Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 93 of 126
Found at i:28266690 original size:16 final size:16
Alignment explanation
Indices: 28266669--28266709 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
28266659 TACTGATTAC
28266669 CCATTACAGATATATT
1 CCATTACAGATATATT
** *
28266685 CCATTACATCTCTATT
1 CCATTACAGATATATT
28266701 CCATTACAG
1 CCATTACAG
28266710 CCATATTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (16 bp):
CCATTACAGATATATT
Found at i:28266716 original size:16 final size:16
Alignment explanation
Indices: 28266669--28266721 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
28266659 TACTGATTAC
**
28266669 CCATTACAGATATATT
1 CCATTACAGCCATATT
*
28266685 CCATTACATCTC-TATT
1 CCATTACAGC-CATATT
28266701 CCATTACAGCCATATT
1 CCATTACAGCCATATT
*
28266717 TCATT
1 CCATT
28266722 CACCTCAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 29 0.97
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (16 bp):
CCATTACAGCCATATT
Found at i:28268000 original size:21 final size:21
Alignment explanation
Indices: 28267952--28268005 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
28267942 TTGCTCTGCT
* * *
28267952 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCCCTCGCTGCAACCG
**
28267973 CCACTTCCCTCGCTGCAACCG
1 CTGCTTCCCTCGCTGCAACCG
28267994 CTGCTTCCCTCG
1 CTGCTTCCCTCG
28268006 TTGCCGCTTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.07, C:0.48, G:0.17, T:0.28
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAACCG
Found at i:28270592 original size:9 final size:8
Alignment explanation
Indices: 28270576--28271131 Score: 101
Period size: 9 Copynumber: 62.1 Consensus size: 8
28270566 TATTATGTAT
28270576 TATGTAAG
1 TATGTAAG
28270584 TACTGTAAG
1 TA-TGTAAG
28270593 TAATGTAAG
1 T-ATGTAAG
28270602 TTATGTAAG
1 -TATGTAAG
*
28270611 TTACT-TAATT
1 -TA-TGTAA-G
28270621 TATGTAAG
1 TATGTAAG
28270629 TTATGTAAG
1 -TATGTAAG
* *
28270638 ATATTTAATT
1 -TATGTAA-G
28270648 TATGTAAG
1 TATGTAAG
28270656 TTATGTAAG
1 -TATGTAAG
*
28270665 TTACT-TAATT
1 -TA-TGTAA-G
*
28270675 TCTGTAAG
1 TATGTAAG
28270683 TTATGTAAG
1 -TATGTAAG
28270692 TTATGTAAG
1 -TATGTAAG
*
28270701 ATAT-TTAG
1 -TATGTAAG
*
28270709 TTTATGTAATT
1 --TATGTAA-G
28270720 TATGTAAG
1 TATGTAAG
28270728 TTATGTAAG
1 -TATGTAAG
* *
28270737 TTATTTAATT
1 -TATGTAA-G
*
28270747 TTTGTAAG
1 TATGTAAG
28270755 TTATGTAAG
1 -TATGTAAG
*
28270764 TTACT-TAATT
1 -TA-TGTAA-G
28270774 TATGTAAG
1 TATGTAAG
28270782 TTATGTAAG
1 -TATGTAAG
28270791 TTATGTAAG
1 -TATGTAAG
* *
28270800 TTATTTAATT
1 -TATGTAA-G
28270810 TATGTAAG
1 TATGTAAG
28270818 TTATGTAAG
1 -TATGTAAG
*
28270827 ATAT-TTAG
1 -TATGTAAG
28270835 TTTATGTAA-
1 --TATGTAAG
*
28270844 AATGTAAG
1 TATGTAAG
28270852 TTATGTAAG
1 -TATGTAAG
* *
28270861 TTATTTAATT
1 -TATGTAA-G
*
28270871 TTTGTAAG
1 TATGTAAG
28270879 TTATGTAAG
1 -TATGTAAG
*
28270888 TTACT-TAATT
1 -TA-TGTAA-G
28270898 TATGTAAG
1 TATGTAAG
28270906 TTATGTAAG
1 -TATGTAAG
28270915 TTATGTAAG
1 -TATGTAAG
*
28270924 ATAT-TTAG
1 -TATGTAAG
28270932 TTTATGTAAG
1 --TATGTAAG
28270942 TTATGTAAG
1 -TATGTAAG
*
28270951 ATAT-TTAG
1 -TATGTAAG
*
28270959 TTAATGTAATT
1 -T-ATGTAA-G
28270970 TATGTAAG
1 TATGTAAG
28270978 TTATGTAAG
1 -TATGTAAG
*
28270987 ATAT-TTAG
1 -TATGTAAG
*
28270995 TTAATGTAATT
1 -T-ATGTAA-G
28271006 TATGTAAG
1 TATGTAAG
28271014 TTATGTAAG
1 -TATGTAAG
* *
28271023 TTATTTAATT
1 -TATGTAA-G
*
28271033 TTTGTAAG
1 TATGTAAG
28271041 TTATGTAAG
1 -TATGTAAG
*
28271050 TTACT-TAATT
1 -TA-TGTAA-G
28271060 TATGTAAG
1 TATGTAAG
28271068 TTATGTAAG
1 -TATGTAAG
* *
28271077 TTATTTAATT
1 -TATGTAA-G
*
28271087 TTTGTAAG
1 TATGTAAG
28271095 TTATGTAAG
1 -TATGTAAG
*
28271104 TTACT-TAATT
1 -TA-TGTAA-G
28271114 TATGTAAG
1 TATGTAAG
28271122 TTATGTAAG
1 -TATGTAAG
28271131 T
1 T
28271132 TATTTAATTT
Statistics
Matches: 416, Mismatches: 75, Indels: 114
0.69 0.12 0.19
Matches are distributed among these distances:
7 6 0.01
8 26 0.06
9 363 0.87
10 21 0.05
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.49
Consensus pattern (8 bp):
TATGTAAG
Found at i:28270606 original size:27 final size:27
Alignment explanation
Indices: 28270587--28271251 Score: 603
Period size: 27 Copynumber: 25.0 Consensus size: 27
28270577 ATGTAAGTAC
* *
28270587 TGTAAGTAATGTAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
** * **
28270614 CTTAATTTATGTAAGTTATGTAAGATA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* * *
28270641 TTTAATTTATGTAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
** * * *
28270668 CTTAATTTCTGTAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* *
28270695 TGTAAGATAT-TTAGTTTATGTAATTTA
1 TGTAAGTTATGTAAG-TTATGTAATTTA
* *
28270722 TGTAAGTTATGTAAGTTATTTAATTTT
1 TGTAAGTTATGTAAGTTATGTAATTTA
28270749 TGTAAGTTATGTAAGTTACT-TAATTTA
1 TGTAAGTTATGTAAGTTA-TGTAATTTA
*
28270776 TGTAAGTTATGTAAGTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* * **
28270803 TTTAATTTATGTAAGTTATGTAAGATA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* * *
28270830 T-TTAGTTTATGTAA--AATGTAAGTTA
1 TGTAAG-TTATGTAAGTTATGTAATTTA
* * * *
28270855 TGTAAGTTATTTAATTTTTGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* *
28270882 TGTAAGTTACT-TAATTTATGTAAGTTA
1 TGTAAGTTA-TGTAAGTTATGTAATTTA
* * *
28270909 TGTAAGTTATGTAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
28270936 TGTAAGTTATGTAAG--A--T-ATTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* * *
28270958 -GT---TAATGTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* * ** *
28270981 TGTAAGATATTTAGTTAATGTAATTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* *
28271008 TGTAAGTTATGTAAGTTATTTAATTTT
1 TGTAAGTTATGTAAGTTATGTAATTTA
28271035 TGTAAGTTATGTAAGTTACT-TAATTTA
1 TGTAAGTTATGTAAGTTA-TGTAATTTA
* *
28271062 TGTAAGTTATGTAAGTTATTTAATTTT
1 TGTAAGTTATGTAAGTTATGTAATTTA
28271089 TGTAAGTTATGTAAGTTACT-TAATTTA
1 TGTAAGTTATGTAAGTTA-TGTAATTTA
*
28271116 TGTAAGTTATGTAAGTTATTTAATTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* * * *
28271143 TGTAAGTTATATAAGATATTTAGTTTA
1 TGTAAGTTATGTAAGTTATGTAATTTA
* *
28271170 TGTAAGATAT-TTAGTTTATGTAATTTA
1 TGTAAGTTATGTAAG-TTATGTAATTTA
* *
28271197 TGTAAGTTATGTAAGTTATTTAATTTT
1 TGTAAGTTATGTAAGTTATGTAATTTA
*
28271224 TGTAAGTTATGTAA-TTAATGTAAGTTA
1 TGTAAGTTATGTAAGTT-ATGTAATTTA
28271251 T
1 T
28271252 TTAATTTGTG
Statistics
Matches: 538, Mismatches: 74, Indels: 52
0.81 0.11 0.08
Matches are distributed among these distances:
18 7 0.01
20 1 0.00
21 2 0.00
22 5 0.01
23 5 0.01
24 2 0.00
25 18 0.03
26 17 0.03
27 471 0.88
28 10 0.02
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (27 bp):
TGTAAGTTATGTAAGTTATGTAATTTA
Found at i:28270629 original size:36 final size:36
Alignment explanation
Indices: 28270588--28271258 Score: 641
Period size: 36 Copynumber: 18.7 Consensus size: 36
28270578 TGTAAGTACT
* * *
28270588 GTAAGTAATGTAAGTTATGTAAGTTACT-TAATTTAT
1 GTAAGTTATGTAAGTTATGTAATTTA-TGTAAGTTAT
* *
28270624 GTAAGTTATGTAAGATATTTAATTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
* * *
28270660 GTAAGTTACT-TAATTTCTGTAAGTTATGTAAGTTAT
1 GTAAGTTA-TGTAAGTTATGTAATTTATGTAAGTTAT
* *
28270696 GTAAGATAT-TTAGTTTATGTAATTTATGTAAGTTAT
1 GTAAGTTATGTAAG-TTATGTAATTTATGTAAGTTAT
* * * *
28270732 GTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTA-T
* *
28270769 -TAATTTATGTAAGTTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
* * ** *
28270804 TTAATTTATGTAAGTTATGTAAGATAT-TTAGTTTAT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAG-TTAT
* * * * *
28270840 GTAA--AATGTAAGTTATGTAAGTTATTTAATTTTT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
28270874 GTAAGTTATGTAAGTTACT-TAATTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTA-TGTAATTTATGTAAGTTAT
* * *
28270910 GTAAGTTATGTAAGATATTTAGTTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
* *
28270946 GTAAGATAT-TTAGTTAATGTAATTTATGTAAGTTAT
1 GTAAGTTATGTAAGTT-ATGTAATTTATGTAAGTTAT
* *
28270982 GTAAGATAT-TTAGTTAATGTAATTTATGTAAGTTAT
1 GTAAGTTATGTAAGTT-ATGTAATTTATGTAAGTTAT
* * * *
28271018 GTAAGTTATTTAATTTTTGTAAGTTATGTAAGTTACT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTA-T
* * * * *
28271055 -TAATTTATGTAAGTTATGTAAGTTATTTAATTTTT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
28271090 GTAAGTTATGTAAGTTACT-TAATTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTA-TGTAATTTATGTAAGTTAT
* * * * *
28271126 GTAAGTTATTTAATTTATGTAAGTTATATAAGATAT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
* * * * *
28271162 -TTAGTTTATGTAAGATATTTAGTTTATGTAATTTAT
1 GTAAG-TTATGTAAGTTATGTAATTTATGTAAGTTAT
* *
28271198 GTAAGTTATGTAAGTTATTTAATTTTTGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
*
28271234 GTAA-TTAATGTAAGTTATTTAATTT
1 GTAAGTT-ATGTAAGTTATGTAATTT
28271259 GTGAACCCTA
Statistics
Matches: 533, Mismatches: 81, Indels: 42
0.81 0.12 0.06
Matches are distributed among these distances:
34 26 0.05
35 22 0.04
36 471 0.88
37 14 0.03
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.50
Consensus pattern (36 bp):
GTAAGTTATGTAAGTTATGTAATTTATGTAAGTTAT
Found at i:28271256 original size:18 final size:17
Alignment explanation
Indices: 28270568--28271257 Score: 470
Period size: 18 Copynumber: 38.6 Consensus size: 17
28270558 CATTTATGTA
28270568 TTATGT-ATTATGTAAG
1 TTATGTAATTATGTAAG
*
28270584 -TACTGTAAGTAATGTAAG
1 TTA-TGTAA-TTATGTAAG
*
28270602 TTATGTAAGTTACT-TAAT
1 TTATGTAA-TTA-TGTAAG
28270620 TTATGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
* *
28270638 ATATTTAATTTATGTAAG
1 TTATGTAA-TTATGTAAG
*
28270656 TTATGTAAGTTACT-TAAT
1 TTATGTAA-TTA-TGTAAG
*
28270674 TTCTGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
* *
28270692 TTATGTAAGATAT-TTAG
1 TTATGTAA-TTATGTAAG
28270709 TTTATGTAATTTATGTAAG
1 -TTATGTAA-TTATGTAAG
* *
28270728 TTATGTAAGTTATTTAAT
1 TTATGTAA-TTATGTAAG
*
28270746 TTTTGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
28270764 TTACT-TAATTTATGTAAG
1 TTA-TGTAA-TTATGTAAG
28270782 TTATGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
*
28270800 TTATTTAATTTATGTAAG
1 TTATGTAA-TTATGTAAG
* *
28270818 TTATGTAAGATAT-TTAG
1 TTATGTAA-TTATGTAAG
*
28270835 TTTATGTAA-AATGTAAG
1 -TTATGTAATTATGTAAG
* *
28270852 TTATGTAAGTTATTTAAT
1 TTATGTAA-TTATGTAAG
*
28270870 TTTTGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
28270888 TTACT-TAATTTATGTAAG
1 TTA-TGTAA-TTATGTAAG
28270906 TTATGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
* * *
28270924 ATATTTAGTTTATGTAAG
1 TTATGTA-ATTATGTAAG
* *
28270942 TTATGTAAGATAT-TTAG
1 TTATGTAA-TTATGTAAG
28270959 TTAATGTAATTTATGTAAG
1 TT-ATGTAA-TTATGTAAG
* *
28270978 TTATGTAAGATAT-TTAG
1 TTATGTAA-TTATGTAAG
28270995 TTAATGTAATTTATGTAAG
1 TT-ATGTAA-TTATGTAAG
* *
28271014 TTATGTAAGTTATTTAAT
1 TTATGTAA-TTATGTAAG
*
28271032 TTTTGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
28271050 TTACT-TAATTTATGTAAG
1 TTA-TGTAA-TTATGTAAG
* *
28271068 TTATGTAAGTTATTTAAT
1 TTATGTAA-TTATGTAAG
*
28271086 TTTTGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
28271104 TTACT-TAATTTATGTAAG
1 TTA-TGTAA-TTATGTAAG
* *
28271122 TTATGTAAGTTATTTAAT
1 TTATGTAA-TTATGTAAG
*
28271140 TTATGTAAGTTATATAAG
1 TTATGTAA-TTATGTAAG
* * *
28271158 ATATTTAGTTTATGTAAG
1 TTATGTA-ATTATGTAAG
* * * *
28271176 ATATTTAGTTTATGTAAT
1 TTATGTA-ATTATGTAAG
28271194 TTATGTAAGTTATGTAAG
1 TTATGTAA-TTATGTAAG
* *
28271212 TTATTTAATTTTTGTAAG
1 TTATGTAA-TTATGTAAG
28271230 TTATGTAATTAATGTAAG
1 TTATGTAATT-ATGTAAG
*
28271248 TTATTTAATT
1 TTATGTAATT
28271258 TGTGAACCCT
Statistics
Matches: 545, Mismatches: 98, Indels: 60
0.78 0.14 0.09
Matches are distributed among these distances:
15 2 0.00
16 13 0.02
17 28 0.05
18 481 0.88
19 21 0.04
