 TTTGAGTACT
* *
5378801 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGAAAAAGT
5378866 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
5378883 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGAAAAAGT
* *
5378948 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
5378965 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
5378992 CTATACTTAT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:5383119 original size:2 final size:2
Alignment explanation
Indices: 5383083--5383111 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5383073 TATGGTTGTA
5383083 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5383112 GGATATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5384560 original size:20 final size:19
Alignment explanation
Indices: 5384535--5384587 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5384525 TATTTTTTTA
*
5384535 ACTTATTAATTTTTTAGTTG
1 ACTTATTAATTTTGTA-TTG
* *
5384555 ACTTATTATATATTGTATTT
1 ACTTATTA-ATTTTGTATTG
5384575 ACTTATTAATTTT
1 ACTTATTAATTTT
5384588 ATTATGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (19 bp):
ACTTATTAATTTTGTATTG
Found at i:5384590 original size:17 final size:17
Alignment explanation
Indices: 5384526--5384590 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 17
5384516 ATTTCACTCT
5384526 ATTTT-TTTAACTTATTA
1 ATTTTATTT-ACTTATTA
*
5384543 ATTTTTTAGTTGACTTATTA
1 A--TTTTA-TTTACTTATTA
5384563 TATATTGTATTTACTTATTA
1 -AT-TT-TATTTACTTATTA
5384583 ATTTTATT
1 ATTTTATT
5384591 ATGTATGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
17 5 0.13
18 2 0.05
19 7 0.18
20 20 0.51
21 5 0.13
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTTATTTACTTATTA
Found at i:5384936 original size:13 final size:13
Alignment explanation
Indices: 5384918--5384944 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5384908 TAGAAAAAAA
5384918 TGTGAACTCCTCC
1 TGTGAACTCCTCC
5384931 TGTGAACTCCTCC
1 TGTGAACTCCTCC
5384944 T
1 T
5384945 TTTATATATA
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:0.15, C:0.37, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTGAACTCCTCC
Found at i:5384978 original size:6 final size:6
Alignment explanation
Indices: 5384969--5384998 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
5384959 TGTGTGTGTG
5384969 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGAT
5384999 AACAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
TTTGAT
Found at i:5388034 original size:13 final size:13
Alignment explanation
Indices: 5388016--5388040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5388006 TAAAACCAAA
5388016 AAATGTTTAGTTG
1 AAATGTTTAGTTG
5388029 AAATGTTTAGTT
1 AAATGTTTAGTT
5388041 TGAATCATAT
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:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AAATGTTTAGTTG
Found at i:5392057 original size:16 final size:16
Alignment explanation
Indices: 5392024--5392083 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
5392014 ACAAATGTAT
*
5392024 AAATATATATAATATA
1 AAATATATAAAATATA
5392040 AAATATATAAAAGT-TA
1 AAATATATAAAA-TATA
* * *
5392056 AAAGAGATAAAATAAA
1 AAATATATAAAATATA
*
5392072 AAAAATATAAAA
1 AAATATATAAAA
5392084 CGTATGTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATATATAAAATATA
Found at i:5392861 original size:24 final size:24
Alignment explanation
Indices: 5392834--5392881 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5392824 AAACTTTCCA
*
5392834 ATATTT-TCTTTTGTATTTCTCTGT
1 ATATTTCTCTGTT-TATTTCTCTGT
5392858 ATATTTCTCTGTTTATTTCTCTGT
1 ATATTTCTCTGTTTATTTCTCTGT
5392882 TTCCCCGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.12, C:0.15, G:0.08, T:0.65
Consensus pattern (24 bp):
ATATTTCTCTGTTTATTTCTCTGT
Found at i:5392882 original size:12 final size:12
Alignment explanation
Indices: 5392847--5392883 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
5392837 TTTTCTTTTG
*
5392847 TATTTCTCTGTA
1 TATTTCTCTGTT
5392859 TATTTCTCTGTT
1 TATTTCTCTGTT
5392871 TATTTCTCTGTT
1 TATTTCTCTGTT
5392883 T
1 T
5392884 CCCCGTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.11, C:0.16, G:0.08, T:0.65
Consensus pattern (12 bp):
TATTTCTCTGTT
Found at i:5394967 original size:13 final size:13
Alignment explanation
Indices: 5394949--5394975 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5394939 TAGCCTCTCC
5394949 ATTTTTTTTTTGG
1 ATTTTTTTTTTGG
5394962 ATTTTTTTTTTGG
1 ATTTTTTTTTTGG
5394975 A
1 A
5394976 ATCAAAGCGC
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:0.11, C:0.00, G:0.15, T:0.74
Consensus pattern (13 bp):
ATTTTTTTTTTGG
Found at i:5402198 original size:20 final size:20
Alignment explanation
Indices: 5402173--5402212 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5402163 TAAAGGTCTT
*
5402173 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
