Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 128 of 171
Found at i:40446193 original size:30 final size:30
Alignment explanation
Indices: 40446042--40446198 Score: 103
Period size: 30 Copynumber: 5.3 Consensus size: 30
40446032 GGTAAAATCA
* *
40446042 GGGTTAAAAACGAAATTTTAGAAGCTTCGG
1 GGGTTAAAAACGGAATTTTAGTAGCTTCGG
* * ***
40446072 GGG-T-AAAATGGTAATTTTCGGTAAAATC-G
1 GGGTTAAAAACGG-AATTTT-AGTAGCTTCGG
*
40446101 GGGTTAAAAACGGAATTTTAGAAGCTTCGG
1 GGGTTAAAAACGGAATTTTAGTAGCTTCGG
* * **
40446131 GGG-T-AAAATGGTAATTTTCGGT-GAAATC-G
1 GGGTTAAAAACGG-AATTTT-AGTAG-CTTCGG
40446160 GGGTTAAAAACGGAATTTTAGTAGCTTCGG
1 GGGTTAAAAACGGAATTTTAGTAGCTTCGG
*
40446190 GGGTCAAAA
1 GGGTTAAAA
40446199 TATAATTTTG
Statistics
Matches: 92, Mismatches: 23, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
28 11 0.12
29 31 0.34
30 38 0.41
31 12 0.13
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (30 bp):
GGGTTAAAAACGGAATTTTAGTAGCTTCGG
Found at i:40446225 original size:30 final size:30
Alignment explanation
Indices: 40446189--40446297 Score: 209
Period size: 30 Copynumber: 3.6 Consensus size: 30
40446179 AGTAGCTTCG
40446189 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
40446219 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
40446249 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
40446279 GGGGTCAAAATATAATTTT
1 GGGGTCAAAATATAATTTT
40446298 TAGACAATTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:40446616 original size:161 final size:162
Alignment explanation
Indices: 40446392--40446708 Score: 435
Period size: 161 Copynumber: 2.0 Consensus size: 162
40446382 ACTAATTCGA
* * * *
40446392 AAACTTTGAAAAAATTTTGGACCAATTTTGTAATTAACTAAGAGTTAATTTAAGGACTAAATTAA
1 AAACCTTGAAAAAATTTTGGACCAATTTCGTAATTAAATAAGAGCTAATTTAAGGACTAAATTAA
* * *
40446457 AATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAA-AAATTGACACGTGGCAACCTC
66 AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAA-TGACACGTGGCAACCTC
**
40446521 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
130 TGGCACAGTCAAACAGTCAAAGGACTAGTTTAT
* * * *
40446554 AAACCTTG-AAAAATTATTGGGCCAATTTCGTAATTAAAATAA-AGCTGATTT-GGGATTAAATT
1 AAACCTTGAAAAAATT-TTGGACCAATTTCGTAATT-AAATAAGAGCTAATTTAAGGACTAAATT
* *
40446616 AAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACATGACACGTGGCAACCT
64 AAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCT
*
40446681 CTGGCACTGTCAAACAGTCAAAGGACTA
129 CTGGCACAGTCAAACAGTCAAAGGACTA
40446709 AATTATAATC
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
161 98 0.72
162 33 0.24
163 5 0.04
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (162 bp):
AAACCTTGAAAAAATTTTGGACCAATTTCGTAATTAAATAAGAGCTAATTTAAGGACTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCTCT
GGCACAGTCAAACAGTCAAAGGACTAGTTTAT
Found at i:40446792 original size:161 final size:160
Alignment explanation
Indices: 40446443--40446792 Score: 386
Period size: 161 Copynumber: 2.2 Consensus size: 160
40446433 GAGTTAATTT
* * *
40446443 AAGGACTAAATTAAAATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAAATTGAC
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
** ** **
40446508 ACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTGAAAAATTATTG
66 ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAG
* * * * **
40446573 GGCCAATTTCGTAATTAAAATAAAGCTGATT
130 GGCAAATTTCGCAAATAAAATAAAGATGAAG
** * * *
40446604 TGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACA-TGA
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAA-AAATTGA
* *
40446668 CACGTGGCAACCTCTGGCACTGTCAAACAGTCAAAGGACTAAATTATAATCCAATT-AAAATTAC
65 CACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAATTAC
40446732 AGGGCAAATTT-GCAAATAATTAA-AAAGATGCAAG
128 AGGGCAAATTTCGCAAATAA--AATAAAGATG-AAG
* *
40446766 AAGGACTAAATTGAAGCAAA-TAAAAAT
1 AAGGACTAAATTAAAACAAATTAAAAAT
40446793 GCGGAAGGAT
Statistics
Matches: 156, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
160 6 0.04
161 128 0.82
162 20 0.13
163 2 0.01
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (160 bp):
AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGG
GCAAATTTCGCAAATAAAATAAAGATGAAG
Found at i:40447477 original size:15 final size:15
Alignment explanation
Indices: 40447457--40447494 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40447447 TATAAAATAT
* *
40447457 TTATTATTATTACTG
1 TTATTATTATCACTA
40447472 TTATTATTATCACTA
1 TTATTATTATCACTA
40447487 TTATTATT
1 TTATTATT
40447495 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:40447497 original size:24 final size:24
Alignment explanation
Indices: 40447461--40447516 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
40447451 AAATATTTAT
*
40447461 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
40447485 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
40447509 TATTATTA
1 TATTATTA
40447517 ACCATCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:40448214 original size:17 final size:18
Alignment explanation
Indices: 40448194--40448264 Score: 67
Period size: 17 Copynumber: 4.0 Consensus size: 18
40448184 TCTATTTGGT
*
40448194 TTTTTTATT-AATTTAAA
1 TTTTTAATTAAATTTAAA
40448211 -TTTTAATTAAATTTAAA
1 TTTTTAATTAAATTTAAA
* **
40448228 -TTTAAAGCAAATTTAAA
1 TTTTTAATTAAATTTAAA
40448245 TTTTTACATTTAAATTTAAA
1 TTTTTA-A-TTAAATTTAAA
40448265 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 7 0.16
17 22 0.51
18 4 0.09
19 1 0.02
20 9 0.21
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (18 bp):
TTTTTAATTAAATTTAAA
Found at i:40448226 original size:6 final size:6
Alignment explanation
Indices: 40448203--40448280 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
40448193 TTTTTTTATT
* **
40448203 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
* *
40448251 CATTTA AATTTA AA-ATA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
40448281 CCATGAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 11 0.19
6 41 0.72
8 5 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:40448291 original size:18 final size:17
Alignment explanation
Indices: 40448203--40448294 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 17
40448193 TTTTTTTATT
* *
40448203 AATTTAAATTTTAATTA
1 AATTTAAATTTAAAATA
**
40448220 AATTTAAATTTAAAGCA
1 AATTTAAATTTAAAATA
*
40448237 AATTTAAATTT---TTA
1 AATTTAAATTTAAAATA
*
40448251 CATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
40448268 AATTTAAATTTAACCATG
1 AATTTAAATTTAA-AATA
40448286 AATTTAAAT
1 AATTTAAAT
40448295 CTTGTTCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
14 11 0.18
17 39 0.64
18 11 0.18
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:40448655 original size:38 final size:39
Alignment explanation
Indices: 40448593--40449273 Score: 535
Period size: 39 Copynumber: 19.0 Consensus size: 39
40448583 TTGCTCTTCA
* * *
40448593 AAGACTTTGCTATCCAACTTTACTTCAATTTCAAGAGGAT-
1 AAGAC-TTGTTATCC-ACTCTACTTCAATTTCAAGGGGATG
*
40448633 AA-ACTTGCTATCCAACTCTACTTCAATTTC-AGGAGGAT-
1 AAGACTTGTTATCC-ACTCTACTTCAATTTCAAGG-GGATG
* * *
40448671 --GAC--G-T-TGCTCT-TACTTCAATTTC-A-GAGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
40448701 AAGACATGTTATCCACTCTACTTCAATTTCAAGGGGAT-
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * *
40448739 --GAC--G-T-TGCTCT-TACTTCAATTTC-A-GAGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
40448769 AAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT-
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * *
40448807 --GAC--G-T-TGCTCT-TACTTCAATTTC-A-GAGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* *
40448837 AAGACGTGTTATCCACTCTACTTTAATTTCAAGGGGAT-
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* *
40448875 --GAC--G-T-TGCTCT-TACTTCAATTTCGAA---GATG
1 AAGACTTGTTATCCACTCTACTTCAATTTC-AAGGGGATG
*
40448905 AAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
40448944 AAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* *
40448983 GAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT-
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * *
40449021 --GAC--G-T-TGCTCT-TACTTCAATTTC-A-GAGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
40449051 AAGACATT-TTATCCACTCTACTTCAATTTCAA-GGGATG
1 AAGAC-TTGTTATCCACTCTACTTCAATTTCAAGGGGATG
40449089 AAGACGTT-TTATCCACTCTACTTCAATTTCAA-GGGATG
1 AAGAC-TTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
40449127 AAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
40449166 AAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGAT-
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
* * *
40449204 --GAC--G-T-TGCTCT-TACTTCAATTTC--GGAGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
*
40449234 AAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATG
1 AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
40449273 A
1 A
40449274 CGTTGAGACC
Statistics
Matches: 532, Mismatches: 43, Indels: 133
0.75 0.06 0.19
Matches are distributed among these distances:
29 23 0.04
30 4 0.01
31 72 0.14
32 42 0.08
33 7 0.01
34 11 0.02
35 7 0.01
36 41 0.08
37 76 0.14
38 104 0.20
39 143 0.27
40 2 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (39 bp):
AAGACTTGTTATCCACTCTACTTCAATTTCAAGGGGATG
Found at i:40448686 original size:31 final size:31
Alignment explanation
Indices: 40448651--40448897 Score: 167
Period size: 31 Copynumber: 7.4 Consensus size: 31
40448641 TATCCAACTC
40448651 TACTTCAATTTCAGGAGGATGACGTTGCTCT
1 TACTTCAATTTCAGGAGGATGACGTTGCTCT
* * * *
40448682 TACTTCAATTTCAGAGATGAAGACATGTTATCCACT
1 TACTTCAATTTCAG-GAGGATGAC--G-T-TGCTCT
40448718 CTACTTCAATTTCAAGG-GGATGACGTTGCTCT
1 -TACTTCAATTTC-AGGAGGATGACGTTGCTCT
* * * *
40448750 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACT
1 TACTTCAATTTCAG-GAGGATGAC--G-T-TGCTCT
40448786 CTACTTCAATTTCAAGG-GGATGACGTTGCTCT
1 -TACTTCAATTTC-AGGAGGATGACGTTGCTCT
* * * *
40448818 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACT
1 TACTTCAATTTCAG-GAGGATGAC--G-T-TGCTCT
*
40448854 CTACTTTAATTTCAAGG-GGATGACGTTGCTCT
1 -TACTTCAATTTC-AGGAGGATGACGTTGCTCT
40448886 TACTTCAATTTC
1 TACTTCAATTTC
40448898 GAAGATGAAG
Statistics
Matches: 167, Mismatches: 26, Indels: 46
0.70 0.11 0.19
Matches are distributed among these distances:
30 4 0.02
31 51 0.31
32 29 0.17
33 3 0.02
34 6 0.04
35 3 0.02
36 27 0.16
37 38 0.23
38 6 0.04
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (31 bp):
TACTTCAATTTCAGGAGGATGACGTTGCTCT
Found at i:40448739 original size:68 final size:68
Alignment explanation
Indices: 40448612--40449166 Score: 740
Period size: 68 Copynumber: 7.9 Consensus size: 68
40448602 CTATCCAACT
* *
40448612 TTACTTCAATTTCAAGAGGAT-AA-ACTTGCTATCCAACTCTACTTCAATTTC-AGGAGGATGAC
1 TTACTTCAATTTC-AGA-GATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGG-GGATGAC
40448674 GTTGCTC
62 GTTGCTC
*
40448681 TTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
40448746 CTC
66 CTC
40448749 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
40448814 CTC
66 CTC
*
40448817 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTTAATTTCAAGGGGATGACGTTG
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
40448882 CTC
66 CTC
*
40448885 TTACTTCAATTTC-GAAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAAGAC
1 TTACTTCAATTTCAG-AGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGAT---GA-
* *
40448949 CTGTTATCCAC
61 C-G-T-TGCTC
* *
40448960 TCTACTTCAATTTCAAGGGGATGGAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
1 T-TACTTCAATTTC-A-GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACG
40449025 TTGCTC
63 TTGCTC
* * *
40449031 TTACTTCAATTTCAGAGATGAAGACATTTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGT
1 TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG--GATGACG-
* *
40449096 TTTATCCAC
63 --T-TGCTC
*
40449105 TCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGA
1 T-TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGA
40449167 AGACCTGTTA
Statistics
Matches: 439, Mismatches: 24, Indels: 41
0.87 0.05 0.08
Matches are distributed among these distances:
67 4 0.01
68 260 0.59
69 26 0.06
70 18 0.04
71 6 0.01
72 2 0.00
73 3 0.01
74 10 0.02
75 18 0.04
76 51 0.12
78 40 0.09
79 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (68 bp):
TTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
CTC
Found at i:40448960 original size:107 final size:109
Alignment explanation
Indices: 40448776--40449273 Score: 523
Period size: 107 Copynumber: 4.6 Consensus size: 109
40448766 ATGAAGACGT
** * * * *
40448776 GTTATCCACTCTACTTCAATTTCAAGGGGATGA-C-G-T-TGCTCT-TACTTCAATTTC-A-GAG
1 GTTATCCACTCTACTTCAATTTCAAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGG
* *
40448834 ATGAAGACGTGTTATCCACTCTACTTTAATTTCAAGGGGATGAC
66 ATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
* *
40448878 G-T-TGCTCT-TACTTCAATTTCGAAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGG
1 GTTATCCACTCTACTTCAATTTC-AAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGG
40448940 GATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGGAGAC
65 GATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGAT---GAC
** * * *
40448988 GTGTTATCCACTCTACTTCAATTTCAAGGGGATGA-C-G-T-TGCTCT-TACTTCAATTTC-A-G
1 --GTTATCCACTCTACTTCAATTTCAAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGG
* * * *
40449046 AGATGAAGACATTTTATCCACTCTACTTCAATTTCAAGGGATGAAGAC
64 GGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGG--GATGAC
*
40449094 GTTTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA
1 G--TTATCCACTCTACTTCAATTTCAA--GATGAAGACCTGTTATCCACTCTACTTCAATTTCAA
40449159 GGGGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