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.50
Consensus pattern (17 bp):
TTATGTAATTATGTAAG
Found at i:28275514 original size:21 final size:20
Alignment explanation
Indices: 28275486--28275524 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28275476 CTTAACACAT
*
28275486 AACCTTAAACCTTAAACCCC
1 AACCTTAAACCATAAACCCC
28275506 AACCTTTAAACCATAAACC
1 AACC-TTAAACCATAAACC
28275525 ATAGACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCTTAAACCATAAACCCC
Found at i:28275795 original size:115 final size:115
Alignment explanation
Indices: 28275597--28276123 Score: 444
Period size: 115 Copynumber: 4.6 Consensus size: 115
28275587 ACCAAAACTT
* * * *
28275597 TGCGTTTTGGTTAAGATATTTTTCGGCGCTTTTCAAAAAGCGCCGCTAATACTATACTTTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* **
28275662 CGATTTCTCG--T-GGACGCCACTAATTCCATTATACATCAAGACTTAAACGC
66 CG--TTCTCGCATATG-CGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * *
28275712 TGCGTTTTTGTTAATATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCTTTAGCGG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* * * * * * * *
28275777 CGTTCCCGCATAAGCGCCACTAAGTCTAATATACCTCATGA-AAAAACTC
66 CGTTCTCGCATATGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * * **** * * *
28275826 TGCGTTTTGGTGAGCATATTTTGCGGCGCTTTTTTCCAAGCGCCGCTAATACTATGATGTAGCAG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
* *** * * *
28275891 CGTTTTTTTAATATGCGCCACTAATTAC-TGTATACATCGAGACAAAAACGT
66 CG-TTCTCGCATATGCGCCACTAATTCCAT-TATACATCAAGACAAAAACGC
* * * * * *
28275942 TGCGTTTTGGTTACCAAATTTTGCGGCGCTTCTCTGAAAA-CCCCGCTAATAGTATGCCTTAGCG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTC-AAAAAGCGCCGCTAATACTATGCTTTAGCG
* * * * * * *
28276006 GCGTGT-TC-CTTTTGCGCCACTAATTCTAGTATACCTCAAGAC-CAAACTC
65 GCGT-TCTCGCATATGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
* * * *
28276055 TACGTTTTGGTTCAGATATTTTGCGGCGCTTCTCACAAAA-CGCCGCTAATATTATGCTTTAGCG
1 TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCA-AAAAGCGCCGCTAATACTATGCTTTAGCG
28276119 GCGTT
65 GCGTT
28276124 TTCCATTAAA
Statistics
Matches: 323, Mismatches: 79, Indels: 23
0.76 0.19 0.05
Matches are distributed among these distances:
112 1 0.00
113 67 0.21
114 84 0.26
115 111 0.34
116 58 0.18
117 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (115 bp):
TGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGG
CGTTCTCGCATATGCGCCACTAATTCCATTATACATCAAGACAAAAACGC
Found at i:28276101 original size:229 final size:230
Alignment explanation
Indices: 28275584--28276125 Score: 580
Period size: 229 Copynumber: 2.4 Consensus size: 230
28275574 ATGCATGGTT
* *
28275584 AAGACCAAAACTTTGCGTTTTGGTTAAGATATTTTTCGGCGCTTTTCA-AAAAGCGCCGCTAATA
1 AAGACC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAA-CGCCGCTAATA
* ** * **
28275648 CTAT-ACTTTAGCGGCG-ATTTCTCGTGGACGCCACTAATTCCATTATACATCAAGACTTAAACG
64 CTATGA-TTTAGCGGCGTTTTTCTAATGGACGCCACTAATTACATTATACATCAAGACAAAAACG
* * * * *
28275711 CTGCGTTTTTGTTAATATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAATATGCTTTAGCG
128 CTGCGTTTTGGTTAACAAATTTTGCGGCGCTTCTCAAAAAGCCCCGCTAATAATATGCCTTAGCG
28275776 GCGTTCCCGCATAAGCGCCACTAAGTCTAATATACCTC
193 GCGTTCCCGCATAAGCGCCACTAAGTCTAATATACCTC
* ** * ** * *
28275814 ATGAAAAAACTCTGCGTTTTGG-TGAGCATATTTTGCGGCGCTTTTTTCCAAGCGCCGCTAATAC
1 AAGACCAAACTCTGCGTTTTGGTTAAG-ATATTTTGCGGCGCTTTTCACAAAACGCCGCTAATAC
* * * * *
28275878 TATGATGTAGCAGCGTTTTTTTAATATG-CGCCACTAATTAC-TGTATACATCGAGACAAAAACG
65 TATGATTTAGCGGCGTTTTTCTAAT-GGACGCCACTAATTACAT-TATACATCAAGACAAAAACG
* * * *
28275941 TTGCGTTTTGGTTACCAAATTTTGCGGCGCTTCTCTGAAAA-CCCCGCTAATAGTATGCCTTAGC
128 CTGCGTTTTGGTTAACAAATTTTGCGGCGCTTCTC-AAAAAGCCCCGCTAATAATATGCCTTAGC
* * ** * *
28276005 GGCGTGT-TC-CTTTTGCGCCACTAATTCTAGTATACCTC
192 GGCGT-TCCCGCATAAGCGCCACTAAGTCTAATATACCTC
* * * *
28276043 AAGACCAAACTCTACGTTTTGGTTCAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATATT
1 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAACGCCGCTAATACT
*
28276108 ATGCTTTAGCGGCGTTTT
66 ATGATTTAGCGGCGTTTT
28276126 CCATTAAACG
Statistics
Matches: 253, Mismatches: 50, Indels: 19
0.79 0.16 0.06
Matches are distributed among these distances:
228 3 0.01
229 145 0.57
230 99 0.39
231 6 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (230 bp):
AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAACGCCGCTAATACT
ATGATTTAGCGGCGTTTTTCTAATGGACGCCACTAATTACATTATACATCAAGACAAAAACGCTG
CGTTTTGGTTAACAAATTTTGCGGCGCTTCTCAAAAAGCCCCGCTAATAATATGCCTTAGCGGCG
TTCCCGCATAAGCGCCACTAAGTCTAATATACCTC
Found at i:28276399 original size:112 final size:113
Alignment explanation
Indices: 28276245--28276477 Score: 299
Period size: 112 Copynumber: 2.1 Consensus size: 113
28276235 GACCAAACTC
* *
28276245 TGCGTTTTGGTTAACATATGTTGCGGCGCTTTTGATAAGCGCCGCTAATACTTCCTTTAGCGGCG
1 TGCGTTTTCGTTAACATATGTTGCGGCGCTTTGGATAAGCGCCGCTAATACTTCCTTTAGCGGCG
* * * *
28276310 GGTTTTCGTCAGCGCCACTAACGCTAATATACAACGAGA-CAAAACGA
66 GGTTTTCATAAACGCCACTAACGCTAATATACAACAAGACCAAAACGA
* * * *
28276357 TGCGTTTTCGTTAAGAT-TTTTGCGGCGCATTTGGCTATGCGCCGCTAATACTTCCTTTAGCGGC
1 TGCGTTTTCGTTAACATATGTTGCGGCGC-TTTGGATAAGCGCCGCTAATACTTCCTTTAGCGGC
** ** * *
28276421 GTTTTTTCATAAACGCCACTAATTCTAGTATACATCAAGACCAAAACGA
65 GGGTTTTCATAAACGCCACTAACGCTAATATACAACAAGACCAAAACGA
28276470 TGCGTTTT
1 TGCGTTTT
28276478 GATCTTCAGA
Statistics
Matches: 103, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
111 10 0.10
112 77 0.75
113 16 0.16
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (113 bp):
TGCGTTTTCGTTAACATATGTTGCGGCGCTTTGGATAAGCGCCGCTAATACTTCCTTTAGCGGCG
GGTTTTCATAAACGCCACTAACGCTAATATACAACAAGACCAAAACGA
Found at i:28279145 original size:18 final size:18
Alignment explanation
Indices: 28279085--28279150 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
28279075 TTTTTAAATT
28279085 TTTTAATATATTTTT-TAA
1 TTTTAA-ATATTTTTATAA
**
28279103 TTTTAAA-ATTTTTATTC
1 TTTTAAATATTTTTATAA
* * *
28279120 GTTAAAATATTTTTAGAA
1 TTTTAAATATTTTTATAA
28279138 TTTTAAATTATTT
1 TTTTAAA-TATTT
28279151 GTTAATGTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
16 6 0.17
17 7 0.19
18 18 0.50
19 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTAAATATTTTTATAA
Found at i:28283608 original size:3 final size:3
Alignment explanation
Indices: 28283600--28283635 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
28283590 GAATCTGCAA
28283600 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
28283636 TAGCATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:28284723 original size:13 final size:12
Alignment explanation
Indices: 28284705--28284738 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28284695 AGGGAGAAGC
*
28284705 AAAATAGAATGAA
1 AAAATAAAAT-AA
28284718 AAAATAAAATAA
1 AAAATAAAATAA
28284730 AAAATAAAA
1 AAAATAAAA
28284739 GTTAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:28289929 original size:17 final size:18
Alignment explanation
Indices: 28289903--28289939 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28289893 GAAAAAGAAA
*
28289903 AAGAACAAGAAGAA-GAG
1 AAGAAAAAGAAGAAGGAG
28289920 AAGAAAAAGAAGAAGGAG
1 AAGAAAAAGAAGAAGGAG
28289938 AA
1 AA
28289940 AAGGAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAGAAGGAG
Found at i:28289932 original size:20 final size:21
Alignment explanation
Indices: 28289892--28289948 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
28289882 TTAGGGTTAG
* *
28289892 AGAAAAAGAAAAAGAACAAGA
1 AGAAAAGGAAAAAGAAGAAGA
* *
28289913 AGAAGAGAAGAAAAAGAAGAAGG
1 AGAA-A-AGGAAAAAGAAGAAGA
28289936 AGAAAAGGAAAAA
1 AGAAAAGGAAAAA
28289949 TAGACATGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 11 0.35
22 2 0.06
23 18 0.58
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (21 bp):
AGAAAAGGAAAAAGAAGAAGA
Found at i:28290518 original size:18 final size:19
Alignment explanation
Indices: 28290495--28290530 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28290485 ATATTTTTTA
28290495 TTTTTTA-TTTTAAAATAT
1 TTTTTTATTTTTAAAATAT
28290513 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
28290531 AATTTTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAT
Found at i:28290536 original size:19 final size:18
Alignment explanation
Indices: 28290496--28290537 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
28290486 TATTTTTTAT
**
28290496 TTTTTATTTTAAAATATT
1 TTTTTATTTTAAAATAAA
28290514 TTTTTATTTTTAAAATAAA
1 TTTTTA-TTTTAAAATAAA
28290533 TTTTT
1 TTTTT
28290538 GGTGTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTATTTTAAAATAAA
Found at i:28290962 original size:19 final size:20
Alignment explanation
Indices: 28290938--28290986 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
28290928 TTGTTTCACA
*
28290938 GAAAATAACTT-GGTCAATG
1 GAAAATAACTTAGGTCAACG
*
28290957 GAAAATGACTTACAGGTCAACG
1 GAAAATAACTT--AGGTCAACG
28290979 GAAAATAA
1 GAAAATAA
28290987 GCTTTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
22 14 0.58
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAAATAACTTAGGTCAACG
Found at i:28291268 original size:13 final size:14
Alignment explanation
Indices: 28291252--28291293 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
28291242 TTTAAATTTT
28291252 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
28291265 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
28291280 ATTTTAAATAATAT
1 ATTTT-AATAATAT
28291294 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:28291278 original size:16 final size:16
Alignment explanation
Indices: 28291256--28291292 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
28291246 AATTTTATTT
28291256 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
28291273 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
28291288 TAATA
1 TAATA
28291293 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:28294706 original size:15 final size:15
Alignment explanation
Indices: 28294674--28294723 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
28294664 TTATCCTATT
**
28294674 AGACACATCACTTTC
1 AGACACATCACTACC
**
28294689 AGATGCATCACTACC
1 AGACACATCACTACC
28294704 AGACACATCACTACC
1 AGACACATCACTACC
28294719 AGACA
1 AGACA
28294724 TTTCTTCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.18
Consensus pattern (15 bp):
AGACACATCACTACC
Found at i:28295191 original size:6 final size:6
Alignment explanation
Indices: 28295176--28295275 Score: 92
Period size: 6 Copynumber: 16.7 Consensus size: 6
28295166 AACCAAACTG
* * * * * **
28295176 AAATCC AAATCA AAATCT AAATCA AAATCT AAATCG AGATCA AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* * * * *
28295224 AAATGA AAATAA AAATCA AAATCA AAATCA AAATTA GAATCG AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
28295272 AAAT
1 AAAT
28295276 TGAAATTGAA
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (6 bp):
AAATCA
Found at i:28295276 original size:18 final size:18
Alignment explanation
Indices: 28295175--28295287 Score: 95
Period size: 18 Copynumber: 6.3 Consensus size: 18
28295165 TAACCAAACT
* *
28295175 GAAATCCAAATCAAAATC
1 GAAATCAAAATTAAAATC
*
28295193 TAAATCAAAATCT-AAATC
1 GAAATCAAAAT-TAAAATC
* *
28295211 GAGATCAAAATTGAAAT-
1 GAAATCAAAATTAAAATC
* *
28295228 GAAAATAAAAATCAAAATC
1 G-AAATCAAAATTAAAATC
* *
28295247 AAAATCAAAATTAGAATC
1 GAAATCAAAATTAAAATC
* *
28295265 GAAATCAAAATTGAAATT
1 GAAATCAAAATTAAAATC
28295283 GAAAT
1 GAAAT
28295288 AACCCTAAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
17 2 0.03
18 72 0.97
ACGTcount: A:0.58, C:0.12, G:0.08, T:0.22
Consensus pattern (18 bp):
GAAATCAAAATTAAAATC
Found at i:28296393 original size:18 final size:19
Alignment explanation