5402193 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
5402213 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:5405706 original size:16 final size:17
Alignment explanation
Indices: 5405687--5405731 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
5405677 AAGGGAAAAA
5405687 AAATATATGTATATA-T
1 AAATATATGTATATATT
* *
5405703 AAAT-TATGCATGTATT
1 AAATATATGTATATATT
5405719 AAA-ATATGTATAT
1 AAATATATGTATAT
5405732 GTATATATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (17 bp):
AAATATATGTATATATT
Found at i:5405863 original size:14 final size:13
Alignment explanation
Indices: 5405837--5405869 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5405827 AAAACAAATG
5405837 TATA-AATATATA
1 TATATAATATATA
5405849 TATATAATATAATA
1 TATATAATAT-ATA
5405863 TATATAA
1 TATATAA
5405870 AAGTTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 5 0.26
14 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATAATATATA
Found at i:5406704 original size:24 final size:24
Alignment explanation
Indices: 5406677--5406724 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5406667 AAACTTTCCA
*
5406677 ATATTT-TCTTTTGTATTTCTCTGT
1 ATATTTCTCTGTT-TATTTCTCTGT
5406701 ATATTTCTCTGTTTATTTCTCTGT
1 ATATTTCTCTGTTTATTTCTCTGT
5406725 TTCCCCGTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.12, C:0.15, G:0.08, T:0.65
Consensus pattern (24 bp):
ATATTTCTCTGTTTATTTCTCTGT
Found at i:5406725 original size:12 final size:12
Alignment explanation
Indices: 5406690--5406726 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
5406680 TTTTCTTTTG
*
5406690 TATTTCTCTGTA
1 TATTTCTCTGTT
5406702 TATTTCTCTGTT
1 TATTTCTCTGTT
5406714 TATTTCTCTGTT
1 TATTTCTCTGTT
5406726 T
1 T
5406727 CCCCGTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.11, C:0.16, G:0.08, T:0.65
Consensus pattern (12 bp):
TATTTCTCTGTT
Found at i:5407230 original size:9 final size:10
Alignment explanation
Indices: 5407212--5407282 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
5407202 ATTTAGCAAG
5407212 TATAAAAAAT
1 TATAAAAAAT
5407222 TATAAAAATAT
1 TATAAAAA-AT
5407233 TATAAAAAAAAGT
1 TAT--AAAAAA-T
*
5407246 TATAGAAAAT
1 TATAAAAAAT
* *
5407256 AATATAAAAT
1 TATAAAAAAT
** *
5407266 TATTCAAATT
1 TATAAAAAAT
5407276 TATAAAA
1 TATAAAA
5407283 GAATATAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 28 0.58
11 10 0.21
12 1 0.02
13 9 0.19
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (10 bp):
TATAAAAAAT
Found at i:5407234 original size:11 final size:11
Alignment explanation
Indices: 5407212--5407269 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
5407202 ATTTAGCAAG
5407212 TATAAAAA-AT
1 TATAAAAATAT
5407222 TATAAAAATAT
1 TATAAAAATAT
*
5407233 TATAAAAAAAAGT
1 TAT-AAAAATA-T
*
5407246 TATAGAAAATAA
1 TATA-AAAATAT
*
5407258 TATAAAATTAT
1 TATAAAAATAT
5407269 T
1 T
5407270 CAAATTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
10 8 0.21
11 11 0.28
12 11 0.28
13 9 0.23
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:5407248 original size:24 final size:24
Alignment explanation
Indices: 5407215--5407264 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
5407205 TAGCAAGTAT
*
5407215 AAAAAATTATA-AAAATATTATAA
1 AAAAAATTATAGAAAATAATATAA
5407238 AAAAAAGTTATAGAAAATAATATAA
1 AAAAAA-TTATAGAAAATAATATAA
5407263 AA
1 AA
5407265 TTATTCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 5 0.21
25 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAAATTATAGAAAATAATATAA
Found at i:5410106 original size:15 final size:15
Alignment explanation
Indices: 5410088--5410136 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5410078 AATGACAATT
5410088 ATAATAAATAATATA
1 ATAATAAATAATATA
*
5410103 ATAATACATAATGAT-
1 ATAATAAATAAT-ATA
5410118 ATAATATAATAATA-A
1 ATAATA-AATAATATA
5410133 ATAA
1 ATAA
5410137 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 22 0.76
16 7 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAATAAATAATATA
Found at i:5410107 original size:8 final size:8
Alignment explanation
Indices: 5410088--5410141 Score: 55
Period size: 7 Copynumber: 7.2 Consensus size: 8
5410078 AATGACAATT
5410088 ATAATA-A
1 ATAATATA
5410095 ATAATATA
1 ATAATATA
*
5410103 ATAATA-C
1 ATAATATA
5410110 ATAATGAT-
1 ATAAT-ATA
5410118 ATAATATA
1 ATAATATA
5410126 ATAATA-A
1 ATAATATA
5410133 ATAA-ATA
1 ATAATATA
5410140 AT
1 AT
5410142 TAAATAGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
6 1 0.02
7 21 0.51
8 19 0.46
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (8 bp):
ATAATATA
Found at i:5410114 original size:34 final size:34
Alignment explanation
Indices: 5410069--5410141 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
5410059 ACATATGTAC
*
5410069 AAATAA-A-ATAATGACA-ATTATAATAA-ATAAT
1 AAATAATACATAATGACATAATATAATAATA-AAT
*
