Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 188 of 230
Found at i:56581392 original size:50 final size:49
Alignment explanation
Indices: 56581336--56581670 Score: 332
Period size: 51 Copynumber: 6.7 Consensus size: 49
56581326 GATGGCCACG
56581336 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCTGAATGATGGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGATGGGTCGCA
** * **
56581386 TGTGTAGTACTATGTGCAGGCTACTATGCATATCGAAT-A-GCTTCGATCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATGATGGGTCG--CA
* * *
56581435 TGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCTGAATGATGGGTCCCA
1 --TGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGATGGGTCGCA
* * * * *
56581487 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-G-ATGGGTCGCA
* * *
56581538 TATGTAATACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACC-GAATGATGGGTCGCA
* * * * * * * *
56581588 TGAGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAAT-G-ATGGGTCGCA
*
56581639 TGTGTAGTACTATGTGCAGGCTACTACGTGTA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTA
56581671 TCAGATGGAA
Statistics
Matches: 231, Mismatches: 42, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
47 4 0.02
48 1 0.00
49 13 0.06
50 99 0.43
51 100 0.43
52 10 0.04
53 1 0.00
54 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGAATGATGGGTCGCA
Found at i:56581451 original size:101 final size:101
Alignment explanation
Indices: 56581332--56581670 Score: 570
Period size: 101 Copynumber: 3.4 Consensus size: 101
56581322 AAGTGATGGC
*
56581332 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCTGAATGATGGGTCGCATGTGTAGTACT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATGGGTCGCATGTGTAGTACT
* *
56581397 ATGTGCAGGCTACTATGCATATCGAATAGCTTCGAT
66 ATGTGCAGGCTACTATGCGTACCGAATAGCTTCGAT
* * *
56581433 CATGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCTGAATGATGGGTCCCATGTGTAGTACT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATGGGTCGCATGTGTAGTACT
56581498 ATGTGCAGGCTACTATGCGTACCGAATAGCTTCGAT
66 ATGTGCAGGCTACTATGCGTACCGAATAGCTTCGAT
* * * * *
56581534 CACATATGTAATACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGAGTAGTACT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATGGGTCGCATGTGTAGTACT
*
56581599 ATGTGCAGGCTACTATGCGTACCGGATAGCTTCGAT
66 ATGTGCAGGCTACTATGCGTACCGAATAGCTTCGAT
56581635 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
56581671 TCAGATGGAA
Statistics
Matches: 220, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 220 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCTGAATGATGGGTCGCATGTGTAGTACT
ATGTGCAGGCTACTATGCGTACCGAATAGCTTCGAT
Found at i:56581462 original size:51 final size:51
Alignment explanation
Indices: 56581336--56581664 Score: 346
Period size: 50 Copynumber: 6.5 Consensus size: 51
56581326 GATGGCCACG
* * * * *
56581336 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCTGAAT-G-ATGGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGCTTCGATCACA
* * **
56581386 TGTGTAGTACTATGTGCAGGCTACTATGCATATCGAATAGCTTCGATCATG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACA
* * * * * * *
56581437 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCTGAAT-G-ATGGGTCCCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGCTTCGATCACA
56581487 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACA
* * * * * * * *
56581538 TATGTAATACTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATGGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACC-GAATAGCTTCGATCACA
* * *
56581588 TGAGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACA
56581639 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
56581665 CGTGTATCAG
Statistics
Matches: 224, Mismatches: 47, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
49 11 0.05
50 104 0.46
51 101 0.45
52 8 0.04
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACA
Found at i:56581697 original size:51 final size:49
Alignment explanation
Indices: 56581339--56581724 Score: 272
Period size: 51 Copynumber: 7.7 Consensus size: 49
56581329 GGCCACGTGT
* * * * *
56581339 GTAGTACTATGTGCAGGCTACTATGTGTACCTGAATGATGGGTCGCATGT
1 GTAGTACTATGTGCAGGCTACTACGTGTACC-GGATGATCGGTCACATGA
* ** * * * * ** *
56581389 GTAGTACTATGTGCAGGCTACTATGCATATCGAATAGCTTCGATCATGTGT
1 GTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-G-ATCGGTCACATGA
* * * * *
56581440 GTAGTACTATGTGTAGGCTACTACGTGTACCTGAATGATGGGTCCCATGT
1 GTAGTACTATGTGCAGGCTACTACGTGTACC-GGATGATCGGTCACATGA
* * * * *
56581490 GTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGATCACAT-A
1 GTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-G-ATCGGTCACATGA
* * *
56581540 TGTAATACTATGTGCAGGCTACTACGTGTACCGGAATGATGGGTCGCATGA
1 -GTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGATCGGTCACATGA
* * * * * *
56581591 GTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACGTGT
1 GTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-G-ATCGGTCACATGA
* * *
56581642 GTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGAAAT-GGTCACCTGA
1 GTAGTACTATGTGCAGGCTACTACGTGTACCGGAT-G--ATCGGTCACATGA
* * * *
56581693 GTAGTACTATGTGTAGACTACTATGTGAACCG
1 GTAGTACTATGTGCAGGCTACTACGTGTACCG
56581725 AGTATCATTG
Statistics
Matches: 264, Mismatches: 61, Indels: 21
0.76 0.18 0.06
Matches are distributed among these distances:
49 10 0.04
50 103 0.39
51 144 0.55
52 7 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
GTAGTACTATGTGCAGGCTACTACGTGTACCGGATGATCGGTCACATGA
Found at i:56581835 original size:33 final size:34
Alignment explanation
Indices: 56581788--56581920 Score: 126
Period size: 33 Copynumber: 3.7 Consensus size: 34
56581778 ATATAAAGGG
*
56581788 GGTTTCTAAGTGCTGATTCC-CCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
* * *
56581821 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGAATC----AT-TG---GT
*
56581863 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
*
56581896 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
56581921 TAACGGATAA
Statistics
Matches: 81, Mismatches: 9, Indels: 19
0.74 0.08 0.17
Matches are distributed among these distances:
33 38 0.47
34 10 0.12
36 2 0.02
37 1 0.01
38 2 0.02
39 2 0.02
41 6 0.07
42 20 0.25
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
Found at i:56581896 original size:75 final size:75
Alignment explanation
Indices: 56581743--56581919 Score: 250
Period size: 75 Copynumber: 2.3 Consensus size: 75
56581733 TGATTATAAA
* * * *
56581743 GTGGTTGCTAAATGTTGATTCCACCGTATCTTTGAATATAAAGGGGGTTTCTAAGTGCTGATTCC
1 GTGGTTGCTAAGTGCTGA-TCCACCGTATCTTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCC
*
56581808 CCGAATCATTG
65 CCGAATCACTG
*
56581819 GTGGTTGCTAAGTGCTGATCCCACCGTATC-TTAAATGTGAAA-GGGGTTGCTAAGTGCTGATTC
1 GTGGTTGCTAAGTGCTGAT-CCACCGTATCTTTAAATAT-AAAGGGGGTTGCTAAGTGCTGATTC
56581882 CCCGAATCACTG
64 CCCGAATCACTG
56581894 GTGGTTGCTAAGTGCTGAATCCACCG
1 GTGGTTGCTAAGTGCTG-ATCCACCG
56581920 ATAACGGATA
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
75 61 0.66
76 31 0.34
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (75 bp):
GTGGTTGCTAAGTGCTGATCCACCGTATCTTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCC
CGAATCACTG
Found at i:56582768 original size:49 final size:49
Alignment explanation
Indices: 56582690--56582788 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
56582680 ATGAGTACTT
* * * *
56582690 TCGGTAAGTGATATGTGATTCCGTATAAGACCATGGCTGGGCTATGGCA
1 TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
* * *
56582739 TCGGTATGTGATATGTGATTACATGTAAGACCATAGTTGGACTATGGCA
1 TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
56582788 T
1 T
56582789 TGAGAAAACG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.31
Consensus pattern (49 bp):
TCGGTAAGTGATATGTGATTACATATAAGACCATAGCTGGACTATGGCA
Found at i:56585544 original size:15 final size:15
Alignment explanation
Indices: 56585524--56585554 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56585514 TATGTGAGTC
56585524 TAGTTTCAGATAAAA
1 TAGTTTCAGATAAAA
56585539 TAGTTTCAGATAAAA
1 TAGTTTCAGATAAAA
56585554 T
1 T
56585555 TAACGGATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
TAGTTTCAGATAAAA
Found at i:56589367 original size:85 final size:85
Alignment explanation
Indices: 56589215--56589384 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 85
56589205 TTTTGCAATC
* * ** *
56589215 ATTGTGTATTCAAACTTTCAAAATGCATAAAAAAAGTTCTCAAAATTTTTCAAAAAAAGTAATTA
1 ATTGGGTACTCAAACTTTCAAAATGCATAAAAAAAGCCCTCAAAATTTTTCAAAAAAAGCAATTA
56589280 AGCCCCTAATTTTTTTATTCA
66 AGCCCCTAATTTTTTT-TTCA
* * *
56589301 ATTGGGTACTCAAACTTTCAACATGCATAAAAAAAAGCCCTC-AATTTTTTC-AAAAATGCAATT
1 ATTGGGTACTCAAACTTTCAAAATGCAT-AAAAAAAGCCCTCAAAATTTTTCAAAAAAAGCAATT
* *
56589364 AAGCCCTTGATTTTTTTTTCA
65 AAGCCCCTAATTTTTTTTTCA
56589385 CTGAATTGGG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 4 0.05
85 25 0.34
86 33 0.45
87 11 0.15
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (85 bp):
ATTGGGTACTCAAACTTTCAAAATGCATAAAAAAAGCCCTCAAAATTTTTCAAAAAAAGCAATTA
AGCCCCTAATTTTTTTTTCA
Found at i:56589571 original size:10 final size:10
Alignment explanation
Indices: 56589558--56589644 Score: 54
Period size: 10 Copynumber: 8.8 Consensus size: 10
56589548 ATAAAAGTTA
56589558 TAAAAAATAT
1 TAAAAAATAT
***
56589568 TAAATTTTAT
1 TAAAAAATAT
56589578 TAAAAAATAT
1 TAAAAAATAT
56589588 T-AAAAATAT
1 TAAAAAATAT
***
56589597 TAAATTTTAT
1 TAAAAAATAT
* *
56589607 TAAAAATTAG
1 TAAAAAATAT
*
56589617 AAAAAAAT-T
1 TAAAAAATAT
56589626 TATAAAAATCA-
1 TA-AAAAAT-AT
56589637 TAAAAAAT
1 TAAAAAAT
56589645 TATAAAATGT
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
9 10 0.18
10 45 0.79
11 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:56589582 original size:29 final size:29
Alignment explanation
Indices: 56589549--56589622 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
56589539 TAAAAATCAA
*
56589549 TAAAAGTTATAAAAAATATTAAATTTTAT
1 TAAAAATTATAAAAAATATTAAATTTTAT
* *
56589578 TAAAAAATATTAAAAATATTAAATTTTAT
1 TAAAAATTATAAAAAATATTAAATTTTAT
*
56589607 TAAAAATTAGAAAAAA
1 TAAAAATTATAAAAAA
56589623 ATTTATAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAAAATTATAAAAAATATTAAATTTTAT
Found at i:56589649 original size:10 final size:10
Alignment explanation
Indices: 56589550--56589651 Score: 50
Period size: 10 Copynumber: 10.3 Consensus size: 10
56589540 AAAAATCAAT
*
56589550 AAAAGTTATA
1 AAAAATTATA
*
56589560 AAAAA-TATT
1 AAAAATTATA
**
56589569 AAATTTTATTA
1 AAAAATTA-TA
*
56589580 AAAAA-TATT
1 AAAAATTATA
*
56589589 AAAAA-TATT
1 AAAAATTATA
** *
56589598 AAATTTTATT
1 AAAAATTATA
*
56589608 AAAAATTAGAA
1 AAAAATTA-TA
56589619 AAAAATT-TA
1 AAAAATTATA
*
56589628 TAAAAATCATA
1 -AAAAATTATA
56589639 AAAAATTATA
1 AAAAATTATA
56589649 AAA
1 AAA
56589652 TGTATCAAAG
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
9 20 0.29
10 36 0.52
11 13 0.19
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (10 bp):
AAAAATTATA
Found at i:56589685 original size:13 final size:13
Alignment explanation
Indices: 56589667--56589693 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56589657 CAAAGAGGCT
56589667 CTTTAACCATTAA
1 CTTTAACCATTAA
56589680 CTTTAACCATTAA
1 CTTTAACCATTAA
56589693 C
1 C
56589694 CGTTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (13 bp):
CTTTAACCATTAA
Found at i:56589955 original size:19 final size:19
Alignment explanation
Indices: 56589933--56589969 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56589923 CTATATTTCT