Indices: 28296356--28296392 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28296346 TTTTTAAAAA
*
28296356 TATAAA-ATTTGAAATTTT
1 TATAAATATTTTAAATTTT
28296374 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
28296393 AAAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:28299129 original size:44 final size:44
Alignment explanation
Indices: 28299047--28299292 Score: 150
Period size: 44 Copynumber: 5.3 Consensus size: 44
28299037 ACCCGCTGTT
* * * * * * *
28299047 ACTTCAGGGAGATGAGACTTGTGGTTTTAGTCTACTCCACTGCA
1 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
28299091 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
1 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
* * * * *
28299135 ACTTCATGAAGATAAAATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTACA
1 ACTTCAGGGAGATAAAA-CTG--G-----TG--GCTTCAATCTGCTCCACTGCA
** * * * * * * *
28299189 ACCCCAGGGAAATAAGATCTGCTGTCTTCAGTCTGCTTCGCTGCA
1 ACTTCAGGGAGATAA-AACTGGTGGCTTCAATCTGCTCCACTGCA
* ** * *
28299234 ACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGTA
1 ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
*
28299278 ACTTCAGGAAGATAA
1 ACTTCAGGGAGATAA
28299293 GATCTGCCAT
Statistics
Matches: 150, Mismatches: 41, Indels: 22
0.70 0.19 0.10
Matches are distributed among these distances:
44 85 0.57
45 28 0.19
47 3 0.02
52 2 0.01
54 31 0.21
55 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (44 bp):
ACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCA
Found at i:28299342 original size:143 final size:142
Alignment explanation
Indices: 28299075--28299494 Score: 536
Period size: 143 Copynumber: 2.9 Consensus size: 142
28299065 TTGTGGTTTT
* * **
28299075 AGTCTACTCCACTGCAACTTCAGGGAGATAAAACTGGTGGCTTCAATCTGCTCCACTGCAACTTC
1 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* * * *
28299140 ATGAAGATAAAATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTACAACCCCAGGGAAATAAG
66 AGGAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAG
28299205 ATCTGC-TGTCTTC
131 AT-T-CATGTCTTC
* * * *
28299218 AGTCTGCTTCGCTGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGTAACTTC
1 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* * **
28299283 AGGAAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACACTGGGGAAATAAG
66 AGGAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAG
28299348 ATTCATTGTCTTC
131 ATTCA-TGTCTTC
* * * * * * * *
28299361 AGTCTGCTCCGCTGTAACTTTAGGGAGATAAGGTTGGTGGCTTCAATCTGCTTCGCTACACCCTC
1 AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
* * * * **
28299426 AGGAAAATAAGATTTACCGTAACTTGTAACTTTAATCTGTTCCACTGCAATGCCAGGGAAATAAG
66 AGGAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAG
28299491 ATTC
131 ATTC
28299495 TCCATAATGA
Statistics
Matches: 237, Mismatches: 38, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
141 1 0.00
142 1 0.00
143 235 0.99
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (142 bp):
AGTCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTC
AGGAAGATAAGATCTGCCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAG
ATTCATGTCTTC
Found at i:28306670 original size:19 final size:19
Alignment explanation
Indices: 28306646--28306689 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
28306636 AAACGACATG
*
28306646 TACAACGAATAAACTCTGA
1 TACAACAAATAAACTCTGA
28306665 TACAACAAATAAACTCTGA
1 TACAACAAATAAACTCTGA
28306684 TACAAC
1 TACAAC
28306690 TTTCTATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (19 bp):
TACAACAAATAAACTCTGA
Found at i:28313394 original size:31 final size:31
Alignment explanation
Indices: 28313304--28313395 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
28313294 GTTATTCAAT
* *
28313304 TTTTACGAATCAACTCAAATAAGTAGTTCGA
1 TTTTATGAATCAACTCAAATAAGTAATTCGA
* * ** * *
28313335 GTTT-TGAATTAA-TTGAATCGAGTTATTCGA
1 TTTTATGAATCAACTCAAAT-AAGTAATTCGA
28313365 TTTTATGAATCAACTCAAATAAGTAATTCGA
1 TTTTATGAATCAACTCAAATAAGTAATTCGA
28313396 GTTTCGAGTT
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
29 4 0.09
30 17 0.39
31 19 0.43
32 4 0.09
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (31 bp):
TTTTATGAATCAACTCAAATAAGTAATTCGA
Found at i:28313792 original size:14 final size:14
Alignment explanation
Indices: 28313775--28313808 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28313765 TTAATATTTT
* *
28313775 TAATTTAATTCGAA
1 TAATTTAACTCAAA
28313789 TAATTTAACTCAAA
1 TAATTTAACTCAAA
28313803 TAATTT
1 TAATTT
28313809 CACTTGGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (14 bp):
TAATTTAACTCAAA
Found at i:28316881 original size:41 final size:41
Alignment explanation
Indices: 28316836--28316916 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
28316826 AAAGAATATC
* **
28316836 TAAAATTAAAATGTGGTATATATAATTGTTTAAAATTAAAG
1 TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAAG
* *
28316877 TAAAATTTAAATGTTATATATATAATTGCATAAAATTAAA
1 TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAA
28316917 ATTTACGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.40
Consensus pattern (41 bp):
TAAAATTAAAATGTGATATATATAATTGCATAAAATTAAAG
Found at i:28318693 original size:23 final size:23
Alignment explanation
Indices: 28318654--28318719 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
28318644 TAATTTACAC
* *
28318654 CGAAGTGCTACTGTCACTTGCAT
1 CGAAGTGCCACTATCACTTGCAT
* *
28318677 GGGAGTGCCACTATCACTTGCAT
1 CGAAGTGCCACTATCACTTGCAT
*
28318700 CGAAGTGCCACCATCACTTG
1 CGAAGTGCCACTATCACTTG
28318720 TTCGCGTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (23 bp):
CGAAGTGCCACTATCACTTGCAT
Found at i:28322760 original size:51 final size:50
Alignment explanation
Indices: 28322680--28322779 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 50
28322670 TGTTTTTTTC
* * *
28322680 CTTTCTTTTGCCTTTTTCCATCTTTTCTTGATTTCTTGCTAGCCACCGTT
1 CTTTCTTTTGCCTTTTTCCAGCTCTTCTTGATTTCTTGCAAGCCACCGTT
* *
28322730 CTTTCTTTTTTCCTTTTTCCAGCTCTTCTTGCTTTCTTGCAAGCCACCGT
1 CTTTC-TTTTGCCTTTTTCCAGCTCTTCTTGATTTCTTGCAAGCCACCGT
28322780 CATCGTCCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 5 0.11
51 39 0.89
ACGTcount: A:0.08, C:0.30, G:0.10, T:0.52
Consensus pattern (50 bp):
CTTTCTTTTGCCTTTTTCCAGCTCTTCTTGATTTCTTGCAAGCCACCGTT
Found at i:28326805 original size:27 final size:27
Alignment explanation
Indices: 28326764--28326826 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
28326754 GGTAATGGAA
*
28326764 TGGCGGCACCAGTGGTGCCATTCTCAT
1 TGGCGGCACCAGTGGTGCCATTCCCAT
**
28326791 TGGCGGCACTGGTGGTGCCATTCCCAT
1 TGGCGGCACCAGTGGTGCCATTCCCAT
28326818 TGGCGGCAC
1 TGGCGGCAC
28326827 AGGACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.13, C:0.30, G:0.33, T:0.24
Consensus pattern (27 bp):
TGGCGGCACCAGTGGTGCCATTCCCAT
Found at i:28330371 original size:25 final size:25
Alignment explanation
Indices: 28330337--28330416 Score: 112
Period size: 25 Copynumber: 3.3 Consensus size: 25
28330327 TACATCAATA
28330337 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
28330362 ATTAAAATAAGGAC--TAATCA-ATA
1 ATTAAAATAAGGACTTTAAT-ATTTT
28330385 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
28330410 ATTAAAA
1 ATTAAAA
28330417 ATCACGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
23 19 0.40
24 2 0.04
25 26 0.55
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (25 bp):
ATTAAAATAAGGACTTTAATATTTT
Found at i:28330388 original size:23 final size:23
Alignment explanation
Indices: 28330330--28330399 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
28330320 TAAAAATTAC
28330330 ATCAATAATTAAAATAAGGACTTTA
1 ATCAATAATTAAAATAAGGAC--TA
* *
28330355 AT-ATTTTATTAAAATAAGGACTA
1 ATCA-ATAATTAAAATAAGGACTA
28330378 ATCAATAATTAAAATAAGGACT
1 ATCAATAATTAAAATAAGGACT
28330400 TTAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 20 0.51
24 2 0.05
25 17 0.44
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
ATCAATAATTAAAATAAGGACTA
Found at i:28330773 original size:16 final size:16
Alignment explanation
Indices: 28330752--28330787 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28330742 ATTGATAGTG
28330752 TGTTCTAATTTTAATA
1 TGTTCTAATTTTAATA
28330768 TGTTCTAATTTTAATA
1 TGTTCTAATTTTAATA
28330784 TGTT
1 TGTT
28330788 GCAGTAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (16 bp):
TGTTCTAATTTTAATA
Found at i:28337517 original size:19 final size:19
Alignment explanation
Indices: 28337493--28337586 Score: 125
Period size: 19 Copynumber: 4.8 Consensus size: 19
28337483 AATCATATCT
28337493 TCCAAGATTACATATCATA
1 TCCAAGATTACATATCATA
28337512 TCCAAGATTACATATCATA
1 TCCAAGATTACATATCATA
*
28337531 TCCAAGATTGCATATATCATA
1 TCCAAGATT--ACATATCATA
* *
28337552 TCTAAGATTGCATATCATA
1 TCCAAGATTACATATCATA
* *
28337571 TCTAAGATTGCATATC
1 TCCAAGATTACATATC
28337587 CTTGAAGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 52 0.75
21 17 0.25
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (19 bp):
TCCAAGATTACATATCATA
Found at i:28337559 original size:40 final size:40
Alignment explanation
Indices: 28337470--28337585 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
28337460 AAATTAAATC
* *
28337470 TCTAAGATTACAAAATCATATCTTCCAAGATT--ACATATCATA
1 TCTAAGATTAC-ATATCATA---TCCAAGATTGCATATATCATA
*
28337512 TCCAAGATTACATATCATATCCAAGATTGCATATATCATA
1 TCTAAGATTACATATCATATCCAAGATTGCATATATCATA
* *
28337552 TCTAAGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTACATATCATATCCAAGATTGCATAT
28337586 CCTTGAAGAT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
38 9 0.14
40 40 0.61
41 7 0.11
42 10 0.15
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (40 bp):
TCTAAGATTACATATCATATCCAAGATTGCATATATCATA
Found at i:28337940 original size:25 final size:25
Alignment explanation
Indices: 28337910--28337959 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28337900 CACTACAACT
28337910 TCAGGGAGATAAGACTTGTATCTTC
1 TCAGGGAGATAAGACTTGTATCTTC
28337935 TCAGGGAGATAAGACTTGTATCTTC
1 TCAGGGAGATAAGACTTGTATCTTC
28337960 GATCTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (25 bp):
TCAGGGAGATAAGACTTGTATCTTC
Found at i:28338192 original size:89 final size:89
Alignment explanation
Indices: 28337955--28338232 Score: 427
Period size: 89 Copynumber: 3.2 Consensus size: 89
28337945 AAGACTTGTA
* * * *
28337955 TCTTCGATCTACTTTGCCACCAGTATGGGAAAACAAGATCTGCTACCTTTGATCTATTTCATGCC
1 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
28338020 GATACATGAAGACAAGATCTACTT
66 AATACATGAAGACAAGATCTACTT
* * * *
28338044 TCTTCGATCTACTTCGCTA--A-TACGTGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
28338106 AATACATGAAGACAAGATCAACTT
66 AATACATGAAGACAAGATCTACTT
*
28338130 TCTTCGATATACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
1 TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
*
28338195 AATACATGAAGACAAGATCTGCTT
66 AATACATGAAGACAAGATCTACTT
28338219 TCTTCGATCTACTT
1 TCTTCGATCTACTT
28338233 CACGATAACC
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
86 74 0.44
87 1 0.01
88 1 0.01
89 92 0.55
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (89 bp):
TCTTCGATCTACTTTGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC
AATACATGAAGACAAGATCTACTT
Found at i:28338235 original size:44 final size:44
Alignment explanation
Indices: 28337987--28338236 Score: 272
Period size: 44 Copynumber: 5.7 Consensus size: 44
28337977 GTATGGGAAA
* * * * *
28337987 ACAAGATCTGCTACCTTTGATCTATTTCATGCCGATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
* * * *
28338031 ACAAGATCTACTTTCTTCGATCTACTT--CGCTAATACGTGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
28338073 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