5410100 ATAATAATACATAATGATATAATATAATAATAAAT
1 A-AATAATACATAATGACATAATATAATAATAAAT
5410135 AAATAAT
1 AAATAAT
5410142 TAAATAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
31 1 0.03
32 5 0.14
33 1 0.03
34 14 0.40
35 13 0.37
36 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (34 bp):
AAATAATACATAATGACATAATATAATAATAAAT
Found at i:5411761 original size:45 final size:44
Alignment explanation
Indices: 5411710--5411797 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
5411700 CTTCAATATA
* * *
5411710 CTCCACTGCAACTTCAGGGAGGTAAAATCTGCCATCTTCGATCTG
1 CTCCACTACAACTT-AGGGAGGCAAAATCTGCAATCTTCGATCTG
** *
5411755 CTCCACTACTGCTTAGGGAGGCAAAATCTGTAATCTTCGATCT
1 CTCCACTACAACTTAGGGAGGCAAAATCTGCAATCTTCGATCT
5411798 ATTTCACCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 26 0.70
45 11 0.30
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (44 bp):
CTCCACTACAACTTAGGGAGGCAAAATCTGCAATCTTCGATCTG
Found at i:5423421 original size:3 final size:3
Alignment explanation
Indices: 5423399--5423461 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
5423389 CATATGTACA
* *
5423399 AAT AA- AAT AAT GAC AAT AAT AAT AAAT AAT -AT AAT AAT ACAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT
*
5423444 GAT -AT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
5423462 ATAAATAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
2 8 0.16
3 35 0.71
4 6 0.12
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5423432 original size:15 final size:15
Alignment explanation
Indices: 5423414--5423465 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
5423404 AATAATGACA
5423414 ATAATAATAAATAAT
1 ATAATAATAAATAAT
*
5423429 ATAATAATACATAAT
1 ATAATAATAAATAAT
5423444 GAT-ATAATATAATAAT
1 -ATAATAATA-AATAAT
5423460 A-AATAA
1 ATAATAA
5423466 ATAATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:5432706 original size:30 final size:28
Alignment explanation
Indices: 5432665--5432726 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 28
5432655 ATATATTTAA
5432665 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTA-TTAAGTAAA-AGATATTT
* *
5432695 ATTATTTATTATTAAGTAAAATATATTT
1 ATTACTTATTATTAAGTAAAAGATATTT
5432723 ATTA
1 ATTA
5432727 ATTAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
29 9 0.30
30 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (28 bp):
ATTACTTATTATTAAGTAAAAGATATTT
Found at i:5433395 original size:17 final size:18
Alignment explanation
Indices: 5433373--5433408 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5433363 TAAATGAGTC
5433373 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5433390 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
5433408 A
1 A
5433409 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:5445673 original size:86 final size:86
Alignment explanation
Indices: 5445572--5445742 Score: 270
Period size: 86 Copynumber: 2.0 Consensus size: 86
5445562 GGGTTTTAAT
* * * *
5445572 TTTTTTTGTAGTATTATTTATTTGTATGTTTGTCACTTAATTAGTATAAAAAAAACTAAATAAAT
1 TTTTTTTGAAGTATTATTTATTTGTATGCTTCTCACTTAATTAATATAAAAAAAACTAAATAAAT
5445637 ACTGAAATGGTATATTTGAGA
66 ACTGAAATGGTATATTTGAGA
* * *
5445658 TTTTTTTGAATTATTATTTATTTGTATGCTTCTTACTTAATTAATATAAAAAAAACTAATTAAAT
1 TTTTTTTGAAGTATTATTTATTTGTATGCTTCTCACTTAATTAATATAAAAAAAACTAAATAAAT
*
5445723 ACTGAAATGGTATGTTTGAG
66 ACTGAAATGGTATATTTGAG
5445743 GCTTTCAAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (86 bp):
TTTTTTTGAAGTATTATTTATTTGTATGCTTCTCACTTAATTAATATAAAAAAAACTAAATAAAT
ACTGAAATGGTATATTTGAGA
Found at i:5446501 original size:33 final size:33
Alignment explanation
Indices: 5446459--5446525 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5446449 AAATCACAAT
5446459 CTGCCATTTGAGGAACGCAAAGAGGATATGGCA
1 CTGCCATTTGAGGAACGCAAAGAGGATATGGCA
5446492 CTGCCATTTGAGGAACGCAAAGAGGATATGGCA
1 CTGCCATTTGAGGAACGCAAAGAGGATATGGCA
5446525 C
1 C
5446526 AGCAAATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (33 bp):
CTGCCATTTGAGGAACGCAAAGAGGATATGGCA
Found at i:5447601 original size:2 final size:2
Alignment explanation
Indices: 5447588--5447626 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5447578 CATGTATGTG
* *
5447588 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5447627 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5451761 original size:27 final size:27
Alignment explanation
Indices: 5451723--5451778 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5451713 ATTAATTTAT
5451723 TTTGTAAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
5451750 TTTGTAAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
5451777 TT
1 TT
5451779 AGCAAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (27 bp):
TTTGTAAAGTAATTATTTATTTTGAAC
Found at i:5462293 original size:21 final size:21
Alignment explanation
Indices: 5462224--5462388 Score: 90