56589933 ATATATTTTATAATTTTTA
1 ATATATTTTATAATTTTTA
*
56589952 ATATTTTTTATAATTTTT
1 ATATATTTTATAATTTTT
56589970 TATTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATATTTTATAATTTTTA
Found at i:56594307 original size:16 final size:15
Alignment explanation
Indices: 56594288--56594335 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
56594278 TAATTATAAA
56594288 TTATTCTATTTATATT
1 TTATT-TATTTATATT
* *
56594304 TTATTTATATAAATAT
1 TTATTTATTTATAT-T
56594320 TTATTTATTTATATT
1 TTATTTATTTATATT
56594335 T
1 T
56594336 ATCTGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTATTTATATT
Found at i:56594310 original size:31 final size:27
Alignment explanation
Indices: 56594275--56594336 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 27
56594265 GTATTTCACA
*
56594275 ATTTAATTATAAATTATTCTATTTATATTTT
1 ATTTAA-TATAAA-TATT-TATTTAT-TTAT
56594306 ATTT-ATATAAATATTTATTTATTTAT
1 ATTTAATATAAATATTTATTTATTTAT
56594332 ATTTA
1 ATTTA
56594337 TCTGTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 7 0.24
27 7 0.24
28 4 0.14
29 6 0.21
30 1 0.03
31 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTAATATAAATATTTATTTATTTAT
Found at i:56594699 original size:84 final size:84
Alignment explanation
Indices: 56594567--56594804 Score: 345
Period size: 84 Copynumber: 2.8 Consensus size: 84
56594557 TATTAAAACT
56594567 AATAAAATCTGTTTTGGGATTTAGTTCC-GCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
1 AATAAAATCTGTTTTGGGATTTA-TTCCAGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
*
56594631 TCTAAATTAGAATTAAATTA
65 TCCAAATTAGAATTAAATTA
* * *
56594651 AATAAAATCTATTTTGGGATTTATTCCAGTCGTTTAACAAGATTTTATTTTATTTTATTTTGTTT
1 AATAAAATCTGTTTTGGGATTTATTCCAGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTTT
*
56594716 CCAAATTCGAATTAAATTA
66 CCAAATTAGAATTAAATTA
* ** * * *
56594735 AACAAAATCTGTTTCAGGATTTATTCCCA-CCGTTTAACAAGATTTTATTCGATATTGTTTTGTT
1 AATAAAATCTGTTTTGGGATTTATT-CCAGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTT
56594799 TCCAAA
65 TCCAAA
56594805 CAAAGACGTA
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
83 4 0.03
84 131 0.95
85 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (84 bp):
AATAAAATCTGTTTTGGGATTTATTCCAGCCGTTTAACAAGATTTTATTTGATTTTATTTTGTTT
CCAAATTAGAATTAAATTA
Found at i:56601586 original size:27 final size:27
Alignment explanation
Indices: 56601556--56601732 Score: 142
Period size: 27 Copynumber: 6.6 Consensus size: 27
56601546 ATATTGAGCC
* *
56601556 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
56601583 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
56601610 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
56601638 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
56601665 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * * *
56601692 C-AACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
56601718 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
56601733 GTACAATTTA
Statistics
Matches: 120, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
26 19 0.16
27 78 0.65
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:56601649 original size:55 final size:54
Alignment explanation
Indices: 56601556--56601732 Score: 178
Period size: 55 Copynumber: 3.3 Consensus size: 54
56601546 ATATTGAGCC
* * *
56601556 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* * ** *
56601610 CGCACACTTAGTGCTACATAGTCAGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCA-ACTCGCACACTTAGTGCCACATAATCAAAT
* ** * * * *
56601665 CGCACACTTAGTGC-ATCATATTCATTTC-AACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
*
56601718 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
56601733 GTACAATTTA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 32 0.31
54 24 0.24
55 46 0.45
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:56609575 original size:27 final size:27
Alignment explanation
Indices: 56609545--56609722 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
56609535 ATATTGAGCC
* * *
56609545 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
56609572 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
56609599 CGCACACTTAGTGCTACATAGTCAGATT
1 CGCACACTTAGTGCTACATAATCA-AAT
** ** *
56609627 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
56609654 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* * *
56609681 CGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
56609708 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
56609723 GTACAATTTA
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 101 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:56609684 original size:82 final size:81
Alignment explanation
Indices: 56609566--56609721 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
56609556 TGCTATATAA
* * * *
56609566 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGATTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCA-AATCGCA
56609631 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
56609648 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCA
*
56609712 CCCTTAGTGC
65 CACTTAGTGC
56609722 TGTACAATTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 17 0.27
82 47 0.73
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTGAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:56609705 original size:54 final size:54
Alignment explanation
Indices: 56609545--56609721 Score: 196
Period size: 54 Copynumber: 3.3 Consensus size: 54
56609535 ATATTGAGCC
* * * *
56609545 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAATTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
56609599 CGCACACTTAGTGC-TACATAGTCAGATTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCA-ATTCGCACACTTAGTGCCACATAGTCAAAT
* * * *
56609654 CGCACACTTAGTGCATCATATTCATTTCGCACACTGAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAATTCGCACACTTAGTGCCACATAGTCAAAT
*
56609708 CGCACCCTTAGTGC
1 CGCACACTTAGTGC
56609722 TGTACAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
52 1 0.01
54 56 0.54
55 45 0.44
56 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAATTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:56612835 original size:43 final size:42
Alignment explanation
Indices: 56612773--56612934 Score: 139
Period size: 43 Copynumber: 3.8 Consensus size: 42
56612763 CAAAAGCTCG
* * **
56612773 TACAATACCAACGTCCCAGACGTGGTCTTACATGTAATCAAA
1 TACAATGCCAATGTCCCAGACGTGGTCTTACACATAATCAAA
* *
56612815 TAACAATGCCATTGTCCCAGACAG-GGTCTTACACATAATCATA
1 T-ACAATGCCAATGTCCCAGAC-GTGGTCTTACACATAATCAAA
* * * * *
56612858 TACGATGCCAATGTCCCAAACATGGTCTTATACGTAAATCTCAAA
1 TACAATGCCAATGTCCCAGACGTGGTCTTACACAT-AA--TCAAA
* * *
56612903 T-CGAGGCCAACGTCCCAGACGTGGTCTTACAC
1 TACAATGCCAATGTCCCAGACGTGGTCTTACAC
56612935 GATGTCACAT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
42 28 0.29
43 36 0.38
44 27 0.28
45 5 0.05
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACGTGGTCTTACACATAATCAAA
Found at i:56617677 original size:10 final size:10
Alignment explanation
Indices: 56617664--56617688 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56617654 TCATTCTCTA
56617664 TCATTTCTTT
1 TCATTTCTTT
56617674 TCATTTCTTT
1 TCATTTCTTT
56617684 TCATT
1 TCATT
56617689 ATTATTCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (10 bp):
TCATTTCTTT
Found at i:56617979 original size:3 final size:3
Alignment explanation
Indices: 56617971--56618000 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
56617961 GCTTTGCTAT
56617971 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
56618001 CTACACTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:56639453 original size:27 final size:27
Alignment explanation
Indices: 56639423--56639764 Score: 332
Period size: 27 Copynumber: 12.7 Consensus size: 27
56639413 GTGAGGTCAA
56639423 TAAAATGACCGAAATACCCCCGTAGGG
1 TAAAATGACCGAAATACCCCCGTAGGG
** *
56639450 TAAAATGACCGAAATACCCCTATATGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* * *
56639477 TAAAATGACCGAAATACCCTCATATGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* * * *
56639504 TAAAATGATCGAAATACTCCTGTAGGA
1 TAAAATGACCGAAATACCCCCGTAGGG
* ** *
56639531 TAAAATGATCGAAATACCCCTATAAGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* * *
56639558 TAAAATGATCC-AAACACCCCCGTAAGA
1 TAAAATGA-CCGAAATACCCCCGTAGGG
** * *
56639585 TAAAATGATTGAAATACCACCGTAAGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* *
56639612 TAAAATGACCGAAA-ACCCTCTTAGGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* *
56639638 TAAAATGATCGAAATAACCCCGTAGGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* *
56639665 TAAAATGATCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* * *
56639692 TAAAATAACCAAAATA-CCCCAT-GGG
1 TAAAATGACCGAAATACCCCCGTAGGG
* *
56639717 TTAAAATGACTGAAATACTCCCGTAGGG
1 -TAAAATGACCGAAATACCCCCGTAGGG
* *
56639745 TGAAATGATCGAAATACCCC
1 TAAAATGACCGAAATACCCC
56639765 TGTCGAAACC
Statistics
Matches: 259, Mismatches: 50, Indels: 12
0.81 0.16 0.04
Matches are distributed among these distances:
25 3 0.01
26 40 0.15
27 212 0.82
28 4 0.02
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCGTAGGG
Found at i:56639763 original size:80 final size:80
Alignment explanation
Indices: 56639423--56639764 Score: 397
Period size: 80 Copynumber: 4.2 Consensus size: 80
56639413 GTGAGGTCAA
* * *
56639423 TAAAATGACCGAAATACCCCCGTAGGGTAAAATGACCGAAATACCCCTATATGGTAAAATGACCG
1 TAAAATGATCGAAATACCCCCGTAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCG
* *
56639488 AAATACCCTCATATGG
66 AAATACCC-CGTAGGG
* * * * * *
56639504 TAAAATGATCGAAATACTCCTGTAGGATAAAATGATCGAAATACCCCTATAAGGTAAAATGATCC
1 TAAAATGATCGAAATACCCCCGTAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCG
* * *
56639569 AAACACCCCCGTAAGA
66 AAATA-CCCCGTAGGG
* * *
56639585 TAAAATGATTGAAATACCACCGTAAGGTAAAATGACCGAAA-ACCCTCT-TAGGGTAAAATGATC
1 TAAAATGATCGAAATACCCCCGTAGGGTAAAATGACCGAAATACCC-CTATAGGGTAAAATGATC
56639648 GAAATAACCCCGTAGGG
65 GAAAT-ACCCCGTAGGG
* * *
56639665 TAAAATGATCGAAATACCCCCATAGGGTAAAATAACCAAAATACCCC-AT-GGGTTAAAATGA-C
1 TAAAATGATCGAAATACCCCCGTAGGGTAAAATGACCGAAATACCCCTATAGGG-TAAAATGATC
56639727 TGAAATACTCCCGTAGGG
65 -GAAATAC-CCCGTAGGG
*
56639745 TGAAATGATCGAAATACCCC
1 TAAAATGATCGAAATACCCC
56639765 TGTCGAAACC
Statistics
Matches: 222, Mismatches: 31, Indels: 17
0.82 0.11 0.06
Matches are distributed among these distances:
79 6 0.03
80 107 0.48
81 106 0.48
82 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (80 bp):
TAAAATGATCGAAATACCCCCGTAGGGTAAAATGACCGAAATACCCCTATAGGGTAAAATGATCG
AAATACCCCGTAGGG
Found at i:56643009 original size:50 final size:50
Alignment explanation
Indices: 56642926--56643799 Score: 696
Period size: 50 Copynumber: 17.5 Consensus size: 50
56642916 GGGGAAGCAT
* * * * * **
56642926 GATTCGCTATTGTGGCTTTAATCTATTCCACTGCACCGCCTGGG-GAGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAG-GTAA
* ** * * * * *
56642976 AATTCGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * * ** *
56643026 GATTCACCGTTATGGCTTTAATCTGTTCCACTGCACCGCCTGAGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * * *
56643076 GACTCACTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * * ***
56643126 GATTCACCGTTATGGCTTTAATCTGTTCCACTGCACCACCTGGGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
** ** * * * * *
56643176 GATTCGTTACTGTAGGTTTAATCTTTTTAACTGCAATACCAGGGAGGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * *
56643226 GATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACA-ACCTGGGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCA-ATGCCTGGGAGGTAA
* * * * *
56643276 GATTCACTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * **
56643326 GATTCACCGTTGT-GACTTTAATCTGTTCCACTGCACCGCCTGGGAGGTAA
1 GATTCACTGTTGTAG-CTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * *
56643376 GATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * *
56643426 GATTCACCGTTGTGGCTTTAATCTATTCCACTGCACTGCCTGGGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * * *
56643476 GATTCGCTGCTGTAGCTTTAATCTTTTTAACTACAATGTCAGGGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * *
56643526 GATTCACAGTTGTGGCTCTAATCTGTTCCACTGC-ATCGCCTGGGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAAT-GCCTGGGAGGTAA
* * * * * * *
56643576 GATTCCCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGAAGGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * *
56643626 GATTCACCGTTGT-GACTTTAATCTGTTCCACTGCACTGCCTGGGAGGTAA
1 GATTCACTGTTGTAG-CTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * * *
56643676 GATTCACTGCTGTAGCTTTAATCTTTTTAACTACAATGTCAGGGAGGCAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* * * * * ** *
56643726 GATTTACCGTTGTGGCTTTAATCTATTCCACTGCACCGCTTGGGAGGTAA
1 GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
* *
56643776 GATTCGCTATTGTAGCTTTAATCT
1 GATTCACTGTTGTAGCTTTAATCT
56643800 GCAATGTCAA
Statistics
Matches: 619, Mismatches: 196, Indels: 18
0.74 0.24 0.02
Matches are distributed among these distances:
49 5 0.01
50 609 0.98
51 5 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
GATTCACTGTTGTAGCTTTAATCTTTTCAACTGCAATGCCTGGGAGGTAA
Found at i:56643044 original size:100 final size:100
Alignment explanation
Indices: 56642891--56643799 Score: 1354
Period size: 100 Copynumber: 9.1 Consensus size: 100
56642881 CGCCATTGTG
* ** * * * ** *
56642891 GCTTTAATCTTTTT-ACTACAATGTTGGGGAAGCATGATTCGCTATTGTGGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* ** *
56642955 ACTGCACCGCCTGGG-GAGTAAAATTCGTTGTTGTA
66 ACTGCACCGCCTGGGAG-GTAAGATTCACTGCTGTA
* * *
56642990 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTATGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* *
56643055 ACTGCACCGCCTGAGAGGTAAGACTCACTGCTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
*
56643090 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTATGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* ** *
56643155 ACTGCACCACCTGGGAGGTAAGATTCGTTACTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
* **
56643190 GGTTTAATCTTTTTAACTGCAATACCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
**
56643255 ACTGCACAACCTGGGAGGTAAGATTCACTGCTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
*
56643290 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGACTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
*
56643355 ACTGCACCGCCTGGGAGGTAAGATTCACTGTTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
*
56643390 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* *
56643455 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
* * * *
56643490 GCTTTAATCTTTTTAACTACAATGTCAGGGAGGTAAGATTCACAGTTGTGGCTCTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* *
56643555 ACTGCATCGCCTGGGAGGTAAGATTCCCTGCTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
* *
56643590 GCTTTAATCTTTTTAACTGCAATGTCAGGAAGGCAAGATTCACCGTTGTGACTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
*
56643655 ACTGCACTGCCTGGGAGGTAAGATTCACTGCTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
* * *
56643690 GCTTTAATCTTTTTAACTACAATGTCAGGGAGGCAAGATTTACCGTTGTGGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * **
56643755 ACTGCACCGCTTGGGAGGTAAGATTCGCTATTGTA
66 ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
56643790 GCTTTAATCT
1 GCTTTAATCT
56643800 GCAATGTCAA
Statistics
Matches: 739, Mismatches: 69, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
99 14 0.02
100 724 0.98
101 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
ACTGCACCGCCTGGGAGGTAAGATTCACTGCTGTA
Found at i:56646036 original size:9 final size:9
Alignment explanation
Indices: 56646022--56646049 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
56646012 TCCATCTAGA
56646022 TTTTTTTCT
1 TTTTTTTCT
56646031 TTTTTTTCT
1 TTTTTTTCT
56646040 TTTTTTTCT
1 TTTTTTTCT
56646049 T
1 T
56646050 CTTTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:56646058 original size:13 final size:13
Alignment explanation
Indices: 56646026--56646061 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
56646016 TCTAGATTTT
*
56646026 TTTCTTTTTTTTC
1 TTTCTTTTTCTTC
56646039 TTT-TTTTTCTTC
1 TTTCTTTTTCTTC
56646051 TTTCTTTTTCT
1 TTTCTTTTTCT
56646062 CTCATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTCTTC
Found at i:56646103 original size:16 final size:15
Alignment explanation
Indices: 56646066--56646100 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56646056 TTTTCTCTCA
56646066 TTTTTT-ATTTTAAT
1 TTTTTTGATTTTAAT
*
56646080 TTTTTTGATTTTGAT
1 TTTTTTGATTTTAAT
56646095 TTTTTT
1 TTTTTT
56646101 TGAAAGGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTTTGATTTTAAT
Found at i:56652444 original size:27 final size:27
Alignment explanation
Indices: 56652348--56652441 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
56652338 TTACAACTCT
*
56652348 AATAGGGTAAAATAACCTAAATAACCCC
1 AATAGGGTAAAATAACCAAAAT-ACCCC
*
56652376 -ATAAGGTAAAATAACCAAAATACCCC
1 AATAGGGTAAAATAACCAAAATACCCC
** * *
56652402 TGTAGGGTAAAATGACCGAAATACCCC
1 AATAGGGTAAAATAACCAAAATACCCC
56652429 AATAGGGTAAAAT
1 AATAGGGTAAAAT
56652442 GACTGTTATA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.09
27 52 0.91
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (27 bp):
AATAGGGTAAAATAACCAAAATACCCC
Found at i:56652647 original size:26 final size:26
Alignment explanation
Indices: 56652618--56652672 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
56652608 TCTATCACAT
*
56652618 ATACTATTACTGCCAGCTTTGCTGCG
1 ATACTATTACTGCCAGCTTTGCTGAG
*
56652644 ATACTATTACTGGCAGCTTTGCTGAG
1 ATACTATTACTGCCAGCTTTGCTGAG
56652670 ATA
1 ATA
56652673 TTGGTGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGCCAGCTTTGCTGAG
Found at i:56658824 original size:6 final size:6
Alignment explanation
Indices: 56658813--56658842 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
56658803 TCCTCCCTCA
56658813 CTTTTT CTTTTT CTTTTT CTTCTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTT-TTT CTTTT
56658843 CGGTTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:56659794 original size:27 final size:27
Alignment explanation
Indices: 56659765--56660123 Score: 429
Period size: 27 Copynumber: 13.3 Consensus size: 27
56659755 GTGAGGTCAA
* *
56659765 TAAAATGACCAAAATACCCTCATAGGA
1 TAAAATGACCGAAATACCCTCATAGGG
*
56659792 TAAAATGACCGAAATACACC-CATAGGA
1 TAAAATGACCGAAATAC-CCTCATAGGG
* * * *
56659819 TAAAACGATCGAAATACCCCCGTAGGG
1 TAAAATGACCGAAATACCCTCATAGGG
* *
56659846 TAAAATAATCGAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCTCATAGGG
* *
56659873 TAAAATGATCAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCTCATAGGG
56659900 TAAAATGACCGAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCTCATAGGG
*
56659927 TAAAATGATCGAAATACCC-CTATAGGG
1 TAAAATGACCGAAATACCCTC-ATAGGG
* *
56659954 TAAAATGATCGAAATACCC-CTGTAGGG
1 TAAAATGACCGAAATACCCTC-ATAGGG
*
56659981 TAAAATGACCGAAATACTCC-CGTAGGG
1 TAAAATGACCGAAATAC-CCTCATAGGG
* *
56660008 TAAAATAACCGAAATACCCTCATAAGG
1 TAAAATGACCGAAATACCCTCATAGGG
* * *
56660035 TAAAAAGACCAAAATACCCTCGTAGGG
1 TAAAATGACCGAAATACCCTCATAGGG
* *
56660062 TAAAATAATCGAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCTCATAGGG
* * *
56660089 TAAAATGACTGAAATACCCCCATAAGG
1 TAAAATGACCGAAATACCCTCATAGGG
56660116 TAAAATGA
1 TAAAATGA
56660124 TTGTTATACC
Statistics
Matches: 293, Mismatches: 34, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.02
27 283 0.97
28 5 0.02
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCATAGGG
Found at i:56663571 original size:23 final size:23
Alignment explanation
Indices: 56663545--56663588 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
56663535 ATGTTAATTT
56663545 AATTAGTAAAAATATA-TATTTTG
1 AATT-GTAAAAATATATTATTTTG
* *
56663568 AATTGTAGAATTATATTATTT
1 AATTGTAAAAATATATTATTT
56663589 AAAGAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
AATTGTAAAAATATATTATTTTG
Found at i:56668141 original size:22 final size:21
Alignment explanation
Indices: 56668109--56668153 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
56668099 ATTTGAAATG
56668109 TTTTATAATATTACTTTTTAAAA
1 TTTTATAATATT--TTTTTAAAA
56668132 TTTTA-AATATTTTTTTAAAA
1 TTTTATAATATTTTTTTAAAA
56668152 TT
1 TT
56668154 ATTTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.50
22 6 0.27
23 5 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATAATATTTTTTTAAAA
Found at i:56668158 original size:14 final size:14
Alignment explanation
Indices: 56668139--56668167 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56668129 AAATTTTAAA
56668139 TATTTTTTTAAAAT
1 TATTTTTTTAAAAT
56668153 TATTTTTTTAAAAT
1 TATTTTTTTAAAAT
56668167 T
1 T
56668168 TTAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTTTTTAAAAT
Found at i:56668184 original size:22 final size:22
Alignment explanation
Indices: 56668144--56668185 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56668134 TTAAATATTT
*
56668144 TTTTAAAATTATTTTTTTAAAA
1 TTTTAAAATTATATTTTTAAAA
56668166 TTTT-AAATATATATTTTTAA
1 TTTTAAAAT-TATATTTTTAA
56668186 TAAATAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAATTATATTTTTAAAA
Found at i:56668391 original size:13 final size:13
Alignment explanation
Indices: 56668375--56668436 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
56668365 TAAATGCATA
*
56668375 TTTTAAATATTTT
1 TTTTAAATATTAT
*
56668388 TTTTAAATATAATT
1 TTTTAAATATTA-T
56668402 TTTATAAATTATTAAT
1 TTT-TAAA-TATT-AT
56668418 TTTTAAA-ATTAT
1 TTTTAAATATTAT
56668430 TTTTAAA
1 TTTTAAA
56668437 GATATTCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
12 9 0.21
13 13 0.31
14 4 0.10
15 8 0.19
16 7 0.17
17 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:56668431 original size:29 final size:30
Alignment explanation
Indices: 56668387--56668450 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
56668377 TTAAATATTT
56668387 TTTTTAAATATAATTTTTATAA-ATTATT-AA
1 TTTTTAAATATAATTTTTA-AAGA-TATTCAA
*
56668417 TTTTTAAA-ATTATTTTTAAAGATATTCAA
1 TTTTTAAATATAATTTTTAAAGATATTCAA
56668446 TTTTT
1 TTTTT
56668451 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 17 0.55
30 8 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTTTAAATATAATTTTTAAAGATATTCAA
Found at i:56674465 original size:20 final size:19
Alignment explanation
Indices: 56674442--56674493 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
56674432 TTTTTTCTAA
*
56674442 TTAATTTAAATTTCACTTTT
1 TTAATTTAAATATCA-TTTT
* *
56674462 TTAAATAAAATATCATTTT
1 TTAATTTAAATATCATTTT
*
56674481 TAAATTTTAAATA
1 TTAA-TTTAAATA
56674494 GAATTTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATTTAAATATCATTTT
Found at i:56674591 original size:41 final size:40
Alignment explanation
Indices: 56674534--56674614 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
56674524 AAATAATTTA
*
56674534 AAAATCATAATTTAAAAAATTATAAATCAAATTAAAAAATT
1 AAAATCATAATTTAAAAAATTATAAAACAAA-TAAAAAATT
* *
56674575 AAAAT-ATACATTTAAAATATTATAAAACAAATAATAAATT
1 AAAATCATA-ATTTAAAAAATTATAAAACAAATAAAAAATT