** * * * * ***
28338117 ACAAGATCAACTTTCTTCGATATACTTTGC-CACCAGTATGGGAAG
1 ACAAGATCTGCTATCTTCGATCTAC-TT-CACGCCAATACATGAAG
*
28338162 ACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAG
1 ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
*
28338206 ACAAGATCTGCTTTCTTCGATCTACTTCACG
1 ACAAGATCTGCTATCTTCGATCTACTTCACG
28338237 ATAACCCAGG
Statistics
Matches: 165, Mismatches: 36, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
42 35 0.21
43 1 0.01
44 96 0.58
45 32 0.19
46 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (44 bp):
ACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAG
Found at i:28338311 original size:88 final size:88
Alignment explanation
Indices: 28338197--28338609 Score: 529
Period size: 88 Copynumber: 4.7 Consensus size: 88
28338187 TTCACGCCAA
* * * * * * * * * *
28338197 TACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACGATAACCCAGGGAGGGAAGGCTGATA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGGGAGGCAAGGCTGGTA
* * *
28338262 TTTTTGATCTGCTTCACTGTGGG
66 TCTTCGATCTGCTTCACTGTCGG
*
28338285 TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGGGAGGCAAGGCTGGTA
28338350 TCTTCGATCTGCTTCACTGTCGG
66 TCTTCGATCTGCTTCACTGTCGG
* * *
28338373 TGCAGGAAGGCAAGATCTGCTATCTTTAACCTACTCCACTACAACCCAGGGAGGAAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGGGAGGCAAGGCTGGTA
*** *
28338438 TCTTCGATCTGCTTTGTTGTCGA
66 TCTTCGATCTGCTTCACTGTCGG
* *
28338461 TGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGAGAGGCAAGGCTGGTA
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGGGAGGCAAGGCTGGTA
* *
28338526 TCTTCGATCTGCTTCACCGTCAG
66 TCTTCGATCTGCTTCACTGTCGG
* * * * * * * *
28338549 TACAAGAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCTGCAAACCAGGAAGGCAAGGCT
1 TACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGGGAGGCAAGGCT
28338610 TTGTGATTTC
Statistics
Matches: 284, Mismatches: 41, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 284 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.25
Consensus pattern (88 bp):
TACAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCCAGGGAGGCAAGGCTGGTA
TCTTCGATCTGCTTCACTGTCGG
Found at i:28338342 original size:44 final size:44
Alignment explanation
Indices: 28338287--28338606 Score: 182
Period size: 44 Copynumber: 7.3 Consensus size: 44
28338277 ACTGTGGGTA
28338287 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
* * * * * * * ****
28338331 CAGGGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACC
* *
28338375 CAGGAAGGCAAGATCTGCTATCTTTAACCTACTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
* * * * * * **** * * **
28338419 CAGGGAGGAAAG-GCTGGTATCTTCGATCTGCTTTGTTGTCGATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-ACAACC
*
28338463 CAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
* * * * * ***
28338507 CA-GAGAGGCAAG-GCTGGTATCTTCGATCTGCTTCACCGT-CAGTA
1 CAGGA-AGGCAAGATCTGCTATCTTCAACCTGCTCCA-C-TACAACC
* * * * * *
28338551 CAAGAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCTGCAAAC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
28338595 CAGGAAGGCAAG
1 CAGGAAGGCAAG
28338607 GCTTTGTGAT
Statistics
Matches: 191, Mismatches: 75, Indels: 20
0.67 0.26 0.07
Matches are distributed among these distances:
43 55 0.29
44 83 0.43
45 53 0.28
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACC
Found at i:28344322 original size:247 final size:243
Alignment explanation
Indices: 28343865--28344357 Score: 860
Period size: 247 Copynumber: 2.0 Consensus size: 243
28343855 TTAGTTGTCG
* *
28343865 AAAAACAAAAATTGGGAGTTGCCACTAATCTTTTATTGAGGTGTGATTGAATCACCTAAAAACGG
1 AAAAACAAAAATTGGGAGTCGCCACCAATCTTTTATTGAGGTGTGATTGAATCACCTAAAAACGG
* **
28343930 CTTTGGTCTACGAGTTTTAGAAAAACGGATCCGGGAGTCGGTTACGTGAGGAAGGATTAGCACCC
66 CTTTGGTCTACGAGTTTTAAAAAAACGGATCCAAGAGTCGGTTACGTGAGGAAGGATTAGCACCC
* *
28343995 TCGTTACGCCCAGAAATTGGTACCTAGTTGATTAATTAGTGTCTTAATGTTGAGAGTTAATAAAT
131 TCGTTACGCCCAGAAATTGGTACCTAGTTGATTAATTAGTATCTTAATGTCGAGAGTTAATAAAT
28344060 ACTATCCTTAGTTAAATTAAATTATTTATTAAGACTTTCTCAACTTTAA
196 ACTATCCTTAGTTAAATTAAATTATTTATTAAGACTTTCTC-ACTTTAA
*
28344109 AAAAAGCAAAAATTGGGAGTCGCCACCAATCTTTTATTGAGGTGTGATTGGATCACCTAAAAACG
1 AAAAA-CAAAAATTGGGAGTCGCCACCAATCTTTTATTGAGGTGTGATTGAATCACCTAAAAACG
28344174 GCTTTGGTCTACGAGTTTTAAAAAAACGGATCCAAGAGTCGGTTACGTACGAGGAAGGATTAGCA
65 GCTTTGGTCTACGAGTTTTAAAAAAACGGATCCAAGAGTCGGTTACGT--GAGGAAGGATTAGCA
*
28344239 CCCTCGTTACGCCTAGAAATTGGTACCTAGTTGATTAATTAGTATCTTAATGTCGAGAGTTAATA
128 CCCTCGTTACGCCCAGAAATTGGTACCTAGTTGATTAATTAGTATCTTAATGTCGAGAGTTAATA
*
28344304 AATACTATCCTTAGTTAAATTAAATTATTTATTAAGACTTTCTCATTTTAA
193 AATACTATCCTTAGTTAAATTAAATTATTTATTAAGACTTTCTCACTTTAA
28344355 AAA
1 AAA
28344358 GAAAAATATC
Statistics
Matches: 236, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
244 5 0.02
245 101 0.43
246 9 0.04
247 121 0.51
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (243 bp):
AAAAACAAAAATTGGGAGTCGCCACCAATCTTTTATTGAGGTGTGATTGAATCACCTAAAAACGG
CTTTGGTCTACGAGTTTTAAAAAAACGGATCCAAGAGTCGGTTACGTGAGGAAGGATTAGCACCC
TCGTTACGCCCAGAAATTGGTACCTAGTTGATTAATTAGTATCTTAATGTCGAGAGTTAATAAAT
ACTATCCTTAGTTAAATTAAATTATTTATTAAGACTTTCTCACTTTAA
Found at i:28344761 original size:15 final size:15
Alignment explanation
Indices: 28344741--28344778 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
28344731 CTTTTTTGGC
28344741 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
28344756 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
28344771 CGATTTGC
1 CGATTTGC
28344779 GTCATCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.26, G:0.21, T:0.45
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:28347077 original size:50 final size:50
Alignment explanation
Indices: 28347018--28347118 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
28347008 AAATTATTTA
28347018 TACATTTCTTAACAAATTTATGAATCATAAATTATAATAATAAAAGTTAT
1 TACATTTCTTAACAAATTTATGAATCATAAATTATAATAATAAAAGTTAT
28347068 TACATTTCTTAACAAATTTATGAATCATAAATTATAATAATAAAAGTTAT
1 TACATTTCTTAACAAATTTATGAATCATAAATTATAATAATAAAAGTTAT
28347118 T
1 T
28347119 TTGAGAGTGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (50 bp):
TACATTTCTTAACAAATTTATGAATCATAAATTATAATAATAAAAGTTAT
Found at i:28347362 original size:48 final size:48
Alignment explanation
Indices: 28347306--28347608 Score: 572
Period size: 48 Copynumber: 6.3 Consensus size: 48
28347296 TAAAAATTAC
28347306 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
***
28347354 ATCAATAATT-AAATAAGGACTTTAATATTTTATTGCTATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
28347401 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
28347449 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
28347497 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
28347545 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
1 ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
28347593 ATCAATAATTAAAATA
1 ATCAATAATTAAAATA
28347609 TTTTAAAACA
Statistics
Matches: 248, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
47 44 0.18
48 204 0.82
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.36
Consensus pattern (48 bp):
ATCAATAATTAAAATAAGGACTTTAATATTTTATTAAAATAAGGACTA
Found at i:28356721 original size:24 final size:24
Alignment explanation
Indices: 28356676--28356721 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28356666 ATTTAAATAT
*
28356676 AAAATTTAATCCACAACTTAACCG
1 AAAATTTAATCCACAACATAACCG
28356700 AAAATTTAATCC-CTAACATAAC
1 AAAATTTAATCCAC-AACATAAC
28356722 TTCCCCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATTTAATCCACAACATAACCG
Found at i:28357387 original size:71 final size:71
Alignment explanation
Indices: 28357305--28357438 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 71
28357295 AACCGCCACA
28357305 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAGTG
1 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAGTG
28357370 ATTAAG
66 ATTAAG
* * * *
28357376 AGAGTAAGTAAGACTTTGATTTTCTGATATTCTGTCATGTATTAAGGAGAAGTTTGTGTTAAG
1 AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAG
28357439 AAATTAACGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (71 bp):
AGAGTAAGTAAGAATTTGATTTTATGATATTCTGTCATATATTAAGGAGAAGTTCGTGTTAAGTG
ATTAAG
Found at i:28362420 original size:20 final size:19
Alignment explanation
Indices: 28362390--28362450 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
28362380 TTTACATCTC
28362390 AAAAAAT-TATAAAAAAACT
1 AAAAAATATAT-AAAAAACT
*
28362409 AAAAAATATATAATAAACT
1 AAAAAATATATAAAAAACT
*
28362428 TAAAAA-ATATAAAAAACT
1 AAAAAATATATAAAAAACT
28362446 AAAAA
1 AAAAA
28362451 CCTTAAACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 15 0.41
19 19 0.51
20 3 0.08
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATATATAAAAAACT
Found at i:28362641 original size:29 final size:28
Alignment explanation
Indices: 28362595--28362651 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
28362585 CATTTTTTTC
*
28362595 TTTAAAAAAGGGCCTAATTAAGTAAATTT
1 TTTAAAAAAGGGCATAATTAA-TAAATTT
* * *
28362624 TTTAAAAATGGGTATAATTTATAAATTT
1 TTTAAAAAAGGGCATAATTAATAAATTT
28362652 AGTCAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTAAAAAAGGGCATAATTAATAAATTT
Found at i:28365569 original size:42 final size:41
Alignment explanation
Indices: 28365518--28365716 Score: 192
Period size: 42 Copynumber: 4.7 Consensus size: 41
28365508 ATGCCATATT
* *
28365518 CCAGATATGGTCTTACATGCTATCAT-ATATCGATGCCAATAG-
1 CCAGCTATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GC
28365560 CCAGCTATGGTCTTACATGAATCTCATATCGATGCCAATGTC
1 CCAGCTATGGTCTTACATGAATCTCATATCGATGCCAATG-C
* *
28365602 CCAGAC-ATGGTCTTACATGAATCTCGTATTGATGCCAATGTC
1 CCAG-CTATGGTCTTACATGAATCTCATATCGATGCCAATG-C
* * *
28365644 CCAGAC-ATGGTCTTAGATGAATCACATAACGATGCCAATGTC
1 CCAG-CTATGGTCTTACATGAATCTCATATCGATGCCAATG-C
* *
28365686 CCAGAC-ATGGTCTTACACGTAATCACATATC
1 CCAG-CTATGGTCTTACATG-AATCTCATATC
28365717 AGTATCCTAA
Statistics
Matches: 140, Mismatches: 12, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
40 2 0.01
41 17 0.12
42 110 0.79
43 11 0.08
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (41 bp):
CCAGCTATGGTCTTACATGAATCTCATATCGATGCCAATGC
Found at i:28365617 original size:84 final size:83
Alignment explanation
Indices: 28365518--28365716 Score: 242
Period size: 84 Copynumber: 2.4 Consensus size: 83
28365508 ATGCCATATT
* *
28365518 CCAGATATGGTCTTACATGCTATCAT-ATATCGATGCCAATAG-CCAG-CTATGGTCTTACATGA
1 CCAGACATGGTCTTACATG-AATC-TCATATCGATGCCAAT-GCCCAGAC-ATGGTCTTACATGA
* *
28365580 ATCTCATATCGATGCCAATGTC
62 ATCACATAACGATGCCAATGTC
* * *
28365602 CCAGACATGGTCTTACATGAATCTCGTATTGATGCCAATGTCCCAGACATGGTCTTAGATGAATC
1 CCAGACATGGTCTTACATGAATCTCATATCGATGCCAATG-CCCAGACATGGTCTTACATGAATC
28365667 ACATAACGATGCCAATGTC
65 ACATAACGATGCCAATGTC
* *
28365686 CCAGACATGGTCTTACACGTAATCACATATC
1 CCAGACATGGTCTTACATG-AATCTCATATC
28365717 AGTATCCTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
82 2 0.02
83 15 0.15
84 73 0.74
85 9 0.09
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (83 bp):
CCAGACATGGTCTTACATGAATCTCATATCGATGCCAATGCCCAGACATGGTCTTACATGAATCA
CATAACGATGCCAATGTC
Found at i:28366000 original size:20 final size:19
Alignment explanation
Indices: 28365969--28366020 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
28365959 ATCTATATAA
* *
28365969 TAACAAAATTTACT-TATT
1 TAACACAATTTACTCAATT
28365987 TAATCACTAATTTACTCAATT
1 TAA-CAC-AATTTACTCAATT
28366008 TAACACAATTTAC
1 TAACACAATTTAC
28366021 ACATTAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
20 11 0.38
21 6 0.21
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (19 bp):