Period size: 21 Copynumber: 8.0 Consensus size: 21
5462214 CGGGTGGATC
**
5462224 AGCTCTTACGAGCTTCTGTGA
1 AGCTCTTACGAGCTTCTGTTT
*
5462245 AGCTCTTACGAGCTTCTTTTTT
1 AGCTCTTACGAGCTTC-TGTTT
* **
5462267 AACTCTTTTGAGCTTCTGTTT
1 AGCTCTTACGAGCTTCTGTTT
**
5462288 AGCTCTTATAAGCTTCTG-TT
1 AGCTCTTACGAGCTTCTGTTT
* * * * * * *
5462308 GGCATGATT-TG-G-GT-GGATC
1 AGC-T-CTTACGAGCTTCTGTTT
5462327 AGCTCTTACGAGCTTCT-TTT
1 AGCTCTTACGAGCTTCTGTTT
**
5462347 CAGCTCTTACGAGCTTCCATTT
1 -AGCTCTTACGAGCTTCTGTTT
*
5462369 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
5462389 GGCATGTTCG
Statistics
Matches: 107, Mismatches: 27, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 5 0.05
20 7 0.07
21 70 0.65
22 20 0.19
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.42
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTT
Found at i:5462383 original size:81 final size:80
Alignment explanation
Indices: 5462245--5462423 Score: 232
Period size: 81 Copynumber: 2.2 Consensus size: 80
5462235 GCTTCTGTGA
* ** **
5462245 AGCTCTTACGAGCTTCTTTTTTAACTCTTTTGAGCTTCTGTTTAGCTCTTATAAGCTTCTGTTGG
1 AGCTCTTACGAGCTTC-TTTTCAACTCTTACGAGCTTCCATTTAGCTCTTATAAGCTTCTGTTGG
* ** *
5462310 CATGATTTGGGTGGATC
65 CATG-TTCGGAAGGACC
* *
5462327 AGCTCTTACGAGCTTCTTTTCAGCTCTTACGAGCTTCCATTTAGCTCTTATGAGCTTCTGTTGGC
1 AGCTCTTACGAGCTTCTTTTCAACTCTTACGAGCTTCCATTTAGCTCTTATAAGCTTCTGTTGGC
5462392 ATGTTCGGAAGGACC
66 ATGTTCGGAAGGACC
*
5462407 AGCTCTTATGAGCTTCT
1 AGCTCTTACGAGCTTCT
5462424 ATTGACGATG
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 24 0.28
81 45 0.53
82 16 0.19
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.41
Consensus pattern (80 bp):
AGCTCTTACGAGCTTCTTTTCAACTCTTACGAGCTTCCATTTAGCTCTTATAAGCTTCTGTTGGC
ATGTTCGGAAGGACC
Found at i:5467487 original size:25 final size:24
Alignment explanation
Indices: 5467444--5467496 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
5467434 AAGTTCAAGC
*
5467444 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATATCAAGAAGCTCACAAA
* *
5467468 GAGCCTATATCAAGATGCTCATAAA
1 GAGCC-ATATCAAGAAGCTCACAAA
5467493 GAGC
1 GAGC
5467497 TGCGGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.17
Consensus pattern (24 bp):
GAGCCATATCAAGAAGCTCACAAA
Found at i:5473860 original size:25 final size:25
Alignment explanation
Indices: 5473782--5473876 Score: 88
Period size: 25 Copynumber: 3.9 Consensus size: 25
5473772 GAAGAGTTAT
* *
5473782 TATCAGGGAGCTC-CAAATAGCCATA
1 TATCAGGAAGCTCACAAAGAGCC-TA
* * **
5473807 TAACAGGAAGTTCA-AGCGAGCC-A
1 TATCAGGAAGCTCACAAAGAGCCTA
5473830 TATCAGGAAGCTCACAAAGAGCCTA
1 TATCAGGAAGCTCACAAAGAGCCTA
* *
5473855 TATCAGGACGCTCATAAAGAGC
1 TATCAGGAAGCTCACAAAGAGC
5473877 TACGGTATGT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
23 13 0.24
24 6 0.11
25 36 0.65
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (25 bp):
TATCAGGAAGCTCACAAAGAGCCTA
Found at i:5473977 original size:64 final size:64
Alignment explanation
Indices: 5473853--5473978 Score: 144
Period size: 64 Copynumber: 2.0 Consensus size: 64
5473843 ACAAAGAGCC
* * * * ** * **
5473853 TATATCAGGACGCTCATAAAGAGCTACGGTATGTTCGTATTATATGCAGGATCCACACCGATTA
1 TATAACAGGACGCTCACAAAGAGCTACGGTATATTCGCAACACATGCAGGATAAACACCGATTA
* * *
5473917 TATAACAGGATGCTCACAAAGAGCTGCGGTATATTCGCAACACATGCAGGATAAATACCGAT
1 TATAACAGGACGCTCACAAAGAGCTACGGTATATTCGCAACACATGCAGGATAAACACCGAT
5473979 CAGGATGCTC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (64 bp):
TATAACAGGACGCTCACAAAGAGCTACGGTATATTCGCAACACATGCAGGATAAACACCGATTA
Found at i:5490587 original size:81 final size:81
Alignment explanation
Indices: 5490465--5490614 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
5490455 TAGAGCACTC
* *
5490465 GCAAGGCATGGTATACTTCATCCATCGTTGAGACCTATAGCAAATCATAGTAATACAATGACCAA
1 GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTATAGCAAATCATAGTAATACAACGACCAA
5490530 CCTCTACTAAGCATTT
66 CCTCTACTAAGCATTT
* * * * *
5490546 GCAAGGCATGGTATACTTCATTCTTCGTCGAGA-TTAGTAGCAGATCATAGTAATACAACGAGCA
1 GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTA-TAGCAAATCATAGTAATACAACGACCA
5490610 ACCTC
65 ACCTC
5490615 CACCAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 2 0.03
81 59 0.97
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (81 bp):
GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTATAGCAAATCATAGTAATACAACGACCAA
CCTCTACTAAGCATTT
Found at i:5492802 original size:13 final size:13
Alignment explanation
Indices: 5492784--5492810 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5492774 TTTGGTACAA
5492784 AAATGTGAGATAT
1 AAATGTGAGATAT
5492797 AAATGTGAGATAT
1 AAATGTGAGATAT
5492810 A
1 A
5492811 TGTGGTAAAT
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:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (13 bp):
AAATGTGAGATAT
Found at i:5497535 original size:27 final size:27