62 GGGGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
* * * *
40449207 G-T-TGCTCT-TACTTCAATTTCGGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
1 GTTATCCACTCTACTTCAATTTC-AAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGG
40449269 GATGA
65 GATGA
40449274 CGTTGAGACC
Statistics
Matches: 332, Mismatches: 34, Indels: 55
0.79 0.08 0.13
Matches are distributed among these distances:
99 12 0.04
100 11 0.03
101 2 0.01
102 2 0.01
103 1 0.00
104 5 0.02
105 12 0.04
106 28 0.08
107 123 0.37
108 18 0.05
109 19 0.06
110 9 0.03
111 2 0.01
112 6 0.02
113 20 0.06
114 12 0.04
115 50 0.15
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (109 bp):
GTTATCCACTCTACTTCAATTTCAAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGG
ATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAC
Found at i:40449131 original size:183 final size:179
Alignment explanation
Indices: 40448603--40449273 Score: 772
Period size: 183 Copynumber: 3.7 Consensus size: 179
40448593 AAGACTTTGC
* * * *
40448603 TATCCAACTTTACTTCAATTTCAAGAGGATAAACTTGCTATCCAACTCTACTTCAATTTC-AGGA
1 TATCC-ACTCTACTTCAATTTCAAGGGGATAGAC-TGTTATCC-ACTCTACTTCAATTTCAAGG-
40448667 GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCA
62 GGATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCA
* * * *
40448732 AGGG--GATGACG--T-TGCTCT-TACTTCAATTTC-AGAGATGAAGACGTGT
127 AGGGATGAAGACGTTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
* * **
40448778 TATCCACTCTACTTCAATTTCAAGGGGAT-GAC-G-T-TGCTCT-TACTTCAATTTCAGAGATGA
1 TATCCACTCTACTTCAATTTCAAGGGGATAGACTGTTATCCACTCTACTTCAATTTCA-AGGGGA
* * * * ** * * *
40448838 AGACGTGTTATCCACTCTACTTTAATTTCA-AGGGGATGAC--G-T-TGCTCT-TACTTCAATTT
65 TGAC--G-T-TGCTCT-TACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTT
* *
40448897 CGAA--GATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGAAGACCTGT
125 C-AAGGGATGAAGACGT-TTATCCACTCTACTTCAATTTCAA-GGGATGAAGACGTGT
40448953 TATCCACTCTACTTCAATTTCAAGGGGATGGAGACGTGTTATCCACTCTACTTCAATTTCAAGGG
1 TATCCACTCTACTTCAATTTCAAGGGGAT--AGAC-TGTTATCCACTCTACTTCAATTTCAAGGG
*
40449018 GATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATTTTATCCACTCTACTTCAATTTCAA
63 GATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAA
40449083 GGGATGAAGACGTTTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
128 GGGATGAAGACG-TTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
40449136 TATCCACTCTACTTCAATTTCAAGGGGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGG
1 TATCCACTCTACTTCAATTTCAAGGGGAT--AGA-CTGTTATCCACTCTACTTCAATTTCAAGGG
* *
40449201 GATGACGTTGCTCTTACTTCAATTTCGGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAA
63 GATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAA
40449266 GGGGATGA
128 -GGGATGA
40449274 CGTTGAGACC
Statistics
Matches: 418, Mismatches: 42, Indels: 63
0.80 0.08 0.12
Matches are distributed among these distances:
166 1 0.00
167 24 0.06
168 18 0.04
169 5 0.01
170 3 0.01
171 3 0.01
172 15 0.04
173 26 0.06
174 23 0.06
175 47 0.11
177 12 0.03
178 14 0.03
179 1 0.00
180 2 0.00
181 2 0.00
182 17 0.04
183 163 0.39
184 41 0.10
185 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (179 bp):
TATCCACTCTACTTCAATTTCAAGGGGATAGACTGTTATCCACTCTACTTCAATTTCAAGGGGAT
GACGTTGCTCTTACTTCAATTTCAGAGATGAAGACATGTTATCCACTCTACTTCAATTTCAAGGG
ATGAAGACGTTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGT
Found at i:40449244 original size:68 final size:69
Alignment explanation
Indices: 40449145--40449278 Score: 234
Period size: 68 Copynumber: 1.9 Consensus size: 69
40449135 TTATCCACTC
*
40449145 TACTTCAATTTCAAGGGGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
1 TACTTCAATTTC-AGGAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
40449210 GCTCT
65 GCTCT
*
40449215 TACTTCAATTTC-GGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 TACTTCAATTTCAGGAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
40449279 AGACCTGCAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 50 0.81
70 12 0.19
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (69 bp):
TACTTCAATTTCAGGAGATGAAGACCTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
CTCT
Found at i:40461228 original size:29 final size:31
Alignment explanation
Indices: 40461188--40461409 Score: 124
Period size: 30 Copynumber: 7.5 Consensus size: 31
40461178 CCGGGGAGGC
*
40461188 AAAATGGTAATTTT-GGTGTAATCGGGGTTA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
*** * *
40461218 AAAATGG-AATTTTAAAAG-ATTCGGGGGT-
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
* * * **
40461246 AAAATGGCAATCTTCGGTGAAATTAGGGTTA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
** ** *
40461277 AAAATGG-AATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
* * *
40461305 AAAATGGTAATTTTCGGTAAAATCGAGGTTA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
** ** *
40461336 AAAATGG-AATTTTAGAAG-CTTCGGGGGT-
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
* *
40461364 AAAATGGTAATTTTTGGTGAAATCGAGGTTA
1 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
*
40461395 AAAACGG-AATTTTAG
1 AAAATGGTAATTTTAG
40461410 TAGCTTCGGG
Statistics
Matches: 134, Mismatches: 48, Indels: 20
0.66 0.24 0.10
Matches are distributed among these distances:
28 21 0.16
29 46 0.34
30 47 0.35
31 20 0.15
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (31 bp):
AAAATGGTAATTTTAGGTGAAATCGGGGTTA
Found at i:40461280 original size:59 final size:59
Alignment explanation
Indices: 40461188--40461436 Score: 351
Period size: 59 Copynumber: 4.2 Consensus size: 59
40461178 CCGGGGAGGC
* * * *
40461188 AAAATGGTAATTTT-GGTGTAATCGGGGTTAAAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
* * *
40461246 AAAATGGCAATCTTCGGTGAAAT-TAGGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGA-GGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
*
40461305 AAAATGGTAATTTTCGGTAAAATCGAGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
* * *
40461364 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAACGGAATTTTAGTAGCTTCGGGGGT
1 AAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
*
40461423 CAAAAT-ATAATTTT
1 -AAAATGGTAATTTT
40461437 GGAAAAGTTT
Statistics
Matches: 171, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
58 12 0.07
59 153 0.89
60 6 0.04
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAGCTTCGGGGGT
Found at i:40461454 original size:30 final size:30
Alignment explanation
Indices: 40461418--40461556 Score: 251
Period size: 30 Copynumber: 4.6 Consensus size: 30
40461408 AGTAGCTTCG
40461418 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
40461448 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
40461478 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
* *
40461508 GGAGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATATAATTTTGGAAAAGTTTT
*
40461538 GGGGTCGAAATATAATTTT
1 GGGGTCAAAATATAATTTT
40461557 TAGACAATTT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 104 1.00
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
GGGGTCAAAATATAATTTTGGAAAAGTTTT
Found at i:40461827 original size:161 final size:161
Alignment explanation
Indices: 40461659--40461967 Score: 444
Period size: 161 Copynumber: 1.9 Consensus size: 161
40461649 GAAAACTTTG
* * * *
40461659 AAAAAATT-TTGGACCAATTTTGTAATT-AACTAAGAGTTAATTTAAGGACTAAATTAAAATAAA
1 AAAAAATTATTGGACCAATTTCGTAATTAAAATAA-AGCTAATTT-AGGACTAAATTAAAACAAA
* * **
40461722 TTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAA-AAATTGACACGTGGCAACCTCTGGTGC
64 TTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAA-TGACACGTGGCAACCTCTGGCAC
40461786 AGTCAAACAGTCAAAGGACTAGTTTATAAACCTT
128 AGTCAAACAGTCAAAGGACTAGTTTATAAACCTT
* * * *
40461820 AAAAAATTATTGGGCCAATTTCGTAATTAAAATAAAGCTGATTTGGGATTAAATTAAAACAAATT
1 AAAAAATTATTGGACCAATTTCGTAATTAAAATAAAGCTAATTTAGGACTAAATTAAAACAAATT
* *
40461885 AAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACATGACACGTGGCAACCTCTGGCACAGT
66 AAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCTCTGGCACAGT
40461950 CAAACAGTCAAAGGACTA
131 CAAACAGTCAAAGGACTA
40461968 AATTATAATC
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
161 100 0.76
162 26 0.20
163 5 0.04
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.25
Consensus pattern (161 bp):
AAAAAATTATTGGACCAATTTCGTAATTAAAATAAAGCTAATTTAGGACTAAATTAAAACAAATT
AAAAATAAAAAGGACTAAATGCAGAAATAAGCCAATAAATGACACGTGGCAACCTCTGGCACAGT
CAAACAGTCAAAGGACTAGTTTATAAACCTT
Found at i:40462051 original size:161 final size:157
Alignment explanation
Indices: 40461702--40462051 Score: 384
Period size: 161 Copynumber: 2.2 Consensus size: 157
40461692 GAGTTAATTT
* * *
40461702 AAGGACTAAATTAAAATAAATTAAAAATAGAAGGGACTAAATGCAGAAATAAGCCAAAAATTGAC
1 AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
** ** **
40461767 ACGTGGCAACCTCTGGTGCAGTCAAACAGTCAAAGGACTAGTTTATAAACCTTAAAAAATTATTG
66 ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTT-AAAAATTACAG
* * *
40461832 GGCCAATTTCGTAATTAAAATAAAGCTG
130 GGCAAATTTCATAATTAAAATAAAGCAG
* * * *
40461860 ATTTGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAATCCAATACA-
1 A---AGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAA-AAAT
*
40461924 TGACACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAATCCAATT-AAAAT
62 TGACACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACC--TTAAAAAT
*
40461988 TACAGGGCAAATTTACAAATAATTAAAA-AGATGCAAG
125 TACAGGGCAAATTT-C--ATAATTAAAATA-AAGC-AG
* *
40462025 AAGGACTAAATTGAAGCAAA-TAAAAAT
1 AAGGACTAAATTAAAACAAATTAAAAAT
40462052 GCGGAAGGAT
Statistics
Matches: 159, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
158 1 0.01
161 123 0.77
162 18 0.11
163 3 0.02
164 12 0.08
165 2 0.01
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (157 bp):
AAGGACTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCAGAAATAAGCCAAAAATTGAC
ACGTGGCAACCTCTGGCACAGTCAAACAGTCAAAGGACTAAATTATAAACCTTAAAAATTACAGG
GCAAATTTCATAATTAAAATAAAGCAG
Found at i:40462732 original size:15 final size:15
Alignment explanation
Indices: 40462712--40462749 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
40462702 TATAAAATAT
* *
40462712 TTATTATTATTACTG
1 TTATTATTATCACTA
40462727 TTATTATTATCACTA
1 TTATTATTATCACTA
40462742 TTATTATT
1 TTATTATT
40462750 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:40462752 original size:24 final size:24
Alignment explanation
Indices: 40462716--40462771 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
40462706 AAATATTTAT
*
40462716 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
40462740 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
40462764 TATTATTA
1 TATTATTA
40462772 ACCATCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:40463474 original size:17 final size:18
Alignment explanation
Indices: 40463454--40463524 Score: 67
Period size: 17 Copynumber: 4.0 Consensus size: 18
40463444 TCTATTTGGT
*
40463454 TTTTTTATT-AATTTAAA
1 TTTTTAATTAAATTTAAA
40463471 -TTTTAATTAAATTTAAA
1 TTTTTAATTAAATTTAAA
* **
40463488 -TTTAAAGCAAATTTAAA
1 TTTTTAATTAAATTTAAA
40463505 TTTTTACATTTAAATTTAAA
1 TTTTTA-A-TTAAATTTAAA
40463525 ATAAATTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 7 0.16
17 22 0.51
18 4 0.09
19 1 0.02
20 9 0.21
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (18 bp):
TTTTTAATTAAATTTAAA
Found at i:40463486 original size:6 final size:6
Alignment explanation
Indices: 40463463--40463540 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
40463453 TTTTTTTATT
* **
40463463 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTA AATTTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA--TTTA
* *
40463511 CATTTA AATTTA AA-ATA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
40463541 CCATGAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
5 11 0.19
6 41 0.72
8 5 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:40463551 original size:18 final size:17
Alignment explanation
Indices: 40463463--40463554 Score: 82
Period size: 17 Copynumber: 5.5 Consensus size: 17
40463453 TTTTTTTATT
* *
40463463 AATTTAAATTTTAATTA
1 AATTTAAATTTAAAATA
**
40463480 AATTTAAATTTAAAGCA
1 AATTTAAATTTAAAATA
*
40463497 AATTTAAATTT---TTA
1 AATTTAAATTTAAAATA
*
40463511 CATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
40463528 AATTTAAATTTAACCATG
1 AATTTAAATTTAA-AATA
40463546 AATTTAAAT
1 AATTTAAAT
40463555 CTTGTTCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
14 11 0.18
17 39 0.64
18 11 0.18
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:40463939 original size:28 final size:28
Alignment explanation
Indices: 40463902--40463972 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 28
40463892 AACAGTCCAG
* *
40463902 AAATTGCATTTTAACCC-AAAATTTTAGA
1 AAATTACATTTTAACCCGAAAATTCTA-A
* *
40463930 AAATTACATTTTGACCCCGAAACTTCTAA
1 AAATTACATTTT-AACCCGAAAATTCTAA
40463959 AAATTATCATTTTA
1 AAATTA-CATTTTA
40463973 CCGTTCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 11 0.31
29 12 0.33
30 13 0.36
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (28 bp):
AAATTACATTTTAACCCGAAAATTCTAA
Found at i:40464088 original size:59 final size:59
Alignment explanation
Indices: 40463957--40464330 Score: 504
Period size: 59 Copynumber: 6.4 Consensus size: 59
40463947 CGAAACTTCT
* ** * * *
40463957 AAAAATTATCATTTTACCGTTCAAAC-TTCTAAAATTCCATTTTTAACCCCGGTTTGACC
1 AAAAATTACCATTTTACC-CCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
40464016 -AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTTACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
40464074 AAAAATTGCCATTTTGCCCCCAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCA-C
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* *
40464132 AAAAATTACTATTTTACCCCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTA--CCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
40464193 AAAAATTACCATTTTACCCTCAAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * * *
40464252 AAAAATTACTATTTTACCCCCGAACTCTCAAAAATTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
*
40464311 -AAAATTACCATTTTGCCCCC
1 AAAAATTACCATTTTACCCCC
40464331 GGGTATCCAA
Statistics
Matches: 279, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
57 5 0.02
58 76 0.27
59 143 0.51
60 39 0.14
61 16 0.06
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:40464178 original size:31 final size:30
Alignment explanation
Indices: 40464090--40464301 Score: 83
Period size: 29 Copynumber: 7.1 Consensus size: 30
40464080 TGCCATTTTG
* *
40464090 CCCCCAAACTTTCCAAAATTTCATTTTTA-
1 CCCCCGAACTTTCCAAAATTACATTTTTAC
*
40464119 ACCCCG-A-TTTCACAAAAATTAC-TATTTTACC
1 CCCCCGAACTTTC-C-AAAATTACAT-TTTTA-C
*
40464150 CCCCCGAACTTTCCAAAATTCCATTTTTA-
1 CCCCCGAACTTTCCAAAATTACATTTTTAC
*
40464179 ACCCCG-A-TTTCACCAAAAATTACCA-TTTTA-
1 CCCCCGAACTTT--CC-AAAATTA-CATTTTTAC
* * * *
40464209 CCCTCAAACTTTCTAAAATTCCATTTTTA-
1 CCCCCGAACTTTCCAAAATTACATTTTTAC
* *
40464238 ACCCCG--GTTTCACCAAAAATTAC-TATTTTA-
1 CCCCCGAACTTT--CC-AAAATTACAT-TTTTAC
* * * *
40464268 CCCCCGAACTCTCAAAAATTCCATTTTTAA
1 CCCCCGAACTTTCCAAAATTACATTTTTAC
40464298 CCCC
1 CCCC
40464302 GATTTCACCA
Statistics
Matches: 137, Mismatches: 23, Indels: 45
0.67 0.11 0.22
Matches are distributed among these distances:
27 10 0.07
28 6 0.04
29 51 0.37
30 38 0.28
31 20 0.15
32 8 0.06
33 4 0.03
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (30 bp):
CCCCCGAACTTTCCAAAATTACATTTTTAC
Found at i:40464205 original size:119 final size:117
Alignment explanation
Indices: 40463978--40464330 Score: 539
Period size: 119 Copynumber: 3.0 Consensus size: 117
40463968 TTTTACCGTT
* * * *
40463978 CAAAC-TTCTAAAATTCCATTTTTAACCCCGGTTTGACCAAAATTACCATTTTACCCCCAAACTT
1 CAAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACAAAAATTACTATTTTACCCCCGAACTT
* * *
40464042 TCCAAAATTCCATTTTTTACCTCGATTTCACCAAAAATTGCCATTTTGCCCC
66 TCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCC
* * *
40464094 CAAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACAAAAATTACTATTTTACCCCCCCGAAC
1 CAAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACAAAAATTACTATTTTA--CCCCCGAAC
* *
40464159 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCT
64 TTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCC
40464213 CAAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACTATTTTACCCCCGAACT
1 CAAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCA-CAAAAATTACTATTTTACCCCCGAACT
* *
40464278 CTCAAAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTGCCCC
65 TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCC
40464330 C
1 C
40464331 GGGTATCCAA
Statistics
Matches: 214, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
116 5 0.02
117 60 0.28
118 41 0.19
119 91 0.43
120 17 0.08
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (117 bp):
CAAACTTTCTAAAATTCCATTTTTAACCCCGGTTTCACAAAAATTACTATTTTACCCCCGAACTT
TCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCC
Found at i:40464295 original size:178 final size:177
Alignment explanation
Indices: 40463987--40464330 Score: 526
Period size: 178 Copynumber: 1.9 Consensus size: 177
40463977 TCAAACTTCT
* *
40463987 AAAATTCCATTTTTAACCCCGGTTTGACCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC
* * * * * * *
40464052 CATTTTTTACCTCGATTTCACCAAAAATTGCCATTTTGCCCCCAAACTTTCCAAAATTTCATTTT
66 CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTT
*
40464117 TAACCCCGATTTCACAAAAATTACTATTTTACCCCCCCGAACTTTCC
131 TAACCCCGATTTCACAAAAATTACCATTTTACCCCCCCGAACTTTCC
* *
40464164 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCAAACTTTCTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCCAAACTTTCCAAAATT
* * *
40464229 CCATTTTTAACCCCGGTTTCACCAAAAATTACTATTTTACCCCCGAACTCTCAAAAATTCCATTT
65 CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTT
* *
40464294 TTAACCCCGATTTCACCAAAATTACCATTTTGCCCCC
130 TTAACCCCGATTTCACAAAAATTACCATTTTACCCCC
40464331 GGGTATCCAA
Statistics
Matches: 149, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
177 27 0.18
178 122 0.82
ACGTcount: A:0.31, C:0.31, G:0.04, T:0.34
Consensus pattern (177 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC
CATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTCTCAAAAATTCCATTTT
TAACCCCGATTTCACAAAAATTACCATTTTACCCCCCCGAACTTTCC
Found at i:40465576 original size:23 final size:23
Alignment explanation
Indices: 40465549--40465598 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
40465539 AATTTTAAAA
40465549 TAAATTTAAAATCAAAGT-AAGTT
1 TAAATTTAAAAT-AAAGTAAAGTT
*
40465572 TAAATTTAAAATAAATTAAAGTT
1 TAAATTTAAAATAAAGTAAAGTT
40465595 TAAA
1 TAAA
40465599 AACAATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (23 bp):
TAAATTTAAAATAAAGTAAAGTT
Found at i:40465598 original size:17 final size:17
Alignment explanation
Indices: 40465531--40465599 Score: 77
Period size: 17 Copynumber: 4.0 Consensus size: 17
40465521 CAATTTATAT
40465531 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
* * *
40465549 TAAATTTAAAATCAAAG
1 TAAATTTAAATTTAAAA
*
40465566 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
40465583 TAAA-TTAAAGTTTAAAA
1 TAAATTTAAA-TTTAAAA
40465600 ACAATTCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
16 5 0.12
17 27 0.64
18 10 0.24
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40465966 original size:21 final size:21
Alignment explanation
Indices: 40465940--40465979 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40465930 TTCATTTTTC
*
40465940 TCATAAAAAATCTTAAAAACA
1 TCATAAAAAATATTAAAAACA
40465961 TCATAAAAAATATTAAAAA
1 TCATAAAAAATATTAAAAA
40465980 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (21 bp):
TCATAAAAAATATTAAAAACA
Found at i:40465967 original size:11 final size:10
Alignment explanation
Indices: 40465940--40465988 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
40465930 TTCATTTTTC
40465940 TCATAAAAAA
1 TCATAAAAAA
*
40465950 TCTTAAAAACA
1 TCATAAAAA-A
40465961 TCATAAAAAA
1 TCATAAAAAA
*
40465971 T-ATTAAAAA
1 TCATAAAAAA
40465980 T-A-AAAAAA
1 TCATAAAAAA
40465988 T
1 T
40465989 TATATAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 6 0.18
9 9 0.26
10 10 0.29
11 9 0.26
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (10 bp):
TCATAAAAAA
Found at i:40466012 original size:29 final size:29
Alignment explanation
Indices: 40465980--40466046 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
40465970 ATATTAAAAA
*
40465980 TAAAAAAATTATATAA-ACTTATAGAAGTT
1 TAAAAAAATTATA-AATACTTATAGAAATT
**
40466009 TAAAAATTTTATAAATACTTATAGAAATT
1 TAAAAAAATTATAAATACTTATAGAAATT
*
40466038 TATAAAAAT
1 TAAAAAAAT
40466047 ATCATTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 2 0.06
29 29 0.94
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (29 bp):
TAAAAAAATTATAAATACTTATAGAAATT
Found at i:40466060 original size:24 final size:22
Alignment explanation
Indices: 40466009--40466068 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 22
40465999 TATAGAAGTT
*
40466009 TAAAAATTT-TATAAATACTTA
1 TAAAAATTTATAAAAATACTTA
*
40466030 TAGAAATTTATAAAAATATCATTA
1 TAAAAATTTATAAAAATA-C-TTA
40466054 TAAAAATTATATAAA
1 TAAAAATT-TATAAA
40466069 CTTATAGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 8 0.25
22 7 0.22
23 1 0.03
24 10 0.31
25 6 0.19
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAAAATTTATAAAAATACTTA
Found at i:40467492 original size:12 final size:12
Alignment explanation
Indices: 40467475--40467501 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40467465 AAGAATTAGT
40467475 AAGTCTATGTTA
1 AAGTCTATGTTA
40467487 AAGTCTATGTTA
1 AAGTCTATGTTA
40467499 AAG
1 AAG
40467502 CATAGACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (12 bp):
AAGTCTATGTTA
Found at i:40470214 original size:10 final size:10
Alignment explanation
Indices: 40470195--40470224 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40470185 TATCGTCGGA
40470195 GTATATTAAT
1 GTATATTAAT
*
40470205 GTATACTAAT
1 GTATATTAAT
40470215 GTATATTAAT
1 GTATATTAAT
40470225 TGTTCAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (10 bp):
GTATATTAAT
Found at i:40473776 original size:625 final size:627
Alignment explanation
Indices: 40472451--40475307 Score: 4912
Period size: 627 Copynumber: 4.6 Consensus size: 627
40472441 ATTATCCGGC
* * * * *
40472451 CAGATTCC-ATCTTCCATCTTCAA-GATTTCTTCTCTAAAGATTATTAG-TCT-CCTCAGCAATA
1 CAGATTCCGA-CTTCGATCTTCAACG-TTTCTTCTCTGAAGACTATT-GTTCTATC-CAACAATA
* **
40472512 GTCTATTAGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTG
62 GCCTATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTG
* *
40472577 AGTTGGAATGAATTATCTGGTAACATTCCGTCAAGTACAGACAAATGCAACAACCTTAAAAATTT
127 AGTTGGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTT
* * *
40472642 GGCATTGTCC-ATTAATCAATTTATGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTC
192 GGCATTGTCCTA-TAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTT
* ** * * *
40472706 GAAAAATTATGGTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTGATGTTTTTAATTTAA
256 GAAGAATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAA
*
40472771 ACATTTGGACCCTTTTGTTTTTAAATTTTTTAAAATATATACTT-GTAATATAAATACCAAAAAT
321 ACATTT-GACCCTTTTGTTTTTAAATTTTTTAAAA-AAATA-TTGGTAATATAAATACCAAAAAT
* * * *
40472835 AAGGGAATTTTCTATGAAAGAAAAATACTTAATTAGCTGAACTGATATACTTATTTTTAGAATCT
383 AAAGGAATTTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCT
*
40472900 TACATATCCATATTATTTCATAACAAAAAAAAAGACTCTTTGATTTAGACTTACAAAATAGTTAG
448 TACATATCCATATTATTTCATAAC-AAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAG
* *
40472965 CTTTAACACCTTCATTTTTC-AACTATGTTAATTTGCAGGTCAAATTCCAGAGGAAATTGGTAAT
512 CTTTAACACCTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAAT
*
40473029 CTTTATAGCTTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
577 CTTTATAGTTTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
* *
40473080 CAGATTCCGACTTCGATCTTTAACATTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
1 CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
40473145 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
66 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
40473210 GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGCA
131 GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGCA
* *
40473275 TTATCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTCGAAGA
196 TTGTCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTTGAAGA
*
40473340 ATTATATTTGGGGTTTAATAACCTTGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
261 ATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
** *
40473405 TGACCCTTTTGTTTTTAAA-TTTTTAAAAAAATATTTATAATATAAATACCAAAAATAAGGGAAT
326 TGACCCTTTTGTTTTTAAATTTTTTAAAAAAATATTGGTAATATAAATACCAAAAATAAAGGAAT
*
40473469 TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTACTTTTAGAATCTTACATATC
391 TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCTTACATATC
*
40473534 CATATTATTTCATAACAAAAAAAACCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
456 CATATTATTTCATAACAAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
* *
40473599 CTTCATTTTTC-AACTATGTTAATTTGCAGGTCAAATCCCTGAGGAAATTGGTAATCTTTATAGT
521 CTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAATCTTTATAGT
* *
40473663 TTGGAAATGCTTAATTTTCAAGCAATTAAAAGTCTTATAGGT
586 TTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
40473705 CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
1 CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
40473770 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
66 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
40473835 GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGCA
131 GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGCA
* *
40473900 TTATCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTGTCTCGACTTGAAGA
196 TTGTCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTTGAAGA
40473965 ATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
261 ATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
*
40474030 TGACCCTTTTGTTTTTAAATTTTTTAAAAAAATATTGGTAATATAAATGCCAAAAATAAAGGAAT
326 TGACCCTTTTGTTTTTAAATTTTTTAAAAAAATATTGGTAATATAAATACCAAAAATAAAGGAAT
40474095 TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCTTACATATC
391 TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCTTACATATC
*
40474160 CATATTATTTCATAGCAAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
456 CATATTATTTCATAACAAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
40474225 CTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAATCTTTATAGT
521 CTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAATCTTTATAGT
40474290 TTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
586 TTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
40474332 CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
1 CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
*
40474397 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACTTGAGTT
66 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
*
40474462 GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGACA
131 GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGCA
* *
40474527 TTGTACTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTGTCTCGACTTGAAGA
196 TTGTCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTTGAAGA
40474592 ATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
261 ATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
*
40474657 TGACCCTTTTGTTTTTAAATTTTTTAAAAAAATATTGGTAATATAAATGCCAAAAATAAAGGAAT
326 TGACCCTTTTGTTTTTAAATTTTTTAAAAAAATATTGGTAATATAAATACCAAAAATAAAGGAAT
40474722 TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCTTACATATC
391 TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCTTACATATC
*
40474787 CATATTATTTCATAGCAAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
456 CATATTATTTCATAACAAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
40474852 CTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAATCTTTATAGT
521 CTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAATCTTTATAGT
*
40474917 TTGGAAATGCTTAATATTCAAGCAATTAAGAGTCTTACAGGT
586 TTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
*
40474959 CAGATTCCGACTTCGACCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
1 CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
*
40475024 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGGGCTTTACTTGAGTT
66 ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
* * * *
40475089 GGAATGAGA-TATCTGGTAACATTCCGTCAAATATAGGCAAATGCAACAACCTTAAAAATTTGAC
131 GGAATGA-ATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGC
* *
40475153 ATTGTACTATAATCAATTTACGGGGATCATTCCAAGAAGTATTGGAAATCTGA-CTCGACTTGAA
195 ATTGTCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCT-ATCTCGACTTGAA
* * *
40475217 -AATT-TATGGTTGGAGTTTAATAACCTAGAAGGTATGCATTTTCTTTGATGTCTTTAGTTTAAA
259 GAATTATAT--TTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAA
*
40475280 CATTTGGCCCCTTTTGTTTTTAAATTTT
322 CATTT-GACCCTTTTGTTTTTAAATTTT
40475308 AAAATAAATT
Statistics
Matches: 2149, Mismatches: 66, Indels: 27
0.96 0.03 0.01
Matches are distributed among these distances:
625 492 0.23
626 291 0.14
627 1027 0.48
628 41 0.02
629 295 0.14
630 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (627 bp):
CAGATTCCGACTTCGATCTTCAACGTTTCTTCTCTGAAGACTATTGTTCTATCCAACAATAGCCT
ATCGGGTAGTTTGCCTAATGATATGTGTCAACATCTTCCCAAGCTTGAAGTGCTTTACTTGAGTT
GGAATGAATTATCTGGTAACATTCCGTCAAGTATAGACCAATGCAACAACCTTAAAAATTTGGCA
TTGTCCTATAATCAGTTTACGGGGATCATTCCAAGAAGTATTGGAAATCTATCTCGACTTGAAGA
ATTATATTTGGGGTTTAATAACCTAGAAGGTATGCATTTTCCTTAATGTCTTTAGTTTAAACATT
TGACCCTTTTGTTTTTAAATTTTTTAAAAAAATATTGGTAATATAAATACCAAAAATAAAGGAAT
TTTCTATGAAGGAAAAATACATAATTAGCTGAACTAATATACTTATTTTTAGAATCTTACATATC
CATATTATTTCATAACAAAAAAAAGCCTCTTTGATTTAGACTTACAAAATAGTTAGCTTTAACAC
CTTCATTTTTCAAACTATGTTAATCTGCAGGTCAAATTCCTGAGGAAATTGGTAATCTTTATAGT
TTGGAAATGCTTAATATTCAAGCAATTAAAAGTCTTACAGGT
Found at i:40475804 original size:16 final size:16
Alignment explanation
Indices: 40475783--40475814 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40475773 ATCAAAATAA
40475783 TAATGAATTATTAATT
1 TAATGAATTATTAATT
*
40475799 TAATGATTTATTAATT
1 TAATGAATTATTAATT
40475815 AATAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TAATGAATTATTAATT
Found at i:40476634 original size:12 final size:12
Alignment explanation
Indices: 40476614--40476661 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
40476604 TTTATTTCAT
40476614 ATAATTAAAAAA
1 ATAATTAAAAAA
*
40476626 ATTATTAAAAATA
1 ATAATTAAAAA-A
*
40476639 ATAAATAAAAAA
1 ATAATTAAAAAA
40476651 TATAATTAAAA
1 -ATAATTAAAA
40476662 TTTACAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATAATTAAAAAA
Found at i:40476670 original size:26 final size:25
Alignment explanation
Indices: 40476619--40476671 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
40476609 TTCATATAAT
* *
40476619 TAAAAAAATTATTAAAAATAATAAA
1 TAAAAAAATAATTAAAAATAACAAA
* *
40476644 TAAAAAATATAATTAAAATTTACAAA
1 TAAAAAA-ATAATTAAAAATAACAAA
40476670 TA
1 TA
40476672 TTTTTAATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAAAAAATAATTAAAAATAACAAA
Found at i:40478115 original size:10 final size:10
Alignment explanation
Indices: 40478102--40478166 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
40478092 AAAAAATAAT
40478102 AAAATTATTA
1 AAAATTATTA
40478112 AAAATTATTA
1 AAAATTATTA
* *
40478122 GAAATTGTTA
1 AAAATTATTA
* * *
40478132 CATATT-GTA
1 AAAATTATTA
*
40478141 AAAAATA-TA
1 AAAATTATTA
40478150 AAAATTATTA
1 AAAATTATTA
*
40478160 GAAATTA
1 AAAATTA
40478167 CAAAAGACAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 13 0.30
10 30 0.70
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (10 bp):
AAAATTATTA
Found at i:40478333 original size:27 final size:28
Alignment explanation
Indices: 40478292--40478353 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
40478282 GTATTTTTAT
*
40478292 AATTTTAGATTA-TTTCTATTTTTTAAAA
1 AATTTTAGATGATTTTCTATTTTTT-AAA
* *
40478320 AATTTTA-ATGATTTTGTATTTTTTAAG
1 AATTTTAGATGATTTTCTATTTTTTAAA
40478347 AATTTTA
1 AATTTTA
40478354 TATTTTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (28 bp):
AATTTTAGATGATTTTCTATTTTTTAAA
Found at i:40483350 original size:23 final size:23
Alignment explanation
Indices: 40483309--40483352 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40483299 ATATGTAATA
*
40483309 TATACATATTTTTCCTATTTTAT
1 TATACATATTTTTCATATTTTAT
* *
40483332 TATATATATTTTTTATATTTT
1 TATACATATTTTTCATATTTT
40483353 CGAAAATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (23 bp):
TATACATATTTTTCATATTTTAT
Found at i:40484207 original size:29 final size:28
Alignment explanation
Indices: 40484165--40484355 Score: 152
Period size: 29 Copynumber: 6.5 Consensus size: 28
40484155 CAAACTTTCA
*
40484165 AAAAAATCTCATTTTTGACCTCGAACTTCC
1 AAAAATTC-CATTTTT-ACCTCGAACTTCC
* *
40484195 AAAAATTCCATTTTTACCCACGAACTTTC
1 AAAAATTCCATTTTTA-CCTCGAACTTCC
* * * *
40484224 AAAAATTCCATTTTTGCCCCCCCAAAATTCC
1 AAAAATTCCATTTTT---ACCTCGAACTTCC
* *
40484255 AAATATTCCATTTTTACCCTCAAAC-TCC
1 AAAAATTCCATTTTTA-CCTCGAACTTCC
*
40484283 TAAAAATTCCATTTTTACCCCGAATCTTTCC
1 -AAAAATTCCATTTTTACCTCGAA-C-TTCC
*
40484314 -AAAATTCCATTTTTTACCTCGAATTTCC
1 AAAAATTCCA-TTTTTACCTCGAACTTCC
* *
40484342 CAAAATTACATTTT
1 AAAAATTCCATTTT
40484356 CGCCTCATAG
Statistics
Matches: 132, Mismatches: 18, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
28 17 0.13
29 71 0.54
30 19 0.14
31 25 0.19
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAAATTCCATTTTTACCTCGAACTTCC
Found at i:40484255 original size:60 final size:60
Alignment explanation
Indices: 40484191--40484303 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
40484181 GACCTCGAAC
* * *
40484191 TTCCAAAAATTCCATTTTTACCCACGAACT-TTCAAAAATTCCATTTTTGCCCCCCCAAAA
1 TTCCAAAAATTCCATTTTTACCCACAAACTCCT-AAAAATTCCATTTTTACCCCCCCAAAA
* *
40484251 TTCCAAATATTCCATTTTTACCCTCAAACTCCTAAAAATTCCATTTTTACCCC
1 TTCCAAAAATTCCATTTTTACCCACAAACTCCTAAAAATTCCATTTTTACCCC
40484304 GAATCTTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 46 0.98
61 1 0.02
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.35
Consensus pattern (60 bp):
TTCCAAAAATTCCATTTTTACCCACAAACTCCTAAAAATTCCATTTTTACCCCCCCAAAA
Found at i:40484543 original size:57 final size:58
Alignment explanation
Indices: 40484368--40484593 Score: 231
Period size: 58 Copynumber: 3.9 Consensus size: 58
40484358 CCTCATAGCA
* * **
40484368 TCCAAAAATTACATTTTCATCCCCGAGCGTCCAAAAATTATCATTTTGTCCCT-AAATG
1 TCCAAAAATTACATTTTCACCCCCGAGCGTCCAAAAATTACCATTTT-TCCCTCGGATG
* * ** * ** * ** *
40484426 TCTAAAAATTTCATTTTTGCTCTTGAGTGTCCAAAAATTATTATTTTTCCCCCGGATG
1 TCCAAAAATTACATTTTCACCCCCGAGCGTCCAAAAATTACCATTTTTCCCTCGGATG
* *
40484484 TCCAAAAATTACATTTTCACCCCCGAGCATCC-AAAATTACCATTTTACCCTCGGATG
1 TCCAAAAATTACATTTTCACCCCCGAGCGTCCAAAAATTACCATTTTTCCCTCGGATG
* ** * *
40484541 TCCAAAAATTACATTTTCTCCCTTGAGTGTCCAAAAATTACCATTTTGCCCTC
1 TCCAAAAATTACATTTTCACCCCCGAGCGTCCAAAAATTACCATTTTTCCCTC
40484594 AACATCAAAA
Statistics
Matches: 134, Mismatches: 32, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
57 52 0.39
58 82 0.61
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (58 bp):
TCCAAAAATTACATTTTCACCCCCGAGCGTCCAAAAATTACCATTTTTCCCTCGGATG
Found at i:40484592 original size:29 final size:29
Alignment explanation
Indices: 40484368--40484593 Score: 146
Period size: 29 Copynumber: 7.8 Consensus size: 29
40484358 CCTCATAGCA
* *
40484368 TCCAAAAATTA-CATTTT-CATCCCCGAGCG
1 TCCAAAAATTATCATTTTGC--CCTCGAGTG
* *
40484397 TCCAAAAATTATCATTTTGTCCCT-AAATG
1 TCCAAAAATTATCATTTTG-CCCTCGAGTG
* * *
40484426 TCTAAAAATT-TCATTTTTGCTCTTGAGTG
1 TCCAAAAATTATCA-TTTTGCCCTCGAGTG
* * *
40484455 TCCAAAAATTATTATTTTTCCCCCG-GATG
1 TCCAAAAATTATCATTTTGCCCTCGAG-TG
* * **
40484484 TCCAAAAATTA-CATTTTCACCCCCGAGCA
1 TCCAAAAATTATCATTTT-GCCCTCGAGTG
* *
40484513 TCC-AAAATTACCATTTTACCCTCG-GATG
1 TCCAAAAATTATCATTTTGCCCTCGAG-TG
* *
40484541 TCCAAAAATTA-CATTTTCTCCCTTGAGTG
1 TCCAAAAATTATCATTTT-GCCCTCGAGTG
*
40484570 TCCAAAAATTACCATTTTGCCCTC
1 TCCAAAAATTATCATTTTGCCCTC
40484594 AACATCAAAA
Statistics
Matches: 157, Mismatches: 25, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.01
28 34 0.22
29 103 0.66
30 18 0.11
32 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTATCATTTTGCCCTCGAGTG
Found at i:40484924 original size:9 final size:10
Alignment explanation
Indices: 40484902--40484926 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40484892 TTGGATATCC
40484902 TTTTCCAAGT
1 TTTTCCAAGT
40484912 TTTTCCAAGT
1 TTTTCCAAGT
40484922 TTTTC
1 TTTTC
40484927 AAATACCTGT
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:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (10 bp):
TTTTCCAAGT
Found at i:40488693 original size:17 final size:17
Alignment explanation
Indices: 40488673--40488718 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
40488663 TAATTTTTAT
*
40488673 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
40488690 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
40488707 TTTAAATTTATT
1 TTTAAATTTATT
40488719 CCCTTAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40491449 original size:97 final size:97
Alignment explanation
Indices: 40491264--40491457 Score: 241
Period size: 97 Copynumber: 2.0 Consensus size: 97
40491254 ACCCTTGAAA
** * * *
40491264 AAGGGTATTTGATTTTCCCGATTTGAAGAAAAGTCGTGTCTGATAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCAATTATCCCGATTTGAAGAAAAATCGTGCCTGATAAGTTAAGGCACAAATTTTCA
*
40491329 AAACCATAGATATAGAAACATTGCCTCGATTT
66 AAACCATAGATAAAGAAACATTGCCTCGATTT
* *
40491361 AAGGGTATTCAATTATCCCGGTTTGAAGAAAAATCGTGCCT-AGTAAGTTAAGGCATAAATTTTC
1 AAGGGTATTCAATTATCCCGATTTGAAGAAAAATCGTGCCTGA-TAAGTTAAGGCACAAATTTTC
* * *
40491425 AAAGCTCGA-A-ATAAAGGAATATTGCCTCGATTT
65 AAAAC-C-ATAGATAAAGAAACATTGCCTCGATTT
40491458 TAAATATTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 1 0.01
97 79 0.95
98 2 0.02
99 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (97 bp):
AAGGGTATTCAATTATCCCGATTTGAAGAAAAATCGTGCCTGATAAGTTAAGGCACAAATTTTCA
AAACCATAGATAAAGAAACATTGCCTCGATTT
Found at i:40492059 original size:30 final size:30
Alignment explanation
Indices: 40491837--40492177 Score: 271
Period size: 29 Copynumber: 11.6 Consensus size: 30
40491827 AAAGTGTGAT
**
40491837 TTTTTGGAAA-TTCAAGGG-CAAAATGGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAAAT-GTAA
* * *
40491866 TTTTTGG-ATGTTTGGGGGT-AAAATGGTAG
1 TTTTTGGAAAGTTTGAGGGTCAAAAT-GTAA
** * *
40491895 TTTTT-TTATGTTCGAGGGT-AAAATGGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAAAT-GTAA
*
40491924 TTTTTGG-AAGTTCGAGGG-CAAATATGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAA-ATGTAA
* * ** *
40491953 TTTTT-GAGAAGTTT-TGGGTAAAAACATGA
1 TTTTTGGA-AAGTTTGAGGGTCAAAATGTAA
*
40491982 TTTTT-GAAAGTTT-AGGGGTAAAAATGTAA
1 TTTTTGGAAAGTTTGA-GGGTCAAAATGTAA
** *
40492011 TTTTAAG-AAGTTTAAGGGTCAAAATGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAAATGTAA
*
40492040 TTTTTGGAAAGTTTGAGGGTTAAAATGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAAATGTAA
* *
40492070 TTTTTAGG-AGGTTTGAGGGTAAAAATGTAA
1 TTTTT-GGAAAGTTTGAGGGTCAAAATGTAA
* *
40492100 TTTTTGAAAAGTTCGAGGGTCAAAATGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAAATGTAA
* *
40492130 TTTTTGGAAAGTTCGAAGGTCAAAATGTAA
1 TTTTTGGAAAGTTTGAGGGTCAAAATGTAA
*
40492160 TTTTTGGAGAGTTT-AGGG
1 TTTTTGGAAAGTTTGAGGG
40492178 ACCTTTTGGG
Statistics
Matches: 259, Mismatches: 38, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.03
29 128 0.49
30 121 0.47
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
TTTTTGGAAAGTTTGAGGGTCAAAATGTAA
Found at i:40492095 original size:60 final size:59
Alignment explanation
Indices: 40491856--40492177 Score: 284
Period size: 60 Copynumber: 5.5 Consensus size: 59
40491846 ATTCAAGGGC
* * * ** * *
40491856 AAAATGGTAATTTTTGG-ATGTTTGGGGGT-AAAATGGTAGTTTTTTTATGTTCGAGGGT-
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGTCAAAAT-GTAATTTTTGGAAGTTTGAGGGTA
* *
40491914 AAAATGGTAATTTTTGG-AAGTTCGAGGG-CAAATATGTAATTTTTGAGAAGTTT-TGGGTA
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGGTCAAA-ATGTAATTTTTG-GAAGTTTGAGGGTA
** * * ** * *
40491973 AAAACATGATTTTT-GAAAGTTT-AGGGGTAAAAATGTAATTTTAAGAAGTTTAAGGGTC
1 AAAATGTAATTTTTGGAAAGTTTGA-GGGTCAAAATGTAATTTTTGGAAGTTTGAGGGTA
* *
40492031 AAAATGTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTTAGGAGGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAATGTAATTTTT-GGAAGTTTGAGGGTA
* * * * *
40492091 AAAATGTAATTTTTGAAAAGTTCGAGGGTCAAAATGTAATTTTTGGAAAGTTCGAAGGTC
1 AAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAATGTAATTTTTGG-AAGTTTGAGGGTA
*
40492151 AAAATGTAATTTTTGGAGAGTTT-AGGG
1 AAAATGTAATTTTTGGAAAGTTTGAGGG
40492178 ACCTTTTGGG
Statistics
Matches: 215, Mismatches: 37, Indels: 23
0.78 0.13 0.08
Matches are distributed among these distances:
57 9 0.04
58 80 0.37
59 44 0.20
60 82 0.38