56674615 TGAAAAGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 11 0.31
41 25 0.69
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (40 bp):
AAAATCATAATTTAAAAAATTATAAAACAAATAAAAAATT
Found at i:56674689 original size:22 final size:21
Alignment explanation
Indices: 56674655--56674728 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
56674645 ATTTTATTTA
56674655 TTAAAAAATATATTTAAAATT
1 TTAAAAAATATATTTAAAATT
*
56674676 TTAAAAAATAATATTATAAAACAT
1 TTAAAAAAT-ATATT-TAAAA-TT
* * *
56674700 TTCAAATATACATTTAAAATT
1 TTAAAAAATATATTTAAAATT
*
56674721 TTATAAAA
1 TTAAAAAA
56674729 CAAATAATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 15 0.36
22 10 0.24
23 9 0.21
24 8 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAAAAATATATTTAAAATT
Found at i:56674761 original size:12 final size:12
Alignment explanation
Indices: 56674723--56674768 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
56674713 TTAAAATTTT
56674723 ATAAAACAAATA
1 ATAAAACAAATA
56674735 AT-AAACAAATAA
1 ATAAAACAAAT-A
*
56674747 ATAAAATAAATA
1 ATAAAACAAATA
*
56674759 ATAAATCAAA
1 ATAAAACAAA
56674769 CGTGTATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 8 0.28
12 14 0.48
13 7 0.24
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (12 bp):
ATAAAACAAATA
Found at i:56691216 original size:11 final size:10
Alignment explanation
Indices: 56691203--56691302 Score: 75
Period size: 10 Copynumber: 9.9 Consensus size: 10
56691193 TAAAAAAAGT
56691203 ATTTT-AAAA
1 ATTTTAAAAA
56691212 ATATTT-AAAA
1 AT-TTTAAAAA
56691222 ATTTTAAAAA
1 ATTTTAAAAA
*
56691232 A-TTAAAAAA
1 ATTTTAAAAA
56691241 GTATTTTAAAAA
1 --ATTTTAAAAA
*
56691253 ATTTTTAAAA
1 ATTTTAAAAA
56691263 A--TTAAAAA
1 ATTTTAAAAA
*
56691271 ATTTAAAAAA
1 ATTTTAAAAA
*
56691281 GTATTTTAAAAGT
1 --ATTTTAAAA-A
56691294 ATTTTAAAA
1 ATTTTAAAA
56691303 TTAAAAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.09
9 12 0.16
10 30 0.41
11 10 0.14
12 15 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:56691239 original size:41 final size:40
Alignment explanation
Indices: 56691187--56691319 Score: 180
Period size: 40 Copynumber: 3.3 Consensus size: 40
56691177 AAATTAAAAC
56691187 AAAAATTAAAAAAAGTATTTTAAAAATATTTAAAAATTTTA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTAAAAA-TTTA
*
56691228 AAAAATT-AAAAAAGTATTTTAAAAAATTTTTAAAAA-TTA
1 AAAAATTAAAAAAAGTATTTT-AAAAATATTTAAAAATTTA
* * * *
56691267 AAAAATTTAAAAAAGTATTTTAAAAGTATTTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTAAAAATTTA
*
56691307 AAAAAATAAAAAA
1 AAAAATTAAAAAA
56691320 TAATAAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
39 22 0.27
40 39 0.48
41 21 0.26
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTAAAAATTTA
Found at i:56691272 original size:8 final size:9
Alignment explanation
Indices: 56691205--56691280 Score: 73
Period size: 9 Copynumber: 8.0 Consensus size: 9
56691195 AAAAAAGTAT
56691205 TTTAAAAATA
1 TTTAAAAA-A
*
56691215 TTTAAAAAT
1 TTTAAAAAA
56691224 TTTAAAAAA
1 TTTAAAAAA
*
56691233 TTAAAAAAGTA
1 TTTAAAAA--A
56691244 TTTTAAAAAA
1 -TTTAAAAAA
*
56691254 TTTTTAAAAA
1 -TTTAAAAAA
56691264 -TTAAAAAA
1 TTTAAAAAA
56691272 TTTAAAAAA
1 TTTAAAAAA
56691281 GTATTTTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
8 7 0.12
9 23 0.41
10 18 0.32
11 1 0.02
12 7 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:56695866 original size:21 final size:22
Alignment explanation
Indices: 56695829--56695881 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
56695819 TCGGCCCATT
**
56695829 TTTTAATAAA-TACAAAAATTTA
1 TTTTAA-AAATTACAAAAAAGTA
56695851 TTTTAAAAATTA-AAAAAAGTA
1 TTTTAAAAATTACAAAAAAGTA
56695872 TTTTAAAAAT
1 TTTTAAAAAT
56695882 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTTAAAAATTACAAAAAAGTA
Found at i:56718732 original size:42 final size:42
Alignment explanation
Indices: 56718676--56718798 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
56718666 AAGCTCATAG
* * * *
56718676 GAGCTGAACGGAAACCCATAAGGGTTAATCTGAAGCTCAGAAA
1 GAGCTAAACTGAAACCAATAAGGGTTAAACTGAA-CTCAGAAA
* * *
56718719 -AGCTAAACTGAAACCTATTAGGGTTAAAATGACACTC-GAAA
1 GAGCTAAACTGAAACCAATAAGGGTTAAACTGA-ACTCAGAAA
* *
56718760 GAGCTAAACTTAAACCAAGAAGGGTTAAACTGAAACTCA
1 GAGCTAAACTGAAACCAATAAGGGTTAAACTG-AACTCA
56718799 TATGAGTTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
41 4 0.06
42 59 0.91
43 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (42 bp):
GAGCTAAACTGAAACCAATAAGGGTTAAACTGAACTCAGAAA
Found at i:56720920 original size:16 final size:15
Alignment explanation
Indices: 56720895--56720927 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
56720885 TTGGGTTGAG
56720895 AAAATAATTTAATTA
1 AAAATAATTTAATTA
56720910 AAAATTAATTTAATTA
1 AAAA-TAATTTAATTA
56720926 AA
1 AA
56720928 CTAAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATAATTTAATTA
Found at i:56721152 original size:18 final size:17
Alignment explanation
Indices: 56721111--56721153 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
56721101 CAAGTGGAAT
56721111 TTTTATTTTTTAATAAA
1 TTTTATTTTTTAATAAA
* *
56721128 TTATATTTTTTAATTATA
1 TTTTATTTTTTAA-TAAA
56721146 TTTTATTT
1 TTTTATTT
56721154 GAATAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTATTTTTTAATAAA
Found at i:56723895 original size:26 final size:27
Alignment explanation
Indices: 56723857--56723929 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
56723847 AATATCGCAA
* *
56723857 CAAAGCTTCCAGTAATAGTATTGC-AG
1 CAAAGCTGCCAGTAATAGTATTCCAAG
*
56723883 CAAAGCTGGCAGT-ATCAGTA-TCCAAG
1 CAAAGCTGCCAGTAAT-AGTATTCCAAG
* *
56723909 CAAAGCTGTCAGTAACAGTAT
1 CAAAGCTGCCAGTAATAGTAT
56723930 ACTTCCTCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 4 0.11
26 33 0.87
27 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (27 bp):
CAAAGCTGCCAGTAATAGTATTCCAAG
Found at i:56731708 original size:26 final size:26
Alignment explanation
Indices: 56731636--56731710 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
56731626 ACCAACATCG
*
56731636 CAGCAAAGCTA-CAGTAATAGTATCA
1 CAGCAAAGCTACCAGTAACAGTATCA
* * *
56731661 CAGTAAAGCTGCCAGTATCAGTATCA
1 CAGCAAAGCTACCAGTAACAGTATCA
* *
56731687 CAGCAAAACTACCAATAACAGTAT
1 CAGCAAAGCTACCAGTAACAGTAT
56731711 ACTTCCTCCA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 9 0.22
26 31 0.77
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (26 bp):
CAGCAAAGCTACCAGTAACAGTATCA
Found at i:56744525 original size:9 final size:9
Alignment explanation
Indices: 56744508--56744760 Score: 157
Period size: 9 Copynumber: 29.9 Consensus size: 9
56744498 TAAGTATAAT
*
56744508 TAAGCTATG
1 TAAGTTATG
56744517 TAAGTTATG
1 TAAGTTATG
*
56744526 TAAGTTATA
1 TAAGTTATG
*
56744535 TAAGTTGTG
1 TAAGTTATG
*
56744544 T-A-TAATG
1 TAAGTTATG
56744551 TAAGTTATG
1 TAAGTTATG
*
56744560 AAAGTTATG
1 TAAGTTATG
56744569 T-A-TTATG
1 TAAGTTATG
56744576 TAAGTTATG
1 TAAGTTATG
56744585 T-A-TTATG
1 TAAGTTATG
*
56744592 TAAGTTATT
1 TAAGTTATG
*
56744601 TAAGTTGTG
1 TAAGTTATG
56744610 T-A-TTATG
1 TAAGTTATG
*
56744617 TAAGTCATG
1 TAAGTTATG
* *
56744626 TAGGCTATG
1 TAAGTTATG
56744635 T-A-TTATG
1 TAAGTTATG
56744642 TAAGTTATG
1 TAAGTTATG
* *
56744651 AAAGTTTCATA
1 TAAG-TT-ATG
*
56744662 TAAGTGAT-
1 TAAGTTATG
*
56744670 TAA-ATATG
1 TAAGTTATG
56744678 T-A-TTATG
1 TAAGTTATG
* *
56744685 TAATTTATT
1 TAAGTTATG
56744694 TAAGTTATG
1 TAAGTTATG
*
56744703 TAAGTTGTG
1 TAAGTTATG
56744712 T-A-TTATG
1 TAAGTTATG
*
56744719 CT-AGTCATG
1 -TAAGTTATG
* *
56744728 TAGGCTATG
1 TAAGTTATG
56744737 T-A-TTATG
1 TAAGTTATG
56744744 TAAGTTATG
1 TAAGTTATG
*
56744753 AAAGTTAT
1 TAAGTTAT
56744761 ATATAAGTTA
Statistics
Matches: 186, Mismatches: 38, Indels: 40
0.70 0.14 0.15
Matches are distributed among these distances:
7 43 0.23
8 19 0.10
9 116 0.62
10 3 0.02
11 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:56744574 original size:16 final size:16
Alignment explanation
Indices: 56744555--56744650 Score: 88
Period size: 16 Copynumber: 5.9 Consensus size: 16
56744545 ATAATGTAAG
*
56744555 TTATGAAAGTTATGTA
1 TTATGTAAGTTATGTA
56744571 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
56744587 TTATGTAAGTTATTTAA
1 TTATGTAAGTTATGT-A
*
56744604 GTTGTGT-A-TTATGTAA
1 -TTATGTAAGTTATGT-A
* * *
56744620 GTCATGTAGGCTATGTA
1 -TTATGTAAGTTATGTA
56744637 TTATGTAAGTTATG
1 TTATGTAAGTTATG
56744651 AAAGTTTCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
16 52 0.80
17 3 0.05
18 10 0.15
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:56744599 original size:25 final size:25
Alignment explanation
Indices: 56744513--56744704 Score: 136
Period size: 25 Copynumber: 8.0 Consensus size: 25
56744503 ATAATTAAGC
*
56744513 TATGTAAGTTATGTAAGTTATATAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
* * *
56744540 TGTGT-A-TAATGTAAGTTATGAAAGT
1 TATGTAAGTTATGTAAGTTATG-TA-T
56744565 TATGT-A-TTATGTAAGTTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* *
56744588 TATGTAAGTTATTTAAGTTGTGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* * *
56744613 TATGTAAGTCATGTAGGCTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* *
56744638 TATGTAAGTTATGAAAGTT-T-CA-
1 TATGTAAGTTATGTAAGTTATGTAT
* *
56744660 TA--TAAGTGAT-TAA-ATATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* *
56744681 TATGTAATTTATTTAAGTTATGTA
1 TATGTAAGTTATGTAAGTTATGTA
56744705 AGTTGTGTAT
Statistics
Matches: 129, Mismatches: 26, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 8 0.06
21 2 0.02
22 2 0.02
23 13 0.10
24 6 0.05
25 89 0.69
26 1 0.01
27 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.46
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTATGTAT
Found at i:56744635 original size:66 final size:66
Alignment explanation
Indices: 56744521--56744650 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
56744511 GCTATGTAAG
* *
56744521 TTATGTAAGTTATATAAGTTGTGTATAATGTAAGTTATGAAAGTTATGTATTATGTAAGTTATGT
1 TTATGTAAGTTATATAAGTTGTGTATAATGTAAGTCATGAAAGCTATGTATTATGTAAGTTATGT
56744586 A
66 A
* * * *
56744587 TTATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGTAGGCTATGTATTATGTAAGTTATG
1 TTATGTAAGTTATATAAGTTGTGTATAATGTAAGTCATGAAAGCTATGTATTATGTAAGTTATG
56744651 AAAGTTTCAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (66 bp):
TTATGTAAGTTATATAAGTTGTGTATAATGTAAGTCATGAAAGCTATGTATTATGTAAGTTATGT
A
Found at i:56744646 original size:41 final size:41
Alignment explanation
Indices: 56744555--56744752 Score: 64
Period size: 41 Copynumber: 5.0 Consensus size: 41
56744545 ATAATGTAAG
* * *
56744555 TTATGAAAGTTATGTATTATGTAAGTTATGT-A-TTATGTAA
1 TTATGTAAGTCATGTACTATGTAAGTTATGTAAGTTATGT-A
* ** * * * *
56744595 GTTATTTAAGTTGTGTATTATGTAAGTCATGTAGGCTATGTA
1 -TTATGTAAGTCATGTACTATGTAAGTTATGTAAGTTATGTA
* * * * * *
56744637 TTATGTAAGTTATGAAAGTTTCATATAAGTGAT-TAA-ATATGTA
1 TTATGTAAGTCATG-TA--CT-ATGTAAGTTATGTAAGTTATGTA
*
56744680 TTATGTAA-T--T-TA-T-T-TAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTCATGTACTATGTAAGTTATGTAAGTTATGTA
56744714 TTATGCT-AGTCATGTAGGCTATGT-A-TTATGTAAGTTATG
1 TTATG-TAAGTCATGTA--CTATGTAAGTTATGTAAGTTATG
56744753 AAAGTTATAT
Statistics
Matches: 121, Mismatches: 18, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
32 7 0.06
33 4 0.03
34 11 0.09
35 3 0.02
37 1 0.01
38 3 0.02
40 1 0.01
41 53 0.44
42 5 0.04
43 20 0.17
44 4 0.03
45 9 0.07
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (41 bp):
TTATGTAAGTCATGTACTATGTAAGTTATGTAAGTTATGTA
Found at i:56744714 original size:102 final size:100
Alignment explanation
Indices: 56744580--56744775 Score: 315