Alignment explanation
Indices: 5497497--5497561 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
5497487 TTTATCGAGG
*
5497497 TTATTAGTTTATCGATAAATAAATATT
1 TTATTAATTTATCGATAAATAAATATT
*
5497524 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATAAATATT
5497551 TTATTAATTTA
1 TTATTAATTTA
5497562 GAGAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATAAATATT
Found at i:5497704 original size:38 final size:33
Alignment explanation
Indices: 5497638--5497709 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 33
5497628 TAGATCAAAG
*
5497638 TTAATTGGTTCATGTAACAAAAAAAAGAGTTAA
1 TTAATTGGTTCATGTAAAAAAAAAAAGAGTTAA
5497671 TTAATTGGTTCATGTAGCCAAAAAGAATAAAGAGTTAA
1 TTAATTGGTTCATGTA---AAAAA-AA-AAAGAGTTAA
5497709 T
1 T
5497710 GGTTTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 16 0.48
36 4 0.12
37 2 0.06
38 11 0.33
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (33 bp):
TTAATTGGTTCATGTAAAAAAAAAAAGAGTTAA
Found at i:5504734 original size:21 final size:20
Alignment explanation
Indices: 5504691--5504751 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
5504681 ATTTATTAAT
* *
5504691 TAGAAATAAATTTATAAAAA
1 TAGAAAAAAAATTATAAAAA
*
5504711 TAGTAAAAAAATTATAAAATA
1 TAGAAAAAAAATTATAAAA-A
5504732 TAGAAAAAAAATTATAAAAA
1 TAGAAAAAAAATTATAAAAA
5504752 ATTATGAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
TAGAAAAAAAATTATAAAAA
Found at i:5504750 original size:9 final size:10
Alignment explanation
Indices: 5504688--5504756 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 10
5504678 ATAATTTATT
*
5504688 AATTAGAAATA
1 AATTATAAA-A
5504699 AATTTATAAAA
1 AA-TTATAAAA
*
5504710 ATAGTA-AAAA
1 A-ATTATAAAA
5504720 AATTATAAAA
1 AATTATAAAA
* * *
5504730 TATAGAAAAAA
1 AAT-TATAAAA
5504741 AATTATAAAA
1 AATTATAAAA
5504751 AATTAT
1 AATTAT
5504757 GAAGTCGTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
9 3 0.07
10 22 0.49
11 13 0.29
12 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (10 bp):
AATTATAAAA
Found at i:5505058 original size:22 final size:21
Alignment explanation
Indices: 5505031--5505084 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
5505021 TTTTACAAAA
5505031 TTTACAATTTTTTTATGATTTT
1 TTTACAATTTTTTTAT-ATTTT
5505053 TTTACAA-TTTTTTATATTTT
1 TTTACAATTTTTTTATATTTT
5505073 TTT-CTAATTTTT
1 TTTAC-AATTTTT
5505085 AATAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.03
20 10 0.33
21 12 0.40
22 7 0.23
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTACAATTTTTTTATATTTT
Found at i:5505063 original size:20 final size:20
Alignment explanation
Indices: 5505039--5505084 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
5505029 AATTTACAAT
5505039 TTTTTTATGATTTTTTTAC-AA
1 TTTTTTAT-ATTTTTTT-CTAA
5505060 TTTTTTATATTTTTTTCTAA
1 TTTTTTATATTTTTTTCTAA
5505080 TTTTT
1 TTTTT
5505085 AATAAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 8 0.33
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTTATATTTTTTTCTAA
Found at i:5505075 original size:10 final size:10
Alignment explanation
Indices: 5505037--5505075 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5505027 AAAATTTACA
5505037 ATTTTTTTAT
1 ATTTTTTTAT
*
5505047 GATTTTTTTAC
1 -ATTTTTTTAT
*
5505058 AATTTTTTAT
1 ATTTTTTTAT
5505068 ATTTTTTT
1 ATTTTTTT
5505076 CTAATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (10 bp):
ATTTTTTTAT
Found at i:5505082 original size:11 final size:11
Alignment explanation
Indices: 5505031--5505084 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
5505021 TTTTACAAAA
*
5505031 TTTACAATTTT
1 TTTATAATTTT
*
5505042 TTTATGATTTT
1 TTTATAATTTT
*
5505053 TTTACAA-TTT
1 TTTATAATTTT
5505063 TTTAT-ATTTT
1 TTTATAATTTT
*
5505073 TTTCTAATTTT
1 TTTATAATTTT
5505084 T
1 T
5505085 AATAAATTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 1 0.03
10 14 0.40
11 20 0.57
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTATAATTTT
Found at i:5507415 original size:43 final size:43
Alignment explanation
Indices: 5507367--5507631 Score: 394
Period size: 43 Copynumber: 6.3 Consensus size: 43
5507357 TTATCTTTAA
* *
5507367 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTATACAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
*
5507410 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTATACAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
*
5507453 AAACGCCGCTAAAGATCATGTTCTTTA---GCGCTTTTTGCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
* * * *
5507493 AAACGCCGCTAAAGCTCATGTTCTTTTGCGGTGCTTTTTACAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
* *
5507536 AAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGTTTTTTACAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
**
5507579 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCAATTTTT-CAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