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAATGTAATTTTTGGAAGTTTGAGGGTA
Found at i:40496931 original size:36 final size:38
Alignment explanation
Indices: 40496869--40497043 Score: 166
Period size: 36 Copynumber: 4.8 Consensus size: 38
40496859 TTGATGCCAC
* * *
40496869 AAAAAAGGTTGGG-TAGCCCTTATCTAAGGCAATC-TT
1 AAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTT
40496905 -AAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTT
1 AAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTT
** * * * * *
40496942 AAAAAAAATTGAGATAAACC-CGTTTAAGGAAACC-TT
1 AAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTT
* * *
40496978 AAAAGA-GTTGAGATAGACCTTGTCTCAGGCAACCTTT
1 AAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTT
* *
40497015 AAAAAAGATTGGGATAGACC-CGTCTAAGG
1 AAAAAAGGTTGGGATAGACCTTGTCTAAGG
40497044 TTGGGATGCA
Statistics
Matches: 111, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
35 23 0.21
36 35 0.32
37 27 0.24
38 26 0.23
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (38 bp):
AAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTT
Found at i:40496970 original size:37 final size:37
Alignment explanation
Indices: 40496891--40497043 Score: 134
Period size: 38 Copynumber: 4.2 Consensus size: 37
40496881 GTAGCCCTTA
* ** * *
40496891 TCTAAGGCAATC-TT-AAAAAGGTTGGGATAGACCTTG
1 TCTAAGGCAACCTTTAAAAAAAATTGAGATAGACC-CG
*
40496927 TCTAAGGCAACCTTTAAAAAAAATTGAGATAAACCCG
1 TCTAAGGCAACCTTTAAAAAAAATTGAGATAGACCCG
* * * * *
40496964 TTTAAGGAAACC-TT-AAAAGAGTTGAGATAGACCTTG
1 TCTAAGGCAACCTTTAAAAAAAATTGAGATAGACC-CG
* * *
40497000 TCTCAGGCAACCTTTAAAAAAGATTGGGATAGACCCG
1 TCTAAGGCAACCTTTAAAAAAAATTGAGATAGACCCG
40497037 TCTAAGG
1 TCTAAGG
40497044 TTGGGATGCA
Statistics
Matches: 91, Mismatches: 21, Indels: 9
0.75 0.17 0.07
Matches are distributed among these distances:
35 16 0.18
36 23 0.25
37 22 0.24
38 30 0.33
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (37 bp):
TCTAAGGCAACCTTTAAAAAAAATTGAGATAGACCCG
Found at i:40496993 original size:73 final size:72
Alignment explanation
Indices: 40496891--40497043 Score: 216
Period size: 73 Copynumber: 2.1 Consensus size: 72
40496881 GTAGCCCTTA
* * *
40496891 TCTAAGGCAATCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAAAATTGAGA
1 TCTAAGGAAACCTT-AAAAGGTTGAGATAGACCTTGTCTAAGGCAACCTTTAAAAAAAATTGAGA
40496956 TAAACCCG
65 TAAACCCG
* * * *
40496964 TTTAAGGAAACCTTAAAAGAGTTGAGATAGACCTTGTCTCAGGCAACCTTTAAAAAAGATTGGGA
1 TCTAAGGAAACCTTAAAAG-GTTGAGATAGACCTTGTCTAAGGCAACCTTTAAAAAAAATTGAGA
*
40497029 TAGACCCG
65 TAAACCCG
40497037 TCTAAGG
1 TCTAAGG
40497044 TTGGGATGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
72 5 0.07
73 65 0.93
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (72 bp):
TCTAAGGAAACCTTAAAAGGTTGAGATAGACCTTGTCTAAGGCAACCTTTAAAAAAAATTGAGAT
AAACCCG
Found at i:40498393 original size:126 final size:126
Alignment explanation
Indices: 40498168--40498492 Score: 443
Period size: 126 Copynumber: 2.6 Consensus size: 126
40498158 AATTAATTCG
* * * * * * * *
40498168 CCAACTCTTTTACAGAGAGTTGGCTAAAGCATTTGTCGATAAGTTTATCCTAATACTTAGGAAAG
1 CCAACTCTTATACAAAGAGTTGGCCAAAGCATATGTCGGTAAGTCTATCCCAACACTTAGGAAAG
* * *
40498233 CGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATATT
66 TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
* * *
40498294 CCAACTCTTATACAAAGAGTTGGCCAAAGCGTATGCCGGTAAGTCTACCCCAACACTTAGGAAAG
1 CCAACTCTTATACAAAGAGTTGGCCAAAGCATATGTCGGTAAGTCTATCCCAACACTTAGGAAAG
* * * *
40498359 TGTCGGCATAGTGTTGGATAAAGTCGACTCTTATTTAAGCGTTGTCTTAGGCATGCATATC
66 TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
* * * * *
40498420 CCAACCCTTATACAAAGAGTTGGCCAAAACATATGTCAGCAACTCTATCCCAACACTTAGGAAAG
1 CCAACTCTTATACAAAGAGTTGGCCAAAGCATATGTCGGTAAGTCTATCCCAACACTTAGGAAAG
40498485 TGTCGGCA
66 TGTCGGCA
40498493 CTCTTATTTA
Statistics
Matches: 173, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 173 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (126 bp):
CCAACTCTTATACAAAGAGTTGGCCAAAGCATATGTCGGTAAGTCTATCCCAACACTTAGGAAAG
TGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATATC
Found at i:40498748 original size:141 final size:139
Alignment explanation
Indices: 40498492--40498884 Score: 452
Period size: 141 Copynumber: 2.8 Consensus size: 139
40498482 AAGTGTCGGC
* * * ** *
40498492 ACTCTTATTTAAGCGTTGCCTTAGGCATGCATATCCCAACCCTTATACAAACTATTGGCCAAAGT
1 ACTCTTATTTAAGTGTTGCTTTAGGCATGCATATCCCAACCATTATACAAAGAATT-GCCAAAGC
* *
40498557 GTATGCCG-CAAGTCTATCCTAACACTTAGGAAAGTGTCAG-CCCAAAAGTGT-AACCATAGTGT
65 GTATGTCGACAAGTCTATCCCAACACTTAGGAAAGTGTC-GCCCCAAAAGTGTGAA-CATAGTGT
* **
40498619 TGGACAAAGCTG
128 TGGACAAAACCA
* * *
40498631 ACTCTTATTTGAGTGTTGCTTTAGGCATGCATATCCTAACCATTATACAAAAGAATTAGCAAAAG
1 ACTCTTATTTAAGTGTTGCTTTAGGCATGCATATCCCAACCATTATAC-AAAGAATT-GCCAAAG
* *
40498696 CGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGTGTCGCCCCAAAAGTGTGGACATATTGTT
64 CGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGTGTCGCCCCAAAAGTGTGAACATAGTGTT
40498761 GGACAAAACCA
129 GGACAAAACCA
* * * * *
40498772 ACTCTTAATTAAGTGTTG-TCTTAGGCATTCATATCCCAACCTTTATACGAAGAGTTGACCAAAG
1 ACTCTTATTTAAGTGTTGCT-TTAGGCATGCATATCCCAACCATTATACAAAGAATTG-CCAAAG
** * * * *
40498836 CGTATGTTTACAAATCTATCCCAACACTTAGAAAATTGTCGCTCCAAAA
64 CGTATGTCGACAAGTCTATCCCAACACTTAGGAAAGTGTCGCCCCAAAA
40498885 AAGTTGTCTT
Statistics
Matches: 217, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
139 44 0.20
140 75 0.35
141 97 0.45
142 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (139 bp):
ACTCTTATTTAAGTGTTGCTTTAGGCATGCATATCCCAACCATTATACAAAGAATTGCCAAAGCG
TATGTCGACAAGTCTATCCCAACACTTAGGAAAGTGTCGCCCCAAAAGTGTGAACATAGTGTTGG
ACAAAACCA
Found at i:40500159 original size:28 final size:28
Alignment explanation
Indices: 40500061--40500217 Score: 78
Period size: 28 Copynumber: 5.5 Consensus size: 28
40500051 TGCCCGGGGC
*
40500061 AAAATGGTAATTTT-GAACTTTCGAGGGT
1 AAAATGGTAATTTTAG-ACATTCGAGGGT
* * * *
40500089 AAAATGGTAATTTTGGAAAGATTTG-GAGTT
1 AAAATGGTAATTTT--AGACATTCGAG-GGT
40500119 AAAACT-G-ACATTTTAGACATTCGAGGGT
1 AAAA-TGGTA-ATTTTAGACATTCGAGGGT
* * *
40500147 AAAATGGTAATTTTTAGAAAAATCGA-GAT
1 AAAATGGTAA-TTTTAG-ACATTCGAGGGT
*
40500176 AAAAAATGG-AATTTTTGGACA-TCG-GGGT
1 --AAAATGGTAA-TTTTAGACATTCGAGGGT
40500204 AAAATGGTAATTTT
1 AAAATGGTAATTTT
40500218 TGCAAGTTTC
Statistics
Matches: 99, Mismatches: 15, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
26 11 0.11
27 3 0.03
28 33 0.33
29 14 0.14
30 30 0.30
31 8 0.08
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (28 bp):
AAAATGGTAATTTTAGACATTCGAGGGT
Found at i:40500190 original size:58 final size:58
Alignment explanation
Indices: 40500061--40500218 Score: 157
Period size: 58 Copynumber: 2.7 Consensus size: 58
40500051 TGCCCGGGGC
* * * * *
40500061 AAAATGGTAATTTTGAACTTTCGAGGGTAAAATGGTAA-TTTTGGAAAGATTTGGAGTTA
1 AAAATGG-AATTTTG-ACATTCGAGGGTAAAATGGTAATTTTTAGAAAGAATCGGAGTAA
*
40500120 AAACT-GACATTTTAGACATTCGAGGGTAAAATGGTAATTTTTAGAAA-AATC-GAGATAA
1 AAAATGGA-ATTTT-GACATTCGAGGGTAAAATGGTAATTTTTAGAAAGAATCGGAG-TAA
40500178 AAAATGGAATTTTTGGACA-TCG-GGGTAAAATGGTAATTTTT
1 AAAATGGAA-TTTT-GACATTCGAGGGTAAAATGGTAATTTTT
40500219 GCAAGTTTCA
Statistics
Matches: 85, Mismatches: 8, Indels: 14
0.79 0.07 0.13
Matches are distributed among these distances:
57 23 0.27
58 39 0.46
59 23 0.27
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTGACATTCGAGGGTAAAATGGTAATTTTTAGAAAGAATCGGAGTAA
Found at i:40500293 original size:28 final size:29
Alignment explanation
Indices: 40500199--40500377 Score: 143
Period size: 29 Copynumber: 6.2 Consensus size: 29
40500189 TTTGGACATC
40500199 GGGGT-AAAATGGTAATTTTT-GCAAGTTTCA
1 GGGGTAAAAAT-GTAATTTTTAG-AAGTTT-A
* * * *
40500229 -GGATCAAAATGAAATTTTTAGAAGTTCA
1 GGGGTAAAAATGTAATTTTTAGAAGTTTA
* * *
40500257 GGGGCAAAATTGTAATTTTTGGAAGTTT-
1 GGGGTAAAAATGTAATTTTTAGAAGTTTA
* * *
40500285 TGGGTAAAAATGTAATTTTCAAAAGTTTA
1 GGGGTAAAAATGTAATTTTTAGAAGTTTA
* *
40500314 GGGGTAAAAATGTAATTTTCAGAAGCTTCA
1 GGGGTAAAAATGTAATTTTTAGAAG-TTTA
* * *
40500344 GGGTTAAAAATGGAATTTTGGAGAAGTTT-
1 GGGGTAAAAATGTAATTTT-TAGAAGTTTA
40500373 GGGGT
1 GGGGT
40500378 CGAAATATGA
Statistics
Matches: 119, Mismatches: 24, Indels: 13
0.76 0.15 0.08
Matches are distributed among these distances:
28 23 0.19
29 63 0.53
30 28 0.24
31 5 0.04
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTAGAAGTTTA
Found at i:40500317 original size:57 final size:58
Alignment explanation
Indices: 40500199--40500332 Score: 162
Period size: 57 Copynumber: 2.3 Consensus size: 58
40500189 TTTGGACATC
* * * *
40500199 GGGGTAAAATGGTAATTTTTGCAAGTTTCAGGATCAAAATGAAATTTTTAGAAGTTCA
1 GGGGTAAAATTGTAATTTTTGCAAGTTTCAGGATAAAAATGAAATTTTCAAAAGTTCA
* * * * * *
40500257 GGGGCAAAATTGTAATTTTTGGAAGTTT-TGGGTAAAAATGTAATTTTCAAAAGTTTA
1 GGGGTAAAATTGTAATTTTTGCAAGTTTCAGGATAAAAATGAAATTTTCAAAAGTTCA
*
40500314 GGGGTAAAAATGTAATTTT
1 GGGGTAAAATTGTAATTTT
40500333 CAGAAGCTTC
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
57 39 0.61
58 25 0.39
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (58 bp):
GGGGTAAAATTGTAATTTTTGCAAGTTTCAGGATAAAAATGAAATTTTCAAAAGTTCA
Found at i:40502279 original size:17 final size:17
Alignment explanation
Indices: 40502259--40502322 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
40502249 AAATATATCT
* *
40502259 TAAATTCAAATTTATAA
1 TAAATTTAAATTTAAAA
40502276 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
40502293 TAAACTT-AATCTTAAAA
1 TAAATTTAAAT-TTAAAA
40502310 TAAATTTAAATTT
1 TAAATTTAAATTT
40502323 TGTTGGGCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
16 3 0.07
17 35 0.85
18 3 0.07
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40503013 original size:206 final size:206
Alignment explanation
Indices: 40502659--40503040 Score: 629
Period size: 206 Copynumber: 1.9 Consensus size: 206
40502649 CTTGGCCTTT
* * * * *
40502659 TTCTCAGTATCCCATCAGGAAGATGACCGCGTTACTTGTTTCAATTCGCTTCTCTGTATCTCATC
1 TTCTCAGTATCCCATCAGGAAGACGACCGCATCACTTGTTTCAATTCACTTCTCGGTATCTCATC
*
40502724 AGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACAATTTTATTGCTTCAAC
66 AGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACAATTTTATTGCTTCAAC
*
40502789 CTGCCTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTGGCATTGAGTCTCAGTTTG
131 CTGCCTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTGGCATTGAGTCTCAGTTTG
40502854 ATTTATTCTTC
196 ATTTATTCTTC
* *
40502865 TTCTCAGTATCTCATCAGGAAGACGACCGCATCGCTTGTTTCAATTCACTTCTCGGTATCTCATC
1 TTCTCAGTATCCCATCAGGAAGACGACCGCATCACTTGTTTCAATTCACTTCTCGGTATCTCATC
* * * * *
40502930 AGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGTTAACCATTTTGTTGCTTCAAC
66 AGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACAATTTTATTGCTTCAAC
*
40502995 CTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCT
131 CTGCCTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCT
40503041 CGCGTCGAGC
Statistics
Matches: 161, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
206 161 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (206 bp):
TTCTCAGTATCCCATCAGGAAGACGACCGCATCACTTGTTTCAATTCACTTCTCGGTATCTCATC
AGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACAATTTTATTGCTTCAAC
CTGCCTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTGGCATTGAGTCTCAGTTTG
ATTTATTCTTC
Found at i:40504219 original size:52 final size:54
Alignment explanation
Indices: 40504111--40504221 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
40504101 CGAACCCCTT
* *
40504111 TTTTTTTTAATCGAGACGCCCTTTGTGGGTTTTCATCTCAATTCTCTCTTCTTC
1 TTTTTTTGAATCGAGACGCCCTTTGCGGGTTTTCATCTCAATTCTCTCTTCTTC
* * *
40504165 TTTTTTTGAATTGAGATGTCCTTTGCGGGTTTTCATCTCAATTCTCTC-TC-TC
1 TTTTTTTGAATCGAGACGCCCTTTGCGGGTTTTCATCTCAATTCTCTCTTCTTC
40504217 TTTTT
1 TTTTT
40504222 CTTAGGTGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
52 7 0.13
53 2 0.04
54 43 0.83
ACGTcount: A:0.13, C:0.22, G:0.14, T:0.52
Consensus pattern (54 bp):
TTTTTTTGAATCGAGACGCCCTTTGCGGGTTTTCATCTCAATTCTCTCTTCTTC
Found at i:40515373 original size:2 final size:2
Alignment explanation
Indices: 40515366--40515395 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40515356 TAAGATTCCA
40515366 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40515396 TTCTCATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40516270 original size:30 final size:29
Alignment explanation
Indices: 40516234--40516332 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 29
40516224 TTGAAAAACT
40516234 CTTATTTGAACACTTTTTAAAGGTTAAGCC
1 CTTATTTGAACACTTTTTAAAGGTTAAG-C
** *
40516264 CTTATTTGTTCA-TTTTGAAAGGTTTAA-C
1 CTTATTTGAACACTTTTTAAAGG-TTAAGC
**
40516292 CTTCATTT-AAGCACTTTTATAAAGGTTTGGTC
1 CTT-ATTTGAA-CACTTTT-TAAAGGTTAAG-C
40516324 CTTATTTGA
1 CTTATTTGA
40516333 GCAACCTCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
28 4 0.08
29 15 0.28
30 20 0.38
31 9 0.17
32 5 0.09
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.45
Consensus pattern (29 bp):
CTTATTTGAACACTTTTTAAAGGTTAAGC
Found at i:40522558 original size:18 final size:18
Alignment explanation
Indices: 40522537--40522573 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40522527 TACATATGAT
40522537 AAAT-TTTATAAATAACAA
1 AAATATTTA-AAATAACAA
40522555 AAATATTTAAAATAACAA
1 AAATATTTAAAATAACAA
40522573 A
1 A
40522574 TTTAGTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATATTTAAAATAACAA
Found at i:40523174 original size:18 final size:19
Alignment explanation
Indices: 40523141--40523176 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40523131 ATGTTTTTAA
*
40523141 AATTATTTTATTTAATTTT
1 AATTAGTTTATTTAATTTT
40523160 AATTAGTTT-TTTAATTT
1 AATTAGTTTATTTAATTT