TAACACAATTTACTCAATT
Found at i:28366965 original size:24 final size:24
Alignment explanation
Indices: 28366933--28366980 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28366923 AACTTTACGA
28366933 TCCGCTTCCACGTTCATCCACATC
1 TCCGCTTCCACGTTCATCCACATC
28366957 TCCGCTTCCACGTTCATCCACATC
1 TCCGCTTCCACGTTCATCCACATC
28366981 ATTCTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.46, G:0.08, T:0.29
Consensus pattern (24 bp):
TCCGCTTCCACGTTCATCCACATC
Found at i:28389116 original size:42 final size:42
Alignment explanation
Indices: 28389053--28389181 Score: 161
Period size: 42 Copynumber: 3.1 Consensus size: 42
28389043 TCGAGTTTAC
* *
28389053 TTTCCGTTGAGCTCTCATGAGCTTCAGTTTAACCCTTATGGG
1 TTTCCGTTAAGCTCTTATGAGCTTCAGTTTAACCCTTATGGG
* * * **
28389095 TTTCCGTTCAGCTTTTTTGAGCTTCAGTTTAACTTTTATGGG
1 TTTCCGTTAAGCTCTTATGAGCTTCAGTTTAACCCTTATGGG
* *
28389137 TTTCTGTTAAGCTCTTATGAGCTTCCA-TTCAACCCTTATGGG
1 TTTCCGTTAAGCTCTTATGAGCTT-CAGTTTAACCCTTATGGG
28389179 TTT
1 TTT
28389182 TTGTTTGGCA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 71 0.97
43 2 0.03
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (42 bp):
TTTCCGTTAAGCTCTTATGAGCTTCAGTTTAACCCTTATGGG
Found at i:28395085 original size:42 final size:42
Alignment explanation
Indices: 28395028--28395127 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
28395018 CTATATGAAC
*
28395028 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
* *
28395070 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGTATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
28395112 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
28395128 TACCGAGAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.35, C:0.10, G:0.28, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
Found at i:28416179 original size:7 final size:7
Alignment explanation
Indices: 28416169--28416197 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
28416159 AAAGTAAATA
28416169 ATATGTG
1 ATATGTG
28416176 ATATGTG
1 ATATGTG
28416183 ATATGTG
1 ATATGTG
28416190 ATATGTG
1 ATATGTG
28416197 A
1 A
28416198 GCATGTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
ATATGTG
Found at i:28417020 original size:20 final size:20
Alignment explanation
Indices: 28416997--28417035 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28416987 AATTAAATCA
28416997 GTTTTCTATAAATTCAATTC
1 GTTTTCTATAAATTCAATTC
*
28417017 GTTTTCTGTAAATTCAATT
1 GTTTTCTATAAATTCAATT
28417036 GATCGGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
GTTTTCTATAAATTCAATTC
Found at i:28418512 original size:48 final size:48
Alignment explanation
Indices: 28418456--28418751 Score: 592
Period size: 48 Copynumber: 6.2 Consensus size: 48
28418446 TGTGGCACCG
28418456 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
1 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
28418504 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
1 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
28418552 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
1 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
28418600 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
1 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
28418648 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
1 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
28418696 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
1 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
28418744 AGGAAAAA
1 AGGAAAAA
28418752 AGAATTTTAC
Statistics
Matches: 248, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 248 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (48 bp):
AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACC
Found at i:28418830 original size:50 final size:50
Alignment explanation
Indices: 28418767--28418933 Score: 144
Period size: 50 Copynumber: 3.3 Consensus size: 50
28418757 TTTACTCATT
*
28418767 CTGGTGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAAAAAAATTAC
1 CTGGTGACACCACATTGAAGTGGCAGGACCGAAAAATTAAAAAAAATTAC
* * ** ** ***
28418817 CTGGTGCCACCACATCTGGAGTATGGACCAGGA-AAAAAGAATT-TTACTCATT--
1 CTGGTGACACCACAT-TGAAG--TGG--CAGGACCGAAA-AATTAAAAAAAATTAC
*
28418869 CTGGTGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAAAAAAATTAC
1 CTGGTGACACCACATTGAAGTGGCAGGACCGAAAAATTAAAAAAAATTAC
*
28418919 CTGGTGCCACCACAT
1 CTGGTGACACCACAT
28418934 CTGGAGTATG
Statistics
Matches: 85, Mismatches: 22, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
47 9 0.11
48 7 0.08
49 3 0.04
50 26 0.31
51 8 0.09
52 13 0.15
53 3 0.04
54 7 0.08
55 9 0.11
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (50 bp):
CTGGTGACACCACATTGAAGTGGCAGGACCGAAAAATTAAAAAAAATTAC
Found at i:28418847 original size:102 final size:102
Alignment explanation
Indices: 28418706--28418994 Score: 569
Period size: 102 Copynumber: 2.8 Consensus size: 102
28418696 AGGAAAAATT
*
28418706 AAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
1 AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
28418771 TGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAA
66 TGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAA
28418808 AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
1 AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
28418873 TGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAA
66 TGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAA
28418910 AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
1 AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
28418975 TGACTCCACATTGAAGTGGC
66 TGACTCCACATTGAAGTGGC
28418995 GGGGACCAGC
Statistics
Matches: 186, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 186 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (102 bp):
AAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGG
TGACTCCACATTGAAGTGGCAGGACCGAAAAATTAAA
Found at i:28418854 original size:144 final size:138
Alignment explanation
Indices: 28418456--28418854 Score: 477
Period size: 144 Copynumber: 2.8 Consensus size: 138
28418446 TGTGGCACCG
*
28418456 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAATTAAAAATT
1 AGGAAAAA-TAAAAATTACCTGGTGACACCACATCTAGAGTATGGACCA-GAAAAATTAAAAATT
28418521 ACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAATTAAAAATTACCTGGTGCCACCACAT
64 ACCTGGTGCCACCACATCTAGAGTATGGACCAGG---AA-TAAAAATTACCTGGTGCCACCACAT
28418586 CTAGAGTATGGACC
125 CTAGAGTATGGACC
*
28418600 AGGAAAAATTAAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAATTAAAAATT
1 AGGAAAAA-TAAAAATTACCTGGTGACACCACATCTAGAGTATGGACCA-GAAAAATTAAAAATT
28418665 ACCTGGTGCCACCACATCTAGAGTATGGACCAGGAAAAATTAAAAATTACCTGGTGCCACCACAT
64 ACCTGGTGCCACCACATCTAGAGTATGGACCAGG---AA-TAAAAATTACCTGGTGCCACCACAT
28418730 CTAGAGTATGGACC
125 CTAGAGTATGGACC
** *
28418744 AGGAAAAA-AGAATTTTACTCATTCTGGTGACTCCACAT-T-GAAGTGGCA-GGACC-GAAAAAT
1 AGGAAAAATA-AAAATTA--C---CTGGTGACACCACATCTAG-AGT---ATGGACCAGAAAAAT
*
28418804 TAAAAAAAATTACCTGGTGCCACCACATCTGGAGTATGGACCAGGAA-AAAA
56 T---AAAAATTACCTGGTGCCACCACATCTAGAGTATGGACCAGGAATAAAA
28418855 GAATTTTACT
Statistics
Matches: 237, Mismatches: 5, Indels: 25
0.89 0.02 0.09
Matches are distributed among these distances:
142 1 0.00
143 5 0.02
144 152 0.64
145 5 0.02
146 1 0.00
147 14 0.06
148 13 0.05
149 5 0.02
150 41 0.17
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (138 bp):
AGGAAAAATAAAAATTACCTGGTGACACCACATCTAGAGTATGGACCAGAAAAATTAAAAATTAC
CTGGTGCCACCACATCTAGAGTATGGACCAGGAATAAAAATTACCTGGTGCCACCACATCTAGAG
TATGGACC
Found at i:28419055 original size:79 final size:79
Alignment explanation
Indices: 28418924--28419076 Score: 279
Period size: 79 Copynumber: 1.9 Consensus size: 79
28418914 ATTACCTGGT
*
28418924 GCCACCACATCTGGAGTATGGACCAGGAAAAAAGAATTTTACTCATTCTGGTGACTCCACATTGA
1 GCCACCACATCTGGAGTATGAACCAGGAAAAAAGAATTTTACTCATTCTGGTGACTCCACATTGA
28418989 AGTGGCGGGGACCA
66 AGTGGCGGGGACCA
* *
28419003 GCCACCACATCTGGAGTATGAACCAGGAAAAAAGAATTTTACTGATTCTGGTGTCTCCACATTGA
1 GCCACCACATCTGGAGTATGAACCAGGAAAAAAGAATTTTACTCATTCTGGTGACTCCACATTGA
28419068 AGTGGCGGG
66 AGTGGCGGG
28419077 ACGGAAAAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (79 bp):
GCCACCACATCTGGAGTATGAACCAGGAAAAAAGAATTTTACTCATTCTGGTGACTCCACATTGA
AGTGGCGGGGACCA
Found at i:28420018 original size:283 final size:283
Alignment explanation
Indices: 28419511--28420078 Score: 1127
Period size: 283 Copynumber: 2.0 Consensus size: 283
28419501 GCACCAAAAA
28419511 TTAATTAAAAATATTTTTTTTCTTTTTACTCTGAGAATACCCGTGAAAATACAATATTTGAGAAA
1 TTAATTAAAAATATTTTTTTTCTTTTTACTCTGAGAATACCCGTGAAAATACAATATTTGAGAAA
28419576 AGTTACACAAAAAAAATTGATTTCTTTTCTTCTAATGATTGAATTAATTATGAGACAATGATTAA
66 AGTTACACAAAAAAAATTGATTTCTTTTCTTCTAATGATTGAATTAATTATGAGACAATGATTAA
*
28419641 AGGCATTTTTGCCGCCTTGGGAAGTGATAACACCCATTTTTATTAAAAGTTTTAAGTTGTTTTCC
131 AGGCATTTTTGCCGCCTTGGGAAGTGATAACACCCATTTTTACTAAAAGTTTTAAGTTGTTTTCC
28419706 TAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAATATAAGATTAATTTTCTAAAAAT
196 TAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAATATAAGATTAATTTTCTAAAAAT
28419771 GCATGTCTTTCCTGTCTAACCCT
261 GCATGTCTTTCCTGTCTAACCCT
28419794 TTAATTAAAAATATTTTTTTTCTTTTTACTCTGAGAATACCCGTGAAAATACAATATTTGAGAAA
1 TTAATTAAAAATATTTTTTTTCTTTTTACTCTGAGAATACCCGTGAAAATACAATATTTGAGAAA
28419859 AGTTACACAAAAAAAATTGATTTCTTTTCTTCTAATGATTGAATTAATTATGAGACAATGATTAA
66 AGTTACACAAAAAAAATTGATTTCTTTTCTTCTAATGATTGAATTAATTATGAGACAATGATTAA
28419924 AGGCATTTTTGCCGCCTTGGGAAGTGATAACACCCATTTTTACTAAAAGTTTTAAGTTGTTTTCC
131 AGGCATTTTTGCCGCCTTGGGAAGTGATAACACCCATTTTTACTAAAAGTTTTAAGTTGTTTTCC
28419989 TAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAATATAAGATTAATTTTCTAAAAAT
196 TAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAATATAAGATTAATTTTCTAAAAAT
28420054 GCATGTCTTTCCTGTCTAACCCT
261 GCATGTCTTTCCTGTCTAACCCT
28420077 TT
1 TT
28420079 CGGGAAAATT
Statistics
Matches: 284, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 284 1.00
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (283 bp):
TTAATTAAAAATATTTTTTTTCTTTTTACTCTGAGAATACCCGTGAAAATACAATATTTGAGAAA
AGTTACACAAAAAAAATTGATTTCTTTTCTTCTAATGATTGAATTAATTATGAGACAATGATTAA
AGGCATTTTTGCCGCCTTGGGAAGTGATAACACCCATTTTTACTAAAAGTTTTAAGTTGTTTTCC
TAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAATATAAGATTAATTTTCTAAAAAT
GCATGTCTTTCCTGTCTAACCCT
Found at i:28421182 original size:96 final size:97
Alignment explanation
Indices: 28420872--28421187 Score: 274
Period size: 101 Copynumber: 3.2 Consensus size: 97
28420862 AGCGACACCT
* * **
28420872 AAAAATTAAAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAGGAAAAAAGAATTT
1 AAAAATT-AAAAAAAA--TA-CTGGTGCCACCACATCTGGAGTAAGGACCAGG-AAAAA-TTTTT
* * * * * *
28420937 TACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGG
60 TATTCATTTTGGTGACTCCATA-TGAAGTGGCGGGACCG
* * * ** ** *
28420976 AAAAATTAAAAAAAATATTGGTGCCGCCATATCTGGACAAAGGACCAGGGAAATTTTATTTTTTT
1 AAAAATTAAAAAAAATACTGGTGCCACCACATCTGGAGTAAGGACCA-GGAAAAATT-TTTTATT
*** * * * *
28421041 ACTATTTTGGTGACTTTGTGTGAAGTGGCAGCACTG
64 -C-ATTTTGGTGACTCCATATGAAGTGGCGGGACCG
* * *
28421077 AAAAATTAAAAAAAATACTAGTGTCACCACATCTGGAGTAGGGACCA-GAAAAATTTTTTATTCA
1 AAAAATTAAAAAAAATACTGGTGCCACCACATCTGGAGTAAGGACCAGGAAAAATTTTTTATTCA
28421141 TTTTGGTGACTCCATATGAAGTGGCGGGACCG
66 TTTTGGTGACTCCATATGAAGTGGCGGGACCG
28421173 AAAAATTAAAAAAAA
1 AAAAATTAAAAAAAA
28421188 CTTATTAGTG
Statistics
Matches: 166, Mismatches: 42, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
96 41 0.25
97 1 0.01
98 6 0.04
99 6 0.04
100 31 0.19
101 56 0.34
102 10 0.06
103 8 0.05
104 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (97 bp):