5507621 AAACGCCGCTA
1 AAACGCCGCTA
5507632 TTTGTTTGGT
Statistics
Matches: 203, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
40 36 0.18
42 14 0.07
43 153 0.75
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTACAC
Found at i:5507512 original size:83 final size:82
Alignment explanation
Indices: 5507367--5507631 Score: 359
Period size: 83 Copynumber: 3.1 Consensus size: 82
5507357 TTATCTTTAA
* *
5507367 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTT
1 AAACGCCGCTAAAGATCATGTTCTTTA---GCGCTTTTTACACAAACGCCGCTAAAGATCATGTT
5507432 CTTTAGCGGCGCTTTATACAC
63 CTTTAGCGGCGCTTT-TACAC
* *
5507453 AAACGCCGCTAAAGATCATGTTCTTTAGCGCTTTTTGCACAAACGCCGCTAAAGCTCATGTTCTT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGCTTTTTACACAAACGCCGCTAAAGATCATGTTCTT
* * *
5507518 TTGCGGTGCTTTTTACAT
66 TAGCGGCGC-TTTTACAC
*
5507536 AAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGTTTTTTACACAAACGCCGCTAAAGATCATGTT
1 AAACGCCGCTAAAGATCATGTTCTTTAGC-GC--TTTTTACACAAACGCCGCTAAAGATCATGTT
** *
5507601 CTTTAGCGGCAATTTTTCAC
63 CTTTAGCGGCGCTTTTACAC
5507621 AAACGCCGCTA
1 AAACGCCGCTA
5507632 TTTGTTTGGT
Statistics
Matches: 159, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
83 74 0.47
84 5 0.03
85 17 0.11
86 63 0.40
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (82 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGCTTTTTACACAAACGCCGCTAAAGATCATGTTCTT
TAGCGGCGCTTTTACAC
Found at i:5507592 original size:126 final size:127
Alignment explanation
Indices: 5507367--5507631 Score: 426
Period size: 126 Copynumber: 2.1 Consensus size: 127
5507357 TTATCTTTAA
*
5507367 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTT
1 AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTT
5507432 CTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTTCTTTAGC-GC-TTTTTGCAC
66 CTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTTCTTTAGCGGCATTTTT-CAC
* * * * *
5507493 AAACGCCGCTAAAGCTCATGTTCTTTTGCGGTGCTTTTTACATAAACGCCGCTAAAGTTCATGTT
1 AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTT
* *
5507558 CTTTAGCGGCGTTTTTTACACAAACGCCGCTAAAGATCATGTTCTTTAGCGGCAATTTTTCAC
66 CTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTTCTTTAGCGGC-ATTTTTCAC
5507621 AAACGCCGCTA
1 AAACGCCGCTA
5507632 TTTGTTTGGT
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
126 107 0.84
127 2 0.02
128 14 0.11
129 5 0.04
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (127 bp):
AAACGCCGCTAAAGCTCATGTTCTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTT
CTTTAGCGGCGCTTTATACACAAACGCCGCTAAAGATCATGTTCTTTAGCGGCATTTTTCAC
Found at i:5508052 original size:66 final size:66
Alignment explanation
Indices: 5507975--5508110 Score: 236
Period size: 66 Copynumber: 2.1 Consensus size: 66
5507965 CTCGCTGCAG
* *
5507975 CCTCTGCTTCTCTGGATGCCGCATCAGCTTTAAGTTGTCGCTGGAGTTCTTCATATTTCTTTTGA
1 CCTCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
5508040 A
66 A
* *
5508041 CCTCTGCTTCTCTCGCTGCCGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
1 CCTCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
5508106 A
66 A
5508107 CCTC
1 CCTC
5508111 AACTGTGGTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.41
Consensus pattern (66 bp):
CCTCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
A
Found at i:5513590 original size:9 final size:9
Alignment explanation
Indices: 5513572--5513733 Score: 113
Period size: 9 Copynumber: 18.4 Consensus size: 9
5513562 TAAGGGATAT
*
5513572 TTATGAAAG
1 TTATGTAAG
5513581 TTATGTAAG
1 TTATGTAAG
5513590 TTATGT-A-
1 TTATGTAAG
* *
5513597 TTAAGTAAA
1 TTATGTAAG
5513606 TTATGTAAG
1 TTATGTAAG
5513615 TTATGT-A-
1 TTATGTAAG
*
5513622 TTATGTAAA
1 TTATGTAAG
5513631 TTATGTAAG
1 TTATGTAAG
5513640 TTATGT-A-
1 TTATGTAAG
* *
5513647 TTAAGTAGG
1 TTATGTAAG
5513656 TTATGTAAG
1 TTATGTAAG
5513665 TTATGTAAG
1 TTATGTAAG
* *
5513674 TTTTTGTGTA-
1 -TTATGT-AAG
*
5513684 TTATGTAAC
1 TTATGTAAG
* * *
5513693 TTTTTTAAT
1 TTATGTAAG
*
5513702 TTATGTAGG
1 TTATGTAAG
*
5513711 TTATGTATTG
1 TTATGTA-AG
*
5513721 TTATATAAG
1 TTATGTAAG
5513730 TTAT
1 TTAT
5513734 TATGTAGGTT
Statistics
Matches: 120, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
7 16 0.13
8 6 0.05
9 85 0.71
10 12 0.10
11 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5513609 original size:16 final size:17
Alignment explanation
Indices: 5513585--5513663 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 17
5513575 TGAAAGTTAT
*
5513585 GTAAGTTATGT-ATTAA
1 GTAAATTATGTAATTAA
*
5513601 GTAAATTATGTAAGTTAT
1 GTAAATTATGTAA-TTAA
*
5513619 GT--ATTATGTAAATTAT
1 GTAAATTATGT-AATTAA
*
5513635 GTAAGTTATGT-ATTAA
1 GTAAATTATGTAATTAA
**
5513651 GTAGGTTATGTAA
1 GTAAATTATGTAA
5513664 GTTATGTAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
16 37 0.71
17 4 0.08