Period size: 102 Copynumber: 1.9 Consensus size: 100
56744570 ATTATGTAAG
*
56744580 TTATGTATTATGTAAGTTATTTAAGTTGTGTATTATG-TAAGTCATGTAGGCTATGTATTATGTA
1 TTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGCT-AGTCATGTAGGCTATGTATTATGTA
56744644 AGTTATGAAAGTT-TCATATAAGTGATTAAATATGTA
65 AGTTATGAAAGTTAT-ATATAAGTGATTAAATATGTA
*
56744680 TTATGTAATTTATTTAAGTTATGTAAGTTGTGTATTATGCTAGTCATGTAGGCTATGTATTATGT
1 TTATGT-A-TTATGTAAGTTATGTAAGTTGTGTATTATGCTAGTCATGTAGGCTATGTATTATGT
*
56744745 AAGTTATGAAAGTTATATATAAGTTATTAAA
64 AAGTTATGAAAGTTATATATAAGTGATTAAA
56744776 AATATATATA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
100 6 0.07
101 1 0.01
102 80 0.90
103 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (100 bp):
TTATGTATTATGTAAGTTATGTAAGTTGTGTATTATGCTAGTCATGTAGGCTATGTATTATGTAA
GTTATGAAAGTTATATATAAGTGATTAAATATGTA
Found at i:56744769 original size:20 final size:20
Alignment explanation
Indices: 56744744--56744786 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
56744734 ATGTATTATG
**
56744744 TAAGTTATGAAAGTTATATA
1 TAAGTTATGAAAAATATATA
*
56744764 TAAGTTATTAAAAATATATA
1 TAAGTTATGAAAAATATATA
56744784 TAA
1 TAA
56744787 ATTTTTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
TAAGTTATGAAAAATATATA
Found at i:56744794 original size:20 final size:19
Alignment explanation
Indices: 56744758--56744803 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
56744748 TTATGAAAGT
*
56744758 TATATATAAGTTATTAAAAA
1 TATATATAAATTATT-AAAA
* *
56744778 TATATATAAATTTTTAATA
1 TATATATAAATTATTAAAA
56744797 TATATAT
1 TATATAT
56744804 TAAAAATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATATATAAATTATTAAAA
Found at i:56744847 original size:23 final size:22
Alignment explanation
Indices: 56744819--56744863 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
56744809 ATGTATATAA
*
56744819 ATATTAATAAGTTATTAAGTTAT
1 ATATTAAAAAGTTA-TAAGTTAT
*
56744842 ATATTAAAAATTTATAAGTTAT
1 ATATTAAAAAGTTATAAGTTAT
56744864 GTAAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
ATATTAAAAAGTTATAAGTTAT
Found at i:56744859 original size:30 final size:30
Alignment explanation
Indices: 56744812--56744872 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
56744802 ATTAAAAATG
* *
56744812 TATATAAATATTAATAAGTTAT-TAAGTTA
1 TATATAAAAATTAATAAGTTATGTAAATTA
*
56744841 TATATTAAAAATTTATAAGTTATGTAAATTA
1 TATA-TAAAAATTAATAAGTTATGTAAATTA
56744872 T
1 T
56744873 GAACTCATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.15
30 16 0.59
31 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (30 bp):
TATATAAAAATTAATAAGTTATGTAAATTA
Found at i:56746223 original size:22 final size:22
Alignment explanation
Indices: 56746195--56746242 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
56746185 TAGAAGGACA
*
56746195 AAAAAAGGTTCAAAGTTGTCCT
1 AAAAAAGGTTCAAAGTTGCCCT
56746217 AAAAAAGGTTCAAAGTTGCCCT
1 AAAAAAGGTTCAAAGTTGCCCT
56746239 AAAA
1 AAAA
56746243 TAAATTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAAAAGGTTCAAAGTTGCCCT
Found at i:56747079 original size:105 final size:102
Alignment explanation
Indices: 56746938--56747186 Score: 295
Period size: 105 Copynumber: 2.4 Consensus size: 102
56746928 CGCAAAATAT
* * * *
56746938 TATTTCATTTTGAATAAAATGACGTCGTTTTGCTATGCACAA-ACTTTTTTTATTTTGTTTTTTA
1 TATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCA-AATAATTTTTTTA--TT-TTTTATA
* * *
56747002 AATTGATTTATTTTTTGCGGCGTTTTTATGGAAAATGCCGC-
62 AATTGATTTATATTTTGCGGCGTTTTTATAG-AAACGCCGCA
* *
56747043 TATTTCATTTTGAACAAAATGACGCCGTTTTCCTATGCAAATAATTTTTTTATTTTTTATAATTT
1 TATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCAAATAATTTTTTTATTTTTTATAAATT
*
56747108 TATTTATATTTTGCGGCGTTTTTATAGAAACGCCGCAAAATA
66 GATTTATATTTTGCGGCGTTTTTATAGAAACGCCGC-----A
56747150 TTATTTCATTTTGAACAAAATGACGCCGTTTTGCTAT
1 -TATTTCATTTTGAACAAAATGACGCCGTTTTGCTAT
56747187 TTTGTTTCTA
Statistics
Matches: 125, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
101 8 0.06
102 33 0.26
103 2 0.02
104 2 0.02
105 45 0.36
108 35 0.28
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (102 bp):
TATTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCAAATAATTTTTTTATTTTTTATAAATT
GATTTATATTTTGCGGCGTTTTTATAGAAACGCCGCA
Found at i:56747104 original size:18 final size:20
Alignment explanation
Indices: 56747083--56747119 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
56747073 TCCTATGCAA
56747083 ATAATTTT-TTTAT-TTTTT
1 ATAATTTTATTTATATTTTT
56747101 ATAATTTTATTTATATTTT
1 ATAATTTTATTTATATTTT
56747120 GCGGCGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
ATAATTTTATTTATATTTTT
Found at i:56747119 original size:19 final size:18
Alignment explanation
Indices: 56747083--56747119 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
56747073 TCCTATGCAA
*
56747083 ATAATTTTTTTATTTTTT
1 ATAATTTTTTTATATTTT
56747101 ATAATTTTATTTATATTTT
1 ATAATTTT-TTTATATTTT
56747120 GCGGCGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATAATTTTTTTATATTTT
Found at i:56747637 original size:22 final size:22
Alignment explanation
Indices: 56747612--56747654 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
56747602 ACCTTAAATC
56747612 TCTAAAACCTAAACCCCTAACG
1 TCTAAAACCTAAACCCCTAACG
**
56747634 TCTAACCCCTAAACCCCTAAC
1 TCTAAAACCTAAACCCCTAAC
56747655 CCCTAAACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.42, G:0.02, T:0.19
Consensus pattern (22 bp):
TCTAAAACCTAAACCCCTAACG
Found at i:56747660 original size:22 final size:22
Alignment explanation
Indices: 56747619--56747660 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56747609 ATCTCTAAAA
**
56747619 CCTAAACCCCTAACGTCTAACC
1 CCTAAACCCCTAACCCCTAACC
56747641 CCTAAACCCCTAACCCCTAA
1 CCTAAACCCCTAACCCCTAA
56747661 ACCTTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.48, G:0.02, T:0.17
Consensus pattern (22 bp):
CCTAAACCCCTAACCCCTAACC
Found at i:56747662 original size:15 final size:15
Alignment explanation
Indices: 56747635--56747663 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56747625 CCCCTAACGT
56747635 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
56747650 CTAACCCCTAAACC
1 CTAACCCCTAAACC
56747664 TTAAATCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.52, G:0.00, T:0.14
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:56747668 original size:22 final size:21
Alignment explanation
Indices: 56747616--56747664 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
56747606 TAAATCTCTA
**
56747616 AAACCTAAACCCCTAACGTCT
1 AAACCTAAACCCCTAACCCCT
*
56747637 AACCCCTAAACCCCTAACCCCT
1 AA-ACCTAAACCCCTAACCCCT
56747659 AAACCT
1 AAACCT
56747665 TAAATCTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.37, C:0.45, G:0.02, T:0.16
Consensus pattern (21 bp):
AAACCTAAACCCCTAACCCCT
Found at i:56747700 original size:14 final size:14
Alignment explanation
Indices: 56747683--56747724 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
56747673 AACCCTTAAA
*
56747683 CCATAATCCCTAAT
1 CCATAATCCCTAAC
56747697 CCATAATCCCTAGAC
1 CCATAATCCCTA-AC
*
56747712 CCATACTCCCTAA
1 CCATAATCCCTAA
56747725 ACCTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.24
Consensus pattern (14 bp):
CCATAATCCCTAAC
Found at i:56748010 original size:14 final size:14
Alignment explanation
Indices: 56747993--56748019 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56747983 AACCCTTAAA
56747993 CCATAATCCCTAAT
1 CCATAATCCCTAAT
56748007 CCATAATCCCTAA
1 CCATAATCCCTAA
56748020 ACCTATACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:56748041 original size:310 final size:302
Alignment explanation
Indices: 56747496--56748105 Score: 854
Period size: 310 Copynumber: 2.0 Consensus size: 302
56747486 AATATATTTG
56747496 ATTTATTATTATCTCTTTTACAACTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATT
1 ATTTATTATTATCTCTTTTACAACTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATT
* *
56747561 AAGCTAAACTCAAAACCTTAACTCGACCCCTGAATCTCTAAACCTTAAATCTCTAAAACCTAAAC
66 AA-C-AAACCCAAAACCTTAACTCGACCCCTGAATCTCTAAACCCTAAATCTCT-AAACCTAAAC
*
56747626 CCCTAACGTCTAACCCCTAAACCCCTAACCCCTAAACCTTAAATCTCAACCCTTAAACCATAATC
128 CCCAAACGTCTAACCCCTAAACCCCTAACCCCTAAACCTTAAATCTCAACCCTTAAACCATAATC
* * * *
56747691 CCTAATCCATAATCCCTAGACCCATACTCCCTAAACCTTAAAATATG-AACTCCTAAACCGGCCT
193 CCTAATCCATAATCCCTAAACCCATACTCCATAAACCTTAAAA-ACGTAACTCCTAAACCGGCAT
* *
56747755 TAAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACAA
257 TAAATCTTAAATAAATCATAGACCCAAAACCAAAAACCCTAAACAA
* *
56747801 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTCAAATATAAATTAAAAAAATTAAT
1 ATTTATTATTATCTCTTTTACAACTATATAAGAACATATTTAAAATATAAATTAAAAAAA-TAAT
* * *
56747866 CTAA-ACACCCAAAATCC-TAACTCGACCCTTGAATC-CTTAAACCCTAAAT-TCCT-AACTCTT
65 -TAACAAACCCAAAA-CCTTAACTCGACCCCTGAATCTC-TAAACCCTAAATCT-CTAAAC-CTA
* *
56747926 AACCCCAAACGTCTAACCCTAAACTCCTAACCCTCTAACCCTTAAACCTTAAATCTCAACCCTTA
125 AACCCCAAACGTCTAACCC----CT--AAACCC-CTAACCCCTAAACCTTAAATCTCAACCCTTA
* *
56747991 AACCATAATCCCTAATCCATAATCCCTAAACCTATACTCCATATACCTTAAAAACGTAACTCCTA
183 AACCATAATCCCTAATCCATAATCCCTAAACCCATACTCCATAAACCTTAAAAACGTAACTCCTA
*
56748056 AACTGGCATTAAATCTTAAATAAATCATAGACCCAAAACCAAAAACCCTA
248 AACCGGCATTAAATCTTAAATAAATCATAGACCCAAAACCAAAAACCCTA
56748106 TGTTTTTTTT
Statistics
Matches: 272, Mismatches: 19, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
302 3 0.01
303 22 0.08
304 38 0.14
305 60 0.22
306 4 0.01
307 5 0.02
309 7 0.03
310 133 0.49
ACGTcount: A:0.42, C:0.28, G:0.03, T:0.27
Consensus pattern (302 bp):
ATTTATTATTATCTCTTTTACAACTATATAAGAACATATTTAAAATATAAATTAAAAAAATAATT
AACAAACCCAAAACCTTAACTCGACCCCTGAATCTCTAAACCCTAAATCTCTAAACCTAAACCCC
AAACGTCTAACCCCTAAACCCCTAACCCCTAAACCTTAAATCTCAACCCTTAAACCATAATCCCT
AATCCATAATCCCTAAACCCATACTCCATAAACCTTAAAAACGTAACTCCTAAACCGGCATTAAA
TCTTAAATAAATCATAGACCCAAAACCAAAAACCCTAAACAA
Found at i:56748246 original size:114 final size:114
Alignment explanation
Indices: 56748110--56748597 Score: 535
Period size: 114 Copynumber: 4.3 Consensus size: 114
56748100 ACCCTATGTT
** * *
56748110 TTTTTTGCGGCGCTTTAC-CAAAAACGCCGCTAAATACCTGAGCATTAGCAGTGCTTTCCT-AAA
1 TTTTTTGCGGCGCTTT-CTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCTAAAA
* *
56748173 AACGCCGTTAAATCCCCGAAAGCTCAGACAACGGCGTCGTTGGGCTTATG
65 AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATG
* *
56748223 TCTTTTTGCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGC-TTCCTAAAA
1 T-TTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCTAAAA
* ** * * * *
56748287 AACGCCACTAAATCAGCGAAAGCTCAAAAAACAGCATCGTTAGGCTTA-G
65 AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATG
* * * * *
56748336 TTTATTTAGCGGCGCTTCCCCAAAAA-GTCGCTAAAGCCCTGAACATTAGCGGTGCTTT-CTAAA
1 TTT-TTT-GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCTAAA
* * * *
56748399 AAACGCCGCTACATCCCCGAAAGCCCAGAAAACGGGGTCGTTGGGCTTAGGTTT
64 AAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA---TG
* * * * *
56748453 TTTTTTGCGGCGCTTTATC-AAAACACTGTTAAAGCCCT-AGAAATTAGCGGCGCTTTCCT-AAA
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAG-CATTAGCGGCGCTTTCCTAAAA
* *
56748515 AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGG
65 AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATG
* * *
56748565 TTTTTTGCGGCACTTTCTGAAAAACGCTGCTAA
1 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
56748598 TGCTTATTTT
Statistics
Matches: 307, Mismatches: 54, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
112 18 0.06
113 92 0.30
114 109 0.36