40523177 GTTATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
AATTAGTTTATTTAATTTT
Found at i:40524490 original size:10 final size:10
Alignment explanation
Indices: 40524475--40524533 Score: 66
Period size: 10 Copynumber: 6.0 Consensus size: 10
40524465 GTAAAATAAG
40524475 AAAATTATTA
1 AAAATTATTA
40524485 AAAATTATTA
1 AAAATTATTA
* *
40524495 GAAATTGTTA
1 AAAATTATTA
* * *
40524505 AATATTGTAA
1 AAAATTATTA
40524515 AAAATTA-TA
1 AAAATTATTA
40524524 AAAATTATTA
1 AAAATTATTA
40524534 GAGACAAGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
9 8 0.20
10 32 0.80
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (10 bp):
AAAATTATTA
Found at i:40524708 original size:17 final size:16
Alignment explanation
Indices: 40524687--40524734 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
40524677 TTTTTAAATA
*
40524687 ATTTTAATAGTTTTGT
1 ATTTTAATAGTTTTCT
*
40524703 ATTTTTAATAATTTTCT
1 A-TTTTAATAGTTTTCT
40524720 ATTTTATATAGTTTT
1 ATTTTA-ATAGTTTT
40524735 TTTTTTGTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (16 bp):
ATTTTAATAGTTTTCT
Found at i:40531049 original size:30 final size:29
Alignment explanation
Indices: 40530963--40531375 Score: 156
Period size: 30 Copynumber: 14.1 Consensus size: 29
40530953 GTAATTTCGA
* * *
40530963 GAAAGTTCGGAATTAAAAATGAAAATTTT-
1 GAAAGTTCGGGA-TAAAAATGTAATTTTTG
40530992 GAAA-TTCGAGCG-T-AAAATGGTAATTTTTG
1 GAAAGTTCG-G-GATAAAAAT-GTAATTTTTG
*
40531021 GAAAGTTCGGGATCAAAAATGAAATTTTTG
1 GAAAGTTCGGGAT-AAAAATGTAATTTTTG
* * *
40531051 GACA-TTTGAGGATAAAAATGTGATTTTTG
1 GAAAGTTCG-GGATAAAAATGTAATTTTTG
* * *
40531080 GAAAGTTTAGGGTTAAAAATGTAATTTTTA
1 GAAAG-TTCGGGATAAAAATGTAATTTTTG
* * * *
40531110 G-CAGTTCGGGGGGTAAATATGTATTTTTTG
1 GAAAGTTC--GGGATAAAAATGTAATTTTTG
* * * *
40531140 GAAAGTTTGGGGGTCAAAATGTGATTTTTG
1 GAAAG-TTCGGGATAAAAATGTAATTTTTG
* * *
40531170 GAAAGTTTAGTG-TCAAAAA--T-ATTTTAG
1 GAAAG-TTCGGGAT-AAAAATGTAATTTTTG
* * *
40531197 G-AAGTTTGGGGGTAAAAATGTGATTTTTAG
1 GAAAG-TTCGGGATAAAAATGTAATTTTT-G
* * **
40531227 AAAATTTAAGG-TCAAAAATGTAA-TTTTG
1 GAAAGTTCGGGAT-AAAAATGTAATTTTTG
* * * * *
40531255 TAAAGTTAAGGGGTTAAAATGTGATTTTTG
1 GAAAGTT-CGGGATAAAAATGTAATTTTTG
* *
40531285 GAAAGTTTAGGG-TCAAAAATGCAATTTTTG
1 GAAAG-TTCGGGAT-AAAAATGTAATTTTTG
* * * *
40531315 G-AAGTTTAAGGG-TAAAATTATGATTTTTG
1 GAAAG-TT-CGGGATAAAAATGTAATTTTTG
* * *
40531344 GAAAGTTTGGGATCAAAATATAATTTTTG
1 GAAAGTTCGGGATAAAAATGTAATTTTTG
40531373 GAA
1 GAA
40531376 GTTGAGGGTC
Statistics
Matches: 299, Mismatches: 54, Indels: 62
0.72 0.13 0.15
Matches are distributed among these distances:
26 13 0.04
27 13 0.04
28 26 0.09
29 94 0.31
30 137 0.46
31 14 0.05
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
GAAAGTTCGGGATAAAAATGTAATTTTTG
Found at i:40531068 original size:29 final size:30
Alignment explanation
Indices: 40531005--40531397 Score: 219
Period size: 30 Copynumber: 13.4 Consensus size: 30
40530995 ATTCGAGCGT
*
40531005 AAAATGGTAATTTTTGGAAAGTTCG-GGATCA
1 AAAAT-GTAATTTTTGGAAAGTTTGAGGAT-A
* *
40531036 AAAATGAAATTTTTGGACA-TTTGAGGATA
1 AAAATGTAATTTTTGGAAAGTTTGAGGATA
* *
40531065 AAAATGTGATTTTTGGAAAGTTT-AGGGTTA
1 AAAATGTAATTTTTGGAAAGTTTGA-GGATA
* * * * *
40531095 AAAATGTAATTTTTAG-CAGTTCGGGGGGTA
1 AAAATGTAATTTTTGGAAAGTT-TGAGGATA
* * * * *
40531125 AATATGTATTTTTTGGAAAGTTTGGGGGTC
1 AAAATGTAATTTTTGGAAAGTTTGAGGATA
*
40531155 AAAATGTGATTTTTGGAAAGTTT-AGTG-TCA
1 AAAATGTAATTTTTGGAAAGTTTGAG-GAT-A
* * *
40531185 AAAA--T-ATTTTAGG-AAGTTTGGGGGTA
1 AAAATGTAATTTTTGGAAAGTTTGAGGATA
* * * *
40531211 AAAATGTGATTTTTAGAAAATTTAAGG-TCA
1 AAAATGTAATTTTTGGAAAGTTTGAGGAT-A
* * * *
40531241 AAAATGTAA-TTTTGTAAAG-TTAAGGGGTT
1 AAAATGTAATTTTTGGAAAGTTTGA-GGATA
* *
40531270 AAAATGTGATTTTTGGAAAGTTT-AGGGTCA
1 AAAATGTAATTTTTGGAAAGTTTGAGGAT-A
* * *
40531300 AAAATGCAATTTTTGG-AAGTTTAAGGGTA
1 AAAATGTAATTTTTGGAAAGTTTGAGGATA
* * * *
40531329 AAATTATGATTTTTGGAAAGTTTG-GGATC
1 AAAATGTAATTTTTGGAAAGTTTGAGGATA
* * *
40531358 AAAATATAATTTTTGG-AAG-TTGAGGGTC
1 AAAATGTAATTTTTGGAAAGTTTGAGGATA
*
40531386 AAAATATAATTT
1 AAAATGTAATTT
40531398 CTAGATAATT
Statistics
Matches: 288, Mismatches: 51, Indels: 49
0.74 0.13 0.13
Matches are distributed among these distances:
26 12 0.04
27 12 0.04
28 25 0.09
29 91 0.32
30 137 0.48
31 11 0.04
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGATA
Found at i:40531098 original size:59 final size:58
Alignment explanation
Indices: 40530947--40531108 Score: 161
Period size: 59 Copynumber: 2.8 Consensus size: 58
40530937 GCTTGGGGGC
* * * *
40530947 AAAATGGTAA-TTTCGAGAAAGTTCGGAATTAAAAATGAAAATTTTGAAATTCGAGCGT
1 AAAATGGTAATTTTTG-GAAAGTTAGGGATTAAAAATGAAATTTTTGAAATTCGAGCGT
* * * *
40531005 AAAATGGTAATTTTTGGAAAGTTCGGGATCAAAAATGAAATTTTTGGACATTTGAG-GAT
1 AAAATGGTAATTTTTGGAAAGTTAGGGATTAAAAATGAAATTTTT-GAAATTCGAGCG-T
* *
40531064 AAAAAT-GTGATTTTTGGAAAGTTTAGGG-TTAAAAATGTAATTTTT
1 -AAAATGGTAATTTTTGGAAAG-TTAGGGATTAAAAATGAAATTTTT
40531109 AGCAGTTCGG
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
58 37 0.42
59 42 0.47
60 10 0.11
ACGTcount: A:0.40, C:0.04, G:0.22, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAGTTAGGGATTAAAAATGAAATTTTTGAAATTCGAGCGT
Found at i:40531320 original size:59 final size:57
Alignment explanation
Indices: 40531134--40531383 Score: 249
Period size: 59 Copynumber: 4.3 Consensus size: 57
40531124 AAATATGTAT
** * *
40531134 TTTTTGGAAAGTTTGGGGGTCAAAATGTGATTTTTGGAAAGTTTAGTGTCAAAAAT-A
1 TTTTTGG-AAGTTAAGGGGTTAAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAATAA
* ** * * * *
40531191 TTTTAGGAAGTTTGGGGGTAAAAATGTGATTTTTAGAAAATTTAAGGTCAAAAATGTAA
1 TTTTTGGAAGTTAAGGGGTTAAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAA--TAA
*
40531250 -TTTTGTAAAGTTAAGGGGTTAAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAATGCAA
1 TTTTTG-GAAGTTAAGGGGTTAAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAAT--AA
*
40531309 TTTTTGGAAGTTTAA-GGG-TAAAATTATGATTTTTGGAAAGTTT-GGGATCAAAATATAA
1 TTTTTGGAAG-TTAAGGGGTTAAAA-TGTGATTTTTGGAAAGTTTAGGG-TCAAAA-ATAA
*
40531367 TTTTTGGAAGTTGAGGG
1 TTTTTGGAAGTTAAGGG
40531384 TCAAAATATA
Statistics
Matches: 164, Mismatches: 17, Indels: 23
0.80 0.08 0.11
Matches are distributed among these distances:
56 42 0.26
57 10 0.06
58 27 0.16
59 74 0.45
60 11 0.07
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (57 bp):
TTTTTGGAAGTTAAGGGGTTAAAATGTGATTTTTGGAAAGTTTAGGGTCAAAAATAA
Found at i:40532438 original size:11 final size:10
Alignment explanation
Indices: 40532414--40532468 Score: 55
Period size: 9 Copynumber: 5.7 Consensus size: 10
40532404 TCATTTTCCT
*
40532414 TTTATTACTA
1 TTTATTAATA
40532424 TTTATTTAATA
1 TTTA-TTAATA
40532435 TTTATTAATA
1 TTTATTAATA
40532445 -TTATT-AT-
1 TTTATTAATA
40532452 TGTTATTAATA
1 T-TTATTAATA
40532463 -TTATTA
1 TTTATTA
40532469 TTAAAGTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
8 2 0.05
9 16 0.41
10 12 0.31
11 9 0.23
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTATTAATA
Found at i:40532459 original size:18 final size:18
Alignment explanation
Indices: 40532436--40532470 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40532426 TATTTAATAT
40532436 TTATTAATATTATTATTG
1 TTATTAATATTATTATTG
40532454 TTATTAATATTATTATT
1 TTATTAATATTATTATT
40532471 AAAGTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTATTAATATTATTATTG
Found at i:40532551 original size:22 final size:22
Alignment explanation
Indices: 40532512--40532560 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
40532502 TAATTATGAA
* *
40532512 ATAATAAATGACAAATATTGAT
1 ATAATAAATAACAAATATTAAT
* *
40532534 ATAATAAATAATAGATATTAAT
1 ATAATAAATAACAAATATTAAT
40532556 A-AATA
1 ATAATA
40532561 TGTACAGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAATAAATAACAAATATTAAT
Found at i:40533181 original size:29 final size:30
Alignment explanation
Indices: 40533131--40533187 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40533121 TGATTTAATT
40533131 TGTAATTGGGCCTAGTGTTTTGGGTTTGGA
1 TGTAATTGGGCCTAGTGTTTTGGGTTTGGA
* *
40533161 TGTATTTGGGCTTAG-GTTTTGGGTTTG
1 TGTAATTGGGCCTAGTGTTTTGGGTTTG
40533188 TTAGGATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.11, C:0.05, G:0.37, T:0.47
Consensus pattern (30 bp):
TGTAATTGGGCCTAGTGTTTTGGGTTTGGA
Found at i:40533331 original size:12 final size:12
Alignment explanation
Indices: 40533292--40533325 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40533282 TAACTAAATT
40533292 TAAATTTAAAAA
1 TAAATTTAAAAA
*
40533304 TAAATATAAAAA
1 TAAATTTAAAAA
40533316 TAAATTTAAA
1 TAAATTTAAA
40533326 TTTAAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:40533862 original size:49 final size:48
Alignment explanation
Indices: 40533752--40533874 Score: 131
Period size: 49 Copynumber: 2.5 Consensus size: 48
40533742 AGATCTGGTT
* * * **
40533752 CACTTCTCTATATCTCATCAAGAAGGTAACCGCTTTATTGTTTTGACC
1 CACTTCTCTGTATCTCATCAAGAAGATAACCGCTCTATTGTTTCAACC
* * *
40533800 CACTTCTCAGTATCTCATCAAGAAGATGAA-CGCATCTCTTGTTTCAATC
1 CACTTCTCTGTATCTCATCAAGAAGAT-AACCGC-TCTATTGTTTCAACC
* *
40533849 CGCTTCTCTGTATCTCATCAGGAAGA
1 CACTTCTCTGTATCTCATCAAGAAGA
40533875 CGAATTTGGT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 27 0.44
49 35 0.56
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (48 bp):
CACTTCTCTGTATCTCATCAAGAAGATAACCGCTCTATTGTTTCAACC
Found at i:40533900 original size:134 final size:134
Alignment explanation
Indices: 40533654--40533951 Score: 366
Period size: 134 Copynumber: 2.2 Consensus size: 134
40533644 GTTTGGTGTC
** * * * * ** *
40533654 ATTGTTTTGGTCCACTTCTTAGTATTTCATCAGGAAGATGATCGCATCACTTGTTTTGATTCACT
1 ATTGTTTTGACCCACTTCTCAGTATCTCATCAAGAAGATGAACGCATCACTTGTTTCAATCCACT
* * * *
40533719 TCTCTATATCTCCTCAGGAAGACAGATCTGGTTCACTTCTCTATATCTCATCAAGAAGGTAACCG
66 TCTCTATATCTCATCAGGAAGACAGATCTGGTCCACTTCTCTATATCTCATCAAGAAGCTAACCA
40533784 CTTT
131 CTTT
* *
40533788 ATTGTTTTGACCCACTTCTCAGTATCTCATCAAGAAGATGAACGCATCTCTTGTTTCAATCCGCT
1 ATTGTTTTGACCCACTTCTCAGTATCTCATCAAGAAGATGAACGCATCACTTGTTTCAATCCACT
* *
40533853 TCTCTGTATCTCATCAGGAAGAC-GAATTTGGTCCACTTCTC-AGTATCTCATCAAGAAGCTAAC
66 TCTCTATATCTCATCAGGAAGACAG-ATCTGGTCCACTTCTCTA-TATCTCATCAAGAAGCTAAC
*
40533916 CATTTT
129 CACTTT
* * * *
40533922 ATTGCTTCGACCTACTTTTCAGTATCTCAT
1 ATTGTTTTGACCCACTTCTCAGTATCTCAT
40533952 TAGGAAGCTG
Statistics
Matches: 140, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
133 2 0.01
134 138 0.99
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (134 bp):
ATTGTTTTGACCCACTTCTCAGTATCTCATCAAGAAGATGAACGCATCACTTGTTTCAATCCACT
TCTCTATATCTCATCAGGAAGACAGATCTGGTCCACTTCTCTATATCTCATCAAGAAGCTAACCA
CTTT
Found at i:40534185 original size:172 final size:172
Alignment explanation
Indices: 40533888--40534254 Score: 574
Period size: 172 Copynumber: 2.1 Consensus size: 172
40533878 ATTTGGTCCA
* * * * * *
40533888 CTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGACCTACTTTTCAGTATCTCATT
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTACTTCTCAATATCTCATC
* *
40533953 AGGAAGCTGGGGTTTGAAGATTTGCTCACTTTGAGCCTGATTTCATTGATTTGATCTTCTTCTCA
66 AGGAAGCTGGGGTTCGAAGATTCGCTCACTTTGAGCCTGATTTCATTGATTTGATCTTCTTCTCA
*
40534018 ATGTCTCATCAGGAAGGTGACCGTATCACTTATTTCAAT-TCG
131 ATGTCTCATCAGGAAGATGACCGTATCACTTATTTCAATCT-G
* *
40534060 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTTGACCTGCTTCTCAATATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTACTTCTCAATATCTCATC
* * * *
40534125 AGGAAGCTGTGGTTCGAAGATTCGCTCACTTTGAGTCTGGTTTCATTGATTTGGTCTTCTTCTCA
66 AGGAAGCTGGGGTTCGAAGATTCGCTCACTTTGAGCCTGATTTCATTGATTTGATCTTCTTCTCA
*
40534190 ATGTCTCATCAGGAAGATGACCGTATCACTTGTTTCAATCTG
131 ATGTCTCATCAGGAAGATGACCGTATCACTTATTTCAATCTG
40534232 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
40534255 ACGAATTTGG
Statistics
Matches: 178, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
172 177 0.99
173 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (172 bp):
CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTACTTCTCAATATCTCATC
AGGAAGCTGGGGTTCGAAGATTCGCTCACTTTGAGCCTGATTTCATTGATTTGATCTTCTTCTCA
ATGTCTCATCAGGAAGATGACCGTATCACTTATTTCAATCTG
Found at i:40534463 original size:205 final size:205
Alignment explanation
Indices: 40534060--40534612 Score: 732
Period size: 205 Copynumber: 2.7 Consensus size: 205
40534050 TTTCAATTCG
* * *
40534060 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTTGACCTGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* * * * * *
40534125 AGGAAGCTGTGGTTCGAAGATTCGCTCACT-TTGAGTCTGGTTTCATTGATTTGGTCTTCTTCTC
66 AGGAAGCTGGGGTTCGAAGTTTCGCTC-GTATTGAG-CT--TTTC-TTGAGTTGGTATACTTCTC
* * * * *
40534189 AATGTCTCATCAGGAAGATGACCGTATCACTTGTTTCAATCTGCTTCTCTGTATCTCATCAGGAA
126 TATATCTCATCAGGAAGATAACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAA
40534254 GACGAATTTGGTCCA
191 GACGAATTTGGTCCA
* * *
40534269 CTTCTCAGTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTATTAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* *
40534334 AGGAAGCTGGGGTTCAAAGTTTCACTCGTATTGAGCTTTAT-TTGAGTTGGTATACTTCTCTATA
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCGTATTGAGCTTT-TCTTGAGTTGGTATACTTCTCTATA
* *
40534398 TCTCATCAGGAAGATAACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACG
130 TCTCATCAGGAAGATAACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACG
*
40534463 AATTTGGTGCA
195 AATTTGGTCCA
* *
40534474 CTTCTCAGTATCTTATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
* * * * *
40534539 AAGAGGCTAGGGTTCGAAGTTTCGCTCGCATTTAGCTTTTTTCCATTGAGTTGGTATACTTCTCT
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCGTATTGAGC--TTTT-C-TTGAGTTGGTATACTTCTCT
*
40534604 GTATCTCAT
127 ATATCTCAT
40534613 TAGGGGGATG
Statistics