AAAAATTAAAAAAAATACTGGTGCCACCACATCTGGAGTAAGGACCAGGAAAAATTTTTTATTCA
TTTTGGTGACTCCATATGAAGTGGCGGGACCG
Found at i:28422767 original size:983 final size:981
Alignment explanation
Indices: 28420859--28422775 Score: 3310
Period size: 983 Copynumber: 2.0 Consensus size: 981
28420849 CACCACATTT
28420859 ACAAGCGACACCTAAAAATTAAAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAG
1 ACAAGCGACACCTAAAAATTAAAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAG
28420924 GAAAAAAGAATTTTACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGGAAAAATTAAAAAA
66 GAAAAAAGAATTTTACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGGAAAAATTAAAAAA
28420989 AATATTGGTGCCGCCATATCTGGACAAAGGACCAGGGAAATTTTATTTTTTTACTATTTTGGTGA
131 AATATTGGTGCCGCCATATCTGGACAAAGGACCAGGGAAATTTTATTTTTTTACTATTTTGGTGA
* *
28421054 CTTTGTGTGAAGTGGCAGCACTGAAAAATTAAAAAAAATACTAGTGTCACCACATCTGGAGTAGG
196 CTTTGTGTGAAGTGGCAGCACTAAAAAATTAAAAAAAATACTAGTGCCACCACATCTGGAGTAGG
* *
28421119 GACCAGAAAAATTTTTTATTCATTTTGGTGACTCCATATGAAGTGGCGGGACCGAAAAATTAAAA
261 GACCAGAAAAATTTTTTATTCATTTTGGTGACTCCATATGAAGTGGCGAGACAGAAAAATTAAAA
**
28421184 AAAACTTATTAGTGTCGTCATATCTAGGGTAGGGACCAAGAGTTTCTTTTTAACTTTTTTAGTGA
326 AAAACTTATTAGTGTCGTCATATCTAGGGTAGGGACCAAGAGTTTCTTTTTAAAATTTTTAGTGA
28421249 CTCCATGTGAAGTGATGGCACCGAAAAATTTTAAAAATGCGGCACCAACAAATATTTTCTTTTAT
391 CTCCATGTGAAGTGATGGCACCGAAAAATTTTAAAAATGCGGCACCAACAAATATTTTCTTTTAT
*
28421314 TCCAATTTAGCGGCGCCACTTATAAGCATGCAACCAAAAATTTTTTTTTTATTCCAATTTGATGC
456 TCCAATTTAGCGGCGCCACTTATAAGCATGCAACC-AAAA-TTTTTTTTTATTACAATTTGATGC
* *
28421379 CTCCATTAAAAGAGGTGGCACCAAAAATTAATTAAAAAATATTTTTTTTTACTCTGGGAATACCC
519 CTCCATTAAAAGAGGTGGCACCAAAAATTAATTAAAAAATATTTATTTTTACTCTGAGAATACCC
* *
28421444 GAGAAAATACAATATTTGAGAAAAGTTACACAAAAAAATTGATTTCTTTTCTTCTAATGATTGAA
584 GAGAAAATACAATATTTGAAAAAAGTTACACAAAAAAATTGATTTCTTTTCATCTAATGATTGAA
* * *
28421509 TTAATTATGAGACAATGATTAAAGGCATTTTTGCCGTCTTGGGAAGTGATAACACCCATTTTTAC
649 TTAATTATGAGACAACGATTAAAGGCATTTTTACCGCCTTGGGAAGTGATAACACCCATTTTTAC
***
28421574 TAAAAGTTTTAAGTTGTTTTCCTAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAAT
714 TAAAAGTTTTAAGCCATTTTCCTAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAAT
28421639 ATAAGATTAATTTTCTAAAAATGCATGTCTTTCCTGTCTAACCCTCTCGGGAAAATTACATATAA
779 ATAAGATTAATTTTCTAAAAATGCATGTCTTTCCTGTCTAACCCTCTCGGGAAAATTACATATAA
* * *
28421704 AAACCCATTTTTTTAAAAATTTACTAAAATGGGCCCAGTATATAATTATTTATCGGAATGGCCCT
844 AAACCCATTTTTTAAAAAATTTACTAAAATGGGCCCAGTATATAATTATTTACCGGAATGACCCT
* * *
28421769 ATTTTCCCGAAAGCGCGTCCACGTTTGCCGACCCATGCTATGTGTTTTCAGCTCTGGTTGATGGC
909 ATTTCCCCAAAAGCGCGTCAACGTTTGCCGACCCATGCTATGTGTTTTCAGCTCTGGTTGATGGC
28421834 CCTCTATA
974 CCTCTATA
28421842 ACAAGCGACACCTAAAAATT-AAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAG
1 ACAAGCGACACCTAAAAATTAAAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAG
28421906 GAAAAAAGAATTTTACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGGAAAAATTAAAAAA
66 GAAAAAAGAATTTTACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGGAAAAATT-AAAAA
*
28421971 AAATATTGGTGCCGCCATATCTGGAGAAAGGACCAGGGAAATTTTATTTTTTTACTATTTTGGTG
130 AAATATTGGTGCCGCCATATCTGGACAAAGGACCAGGGAAATTTTATTTTTTTACTATTTTGGTG
*
28422036 ACTTTGTGTGAAGTGGCAGCACTAAAAAATTAAAAAAAATACTAGTGCCATCACATCTGGAGTAG
195 ACTTTGTGTGAAGTGGCAGCACTAAAAAATTAAAAAAAATACTAGTGCCACCACATCTGGAGTAG
*
28422101 GGACCA-AAAAATTTTTTTATTCATTTTGGTGACTCCATATGAAGTGGTGAGACAGAAAAATTAA
260 GGACCAGAAAAA-TTTTTTATTCATTTTGGTGACTCCATATGAAGTGGCGAGACAGAAAAATT--
*
28422165 AAAAAAAACTTATTGGTGTCGTCATATCTAGGGTAGGGACCAAGAGTTTC-TTTTAAAATTTTTA
322 AAAAAAAACTTATTAGTGTCGTCATATCTAGGGTAGGGACCAAGAGTTTCTTTTTAAAATTTTTA
28422229 GTGACTCCATGTGAAGTGATGGCACCGAAAAATTTTAAAAATGCGGCACCAACAAATATTTTCTT
387 GTGACTCCATGTGAAGTGATGGCACCGAAAAATTTTAAAAATGCGGCACCAACAAATATTTTCTT
* * *
28422294 TTATTCCAATTTGGCTGCGCCACTTATAAGCATGCAACC-AAA-TTTTTTTTATTACAATTTGGT
452 TTATTCCAATTTAGCGGCGCCACTTATAAGCATGCAACCAAAATTTTTTTTTATTACAATTTGAT
28422357 GCCTCCATTAAAAGAGGTGGCACCAAAAATTAATTAAAAATATATATATATTTTTACTCTGAGAA
517 GCCTCCATTAAAAGAGGTGGCACCAAAAATTAATTAAAAA-ATAT-T-TATTTTTACTCTGAGAA
* *
28422422 TTCCCGTGAAAATACAATATTTGAAAAAAGTTACACAAAAAAATTGATTTCTTTTCATCTAATGA
579 TACCCGAGAAAATACAATATTTGAAAAAAGTTACACAAAAAAATTGATTTCTTTTCATCTAATGA
* *
28422487 TTGACTTAATTATGAGACAACGATTAAAGGCATTTTTACCGCCTTGGGAAGTGATTACACCCATT
644 TTGAATTAATTATGAGACAACGATTAAAGGCATTTTTACCGCCTTGGGAAGTGATAACACCCATT
*
28422552 TTTACTAAAAGTTTTAAGCCATTTTCCTAAATAATCTGATA-AGTGATTATTTTTGTGATTTTTT
709 TTTACTAAAAGTTTTAAGCCATTTTCCTAAATAATCTGATACA-TGATTATTTTCGTGATTTTTT
* *
28422616 AATATTATAAGATTAATTTTCTAAAAATGCATGTCTTTCCTGTCTAACCCTCT-TGGACAAATTA
773 AATAATATAAGATTAATTTTCTAAAAATGCATGTCTTTCCTGTCTAACCCTCTCGGGA-AAATTA
* * *
28422680 CATATAAAAGCTCATTTTTTAAAAAATTTACTGAAATGGGCCC-GATATATAATTATTTACCGGA
837 CATATAAAAACCCATTTTTTAAAAAATTTACTAAAATGGGCCCAG-TATATAATTATTTACCGGA
28422744 ATGACCCTATTTCCCCAAAAGCGCGTCAACGT
901 ATGACCCTATTTCCCCAAAAGCGCGTCAACGT
28422776 CAACGCGATG
Statistics
Matches: 884, Mismatches: 40, Indels: 20
0.94 0.04 0.02
Matches are distributed among these distances:
980 59 0.07
981 4 0.00
982 117 0.13
983 541 0.61
984 114 0.13
985 49 0.06
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (981 bp):
ACAAGCGACACCTAAAAATTAAAAAAAAATTTACCTGGTGCCACCACATCTGGAGTATGAACCAG
GAAAAAAGAATTTTACTGATTCTGGTGTCTCCACATTGAAGTGGCGGGACGGAAAAATTAAAAAA
AATATTGGTGCCGCCATATCTGGACAAAGGACCAGGGAAATTTTATTTTTTTACTATTTTGGTGA
CTTTGTGTGAAGTGGCAGCACTAAAAAATTAAAAAAAATACTAGTGCCACCACATCTGGAGTAGG
GACCAGAAAAATTTTTTATTCATTTTGGTGACTCCATATGAAGTGGCGAGACAGAAAAATTAAAA
AAAACTTATTAGTGTCGTCATATCTAGGGTAGGGACCAAGAGTTTCTTTTTAAAATTTTTAGTGA
CTCCATGTGAAGTGATGGCACCGAAAAATTTTAAAAATGCGGCACCAACAAATATTTTCTTTTAT
TCCAATTTAGCGGCGCCACTTATAAGCATGCAACCAAAATTTTTTTTTATTACAATTTGATGCCT
CCATTAAAAGAGGTGGCACCAAAAATTAATTAAAAAATATTTATTTTTACTCTGAGAATACCCGA
GAAAATACAATATTTGAAAAAAGTTACACAAAAAAATTGATTTCTTTTCATCTAATGATTGAATT
AATTATGAGACAACGATTAAAGGCATTTTTACCGCCTTGGGAAGTGATAACACCCATTTTTACTA
AAAGTTTTAAGCCATTTTCCTAAATAATCTGATACATGATTATTTTCGTGATTTTTTAATAATAT
AAGATTAATTTTCTAAAAATGCATGTCTTTCCTGTCTAACCCTCTCGGGAAAATTACATATAAAA
ACCCATTTTTTAAAAAATTTACTAAAATGGGCCCAGTATATAATTATTTACCGGAATGACCCTAT
TTCCCCAAAAGCGCGTCAACGTTTGCCGACCCATGCTATGTGTTTTCAGCTCTGGTTGATGGCCC
TCTATA
Found at i:28423228 original size:96 final size:97
Alignment explanation
Indices: 28423128--28423310 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 97
28423118 AGGTTTAGGG
*
28423128 TTACTTGAGTAATTTAATTA-AAAGTTATTTA-AAAA-TCAAATAAGGGTTTAGAGTTAAGGGTT
1 TTACTTGAGTAAATTAATTATAAA-TT-TTTATAAAATTCAAATAAGGG-TTAGAGTTAAGGGTT
28423190 TTTAAGGAAAAA-TCAAATAAATTAGGGTGCAAGA
63 TTTAAGGAAAAACTCAAATAAATTAGGGTGCAAGA
** * * * *
28423224 TTACTTGAGTAAATTAATTATAAATTTTTATAAAATTTGATTAAGGGTTAGTGTTTAGTGTTTTT
1 TTACTTGAGTAAATTAATTATAAATTTTTATAAAATTCAAATAAGGGTTAGAGTTAAGGGTTTTT
*
28423289 AAGTAAAAACTCAAATAAATTA
66 AAGGAAAAACTCAAATAAATTA
28423311 AGGTTTGGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
95 4 0.05
96 48 0.64
97 23 0.31
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (97 bp):
TTACTTGAGTAAATTAATTATAAATTTTTATAAAATTCAAATAAGGGTTAGAGTTAAGGGTTTTT
AAGGAAAAACTCAAATAAATTAGGGTGCAAGA
Found at i:28423580 original size:126 final size:126
Alignment explanation
Indices: 28423355--28423897 Score: 825
Period size: 126 Copynumber: 4.3 Consensus size: 126
28423345 TTTTTAATTT
* * * * **
28423355 AAAGAAGCTTCCACGTGGACGCGCTTTAGTTGCAGTAACTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* *
28423420 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAAGATGCTTTGTCAGCAGAAGTAATG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
28423481 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTAGAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* * *
28423546 GTTTCTGAGCAAATAGTGTCAAAAACGTTTTAAGCGGGATACTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
* * *
28423607 AAAGAAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCCTCAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* * **
28423672 GTTTCTGAGCAAATAGTGTCAAAAAAGCTTTAAGCAGGATGTTTTGTCAATAGAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
** * * *
28423733 AAAGAAGCTCTTACGTAGACGCGCTTTTGCTATAGTGGCTCCTGAAAAAATAATTTCTAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
* ** *
28423798 ATTTCTGAGCAAATAGTGTCAAAAATACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTG
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
*
28423859 AAAGAAACTCCCACGTGGACGCGCTTTTGCTACAGTGGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGC
28423898 GCATGTTTGG
Statistics
Matches: 374, Mismatches: 43, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 374 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTGGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:28429313 original size:12 final size:12
Alignment explanation
Indices: 28429296--28429326 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
28429286 AGAGGAATTT
28429296 GAGAGAATACTA
1 GAGAGAATACTA
28429308 GAGAGAATACTA
1 GAGAGAATACTA
28429320 GAGAGAA
1 GAGAGAA
28429327 ATTGAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.29, T:0.13
Consensus pattern (12 bp):
GAGAGAATACTA
Found at i:28429338 original size:10 final size:11
Alignment explanation
Indices: 28429277--28429337 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 11
28429267 TCTTTTAAAT
*
28429277 AGAAATTTGAG
1 AGAAACTTGAG
* *
28429288 AGGAATTTGAG
1 AGAAACTTGAG
*
28429299 AGAATACTAGAG
1 AGAA-ACTTGAG
*
28429311 AGAATACTAGAG
1 AGAA-ACTTGAG
28429323 AGAAA-TTGAG
1 AGAAACTTGAG
28429333 AGAAA
1 AGAAA
28429338 TGATTTAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
10 9 0.20
11 14 0.32
12 21 0.48
ACGTcount: A:0.49, C:0.03, G:0.28, T:0.20
Consensus pattern (11 bp):
AGAAACTTGAG
Found at i:28430718 original size:18 final size:18
Alignment explanation
Indices: 28430680--28430715 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28430670 TTATTATTTT
*
28430680 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
28430698 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
28430716 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:28436151 original size:6 final size:6
Alignment explanation
Indices: 28436140--28436164 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28436130 TTACAATAAT
28436140 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
28436165 TGAGATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:28454005 original size:14 final size:14
Alignment explanation
Indices: 28453986--28454022 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28453976 TTAGCAATGC
28453986 TAAAGAAAGAAATA
1 TAAAGAAAGAAATA
28454000 TAAAGAATA-AAATA
1 TAAAGAA-AGAAATA
28454014 -AAAGAAAGA
1 TAAAGAAAGA
28454023 GATGCTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 7 0.33
14 12 0.57
15 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
TAAAGAAAGAAATA
Found at i:28454868 original size:18 final size:18
Alignment explanation
Indices: 28454845--28454879 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28454835 AATAAAAATG
*
28454845 AAAAAAATAAAAATAAAC
1 AAAAAAAGAAAAATAAAC
*
28454863 AAAAAAGGAAAAATAAA
1 AAAAAAAGAAAAATAAA
28454880 AAATTTGACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (18 bp):
AAAAAAAGAAAAATAAAC
Found at i:28456772 original size:13 final size:14
Alignment explanation
Indices: 28456747--28456779 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
28456737 TGGTTTGGAA
28456747 AAATAACTAAACTC
1 AAATAACTAAACTC
28456761 AAATAA-TAAACTC
1 AAATAACTAAACTC
28456774 AAATAA
1 AAATAA
28456780 AATTCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAACTAAACTC
Found at i:28460663 original size:24 final size:23
Alignment explanation
Indices: 28460636--28460688 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
28460626 TGCACATTAT
* * *
28460636 ATATATCCTAATTAAATTTATTTA
1 ATATATACTAAATAAATTTA-TCA
*
28460660 ATATATATTAAATAAATTTATCA
1 ATATATACTAAATAAATTTATCA
28460683 ATATAT
1 ATATAT
28460689 GTATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATATACTAAATAAATTTATCA
Found at i:28463877 original size:22 final size:22
Alignment explanation
Indices: 28463787--28463886 Score: 78
Period size: 22 Copynumber: 4.6 Consensus size: 22
28463777 TGACTTATCC
* *
28463787 CAACTTATTGGTAGCTTGTCTG
1 CAACTTACTGGCAGCTTGTCTG
* * * *
28463809 CAATTTGCTAGCAGCTTGTCTA
1 CAACTTACTGGCAGCTTGTCTG
* * *
28463831 CAACTAACTGG-TGACTTAT-TG
1 CAACTTACTGGCAG-CTTGTCTG
*
28463852 CAACTTACTGGCATCTTGTCTG
1 CAACTTACTGGCAGCTTGTCTG
*
28463874 CAACTTATTGGCA
1 CAACTTACTGGCA
28463887 ATTCTACTGC
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
21 16 0.28
22 41 0.72
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (22 bp):
CAACTTACTGGCAGCTTGTCTG
Found at i:28470440 original size:18 final size:18
Alignment explanation
Indices: 28470399--28470524 Score: 135
Period size: 18 Copynumber: 7.0 Consensus size: 18
28470389 TATCTACCGT
*
28470399 ATATAAGGGTTCGCTTAC
1 ATATAAGGGTTCGCATAC
** *
28470417 GCATAAGAGTTCGCATAC
1 ATATAAGGGTTCGCATAC
* *
28470435 ATATAAGGGTTTGCATGC
1 ATATAAGGGTTCGCATAC
* *
28470453 ATATAAAGGTTCACATAC
1 ATATAAGGGTTCGCATAC
* *
28470471 ATATAAAGGTTCGCATGC
1 ATATAAGGGTTCGCATAC
* *
28470489 ATATAAGGGTCCACATAC
1 ATATAAGGGTTCGCATAC
*
28470507 ATATAAGGGTTCACATAC
1 ATATAAGGGTTCGCATAC
28470525 CAACAATTTG
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 88 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (18 bp):
ATATAAGGGTTCGCATAC
Found at i:28472729 original size:286 final size:286
Alignment explanation
Indices: 28472217--28472788 Score: 1117
Period size: 286 Copynumber: 2.0 Consensus size: 286
28472207 ATGACATAGA
*
28472217 AGTTAATATACTCTTCTTGAGATGTCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
1 AGTTAATATACTCTTCTTGAGATATCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
28472282 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
66 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
28472347 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
131 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
28472412 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCAAATTATAG
196 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCAAATTATAG
*
28472477 TAGATCAAGTAATTCTTCTACAAATT
261 CAGATCAAGTAATTCTTCTACAAATT
28472503 AGTTAATATACTCTTCTTGAGATATCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
1 AGTTAATATACTCTTCTTGAGATATCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
28472568 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
66 CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
28472633 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
131 TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
*
28472698 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCGAATTATAG
196 CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCAAATTATAG
28472763 CAGATCAAGTAATTCTTCTACAAATT
261 CAGATCAAGTAATTCTTCTACAAATT
28472789 TGATGTTGAA
Statistics
Matches: 283, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
286 283 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (286 bp):
AGTTAATATACTCTTCTTGAGATATCTTCAAGGGTATGTTGCGACACACTTAGGCTGCATCACGA
CATCGAAGGCAGTCTTGTGATTTCTCTATTCTGTTCCCTATGTTGCAACATTGATCATTCTGTGT
TGCGATATAGTGACTAGAATCGGTTTAGTACGCCTTCTAATGGTCTCCTAAACACTTACAAAGTT
CAATTTGAACACTTTCAAACTCCTAAAGTGCGAAAATTAGTTTAATCTATTTCACCAAATTATAG
CAGATCAAGTAATTCTTCTACAAATT
Found at i:28473534 original size:22 final size:22
Alignment explanation
Indices: 28473501--28473545 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28473491 TAATTTTAGG
28473501 TTTAGTTTTCTCTA-AGTTTTC
1 TTTAGTTTTCTCTACAGTTTTC
*
28473522 TTTAGTTTTTCTCTACATTTTTC
1 TTTAG-TTTTCTCTACAGTTTTC
28473545 T
1 T
28473546 AGGGTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.13, C:0.16, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTAGTTTTCTCTACAGTTTTC
Found at i:28480977 original size:24 final size:24
Alignment explanation
Indices: 28480932--28480986 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
28480922 GTTGCGCATT
* *
28480932 ATATATATGCTAATTAAATTTATTTA
1 ATATATAT-CTAAATAAATTTA-TCA
*
28480958 ATATATAT-TAAATAAGTTTATCA
1 ATATATATCTAAATAAATTTATCA
28480981 ATATAT
1 ATATAT
28480987 GTATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 8 0.31
24 10 0.38
26 8 0.31
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATATATCTAAATAAATTTATCA
Found at i:28481258 original size:11 final size:12
Alignment explanation
Indices: 28481216--28481264 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
28481206 AATAAATACC
28481216 AAAAATTTATTTT
1 AAAAA-TTATTTT
*
28481229 AAAAATTA---A
1 AAAAATTATTTT
28481238 AAAAATTATTTT
1 AAAAATTATTTT
28481250 AAAAA-TATTTT
1 AAAAATTATTTT
28481261 AAAA
1 AAAA
28481265 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 8 0.26
11 10 0.32
12 8 0.26
13 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:28481267 original size:22 final size:21
Alignment explanation
Indices: 28481216--28481255 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28481206 AATAAATACC
*
28481216 AAAAATTTATTTTAAAAATTA
1 AAAAAATTATTTTAAAAATTA
28481237 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
28481256 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAATTATTTTAAAAATTA
Found at i:28482014 original size:20 final size:20
Alignment explanation
Indices: 28481989--28482030 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
28481979 ATACTTTCAT
*
28481989 CTGCGAAGTCGCAGGGTTGA
1 CTGCGAAATCGCAGGGTTGA
28482009 CTGCGAAATCGCAGGGTTGA
1 CTGCGAAATCGCAGGGTTGA
28482029 CT
1 CT
28482031 TGAATAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.21
Consensus pattern (20 bp):
CTGCGAAATCGCAGGGTTGA
Found at i:28485196 original size:30 final size:30
Alignment explanation
Indices: 28485160--28485218 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
28485150 GTACATCATT
28485160 ATAACACTAAAGTCCATTTAAATAAGTTCC
1 ATAACACTAAAGTCCATTTAAATAAGTTCC
28485190 ATAACACTAAAGTCCATTTAAATAAGTTC
1 ATAACACTAAAGTCCATTTAAATAAGTTC
28485219 AATAGTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.31
Consensus pattern (30 bp):
ATAACACTAAAGTCCATTTAAATAAGTTCC
Found at i:28493709 original size:62 final size:62
Alignment explanation
Indices: 28493643--28493760 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
28493633 CATCAGCGTG
*
28493643 TCTCTAGGCCGTGTGAGTCACACGGTATTTCGAATGGCC-ACACGACCTAAGACACGACCATC
1 TCTCTAGGCCGTCTGAGTCACACGGTATTTCG-ATGGCCTACACGACCTAAGACACGACCATC
* * * *
28493705 TCTCTTGGCCGTCTGAGTCACACGGTATTTCGATTGCCTACACGGCCTAAGGCACG
1 TCTCTAGGCCGTCTGAGTCACACGGTATTTCGATGGCCTACACGACCTAAGACACG
28493761 GGCGTGTCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 5 0.10
62 45 0.90
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.24
Consensus pattern (62 bp):
TCTCTAGGCCGTCTGAGTCACACGGTATTTCGATGGCCTACACGACCTAAGACACGACCATC
Found at i:28498553 original size:22 final size:21
Alignment explanation
Indices: 28498528--28498571 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
28498518 AAAAAGTGAC
*
28498528 TTCACAACTATATAAAAACTCG
1 TTCACAACTACAT-AAAACTCG
**
28498550 TTCATTACTACATAAAACTCG
1 TTCACAACTACATAAAACTCG
28498571 T
1 T
28498572 GAGCTAGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (21 bp):
TTCACAACTACATAAAACTCG
Found at i:28504342 original size:33 final size:33
Alignment explanation
Indices: 28504273--28504354 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
28504263 ATTTTATATA
* *
28504273 TTTATATGATTTAAAATTTTAAAAAAATTTAGTTT
1 TTTATAT-ATTT-ATATTTTAAAAAAATTTAATTT
* **
28504308 TTTATATATTTATATTTTGAAAATTTTTAATTT
1 TTTATATATTTATATTTTAAAAAAATTTAATTT
*
28504341 TTTATAAATTTATA
1 TTTATATATTTATA
28504355 AATTATTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 30 0.73
34 4 0.10
35 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (33 bp):
TTTATATATTTATATTTTAAAAAAATTTAATTT
Found at i:28510500 original size:30 final size:31
Alignment explanation
Indices: 28510434--28510506 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
28510424 ATGTTAATGG
* *
28510434 GTGACTGATTTGTCACTTTTCGATAACGTTA
1 GTGACTGTTTTGTAACTTTTCGATAACGTTA
*
28510465 GTGACTGTTTTGTAATTTTTCGA-AA-GTTGA
1 GTGACTGTTTTGTAACTTTTCGATAACGTT-A
28510495 GTGACTGTTTTG
1 GTGACTGTTTTG
28510507 CCAACTGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.08
30 15 0.39
31 20 0.53
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.45
Consensus pattern (31 bp):
GTGACTGTTTTGTAACTTTTCGATAACGTTA
Found at i:28513334 original size:17 final size:17
Alignment explanation
Indices: 28513312--28513346 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28513302 TAATACAATG
28513312 ATCTTTATGTTTCCATT
1 ATCTTTATGTTTCCATT
28513329 ATCTTTATGTTTCCATT
1 ATCTTTATGTTTCCATT
28513346 A
1 A
28513347 CAGGAGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (17 bp):
ATCTTTATGTTTCCATT
Found at i:28515616 original size:16 final size:18
Alignment explanation
Indices: 28515575--28515608 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28515565 CAAAATTAGA
28515575 GTTTCTCTCATTCTTTTC
1 GTTTCTCTCATTCTTTTC
*
28515593 GATTCTCTCA-TCTTTT
1 GTTTCTCTCATTCTTTT
28515609 TTTTCTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.26, G:0.06, T:0.59
Consensus pattern (18 bp):
GTTTCTCTCATTCTTTTC
Found at i:28517052 original size:13 final size:14
Alignment explanation
Indices: 28517036--28517073 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
28517026 GAGAATTTGA
28517036 TTAAAAAATTT-TC
1 TTAAAAAATTTATC
*
28517049 TTAAAAAATTTATT
1 TTAAAAAATTTATC
28517063 TTGAAAAAATT
1 TT-AAAAAATT
28517074 CAATGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (14 bp):
TTAAAAAATTTATC
Found at i:28517622 original size:37 final size:37
Alignment explanation
Indices: 28517558--28517634 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
28517548 ATTCCAAAAA
*
28517558 TAATACTATTTTAATTATTATAATATTAAATTTAAT-T
1 TAATACTATTTTAATTAGTATAATATT-AATTTAATAT
**
28517595 TAATACTTATTTTAATT-GTATTTTATTAATTTAATAT
1 TAATAC-TATTTTAATTAGTATAATATTAATTTAATAT
28517632 TAA
1 TAA
28517635 AGTGATTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 8 0.23
37 17 0.49
38 10 0.29
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (37 bp):
TAATACTATTTTAATTAGTATAATATTAATTTAATAT
Found at i:28517816 original size:11 final size:9
Alignment explanation
Indices: 28517788--28517813 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28517778 ATTATAGTTG
28517788 AACTCTCTA
1 AACTCTCTA
28517797 AACTCTCTA
1 AACTCTCTA
28517806 AACTCTCT
1 AACTCTCT
28517814 CTATATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (9 bp):
AACTCTCTA
Found at i:28520757 original size:28 final size:28
Alignment explanation
Indices: 28520717--28520801 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
28520707 CAAAAATTTG
*
28520717 ACCATTACAATATGGTTGTTGGAATCTA
1 ACCATTACAATATGGCTGTTGGAATCTA
** ** * *
28520745 ATTATTACAATATGGCCATTGGAATTTG
1 ACCATTACAATATGGCTGTTGGAATCTA
28520773 ACCATTACAA-ATGGCTGTTGGAATCTA
1 ACCATTACAATATGGCTGTTGGAATCTA
28520800 AC
1 AC
28520802 TGTTGCAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 15 0.34
28 29 0.66
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (28 bp):