18 11 0.21
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (17 bp):
GTAAATTATGTAATTAA
Found at i:5513609 original size:25 final size:25
Alignment explanation
Indices: 5513581--5513671 Score: 155
Period size: 25 Copynumber: 3.6 Consensus size: 25
5513571 TTTATGAAAG
5513581 TTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTATTAAGTAAA
*
5513606 TTATGTAAGTTATGTATTATGTAAA
1 TTATGTAAGTTATGTATTAAGTAAA
**
5513631 TTATGTAAGTTATGTATTAAGTAGG
1 TTATGTAAGTTATGTATTAAGTAAA
5513656 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
5513672 AGTTTTTGTG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTAAGTAAA
Found at i:5513744 original size:12 final size:12
Alignment explanation
Indices: 5513729--5513769 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5513719 TGTTATATAA
5513729 GTTATTATGTAG
1 GTTATTATGTAG
*
5513741 GTTATTATGTAA
1 GTTATTATGTAG
* *
5513753 GTCATTATGTTG
1 GTTATTATGTAG
5513765 GTTAT
1 GTTAT
5513770 GTAAGTTGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.51
Consensus pattern (12 bp):
GTTATTATGTAG
Found at i:5513753 original size:24 final size:24
Alignment explanation
Indices: 5513721--5513769 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5513711 TTATGTATTG
*
5513721 TTATATAAGTTATTATGTAGGTTA
1 TTATATAAGTCATTATGTAGGTTA
* *
5513745 TTATGTAAGTCATTATGTTGGTTA
1 TTATATAAGTCATTATGTAGGTTA
5513769 T
1 T
5513770 GTAAGTTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (24 bp):
TTATATAAGTCATTATGTAGGTTA
Found at i:5514038 original size:9 final size:9
Alignment explanation
Indices: 5514024--5514080 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
5514014 ATTATAAATT
*
5514024 TAAATTTTG
1 TAAATTATG
5514033 TAAATTATG
1 TAAATTATG
5514042 --AATTATG
1 TAAATTATG
5514049 TAAATTATG
1 TAAATTATG
* *
5514058 TAAAATACG
1 TAAATTATG
*
5514067 TAAGTTATG
1 TAAATTATG
5514076 -AAATT
1 TAAATT
5514081 TGAACTTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 7 0.18
8 4 0.10
9 28 0.72
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (9 bp):
TAAATTATG
Found at i:5514050 original size:16 final size:16
Alignment explanation
Indices: 5513999--5514057 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
5513989 TATTAATAAG
* *
5513999 TTATGTAAGTTATGTA
1 TTATGTAAATTATGAA
*
5514015 TTA--TAAATT-TAAA
1 TTATGTAAATTATGAA
*
5514028 TTTTGTAAATTATGAA
1 TTATGTAAATTATGAA
5514044 TTATGTAAATTATG
1 TTATGTAAATTATG
5514058 TAAAATACGT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 6 0.18
16 19 0.56
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (16 bp):
TTATGTAAATTATGAA
Found at i:5517426 original size:41 final size:41
Alignment explanation
Indices: 5517381--5517557 Score: 203
Period size: 41 Copynumber: 4.3 Consensus size: 41
5517371 TAAAAAAGCA
* * * * *
5517381 CCGCTAAAGGCCTGAGA-ATTAGCAGTGCATCCATAAAAACG
1 CCGCTAAAGCCCAGA-ACATTAGCGGCGCATACATAAAAACG
* * * *
5517422 CCGCTAAATCCCAGAATATTAGCGGCGCATAAATAAAAACA
1 CCGCTAAAGCCCAGAACATTAGCGGCGCATACATAAAAACG
*
5517463 CCGCTAAAGCCCAGAACATTAGCGGCGCTTACATAAAAACG
1 CCGCTAAAGCCCAGAACATTAGCGGCGCATACATAAAAACG
* * * * *
5517504 CCGCTAAAGCACAGAACATTAGCGGCACTTCCATAAAATCG
1 CCGCTAAAGCCCAGAACATTAGCGGCGCATACATAAAAACG
5517545 CCGCTAAAGCCCA
1 CCGCTAAAGCCCA
5517558 CGAAAAGTCA
Statistics
Matches: 117, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
40 1 0.01
41 116 0.99
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (41 bp):
CCGCTAAAGCCCAGAACATTAGCGGCGCATACATAAAAACG
Found at i:5518416 original size:32 final size:32
Alignment explanation
Indices: 5518378--5518458 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
5518368 AACCACTACC
5518378 ATAAATATATTAAATATTTTATTATATTAAAA
1 ATAAATATATTAAATATTTTATTATATTAAAA
* * * * *
5518410 ATAAATAAAATAAATGTTTTATTGTATTAAAT
1 ATAAATATATTAAATATTTTATTATATTAAAA
5518442 AT-AATAT-TTAAA-ATTTT
1 ATAAATATATTAAATATTTT
5518459 TATATTTTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 4 0.10
30 4 0.10
31 4 0.10
32 29 0.71
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (32 bp):
ATAAATATATTAAATATTTTATTATATTAAAA
Found at i:5520273 original size:42 final size:42
Alignment explanation
Indices: 5520214--5520348 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
5520204 CCACATAGCC
* *
5520214 AAGGACATGGGCGTGTGCCCAGGCCGTGTGAGTCACACGGGT
1 AAGGACATGGGTGTGTGCCCAGGCCGTGTGAGCCACACGGGT
* * *
5520256 AAGGACATGGGTGTGTGCCCAAGTCGTGTGAGCCTCACGGGT
1 AAGGACATGGGTGTGTGCCCAGGCCGTGTGAGCCACACGGGT
* * * *
5520298 AAGGACATGGATGTGTGCCCAGGCCATGTGAGCCACATGGGC
1 AAGGACATGGGTGTGTGCCCAGGCCGTGTGAGCCACACGGGT
5520340 AAGGACATG
1 AAGGACATG
5520349 TGCATGTGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.22, C:0.22, G:0.38, T:0.18
Consensus pattern (42 bp):
AAGGACATGGGTGTGTGCCCAGGCCGTGTGAGCCACACGGGT
Found at i:5523219 original size:30 final size:29