Matches: 302, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
205 177 0.59
206 3 0.01
207 4 0.01
208 3 0.01
209 115 0.38
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (205 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATC
AGGAAGCTGGGGTTCGAAGTTTCGCTCGTATTGAGCTTTTCTTGAGTTGGTATACTTCTCTATAT
CTCATCAGGAAGATAACCGCATCACTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGA
ATTTGGTCCA
Found at i:40546863 original size:29 final size:29
Alignment explanation
Indices: 40546758--40547175 Score: 216
Period size: 30 Copynumber: 14.1 Consensus size: 29
40546748 GCCCGAGGGT
* *
40546758 AAAATGGTAATTTTGAGAAAGTTTAGGATCA
1 AAAAT-GTAATTTT-TGAAAGTTTGGGATCA
* * * *
40546789 AAAATGAAAATTTTGGACA-TTTGAGAGT--
1 AAAATG-TAATTTTTGAAAGTTTGGGA-TCA
40546817 AAAATGGTAATTTTTTGAAAGTTTGGGATCA
1 AAAAT-GTAA-TTTTTGAAAGTTTGGGATCA
* * *
40546848 AAAATGAAATTTTTGAACA-TTCAGGG-TTA
1 AAAATGTAATTTTTGAA-AGTT-TGGGATCA
* *
40546877 AAAATGTGATTTTTGGAAAGTTTGGGGTCA
1 AAAATGTAATTTTT-GAAAGTTTGGGATCA
* * * *
40546907 AAAATGTCATTTTTGGAAGTTCGAGGGT-A
1 AAAATGTAATTTTTGAAAGTTTG-GGATCA
* * * *
40546936 AAGATGTGATTTTTGGAAGTTTGAGGGT-A
1 AAAATGTAATTTTTGAAAGTTTG-GGATCA
* * * *
40546965 AAAATGTGAGTTTTCGAAAGTTTAGCG-TTA
1 AAAATGT-AATTTTTGAAAGTTT-GGGATCA
*
40546995 AAAATGTAA-TTTTGGAAGTTTAGAGG-T-A
1 AAAATGTAATTTTTGAAAGTTT-G-GGATCA
* * *
40547023 AAAATGTGATTTTTGGAAAGTTCGGGGTCA
1 AAAATGTAATTTTT-GAAAGTTTGGGATCA
* *
40547053 AAAATGTGATTTTTGAAAAGTTTAGGGGTC-
1 AAAATGTAATTTTTG-AAAGTTT-GGGATCA
** *
40547083 AAAATGTGCTTTTTGGAAAGTTTAGTG-TCA
1 AAAATGTAATTTTT-GAAAGTTT-GGGATCA
*
40547113 AAAATGTAATTTTTGGAAAGTTT-AGAGTCA
1 AAAATGTAATTTTT-GAAAGTTTGGGA-TCA
* *
40547143 AAAATGTAATTTTTGGAAGTTAGGGAGTCA
1 AAAATGTAATTTTTGAAAGTTTGGGA-TCA
40547173 AAA
1 AAA
40547176 TATGATTTTG
Statistics
Matches: 315, Mismatches: 44, Indels: 57
0.76 0.11 0.14
Matches are distributed among these distances:
28 31 0.10
29 101 0.32
30 159 0.50
31 24 0.08
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTGGGATCA
Found at i:40546943 original size:59 final size:59
Alignment explanation
Indices: 40546731--40547163 Score: 329
Period size: 59 Copynumber: 7.3 Consensus size: 59
40546721 AGTCGAGATT
* ** * * *
40546731 AAATGTAATTTTTGGATGCCCGAGGGT-AAAATG-GTAATTTTGAGAAAGTTTAGGATCAA
1 AAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTG-ATTTTTG-GAAAGTTTGGGGTCAA
* * * * * * *
40546790 AAATGAAAATTTTGGACA-TTTGAGAGT-AAAATGGTAATTTTTTGAAAGTTTGGGATCAA
1 AAATGTAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTGATTTTTGGAAAGTTTGGGGTCAA
* *
40546849 AAATGAAATTTTT-GAACATTC-AGGGTTAAAAATGTGATTTTTGGAAAGTTTGGGGTCAA
1 AAATGTAATTTTTGGAA-GTTCGAGGG-TAAAAATGTGATTTTTGGAAAGTTTGGGGTCAA
* *
40546908 AAATGTCATTTTTGGAAGTTCGAGGGTAAAGATGTGATTTTTGG-AAGTTTGAGGGT-AA
1 AAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAAGTTTG-GGGTCAA
* * * * * * *
40546966 AAATGTGAGTTTTCGAAAGTT-TAGCGTTAAAAATGT-AATTTTGG-AAGTTTAGAGGT-AA
1 AAATGT-AATTTTTGGAAGTTCGAG-GGTAAAAATGTGATTTTTGGAAAGTTT-GGGGTCAA
* *
40547024 AAATGTGATTTTTGGAAAGTTCG-GGGTCAAAAATGTGATTTTTGAAAAGTTTAGGGGTC-A
1 AAATGTAATTTTTGG-AAGTTCGAGGGT-AAAAATGTGATTTTTGGAAAGTTT-GGGGTCAA
** * * * * *
40547084 AAATGTGCTTTTTGGAAAGTT-TAGTGTCAAAAATGTAATTTTTGGAAAGTTTAGAGTCAA
1 AAATGTAATTTTTGG-AAGTTCGAGGGT-AAAAATGTGATTTTTGGAAAGTTTGGGGTCAA
40547144 AAATGTAATTTTTGGAAGTT
1 AAATGTAATTTTTGGAAGTT
40547164 AGGGAGTCAA
Statistics
Matches: 305, Mismatches: 48, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
57 8 0.03
58 60 0.20
59 147 0.48
60 90 0.30
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (59 bp):
AAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGGAAAGTTTGGGGTCAA
Found at i:40547008 original size:58 final size:57
Alignment explanation
Indices: 40546872--40547160 Score: 294
Period size: 60 Copynumber: 4.9 Consensus size: 57
40546862 GAACATTCAG
* * *
40546872 GGTTAAAAATGTGATTTTTGGAAAGTTTGGGGTCAAAAATGTCATTTTTGG-AAGTTCGA
1 GGTTAAAAATGTGATTTTTGG-AAGTTTAGGGT-AAAAATGTGATTTTTGGAAAGTT-TA
* * * *
40546931 GGGTAAAGATGTGATTTTTGGAAGTTTGAGGGTAAAAATGTGAGTTTTCGAAAGTTTA
1 GGTTAAAAATGTGATTTTTGGAAGTTT-AGGGTAAAAATGTGATTTTTGGAAAGTTTA
* **
40546989 GCGTTAAAAATGT-AATTTTGGAAGTTTAGAGGTAAAAATGTGATTTTTGGAAAGTTCGG
1 G-GTTAAAAATGTGATTTTTGGAAGTTTAG-GGTAAAAATGTGATTTTTGGAAAGTT-TA
* * * *
40547048 GGTCAAAAATGTGATTTTTGAAAAGTTTAGGGGTCAAAATGTGCTTTTTGGAAAGTTTA
1 GGTTAAAAATGTGATTTTTG-GAAGTTTA-GGGTAAAAATGTGATTTTTGGAAAGTTTA
* * * *
40547107 GTGTCAAAAATGTAATTTTTGGAAAGTTTAGAGTCAAAAATGTAATTTTTGGAA
1 G-GTTAAAAATGTGATTTTTGG-AAGTTTAGGGT-AAAAATGTGATTTTTGGAA
40547161 GTTAGGGAGT
Statistics
Matches: 192, Mismatches: 27, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.01
58 69 0.36
59 48 0.25
60 72 0.38
61 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (57 bp):
GGTTAAAAATGTGATTTTTGGAAGTTTAGGGTAAAAATGTGATTTTTGGAAAGTTTA
Found at i:40547183 original size:29 final size:29
Alignment explanation
Indices: 40546877--40547184 Score: 256
Period size: 30 Copynumber: 10.4 Consensus size: 29
40546867 TTCAGGGTTA
40546877 AAAATGTGATTTTTGGAAAGTTT-GGGGTC
1 AAAATGTGATTTTTGG-AAGTTTAGGGGTC
* *
40546906 AAAAATGTCATTTTTGGAAG-TTCGAGGGT-
1 -AAAATGTGATTTTTGGAAGTTTAG-GGGTC
*
40546935 AAAGATGTGATTTTTGGAAGTTT-GAGGGTA
1 AAA-ATGTGATTTTTGGAAGTTTAG-GGGTC
* * * * *
40546965 AAAATGTGAGTTTTCGAAAGTTTAGCGTTA
1 AAAATGTGA-TTTTTGGAAGTTTAGGGGTC
* * *
40546995 AAAATGT-AATTTTGGAAGTTTAGAGGTA
1 AAAATGTGATTTTTGGAAGTTTAGGGGTC
*
40547023 AAAATGTGATTTTTGGAAAG-TTCGGGGTC
1 AAAATGTGATTTTTGG-AAGTTTAGGGGTC
*
40547052 AAAAATGTGATTTTTGAAAAGTTTAGGGGTC
1 -AAAATGTGATTTTTG-GAAGTTTAGGGGTC
* *
40547083 AAAATGTGCTTTTTGGAAAGTTTA-GTGTC
1 AAAATGTGATTTTTGG-AAGTTTAGGGGTC
* *
40547112 AAAAATGTAATTTTTGGAAAGTTTA-GAGTC
1 -AAAATGTGATTTTTGG-AAGTTTAGGGGTC
*
40547142 AAAAATGTAATTTTTGGAAG-TTAGGGAGTC
1 -AAAATGTGATTTTTGGAAGTTTAGGG-GTC
*
40547172 AAAATATGATTTT
1 AAAATGTGATTTT
40547185 GGACAATTCA
Statistics
Matches: 236, Mismatches: 26, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
28 30 0.13
29 64 0.27
30 133 0.56
31 9 0.04
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAATGTGATTTTTGGAAGTTTAGGGGTC
Found at i:40548435 original size:22 final size:22
Alignment explanation
Indices: 40548396--40548444 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
40548386 TAATTACGAA
* *
40548396 ATAATAAATGACAAATATTGAT
1 ATAATAAATAACAAATATTAAT
* *
40548418 ATAATAAATAATAGATATTAAT
1 ATAATAAATAACAAATATTAAT
40548440 A-AATA
1 ATAATA
40548445 TGTATAGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAATAAATAACAAATATTAAT
Found at i:40549186 original size:6 final size:6
Alignment explanation
Indices: 40549175--40549208 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
40549165 CAAATTTAAC
**
40549175 TAAATT TAAATT TAAATT TAAAAA TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
40549209 ACCAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:40551577 original size:103 final size:102
Alignment explanation
Indices: 40551393--40551706 Score: 493
Period size: 103 Copynumber: 3.1 Consensus size: 102
40551383 ATCTTAAGGA
*
40551393 CTCTCTAAACATCTCTAGAAGATAGCATTAACAACAACAATTCCTAATCTCACTTTCTCTAGAAT
1 CTCTTTAAACATCTCTAGAAGATAGCATTAACAACAACAATTCCTAATCTCACTTTCTCTAGAAT
* *
40551458 TTCAGCCAAAACTCAAGAATTCGCTATCTCACTAAAAT
66 TTCA-ACAAAACTCAAGAATTCACTATCTCACTAAAAT
* * * *
40551496 CTCTTTAAACATCCCTAGAAGTTAGCATTAACAAAAACAATTCCTAATCTCATTTTCTCTAGAAT
1 CTCTTTAAACATCTCTAGAAGATAGCATTAACAACAACAATTCCTAATCTCACTTTCTCTAGAAT
*
40551561 TTCAATCAAAACTCAAGAACTCACTATCTCACTAAAAT
66 TTCAA-CAAAACTCAAGAATTCACTATCTCACTAAAAT
* * *
40551599 CTTTTTAAACATCTCTAGAACATAGCATTAACAACAACAATTTCTAATCTCACTTTCTCTAGAAT
1 CTCTTTAAACATCTCTAGAAGATAGCATTAACAACAACAATTCCTAATCTCACTTTCTCTAGAAT
* *
40551664 TTCAACCAAACTCAAGAATTCACTTTCTCACTAAAAT
66 TTCAACAAAACTCAAGAATTCACTATCTCACTAAAAT
40551701 CTCTTT
1 CTCTTT
40551707 CTAACTTGAA
Statistics
Matches: 191, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
102 34 0.18
103 157 0.82
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (102 bp):
CTCTTTAAACATCTCTAGAAGATAGCATTAACAACAACAATTCCTAATCTCACTTTCTCTAGAAT
TTCAACAAAACTCAAGAATTCACTATCTCACTAAAAT
Found at i:40554505 original size:15 final size:15
Alignment explanation
Indices: 40554485--40554519 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40554475 GTTCCTTTGG
40554485 TGAAAATTCTC-CAGT
1 TGAAAATTCTCTC-GT
40554500 TGAAAATTCTCTCGT
1 TGAAAATTCTCTCGT
40554515 TGAAA
1 TGAAA
40554520 GCTCCCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TGAAAATTCTCTCGT
Found at i:40560855 original size:18 final size:17
Alignment explanation
Indices: 40560838--40560881 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 17
40560828 AATACAAAAT
40560838 TAAATATCTAAAATAAA
1 TAAATATCTAAAATAAA
40560855 TAAATA-C--AAATAAA
1 TAAATATCTAAAATAAA
*
40560869 TAAATATATAAAA
1 TAAATATCTAAAA
40560882 AATTGAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 13 0.57
16 1 0.04
17 9 0.39
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATATCTAAAATAAA
Found at i:40560856 original size:13 final size:13
Alignment explanation
Indices: 40560775--40560874 Score: 62
Period size: 14 Copynumber: 7.4 Consensus size: 13
40560765 AATAAATCCA
40560775 AAATAAAATAACAT
1 AAATAAAATAA-AT
*
40560789 AACAATTAAATAAAT
1 -A-AATAAAATAAAT
40560804 GAAATAAAATAAA-
1 -AAATAAAATAAAT
*
40560817 AACCAT-AATTAAAT
1 AA--ATAAAATAAAT
* *
40560831 ACA-AAATTAAAT
1 AAATAAAATAAAT
**
40560843 ATCTAAAATAAAT
1 AAATAAAATAAAT
40560856 AAATACAAATAAAT
1 AAATA-AAATAAAT
40560870 AAATA
1 AAATA
40560875 TATAAAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
12 12 0.18
13 17 0.25
14 26 0.38
15 4 0.06
16 9 0.13
ACGTcount: A:0.68, C:0.07, G:0.01, T:0.24
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:40560884 original size:29 final size:29
Alignment explanation
Indices: 40560821--40560881 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
40560811 AATAAAAACC
* * *
40560821 ATAATTAAATACAAAATTAAATATCTAAA
1 ATAAATAAATACAAAAATAAATATATAAA
40560850 ATAAATAAATACAAATAAATAAATATATAAA
1 ATAAATAAATAC-AA-AAATAAATATATAAA
40560881 A
1 A
40560882 AATTGAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 11 0.41
30 2 0.07
31 14 0.52
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (29 bp):
ATAAATAAATACAAAAATAAATATATAAA
Found at i:40560954 original size:26 final size:25
Alignment explanation
Indices: 40560925--40560994 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
40560915 AATAATGGGA
*
40560925 AAAATTAAAAAAGAAAAAATTAAAAT
1 AAAATTAAAAAA-AAAAAATAAAAAT
**
40560951 AAAATTTAAAGCAAAAAAATAAAAAT
1 AAAA-TTAAAAAAAAAAAATAAAAAT
*
40560977 TAAA-TAAAAAATAAAAAA
1 AAAATTAAAAAA-AAAAAA
40560995 GTATAGGGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
24 5 0.14
25 6 0.17
26 19 0.53
27 6 0.17
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAATTAAAAAAAAAAAATAAAAAT
Found at i:40560969 original size:20 final size:18
Alignment explanation
Indices: 40560946--40560993 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
40560936 AGAAAAAATT
*
40560946 AAAATAAAATTTAAAGCAAA
1 AAAATAAAAATTAAA--AAA
*
40560966 AAAATAAAAATTAAATAA
1 AAAATAAAAATTAAAAAA
40560984 AAAATAAAAA
1 AAAATAAAAA
40560994 AGTATAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAATAAAAATTAAAAAA
Found at i:40562178 original size:30 final size:30
Alignment explanation
Indices: 40562142--40562509 Score: 140
Period size: 30 Copynumber: 12.4 Consensus size: 30
40562132 AAAACGGTGA
*
40562142 TTTTGGAAACTTCGAGGGC-AAAATAGTAAT
1 TTTTGGAAAGTTCGAGGGCAAAAAT-GTAAT
* *
40562172 TTTTGG-ATGTTC-AGGGGTAAAAATGTAAT
1 TTTTGGAAAGTTCGA-GGGCAAAAATGTAAT
* *
40562201 TTTTGGAATGTTCGAGGTCAAAAATGTAAT
1 TTTTGGAAAGTTCGAGGGCAAAAATGTAAT
* * * *
40562231 TTTTGGACA-TTTGAGGG-TAAAATAGCAATT
1 TTTTGGAAAGTTCGAGGGCAAAAAT-GTAA-T
* * * * *
40562261 TTTTAGAAATTTTG-GGGTTAAAAATGGAAT
1 TTTTGGAAAGTTCGAGGG-CAAAAATGTAAT
* * * * * ** *
40562291 TTTTAGACATTTAG-GGGTAAATTTGTAAG
1 TTTTGGAAAGTTCGAGGGCAAAAATGTAAT
* * *
40562320 TTTTGGAAAGTTTG-GGGTTAAAAATGGAA-
1 TTTTGGAAAGTTCGAGGG-CAAAAATGTAAT
* *** *
40562349 TTTTCGAAAGTTCGAGTATAAAAATATAAT
1 TTTTGGAAAGTTCGAGGGCAAAAATGTAAT
** *
40562379 TTTTGAGAAA-TTCGAGGTTAAAGAT-TCAA-
1 TTTTG-GAAAGTTCGAGGGCAAAAATGT-AAT
*
40562408 TTTTGGAAAGTT-TAGGGGCAAAAATGTAAT
1 TTTTGGAAAGTTCGA-GGGCAAAAATGTAAT
*
40562438 TTTTGAAAAGTTCG-GGAGTCAAAACA--TAAT
1 TTTTGGAAAGTTCGAGG-G-CAAAA-ATGTAAT
* * * *
40562468 TTTT-GAGAAGTTTGAGGGCTAAAATATGAT
1 TTTTGGA-AAGTTCGAGGGCAAAAATGTAAT
*
40562498 TTTTGGATAGTT
1 TTTTGGAAAGTT
40562510 TAGGGACCTT
Statistics
Matches: 262, Mismatches: 49, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
28 12 0.05
29 93 0.35
30 130 0.50
31 21 0.08
32 6 0.02
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTCGAGGGCAAAAATGTAAT
Found at i:40562249 original size:59 final size:60
Alignment explanation
Indices: 40562142--40562509 Score: 219
Period size: 59 Copynumber: 6.2 Consensus size: 60
40562132 AAAACGGTGA
* * * *
40562142 TTTTGGAAACTTCGAGGGC-AAAATAGTAATTTTTGGATG-TTCAGGGGTAAAAATGTAAT
1 TTTTGGAAAGTTCGAGGTCAAAAAT-GTAATTTTTGGAAGTTTGAGGGGTAAAAATGTAAT
* *
40562201 TTTTGGAATGTTCGAGGTCAAAAATGTAATTTTTGGACA-TTTGA-GGGT-AAAATAGCAATT
1 TTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTGGA-AGTTTGAGGGGTAAAAAT-GTAA-T
* * * * * * * ** *
40562261 TTTTAGAAATTTTGGGGTTAAAAATGGAATTTTTAGACA-TTT-AGGGGTAAATTTGTAAG
1 TTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTGGA-AGTTTGAGGGGTAAAAATGTAAT
* * * * * * * ** *
40562320 TTTTGGAAAGTTTGGGGTTAAAAATGGAATTTTCGAAAGTTCGA-GTATAAAAATATAAT
1 TTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTGGAAGTTTGAGGGGTAAAAATGTAAT
* * *