115 80 0.26
116 5 0.02
117 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (114 bp):
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCCTAAAAA
ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATG
Found at i:56748833 original size:26 final size:27
Alignment explanation
Indices: 56748786--56748841 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
56748776 GATTTCGAGG
56748786 GGGGAAAAGAATAAGGAGAAAAA-GTT
1 GGGGAAAAGAATAAGGAGAAAAAGGTT
56748812 GGGGAAAA-AAGTAGAGGA-AAAAAGGTT
1 GGGGAAAAGAA-TA-AGGAGAAAAAGGTT
56748839 GGG
1 GGG
56748842 CTACAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.07
26 15 0.56
27 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.39, T:0.11
Consensus pattern (27 bp):
GGGGAAAAGAATAAGGAGAAAAAGGTT
Found at i:56749165 original size:113 final size:114
Alignment explanation
Indices: 56749018--56749355 Score: 341
Period size: 113 Copynumber: 3.0 Consensus size: 114
56749008 TTTATCAACA
* * * **
56749018 AGCGCCGCTAAATCCCTACATATTGCGGCG-TTTGACCAAAAATACCACTTAAAACCTACAAAAA
1 AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTGACCAAAAACACCAC-TAAAAAATACAAAAA
***
56749082 CGACGTCGTTTTGATTAAAACAAAATAACATTTTGCGGCGTTTTT-TGGT
65 CGACGTCGTTTTGATTAAAACAAAATAACATTTTGCGGCGTTTTTCACCT
* * *
56749131 AGCGCCACTAAATCCCAACCTATT-CGGCGTTTTGA-CGAAAACGCCACTAAAAAAT-CAAATAA
1 AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTGACCAAAAACACCACTAAAAAATACAAA-AA
* *
56749193 C-ACGGCTCCGTTTTGATTAAAA-ATAAATTAACCTTTTGCGGTGTTTTTCACCT
65 CGAC-G-T-CGTTTTGATTAAAACA-AAA-TAACATTTTGCGGCGTTTTTCACCT
* * *
56749246 TGCGCCGCTAAATCCCGACCTATTGCGGCGTTTT-ACCAAAAACACCACTAAAAAATCAAATAAA
1 AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTGACCAAAAACACCACTAAAAAAT-ACA-AAA
* * * * * *
56749310 AAGGCGCCGTTTTGATAAAAACAGAATAACTTTTTGCGGCGTTTTT
64 ACGACGTCGTTTTGATTAAAACAAAATAACATTTTGCGGCGTTTTT
56749356 GGTGAAACGC
Statistics
Matches: 184, Mismatches: 26, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
110 6 0.03
111 10 0.05
112 16 0.09
113 43 0.23
114 18 0.10
115 41 0.22
116 42 0.23
117 1 0.01
118 4 0.02
119 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (114 bp):
AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTGACCAAAAACACCACTAAAAAATACAAAAAC
GACGTCGTTTTGATTAAAACAAAATAACATTTTGCGGCGTTTTTCACCT
Found at i:56749299 original size:115 final size:113
Alignment explanation
Indices: 56749018--56749470 Score: 368
Period size: 115 Copynumber: 4.0 Consensus size: 113
56749008 TTTATCAACA
* * * * **
56749018 AGCGCCGCTAAATCCCTACATATTGCGGCGTTTGACCAAAAATACCACTTAAAACCTACAAA-AA
1 AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTACCAAAAACACCAC-TAAAAAAT-CAAATAA
***
56749082 CGAC-G-T-CGTTTTGATTAAAACAAAATAACATTTTGCGGCGTTTTTTGGT
64 C-ACGGCTCCGTTTTGATTAAAA-AAAATAACATTTTGCGGCGTTTTTACCT
* * *
56749131 AGCGCCACTAAATCCCAACCTATT-CGGCGTTTTGA-CGAAAACGCCACTAAAAAATCAAATAAC
1 AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTT-ACCAAAAACACCACTAAAAAATCAAATAAC
* *
56749194 ACGGCTCCGTTTTGATTAAAAATAAATTAACCTTTTGCGGTGTTTTTCACCT
65 ACGGCTCCGTTTTGATTAAAAA-AAA-TAACATTTTGCGGCGTTTTT-ACCT
* * *
56749246 TGCGCCGCTAAATCCCGACCTATTGCGGCGTTTTACCAAAAACACCACTAAAAAATCAAATAAAA
1 AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTACCAAAAACACCACTAAAAAATCAAATAACA
* * * **
56749311 AGGCGCCGTTTTGA-TAAAAACAGAATAACTTTTTGCGGCGTTTTT-GGT
66 CGGCTCCGTTTTGATTAAAAA-A-AATAACATTTTGCGGCGTTTTTACCT
* * * * ** * * * * *
56749359 GAAACGCCGCTACAGCCCAACATATTGCGGTATTTCACTAAAAACGCCACTAAGAAATCCAATAA
1 --AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTACCAAAAACACCACTAAAAAATCAAATAA
* * * * *
56749424 AACGGCCCCGTTTTTG-TTAAAACAAAATGA-TTTTTGCGGAGTTTTTA
64 CACGGCTCCG-TTTTGATTAAAA-AAAATAACATTTTGCGGCGTTTTTA
56749471 GAAAAATGCC
Statistics
Matches: 279, Mismatches: 44, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
110 6 0.02
111 10 0.04
112 19 0.07
113 40 0.14
114 33 0.12
115 110 0.39
116 60 0.22
117 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (113 bp):
AGCGCCGCTAAATCCCAACCTATTGCGGCGTTTTACCAAAAACACCACTAAAAAATCAAATAACA
CGGCTCCGTTTTGATTAAAAAAAATAACATTTTGCGGCGTTTTTACCT
Found at i:56749953 original size:8 final size:7
Alignment explanation
Indices: 56749935--56750190 Score: 94
Period size: 7 Copynumber: 35.9 Consensus size: 7
56749925 ACTAATTAAT
56749935 CTAAACC
1 CTAAACC
56749942 CTAAACCC
1 CTAAA-CC
*
56749950 CT-AACT
1 CTAAACC
*
56749956 C-ATATCC
1 CTA-AACC
56749963 CTTAAACC
1 C-TAAACC
*
56749971 CTAAATC
1 CTAAACC
* *
56749978 ATAAAAC
1 CTAAACC
* *
56749985 ATAAATC
1 CTAAACC
*
56749992 CTGAACC
1 CTAAACC
*
56749999 ATAAACC
1 CTAAACC
56750006 CTTAAACC
1 C-TAAACC
*
56750014 C-CAACC
1 CTAAACC
56750020 CTTAAACC
1 C-TAAACC
56750028 CTAAACC
1 CTAAACC
*
56750035 GTAAACC
1 CTAAACC
* *
56750042 ATAATCC
1 CTAAACC
* *
56750049 ATAATCC
1 CTAAACC
*
56750056 ATAAACC
1 CTAAACC
*
56750063 TTAAA--
1 CTAAACC
*
56750068 ATAGTAACTC
1 CTA--AAC-C
56750078 CTAAACC
1 CTAAACC
*
56750085 TTAAACC
1 CTAAACC
56750092 CTAAACC
1 CTAAACC
* *
56750099 ATAATCC
1 CTAAACC
56750106 CTAAACC
1 CTAAACC
*
56750113 CATAATCC
1 C-TAAACC
* *
56750121 ATGAACC
1 CTAAACC
*
56750128 TTAAA--
1 CTAAACC
*
56750133 ATAGTAACTC
1 CTA--AAC-C
56750143 CTAAACC
1 CTAAACC
*
56750150 TTAAACC
1 CTAAACC
56750157 CTAAACC
1 CTAAACC
* *
56750164 ATATACC
1 CTAAACC
56750171 CTAAACC
1 CTAAACC
56750178 CTAAACC
1 CTAAACC
56750185 CTAAAC
1 CTAAAC
56750191 TATAATGATA
Statistics
Matches: 187, Mismatches: 43, Indels: 38
0.70 0.16 0.14
Matches are distributed among these distances:
5 4 0.02
6 7 0.04
7 140 0.75
8 31 0.17
9 1 0.01
10 4 0.02
ACGTcount: A:0.43, C:0.33, G:0.02, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:56750096 original size:14 final size:14
Alignment explanation
Indices: 56749935--56750195 Score: 109
Period size: 14 Copynumber: 17.8 Consensus size: 14
56749925 ACTAATTAAT
*
56749935 CTAAACCCTAAACCC
1 CTAAACCATAAA-CC
*
56749950 CT-AACTCAT-ATCC
1 CTAAAC-CATAAACC
* *
56749963 CTTAAACCCTAAATC
1 C-TAAACCATAAACC
* * *
56749978 ATAAAACATAAATC
1 CTAAACCATAAACC
*
56749992 CTGAACCATAAACC
1 CTAAACCATAAACC
**
56750006 CTTAAACC-CCAACC
1 C-TAAACCATAAACC
*
56750020 CTTAAACCCTAAACC
1 C-TAAACCATAAACC
* *
56750035 GTAAACCATAATCC
1 CTAAACCATAAACC
* *
56750049 ATAATCCATAAACC
1 CTAAACCATAAACC
*
56750063 TTAAA--ATAGTAACTC
1 CTAAACCATA--AAC-C
*
56750078 CTAAACCTTAAACC
1 CTAAACCATAAACC
*
56750092 CTAAACCATAATCC
1 CTAAACCATAAACC
*
56750106 CTAAACCCATAATCC
1 CTAAA-CCATAAACC
* *
56750121 ATGAACCTTAAAATAGTAACTC
1 CTAAACC-----ATA--AAC-C
*
56750143 CTAAACCTTAAACC
1 CTAAACCATAAACC
*
56750157 CTAAACCATATACC
1 CTAAACCATAAACC
*
56750171 CTAAACCCTAAACC
1 CTAAACCATAAACC
*
56750185 CTAAACTATAA
1 CTAAACCATAA
56750196 TGATAATTAA
Statistics
Matches: 185, Mismatches: 41, Indels: 41
0.69 0.15 0.15
Matches are distributed among these distances:
12 3 0.02
13 3 0.02
14 123 0.66
15 41 0.22
17 4 0.02
19 3 0.02
21 2 0.01
22 6 0.03
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.22
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:56750128 original size:65 final size:65
Alignment explanation
Indices: 56750019--56750178 Score: 252
Period size: 65 Copynumber: 2.5 Consensus size: 65
56750009 AAACCCCAAC
* * * *
56750019 CCTTAAACCCTAAACCGTAAACCAT-AATCCATAATCCATAAACCTTAAAATAGTAACTCCTAAA
1 CCTTAAACCCTAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCCTAAA
*
56750083 CCTTAAACCCTAAACCATAATCCCTAAACCCATAATCCATGAACCTTAAAATAGTAACTCCTAAA
1 CCTTAAACCCTAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCCTAAA
56750148 CCTTAAACCCTAAACCAT-ATACCCTAAACCC
1 CCTTAAACCCTAAACCATAAT-CCCTAAACCC
56750179 TAAACCCTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
64 24 0.27
65 65 0.73
ACGTcount: A:0.43, C:0.32, G:0.03, T:0.23
Consensus pattern (65 bp):
CCTTAAACCCTAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAAATAGTAACTCCTAAA
Found at i:56753302 original size:20 final size:19
Alignment explanation
Indices: 56753279--56753327 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
56753269 TTTTACATTA
*
56753279 ATTTCTTTTTCTTTTTTTCT
1 ATTTCTTTTT-TTTCTTTCT
56753299 ATTTGCTTTTTTTTCTTTCT
1 ATTT-CTTTTTTTTCTTTCT
56753319 -TCTTCTTTT
1 AT-TTCTTTT
56753328 ATAATGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (19 bp):
ATTTCTTTTTTTTCTTTCT
Found at i:56756473 original size:18 final size:21
Alignment explanation
Indices: 56756445--56756492 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
56756435 AAAGTAGTGG
56756445 AAATT-TATTTT-A-AGAA-T
1 AAATTCTATTTTCAGAGAATT
56756462 AAATTCTATTTTCAGAGAATT
1 AAATTCTATTTTCAGAGAATT
56756483 ACAATTCTAT
1 A-AATTCTAT
56756493 CCGTTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 6 0.23
19 1 0.04
20 4 0.15
21 2 0.08
22 8 0.31
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (21 bp):
AAATTCTATTTTCAGAGAATT
Found at i:56764076 original size:37 final size:37
Alignment explanation
Indices: 56764026--56764104 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
56764016 TTATTACGAA
* * *
56764026 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
56764063 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
56764100 GTCTT
1 GTCTT
56764105 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:56764292 original size:47 final size:47
Alignment explanation
Indices: 56764223--56764865 Score: 955
Period size: 47 Copynumber: 13.4 Consensus size: 47
56764213 CCTTTCGGGA
* * *
56764223 CTTATCACATTTATGCACTTTCACATTCATTACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56764270 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
56764317 CTTATCACATATATACACTTTCACATTCATCACATC-GCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56764363 CTTATTACATATATACACTTTCACATTCATCACATCGGCGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
56764410 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56764457 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
56764504 CTTATTACATATATACATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTA-T-CACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56764555 CTTATCACATATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56764602 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56764649 CTTATTACATATATACATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATAC----ACTTTCACATTCATCACATCGGCCATTAGGC
56764700 CTTATCACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
56764751 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56764800 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56764847 CTTATCACACATATACACT
1 CTTATCACATATATACACT
56764866 CTCTTGGCTG
Statistics
Matches: 555, Mismatches: 28, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
46 45 0.08
47 323 0.58
48 1 0.00
49 63 0.11
50 1 0.00
51 114 0.21
53 4 0.01
55 4 0.01
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:56764580 original size:145 final size:141
Alignment explanation
Indices: 56764223--56764865 Score: 982
Period size: 145 Copynumber: 4.5 Consensus size: 141
56764213 CCTTTCGGGA
* * * *
56764223 CTTATCACATTTATGCACTTTCACATTCATTACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
56764288 TTTCACATTCATCGCATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
56764353 -GCCATTAGGC
131 GGCCATTAGGC
* *
56764363 CTTATTACATATATACACTTTCACATTCATCACATCGGCGATTAGGCCTTATCACACATATACAC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* *
56764428 TTTCACATTCATCACGTCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
*
56764493 GGCTATTAGGC
131 GGCCATTAGGC