Alignment explanation
Indices: 5523180--5523240 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
5523170 ATTGAACTTT
5523180 AACTATT-AAATCAAAATAGTAGAGAGATTA
1 AACTATTAAAATCAAAA-A-TAGAGAGATTA
* * *
5523210 AACTCTTAAAATTAAAAATAGATAGATTA
1 AACTATTAAAATCAAAAATAGAGAGATTA
5523239 AA
1 AA
5523241 TTTTAAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.44
30 7 0.26
31 8 0.30
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.28
Consensus pattern (29 bp):
AACTATTAAAATCAAAAATAGAGAGATTA
Found at i:5524558 original size:43 final size:43
Alignment explanation
Indices: 5524496--5524621 Score: 130
Period size: 43 Copynumber: 2.9 Consensus size: 43
5524486 ACATAGGTTG
*
5524496 TCGATATGTGTTTCCGTGTAAGACCACGTCTGGGACGTTGCCA
1 TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGCCA
* * * *
5524539 TCGATTTGTGTTTATGTGTAAGACC-CTGTCCGGGACAG-TGGCA
1 TCGATATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGCCA
* * * * *
5524582 TTGATATGCGATTACATGTAAGACCACGTCTGGGCCGTTG
1 TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTG
5524622 GCATTGTACG
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.03
43 62 0.94
44 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (43 bp):
TCGATATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGCCA
Found at i:5531605 original size:40 final size:40
Alignment explanation
Indices: 5531528--5531638 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 40
5531518 GGCGTTTGTA
* * *
5531528 CAAAAAATGCTGCTAAAAATCGAGCATTAGCGACGCTTTC
1 CAAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTCC
*
5531568 CAAAAAACGCCGCTAAAGATCGAGCATTAGC-AGCGCTTCC
1 CAAAAAACGCCGCTAAAAATCGAGCATTAGCGA-CGCTTCC
* * * *
5531608 CTAGAAGCGCCGCTAAAAAT-GATCATTAGCG
1 CAAAAAACGCCGCTAAAAATCGAGCATTAGCG
5531639 GCGTTTTTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 10 0.17
40 50 0.83
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (40 bp):
CAAAAAACGCCGCTAAAAATCGAGCATTAGCGACGCTTCC
Found at i:5531766 original size:41 final size:40
Alignment explanation
Indices: 5531704--5532022 Score: 341
Period size: 41 Copynumber: 7.8 Consensus size: 40
5531694 CCTTTAGGGT
* * * * *
5531704 TTTTAGCAGCGTTTTTGAAAAAGCACCGCTAAAGATCGGGA
1 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-AGA
* * * * * *
5531745 TTTTAGCGGCATTTTTTAAAAAGCGCAGCTAATGCCCTGG
1 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* *
5531785 TCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGA
1 T-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* * * *
5531826 GATTTAGCGGCGTTTTTGAAAAATCACCGCTAATGTTCAGA
1 -TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* * * * * *
5531867 GCTTTAGCAGCATTTTTGGAGAAGCGACGCTAATGCTCAGA
1 -TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
* *
5531908 TCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAGTGCTCAGA
1 T-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
*
5531949 TCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAGC
1 T-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-AGA
5531991 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
1 TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
5532023 AATATTTTAT
Statistics
Matches: 232, Mismatches: 42, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
40 2 0.01
41 227 0.98
42 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGA
Found at i:5531924 original size:123 final size:121
Alignment explanation
Indices: 5531705--5532022 Score: 402
Period size: 123 Copynumber: 2.6 Consensus size: 121
5531695 CTTTAGGGTT
* * * * *
5531705 TTTAGCAGCGTTTTTGAAAAAGCACCGCTAAAGATCGGGATTTTAGCGGCATTTTTTAAAAAGCG
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGATCGAG-CTTTAGCGGCATTTTTGAAAAAGCG
* * *
5531770 CAGCTAATGCCCTGGTCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCAGAGA
65 C-GCTAATGCCCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGA
* * * * *
5531828 TTTAGCGGCGTTTTTGAAAAATCACCGCTAATGTTCAGAGCTTTAGCAGCATTTTTGGAGAAGCG
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGATC-GAGCTTTAGCGGCATTTTTGAAAAAGCG
* * **
5531893 ACGCTAATGCTCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAGTGCTCAGATC
65 -CGCTAATGCCCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGA
* * *
5531951 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGAGCTTTTAGCGGCGTTTTTGAAAAAGCG
1 TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGATCGAGC-TTTAGCGGCATTTTTGAAAAAGCG
5532016 CCGCTAA
65 -CGCTAA
5532023 AATATTTTAT
Statistics
Matches: 167, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
122 4 0.02
123 160 0.96
124 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (121 bp):
TTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGATCGAGCTTTAGCGGCATTTTTGAAAAAGCGC
GCTAATGCCCAGATCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAGA
Done.