40562379 TTTTGAGAAA-TTCGAGGTTAAAGAT-TCAA-TTTTGGAAAGTTT-AGGGGCAAAAATGTAAT
1 TTTTG-GAAAGTTCGAGGTCAAAAATGT-AATTTTTGG-AAGTTTGAGGGGTAAAAATGTAAT
* * *
40562438 TTTTGAAAAGTTCGGGAGTCAAAACA--TAATTTTTGAGAAGTTTGAGGGCTAAAATATG--AT
1 TTTTGGAAAGTTCGAG-GTCAAAA-ATGTAATTTTTG-GAAGTTTGAGGGGTAAAA-ATGTAAT
*
40562498 TTTTGGATAGTT
1 TTTTGGAAAGTT
40562510 TAGGGACCTT
Statistics
Matches: 240, Mismatches: 49, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
58 14 0.06
59 126 0.52
60 84 0.35
61 13 0.05
62 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (60 bp):
TTTTGGAAAGTTCGAGGTCAAAAATGTAATTTTTGGAAGTTTGAGGGGTAAAAATGTAAT
Found at i:40562294 original size:60 final size:59
Alignment explanation
Indices: 40562220--40562352 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 59
40562210 GTTCGAGGTC
* * * *
40562220 AAAAATGTAATTTTTGGACATTT-GAGGGTAAAATAGCAATTTTTTAGAAATTTTGGGGTT
1 AAAAATGGAATTTTTAGACATTTAG-GGGTAAAATAGCAA-GTTTTAGAAAGTTTGGGGTT
* * * *
40562280 AAAAATGGAATTTTTAGACATTTAGGGGTAAATTTGTAAGTTTTGGAAAGTTTGGGGTT
1 AAAAATGGAATTTTTAGACATTTAGGGGTAAAATAGCAAGTTTTAGAAAGTTTGGGGTT
40562339 AAAAATGGAATTTT
1 AAAAATGGAATTTT
40562353 CGAAAGTTCG
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 31 0.48
60 32 0.50
61 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGACATTTAGGGGTAAAATAGCAAGTTTTAGAAAGTTTGGGGTT
Found at i:40563560 original size:3 final size:3
Alignment explanation
Indices: 40563554--40563603 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
40563544 CATTTTTTTT
* *
40563554 TTA TTA -TA TTA TTA TTA TTA TTA ATG TTA -TA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
40563598 TTA TTA
1 TTA TTA
40563604 AGTATTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:40564270 original size:16 final size:19
Alignment explanation
Indices: 40564233--40564270 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
40564223 TTTGTAAAAA
40564233 TGGACACTTTGTTTATATT
1 TGGACACTTTGTTTATATT
40564252 TGGAC-CTTT-TTTA-ATT
1 TGGACACTTTGTTTATATT
40564268 TGG
1 TGG
40564271 GCTTGTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 4 0.21
18 4 0.21
19 5 0.26
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (19 bp):
TGGACACTTTGTTTATATT
Found at i:40564303 original size:6 final size:6
Alignment explanation
Indices: 40564282--40564327 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
40564272 CTTGTATTCT
* *
40564282 TTTAAA TTTAGA -TTAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40564328 ATAAACTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:40564304 original size:17 final size:17
Alignment explanation
Indices: 40564282--40564352 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
40564272 CTTGTATTCT
*
40564282 TTTAAATTTAGATTAAA
1 TTTAAATTTAAATTAAA
*
40564299 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
*
40564316 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
* *
40564333 CTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAATTAAA
40564350 TTT
1 TTT
40564353 TAAAATGGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 3 0.06
17 44 0.94
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:40564320 original size:34 final size:34
Alignment explanation
Indices: 40564282--40564352 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
40564272 CTTGTATTCT
* * * *
40564282 TTTAAATTTAGATTAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAACTTAAACTTAAAATAAA
*
40564316 TTTAAATTTAAAATAAACTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAACTTAAACTTAAAATAAA
40564350 TTT
1 TTT
40564353 TAAAATGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (34 bp):
TTTAAATTTAAAATAAACTTAAACTTAAAATAAA
Found at i:40564332 original size:11 final size:12
Alignment explanation
Indices: 40564283--40564327 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
40564273 TTGTATTCTT
*
40564283 TTAAATTTAGA-
1 TTAAATTTAAAC
40564294 TTAAATTTAAAC
1 TTAAATTTAAAC
*
40564306 TTAAA-TTAAAT
1 TTAAATTTAAAC
40564317 TTAAATTTAAA
1 TTAAATTTAAA
40564328 ATAAACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:40564344 original size:23 final size:23
Alignment explanation
Indices: 40564294--40564337 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
40564284 TAAATTTAGA
*
40564294 TTAAATTTAAACTTAAATTAAAT
1 TTAAATTTAAACATAAATTAAAT
40564317 TTAAATTTAAA-ATAAACTTAA
1 TTAAATTTAAACATAAA-TTAA
40564338 TCTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAAATTTAAACATAAATTAAAT
Found at i:40565018 original size:209 final size:209
Alignment explanation
Indices: 40564647--40565360 Score: 1025
Period size: 209 Copynumber: 3.4 Consensus size: 209
40564637 CTTTAGTGGT
* ** *
40564647 TTGGCGTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATTGCTTGTTTT
1 TTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTC
* * * * * * * *
40564712 GATCCACTTCTCTGTGTCTCATTAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAAGAA
66 AATCCGCTTCTCTGTATCTCATTAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
* ** * * * *
40564777 GGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGATGGGGTTCAAAGATT
131 GCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATT
40564842 TGCTCACTTTGAGC
196 TGCTCACTTTGAGC
* *
40564856 TTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCACATTACTTGTTTC
1 TTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTC
* * * *
40564921 AATCCGCTTCTCTATATCTGATCAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAGGAA
66 AATCCGCTTCTCTGTATCTCATTAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
* * *
40564986 GCTAATCATTTTATTGCTTCGACCTTCTTCTCAGTATCTCATCAGGAAGCTAAGGTTCGAAGATT
131 GCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATT
40565051 TGCTCACTTTGAGC
196 TGCTCACTTTGAGC
* * *
40565065 TTGGCTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTATTTC
1 TTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTC
* * *
40565130 AATCCGCTTCTTTGTATCTCATTAGGAAGATGAATTTGGTCCACTTCTCAGTATCTCATCAATAA
66 AATCCGCTTCTCTGTATCTCATTAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
*
40565195 GCTAACCATTTTATTGCTTCAACCTACTTCTCAAG-ATCTCATCAGGAAGCTAGGGTTCGAAGAT
131 GCTAACCATTTTATTGCTTCGACCTACTTCTC-AGTATCTCATCAGGAAGCTAGGGTTCGAAGAT
40565259 TTGCTCACTTTGAGC
195 TTGCTCACTTTGAGC
* * * * * *
40565274 TTGGCTTCATTGGTTTAGTCTTCTTCTTAGTATCTAATCAGGAAGATAACCGCATCACTTGTTTC
1 TTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTC
* *
40565339 AATCTGCTTCTCTGTATTTCAT
66 AATCCGCTTCTCTGTATCTCAT
40565361 CAAGAAAAAT
Statistics
Matches: 453, Mismatches: 51, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
209 451 1.00
210 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
TTGGCTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTC
AATCCGCTTCTCTGTATCTCATTAGGAAGAAGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
GCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATT
TGCTCACTTTGAGC
Found at i:40574245 original size:22 final size:22
Alignment explanation
Indices: 40574205--40574246 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40574195 TATCCTCAAC
**
40574205 TTATTGGCAATTTGTCTGCAAA
1 TTATTGGCAATTTAACTGCAAA
40574227 TTATTGGCAATTTAACTGCA
1 TTATTGGCAATTTAACTGCA
40574247 TATTGTTATT
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:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (22 bp):
TTATTGGCAATTTAACTGCAAA
Found at i:40575421 original size:18 final size:19
Alignment explanation
Indices: 40575389--40575424 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40575379 TTAAAGAGAA
40575389 AATATCAATACAAAGATAT
1 AATATCAATACAAAGATAT
*
40575408 AATA-CAATAGAAAGATA
1 AATATCAATACAAAGATA
40575425 AATGGGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.22
Consensus pattern (19 bp):
AATATCAATACAAAGATAT
Found at i:40576427 original size:42 final size:42
Alignment explanation
Indices: 40576368--40576513 Score: 148
Period size: 42 Copynumber: 3.2 Consensus size: 42
40576358 CTATAAAAAA
40576368 CATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC
1 CATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC
* * *
40576410 CATTTATTTTTCATTGCATTTAGAGTACCAAATGTGATCCAGGAGTGGAGGTC
1 CATTTACTTTTCATTGCATTTAGAG-GCCCAA---G-T------GTGGAGGTC
*
40576463 CATTTACTTTTCATTGCATTTAGAGGCTCAAGTGTGGAGGTC
1 CATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC
*
40576505 CATCTACTT
1 CATTTACTT
40576514 CTTTTTTCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
42 41 0.48
43 4 0.05
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
52 3 0.04
53 33 0.39
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (42 bp):
CATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTC
Found at i:40577959 original size:43 final size:40
Alignment explanation
Indices: 40577912--40578029 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 40
40577902 GGGTGATTCC
* * *
40577912 AGGGTGTGTGTCTATATTGTTTGGAGGAACACGGGTGTGGGTT
1 AGGGTGT-TGT-TATATTGTTT-GAGGCACACGAGCGTGGGTT
*
40577955 AGGGTGTATG-TATACTGTTCTGAGGCACACGAGCGTGGGTT
1 AGGGTGT-TGTTATATTGTT-TGAGGCACACGAGCGTGGGTT
*
40577996 AGGGTCTT-TGTATATTGTTTTGAGGCACACGAGC
1 AGGGTGTTGT-TATATTG-TTTGAGGCACACGAGC
40578030 TGGCACACGG
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.02
41 51 0.80
42 3 0.05
43 9 0.14
ACGTcount: A:0.19, C:0.12, G:0.36, T:0.33
Consensus pattern (40 bp):
AGGGTGTTGTTATATTGTTTGAGGCACACGAGCGTGGGTT
Found at i:40577993 original size:41 final size:41
Alignment explanation
Indices: 40577948--40578029 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
40577938 GAACACGGGT
*
40577948 GTGGGTTAGGGTGTATGTATACTGTTCTGAGGCACACGAGC
1 GTGGGTTAGGGTCTATGTATACTGTTCTGAGGCACACGAGC
* * *
40577989 GTGGGTTAGGGTCTTTGTATATTGTTTTGAGGCACACGAGC
1 GTGGGTTAGGGTCTATGTATACTGTTCTGAGGCACACGAGC
40578030 TGGCACACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.18, C:0.13, G:0.35, T:0.33
Consensus pattern (41 bp):
GTGGGTTAGGGTCTATGTATACTGTTCTGAGGCACACGAGC
Found at i:40578061 original size:53 final size:53
Alignment explanation
Indices: 40577978--40578175 Score: 227
Period size: 53 Copynumber: 3.7 Consensus size: 53
40577968 ACTGTTCTGA
* * * * * *
40577978 GGCACACGAGCGTGGGTTAGGGTCTTTGTATATTGTTTTGAGGCACACGAGCT
1 GGCACACGGGCGTGGGTTAGGGTGTGTGTATACTATTCTGAGGCACACGAGCT
* *
40578031 GGCACACGGGCGTGGGTTAGGGTGTGTGTATACTATTCTGAGGCACACGGGTT
1 GGCACACGGGCGTGGGTTAGGGTGTGTGTATACTATTCTGAGGCACACGAGCT
** * * * *
40578084 GGCACACGGGTATGGGTCAAGGTGTTTGTATACTATTCTGGGGCACAC-AGGCT
1 GGCACACGGGCGTGGGTTAGGGTGTGTGTATACTATTCTGAGGCACACGA-GCT
* * *
40578137 GACACATGGGCGTGTGTTAGGGTGTGTGTATACTATTCT
1 GGCACACGGGCGTGGGTTAGGGTGTGTGTATACTATTCT
40578176 AGGGAACATG
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
53 120 1.00
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (53 bp):
GGCACACGGGCGTGGGTTAGGGTGTGTGTATACTATTCTGAGGCACACGAGCT
Found at i:40578839 original size:29 final size:29
Alignment explanation
Indices: 40578774--40578829 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
40578764 ACGGATGGGG
* *
40578774 GTATCACGTCTGCATCTGTAACTATATTT
1 GTATCATGTCTGCACCTGTAACTATATTT
40578803 GTATCATGTCTGCACCTGTAACTATAT
1 GTATCATGTCTGCACCTGTAACTATAT
40578830 CTCTGACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (29 bp):
GTATCATGTCTGCACCTGTAACTATATTT
Found at i:40584822 original size:13 final size:13
Alignment explanation
Indices: 40584802--40584832 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40584792 ATTTAAATTC
40584802 TATT-TTTAGGAT
1 TATTATTTAGGAT
40584814 TATTATTTAGGAT
1 TATTATTTAGGAT
40584827 TATTAT
1 TATTAT
40584833 GATATTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (13 bp):
TATTATTTAGGAT
Found at i:40587489 original size:79 final size:79
Alignment explanation
Indices: 40587355--40587587 Score: 292
Period size: 79 Copynumber: 3.0 Consensus size: 79
40587345 AAATTGGTTG
* *
40587355 TTTGATGGATGTTGTTGGTTAATCCAACTAGAGCTGGGCTCACAATTGCAGTTTATCAGCTAGGC
1 TTTGATAGATATTGTTGGTTAATCCAACTAGAGCTGGGCTCACAATTGCAGTTTATCAGCTAGGC
40587420 ACTAGGTGCCAGGA
66 ACTAGGTGCCAGGA
* *
40587434 TTTGATAGATATTGTTGGTTAATCCAACTAGAGCTGGGCTCAGAATTGC-GATTTATCCGCTAGG
1 TTTGATAGATATTGTTGGTTAATCCAACTAGAGCTGGGCTCACAATTGCAG-TTTATCAGCTAGG
* *
40587498 CACTGGGTGCTAGGA
65 CACTAGGTGCCAGGA
* * * * * * *
40587513 TTTGA-CGATATTGTTGGTTAATCTAACTAGAGCTAGGTTCACATTTG-AGGTTTATCAACTACG
1 TTTGATAGATATTGTTGGTTAATCCAACTAGAGCTGGGCTCACAATTGCA-GTTTATCAGCTAGG
* *
40587576 CATTGGGTGCCA
65 CACTAGGTGCCA
40587588 TAATTGCCGG
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
78 57 0.43
79 77 0.57
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (79 bp):
TTTGATAGATATTGTTGGTTAATCCAACTAGAGCTGGGCTCACAATTGCAGTTTATCAGCTAGGC
ACTAGGTGCCAGGA
Found at i:40595852 original size:29 final size:29
Alignment explanation
Indices: 40595820--40595894 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
40595810 TGTTTTATAA
* *
40595820 TTTTATAATTTATAAAA-TTACATTTAATT
1 TTTTAAAAATTATAAAATTTA-ATTTAATT
*
40595849 TTTTAAAAATGATAAAAATTTAATTTAATT
1 TTTTAAAAATTAT-AAAATTTAATTTAATT
40595879 TTTTAAAAATTATAAA
1 TTTTAAAAATTATAAA
40595895 GATATAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
29 13 0.32
30 24 0.60
31 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTTAAAAATTATAAAATTTAATTTAATT
Found at i:40595875 original size:30 final size:30
Alignment explanation
Indices: 40595833--40595894 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
40595823 TATAATTTAT
40595833 AAAATTACATTTAATTTTTTAAAAATGATA
1 AAAATTACATTTAATTTTTTAAAAATGATA
*
40595863 AAAATTTA-ATTTAATTTTTTAAAAATTATA
1 AAAA-TTACATTTAATTTTTTAAAAATGATA
40595893 AA
1 AA
40595895 GATATAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
AAAATTACATTTAATTTTTTAAAAATGATA
Done.