* *
56764504 CTTATTACATATATACATACACTTTCACATTCATCACATCGACTATTAGGCCTTATCACATATAT
1 CTTATTAC--ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
* *
56764569 ACACTTTCACATTCATCACGTCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCA
62 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCA
*
56764634 CATCGGCTATTAGGC
127 CATCGGCCATTAGGC
56764649 CTTATTACATATATACATATACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 CTTATTACATATATAC----ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATAT
*
56764714 ACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACAT
60 --ATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACAT--ATACACTTTCACAT
56764779 TCATCACATCGGCCATTAGGC
121 TCATCACATCGGCCATTAGGC
* *
56764800 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATACAC
1 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
56764865 T
66 T
56764866 CTCTTGGCTG
Statistics
Matches: 466, Mismatches: 22, Indels: 27
0.90 0.04 0.05
Matches are distributed among these distances:
140 120 0.26
141 21 0.05
143 15 0.03
145 174 0.37
147 42 0.09
149 44 0.09
151 50 0.11
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (141 bp):
CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:56768633 original size:9 final size:9
Alignment explanation
Indices: 56768616--56768652 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
56768606 TATAGTTTGA
56768616 TATTCGAAT
1 TATTCGAAT
*
56768625 TATTTGAAT
1 TATTCGAAT
*
56768634 TATTCGAGT
1 TATTCGAAT
56768643 TATTCGAAT
1 TATTCGAAT
56768652 T
1 T
56768653 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:56774375 original size:30 final size:30
Alignment explanation
Indices: 56774341--56774407 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
56774331 TCATCGCTAA
*
56774341 CCATTTTCTGTTAAAGACGTAACAAAGTTG
1 CCATTTTCCGTTAAAGACGTAACAAAGTTG
** * *
56774371 CCATTTTCCGTTGTAGACTTAACAGAGTTG
1 CCATTTTCCGTTAAAGACGTAACAAAGTTG
56774401 CCATTTT
1 CCATTTT
56774408 TCATCCTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (30 bp):
CCATTTTCCGTTAAAGACGTAACAAAGTTG
Found at i:56775294 original size:30 final size:30
Alignment explanation
Indices: 56775258--56775325 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
56775248 GAGAAGGATG
*
56775258 GAAAATGGAAACTTCGTTAAGTCTGTAACA
1 GAAAATGGAAACTCCGTTAAGTCTGTAACA
* * *
56775288 GAAAATGGCAACTCCGTTACGTTTGTAACA
1 GAAAATGGAAACTCCGTTAAGTCTGTAACA
*
56775318 GGAAATGG
1 GAAAATGG
56775326 TTAGTGATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (30 bp):
GAAAATGGAAACTCCGTTAAGTCTGTAACA
Found at i:56779984 original size:76 final size:76
Alignment explanation
Indices: 56779892--56780056 Score: 267
Period size: 76 Copynumber: 2.2 Consensus size: 76
56779882 TATCTCCCGT
* *
56779892 ACATAAAGGTATCGTCGATTTGTACCAGTGGCTTGTAGTATTGGAATGCCTGTCGACATTGCATC
1 ACATAAAGGTACCGTCGATTTGTACCAGGGGCTTGTAGTATTGGAATGCCTGTCGACATTGCATC
56779957 AGATATCCCAC
66 AGATATCCCAC
* * *
56779968 ATATAAAGGTACCGTCGATTTGTACCAGGGGCTTGTAGTATTGGGATGCCTGTCGACATTGCATT
1 ACATAAAGGTACCGTCGATTTGTACCAGGGGCTTGTAGTATTGGAATGCCTGTCGACATTGCATC
**
56780033 AGATATCCCGT
66 AGATATCCCAC
56780044 ACATAAAGGTACC
1 ACATAAAGGTACC
56780057 ATCCTACATG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (76 bp):
ACATAAAGGTACCGTCGATTTGTACCAGGGGCTTGTAGTATTGGAATGCCTGTCGACATTGCATC
AGATATCCCAC
Found at i:56780337 original size:17 final size:16
Alignment explanation
Indices: 56780315--56780356 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
56780305 TAAATAATTC
56780315 AAATATACGATTGGTT-T
1 AAATAT-CGATT-GTTGT
56780332 AAATAT-GATTGTTGT
1 AAATATCGATTGTTGT
56780347 AAATATCGAT
1 AAATATCGAT
56780357 GTAAGTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 11 0.48
16 3 0.13
17 6 0.26
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (16 bp):
AAATATCGATTGTTGT
Found at i:56782602 original size:9 final size:9
Alignment explanation
Indices: 56782588--56782617 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56782578 TCCATTGATG
*
56782588 AGATATTGA
1 AGATATTAA
56782597 AGATATTAA
1 AGATATTAA
56782606 AGATATTAA
1 AGATATTAA
56782615 AGA
1 AGA
56782618 ATCGTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (9 bp):
AGATATTAA
Found at i:56788343 original size:27 final size:27
Alignment explanation
Indices: 56788313--56788366 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
56788303 TTAATTTATC
56788313 TTAATCTAATTCTAACATAATATAAAT
1 TTAATCTAATTCTAACATAATATAAAT
* *
56788340 TTAATTTAATTTTAACATAATATAAAT
1 TTAATCTAATTCTAACATAATATAAAT
56788367 CTGTCATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAATCTAATTCTAACATAATATAAAT
Found at i:56789127 original size:34 final size:34
Alignment explanation
Indices: 56789072--56789137 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
56789062 CAAACACCAA
*
56789072 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
*
56789107 AAAACATTTTCCCG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
56789138 ATATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:56792037 original size:43 final size:43
Alignment explanation
Indices: 56791938--56792093 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 43
56791928 TAGGGTTATC
* * *
56791938 GAGATTACGTGTAAGAACATATCTGGGATA-TGGAATCAATAT
1 GAGATTACGTGTAAGACCATATCTGGGACATTGGAATCGATAT
* *
56791980 GAGAATT-CGTGTAAGACCATGTCTGGGACATTGGGATCGATAT
1 GAG-ATTACGTGTAAGACCATATCTGGGACATTGGAATCGATAT
* * * * * *
56792023 GTGATTTCGTGTAAGACCA-AGGCCGGG-CTATTGGCATCGATAC
1 GAGATTACGTGTAAGACCATA-TCTGGGAC-ATTGGAATCGATAT
*
56792066 GAGATTACATGTAAGACCATATCTGGGA
1 GAGATTACGTGTAAGACCATATCTGGGA
56792094 TATGACATTG
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
42 27 0.30
43 63 0.69
44 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (43 bp):
GAGATTACGTGTAAGACCATATCTGGGACATTGGAATCGATAT
Found at i:56796971 original size:14 final size:14
Alignment explanation
Indices: 56796952--56796986 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
56796942 ATATATCAAA
56796952 TAATTTTCTCACCC
1 TAATTTTCTCACCC
56796966 TAATTTTCTCACCC
1 TAATTTTCTCACCC
56796980 TAATTTT
1 TAATTTT
56796987 AACCGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.29, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTTTCTCACCC
Found at i:56797140 original size:12 final size:12
Alignment explanation
Indices: 56797112--56797147 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
56797102 GCAAATAAGT
*
56797112 CATTTCTCATTTT
1 CATTTC-CATTTC
56797125 CATTTCCATTTC
1 CATTTCCATTTC
56797137 CATTTCCATTT
1 CATTTCCATTT
56797148 TGAGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
CATTTCCATTTC
Found at i:56797146 original size:18 final size:19
Alignment explanation
Indices: 56797112--56797147 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
56797102 GCAAATAAGT
*
56797112 CATTTCTCATTTTCATTTC
1 CATTTCTCATTTCCATTTC
56797131 CATTTC-CATTTCCATTT
1 CATTTCTCATTTCCATTT
56797148 TGAGAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (19 bp):
CATTTCTCATTTCCATTTC
Found at i:56809028 original size:188 final size:187
Alignment explanation
Indices: 56808710--56809084 Score: 597
Period size: 188 Copynumber: 2.0 Consensus size: 187
56808700 TGCAGATTTT
*
56808710 GTTAACTATCTAGTGTGTAGAAAACTCCCATTGGGTGTCACAAGCCATAAAAAGAAAGATTTATT
1 GTTAACTATATAGTGTGTAGAAAACTCCCATTGGGTGTCACAAGCCATAAAAAGAAAGATTTATT
* * * * * *
56808775 CGTGACATAATGAAGTATCATTGGATCGAGCCGTATTTATTCAAAGTATGCAATGACAGTATCAT
66 CATAACATAATAAAGTATCATTAGAACGAGCCGTATTTATTCAAAGTATGCAATGACAATATCAT
56808840 TCGACTCTGTGTTCCGGAAGAAGAGATGCTTTCAATCCTAAAGCATTGTCATGATGC
131 TCGACTCTGTGTTCCGGAAGAAGAGATGCTTTCAATCCTAAAGCATTGTCATGATGC
* * *
56808897 GTTAACTATATAGTGTGTAGAAAACTCCCATTGGGTGTCACAGGCCATAAAAAAGAAAGGTTTCT
1 GTTAACTATATAGTGTGTAGAAAACTCCCATTGGGTGTCACAAGCCAT-AAAAAGAAAGATTTAT
* * *
56808962 TTATAACATAATAAAGTATCATTAGAACGAGCTGTATTTATTCAAAGTATGCGATGACAATATCA
65 TCATAACATAATAAAGTATCATTAGAACGAGCCGTATTTATTCAAAGTATGCAATGACAATATCA
* * *
56809027 TTCGACTTTGTGTTCCGGAAGAAGAGATGCTTTCAATCCTGAAGCATTGTCGTGATGC
130 TTCGACTCTGTGTTCCGGAAGAAGAGATGCTTTCAATCCTAAAGCATTGTCATGATGC
56809085 TCCTTATGGA
Statistics
Matches: 171, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
187 46 0.27
188 125 0.73
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (187 bp):
GTTAACTATATAGTGTGTAGAAAACTCCCATTGGGTGTCACAAGCCATAAAAAGAAAGATTTATT
CATAACATAATAAAGTATCATTAGAACGAGCCGTATTTATTCAAAGTATGCAATGACAATATCAT
TCGACTCTGTGTTCCGGAAGAAGAGATGCTTTCAATCCTAAAGCATTGTCATGATGC
Found at i:56811985 original size:18 final size:18
Alignment explanation
Indices: 56811962--56812008 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
56811952 TTGGTGCTAT
*
56811962 AGAAGAAGAAGTTGTTGC
1 AGAAGAAGAAGTTATTGC
* *
56811980 AGAAGAGGAAATTATTGC
1 AGAAGAAGAAGTTATTGC
*
56811998 TGAAGAAGAAG
1 AGAAGAAGAAG
56812009 AAATTGTTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.32, T:0.19
Consensus pattern (18 bp):
AGAAGAAGAAGTTATTGC
Found at i:56812484 original size:17 final size:17
Alignment explanation
Indices: 56812459--56812495 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
56812449 AATAAGTATA
*
56812459 CATTGTCATTGCATTTT
1 CATTGTCATTACATTTT
*
56812476 CATTTTCATTACATTTT
1 CATTGTCATTACATTTT
56812493 CAT
1 CAT
56812496 GTTAGTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (17 bp):
CATTGTCATTACATTTT
Found at i:56816332 original size:47 final size:48
Alignment explanation
Indices: 56816280--56816378 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
56816270 AACTAACATT
* * *
56816280 TGTTCTGGCAACTTGACTGCAATTCTGGTGGC-TTGACCACGTATATC
1 TGTTCTGACAACTTGACTACAATTCTGGTGGCTTTGACCACATATATC
* * *
56816327 TGTTCTGACAGCTTGACTACAATTTTGGTGGCTTTGTCCACATATATC
1 TGTTCTGACAACTTGACTACAATTCTGGTGGCTTTGACCACATATATC
56816375 TGTT
1 TGTT
56816379 GGTGTGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 28 0.62
48 17 0.38
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (48 bp):
TGTTCTGACAACTTGACTACAATTCTGGTGGCTTTGACCACATATATC
Found at i:56817405 original size:94 final size:94
Alignment explanation
Indices: 56817213--56817386 Score: 251
Period size: 94 Copynumber: 1.9 Consensus size: 94
56817203 GGGGGTTACA
* * * *
56817213 ACAACCTAAGTTTATTGATTTATGATCATGAACAATCTTCTTTGAGTTAGCTGATTTACAATCAC
1 ACAACCTAAGTTAATTGATTTACGATCATGAACAATCTTCTCTAAGTTAGCTGATTTACAATCAC
*
56817278 AACTTCAAATAGCTCTCTAATTTACAATC
66 AACTCCAAATAGCTCTCTAATTTACAATC
* * * *
56817307 ACAACCTAAGTTAATTGATTTACGATCATGAACAATCTT-TCCTAAGTTAGTTGGTTTACGATCG
1 ACAACCTAAGTTAATTGATTTACGATCATGAACAATCTTCT-CTAAGTTAGCTGATTTACAATCA
56817371 CAACTCCAAATAGCTC
65 CAACTCCAAATAGCTC
56817387 ATTGATTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
93 1 0.01
94 69 0.99
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (94 bp):
ACAACCTAAGTTAATTGATTTACGATCATGAACAATCTTCTCTAAGTTAGCTGATTTACAATCAC
AACTCCAAATAGCTCTCTAATTTACAATC
Found at i:56817454 original size:130 final size:129
Alignment explanation
Indices: 56817297--56817566 Score: 344
Period size: 130 Copynumber: 2.1 Consensus size: 129
56817287 TAGCTCTCTA
* **
56817297 ATTTACAATCACAACCTAAGTTAATTGATTTACGATCATGAACAATCTT-TCCTAAGTTAGTTGG
1 ATTTACAATCACAACCTAAGTTAATTGATTTACGATCATGAACAATCTTCTCC-AAGTTAGCTAA
* * * * *
56817361 TTTACGATCGCAACTCCAAATAGCTCATTGATTTATGATCACAACTGATATTATTAAGACTTGTT
65 CTTACAATCGCAACTCCAAACAGCTCACTAATTTA-GATCACAACTGATATTATTAAGACTTGTT
56817426 G
129 G
* * * * *
56817427 ATTTACGATCACAACCTAAGTTCATTGATTTACGATCATGAATAGTCTTCTCCGAGTTAGCTAAC