ACCATTACAATATGGCTGTTGGAATCTA
Found at i:28523405 original size:31 final size:31
Alignment explanation
Indices: 28523370--28523428 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
28523360 ATGTGTATAG
28523370 TTGAATCACAATAAAAATTTCATATATACAT
1 TTGAATCACAATAAAAATTTCATATATACAT
* * *
28523401 TTGAATTACAATCAAAGTTTCATATATA
1 TTGAATCACAATAAAAATTTCATATATA
28523429 TTGTTAGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (31 bp):
TTGAATCACAATAAAAATTTCATATATACAT
Found at i:28528889 original size:21 final size:21
Alignment explanation
Indices: 28528859--28528899 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28528849 TCTGTTGCCC
28528859 TTTCTTTCTTTTTT-CTTTTA
1 TTTCTTTCTTTTTTCCTTTTA
28528879 TTTCTATTCTTTTTTCCTTTT
1 TTTCT-TTCTTTTTTCCTTTT
28528900 TTAATCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTCTTTCTTTTTTCCTTTTA
Found at i:28537687 original size:19 final size:20
Alignment explanation
Indices: 28537646--28537687 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
28537636 TTAAAAATAA
**
28537646 TTTAATTCAATTCACTTGGT
1 TTTAATTCAATTCACTTAAT
*
28537666 TTTAATTC-ATTCATTTAAT
1 TTTAATTCAATTCACTTAAT
28537685 TTT
1 TTT
28537688 CAGTTTTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTAATTCAATTCACTTAAT
Found at i:28543672 original size:10 final size:10
Alignment explanation
Indices: 28543657--28543685 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28543647 AAGCAATCAG
28543657 GAATCAAAAT
1 GAATCAAAAT
28543667 GAATCAAAAT
1 GAATCAAAAT
28543677 GAATCAAAA
1 GAATCAAAA
28543686 CATAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (10 bp):
GAATCAAAAT
Found at i:28544777 original size:20 final size:20
Alignment explanation
Indices: 28544714--28544819 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 20
28544704 TGCAAAATAA
* * *
28544714 GGGCACCAAAGTGTAATCAG
1 GGGCACCAGAGTGCATTCAG
* ** * *
28544734 GAGCACCAGTCTGCAATCAA
1 GGGCACCAGAGTGCATTCAG
*
28544754 GGGCACCAGAGTGCATTTAG
1 GGGCACCAGAGTGCATTCAG
* *
28544774 GGGCACGA-ATGTGC-TGCCAG
1 GGGCACCAGA-GTGCAT-TCAG
*
28544794 GGGCACCGGAGTGCATTCAG
1 GGGCACCAGAGTGCATTCAG
28544814 GGGCAC
1 GGGCAC
28544820 GTATGTGCAA
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
19 2 0.03
20 60 0.94
21 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.34, T:0.15
Consensus pattern (20 bp):
GGGCACCAGAGTGCATTCAG
Found at i:28544827 original size:20 final size:20
Alignment explanation
Indices: 28544764--28544828 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
28544754 GGGCACCAGA
*
28544764 GTGCATTTAGGGGCACGAAT
1 GTGCATTCAGGGGCACGAAT
* *
28544784 GTGC-TGCCAGGGGCACCGGA-
1 GTGCAT-TCAGGGGCA-CGAAT
*
28544804 GTGCATTCAGGGGCACGTAT
1 GTGCATTCAGGGGCACGAAT
28544824 GTGCA
1 GTGCA
28544829 AACATGGACA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 28 0.78
21 4 0.11
ACGTcount: A:0.20, C:0.22, G:0.38, T:0.20
Consensus pattern (20 bp):
GTGCATTCAGGGGCACGAAT
Found at i:28544841 original size:40 final size:40
Alignment explanation
Indices: 28544753--28544872 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 40
28544743 TCTGCAATCA
* * * ***
28544753 AGGG-CACCAGAGTGCATTTAGGGGCACGAATGTGCTGCC
1 AGGGACACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
*
28544792 AGGGGCACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
1 AGGGACACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
* * *
28544832 ATGGACACCGAAGTG-TTTACAGGGGCACAGT-TGTGCAAAC
1 AGGGACACCGGAGTGCATT-CAGGGGCAC-GTATGTGCAAAC
28544872 A
1 A
28544873 AGAACATCGA
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 6 0.09
40 60 0.88
41 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.34, T:0.17
Consensus pattern (40 bp):
AGGGACACCGGAGTGCATTCAGGGGCACGTATGTGCAAAC
Found at i:28544884 original size:40 final size:40
Alignment explanation
Indices: 28544811--28544888 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
28544801 GGAGTGCATT
* *
28544811 CAGGGGCACGTATGTGCAAACATGGACACCGAAGTGTTTA
1 CAGGGGCACGTATGTGCAAACAAGAACACCGAAGTGTTTA
*
28544851 CAGGGGCACAGT-TGTGCAAACAAGAACATCGAAGTGTT
1 CAGGGGCAC-GTATGTGCAAACAAGAACACCGAAGTGTT
28544889 ATGAAGGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.19
Consensus pattern (40 bp):
CAGGGGCACGTATGTGCAAACAAGAACACCGAAGTGTTTA
Found at i:28545321 original size:29 final size:29
Alignment explanation
Indices: 28545289--28545349 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
28545279 GACCCTTCAA
28545289 TTTT-CATTAATTACATATTT-TCCCTAAAC
1 TTTTACATT-ATTACA-ATTTATCCCTAAAC
*
28545318 TTTTACATTTTTACAATTTAGTCCCTAAAC
1 TTTTACATTATTACAATTTA-TCCCTAAAC
28545348 TT
1 TT
28545350 AAAATCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.14
29 9 0.32
30 15 0.54
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.49
Consensus pattern (29 bp):
TTTTACATTATTACAATTTATCCCTAAAC
Found at i:28559148 original size:59 final size:62
Alignment explanation
Indices: 28559050--28559176 Score: 163
Period size: 59 Copynumber: 2.1 Consensus size: 62
28559040 ATACACCAAT
* * * *
28559050 AGTCACTCAACTTTGATTAAAACAACAAAATAGTCACTAAAC-TT-T-GAAAAGTTACAACTC
1 AGTCACTCAACTTTGATGAAAACAACAAAATAATCACT-AACGTTATCGAAAAGTGACAAATC
* *
28559110 AGTCGCTCAACTTT-ATGAAAATAACAAAATAATCACTAACGTTATCGAAAAGTGACAAATC
1 AGTCACTCAACTTTGATGAAAACAACAAAATAATCACTAACGTTATCGAAAAGTGACAAATC
28559171 AGTCAC
1 AGTCAC
28559177 CCACTAACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 3 0.05
59 22 0.39
60 14 0.25
61 18 0.32
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (62 bp):
AGTCACTCAACTTTGATGAAAACAACAAAATAATCACTAACGTTATCGAAAAGTGACAAATC
Found at i:28562178 original size:20 final size:20
Alignment explanation
Indices: 28562128--28562179 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
28562118 TAAAATAATA
*
28562128 TTATATT-AATTATATATGT
1 TTATATTAAATTATATATAT
*
28562147 TTA-ATAATAATTATATATAT
1 TTATATTA-AATTATATATAT
28562167 TTATATTAAATTA
1 TTATATTAAATTA
28562180 CTAATCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.07
19 3 0.11
20 19 0.70
21 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATATTAAATTATATATAT
Found at i:28562366 original size:35 final size:35
Alignment explanation
Indices: 28562327--28562417 Score: 80
Period size: 35 Copynumber: 2.6 Consensus size: 35
28562317 ACAGTATTTT
*
28562327 TTAATATGTTTTTATTGTGTTAGAAAACTTTTA-TA
1 TTAATATGTTTTTATTGTGTTAGAAAA-TTATATTA
* * * * *
28562362 TTAATCT-TTTTTAGTGCAT-TTAGTATATTATATTT
1 TTAATATGTTTTTATTG--TGTTAGAAAATTATATTA
28562397 TTAATATGTTTTTATTGTGTT
1 TTAATATGTTTTTATTGTGTT
28562418 TTTTAGTGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
34 13 0.30
35 21 0.49
36 9 0.21
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.59
Consensus pattern (35 bp):
TTAATATGTTTTTATTGTGTTAGAAAATTATATTA
Found at i:28564516 original size:18 final size:18
Alignment explanation
Indices: 28564493--28564528 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
28564483 CCAAGAACAT
28564493 AAAATACAACA-GGCCCAA
1 AAAATACAA-ATGGCCCAA
28564511 AAAATACAAATGGCCCAA
1 AAAATACAAATGGCCCAA
28564529 TTTTTAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.08
Consensus pattern (18 bp):
AAAATACAAATGGCCCAA
Found at i:28567634 original size:39 final size:39
Alignment explanation
Indices: 28567538--28567636 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
28567528 ATATTCACTT
* * * *
28567538 AAGCATATATCACATTACACATATAATTAGATAATGTTC
1 AAGCATATATCGCAATACTCATATAATTAGATAACGTTC
* *
28567577 AAGCACATATCGCAATACTCATATAA-TCGCATAACGTTC
1 AAGCATATATCGCAATACTCATATAATTAG-ATAACGTTC
28567616 AAGCATATATCGCAATACTCA
1 AAGCATATATCGCAATACTCA
28567637 AAAACATGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
38 2 0.04
39 50 0.96
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.28
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATTAGATAACGTTC
Found at i:28575736 original size:12 final size:12
Alignment explanation
Indices: 28575698--28575749 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
28575688 GAAATATATA
*
28575698 AATAATATCAAT
1 AATAATATTAAT
*
28575710 AATAATAGTAAT
1 AATAATATTAAT
*
28575722 AATAATATTATT
1 AATAATATTAAT
* *
28575734 AATTA-ATTAAA
1 AATAATATTAAT
28575745 AATAA
1 AATAA
28575750 ATAGCAAGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:28578545 original size:9 final size:9
Alignment explanation
Indices: 28578531--28578562 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
28578521 AACTTGGTGC
28578531 ATTTTGTTT
1 ATTTTGTTT
28578540 ATTTTGTTT
1 ATTTTGTTT
28578549 ATTTTGTTT
1 ATTTTGTTT
28578558 ATTTT
1 ATTTT
28578563 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:28578643 original size:23 final size:23
Alignment explanation
Indices: 28578613--28578664 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
28578603 TGCAACTTGG
28578613 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
28578636 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
28578659 TTTCAT
1 TTTCAT
28578665 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:28583007 original size:9 final size:9
Alignment explanation
Indices: 28582993--28583024 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
28582983 AACTTGGTGC
28582993 ATTTTGTTT
1 ATTTTGTTT
28583002 ATTTTGTTT
1 ATTTTGTTT
28583011 ATTTTGTTT
1 ATTTTGTTT
28583020 ATTTT
1 ATTTT
28583025 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:28583105 original size:23 final size:23
Alignment explanation
Indices: 28583075--28583126 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
28583065 TGCAACTTGG
28583075 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
28583098 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
28583121 TTTCAT
1 TTTCAT
28583127 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:28584759 original size:27 final size:28
Alignment explanation
Indices: 28584704--28584778 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 28
28584694 CGGTTTTGTT
*
28584704 TAATT-TTCGTATTTCATAATTTAATTATA
1 TAATTATTC-TATTT-ATATTTTAATTATA
*
28584733 -AATTATTCTATTTATATTTTATTTATA
1 TAATTATTCTATTTATATTTTAATTATA
*
28584760 TAAATATT-TATTTATATTT
1 TAATTATTCTATTTATATTT
28584779 ATCTATTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 23 0.56
28 15 0.37
29 3 0.07
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (28 bp):
TAATTATTCTATTTATATTTTAATTATA
Found at i:28595969 original size:21 final size:21
Alignment explanation
Indices: 28595930--28595969 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28595920 ACACACAAAC
*
28595930 ATTTATAAAAGTCTTTATACA
1 ATTTATAAAAGTCTCTATACA
28595951 ATTTATAAAAAGTC-CTATA
1 ATTTAT-AAAAGTCTCTATA
28595970 ACAACACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
ATTTATAAAAGTCTCTATACA
Found at i:28595973 original size:22 final size:21
Alignment explanation
Indices: 28595930--28595973 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
28595920 ACACACAAAC
*
28595930 ATTTATAAAAGTCTTTATACA
1 ATTTATAAAAGTCTATATACA
28595951 ATTTATAAAAAGTCCTATA-ACA
1 ATTTAT-AAAAGT-CTATATACA
28595973 A
1 A
28595974 CACAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTTATAAAAGTCTATATACA
Found at i:28599072 original size:17 final size:16
Alignment explanation
Indices: 28599052--28599105 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
28599042 AGTTAAATTT
28599052 TTTTGTTTCTTGTTTAG
1 TTTTGTTTCTT-TTTAG
*
28599069 TTTTATTTCTATTTGTAG
1 TTTTGTTTCT-TTT-TAG
*
28599087 TTTAGGTTTCTTTTTAG
1 TTT-TGTTTCTTTTTAG
28599104 TT
1 TT
28599106 GTAATCGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 16 0.52
18 10 0.32
19 5 0.16
ACGTcount: A:0.11, C:0.06, G:0.15, T:0.69
Consensus pattern (16 bp):
TTTTGTTTCTTTTTAG
Done.