1 ATTTACAATCACAACCTAAGTTAATTGATTTACGATCATGAACAATCTTCTCCAAGTTAGCTAAC
** * * *
56817492 TTACAATCGCAACTCCAAACAGCTTGCTAATTTAGATCACAACTGATATTATTAAGGCTCGCTG
66 TTACAATCGCAACTCCAAACAGCTCACTAATTTAGATCACAACTGATATTATTAAGACTTGTTG
*
56817556 ATTTATAATCA
1 ATTTACAATCA
56817567 TGAATAATCT
Statistics
Matches: 119, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
129 36 0.30
130 80 0.67
131 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (129 bp):
ATTTACAATCACAACCTAAGTTAATTGATTTACGATCATGAACAATCTTCTCCAAGTTAGCTAAC
TTACAATCGCAACTCCAAACAGCTCACTAATTTAGATCACAACTGATATTATTAAGACTTGTTG
Found at i:56818536 original size:21 final size:20
Alignment explanation
Indices: 56818490--56818536 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
56818480 CCTCTAGCCA
56818490 TTTATTTTGATTCACCAATT
1 TTTATTTTGATTCACCAATT
*
56818510 TCTTATTTT-CTTCAACCAATT
1 T-TTATTTTGATTC-ACCAATT
56818531 GTTTAT
1 -TTTAT
56818537 ACAGTTCACG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 18 0.78
22 1 0.04
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTATTTTGATTCACCAATT
Found at i:56819577 original size:20 final size:20
Alignment explanation
Indices: 56819514--56819577 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
56819504 TCGAGCCACT
* *
56819514 AGTATCGTAGATAAACTGCC
1 AGTATTGTAGATAAACTACC
* * * *
56819534 AATAATGCAGA-AAAGCTACT
1 AGTATTGTAGATAAA-CTACC
56819554 AGTATTGTAGATAAACTACC
1 AGTATTGTAGATAAACTACC
56819574 AGTA
1 AGTA
56819578 ATATGGTCAA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (20 bp):
AGTATTGTAGATAAACTACC
Found at i:56839132 original size:23 final size:23
Alignment explanation
Indices: 56839106--56839159 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
56839096 CAAACTAATC
*
56839106 CTCTCAAATTTCCTTTC-AATTT
1 CTCTCAAATTTCCTTCCAAATTT
56839128 GCTCTCAAA-TTCCTTCCAAATTT
1 -CTCTCAAATTTCCTTCCAAATTT
56839151 CTCTCAAAT
1 CTCTCAAAT
56839160 CTATATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.43
Consensus pattern (23 bp):
CTCTCAAATTTCCTTCCAAATTT
Found at i:56839158 original size:11 final size:12
Alignment explanation
Indices: 56839104--56839159 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
56839094 CACAAACTAA
56839104 TCCTCTCAAATT
1 TCCTCTCAAATT
*
56839116 TCCTTTC-AATT
1 TCCTCTCAAATT
*
56839127 TGCTCTCAAA-T
1 TCCTCTCAAATT
56839138 TCCT-TCCAAATT
1 TCCTCT-CAAATT
56839150 T-CTCTCAAAT
1 TCCTCTCAAAT
56839160 CTATATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 1 0.03
11 24 0.67
12 11 0.31
ACGTcount: A:0.25, C:0.30, G:0.02, T:0.43
Consensus pattern (12 bp):
TCCTCTCAAATT
Found at i:56841050 original size:18 final size:18
Alignment explanation
Indices: 56841023--56841057 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56841013 CAGGTGAGTT
* *
56841023 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
56841041 TCCTAACCCTTATATGT
1 TCCTAACCCTTATATGT
56841058 TTTCTTTTCC
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:0.20, C:0.29, G:0.09, T:0.43
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:56841632 original size:21 final size:21
Alignment explanation
Indices: 56841629--56842077 Score: 467
Period size: 21 Copynumber: 21.0 Consensus size: 21
56841619 TAAAACCCCT
*
56841629 AACCCTAACCTTTAA-TTGAAA
1 AACCCTAACCCTTAACTT-AAA
*
56841650 AACCCTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAA
*
56841671 AACCCTAAACCATTAACTT-AA
1 AACCCT-AACCCTTAACTTAAA
*
56841692 AACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
*
56841714 AACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
56841736 AACACTAAACCTTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
56841758 AACCCTAGCCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
56841779 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
** *
56841801 AACTATAACCCTTAAATT-AA
1 AACCCTAACCCTTAACTTAAA
*
56841821 AACCCTAAACCCTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAA
* * *
56841843 AACCGTAACCCTTAAATAAAA
1 AACCCTAACCCTTAACTTAAA
56841864 AACCCTAATCCCTTAACTTAAA
1 AACCCTAA-CCCTTAACTTAAA
* * *
56841886 AACCCAAACCCTTAAATTTAA
1 AACCCTAACCCTTAACTTAAA
* *
56841907 AACCCTAAACCATTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
*
56841929 AACCCTAAGCCCTTAAATTAAA
1 AACCCTAA-CCCTTAACTTAAA
*
56841951 AACCATAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
56841973 AACCATAACCCTTAAATT-AA
1 AACCCTAACCCTTAACTTAAA
* *
56841993 AACCCTAAACCTTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAA
* * *
56842015 AATCGTAACCCTTAA-ATAAA
1 AACCCTAACCCTTAACTTAAA
*
56842035 AACCCCTAACACTTAACTTAAA
1 AA-CCCTAACCCTTAACTTAAA
56842057 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
56842078 TATAGTTTGA
Statistics
Matches: 364, Mismatches: 50, Indels: 28
0.82 0.11 0.06
Matches are distributed among these distances:
20 18 0.05
21 176 0.48
22 168 0.46
23 2 0.01
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.25
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:56841662 original size:22 final size:21
Alignment explanation
Indices: 56841629--56842077 Score: 355
Period size: 22 Copynumber: 21.0 Consensus size: 21
56841619 TAAAACCCCT
56841629 AACCCTAA-CCTTTAATTGAAA
1 AACCCTAACCCTTTAATT-AAA
*
56841650 AACCCTAACCCTTAAATTAAA
1 AACCCTAACCCTTTAATTAAA
* *
56841671 AACCCTAAACCATTAACTT-AA
1 AACCCTAACCCTTTAA-TTAAA
*
56841692 AACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTTAATTAAA
*
56841714 AACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTTAATTAAA
* *
56841736 AACACTAAACCTTTAACTTAAA
1 AACCCTAACCCTTTAA-TTAAA
* *
56841758 AACCCTAGCCC-TTAACTTTAA
1 AACCCTAACCCTTTAA-TTAAA
56841779 AACCCTAAACCC-TTAACTTAAA
1 AACCCT-AACCCTTTAA-TTAAA
** *
56841801 AACTATAACCCTTAAATT-AA
1 AACCCTAACCCTTTAATTAAA
*
56841821 AACCCTAAACCC-TTAACTTTAA
1 AACCCT-AACCCTTTAA-TTAAA
* * *
56841843 AACCGTAACCCTTAAATAAAA
1 AACCCTAACCCTTTAATTAAA
56841864 AACCCTAATCCC-TTAACTTAAA
1 AACCCTAA-CCCTTTAA-TTAAA
* * *
56841886 AACCCAAACCCTTAAATTTAA
1 AACCCTAACCCTTTAATTAAA
* *
56841907 AACCCTAAACCATTAAATTAAA
1 AACCCT-AACCCTTTAATTAAA
*
56841929 AACCCTAAGCCCTTAAATTAAA
1 AACCCTAA-CCCTTTAATTAAA
*
56841951 AACCATAAACCC-TTAACTTAAA
1 AACCCT-AACCCTTTAA-TTAAA
* *
56841973 AACCATAACCCTTAAATT-AA
1 AACCCTAACCCTTTAATTAAA
* *
56841993 AACCCTAAACCTTTAACTTTAA
1 AACCCTAACCCTTTAA-TTAAA
* * *
56842015 AATCGTAACCC-TTAAATAAA
1 AACCCTAACCCTTTAATTAAA
*
56842035 AACCCCTAACAC-TTAACTTAAA
1 AA-CCCTAACCCTTTAA-TTAAA
56842057 AACCCTAACCC-TTAACTTAAA
1 AACCCTAACCCTTTAA-TTAAA
56842078 TATAGTTTGA
Statistics
Matches: 353, Mismatches: 52, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
20 29 0.08
21 147 0.42
22 175 0.50
23 2 0.01
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.25
Consensus pattern (21 bp):
AACCCTAACCCTTTAATTAAA
Found at i:56841703 original size:43 final size:42
Alignment explanation
Indices: 56841629--56842077 Score: 535
Period size: 43 Copynumber: 10.5 Consensus size: 42
56841619 TAAAACCCCT
* *
56841629 AACCCTAA-CCTTTAATTGAAAAACCCT-AACCCTTAAATTAAA
1 AACCCTAACCCTTAAATT--AAAACCCTAAACCCTTAACTTAAA
* * *
56841671 AACCCTAAACCATTAACTTAAAACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAAATTAAAACCCTAAACCCTTAACTTAAA
* *
56841714 AACCCTAAACCCTTAAATTAAAAACACTAAACCTTTAACTTAAA
1 AACCCT-AACCCTTAAATT-AAAACCCTAAACCCTTAACTTAAA
* *
56841758 AACCCTAGCCCTTAACTTTAAAACCCTAAACCCTTAACTTAAA
1 AACCCTAACCCTTAA-ATTAAAACCCTAAACCCTTAACTTAAA
** *
56841801 AACTATAACCCTTAAATTAAAACCCTAAACCCTTAACTTTAA
1 AACCCTAACCCTTAAATTAAAACCCTAAACCCTTAACTTAAA
* * *
56841843 AACCGTAACCCTTAAATAAAAAACCCTAATCCCTTAACTTAAA
1 AACCCTAACCCTTAAAT-TAAAACCCTAAACCCTTAACTTAAA
* * *
56841886 AACCCAAACCCTTAAATTTAAAACCCTAAACCATTAAATTAAA
1 AACCCTAACCCTTAAA-TTAAAACCCTAAACCCTTAACTTAAA
*
56841929 AACCCTAAGCCCTTAAATTAAAAACCATAAACCCTTAACTTAAA
1 AACCCTAA-CCCTTAAATT-AAAACCCTAAACCCTTAACTTAAA
* * *
56841973 AACCATAACCCTTAAATTAAAACCCTAAACCTTTAACTTTAA
1 AACCCTAACCCTTAAATTAAAACCCTAAACCCTTAACTTAAA
* * * *
56842015 AATCGTAACCCTTAAATAAAAACCCCT-AACACTTAACTTAAA
1 AACCCTAACCCTTAAATTAAAA-CCCTAAACCCTTAACTTAAA
*
56842057 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAAATTAAA
56842078 TATAGTTTGA
Statistics
Matches: 351, Mismatches: 46, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
42 123 0.35
43 156 0.44
44 72 0.21
ACGTcount: A:0.47, C:0.27, G:0.01, T:0.25
Consensus pattern (42 bp):
AACCCTAACCCTTAAATTAAAACCCTAAACCCTTAACTTAAA
Found at i:56844063 original size:18 final size:18
Alignment explanation
Indices: 56844040--56844074 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56844030 CTTTTTTCTC
56844040 TAAAAACCCTAAAAATCT
1 TAAAAACCCTAAAAATCT
*
56844058 TAAAAACCTTAAAAATC
1 TAAAAACCCTAAAAATC
56844075 CTAACGTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAAACCCTAAAAATCT
Found at i:56856553 original size:15 final size:16
Alignment explanation
Indices: 56856525--56856554 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56856515 GTTGGACTAA
56856525 ATTGAATGTGAGTTAT
1 ATTGAATGTGAGTTAT
56856541 ATTGAAT-TGAGTTA
1 ATTGAATGTGAGTTA
56856555 AATTTATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (16 bp):
ATTGAATGTGAGTTAT
Found at i:56856579 original size:23 final size:23
Alignment explanation
Indices: 56856553--56856599 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
56856543 TGAATTGAGT
*
56856553 TAAATTTATTCGTAAAGATTCAG
1 TAAATTCATTCGTAAAGATTCAG
*
56856576 TAAATTCATTCGTACAGATTCAG
1 TAAATTCATTCGTAAAGATTCAG
56856599 T
1 T
56856600 TAGACATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (23 bp):
TAAATTCATTCGTAAAGATTCAG
Found at i:56856891 original size:25 final size:24
Alignment explanation
Indices: 56856863--56856953 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 24
56856853 TACCGATTTT
* *
56856863 AGCTCGTATGAGCTTACTGATATTG
1 AGCTCG-AGGAGCTTACTGATATTC
* * * *
56856888 AGCTCGCATGAGCTTACCGTTATTT
1 AGCTCG-AGGAGCTTACTGATATTC
56856913 AGCTCAGAGGAGCTTACT-ATTATTC
1 AGCTC-GAGGAGCTTACTGA-TATTC
56856938 AGCTCGGAGGAGCTTA
1 AGCTC-GAGGAGCTTA
56856954 TCGTTTATAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (24 bp):
AGCTCGAGGAGCTTACTGATATTC
Found at i:56857209 original size:22 final size:24
Alignment explanation
Indices: 56857169--56857213 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
56857159 GTGATGTTAC
56857169 ATAATACATTGATATATGAAATGA
1 ATAATACATTGATATATGAAATGA
56857193 ATAATACA-TG-TATATGAAATG
1 ATAATACATTGATATATGAAATG
56857214 TGATTACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.52
23 2 0.10
24 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (24 bp):
ATAATACATTGATATATGAAATGA
Found at i:56871729 original size:39 final size:40
Alignment explanation
Indices: 56871629--56871891 Score: 278
Period size: 39 Copynumber: 6.7 Consensus size: 40
56871619 TTGAATGATG
* *
56871629 TCCGGGCTATGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
56871668 ATCCGGACCAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
56871709 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACT-AAT
* *
56871749 T-CGGACCAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
56871788 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
56871827 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
56871865 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
56871892 AACGAGGAGC
Statistics
Matches: 191, Mismatches: 18, Indels: 28
0.81 0.08 0.12
Matches are distributed among these distances:
38 1 0.01
39 101 0.53
40 75 0.39
41 13 0.07
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Done.